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Sample records for clonally expanded plasma

  1. Antibodies produced by clonally expanded plasma cells in multiple sclerosis cerebrospinal fluid cause demyelination of spinal cord explants.

    Science.gov (United States)

    Blauth, Kevin; Soltys, John; Matschulat, Adeline; Reiter, Cory R; Ritchie, Alanna; Baird, Nicholas L; Bennett, Jeffrey L; Owens, Gregory P

    2015-12-01

    B cells are implicated in the etiology of multiple sclerosis (MS). Intrathecal IgG synthesis, cerebrospinal fluid (CSF) oligoclonal bands and lesional IgG deposition suggest a role for antibody-mediated pathology. We examined the binding of IgG1 monoclonal recombinant antibodies (rAbs) derived from MS patient CSF expanded B cell clones to central nervous system (CNS) tissue. MS rAbs displaying CNS binding to mouse and human CNS tissue were further tested for their ability to induce complement-mediated tissue injury in ex vivo spinal cord explant cultures. The staining of CNS tissue, primary human astrocytes and human neurons revealed a measurable bias in MS rAb binding to antigens preferentially expressed on astrocytes and neurons. MS rAbs that recognize myelin-enriched antigens were rarely detected. Both myelin-specific and some astrocyte/neuronal-specific MS rAbs caused significant myelin loss and astrocyte activation when applied to spinal cord explant cultures in the presence of complement. Overall, the intrathecal B cell response in multiple sclerosis binds to both glial and neuronal targets and produces demyelination in spinal cord explant cultures implicating intrathecal IgG in MS pathogenesis.

  2. Carbohydrate plasma expanders for passive tumor targeting

    DEFF Research Database (Denmark)

    Hoffmann, Stefan; Caysa, Henrike; Kuntsche, Judith

    2013-01-01

    The objective of this study was to investigate the suitability of carbohydrate plasma volume expanders as a novel polymer platform for tumor targeting. Many synthetic polymers have already been synthesized for targeted tumor therapy, but potential advantages of these carbohydrates include...... inexpensive synthesis, constant availability, a good safety profile, biodegradability and the long clinical use as plasma expanders. Three polymers have been tested for cytotoxicity and cytokine activation in cell cultures and conjugated with a near-infrared fluorescent dye: hydroxyethyl starches (HES 200 k...

  3. Particles formation in an expanding plasma

    Energy Technology Data Exchange (ETDEWEB)

    Lescoute, E.; Hallo, L.; Chimier, B.; Tikhonchuk, V.T.; Stenz, C. [Bordeaux-1 Univ., CELIA, CNRS-CEA, 33 - Talence (France); Hebert, D.; Chevalier, J.M.; Rullier, J.L.; Palmier, S. [CEA Centre d' Etudes Scientifiques et Techniques d' Aquitaine, 33 - Le Barp (France)

    2009-08-15

    Interaction of a laser beam with a target generates a high velocity expanding plasma plume, solid debris and liquid nano- and micro-particles. They are produced from plasma recombination and vapor condensation and can be deposited on optical elements located nearby the target. Two distinct kinds of particles were observed depending on the temperature achieved in the plasma plume: large micrometer-size fragments for temperatures lower than the critical temperature, and very small nanometer-size particles for higher temperatures. The paper presents experimental observations of fragments and nano-particles in plasma plumes and a comparison with models. A good agreement has been found for nano-particle sizes and distributions. This simple modeling can also be used for nuclei production in the nanosecond time scale. Our estimates show that particle size can be correlated to laser wavelength and fluences.

  4. CD8+ clonality is associated with prolonged acute plasma viremia and altered mRNA cytokine profiles during the course of feline immunodeficiency virus infection.

    Science.gov (United States)

    Miller, Michelle M; Thompson, Elizabeth M; Suter, Steven E; Fogle, Jonathan E

    2013-04-15

    Acute lentiviral infection is characterized by early CD8(+) cytotoxic T cell (CTL) activity and a subsequent decline in plasma viremia. However, CD8(+) lymphocytes fail to eliminate the virus and a progressive T cell immune dysfunction develops during the course of chronic lentiviral infection. To further define this CD8(+) immune dysfunction we utilized PARR (PCR for antigen receptor rearrangements), a technique which measures clonally expanded lymphocyte populations by comparison of highly conserved T cell receptor (TCR) regions to identify the prevalence of clonal CD8(+) T cells following FIV infection. We then compared phenotype, mRNA profiles, CD8(+) proliferation and plasma viremia during acute and chronic infection for PARR positive (PARR(+)) and PARR negative (PARR(-)) Feline Immunodeficiency Virus (FIV) infected cats. We demonstrated that approximately forty percent of the FIV(+) cats examined exhibit CD8(+) clonality compared to none of the FIV(-) control cats. There were no phenotypic differences between PARR(+) and PARR(-) CD8(+) lymphocytes from FIV(+) cats but retrospective analysis of plasma viremia over the course of infection revealed a delayed peak in plasma viremia and a decline in lymphocyte counts were observed in the PARR(+) group during acute infection. CD8(+) lymphocytes isolated from chronically infected PARR(-) cats exhibited significantly higher mRNA expression of IFN-γ and IL-2 following mitogenic stimulation when compared to PARR(+) CD8(+) lymphocytes. These data suggest that clonal CD8(+) expansion may be related to impaired control of acute viremia and less effective CD8(+) anti-viral function. Using PARR to assess changes in CD8(+) clonality during the progression from acute to chronic FIV infection may help to better characterize the factors which contribute to CD8(+) anergy and lentiviral persistence. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Recombinant antibodies generated from both clonal and less abundant plasma cell immunoglobulin G sequences in subacute sclerosing panencephalitis brain are directed against measles virus

    Science.gov (United States)

    Burgoon, Mark P; Caldas, Yupanqui A; Keays, Kathryne M; Yu, Xiaoli; Gilden, Donald H; Owens, Gregory P

    2012-01-01

    Increased immunoglobulin G (IgG) and intrathecally produced oligoclonal bands (OGBs) are characteristic of a limited number of inflammatory central nervous system (CNS) diseases and are often directed against the cause of disease. In subacute sclerosing panencephalitis (SSPE), the cause of disease and the target of the oligoclonal response is measles virus (MV). The authors previously showed that clonally expanded populations of CD38+ plasma cells in SSPE brain, the likely source of OGBs, are directed against MV. In characterizing the breadth of the plasma cell reactivities, the authors found that a large proportion of the less abundant plasma cells are also directed against MV. The intrathecal response may be useful in determining the causes of other inflammatory CNS diseases, such as multiple sclerosis, Behcet’s disease, and neurosarcoidosis. PMID:17065133

  6. Waves and Fine Structure in Expanding Laser-Produced Plasmas

    Science.gov (United States)

    Collette, Andrew; Gekelman, Walter

    2009-11-01

    The behavior of expanding dense plasmas has long been a topic of interest in space plasma research, particularly in the case of expansion within a magnetized background. Previous laser-plasma experiments at the UCLA Large Plasma Device have observed the creation of strong (δBB > 50%) diamagnetic cavities, along with large-scale wave activity and hints of fine-scale structure. A new series of experiments conducted recently at the LaPD performs direct measurement of the fields inside the expanding plasma via a novel 2D probe drive system. This system combines small-scale (0.5mm-1mm) magnetic and electric field probes with high-accuracy vacuum ceramic motors, to allow measurement of the plasma volume over a 2000-point grid at 1mm resolution. The data reveal both coherent high-amplitude waves associated with the formation of these magnetic features, and complicated small-scale structure in both the magnetic field and floating potential. In addition, we will present correlation techniques using multiple independent B and E field probes. This reveals behavior of turbulent, non-phase-locked phenomena. Both the case of a single expanding plasma and two colliding plasmas were studied.

  7. Spatial structure of ion beams in an expanding plasma

    Science.gov (United States)

    Aguirre, E. M.; Scime, E. E.; Thompson, D. S.; Good, T. N.

    2017-12-01

    We report spatially resolved perpendicular and parallel, to the magnetic field, ion velocity distribution function (IVDF) measurements in an expanding argon helicon plasma. The parallel IVDFs, obtained through laser induced fluorescence (LIF), show an ion beam with v ≈ 8000 m/s flowing downstream and confined to the center of the discharge. The ion beam is measurable for tens of centimeters along the expansion axis before the LIF signal fades, likely a result of metastable quenching of the beam ions. The parallel ion beam velocity slows in agreement with expectations for the measured parallel electric field. The perpendicular IVDFs show an ion population with a radially outward flow that increases with distance from the plasma axis. Structures aligned to the expanding magnetic field appear in the DC electric field, the electron temperature, and the plasma density in the plasma plume. These measurements demonstrate that at least two-dimensional and perhaps fully three-dimensional models are needed to accurately describe the spontaneous acceleration of ion beams in expanding plasmas.

  8. Hydrodynamization and transient modes of expanding plasma in kinetic theory

    CERN Document Server

    Heller, Michal P; Spalinski, Michal

    2016-01-01

    We study the transition to hydrodynamics in a weakly-coupled model of quark-gluon plasma given by kinetic theory in the relaxation time approximation. Our studies uncover qualitative similarities to the results on hydrodynamization in strongly coupled gauge theories. In particular, we demonstrate that the gradient expansion in this model has vanishing radius of convergence. The asymptotic character of the hydrodynamic gradient expansion is crucial for the recently discovered applicability of hydrodynamics at large gradients. Furthermore, the analysis of the resurgent properties of the series provides, quite remarkably, indication for the existence of a novel transient, damped oscillatory mode of expanding plasmas in kinetic theory.

  9. H3N2 influenza infection elicits more cross-reactive and less clonally expanded anti-hemagglutinin antibodies than influenza vaccination.

    Directory of Open Access Journals (Sweden)

    M Anthony Moody

    Full Text Available BACKGROUND: During the recent H1N1 influenza pandemic, excess morbidity and mortality was seen in young but not older adults suggesting that prior infection with influenza strains may have protected older subjects. In contrast, a history of recent seasonal trivalent vaccine in younger adults was not associated with protection. METHODS AND FINDINGS: To study hemagglutinin (HA antibody responses in influenza immunization and infection, we have studied the day 7 plasma cell repertoires of subjects immunized with seasonal trivalent inactivated influenza vaccine (TIV and compared them to the plasma cell repertoires of subjects experimentally infected (EI with influenza H3N2 A/Wisconsin/67/2005. The majority of circulating plasma cells after TIV produced influenza-specific antibodies, while most plasma cells after EI produced antibodies that did not react with influenza HA. While anti-HA antibodies from TIV subjects were primarily reactive with single or few HA strains, anti-HA antibodies from EI subjects were isolated that reacted with multiple HA strains. Plasma cell-derived anti-HA antibodies from TIV subjects showed more evidence of clonal expansion compared with antibodies from EI subjects. From an H3N2-infected subject, we isolated a 4-member clonal lineage of broadly cross-reactive antibodies that bound to multiple HA subtypes and neutralized both H1N1 and H3N2 viruses. This broad reactivity was not detected in post-infection plasma suggesting this broadly reactive clonal lineage was not immunodominant in this subject. CONCLUSION: The presence of broadly reactive subdominant antibody responses in some EI subjects suggests that improved vaccine designs that make broadly reactive antibody responses immunodominant could protect against novel influenza strains.

  10. H3N2 Influenza Infection Elicits More Cross-Reactive and Less Clonally Expanded Anti-Hemagglutinin Antibodies Than Influenza Vaccination

    Science.gov (United States)

    Walter, Emmanuel B.; Woods, Christopher W.; Ginsburg, Geoffrey S.; McClain, Micah T.; Denny, Thomas N.; Chen, Xi; Munshaw, Supriya; Marshall, Dawn J.; Whitesides, John F.; Drinker, Mark S.; Amos, Joshua D.; Gurley, Thaddeus C.; Eudailey, Joshua A.; Foulger, Andrew; DeRosa, Katherine R.; Parks, Robert; Meyerhoff, R. Ryan; Yu, Jae-Sung; Kozink, Daniel M.; Barefoot, Brice E.; Ramsburg, Elizabeth A.; Khurana, Surender; Golding, Hana; Vandergrift, Nathan A.; Alam, S. Munir; Tomaras, Georgia D.; Kepler, Thomas B.; Kelsoe, Garnett; Liao, Hua-Xin; Haynes, Barton F.

    2011-01-01

    Background During the recent H1N1 influenza pandemic, excess morbidity and mortality was seen in young but not older adults suggesting that prior infection with influenza strains may have protected older subjects. In contrast, a history of recent seasonal trivalent vaccine in younger adults was not associated with protection. Methods and Findings To study hemagglutinin (HA) antibody responses in influenza immunization and infection, we have studied the day 7 plasma cell repertoires of subjects immunized with seasonal trivalent inactivated influenza vaccine (TIV) and compared them to the plasma cell repertoires of subjects experimentally infected (EI) with influenza H3N2 A/Wisconsin/67/2005. The majority of circulating plasma cells after TIV produced influenza-specific antibodies, while most plasma cells after EI produced antibodies that did not react with influenza HA. While anti-HA antibodies from TIV subjects were primarily reactive with single or few HA strains, anti-HA antibodies from EI subjects were isolated that reacted with multiple HA strains. Plasma cell-derived anti-HA antibodies from TIV subjects showed more evidence of clonal expansion compared with antibodies from EI subjects. From an H3N2-infected subject, we isolated a 4-member clonal lineage of broadly cross-reactive antibodies that bound to multiple HA subtypes and neutralized both H1N1 and H3N2 viruses. This broad reactivity was not detected in post-infection plasma suggesting this broadly reactive clonal lineage was not immunodominant in this subject. Conclusion The presence of broadly reactive subdominant antibody responses in some EI subjects suggests that improved vaccine designs that make broadly reactive antibody responses immunodominant could protect against novel influenza strains. PMID:22039424

  11. Modeling of Plasma Irregularities in Expanding Ionospheric Dust Clouds

    Science.gov (United States)

    Fu, H.; Scales, W.; Mahmoudian, A.; Bordikar, M. R.

    2009-12-01

    Natural dust layers occur in the earth’s mesosphere (50km-85km). Plasma irregularities are associated with these natural dust layers that produce radar echoes. Recently, an Ionospheric sounding rocket experiment was performed to investigate the plasma irregularities in upper atmospheric dust layers. The Charged Aerosol Release Experiment (CARE) uses a rocket payload injection of particles in the ionosphere to determine the mechanisms for enhanced radar scatter from plasma irregularities embedded in artificial dusty plasma in space. A 2-D hybrid computational model is described that may be used to study a variety of irregularities in dusty space plasmas which may lead to radar echoes. In this model, the dust and ions are both treated with Particle-In-Cell method while the dust charge varies with time based on the standard dust Orbit Motion Limited charging model. A stochastic model is adopted to remove particle ions due to the dust charging process. Electrons are treated with a fluid model including the parallel dynamics of magnetic fields. Fourier spectral methods with a predictor-corrector time advance are used to solve it. This numerical model will be used to investigate the electrodynamics and several possible plasma irregularity generation mechanisms after the creation of an artificial dust layer. The first is the dust ion-acoustic instability due to the drift of dust relative to the plasma. The instability saturates by trapping some ions. The effects of dust radius and dust drift velocity on plasma irregularities will be analyzed further. Also, a shear- driven instability in expanding dusty clouds is investigated.

  12. Expanding plasmas from anti de Sitter black holes

    Energy Technology Data Exchange (ETDEWEB)

    Camilo, Giancarlo [Instituto de Fisica, Universidade de Sao Paulo, Departamento de Fisica Matematica, Sao Paulo (Brazil)

    2016-12-15

    We introduce a new foliation of AdS{sub 5} black holes such that the conformal boundary takes the form of a 4-dimensional FLRW spacetime with scale factor a(t). The foliation employs Eddington-Finkelstein-like coordinates and is applicable to a large class of AdS black holes, supported by matter fields or not, considerably extending previous efforts in the literature. We argue that the holographic dual picture of a CFT plasma on a FLRW background provides an interesting prototype to study the nonequilibrium dynamics of expanding plasmas and use holographic renormalization to extract the renormalized energy-momentum tensor of the dual plasma. We illustrate the procedure for three black holes of interest, namely AdS-Schwarzschild, AdS-Gauss-Bonnet, and AdS-Reissner-Nordstroem. For the latter, as a by-product, we show that the nonequilibrium dynamics of a CFT plasma subject to a quench in the chemical potential (i.e., a time-dependent chemical potential) resembles a cosmological evolution with the scale factor a(t) being inversely related to the quench profile μ(t). (orig.)

  13. Spatial Studies of Ion Beams in an Expanding Plasma

    Science.gov (United States)

    Aguirre, Evan; Good, Timothy; Scime, Earl; Thompson, Derek

    2017-10-01

    We report spatially resolved perpendicular and parallel ion velocity distribution function (IVDF) measurements in an expanding argon helicon plasma. The parallel IVDFs, obtained through laser induced fluorescence (LIF), show an ion beam with v 8 km/s flowing downstream that is confined to the center of the discharge. The ion beam is confined to within a few centimeters radially and is measurable for tens of centimeters axially before the LIF signal fades, likely a result of metastable quenching of the beam ions. The axial ion beam velocity slows in agreement with collisional processes. The perpendicular IVDFs show an ion population with a radially outward flow that increases with radial location. The DC electric field, electron temperature, and the plasma density in the double layer plume are all consistent with magnetic field aligned structures. The upstream and downstream electric field measurements show clear evidence of an ion hole that maps along the magnetic field at the edge of the plasma. Current theories and simulations of double layers, which are one-dimensional, completely miss these critically important two-dimensional features.

  14. Nanosecond spectroscopy of expanding laser-produced tin plasma

    Energy Technology Data Exchange (ETDEWEB)

    O' Shay, B; Najmabadi, F; Harilal, S S; Tillack, M S [Center for Energy Research, University of California San Diego 9500 Gilman Drive, La Jolla, CA 92093-0438 (United States)

    2007-04-15

    Time dependent behavior of laser-produced tin plasma has been investigated using gated optical emission spectroscopy. Plasma was generated by focusing 1.064 m Nd:YAG laser light onto a solid density, planar tin target in vacuum at a laser irradiance of 3.8 x 10{sup 11} W/cm{sup 2}. Estimates of the electron temperature and density were made by assuming Boltzmann distributed population levels and Stark broadened singly ionized tin spectral lines, respectively. An initial temperature of 1.4 eV and density of 4.1 x 10{sup 17} cm{sup -3} were calculated from the analysis of spectral data. Experimental data were interpreted alongside numerical results from HYADES - a onedimensional radiation hydrodynamics plasma simulation code. An energy balance was calculated to determine the fraction of incident laser energy converted to directed kinetic energy of expansion.

  15. A new diagnostic for very high magnetic fields in expanding plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Eliezer, S. [Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom) ; Mendonca, J.T. [Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom) ]. E-mail: t.mendonca@rl.ac.uk; Bingham, R. [Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom) ; Norreys, P. [Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom)

    2005-03-14

    Here we propose a new diagnostic method for the magnetic field inside an expanding plasma, based on the idea of photon acceleration, or photon frequency shift of radiation coming out of the plasma. Examples of application for laser-target interaction in the Peta-Watt regime, and for intense magnetic fields in astrophysical environments are considered.

  16. Expanding thermal plasma chemical vapour deposition of ZnO:Al layers for CIGS solar cells

    NARCIS (Netherlands)

    Sharma, K.; Williams, B.L.; Mittal, A.; Knoops, H.C.M.; Kniknie, B.J.; Bakker, N.J.; Kessels, W.M.M.; Schropp, R.E.I.; Creatore, M.

    2014-01-01

    Aluminium-doped zinc oxide (ZnO:Al) grown by expanding thermal plasma chemical vapour deposition (ETP-CVD) has demonstrated excellent electrical and optical properties, which make it an attractive candidate as a transparent conductive oxide for photovoltaic applications. However, when depositing

  17. Expanding thermal plasma CVD of textured ZNO with focus on solar cell applications

    NARCIS (Netherlands)

    Groenen, R.; Sanden, M.C.M. van de; Löffler, J.; Schropp, R.E.I.; Linden, J.L.

    2000-01-01

    A new method for low temperature deposition of surface textured ZnO is presented utilizing an expanding thermal plasma created by a cascaded arc. Films have been deposited at 150-350°C at a rate of typically 0.65-0.75 nm/s, exhibiting low sheet resistance (> 10 Ω/□), high transmittance (>80%) and a

  18. Practical diagnostic approaches to composite plasma cell neoplasm and low grade B-cell lymphoma/clonal infiltrates in the bone marrow.

    Science.gov (United States)

    Hussein, Shafinaz; Gill, Kamraan; Baer, Lea N; Hoehn, Daniela; Mansukhani, Mahesh; Jobanputra, Vaidehi; Bhagat, Govind; Alobeid, Bachir

    2015-03-01

    Composite plasma cell neoplasm (PCN) and low grade B-cell lymphoma (B-NHL) in the bone marrow are uncommon and raise the differential diagnosis of B-NHL with plasmacytic differentiation and PCN with lymphoplasmacytic morphology. This can be a challenging differential diagnosis, and the distinctions are important because of differences in management. We report five cases of composite PCN with B-NHL or clonal B-cell infiltrates involving the bone marrow. By using multiple different diagnostic modalities, including immunophenotyping by flow cytometry and immunohistochemistry, cytogenetic analysis and IGH gene rearrangement studies by polymerase chain reaction, we were able to distinguish two distinct clonally unrelated neoplasms in all cases. We describe the utility and pitfalls of these different diagnostic modalities. Flow cytometric analysis with a panel of antibodies that includes CD19, CD56, CD138, CD45 and other aberrant markers commonly expressed by PCN will allow identification of clonally unrelated PCN and B-NHL in a composite neoplasm, and distinguish them from B-NHL with plasmacytic differentiation and PCN with lymphoplasmacytic morphology. Cytogenetic and molecular analyses can give false-negative or false-positive results. In summary, a multimodal approach utilizing these different tools, including clinical data, should be used to arrive at the correct diagnosis. Copyright © 2014 John Wiley & Sons, Ltd.

  19. Plasma techniques for nanostructured carbon materials synthesis. A case study: carbon nanowall growth by low pressure expanding RF plasma

    Science.gov (United States)

    Vizireanu, S.; Stoica, S. D.; Luculescu, C.; Nistor, L. C.; Mitu, B.; Dinescu, G.

    2010-06-01

    A short description of approaches for carbon nanostructures synthesis is made and the advantages of using plasma during the growth are presented. As a particular example of a plasma based technique we detail the process of downstream carbon nanowall (CNW) synthesis by a radiofrequency expanding plasma beam. The technique combines magnetron sputtering for catalyst deposition and plasma enhanced chemical vapor deposition (main gas: argon, active gas: hydrogen, precursor gas: acetylene) for carbon growth in a single reactor. The analysis focuses on the correlation between the material properties and the plasma characteristics measured at different points along the flow axis, aiming to reveal the importance of plasma species in the growth process. The material properties were investigated by scanning and transmission electron microscopy, whereas the plasma data were obtained by optical emission spectroscopy, Langmuir probes and mass spectrometry. CNWs with a large area and well isolated from each other are obtained at an optimum distance from the precursor injection point where the plasma presents an enhanced content of carbon nanoclusters. The possible processes responsible for the growth are discussed.

  20. Plasma techniques for nanostructured carbon materials synthesis. A case study: carbon nanowall growth by low pressure expanding RF plasma

    Energy Technology Data Exchange (ETDEWEB)

    Vizireanu, S; Stoica, S D; Luculescu, C; Mitu, B; Dinescu, G [National Institute for Laser, Plasma and Radiation Physics Magurele-Bucharest, PO Box MG-16, 077125 (Romania); Nistor, L C, E-mail: dinescug@infim.r [National Institute for Materials Physics Magurele-Bucharest, 077125 (Romania)

    2010-06-15

    A short description of approaches for carbon nanostructures synthesis is made and the advantages of using plasma during the growth are presented. As a particular example of a plasma based technique we detail the process of downstream carbon nanowall (CNW) synthesis by a radiofrequency expanding plasma beam. The technique combines magnetron sputtering for catalyst deposition and plasma enhanced chemical vapor deposition (main gas: argon, active gas: hydrogen, precursor gas: acetylene) for carbon growth in a single reactor. The analysis focuses on the correlation between the material properties and the plasma characteristics measured at different points along the flow axis, aiming to reveal the importance of plasma species in the growth process. The material properties were investigated by scanning and transmission electron microscopy, whereas the plasma data were obtained by optical emission spectroscopy, Langmuir probes and mass spectrometry. CNWs with a large area and well isolated from each other are obtained at an optimum distance from the precursor injection point where the plasma presents an enhanced content of carbon nanoclusters. The possible processes responsible for the growth are discussed.

  1. Confinement and dynamics of laser-produced plasma expanding across a transverse magnetic field.

    Science.gov (United States)

    Harilal, S S; Tillack, M S; O'Shay, B; Bindhu, C V; Najmabadi, F

    2004-02-01

    The dynamics and confinement of laser-created plumes expanding across a transverse magnetic field have been investigated. 1.06 microm, 8 ns pulses from a neodymium-doped yttrium aluminum garnet laser were used to create an aluminum plasma which was allowed to expand across a 0.64 T magnetic field. Fast photography, emission spectroscopy, and time of flight spectroscopy were used as diagnostic tools. Changes in plume structure and dynamics, enhanced emission and ionization, and velocity enhancement were observed in the presence of the magnetic field. Photographic studies showed that the plume is not fully stopped and diffuses across the field. The temperature of the plume was found to increase due to Joule heating and adiabatic compression. The time of flight studies showed that all of the species are slowed down significantly. A multiple peak temporal distribution was observed for neutral species.

  2. Expanding thermal plasma chemical vapour deposition of ZnO:Al layers for CIGS solar cells

    OpenAIRE

    Sharma, K; Williams, B. L.; Mittal, A.; Knoops, H. C. M.; Kniknie, B.J.; Bakker, N J; Kessels, W. M. M.; Schropp, R.E.I.; Creatore, M.

    2014-01-01

    Aluminium-doped zinc oxide (ZnO:Al) grown by expanding thermal plasma chemical vapour deposition (ETP-CVD) has demonstrated excellent electrical and optical properties, which make it an attractive candidate as a transparent conductive oxide for photovoltaic applications. However, when depositing ZnO:Al on CIGS solar cell stacks, one should be aware that high substrate temperature processing (i.e., >200°C) can damage the crucial underlying layers/interfaces (such as CIGS/CdS and CdS/i-ZnO). In...

  3. Fast deposition of amorphous carbon films by an expanding cascaded arc plasma jet

    Science.gov (United States)

    Buuron, A. J. M.; van de Sanden, M. C. M.; van Ooij, W. J.; Driessens, R. M. A.; Schram, D. C.

    1995-07-01

    Using an expanding cascaded arc plasma jet, amorphous hydrogenated and fluorohydrogenated carbon films were deposited on silicon, glass, and steel substrates at high rates of tens of nanometers per second and on large areas of up to 100 cm2. The present work was aimed at depositing amorphous carbon films suited for optical and protective applications. Films deposited with the common argon/methane or argon/acetylene mixture tend to delaminate from the substrate when the film is thicker than about 1 μm. For this reason, also trials using other compounds like C7H8 (toluene), CF4, and H2, and mixtures of these, were carried out. Using toluene, several-μm-thick films with good adhesion to the substrate were deposited. With spectroscopic ellipsometry and infrared absorption spectroscopy optical parameters were obtained. Appropriate numerical models were developed for analyzing the data, taking into account interference fringes in the spectra due to multiple reflections in the thin film. The hydrogen and oxygen content in the films were determined with nuclear recoil techniques. Films deposited with the use of methane and acetylene are diamondlike with mainly sp3 bonding types, and a hydrogen content ranging from 36 to 26 at. % (with a low oxygen contamination of 1-2 at. %). Films deposited with the use of toluene are more polymerlike, with also sp1 and sp2 bonding types. These films have a high hydrogen content (35 at. %), and can be partially oxidized (up to 13 at. %). In general, going from the polymerlike to the more diamondlike films, the refractive index increases from 1.3 to 2.2, and the band gap decreases from about 2 to 1 eV. By the admixture of hydrogen in the deposition plasma diamondlike films were produced with a larger band gap of 2.2 eV. The corrosion performance of the films was studied by storing them in a humidity cabinet. The corrosion resistance of films deposited with hydrocarbon/argon plasma mixtures appears to be limited. Thick films with a good

  4. Quantification of circulating clonal plasma cells via multiparametric flow cytometry identifies patients with smoldering multiple myeloma at high risk of progression.

    Science.gov (United States)

    Gonsalves, W I; Rajkumar, S V; Dispenzieri, A; Dingli, D; Timm, M M; Morice, W G; Lacy, M Q; Buadi, F K; Go, R S; Leung, N; Kapoor, P; Hayman, S R; Lust, J A; Russell, S J; Zeldenrust, S R; Hwa, L; Kourelis, T V; Kyle, R A; Gertz, M A; Kumar, S K

    2017-01-01

    The presence of high numbers of circulating clonal plasma cells (cPCs) in patients with smoldering multiple myeloma (SMM), detected by a slide-based immunofluorescence assay, has been associated with a shorter time to progression (TTP) to MM. The significance of quantifying cPCs via multiparameter flow cytometry, a much more readily available diagnostic modality, in patients with SMM has not been evaluated. This study evaluated 100 patients with a known or new diagnosis of SMM who were seen at the Mayo Clinic, Rochester from January 2008 until December 2013. Patients with ⩾150 cPCs (N=9) were considered to have high number of cPCs based on the 97% specificity and 78% PPV of progression to MM within 2 years of cPC assessment. The median TTP of patients with ⩾150 cPCs was 9 months compared with not reached for patients with <150 cPCs (P<0.001). Thus, quantification of cPCs via multiparametric flow cytometry identifies patients with SMM at very high risk of progression to MM within 2 years and warrants confirmation in larger studies. In the future, this may allow reclassification of such patients as having MM requiring therapy prior to them enduring end-organ damage.

  5. Expanding Thermal Plasma Chemical Vapour Deposition of ZnO:Al Layers for CIGS Solar Cells

    Directory of Open Access Journals (Sweden)

    K. Sharma

    2014-01-01

    Full Text Available Aluminium-doped zinc oxide (ZnO:Al grown by expanding thermal plasma chemical vapour deposition (ETP-CVD has demonstrated excellent electrical and optical properties, which make it an attractive candidate as a transparent conductive oxide for photovoltaic applications. However, when depositing ZnO:Al on CIGS solar cell stacks, one should be aware that high substrate temperature processing (i.e., >200°C can damage the crucial underlying layers/interfaces (such as CIGS/CdS and CdS/i-ZnO. In this paper, the potential of adopting ETP-CVD ZnO:Al in CIGS solar cells is assessed: the effect of substrate temperature during film deposition on both the electrical properties of the ZnO:Al and the eventual performance of the CIGS solar cells was investigated. For ZnO:Al films grown using the high thermal budget (HTB condition, lower resistivities, ρ, were achievable (~5 × 10−4 Ω·cm than those grown using the low thermal budget (LTB conditions (~2 × 10−3 Ω·cm, whereas higher CIGS conversion efficiencies were obtained for the LTB condition (up to 10.9% than for the HTB condition (up to 9.0%. Whereas such temperature-dependence of CIGS device parameters has previously been linked with chemical migration between individual layers, we demonstrate that in this case it is primarily attributed to the prevalence of shunt currents.

  6. Redirection of the spherical expanding shock wave on the interface with plasma

    Energy Technology Data Exchange (ETDEWEB)

    Markhotok, A.; Popovic, S. [Physics Department, Old Dominion University, Norfolk, Virginia 23529 (United States)

    2014-02-15

    We study a strong spherical expanding shock wave interacting with the finite-gradient interface between neutral cold gas and weakly ionized plasma. We want to see how the interaction with the interface can alter the shock structure compared to the case of its free propagation through the media with the exponentially varying density. From our comparative calculations based on the 2D model, we found substantial difference in the shock structure including strong deformation of the shock front followed with its gradual flattening and the redirection in its propagation. There are a number of factors that can be used to control this phenomenon in order to strengthen or lessen the effect. The calculations can be made on any scale, limited with the requirement for the shock wave to be strong. The study points at the possibility in certain applications to avoid the shock wave with its redirection rather than attenuation. The results can be applicable to optimization of the energy deposition into the supersonic flux, the drag reduction in hypersonic flight, in the detonation theory, and combustion through the control of the ignition conditions, and for environmental improvements through sonic boom reduction. Cartesian coordinates were used in order to visualize the phenomenon.

  7. Hydrodynamic analysis of the high electric fields and double layers in expanding inhomogeneous plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Goldsworthy, M.P.; Green, F.; Lalousis, P.; Stening, R.J.; Eliezer, S.; Hora, H.

    1986-12-01

    A genuine two-fluid model of plasmas with collisions permits the calculation of dynamic electric fields and double layers inside of plasmas including oscillations and damping. For the first time, a macroscopic model for coupling of electromagnetic and Langmuir waves was achieved with realistic damping. Starting points were laser-produced plasmas showing very high dynamic electric fields in nonlinear force-produced cavitons and inverted layers, in agreement with experiments. Applications for any inhomogeneous plasma as in laboratory or in astrophysical plasmas can then be followed up by a transparent hydrodynamic description. The authors find the rotation of plasmas in magnetic fields and a new second harmonic resonance. Explanation of inverted double layers, second harmonic emission from laser-produced plasmas, and laser acceleration of charged particles by the very high fields of the double layers is given.

  8. The evolutionary ecology of clonally propagated domesticated plants.

    Science.gov (United States)

    McKey, Doyle; Elias, Marianne; Pujol, Benoît; Duputié, Anne

    2010-04-01

    While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

  9. Using a plasma physics experiment to expand student understanding of the index of refraction

    Science.gov (United States)

    Wise, Joe; Gekelman, Walter; Baker, Robert; Pribyl, Patrick

    2010-02-01

    The Los Angeles Physics Alliance Group (LAPTAG) Plasma Lab has met regularly at UCLA for the past 9 years. High school students have been involved in the construction of probes, amplifiers, antennae, machine shop use, printed circuit construction, experimental design, and scientific programming for the analysis of data. We describe a unique opportunity for high school students to participate in the process of science. Using plasma physics as an educational ``hook,'' students are engaged through a series of experiments, lectures, presentations, and group discussions. The outcome is that students gain a deeper understanding of the scientific method and in this case, the concepts of index of refraction and its effects on wave propagation. For example, students comprehend such advanced topics as dispersion, k-space, plasma properties, and wave group and phase velocities. This engagement supports efforts to improve STEM career choices by exposing high school students to challenging and interesting experiences in preparation for advanced study. )

  10. The thermalization of soft modes in non-expanding isotropic quark gluon plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Blaizot, Jean-Paul, E-mail: jean-paul.blaizot@cea.fr [Institut de Physique Théorique, CNRS/UMR 3681, CEA Saclay, F-91191 Gif-sur-Yvette (France); Liao, Jinfeng [Physics Department and Center for Exploration of Energy and Matter, Indiana University, 2401 N Milo B. Sampson Lane, Bloomington, IN 47408 (United States); RIKEN BNL Research Center, Bldg. 510A, Brookhaven National Laboratory, Upton, NY 11973 (United States); Mehtar-Tani, Yacine [Institute for Nuclear Theory, University of Washington, Seattle, WA 98195-1550 (United States)

    2017-05-15

    We discuss the role of elastic and inelastic collisions and their interplay in the thermalization of the quark–gluon plasma. We consider a simplified situation of a static plasma, spatially uniform and isotropic in momentum space. We focus on the small momentum region, which equilibrates first, and on a short time scale. We obtain a simple kinetic equation that allows for an analytic description of the most important regimes. The present analysis suggests that the formation of a Bose condensate, expected when only elastic collisions are present, is strongly hindered by the inelastic, radiative, processes.

  11. Evolution of the plasma parameters in the expanding laser ablation plume of silver

    DEFF Research Database (Denmark)

    Christensen, Bo Toftmann; Schou, Jørgen; Hansen, T.N.

    2002-01-01

    The angular and radial variation of the ion density and electron temperature in the plasma plume produced by laser ablation of silver at fluences of 0.8-1.3 J cm(-2) at 355 nm have been studied using a time-resolving Langmuir probe. The angular dependence of the electron temperature...

  12. Comparison of three plasma expanders used as priming fluids in cardiopulmonary bypass patients

    NARCIS (Netherlands)

    Tigchelaar, Izaak; Huet, Rolf C. G. Gallandat; Boonstra, Piet W.; van Oeveren, Willem

    Ten per cent low molecular weight hydroxyethyl starch is a plasma substitute only recently used as priming solution in an extracorporeal circuit, in contrast to human albumin and gelatin. To evaluate the effect of priming solutions on haemodynamics and colloid osmotic pressure, we studied 36

  13. Clonal expansion of renal cell carcinoma-infiltrating T lymphocytes

    NARCIS (Netherlands)

    Sittig, S.P.; Kollgaard, T.; Gronbaek, K.; Idorn, M.; Hennenlotter, J.; Stenzl, A.; Gouttefangeas, C.; Straten, P. Thor

    2013-01-01

    T lymphocytes can mediate the destruction of cancer cells by virtue of their ability to recognize tumor-derived antigenic peptides that are presented on the cell surface in complex with HLA molecules and expand. Thus, the presence of clonally expanded T cells within neoplastic lesions is an

  14. Emission spectroscopy of expanding laser-induced gaseous hydrogen-nitrogen plasma.

    Science.gov (United States)

    Gautam, Ghaneshwar; Parigger, Christian G; Helstern, Christopher M; Drake, Kyle A

    2017-11-20

    Microplasma is generated in an ultra-high-pure H2 and N2 gas mixture with a Nd:YAG laser device that is operated at the fundamental wavelength of 1064 nm. The gas mixture ratio of H2 and N2 is 9 to 1 at a pressure of 1.21 ± 0.03 105 Pa inside a chamber. A Czerny-Turner-type spectrometer and an intensified charge-coupled device are utilized for the recording of plasma emission spectra. The line-of-sight measurements are Abel inverted to determine the radial distributions of electron number density and temperature. Recently derived empirical formulas are utilized for the extraction of values for electron density. The Boltzmann plot and line-to-continuum methods are implemented for the diagnostic of electron excitation temperature. The expansion speed of the plasma kernel maximum electron temperature amounts to 1  km/s at a time delay of 300 ns. The microplasma, initiated by focusing 14 ns, 140 mJ pulses, can be described by an isentropic expansion model.

  15. Particle dynamics and current-free double layers in an expanding, collisionless, two-electron-population plasma

    Science.gov (United States)

    Hairapetian, G.; Stenzel, R. L.

    1991-01-01

    The expansion of a two-electron-population, collisionless plasma into vacuum has been examined in detail. Plasma density, plasma potential, electric field, and particle disribution functions have been measured in situ. It is demonstrated that the presence of a low-pressure (P not less than 2 x 10 to the -5th torr) background neutral gas modifies the expansion of the plasma. A new plasma source creating dense, pulsed discharge plasma with a low background pressure (P not greater than 2 x 10 to the -6th torr) has been developed to perform in situ measurements of the temporal and spatial plasma evolution during its expansion into vacuum.

  16. An expanded self-antigen peptidome is carried by the human lymph as compared to the plasma.

    Directory of Open Access Journals (Sweden)

    Cristina C Clement

    2010-03-01

    Full Text Available The pre-nodal afferent lymph is the fluid which directly derives from the extracellular milieu from every parenchymal organ and, as it continues to circulate between the cells, it collects products deriving from the organ metabolism/catabolism. A comprehensive qualitative and quantitative investigation of the self-antigenic repertoire transported by the human lymph is still missing.A major difference between lymph and plasma could be visualized by FPLC and 2D gel in the amount of low molecular weight products corresponding to peptide fragments. Naturally processed peptides in normal pre-nodal human lymph were then fractionated by HPLC and characterized by multidimensional mass spectrometry. Analysis of more then 300 sequences identified self-peptides derived from both intracellular and extracellular proteins revealing the variety of catabolic products transported by human lymph. Quantitative analysis established that at least some of these peptides are present in the circulating lymph in nanomolar concentration.The peptidome, generated by physiological tissue catabolism and transported by the pre-nodal lymph, is in addition to the self-peptidome generated in endosomal compartment. Unlike self antigen processed by local or nodal APC, which mostly produce epitopes constrained by the endosomal processing activity, self antigens present in the lymph could derived from a wider variety of processing pathways; including caspases, involved in cellular apoptosis, and ADAM and other metalloproteinases involved in surface receptor editing, cytokines processing and matrix remodeling. Altogether, expanding the tissue-specific self-repertoire available for the maintenance of immunological tolerance.

  17. Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides.

    Science.gov (United States)

    Egan, Jan B; Shi, Chang-Xin; Tembe, Waibhav; Christoforides, Alexis; Kurdoglu, Ahmet; Sinari, Shripad; Middha, Sumit; Asmann, Yan; Schmidt, Jessica; Braggio, Esteban; Keats, Jonathan J; Fonseca, Rafael; Bergsagel, P Leif; Craig, David W; Carpten, John D; Stewart, A Keith

    2012-08-02

    The longitudinal evolution of a myeloma genome from diagnosis to plasma cell leukemia has not previously been reported. We used whole-genome sequencing (WGS) on 4 purified tumor samples and patient germline DNA drawn over a 5-year period in a t(4;14) multiple myeloma patient. Tumor samples were acquired at diagnosis, first relapse, second relapse, and end-stage secondary plasma cell leukemia (sPCL). In addition to the t(4;14), all tumor time points also shared 10 common single-nucleotide variants (SNVs) on WGS comprising shared initiating events. Interestingly, we observed genomic sequence variants that waxed and waned with time in progressive tumors, suggesting the presence of multiple independent, yet related, clones at diagnosis that rose and fell in dominance. Five newly acquired SNVs, including truncating mutations of RB1 and ZKSCAN3, were observed only in the final sPCL sample suggesting leukemic transformation events. This longitudinal WGS characterization of the natural history of a high-risk myeloma patient demonstrated tumor heterogeneity at diagnosis with shifting dominance of tumor clones over time and has also identified potential mutations contributing to myelomagenesis as well as transformation from myeloma to overt extramedullary disease such as sPCL.

  18. Investigating the flow dynamics and chemistry of an expanding thermal plasma through CH(A-X) emission spectra

    NARCIS (Netherlands)

    Hansen, T. A. R.; Colsters, P. G. J.; M. C. M. van de Sanden,; Engeln, R.

    2011-01-01

    The gas flow in a linear plasma reactor and the plasma chemistry during hydrogenated amorphous carbon and graphite etching are investigated via time and spatially resolved measurements of the ion density and CH emission. A convolution of the ion and hydrocarbon density shows the importance of charge

  19. Clonal evolution in myelodysplastic syndromes

    NARCIS (Netherlands)

    da Silva-Coelho, Pedro; Kroeze, Leonie I.; Yoshida, Kenichi; Koorenhof-Scheele, Theresia N.; Knops, Ruth; van de Locht, Louis T.; de Graaf, Aniek O.; Massop, Marion; Sandmann, Sarah; Dugas, Martin; Stevens-Kroef, Marian J.; Cermak, Jaroslav; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; de Witte, Theo; Blijlevens, Nicole M. A.; Muus, Petra; Huls, Gerwin; van der Reijden, Bert A.; Ogawa, Seishi; Jansen, Joop H.

    2017-01-01

    Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide

  20. Clonality evaluation in human tissues

    Directory of Open Access Journals (Sweden)

    Villamizar-Rivera, Nicolás

    2015-07-01

    Full Text Available Malignant proliferations are usually clonal. While most times the biological potential can be established through routine pathologic and clinical examinations, some cases are difficult to classify. Moreover, in some situations there are dominant clones whose analysis is important, such as in autoimmune diseases and immunodeficiency. This paper presents in an understandable way the main techniques for the study of clonality, namely: evaluation of gene rearrangements of antigen receptor, and evaluation of human antigen receptor gene.

  1. Kinetic approach to the formation of 3D electromagnetic structures in flows of expanding plasma coronas. II. flow anisotropy parameters

    Science.gov (United States)

    Gubchenko, V. M.

    2015-12-01

    The formation of magnetic structures in moving hot solar coronal plasma and hot collisionless laser-produced plasma, as determined by nonlinear criteria for weak and strong magnetization on the basis of the friction parameter Γ B and Alfven number M A, is considered within the Vlasov and Maxwell equations in the second part of the work. The flow velocities are lower then the thermal electron velocity. The energy and pulse anisotropy parameters of a flow, which determine its electromagnetic properties in the Cherenkov resonance line, are calculated by shape of particle distribution function (PDF). The ratio of these parameters is the Q-factor G V ; it characterizes the electromagnetic properties of a plasma flow and is expressed via the ratio of diamagnetic and resistive current densities or via the ratio of irregular and diamagnetic plasma scales. A particle flow is similar to a conductive medium at G V ≪ 1 and a diamagnetic medium at G V ≫ 1. The following cases are considered. (1) A plasma flow is specified by an isotropic PDF and interacts with distributed magnetization. Expressions for anisotropy parameters are derived, 3D field structures in the tail wake are found, and a possibility of topological reconstruction into a compact state under variation in the parameter G V is shown. (2) A plasma flow is specified by an isotropic PDF; a steady-state diamagnetic current layer, characterized by an anisotropic PDF, is immersed inside it. The system is in the diamagnetic state G ≫ 1. The generalized anisotropy parameter is calculated and a possibility of the excitation of three types of diamagnetic structures with low resistive currents is shown. (3) The nonlinear dynamics of anisotropic quasi-current-free plasma ( G =-1), in which the diamagnetic and resistive current densities locally compensate each other in the phase space of particle velocities, is studied. This dynamics is implemented in the long wavelength limit in plasma with an anisotropic PDF.

  2. Clonality of HTLV-2 in natural infection.

    Directory of Open Access Journals (Sweden)

    Anat Melamed

    2014-03-01

    Full Text Available Human T-lymphotropic virus type 1 (HTLV-1 and type 2 (HTLV-2 both cause lifelong persistent infections, but differ in their clinical outcomes. HTLV-1 infection causes a chronic or acute T-lymphocytic malignancy in up to 5% of infected individuals whereas HTLV-2 has not been unequivocally linked to a T-cell malignancy. Virus-driven clonal proliferation of infected cells both in vitro and in vivo has been demonstrated in HTLV-1 infection. However, T-cell clonality in HTLV-2 infection has not been rigorously characterized. In this study we used a high-throughput approach in conjunction with flow cytometric sorting to identify and quantify HTLV-2-infected T-cell clones in 28 individuals with natural infection. We show that while genome-wide integration site preferences in vivo were similar to those found in HTLV-1 infection, expansion of HTLV-2-infected clones did not demonstrate the same significant association with the genomic environment of the integrated provirus. The proviral load in HTLV-2 is almost confined to CD8+ T-cells and is composed of a small number of often highly expanded clones. The HTLV-2 load correlated significantly with the degree of dispersion of the clone frequency distribution, which was highly stable over ∼8 years. These results suggest that there are significant differences in the selection forces that control the clonal expansion of virus-infected cells in HTLV-1 and HTLV-2 infection. In addition, our data demonstrate that strong virus-driven proliferation per se does not predispose to malignant transformation in oncoretroviral infections.

  3. [Cell clonality in myelodysplastic syndrome].

    Science.gov (United States)

    Krejcová, H; Neuwirtová, R; Cermák, J; Belicková, M; Brdicka, R

    2002-01-01

    Myelodysplastic syndromes (MDS) are classified as oncohematologic, clonal diseases. However, some MDS subtypes lack malignant clinical features. Literary data on the clonality of blood cells in MDS are controversial. Therefore we examined the clonality in the group of our own MDS patients. We were especially interested in the comparison of the clonality of myeloid and lymphoid cell line-ages. Using X-chromosome inactivation methods based on polymorphism in human androgen receptor gene (HUMARA), iduronate sulphatase gene (IDS) and protein p55 gene, we assessed the clonality of granulocytes, monocytes and T-lymphocytes of 49 female patients with MDS and 12 control women of various ages. Though the results were heterogeneous, certain trends were observed: most frequently monoclonality of monocytes was found (51%), granulocytes were monoclonal in 33% of cases, monoclonal T lymphocytes only in 8% of cases. There was no case with monoclonal T lymphocytes and simultaneously polyclonal myeloid cell fractions. Results differ in relation to the subtypes of MDS. Among controls we observed monoclonality of myeloid cells in one case of an old lady. WE CONCLUDE: The results confirm the presence of malignant clone of myeloid cells in MDS, which can be of variable size. The examination of the clonality in MDS can be significant for the therapy decision. Monoclonal myeloid cells are found least frequently in refractory anemia, most frequently in RAEB-T. Monoclonality of cells in sideroblastic anemia is interesting. The prevailing polyclonality of T lymphocytes in MDS can be explained by the presence of a long-lived cell population originating from the period before the development of MDS. The role of the polyclonal memory T cells in the antitumor immunity in MDS is discussed.

  4. Role of Parallel and Oblique Ion-Cyclotron Waves in Heating Ions in an Inhomogeneous Expanding Solar Wind Plasma

    Science.gov (United States)

    Ofman, L.; Ozak, N. O.; Vinas, A. F.

    2014-12-01

    In-situ observations of fast solar wind streams at distances of 0.29 AU and beyond by Helios and recently by MESSENGER, and at ~1 AU by STEREO, ACE, and Wind spacecraft provide direct evidence for the presence of turbulent Alfvén wave spectrum and of left-hand polarized ion-cyclotron waves as well as He++ - proton drift in the solar wind plasma. The waves and the super-Alfvénic drift can produce temperature anisotropies by resonant absorption and perpendicular heating of the ions. Measurements indicate that proton velocity distributions are generally non-Maxwellian with evidence for beams, while remote sensing observations of coronal holes have shown that heavy ions are hotter than protons with a temperature anisotropy greater than one (Ti,perp> Ti,||). In addition to the anisotropy, it is expected that the solar wind will be inhomogeneous on decreasing scales approaching the Sun. Here we use a 2.5 D hybrid code and extend previous work to study the heating of solar wind ions (H+, He+) in an inhomogeneous plasma background. We explore the effects of an initial ion drift and of a turbulent wave spectrum on the perpendicular ion heating and cooling and on the spectrum of the magnetic fluctuations in the inhomogeneous background solar wind. Using the 2D hybrid model we find that inhomogeneities in the plasma generate significant power of oblique waves in the solar wind plasma, in addition to enhanced heating compared to the homogenous solar wind case. We find that the cooling effect due to the solar wind expansion is only significant when sub-Alfvénic drifts are explored. On the other hand, the cooling is not significant in the presence of a super-Alfvénic drift, and it is even less significant when we include an inhomogeneous background density. We are able to reproduce the ion temperature anisotropy seen in observations and previous models and find that small-scale inhomogeneities in the inner heliosphere can have a significant impact on resonant wave ion

  5. Surface reactivity of molybdenum thin films exposed to (Ar-N{sub 2}-H{sub 2}) expanding microwave plasma at low temperature: influence of the addition of H{sub 2} gas in the plasma

    Energy Technology Data Exchange (ETDEWEB)

    Jauberteau, I [UMR 6638 CNRS, SPCTS, Faculte des Sciences et Techniques, F-87060 Limoges cedex (France); Jauberteau, J L [UMR 6638 CNRS, SPCTS, Faculte des Sciences et Techniques, F-87060 Limoges cedex (France); Cahoreau, M [UMR 6630 CNRS, SP2MI, UFR des Sciences, Bd3, Teleport 2, BP 179, F-86960 Futuroscope (France); Aubreton, J [UMR 6638 CNRS, SPCTS, Faculte des Sciences et Techniques, F-87060 Limoges cedex (France)

    2005-10-07

    The rapid transfer of a large amount of nitrogen into the surface layers followed by diffusion into the inner layers occurs in thin molybdenum films exposed to expanding microwave plasma using (Ar-35%N{sub 2}) and (Ar-25%N{sub 2}-30%H{sub 2}) gas mixtures. The nitrogen transfer into the surface layers nearly correlates to a Gaussian distribution law, which is explained by the formation of a large number of defects at the film surface in which nitrogen piles up before diffusing into the inner metal layers. Such an effect could be induced by the impinging energetic plasma species as ions, NH{sub x<3} radicals. The diffusion part is successfully fitted to Fick's second law by introducing diffusion coefficients of about (5-7) x 10{sup -14} cm{sup 2} s{sup -1} at 673 K. These values are lower than the diffusion coefficient calculated for a solid solution of nitrogen in molybdenum which is equal to about 4 x 10{sup -13} cm{sup 2} s{sup -1}. A surprisingly high diffusion coefficient of about 3 x 10{sup -13} cm{sup 2} s{sup -1} is found for the molybdenum film exposed to (Ar-25%N{sub 2}-30%H{sub 2}) plasma at room temperature. These results highlight the role of plasma hydrogen species on the enhancement of the metal surface reactivity and nitrogen diffusion into the inner metal layers. A modification of the morphology of the film surface exposed to hydrogen species is also seen. The values of electron densities measured in the various (Ar-N{sub 2}-H{sub 2}) gas mixtures are consistent with the formation of expanded plasma far from the centre of the discharge, apart from(Ar-30%N{sub 2}-12%H{sub 2}) where the plasma expansion is very low. At a distance of 10.5 cm from the centre of the discharge, the electron density is equal to about 1.66 x 10{sup 17} m{sup -3} and 1.16 x 10{sup 17} m{sup -3} for (Ar-25%N{sub 2}-30%H{sub 2}) and (Ar-35%N{sub 2}) gas mixtures, respectively.

  6. Clonal nature of odontogenic tumours.

    Science.gov (United States)

    Gomes, Carolina Cavaliéri; Oliveira, Carla da Silveira; Castro, Wagner Henriques; de Lacerda, Júlio César Tanos; Gomez, Ricardo Santiago

    2009-04-01

    Although clonal origin is an essential step in the comprehension of neoplasias, there have been no studies to examine whether odontogenic tumours are derived from a single somatic progenitor cell. The purpose of this study was to investigate the clonal origin of odontogenic tumours. Fresh samples of seven ameloblastomas, two odontogenic mixomas, two adenomatoid odontogenic tumour, one calcifying odontogenic cyst, one calcifying epithelial odontogenic tumour (CEOT) and six odontogenic keratocyst (OKC) of female patients were included in this study. After DNA extraction, the HUMARA gene polymorphism assay was performed. Most of the informative odontogenic lesions studied (12 out of 16) showed a monoclonal pattern. Among the polyclonal cases, two were OKC, one CEOT and one odontogenic mixoma. Our results suggest that most odontogenic tumours are monoclonal.

  7. Clonal evolution in myelodysplastic syndromes

    OpenAIRE

    da Silva-Coelho, Pedro; Kroeze, Leonie I.; Yoshida, Kenichi; Koorenhof-Scheele, Theresia N.; Knops, Ruth; van de Locht, Louis T.; de Graaf, Aniek O.; Massop, Marion; Sandmann, Sarah; Dugas, Martin; Stevens-Kroef, Marian J.; Cermak, Jaroslav; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko

    2017-01-01

    Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5?11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without...

  8. Measles virus–specific plasma cells are prominent in subacute sclerosing panencephalitis CSF

    Science.gov (United States)

    Owens, G.P.; Ritchie, A.M.; Gilden, D.H.; Burgoon, M.P.; Becker, D.; Bennett, J.L.

    2012-01-01

    Objective To demonstrate the specificity of expanded CD138+ plasma cell clones recovered from the CSF of a patient with subacute sclerosing panencephalitis (SSPE) for measles virus (MV). Methods IgG variable region sequences of single-antibody-secreting CD138+ cells sorted from SSPE CSF were amplified by single-cell PCR and analyzed. Human IgG1 recombinant antibodies (rAbs) were produced from four expanded CD138+ clones and assayed for immunoreactivity against MV proteins. Results Clonal expansion was a prominent feature of the SSPE plasma cell repertoire, and each of the four rAbs assayed was specific for either the MV fusion or the MV nucleocapsid protein. Conclusions Expanded plasma cell clones in the CSF of patients with subacute sclerosing panencephalitis produce disease-relevant antibodies. Recombinant antibodies derived from CSF B cells could provide a tool to identify target antigens in idiopathic inflammatory disorders. PMID:17515543

  9. Differential effect of platelet-rich plasma and fetal calf serum on bone marrow-derived human mesenchymal stromal cells expanded in vitro.

    Science.gov (United States)

    Goedecke, Anja; Wobus, Manja; Krech, Mathias; Münch, Nadine; Richter, Katja; Hölig, Kristina; Bornhauser, Martin

    2011-08-01

    Mesenchymal stromal cells (MSCs) derived from various sources have great potential for use in cell-based therapies. Since the proportion of primary MSCs contained in bone marrow or adipose tissue is low, plastic adherence and in vitro expansion are necessary to expand MSCs prior to clinical application. Human platelet-rich plasma has been introduced as an alternative serum source but functional differences have so far not been described. Here we cultured MSCs derived from human bone marrow in medium supplemented with either 10% fetal calf serum (FCS) or 5% and 10% platelet-rich plasma (PRP) until the first or second passage. Parameters under investigation were cell yield, clonogenicity, phenotype as well as migratory and differentiation potential. In addition, the secretion of SDF-1α and the induced migration of CD34(+) haematopoietic stem cells (HSCs) were investigated with regard to the different serum source. The use of PRP resulted in a significantly higher expansion rate and yield at passages 0 and 1. In addition, the level of secreted SDF-1α was significantly increased in the supernatant of MSCs cultured with FCS instead of human PRP. Consistent with this, the migration capacity of MSCs cultured with 10% FCS as well as their capability to induce the migration of CD34(+) haematopoietic progenitors in a transwell assay was higher. Our results demonstrate that human PRP can be seen as an alternative serum source to FCS for MSC cultivation. However, the requirements of the specific clinical application must be carefully considered before the respective serum source is selected. Copyright © 2010 John Wiley & Sons, Ltd.

  10. Clonality as a driver of spatial genetic structure in populations of clonal tree species.

    Science.gov (United States)

    Dering, Monika; Chybicki, Igor Jerzy; Rączka, Grzegorz

    2015-09-01

    Random genetic drift, natural selection and restricted gene dispersal are basic factors of the spatial genetic structure (SGS) in plant populations. Clonal reproduction has a profound effect on population dynamics and genetic structure and thus emerges as a potential factor in contributing to and modelling SGS. In order to assess the impact of clonality on SGS we studied clonal structure and SGS in the population of Populus alba. Six hundred and seventy-two individuals were mapped and genotyped with 16 nuclear microsatellite markers. To answer the more general question regarding the relationship between SGS and clonality we used Sp statistics, which allows for comparisons of the extent of SGS among different studies, and the comparison of published data on SGS in clonal and non-clonal tree species. Sp statistic was extracted for 14 clonal and 27 non-clonal species belonging to 7 and 18 botanical families, respectively. Results of genetic investigations conducted in the population of P. alba showed over-domination of clonal reproduction, which resulted in very low clonal diversity (R = 0.12). Significant SGS was found at both ramet (Sp = 0.095) and genet level (Sp = 0.05) and clonal reproduction was indicated as an important but not sole driving factor of SGS. Within-population structure, probably due to family structure also contributed to high SGS. High mean dominance index (D = 0.82) indicated low intermingling among genets. Literature survey revealed that clonal tree species significantly differ from non-clonal species with respect to SGS, having 2.8-fold higher SGS. This led us to conclude that clonality is a life-history trait that can have deep impact on processes acting in populations of clonal tree species leading to significant SGS.

  11. Replacing the Transfusion of 1–2 Units of Blood with Plasma Expanders that Increase Oxygen Delivery Capacity: Evidence from Experimental Studies

    Directory of Open Access Journals (Sweden)

    Amy G. Tsai

    2014-10-01

    Full Text Available At least a third of the blood supply in the world is used to transfuse 1–2 units of packed red blood cells for each intervention and most clinical trials of blood substitutes have been carried out at this level of oxygen carrying capacity (OCC restoration. However, the increase of oxygenation achieved is marginal or none at all for molecular hemoglobin (Hb products, due to their lingering vasoactivity. This has provided the impetus for the development of “oxygen therapeutics” using Hb-based molecules that have high oxygen affinity and target delivery of oxygen to anoxic areas. However it is still unclear how these oxygen carriers counteract or mitigate the functional effects of anemia due to obstruction, vasoconstriction and under-perfusion. Indeed, they are administered as a low dosage/low volume therapeutic Hb (subsequently further diluted in the circulatory pool and hence induce extremely small OCC changes. Hyperviscous plasma expanders provide an alternative to oxygen therapeutics by increasing the oxygen delivery capacity (ODC; in anemia they induce supra-perfusion and increase tissue perfusion (flow by as much as 50%. Polyethylene glycol conjugate albumin (PEG-Alb accomplishes this by enhancing the shear thinning behavior of diluted blood, which increases microvascular endothelial shear stress, causes vasodilation and lowering peripheral vascular resistance thus facilitating cardiac function. Induction of supra-perfusion takes advantage of the fact that ODC is the product of OCC and blood flow and hence can be maintained by increasing either or both. Animal studies suggest that this approach may save a considerable fraction of the blood supply. It has an additional benefit of enhancing tissue clearance of toxic metabolites.

  12. Clonal evolution in myelodysplastic syndromes

    Science.gov (United States)

    da Silva-Coelho, Pedro; Kroeze, Leonie I.; Yoshida, Kenichi; Koorenhof-Scheele, Theresia N.; Knops, Ruth; van de Locht, Louis T.; de Graaf, Aniek O.; Massop, Marion; Sandmann, Sarah; Dugas, Martin; Stevens-Kroef, Marian J.; Cermak, Jaroslav; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; de Witte, Theo; Blijlevens, Nicole M. A.; Muus, Petra; Huls, Gerwin; van der Reijden, Bert A.; Ogawa, Seishi; Jansen, Joop H.

    2017-01-01

    Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5–11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions. PMID:28429724

  13. Importance of the infusion rate for the plasma expanding effect of 5% albumin, 6% HES 130/0.4, 4% gelatin, and 0.9% NaCl in the septic rat.

    Science.gov (United States)

    Bark, Björn P; Persson, Johan; Grände, Per-Olof

    2013-03-01

    To compare the plasma volume (PV) expanding effect of a fast infusion rate with that of a slow infusion rate of a fixed volume of 5% albumin, of the synthetic colloids, 6% hydroxyethyl starch 130/0.4 and 4% gelatin, and of 0.9% NaCl in a rat sepsis model and to compare the plasma-expanding effect among these fluids. Prospective, randomized animal study. University hospital laboratory. One hundred and twelve adult male rats. Sepsis was induced by cecal ligation and incision followed by closure of the abdomen. After 3 hrs, an infusion of the PV expander under study was started at a volume of 12mL/kg for the colloids and of 48mL/kg for 0.9% NaCl, either for 15 mins or for 3 hrs. A control group underwent the same experimental procedure but no fluid was given. Three hours after start of the infusion (end of experiment), the plasma-expanding effect was better with a slow than a fast infusion rate for the colloids, especially albumin, but the NaCl groups did not differ significantly from the control group. The PV for the control group was 28.7±3mL/kg. In the slow and the fast infusion groups, it was 38.9±4.3 and 32.6±4.2mL/kg for albumin (p colloid was greater when given at a slow than at a fast infusion rate, an effect more pronounced for albumin. This difference was not seen for NaCl. The PV-expanding effect was poor for NaCl and better for albumin than for the other colloids.

  14. [Pooled Umbilical Cord Blood Plasma for Culturing UCMSC and Ex Vivo Expanding Umbilical Cord Blood CD34⁺ Cells].

    Science.gov (United States)

    Wu, Jie-Ying; Lu, Yan; Chen, Jin-Song; Wu, Shao-Qing; Tang, Xue-Wei; Li, Yan

    2015-08-01

    To investigate the feasibility of umbilical cord blood plasma (UCP) as a replacement for fetal bovine serum (FBS) for culturing mesenchymal stem cells (MSC) derived from umbilical cord, and to observe the supporting effects of these cells (served as a feeder layer) on ex vivo expanding of human umbilical cord blood CD34(+) cells. Umbilical cord blood (UCB) units were suitable if the Guangzhou cord blood bank donor selection criteria strictly were fulfilled. UCP were ready to use after the collection from the plasma depletion/reduction during the processing and pooling of suitable UCB units (at least 30 units were screened for pathogens and microorganisms, and qualified). Umbilical cord mesenchymal stem cells (UCMSC) were harvested from the umbilical cord tissue of health full-term newborns after delivery by enzyme digestion and divided into 3 groups: group 1 and 2 were cultured in the presence of DMEM/F12 containing either FBS or UCP; and group 3 was cultured in serum-free medium (StemPro® MSC SFM CTS™). Morphology, proliferation and surface marker expression were examined by flow cytometry, and the differentiation toward adipogenic and osteogenic lineages was used for investigating the effect of media on UCMSC after 3-5 passages. Next, the cells cultured in the three different media were cryopreserved and thawed, then prepared as feeder layers with the name of UCMSC(FBS), UCMSC(UCP), and UCMSC(SFM), respectively. The CD34⁺ cells were separated from UCB by magnetic activated cell sorting (MACS) and divided into 4 groups cultured in StemPro(-34) SFM medium added with hematopoietic cytokine combination (StemSpan® CC100). The control group included only CD34⁺ cells as group A (blank control) and experimental groups included UCMSC(FBS) + CD34⁺ cells as group B, UCMSC(UCP) + CD34⁺ cells as group C, UCMSC(SFM) + CD34⁺ cells as group D, and cells in all groups were cultured ex vivo for 7 days. The nucleated cell (NC) number was counted by cell counter, CD34

  15. Expanding subjectivities

    DEFF Research Database (Denmark)

    Lundgaard Andersen, Linda; Soldz, Stephen

    2012-01-01

    A major theme in recent psychoanalytic thinking concerns the use of therapist subjectivity, especially “countertransference,” in understanding patients. This thinking converges with and expands developments in qualitative research regarding the use of researcher subjectivity as a tool to understa...

  16. Expander Codes

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 1. Expander Codes - The Sipser–Spielman Construction. Priti Shankar. General Article Volume 10 ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science Bangalore 560 012, India.

  17. Porphyromonas gingivalis: a clonal pathogen?

    Directory of Open Access Journals (Sweden)

    Morten Enersen

    2011-11-01

    Full Text Available The introduction of multilocus sequence typing (MLST in infectious disease research has allowed standardized typing of bacterial clones. Through multiple markers around the genome, it is possible to determine the sequence type (ST of bacterial isolates to establish the population structure of a species. For the periodontal pathogen, Porphyromonas gingivalis, the MLST scheme has been established at www.pubmlst.org/pgingivalis, and data from the database indicate a high degree of genetic diversity and a weakly clonal population structure comparable with Neisseria menigitidis. The major fimbriae (FimA have been held responsible for the adhesive properties of P. gingivalis and represent an important virulence factor. The fimA genotyping method (PCR based indicate that fimA genotype II, IV and Ib are associated with diseased sites in periodontitis and tissue specimens from cardiovascular disease. fimA genotyping of the isolates in the MLST database supports the association of genotypes II and IV with periodontitis. As a result of multiple positive PCR reactions in the fimA genotyping, sequencing of the fimA gene revealed only minor nucleotide variation between isolates of the same and different genotypes, suggesting that the method should be redesigned or re-evaluated. Results from several investigations indicate a higher intraindividual heterogeneity of P. gingivalis than found earlier. Detection of multiple STs from one site in several patients with “refractory” periodontitis, showed allelic variation in two housekeeping genes indicating recombination between different clones within the periodontal pocket.

  18. Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing

    Science.gov (United States)

    Ding, Li; Ley, Timothy J.; Larson, David E.; Miller, Christopher A.; Koboldt, Daniel C.; Welch, John S.; Ritchey, Julie K.; Young, Margaret A.; Lamprecht, Tamara; McLellan, Michael D.; McMichael, Joshua F.; Wallis, John W.; Lu, Charles; Shen, Dong; Harris, Christopher C.; Dooling, David J.; Fulton, Robert S.; Fulton, Lucinda L.; Chen, Ken; Schmidt, Heather; Kalicki-Veizer, Joelle; Magrini, Vincent J.; Cook, Lisa; McGrath, Sean D.; Vickery, Tammi L.; Wendl, Michael C.; Heath, Sharon; Watson, Mark A.; Link, Daniel C.; Tomasson, Michael H.; Shannon, William D.; Payton, Jacqueline E.; Kulkarni, Shashikant; Westervelt, Peter; Walter, Matthew J.; Graubert, Timothy A.; Mardis, Elaine R.; Wilson, Richard K.; DiPersio, John F.

    2011-01-01

    Summary Most patients with acute myeloid leukemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level1,2. To determine the mutational spectrum associated with relapse, we sequenced the primary tumor and relapse genomes from 8 AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to precisely define clonality and clonal evolution patterns at relapse. Besides discovering novel, recurrently mutated genes (e.g. WAC, SMC3, DIS3, DDX41, and DAXX) in AML, we found two major clonal evolution patterns during AML relapse: 1) the founding clone in the primary tumor gained mutations and evolved into the relapse clone, or 2) a subclone of the founding clone survived initial therapy, gained additional mutations, and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific vs. primary tumor mutations in all 8 cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped in part by the chemotherapy that the patients receive to establish and maintain remissions. PMID:22237025

  19. Clonal expansion under the microscope: studying lymphocyte activation and differentiation using live-cell imaging.

    Science.gov (United States)

    Polonsky, Michal; Chain, Benjamin; Friedman, Nir

    2016-03-01

    Clonal expansion of lymphocytes is a hallmark of vertebrate adaptive immunity. A small number of precursor cells that recognize a specific antigen proliferate into expanded clones, differentiate and acquire various effector and memory phenotypes, which promote effective immune responses. Recent studies establish a large degree of heterogeneity in the level of expansion and in cell state between and within expanding clones. Studying these processes in vivo, while providing insightful information on the level of heterogeneity, is challenging due to the complex microenvironment and the inability to continuously track individual cells over extended periods of time. Live cell imaging of ex vivo cultures within micro fabricated arrays provides an attractive methodology for studying clonal expansion. These experiments facilitate continuous acquisition of a large number of parameters on cell number, proliferation, death and differentiation state, with single-cell resolution on thousands of expanding clones that grow within controlled environments. Such data can reveal stochastic and instructive mechanisms that contribute to observed heterogeneity and elucidate the sequential order of differentiation events. Intercellular interactions can also be studied within these arrays by following responses of a controlled number of interacting cells, all trapped within the same microwell. Here we describe implementations of live-cell imaging within microwell arrays for studies of lymphocyte clonal expansion, portray insights already gained from these experiments and outline directions for future research. These tools, together with in vivo experiments tracking single-cell responses, will expand our understanding of adaptive immunity and the ways by which it can be manipulated.

  20. Partition expanders

    Czech Academy of Sciences Publication Activity Database

    Gavinsky, Dmitry; Pudlák, Pavel

    2017-01-01

    Roč. 60, č. 3 (2017), s. 378-395 ISSN 1432-4350 R&D Projects: GA ČR GBP202/12/G061 Institutional support: RVO:67985840 Keywords : expanders * pseudorandomness * communication complexity Subject RIV: BA - General Mathematics Impact factor: 0.645, year: 2016 http://link.springer.com/article/10.1007%2Fs00224-016-9738-5

  1. Expanding versus non expanding universe

    CERN Document Server

    Alfonso-Faus, Antonio

    2012-01-01

    In cosmology the number of scientists using the framework of an expanding universe is very high. This model, the big-bang, is now overwhelmingly present in almost all aspects of society. It is the main stream cosmology of today. A small number of scientists are researching on the possibility of a non-expanding universe. The existence of these two groups, one very large and the other very small, is a good proof of the use of the scientific method: it does not drive to an absolute certainty. All models have to be permanently validated, falsified. Ockham's razor, a powerful philosophical tool, will probably change the amount of scientists working in each of these groups. We present here a model where a big-bang is unnecessary. It ends, in a finite time, in a second INFLATION, or a disaggregation to infinity. We also discuss the possibilities of a non-expanding universe model. Only a few references will be cited, mainly concerned with our own work in the past, thus purposely avoiding citing the many thousands of ...

  2. Transmission of clonal chromosomal abnormalities in human hematopoietic stem and progenitor cells surviving radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Kraft, Daniela, E-mail: d.kraft@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Ritter, Sylvia, E-mail: s.ritter@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Durante, Marco, E-mail: m.durante@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Institute for Condensed Matter Physics, Physics Department, Technical University Darmstadt, Hochschulstraße 6-8, 64289 Darmstadt (Germany); Seifried, Erhard, E-mail: e.seifried@blutspende.de [Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Fournier, Claudia, E-mail: c.fournier@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Tonn, Torsten, E-mail: t.tonn@blutspende.de [Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Technische Universität Dresden, Med. Fakultät Carl Gustav Carus, Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, Blasewitzer Straße 68/70, 01307 Dresden (Germany)

    2015-07-15

    Highlights: • Radiation induced formation and transmission of chromosomal aberrations were assessed. • Cytogenetic analysis was performed in human CD34+ HSPC by mFISH. • We report transmission of stable aberrations in irradiated, clonally expanded HSPC. • Unstable aberrations in clonally expanded HSPC occur independently of irradiation. • Carbon ions and X-rays bear a similar risk for propagation of cytogenetic changes. - Abstract: In radiation-induced acute myeloid leukemia (rAML), clonal chromosomal abnormalities are often observed in bone marrow cells of patients, suggesting that their formation is crucial in the development of the disease. Since rAML is considered to originate from hematopoietic stem and progenitor cells (HSPC), we investigated the frequency and spectrum of radiation-induced chromosomal abnormalities in human CD34{sup +} cells. We then measured stable chromosomal abnormalities, a possible biomarker of leukemia risk, in clonally expanded cell populations which were grown for 14 days in a 3D-matrix (CFU-assay). We compared two radiation qualities used in radiotherapy, sparsely ionizing X-rays and densely ionizing carbon ions (29 and 60–85 keV/μm, doses between 0.5 and 4 Gy). Only a negligible number of de novo arising, unstable aberrations (≤0.05 aberrations/cell, 97% breaks) were measured in the descendants of irradiated HSPC. However, stable aberrations were detected in colonies formed by irradiated HSPC. All cells of the affected colonies exhibited one or more identical aberrations, indicating their clonal origin. The majority of the clonal rearrangements (92%) were simple exchanges such as translocations (77%) and pericentric inversions (15%), which are known to contribute to the development of rAML. Carbon ions were more efficient in inducing cell killing (maximum of ∼30–35% apoptotic cells for 2 Gy carbon ions compared to ∼25% for X-rays) and chromosomal aberrations in the first cell-cycle after exposure (∼70% and

  3. Expanded Dengue.

    Science.gov (United States)

    Kadam, D B; Salvi, Sonali; Chandanwale, Ajay

    2016-07-01

    The World Health Organization (WHO) has coined the term expanded dengue to describe cases which do not fall into either dengue shock syndrome or dengue hemorrhagic fever. This has incorporated several atypical findings of dengue. Dengue virus has not been enlisted as a common etiological agent in several conditions like encephalitis, Guillain Barre syndrome. Moreover it is a great mimic of co-existing epidemics like Malaria, Chikungunya and Zika virus disease, which are also mosquito-borne diseases. The atypical manifestations noted in dengue can be mutisystemic and multifacetal. In clinical practice, the occurrence of atypical presentation should prompt us to investigate for dengue. Knowledge of expanded dengue helps to clinch the diagnosis of dengue early, especially during ongoing epidemics, avoiding further battery of investigations. Dengue has proved to be the epidemic with the ability to recur and has a diverse array of presentation as seen in large series from India, Srilanka, Indonesia and Taiwan. WHO has given the case definition of dengue fever in their comprehensive guidelines. Accordingly, a probable case is defined as acute febrile illness with two or more of any findings viz. headache, retro-orbital pain, myalgia, arthralgia, rash, hemorrhagic manifestations, leucopenia and supportive serology. There have been cases of patients admitted with fever, altered mentation with or without neck stiffness and pyramidal tract signs. Some had seizures or status epilepticus as presentation. When they were tested for serology, dengue was positive. After ruling out other causes, dengue remained the only culprit. We have come across varied presentations of dengue fever in clinical practice and the present article throws light on atypical manifestations of dengue. © Journal of the Association of Physicians of India 2011.

  4. Clonal integration increases tolerance of a phalanx clonal plant to defoliation.

    Science.gov (United States)

    Wang, Pu; Li, Huan; Pang, Xiao-Yu; Wang, Ao; Dong, Bi-Cheng; Lei, Jing-Pin; Yu, Fei-Hai; Li, Mai-He

    2017-09-01

    Defoliation by herbivores commonly imposes negative effects on plants, and physiological integration (resource sharing) can enhance the ability of guerilla clonal plants to tolerate stresses. Here we examined whether physiological integration can increase the ability of phalanx clonal plants to withstand defoliation. On a high mountain grassland in southwestern China, we subjected the phalanx clonal plant Iris delavayi within 10cm×10cm plots to three levels of defoliation intensity, i.e., control (no defoliation), moderate (50% shoot removal to simulate moderate herbivory) and heavy defoliation (100% shoot removal to simulate heavy herbivory), and kept rhizomes at the plot edges connected (allowing physiological integration) or disconnected (preventing integration) with intact ramets outside the plots. Defoliation significantly reduced leaf biomass, root biomass and ramet number of I. delavayi. Clonal integration did not affect the growth of I. delavayi under control, but significantly increased total biomass, rhizome and root biomass under heavy defoliation, and leaf biomass and ramet number under moderate defoliation. We conclude that clonal integration associated with resource reallocation plays an important role in maintaining the productivity of the alpine and subalpine grassland ecosystems in SW China where clonal plants are a dominant component of the grasslands and are commonly extensively managed with moderate grazing intensity. Our results also help to better understand the adaption and tolerance of phalanx clonal plants subjected to long-term grazing in the high mountain environment. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Phenotypic plasticity and specialization in clonal versus non-clonal plants: A data synthesis

    Science.gov (United States)

    Fazlioglu, Fatih; Bonser, Stephen P.

    2016-11-01

    Reproductive strategies can be associated with ecological specialization and generalization. Clonal plants produce lineages adapted to the maternal habitat that can lead to specialization. However, clonal plants frequently display high phenotypic plasticity (e.g. clonal foraging for resources), factors linked to ecological generalization. Alternately, sexual reproduction can be associated with generalization via increasing genetic variation or specialization through rapid adaptive evolution. Moreover, specializing to high or low quality habitats can determine how phenotypic plasticity is expressed in plants. The specialization hypothesis predicts that specialization to good environments results in high performance trait plasticity and specialization to bad environments results in low performance trait plasticity. The interplay between reproductive strategies, phenotypic plasticity, and ecological specialization is important for understanding how plants adapt to variable environments. However, we currently have a poor understanding of these relationships. In this study, we addressed following questions: 1) Is there a relationship between phenotypic plasticity, specialization, and reproductive strategies in plants? 2) Do good habitat specialists express greater performance trait plasticity than bad habitat specialists? We searched the literature for studies examining plasticity for performance traits and functional traits in clonal and non-clonal plant species from different habitat types. We found that non-clonal (obligate sexual) plants expressed greater performance trait plasticity and functional trait plasticity than clonal plants. That is, non-clonal plants exhibited a specialist strategy where they perform well only in a limited range of habitats. Clonal plants expressed less performance loss across habitats and a more generalist strategy. In addition, specialization to good habitats did not result in greater performance trait plasticity. This result was

  6. Phenotypic plasticity, clonal architecture and biomass partitioning in ...

    African Journals Online (AJOL)

    , clonal architecture and biomass partitioning for an aquatic clonal species ... The reduction in size, higher biomass allocations to belowground organs and a more compact growth form (reduced spacer lengths) in case of running water ...

  7. HIV genetic information and clonal growth

    Science.gov (United States)

    Based on an analysis of blood cells from five HIV-infected individuals, NCI researchers have identified more than 2,400 HIV DNA insertion sites. Analysis of these sites showed that there is extensive clonal expansion (growth) of HIV infected cells.

  8. Rhizome elongation and seagrass clonal growth

    NARCIS (Netherlands)

    Marbà, N.; Duarte, C.M.

    1998-01-01

    A compilation of published and original data on rhizome morphometry, horizontal and vertical elongation rates and branching patterns for 27 seagrass species developing in 192 seagrass stands allowed an examination of the variability of seagrass rhizome and clonal growth programmes across and within

  9. PCR clonality detection in Hodgkin lymphoma.

    NARCIS (Netherlands)

    Hebeda, K.M.; Altena, M.C. van; Rombout, P.D.M.; Krieken, J.H.J.M. van; Groenen, P.J.T.A.

    2009-01-01

    B-cell clonality detection in whole tissue is considered indicative of B-cell non-Hodgkin lymphoma (NHL). We tested frozen tissue of 24 classical Hodgkin lymphomas (cHL) with a varying tumor cell load with the multiplex polymerase chain reaction (PCR) primer sets for IGH and IGK gene rearrangement

  10. Assessment of various strategies for the preservation of clonal ...

    African Journals Online (AJOL)

    Field observations carried out on palms originating from somatic embryos cryopreserved at -196 °C showed floral conformity rates comparable to those obtained from standard not-cryopreserved clonal palms, for 6 out of the 8 clonal lines studied. From the 2 remaining clonal lines, a few regenerant palms originating from ...

  11. Multi-jet propulsion organized by clonal development in a colonial siphonophore

    Science.gov (United States)

    Costello, John; Colin, Sean; Gemmell, Brad; Dabiri, John; Sutherland, Kelly

    2015-11-01

    Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labor in thrust and torque production that controls direction and magnitude of whole colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater distributed propulsion vehicle design.

  12. Big Bang Tumor Growth and Clonal Evolution.

    Science.gov (United States)

    Sun, Ruping; Hu, Zheng; Curtis, Christina

    2017-07-14

    The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  13. Drug hypersensitivity in clonal mast cell disorders

    DEFF Research Database (Denmark)

    Bonadonna, P; Pagani, M; Aberer, W

    2015-01-01

    and severity of immediate hypersensitivity reactions. Mastocytosis in adults is associated with a history of anaphylaxis in 22-49%. Fatal anaphylaxis has been described particularly following hymenoptera stings, but also occasionally after the intake of drugs such as nonsteroidal anti-inflammatory drugs...... tryptase determination, physical examination for cutaneous mastocytosis lesions, and clinical characteristics of anaphylactic reaction might be useful for differential diagnosis. In this position paper, the ENDA group performed a literature search on immediate drug hypersensitivity reactions in clonal MC......, opioids and drugs in the perioperative setting. However, data on the frequency of drug hypersensitivity in mastocytosis and vice versa are scarce and evidence for an association appears to be limited. Nevertheless, clonal MC disorders should be ruled out in cases of severe anaphylaxis: basal serum...

  14. Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy.

    Science.gov (United States)

    Mullins, James I; Frenkel, Lisa M

    2017-03-15

    The latent HIV-1 reservoir in blood decays very slowly, even during prolonged suppression of viral replication by antiretroviral therapy (ART). Mechanisms for reservoir persistence include replenishment through low-level viral replication, longevity and homeostatic proliferation of memory T cells, and most recently appreciated, clonal expansion of HIV-infected cells. Clonally expanded cells make up a large and increasing fraction of the residual infected cell population on ART, and insertion of HIV proviruses into certain host cellular genes has been associated with this proliferation. That the vast majority of proviruses are defective clouds our assessment of the degree to which clonally expanded cells harbor infectious viruses, and thus the extent to which they contribute to reservoirs relevant to curing infection. This review summarizes past studies that have defined our current understanding and the gaps in our knowledge of the mechanisms by which proviral integration and clonal expansion sustain the HIV reservoir. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  15. The clonal nature of pityriasis lichenoides.

    Science.gov (United States)

    Weinberg, Jeffrey M; Kristal, Leonard; Chooback, Lillian; Honig, Paul J; Kramer, E Michael; Lessin, Stuart R

    2002-08-01

    Pityriasis lichenoides et varioliformis acuta (PLEVA) and pityriasis lichenoides chronica (PLC) are benign lymphocytic infiltrates of the skin that classically present as either a recurrent papulonecrotic eruption (PLEVA) or a persistent, scaling, papular eruption (PLC). Observations of both types of lesions present on individual patients have led to speculation that both entities are related. Previous studies evaluating the DNA of biopsy specimens from patients with PLEVA and PLC revealed clonal T-cell receptor beta gene rearrangements. To analyze and compare the T-cell populations between lesions of PLEVA and PLC. Retrospective and prospective analysis of patient tissue samples, classified by histologic analysis. Extracted DNA from 13 skin biopsy specimens with the diagnosis of PLC and 14 skin biopsy specimens with the diagnosis of PLEVA was analyzed by polymerase chain reaction/denaturing gradient gel electrophoresis (PCR/DGGE). Molecular diagnostic laboratory at an academic medical center. Twenty-seven tissue samples were obtained from patients with a histologic diagnosis of PLEVA or PLC. These samples were analyzed by PCR/DGGE. The presence or absence of T-cell receptor gene rearrangements on PCR/DGGE analysis corresponding to a clonal population of T cells. Of 14 PLEVA specimens, 8 (57%) demonstrated monoclonal T-cell receptor gene rearrangements; 1 (8%) of 13 PLC specimens showed a gene rearrangement (P =.008, Fisher exact test). Our results demonstrate the polyclonal nature of the lymphocytic infiltrate found in almost all of the PLC specimens, which contrasts with the monoclonal nature found in most of the PLEVA specimens. These differences may represent different stages of the clinical evolution of a single entity that results from varying host immune responses to pathogenic factors. Specifically, we propose that PLEVA is a benign clonal T-cell disorder in which the clone arises from a subset of T cells in lesions of PLC. The host immune response to this

  16. Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.

    Directory of Open Access Journals (Sweden)

    Peter Ashcroft

    2017-10-01

    Full Text Available Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously migrating between these two compartments. Here we construct an individual-based mathematical model of this process, which is parametrised using existing empirical findings from mice. This approach allows us to quantify the amount of migration between the bone marrow niches and the peripheral blood. We use this model to investigate clonal hematopoiesis, which is a significant risk factor for hematologic cancers. We also analyse the engraftment of donor stem cells into non-conditioned and conditioned hosts, quantifying the impact of different treatment scenarios. The simplicity of the model permits a thorough mathematical analysis, providing deeper insights into the dynamics of both the model and of the real-world system. We predict the time taken for mutant clones to expand within a host, as well as chimerism levels that can be expected following transplantation therapy, and the probability that a preconditioned host is reconstituted by donor cells.

  17. Extensive clonal spread and extreme longevity in saw palmetto, a foundation clonal plant.

    Science.gov (United States)

    Takahashi, Mizuki K; Horner, Liana M; Kubota, Toshiro; Keller, Nathan A; Abrahamson, Warren G

    2011-09-01

    The lack of effective tools has hampered out ability to assess the size, growth and ages of clonal plants. With Serenoa repens (saw palmetto) as a model, we introduce a novel analytical framework that integrates DNA fingerprinting and mathematical modelling to simulate growth and estimate ages of clonal plants. We also demonstrate the application of such life-history information of clonal plants to provide insight into management plans. Serenoa is an ecologically important foundation species in many Southeastern United States ecosystems; yet, many land managers consider Serenoa a troublesome invasive plant. Accordingly, management plans have been developed to reduce or eliminate Serenoa with little understanding of its life history. Using Amplified Fragment Length Polymorphisms, we genotyped 263 Serenoa and 134 Sabal etonia (a sympatric non-clonal palmetto) samples collected from a 20 × 20 m study plot in Florida scrub. Sabal samples were used to assign small field-unidentifiable palmettos to Serenoa or Sabal and also as a negative control for clone detection. We then mathematically modelled clonal networks to estimate genet ages. Our results suggest that Serenoa predominantly propagate via vegetative sprouts and 10,000-year-old genets may be common, while showing no evidence of clone formation by Sabal. The results of this and our previous studies suggest that: (i) Serenoa has been part of scrub associations for thousands of years, (ii) Serenoa invasion are unlikely and (ii) once Serenoa is eliminated from local communities, its restoration will be difficult. Reevaluation of the current management tools and plans is an urgent task. © 2011 Blackwell Publishing Ltd.

  18. Clonal Evolution of Autoreactive Germinal Centers.

    Science.gov (United States)

    Degn, Søren E; van der Poel, Cees E; Firl, Daniel J; Ayoglu, Burcu; Al Qureshah, Fahd A; Bajic, Goran; Mesin, Luka; Reynaud, Claude-Agnès; Weill, Jean-Claude; Utz, Paul J; Victora, Gabriel D; Carroll, Michael C

    2017-08-24

    Germinal centers (GCs) are the primary sites of clonal B cell expansion and affinity maturation, directing the production of high-affinity antibodies. This response is a central driver of pathogenesis in autoimmune diseases, such as systemic lupus erythematosus (SLE), but the natural history of autoreactive GCs remains unclear. Here, we present a novel mouse model where the presence of a single autoreactive B cell clone drives the TLR7-dependent activation, expansion, and differentiation of other autoreactive B cells in spontaneous GCs. Once tolerance was broken for one self-antigen, autoreactive GCs generated B cells targeting other self-antigens. GCs became independent of the initial clone and evolved toward dominance of individual clonal lineages, indicating affinity maturation. This process produced serum autoantibodies to a breadth of self-antigens, leading to antibody deposition in the kidneys. Our data provide insight into the maturation of the self-reactive B cell response, contextualizing the epitope spreading observed in autoimmune disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. The role of Aire in clonal selection.

    Science.gov (United States)

    Taniguchi, Ruth T; Anderson, Mark S

    2011-01-01

    In his clonal selection theory, Frank Macfarlane Burnet predicted that autoreactive lymphocytes are deleted to prevent autoimmunity. This and other principles of lymphocyte behavior outlined by Burnet guided many studies that lead to our current understanding of thymic selection. Thus, when the genetic mutation responsible for autoimmune polyglandular syndrome type 1 was mapped to the autoimmune regulator (AIRE) gene, and Aire was found to be highly expressed in thymic epithelium, studying the role of Aire in negative selection made sense in the context of modern models of thymic selection. We now know Aire is a transcription factor required for the expression of many tissue-specific antigens (TSAs) in the thymus. In the absence of functional Aire, human patients and mice develop multi-organ autoimmune disease because of a defect in thymic negative selection. In addition to its role in the thymus, recent work in our lab suggests that extrathymic Aire-expressing cells have an important role in the clonal deletion of autoreactive CD8+ T cells. In this review, we summarize the latest studies on thymic and peripheral Aire-expressing cells, as well as other TSA-expressing stromal cell populations in peripheral lymphoid organs. We also discuss theoretical differences in thymic and peripheral Aire function that warrant further studies.

  20. (Coffea canephora Pierre) Clonal Materials and their Seedling ...

    African Journals Online (AJOL)

    Abstract. The propagation and distribution of robusta coffee (Coffea canephora Pierre), clonal selections in. Uganda has been hampered by logistics. These clonal selections also exhibit a substantial degree of genotype-environmental interaction. Our objectives were to further elucidate the differences between these clones ...

  1. Clonal propagation and storage of subtropical pines in Queensland ...

    African Journals Online (AJOL)

    Clonal forestry is the approach used for deployment of Pinus elliottii x P. caribaea hybrids in Queensland, Australia. Clonal forestry relies on the ability to maintain juvenility of stock plants while selections are made in field tests, so that genetic gains are not eroded by the effects of stock plant maturation. Two parallel ...

  2. Clonality Testing in Veterinary Medicine: A Review With Diagnostic Guidelines.

    Science.gov (United States)

    Keller, S M; Vernau, W; Moore, P F

    2016-07-01

    The accurate distinction of reactive and neoplastic lymphoid proliferations can present challenges. Given the different prognoses and treatment strategies, a correct diagnosis is crucial. Molecular clonality assays assess rearranged lymphocyte antigen receptor gene diversity and can help differentiate reactive from neoplastic lymphoid proliferations. Molecular clonality assays are commonly used to assess atypical, mixed, or mature lymphoid proliferations; small tissue fragments that lack architecture; and fluid samples. In addition, clonality testing can be utilized to track neoplastic clones over time or across anatomic sites. Molecular clonality assays are not stand-alone tests but useful adjuncts that follow clinical, morphologic, and immunophenotypic assessment. Even though clonality testing provides valuable information in a variety of situations, the complexities and pitfalls of this method, as well as its dependency on the experience of the interpreter, are often understated. In addition, a lack of standardized terminology, laboratory practices, and interpretational guidelines hinders the reproducibility of clonality testing across laboratories in veterinary medicine. The objectives of this review are twofold. First, the review is intended to familiarize the diagnostic pathologist or interested clinician with the concepts, potential pitfalls, and limitations of clonality testing. Second, the review strives to provide a basis for future harmonization of clonality testing in veterinary medicine by providing diagnostic guidelines. © The Author(s) 2016.

  3. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Full Length Research Paper. Molecular marker analysis to differentiate a clonal ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal ... (Qiagen, Hilden, Germany), following the supplier's instructions. The DNA concentration was ...

  4. Introduction to special issue on the ecology of clonal plants

    Czech Academy of Sciences Publication Activity Database

    Gross, K. L.; Herben, T.; Klimešová, Jitka

    2017-01-01

    Roč. 52, 3-4 (2017), s. 265-267 ISSN 1211-9520 Institutional support: RVO:67985939 Keywords : Introduction to special issue * clonal plants * clonal meeting Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.017, year: 2016

  5. Distribution of clonal growth traits among wetland habitats

    NARCIS (Netherlands)

    Sosnova, Monika; van Diggelen, Rudy; Macek, Petr; Klimesova, Jitka

    Clonality resulting from the growth of specialized organs is common among plants in wetland habitats. We hypothesize that different wetland habitats select for different attributes of clonal traits. This hypothesis is based on studies of individual species but has not been previously tested at the

  6. Effect of clonal integration on nitrogen cycling in rhizosphere of rhizomatous clonal plant, Phyllostachys bissetii, under heterogeneous light.

    Science.gov (United States)

    Li, Yang; Chen, Jing-Song; Xue, Ge; Peng, Yuanying; Song, Hui-Xing

    2018-02-14

    Clonal integration plays an important role in clonal plant adapting to heterogeneous habitats. It was postulated that clonal integration could exhibit positive effects on nitrogen cycling in the rhizosphere of clonal plant subjected to heterogeneous light conditions. An in-situ experiment was conducted using clonal fragments of Phyllostachys bissetii with two successive ramets. Shading treatments were applied to offspring or mother ramets, respectively, whereas counterparts were treated to full sunlight. Rhizomes between two successive ramets were either severed or connected. Extracellular enzyme activities and nitrogen turnover were measured, as well as soil properties. Abundance of functional genes (archaeal or bacterial amoA, nifH) in the rhizosphere of shaded, offspring or mother ramets were determined using quantitative polymerase chain reaction. Carbon or nitrogen availabilities were significantly influenced by clonal integration in the rhizosphere of shaded ramets. Clonal integration significantly increased extracellular enzyme activities and abundance of functional genes in the rhizosphere of shaded ramets. When rhizomes were connected, higher nitrogen turnover (nitrogen mineralization or nitrification rates) was exhibited in the rhizosphere of shaded offspring ramets. However, nitrogen turnover was significantly decreased by clonal integration in the rhizosphere of shaded mother ramets. Path analysis indicated that nitrogen turnover in the rhizosphere of shaded, offspring or mother ramets were primarily driven by the response of soil microorganisms to dissolved organic carbon or nitrogen. This unique in-situ experiment provided insights into the mechanism of nutrient recycling mediated by clonal integration. It was suggested that effects of clonal integration on the rhizosphere microbial processes were dependent on direction of photosynthates transport in clonal plant subjected to heterogeneous light conditions. Copyright © 2018 Elsevier B.V. All rights

  7. Detection of clonal evolution in hematopoietic malignancies by combining comparative genomic hybridization and single nucleotide polymorphism arrays.

    Science.gov (United States)

    Hartmann, Luise; Stephenson, Christine F; Verkamp, Stephanie R; Johnson, Krystal R; Burnworth, Bettina; Hammock, Kelle; Brodersen, Lisa Eidenschink; de Baca, Monica E; Wells, Denise A; Loken, Michael R; Zehentner, Barbara K

    2014-12-01

    Array comparative genomic hybridization (aCGH) has become a powerful tool for analyzing hematopoietic neoplasms and identifying genome-wide copy number changes in a single assay. aCGH also has superior resolution compared with fluorescence in situ hybridization (FISH) or conventional cytogenetics. Integration of single nucleotide polymorphism (SNP) probes with microarray analysis allows additional identification of acquired uniparental disomy, a copy neutral aberration with known potential to contribute to tumor pathogenesis. However, a limitation of microarray analysis has been the inability to detect clonal heterogeneity in a sample. This study comprised 16 samples (acute myeloid leukemia, myelodysplastic syndrome, chronic lymphocytic leukemia, plasma cell neoplasm) with complex cytogenetic features and evidence of clonal evolution. We used an integrated manual peak reassignment approach combining analysis of aCGH and SNP microarray data for characterization of subclonal abnormalities. We compared array findings with results obtained from conventional cytogenetic and FISH studies. Clonal heterogeneity was detected in 13 of 16 samples by microarray on the basis of log2 values. Use of the manual peak reassignment analysis approach improved resolution of the sample's clonal composition and genetic heterogeneity in 10 of 13 (77%) patients. Moreover, in 3 patients, clonal disease progression was revealed by array analysis that was not evident by cytogenetic or FISH studies. Genetic abnormalities originating from separate clonal subpopulations can be identified and further characterized by combining aCGH and SNP hybridization results from 1 integrated microarray chip by use of the manual peak reassignment technique. Its clinical utility in comparison to conventional cytogenetic or FISH studies is demonstrated. © 2014 American Association for Clinical Chemistry.

  8. Nonclassical Kinetics of Clonal yet Heterogeneous Enzymes.

    Science.gov (United States)

    Park, Seong Jun; Song, Sanggeun; Jeong, In-Chun; Koh, Hye Ran; Kim, Ji-Hyun; Sung, Jaeyoung

    2017-07-06

    Enzyme-to-enzyme variation in the catalytic rate is ubiquitous among single enzymes created from the same genetic information, which persists over the lifetimes of living cells. Despite advances in single-enzyme technologies, the lack of an enzyme reaction model accounting for the heterogeneous activity of single enzymes has hindered a quantitative understanding of the nonclassical stochastic outcome of single enzyme systems. Here we present a new statistical kinetics and exactly solvable models for clonal yet heterogeneous enzymes with possibly nonergodic state dynamics and state-dependent reactivity, which enable a quantitative understanding of modern single-enzyme experimental results for the mean and fluctuation in the number of product molecules created by single enzymes. We also propose a new experimental measure of the heterogeneity and nonergodicity for a system of enzymes.

  9. Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China.

    Directory of Open Access Journals (Sweden)

    Zhi Ruan

    Full Text Available Ureaplasma spp. have gained increasing recognition as pathogens in both adult and neonatal patients with multiple clinical presentations. However, the clonality of this organism in the male population and infertile couples in China is largely unknown. In this study, 96 (53 U. parvum and 43 U. urealyticum of 103 Ureaplasma spp. strains recovered from genital specimens from male patients and 15 pairs of infertile couples were analyzed using multilocus sequence typing (MLST/expanded multilocus sequence typing (eMLST schemes. A total of 39 sequence types (STs and 53 expanded sequence types (eSTs were identified, with three predominant STs (ST1, ST9 and ST22 and eSTs (eST16, eST41 and eST82. Moreover, phylogenetic analysis revealed two distinct clusters that were highly congruent with the taxonomic differences between the two Ureaplasma species. We found significant differences in the distributions of both clusters and sub-groups between the male and female patients (P 0.80. However, this concordance was observed only for the detection of U. urealyticum within the infertile couples. In conclusion, the distributions of the clusters and sub-groups significantly differed between the male and female patients. U. urealyticum is more likely to transmit between infertile couples and be associated with clinical manifestations by the specific epidemic clonal lineages.

  10. Multiobjective clonal selection algorithm for solving forecasting problems

    Science.gov (United States)

    Astakhova, N. N.; Demidova, L. A.; Kuzovnikov, A. V.; Tishkin, R. V.

    2017-02-01

    The multiobjective modified clonal selection algorithm based on the use of the notion “Pareto dominance”, which can be applied for the development of the forecasting models on the base of the strictly binary trees has been offered. It is suggested to use the affinity indicator based on the average forecasting error rate, and the tendencies discrepancy indicator in the role of the objective functions of this algorithm. The multiobjective modified clonal selection algorithm can be applied for solving problems of individual and groups’ forecasting. The experimental results which confirm the efficiency of the offered algorithm in comparison with the basic modified clonal selection algorithm have been given.

  11. VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma.

    Science.gov (United States)

    Jiang, Yanwen; Nie, Kui; Redmond, David; Melnick, Ari M; Tam, Wayne; Elemento, Olivier

    2015-12-28

    Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas. In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.

  12. Clonal integration in Ludwigia hexapetala under different light regimes

    Science.gov (United States)

    Physiological integration among ramets of invasive plant species may support their colonization and spread in novel aquatic environments where growth-limiting resources are spatially heterogeneous. Under contrasting light conditions, we investigated how clonal integration influences growth, biomass...

  13. Adjusting to global change through clonal growth and epigenetic variation

    Directory of Open Access Journals (Sweden)

    Richard S Dodd

    2016-07-01

    Full Text Available The earth is experiencing major changes in global and regional climates and changes are predicted to accelerate in the future. Many species will be under considerable pressure to evolve, to migrate, or be faced with extinction. Clonal plants would appear to be at a particular disadvantage due to their limited mobility and limited capacity for adaptation. However, they have outlived previous environmental shifts and clonal species have persisted for millenia. Clonal spread offers unique ecological advantages, such as resource sharing, risk sharing, and economies of scale among ramets within genotypes. We suggest that ecological attributes of clonal plants, in tandem with variation in gene regulation through epigenetic mechanisms that facilitate and optimize phenotype variation in response to environmental change may permit them to be well suited to projected conditions.

  14. Clonality of mouse and human cardiomyogenesis in vivo

    OpenAIRE

    Hosoda, Toru; D'Amario, Domenico; Cabral-Da-Silva, Mauricio Castro; Zheng, Hanqiao; Padin-Iruegas, M. Elena; Ogorek, Barbara; Ferreira-Martins, João; Yasuzawa-Amano, Saori; Amano, Katsuya; Ide-Iwata, Noriko; Cheng, Wei; Rota, Marcello; Urbanek, Konrad; Kajstura, Jan; Anversa, Piero

    2009-01-01

    An analysis of the clonality of cardiac progenitor cells (CPCs) and myocyte turnover in vivo requires genetic tagging of the undifferentiated cells so that the clonal marker of individual mother cells is traced in the specialized progeny. CPC niches in the atria and apex of the mouse heart were infected with a lentivirus carrying EGFP, and the destiny of the tagged cells was determined 1–5 months later. A common integration site was identified in isolated CPCs, cardiomyocytes, endothelial cel...

  15. What Expands in an Expanding Universe?

    Directory of Open Access Journals (Sweden)

    JOSÉ A. DE FREITAS PACHECO

    2015-12-01

    Full Text Available ABSTRACT In the present investigation, the possible effects of the expansion of the Universe on systems bonded either by gravitational or electromagnetic forces, are reconsidered. It will be shown that the acceleration (positive or negative of the expanding background, is the determinant factor affecting planetary orbits and atomic sizes. In the presently accepted cosmology (ΛCDM all bonded systems are expanding at a decreasing rate that tends to be zero as the universe enters in a de Sitter phase. It is worth mentioning that the estimated expansion rates are rather small and they can be neglected for all practical purposes.

  16. What Expands in an Expanding Universe?

    Science.gov (United States)

    Pacheco, José A De Freitas

    2015-01-01

    In the present investigation, the possible effects of the expansion of the Universe on systems bonded either by gravitational or electromagnetic forces, are reconsidered. It will be shown that the acceleration (positive or negative) of the expanding background, is the determinant factor affecting planetary orbits and atomic sizes. In the presently accepted cosmology (ΛCDM) all bonded systems are expanding at a decreasing rate that tends to be zero as the universe enters in a de Sitter phase. It is worth mentioning that the estimated expansion rates are rather small and they can be neglected for all practical purposes.

  17. Parasites, sex, and clonal diversity in natural snail populations.

    Science.gov (United States)

    King, Kayla C; Jokela, Jukka; Lively, Curtis M

    2011-05-01

    Under the Red Queen hypothesis, host-parasite coevolution selects against common host genotypes. Although this mechanism might underlie the persistence of sexual reproduction, it might also maintain high clonal diversity. Alternatively, clonal diversity might be maintained by multiple origins of parthenogens from conspecific sexuals, a feature in many animal groups. Herein, we addressed the maintenance of overall genetic diversity by coevolving parasites, as predicted by the Red Queen hypothesis. We specifically examined the contribution of parasites to host clonal diversity and the frequency of sexually reproducing individuals in natural stream populations of Potamopyrgus antipodarum snails. We also tested the alternative hypothesis that clonal diversity is maintained by the input of clones by mutation from sympatric sexuals. Clonal diversity and the frequency of sexual individuals were both positively related to infection frequency. Surprisingly, although clones are derived by mutation from sexual snails, parasites explained more of the genotypic variation among parthenogenetic subpopulations. Our findings thus highlight the importance of parasites as drivers of clonal diversity, as well as sex. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  18. Diagnosis and management of smoldering multiple myeloma: the razor's edge between clonality and cancer.

    Science.gov (United States)

    Muchtar, Eli; Kumar, Shaji K; Magen, Hila; Gertz, Morie A

    2018-02-01

    Smoldering multiple myeloma (SMM) is a rare plasma cell disorder, and as the disease is asymptomatic, diagnosis is often incidental. SMM is characterized by increased marrow infiltration by clonal plasma cells and/or elevated serum M-protein in the absence of a myeloma-defining event (MDE). In recent years, SMM has gained increased attention owing to a broadening of the criteria for MDE, which include apart from the CRAB criteria, three additional parameters. Survival advantage may be offered by early treatment in the high-risk subset, based on a single trial. In this review, we assess the risk factors and models for progression to multiple myeloma. A review of our diagnostic and management approaches to SMM is presented.

  19. EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations

    National Research Council Canada - National Science Library

    Langerak, A.W; Groenen, P.J.T.A; Bruggemann, M; Beldjord, K; Bellan, C; Bonello, L; Boone, E; Carter, G.I; Catherwood, M; Davi, F; Delfau-Larue, M.H; Diss, T; Evans, P.A; Gameiro, P; Garcia Sanz, R; Gonzalez, D; Grand, D; Hakansson, A; Hummel, M; Liu, H; Lombardia, L; Macintyre, E.A; Milner, B.J; Montes-Moreno, S; Schuuring, E; Spaargaren, M; Hodges, E; Dongen, J.J. van

    2012-01-01

    PCR-based immunoglobulin (Ig)/T-cell receptor (TCR) clonality testing in suspected lymphoproliferations has largely been standardized and has consequently become technically feasible in a routine diagnostic setting...

  20. A predictive relationship between population and genetic sex ratios in clonal species

    Science.gov (United States)

    McLetchie, D. Nicholas; García-Ramos, Gisela

    2017-04-01

    Sexual reproduction depends on mate availability that is reflected by local sex ratios. In species where both sexes can clonally expand, the population sex ratio describes the proportion of males, including clonally derived individuals (ramets) in addition to sexually produced individuals (genets). In contrast to population sex ratio that accounts for the overall abundance of the sexes, the genetic sex ratio reflects the relative abundance of genetically unique mates, which is critical in predicting effective population size but is difficult to estimate in the field. While an intuitive positive relationship between population (ramet) sex ratio and genetic (genet) sex ratio is expected, an explicit relationship is unknown. In this study, we determined a mathematical expression in the form of a hyperbola that encompasses a linear to a nonlinear positive relationship between ramet and genet sex ratios. As expected when both sexes clonally have equal number of ramets per genet both sex ratios are identical, and thus ramet sex ratio becomes a linear function of genet sex ratio. Conversely, if sex differences in ramet number occur, this mathematical relationship becomes nonlinear and a discrepancy between the sex ratios amplifies from extreme sex ratios values towards intermediate values. We evaluated our predictions with empirical data that simultaneously quantified ramet and genet sex ratios in populations of several species. We found that the data support the predicted positive nonlinear relationship, indicating sex differences in ramet number across populations. However, some data may also fit the null model, which suggests that sex differences in ramet number were not extensive, or the number of populations was too small to capture the curvature of the nonlinear relationship. Data with lack of fit suggest the presence of factors capable of weakening the positive relationship between the sex ratios. Advantages of this model include predicting genet sex ratio using

  1. Clonality of erythromycin resistance in Francisella tularensis.

    Science.gov (United States)

    Karlsson, Edvin; Golovliov, Igor; Lärkeryd, Adrian; Granberg, Malin; Larsson, Eva; Öhrman, Caroline; Niemcewicz, Marcin; Birdsell, Dawn; Wagner, David M; Forsman, Mats; Johansson, Anders

    2016-10-01

    We analysed diverse strains of Francisella tularensis subsp. holarctica to assess if its division into biovars I and II is associated with specific mutations previously linked to erythromycin resistance and to determine the distribution of this resistance trait across this subspecies. Three-hundred and fourteen F. tularensis subsp. holarctica strains were tested for erythromycin susceptibility and whole-genome sequences for these strains were examined for SNPs in genes previously associated with erythromycin resistance. Each strain was assigned to a global phylogenetic framework using genome-wide canonical SNPs. The contribution of a specific SNP to erythromycin resistance was examined using allelic exchange. The geographical distribution of erythromycin-resistant F. tularensis strains was further investigated by literature search. There was a perfect correlation between biovar II strains (erythromycin resistance) and the phylogenetic group B.12. Only B.12 strains had an A → C SNP at position 2059 in the three copies of the rrl gene. Introducing 2059C into an rrl gene of an erythromycin-susceptible F. tularensis strain resulted in resistance. An additional 1144 erythromycin-resistant strains were identified from the scientific literature, all of them from Eurasia. Erythromycin resistance in F. tularensis is caused by an A2059C rrl gene mutation, which exhibits a strictly clonal inheritance pattern found only in phylogenetic group B.12. This group is an extremely successful clone, representing the most common type of F. tularensis throughout Eurasia. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Intrathecal T-cell clonal expansions in patients with multiple sclerosis.

    Science.gov (United States)

    de Paula Alves Sousa, Alessandra; Johnson, Kory R; Nicholas, Richard; Darko, Sam; Price, David A; Douek, Daniel C; Jacobson, Steven; Muraro, Paolo A

    2016-06-01

    Analysis of the T-cell receptor (TCR) repertoire in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS) can reveal antigen-specific immune responses potentially implicated in the disease process. We applied a new unbiased deep-sequencing method for TCR repertoire analysis to accurately measure and compare receptor diversity and clonal expansions within the peripheral and CSF-trafficking T-cell populations of patients with MS and control individuals with idiopathic intracranial hypertension (IIH). Paired blood and CSF TCR β-chain libraries from five MS patients and five IIH controls were sequenced, yielding a total of 80 million reads. Although TCR repertoire diversity was greater in the blood and CSF compartments of MS patients when compared with IIH controls, it is notable that the frequency of clonal expansions was also significantly higher in both compartments of MS patients. Highly expanded T-cell clones were enriched in the CSF compartment of MS patients compared to peripheral blood, very few of them were detected in both compartments. Collectively, our data provide a proof of principle that private compartmentalized T-cell expansion exists in the intrathecal space of MS patients.

  3. Mitochondria: Biogenesis and mitophagy balance in segregation and clonal expansion of mitochondrial DNA mutations.

    Science.gov (United States)

    Carelli, Valerio; Maresca, Alessandra; Caporali, Leonardo; Trifunov, Selena; Zanna, Claudia; Rugolo, Michela

    2015-06-01

    Mitochondria are cytoplasmic organelles containing their own multi-copy genome. They are organized in a highly dynamic network, resulting from balance between fission and fusion, which maintains homeostasis of mitochondrial mass through mitochondrial biogenesis and mitophagy. Mitochondrial DNA (mtDNA) mutates much faster than nuclear DNA. In particular, mtDNA point mutations and deletions may occur somatically and accumulate with aging, coexisting with the wild type, a condition known as heteroplasmy. Under specific circumstances, clonal expansion of mutant mtDNA may occur within single cells, causing a wide range of severe human diseases when mutant overcomes wild type. Furthermore, mtDNA deletions accumulate and clonally expand as a consequence of deleterious mutations in nuclear genes involved in mtDNA replication and maintenance, as well as in mitochondrial fusion genes (mitofusin-2 and OPA1), possibly implicating mtDNA nucleoids segregation. We here discuss how the intricacies of mitochondrial homeostasis impinge on the intracellular propagation of mutant mtDNA. This article is part of a Directed Issue entitled: Energy Metabolism Disorders and Therapies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. The two-stage clonal expansion model in occupational cancer epidemiology: results from three cohort studies.

    Science.gov (United States)

    Zeka, Ariana; Gore, Rebecca; Kriebel, David

    2011-08-01

    The objective of this work was to apply the two-stage clonal expansion model, with the intention to expand the literature on epidemiological applications of the model and demonstrate the feasibility of incorporating biologically based modelling methods into the widely used retrospective cohort study. The authors fitted the two-stage clonal expansion model model to three occupational cohort studies: (1) a cohort of textile workers exposed to asbestos and followed for lung cancer mortality; (2) a cohort of diatomaceous earth workers exposed to silica and also followed for lung cancer mortality; and (3) a cohort of automotive manufacturing workers exposed to straight metalworking fluid (MWF) and followed for larynx cancer incidence. The model allowed the authors to estimate exposure effects in three stages: cancer initiation (early effects), promotion or malignant transformation (late effects). In the first cohort, the authors found strong evidence for an early effect of asbestos on lung cancer risk. Findings from analyses of the second cohort suggested early and less evidently late effects of silica on lung cancer risk. In the MWF (third) cohort, there was only weak evidence of straight MWF exposure effects on both early and late stages. The authors also observed a late birth cohort effect on larynx cancer risk. The findings for asbestos and silica were essentially confirmatory, supporting evidence for their early effects on lung cancer from a large body of literature. The effect of straight MWF on larynx cancer was less clear.

  5. Layouts of Expander Graphs

    OpenAIRE

    Dujmović, Vida; Sidiropoulos, Anastasios; Wood, David R.

    2015-01-01

    Bourgain and Yehudayoff recently constructed $O(1)$-monotone bipartite expanders. By combining this result with a generalisation of the unraveling method of Kannan, we construct 3-monotone bipartite expanders, which is best possible. We then show that the same graphs admit 3-page book embeddings, 2-queue layouts, 4-track layouts, and have simple thickness 2. All these results are best possible.

  6. Sex and clonality in the little fire ant.

    Science.gov (United States)

    Foucaud, Julien; Fournier, Denis; Orivel, Jérôme; Delabie, Jacques H C; Loiseau, Anne; Le Breton, Julien; Kergoat, Gaël J; Estoup, Arnaud

    2007-11-01

    Reproduction systems are controlling the creation of new genetic variants as well as how natural selection can operate on these variants. Therefore, they had historically been one of the main foci of evolutionary biology studies. The little fire ant, Wasmannia auropunctata, has been found to display an extraordinary reproduction system, in which both males and female queens are produced clonally. So far, native sexual populations of W. auropunctata have not been identified. Our goals were to identify such sexual populations and investigate the origins of female parthenogenesis and male clonality. Using mitochondrial DNA and microsatellite markers in 17 native populations, we found that traditional sexual populations occurred in W. auropunctata and are likely the recent source of neighboring clonal populations. Queen parthenogenesis has probably evolved several times through mutational events. Male clonality is tightly linked to queen parthenogenesis and thus appears to be female controlled. Its origin could be accounted for by 2 mutually exclusive hypotheses: either by the expected coevolution of the 2 sexes (i.e., a variant of the maternal genome elimination hypothesis) or by a shared mechanistic origin (i.e., by the production of anucleate ovules by parthenogenetic queens). Our results also show that W. auropunctata males and females do not form separate evolutionary units and are unlikely to be engaged in an all-out battle of sexes. This work opens up new perspectives for studies on the adaptive significance and evolutionary stability of mixed sexual and clonal reproduction systems in living organisms.

  7. New insights into clonality and panmixia in Plasmodium and toxoplasma.

    Science.gov (United States)

    Tibayrenc, Michel; Ayala, Francisco J

    2014-01-01

    Until the 1990s, Plasmodium and Toxoplasma were widely considered to be potentially panmictic species, because they both undergo a meiotic sexual cycle in their definitive hosts. We have proposed that both parasites are able of clonal (nonrecombining) propagation, at least in some cycles. Toxoplasma was soon shown to be a paradigmatic case of clonal population structure in North American and in European cycles. But the proposal provoked an outcry in the case of Plasmodium and still appears as doubtful to many scientists. However, the existence of Plasmodium nonrecombining lines has been fully confirmed, although the origin of these lines is debatable. We discuss the current state of knowledge concerning the population structure of both parasites in the light of the recent developments of pathogen clonal evolution proposed by us and of new hypotheses presented here. © 2014 Elsevier Ltd All rights reserved.

  8. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

    Directory of Open Access Journals (Sweden)

    Zhian N. Kamvar

    2014-03-01

    Full Text Available Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.

  9. Clonal expansion of Epstein-Barr virus (EBV)-infected γδ T cells in patients with chronic active EBV disease and hydroa vacciniforme-like eruptions.

    Science.gov (United States)

    Wada, Taizo; Toga, Akiko; Sakakibara, Yasuhisa; Toma, Tomoko; Hasegawa, Minoru; Takehara, Kazuhiko; Shigemura, Tomonari; Agematsu, Kazunaga; Yachie, Akihiro

    2012-10-01

    Chronic active Epstein-Barr virus (EBV) disease (CAEBV) is a systemic EBV-positive lymphoproliferative disorder characterized by fever, lymphadenopathy, and splenomegaly. Patients with CAEBV may present with cutaneous symptoms, including hypersensitivity to mosquito bites and hydroa vacciniforme (HV)-like eruptions. HV is a rare photodermatosis characterized by vesicles and crust formation after exposure to sunlight, with onset in childhood, and is associated with latent EBV infection. While γδ T cells have recently been demonstrated to be the major EBV-infected cell population in HV, the immunophenotypic features of EBV-infected γδ T cells in CAEBV with HV-like eruptions or HV remain largely undetermined. We describe three patients with CAEBV whose γδ T cells were found to be the major cellular target of EBV. HV-like eruptions were observed in two of these patients. A clonally expanded subpopulation of γδ T cells that were highly activated and T cell receptor Vγ9- and Vδ2-positive cells was demonstrated in all patients. We also show that the clonally expanded γδ T cells infiltrated into the HV-like eruptions in one patient from whom skin biopsy specimens were available. These results suggest the pathogenic roles of clonally expanded γδ T cells infected by EBV in patients with CAEBV and HV-like eruptions.

  10. High degree of clonal reproduction and lack of large-scale geographic patterning mark the introduced range of the invasive vine, kudzu (Pueraria montana var. lobata), in North America.

    Science.gov (United States)

    Bentley, Kerin E; Mauricio, Rodney

    2016-08-01

    Pueraria montana var. lobata, or kudzu, is an invasive species whose invasion in North America is not genetically well characterized. The clonality of kudzu introduces challenges to population genetic analyses that can bias the assessment of spatial patterns of genotypes. Assessing patterns of genetic diversity while considering clonality is necessary to understand the invasion and spread of kudzu in its invasive range. We screened 1747 individuals from 87 populations across the invasive range with 15 microsatellite markers and a 789 bp chloroplast region. We performed detailed clonal analyses and tested levels of genetic diversity, population structure, and phylogeographic relationships. Kudzu exhibited a clonal rate of 80%, and was more heterozygous than other long-lived perennials. We detected only 353 distinct clonal lineages, with over 60% sharing a maternal haplotype. Populations were established with few genotypes, many consisting of only a single clone. We found no isolation by distance. Despite high genetic diversity, we found little geographic patterning. Kudzu is highly clonal with few genetically distinct lineages and haplotypes existing in the introduced range. Our data are consistent with a large single introduction, or a few at most. Introduced lineages are geographically randomly distributed but isolated, suggesting that genotypes rarely expand into already established populations. No route of expansion was detectable from an original introduction. The invasion of kudzu does not seem to have been dominated by a single genotype, thus standing genetic variation and phenotypic plasticity are more likely mechanisms explaining kudzu's invasion success. © 2016 Botanical Society of America.

  11. Expanding Thurston maps

    CERN Document Server

    Bonk, Mario

    2017-01-01

    This monograph is devoted to the study of the dynamics of expanding Thurston maps under iteration. A Thurston map is a branched covering map on a two-dimensional topological sphere such that each critical point of the map has a finite orbit under iteration. It is called expanding if, roughly speaking, preimages of a fine open cover of the underlying sphere under iterates of the map become finer and finer as the order of the iterate increases. Every expanding Thurston map gives rise to a fractal space, called its visual sphere. Many dynamical properties of the map are encoded in the geometry of this visual sphere. For example, an expanding Thurston map is topologically conjugate to a rational map if and only if its visual sphere is quasisymmetrically equivalent to the Riemann sphere. This relation between dynamics and fractal geometry is the main focus for the investigations in this work.

  12. Dynamic evolution of clonal epialleles revealed by methclone.

    Science.gov (United States)

    Li, Sheng; Garrett-Bakelman, Francine; Perl, Alexander E; Luger, Selina M; Zhang, Chao; To, Bik L; Lewis, Ian D; Brown, Anna L; D'Andrea, Richard J; Ross, M Elizabeth; Levine, Ross; Carroll, Martin; Melnick, Ari; Mason, Christopher E

    2014-09-27

    We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.

  13. South American Plasmodium falciparum after the malaria eradication era: clonal population expansion and survival of the fittest hybrids.

    Directory of Open Access Journals (Sweden)

    Sean M Griffing

    Full Text Available Malaria has reemerged in many regions where once it was nearly eliminated. Yet the source of these parasites, the process of repopulation, their population structure, and dynamics are ill defined. Peru was one of malaria eradication's successes, where Plasmodium falciparum was nearly eliminated for two decades. It reemerged in the 1990s. In the new era of malaria elimination, Peruvian P. falciparum is a model of malaria reinvasion. We investigated its population structure and drug resistance profiles. We hypothesized that only populations adapted to local ecological niches could expand and repopulate and originated as vestigial populations or recent introductions. We investigated the genetic structure (using microsatellites and drug resistant genotypes of 220 parasites collected from patients immediately after peak epidemic expansion (1999-2000 from seven sites across the country. The majority of parasites could be grouped into five clonal lineages by networks and AMOVA. The distribution of clonal lineages and their drug sensitivity profiles suggested geographic structure. In 2001, artesunate combination therapy was introduced in Peru. We tested 62 parasites collected in 2006-2007 for changes in genetic structure. Clonal lineages had recombined under selection for the fittest parasites. Our findings illustrate that local adaptations in the post-eradication era have contributed to clonal lineage expansion. Within the shifting confluence of drug policy and malaria incidence, populations continue to evolve through genetic outcrossing influenced by antimalarial selection pressure. Understanding the population substructure of P. falciparum has implications for vaccine, drug, and epidemiologic studies, including monitoring malaria during and after the elimination phase.

  14. Aging in a long-lived clonal tree.

    Directory of Open Access Journals (Sweden)

    Dilara Ally

    2010-08-01

    Full Text Available From bacteria to multicellular animals, most organisms exhibit declines in survivorship or reproductive performance with increasing age ("senescence". Evidence for senescence in clonal plants, however, is scant. During asexual growth, we expect that somatic mutations, which negatively impact sexual fitness, should accumulate and contribute to senescence, especially among long-lived clonal plants. We tested whether older clones of Populus tremuloides (trembling aspen from natural stands in British Columbia exhibited significantly reduced reproductive performance. Coupling molecular-based estimates of clone age with male fertility data, we observed a significant decline in the average number of viable pollen grains per catkin per ramet with increasing clone age in trembling aspen. We found that mutations reduced relative male fertility in clonal aspen populations by about 5.8 x 10(-5 to 1.6 x 10(-3 per year, leading to an 8% reduction in the number of viable pollen grains, on average, among the clones studied. The probability that an aspen lineage ultimately goes extinct rises as its male sexual fitness declines, suggesting that even long-lived clonal organisms are vulnerable to senescence.

  15. PCR-based clonality assessment in patients with lymphocytic ...

    Indian Academy of Sciences (India)

    indicate that bone marrow analysis has higher sensitivity compared to analysis of peripheral blood. [Cikota B. M., Tukic L. J., Tarabar O. T., Stamotovic D. T., Elez M. N. and Magic Z. M. 2009 PCR-based clonality assessment in patients with lymphocyte leukaemias: a single-institution experience. J. Genet. 88, 309–314].

  16. AGROBIOLOGICAL AND TECHNOLOGICAL EVALUATION OF CHASSELAS DORÉ ELITE CLONAL ACCESSIONS

    Directory of Open Access Journals (Sweden)

    Elena Brînduse

    2017-07-01

    Full Text Available Four elite clonal accessions of Vitis vinifera L., Chasselas doré variety were identified in a very old plantation, of 110 years, located in Valea Cãlugãreascã, on the St. Nicolas Monastery vineyard. The vines, grafted on the SO4 (Selection Oppenheim 4 rootstock, were planted in 2007 in the germplasm collection belonging to the Research and Development Institute for Viticulture and Enology, Valea Cãlugãreascã. The evaluation of elite clonal accessions focused on the duration of their phenological cycles, grape fertility and productivity, resistance to diseases, quantity and quality of the grapes production. The elite clonal accessions have been distinguished from Chasselas doré through the grape production which is double at one of elite and higher for the other elites as a results of the average weight of the grapes. The potential of sugar accumulations in the must was approximately twice at the elite clonal accessions, with balanced total acidity and pH values. The elites will be further studied for confirming the genetic stability and to propose the most competitive for homologation.

  17. Determination of optimal levels of Resource Use in Clonal Robusta ...

    African Journals Online (AJOL)

    In spite of the current decline in World Market Prices, coffee remains Uganda's major export crop. However, coffee yield in Uganda remains sub optimal. One of the contributing factors could be an imbalance in the use of the factors of production. Optimal combinations of factors of production for clonal coffee production in ...

  18. Negative plant soil feedback explaining ring formation in clonal plants

    NARCIS (Netherlands)

    Carteni, F.; Marasco, A.; Bonanomi, G.; Mazzoleni, S.; Rietkerk, M.G.; Giannino, F.

    2012-01-01

    Ring shaped patches of clonal plants have been reported in different environments, but the mechanisms underlying such pattern formation are still poorly explained. Water depletion in the inner tussocks zone has been proposed as a possible cause, although ring patterns have been also observed in

  19. Stomatal characteristics of Eucalyptus grandis clonal hybrids in ...

    African Journals Online (AJOL)

    The aim was to investigate the degree to which stomatal conductance (gs) and stomatal density differ between the clonal hybrids across seasons and in response to water stress. Plants from one E. grandis x E. camaldulensis (GC) and two E. grandis x E. urophylla (GU1 and GU2) clones were grown for 18 months in 80 l ...

  20. EVIDENCE FOR CLONAL GROWTH IN FAGUS SYLVATICA L. IN ITALY

    Directory of Open Access Journals (Sweden)

    C. Wellstein

    2012-06-01

    Full Text Available Based on our recent observations in Central Italy we show evidence for root sprouting and subsequent capacity of clonal growth in Fagus sylvatica L. The typology of resprouting in this species is still unclear according to the existing literature. We review Italian, European and global sources and discuss our finding in the light of environmental factors and genetic differences.

  1. European 1: a globally important clonal complex of Mycobacterium bovis.

    NARCIS (Netherlands)

    Smith, N.H.; Berg, S.; Dale, J.; Allen, A.; Rodriguez, S.; Romero, B.; Matos, F.; Ghebremichael, S.; Karoui, C.; Donati, C.; Machado Ada, C.; Mucavele, C.; Kazwala, R.R.; Hilty, M.; Cadmus, S.; Ngandolo, B.N.; Habtamu, M.; Oloya, J.; Muller, Annélle; Milian-Suazo, F.; Andrievskaia, O.; Projahn, M.; Barandiaran, S.; Macias, A.; Muller, B.; Zanini, M.S.; Ikuta, C.Y.; Rodriguez, C.A.; Pinheiro, S.R.; Figueroa, A.; Cho, S.N.; Mosavari, N.; Chuang, P.C.; Jou, R.; Zinsstag, J.; Soolingen, D. van; Costello, E.; Aseffa, A.; Proano-Perez, F.; Portaels, F.; Rigouts, L.; Cataldi, A.A.; Collins, D.M.; Boschiroli, M.L.; Hewinson, R.G.; Ferreira Neto, J.S.; Surujballi, O.; Tadyon, K.; Botelho, A.; Zarraga, A.M.; Buller, N.; Skuce, R.; Michel, A.; Aranaz, A.; Gordon, S.V.; Jeon, B.Y.; Kallenius, G.; Niemann, S.; Boniotti, M.B.; Helden, P.D. van; Harris, B.; Zumarraga, M.J.; Kremer, K.

    2011-01-01

    We have identified a globally important clonal complex of Mycobacterium bovis by deletion analysis of over one thousand strains from over 30 countries. We initially show that over 99% of the strains of M. bovis, the cause of bovine tuberculosis, isolated from cattle in the Republic of Ireland and

  2. [Plant regeneration and clonal propagation system of Datura metel].

    Science.gov (United States)

    Wang, Feng-Ying; Sun, Yi-Ming; Zhang, Hong; Cheng, Meng-Qi; Zhang, Lai; Sun, Min

    2014-02-01

    To study the condition of plant regeneration and clonal propagation system of Datura metel. Stems and leaves of Datura metel were used as explants, effects of different hormones for callus induction and plant regeneration of leaves and clonal propagation system of stems were studied and optimized. The optimal way to obtain sterile explant for leaves were sterilized in 75% ethyl alcohol for 6 s then 0.1% HgCl2 for 6 min; Stems were sterilized in 75% ethyl alcohol for 8 s then 0.1% HgCl2 for 7 min. The optimal medium for callus of leaves was MS + 1.0 mg/L 6-BA + 0.1 mg/L NAA; The optimal medium for callus induction of clustered buds was MS + 2.0 mg/L 6-BA + 0.2 mg/L NAA; The optimal medium for clonal propagation system of stems was MS + 3.0 mg/L 6-BA + 0.05 mg/L NAA. The best medium for rooting induction was MS + 0.5 mg/L IBA. Transplant survival rate of plantlet was greater than 90% in humus soil-pearlite (5:1). The condition of plant regeneration and clonal propagation system of Datura metel is established.

  3. Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama

    Science.gov (United States)

    Obaldia, Nicanor; Baro, Nicholas K.; Calzada, Jose E.; Santamaria, Ana M.; Daniels, Rachel; Wong, Wesley; Chang, Hsiao-Han; Hamilton, Elizabeth J.; Arevalo-Herrera, Myriam; Herrera, Socrates; Wirth, Dyann F.; Hartl, Daniel L.; Marti, Matthias; Volkman, Sarah K.

    2015-01-01

    Identifying the source of resurgent parasites is paramount to a strategic, successful intervention for malaria elimination. Although the malaria incidence in Panama is low, a recent outbreak resulted in a 6-fold increase in reported cases. We hypothesized that parasites sampled from this epidemic might be related and exhibit a clonal population structure. We tested the genetic relatedness of parasites, using informative single-nucleotide polymorphisms and drug resistance loci. We found that parasites were clustered into 3 clonal subpopulations and were related to parasites from Colombia. Two clusters of Panamanian parasites shared identical drug resistance haplotypes, and all clusters shared a chloroquine-resistance genotype matching the pfcrt haplotype of Colombian origin. Our findings suggest these resurgent parasite populations are highly clonal and that the high clonality likely resulted from epidemic expansion of imported or vestigial cases. Malaria outbreak investigations that use genetic tools can illuminate potential sources of epidemic malaria and guide strategies to prevent further resurgence in areas where malaria has been eliminated. PMID:25336725

  4. In vitro clonal propagation of Fuchsia magellanica Lam. | Parveen ...

    African Journals Online (AJOL)

    Fuchsia magellanica Lam. is a famous ornamental plant which is rarely found in Pakistan. Its beauty and ... This study is undertaken to perform in vitro clonal propagation and acclimatization of F. magellanica in order to get hundreds of F. magellanica plants in the laboratory in comparatively less time. Hence, it would be ...

  5. Productivity gains by fertilisation in Eucalyptus urophylla clonal ...

    African Journals Online (AJOL)

    Fertilisation is routinely used to improve tree nutrition, providing profitable returns on large investments. Growth responses to fertilisation differ ... We used this approach with 131 blocks of twin-plots to represent an area of 34 540 ha in the state of São Paulo, Brazil. Clonal plantations of Eucalyptus urophylla were ...

  6. Clonal evaluation of yam tubers raised from yam true seed ...

    African Journals Online (AJOL)

    Clonal evaluation of second generation yam (Dioscorea rotundata) plants raised from gamma ray treated and untreated yam true seeds, showed that, at the MV1 generation, increasing doses of gamma rays decreased plant heights, number of leaves, and tuber yield. At the MV2 generation however, these disappeared.

  7. Clonal differences in log end splitting in Eucalyptus grandis in ...

    African Journals Online (AJOL)

    This paper discusses the juvenile–mature correlation of log end splitting among Eucalyptus grandis clones from two trials and how differences in splitting relate to differences in wood density, pith-to-bark gradient and growth rate. Two approximately 20-year-old Eucalyptus grandis clonal trials at Bergvliet plantation were ...

  8. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Three AFLP markers were polymorphic; two markers were present only in Centennial Seedless, whereas one was present only in Manjari Naveen. These markers will be useful for establishing genetic identity, variety registration and protection of breeder's right. Keywords: Vitis vinifera, AFLP, microsatellites, clonal selection

  9. THE EXTENT OF CLONAL STRUCTURE IN DIFFERENT LYMPHOID ORGANS

    NARCIS (Netherlands)

    HERMANS, MHA; WUBBENA, A; KROESE, FGM; HUNT, SV; COWAN, R; OPSTELTEN, D

    1992-01-01

    To gain insight into the clonal organization of lymphoid organs, we studied the distribution in situ of donor-derived cells in near-physiological chimeras. We introduced RT7b fetal liver cells into nonirradiated congenic RT7a neonatal rats. The chimerism 6-20 wk after injection ranged from 0.3 to

  10. Silicon microfabricated beam expander

    Energy Technology Data Exchange (ETDEWEB)

    Othman, A., E-mail: aliman@ppinang.uitm.edu.my; Ibrahim, M. N.; Hamzah, I. H.; Sulaiman, A. A. [Faculty of Electrical Engineering, Universiti Teknologi MARA Malaysia, 40450, Shah Alam, Selangor (Malaysia); Ain, M. F. [School of Electrical and Electronic Engineering, Engineering Campus, Universiti Sains Malaysia, Seri Ampangan, 14300,Nibong Tebal, Pulau Pinang (Malaysia)

    2015-03-30

    The feasibility design and development methods of silicon microfabricated beam expander are described. Silicon bulk micromachining fabrication technology is used in producing features of the structure. A high-precision complex 3-D shape of the expander can be formed by exploiting the predictable anisotropic wet etching characteristics of single-crystal silicon in aqueous Potassium-Hydroxide (KOH) solution. The beam-expander consist of two elements, a micromachined silicon reflector chamber and micro-Fresnel zone plate. The micro-Fresnel element is patterned using lithographic methods. The reflector chamber element has a depth of 40 µm, a diameter of 15 mm and gold-coated surfaces. The impact on the depth, diameter of the chamber and absorption for improved performance are discussed.

  11. TRIPLE ACTION PALATE EXPANDER

    Directory of Open Access Journals (Sweden)

    Svetlana Yordanova

    2011-09-01

    Full Text Available Malocclusion correction essentially involves expansion of the maxilla, protrusion of anterior teeth and opening the bite. Expansion is often the stage preceding the treatment with fixed appliances. The elevation of the occlusion using accomplished with different devices (bite planes -fixed or removable, composite material on the occlusall surface of molars carries the risk of breaking or debonding them.The present article proposes an expanding appliance with triple action as a therapeutic means of choice in an orthodontic treatment with fixed appliances. The expander can simultaneously be used to protrude upper teeth, to expand the upper jaw and disarticulate the occlusion. It can be easily fabricated in clinical conditions, causes no discomfort and does not hamper oral hygiene because it can be removed and cleaned.

  12. Stem cell clonality -- theoretical concepts, experimental techniques, and clinical challenges.

    Science.gov (United States)

    Glauche, Ingmar; Bystrykh, Leonid; Eaves, Connie; Roeder, Ingo

    2013-04-01

    Here we report highlights of discussions and results presented at an International Workshop on Concepts and Models of Stem Cell Organization held on July 16th and 17th, 2012 in Dresden, Germany. The goal of the workshop was to undertake a systematic survey of state-of-the-art methods and results of clonality studies of tissue regeneration and maintenance with a particular emphasis on the hematopoietic system. The meeting was the 6th in a series of similar conceptual workshops, termed StemCellMathLab,(2) all of which have had the general objective of using an interdisciplinary approach to discuss specific aspects of stem cell biology. The StemCellMathLab 2012, which was jointly organized by the Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Dresden University of Technology and the Institute for Medical Informatics, Statistics and Epidemiology, Medical Faculty, University of Leipzig, brought together 32 scientists from 8 countries, with scientific backgrounds in medicine, cell biology, virology, physics, computer sciences, bioinformatics and mathematics. The workshop focused on the following questions: (1) How heterogeneous are stem cells and their progeny? and (2) What are the characteristic differences in the clonal dynamics between physiological and pathophysiological situations? In discussing these questions, particular emphasis was placed on (a) the methods for quantifying clones and their dynamics in experimental and clinical settings and (b) general concepts and models for their description. In this workshop summary we start with an introduction to the current state of clonality research and a proposal for clearly defined terminology. Major topics of discussion include clonal heterogeneity in unperturbed tissues, clonal dynamics due to physiological and pathophysiological pressures and conceptual and technical issues of clone quantification. We conclude that an interactive cross-disciplinary approach to research in this

  13. Potential for clonal animals in longevity and ageing studies.

    Science.gov (United States)

    Nilsson Sköld, Helen; Obst, Matthias

    2011-10-01

    Ageing is defined as a decline in reproductive and/or somatic performance over time, and as such is experienced by most organisms. Evolutionary theories explain ageing as a consequence of reduced selection pressure against mutations and reduced allocation to somatic maintenance in post-reproductive individuals. In addition, the fecundity of younger age-groups makes a more significant contribution than infinite maintenance of the parental body to the production of subsequent generations. However, in clonal animals, as well as in plants that reproduce by agametic cloning, the adult body is itself a reproductive unit that increases its fitness as a function of genet size. Given the apparent longevity of many such clonal organisms, species undergoing agametic cloning are often assumed to be non-ageing and even potentially immortal. Here, we present a brief overview of ageing in organisms undergoing agametic cloning, focusing on animals and molecular investigation. We discuss molecular and evolutionary aspects of ageing or non-ageing with respect to selection in clonal species. Of particular relevance to the search for potential mechanistic processes behind longevity is the notion that clonal organisms are frequently smaller than their obligate sexual counterparts. In conclusion, we find that while clonal animals also commonly age, evolutionary arguments together with empirical evidence suggest that they are likely to be long-lived and stress resistant at the genet level. However, theoretical modeling continues to predict the possibility of immortality, if the contribution from sexual reproduction is low. Future in-depth study of long-lived clones should present an excellent opportunity to discover novel mechanisms for renewal and long-term somatic maintenance and health.

  14. Clonal Expansion of New Penicillin-Resistant Clade of Neisseria meningitidis Serogroup W Clonal Complex 11, Australia.

    Science.gov (United States)

    Mowlaboccus, Shakeel; Jolley, Keith A; Bray, James E; Pang, Stanley; Lee, Yung Thin; Bew, Jane D; Speers, David J; Keil, Anthony D; Coombs, Geoffrey W; Kahler, Charlene M

    2017-08-01

    In Western Australia, Neisseria meningitidis serogroup W clonal complex 11 became the predominant cause of invasive meningococcal disease in 2016. We used core-genome analysis to show emergence of a penicillin-resistant clade that had the penA_253 allele. This new penicillin-resistant clade might affect treatment regimens for this disease.

  15. Expandable gastroretentive dosage forms.

    Science.gov (United States)

    Klausner, Eytan A; Lavy, Eran; Friedman, Michael; Hoffman, Amnon

    2003-06-24

    Expandable gastroretentive dosage forms (GRDFs) have been designed for the past 3 decades. They were originally created for possible veterinary use, but later the design was modified for enhanced drug therapy in humans. These GRDFs are easily swallowed and reach a significantly larger size in the stomach due to swelling or unfolding processes that prolong their gastric retention time (GRT). After drug release, their dimensions are minimized with subsequent evacuation from the stomach. Gastroretentivity is enhanced by the combination of substantial dimensions with high rigidity of the dosage form to withstand the peristalsis and mechanical contractility of the stomach. Positive results were obtained in preclinical and clinical studies evaluating GRT of expandable GRDFs. Narrow absorption window drugs compounded in such systems have improved in vivo absorption properties. These findings are an important step towards the implementation of expandable GRDFs in the clinical setting. The current review deals with expandable GRDFs reported in articles and patents, and describes the physiological basis of their design. Using the dog as a preclinical screening model prior to human studies, relevant imaging techniques and pharmacokinetic-pharmacodynamic aspects of such delivery systems are also discussed.

  16. The Importance of an In-depth Study of Immunoglobulin Gene Rearrangements When Ascertaining the Clonal Relationship between Concomitant Chronic Lymphocytic Leukemia and Multiple Myeloma

    Science.gov (United States)

    Trudel, Stéphanie; Ghamlouch, Hussein; Dremaux, Julie; Delette, Caroline; Harrivel, Véronique; Marolleau, Jean-Pierre; Gubler, Brigitte

    2016-01-01

    Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are hematological disorders that occur at different stages of B-cell development. It has been shown that CLL B-cells can differentiate into plasma cells in vitro and in vivo. CLL is the most frequent adult leukemia in the western world. It is a heterogeneous disease, characterized by clonal proliferation and the accumulation of mature CD5+ B lymphocytes (1). MM is a clonal plasma cell malignancy that accounts for more than 10% of all hematologic cancers (2). Although secondary cancers [particularly solid tumors (3–5)] can occur with CLL and MM, the concomitant occurrence of these two disorders in the same patient is rare [for a review of the few reported cases, see Ref. (6)]. The clonal relationship between these diseases has not always been clarified but is important in terms of understanding the pathogenesis and optimizing treatment. The clonal relationship between CLL and MM can be evaluated by (i) analyzing immunoglobulin (Ig) heavy chain and light chain (Ig kappa light chain and Ig lambda light chain) gene rearrangement, (ii) identifying and comparing somatic mutations, and (iii) studying chromosomic aberrations. Nevertheless, Ig rearrangements must always be interpreted in the light of specific phenomena such as allelic exclusion, B-cell receptor (BCR) revision (VH and DH gene replacement), BCR editing, and somatic mutations—events that were not considered in previous studies. These issues can be addressed by sequencing the rearranged Ig genes from sorted populations and interpreting the generated data. In the present study, we evaluated the putative clonal relationship between the two diseases by combining DNA copy number analysis with an assessment of Ig gene rearrangements [clonality assessment, V(D)J sequencing, and somatic hypermutation analysis] in highly enriched CD19+ CD5+ (CLL) and CD38+ CD138+ (MM) cell populations. Array comparative genomic hybridization data suggested a possible

  17. Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives.

    Science.gov (United States)

    Wang, Yong-Jian; Müller-Schärer, Heinz; van Kleunen, Mark; Cai, Ai-Ming; Zhang, Ping; Yan, Rong; Dong, Bi-Cheng; Yu, Fei-Hai

    2017-12-01

    What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants in China, and grew pairs of connected and disconnected ramets under heterogeneous light, soil nutrient and water conditions that are commonly encountered by alien plants during their invasion into new areas. Clonal integration increased biomass of all plants in all three heterogeneous resource environments. However, invasive plants benefited more from clonal integration than natives. Consequently, invasive plants produced more biomass than natives. Our results indicate that clonal integration may confer invasive alien clonal plants a competitive advantage over natives. Therefore, differences in the ability of clonal integration could potentially explain, at least partly, the invasion success of alien clonal plants in areas where resources are heterogeneously distributed. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  18. Quantifying heterogeneity and dynamics of clonal fitness in response to perturbation.

    Science.gov (United States)

    Frick, Peter L; Paudel, Bishal B; Tyson, Darren R; Quaranta, Vito

    2015-07-01

    The dynamics of heterogeneous clonal lineages within a cell population, in aggregate, shape both normal and pathological biological processes. Studies of clonality typically relate the fitness of clones to their relative abundance, thus requiring long-term experiments and limiting conclusions about the heterogeneity of clonal fitness in response to perturbation. We present, for the first time, a method that enables a dynamic, global picture of clonal fitness within a mammalian cell population. This novel assay allows facile comparison of the structure of clonal fitness in a cell population across many perturbations. By utilizing high-throughput imaging, our methodology provides ample statistical power to define clonal fitness dynamically and to visualize the structure of perturbation-induced clonal fitness within a cell population. We envision that this technique will be a powerful tool to investigate heterogeneity in biological processes involving cell proliferation, including development and drug response. © 2015 Wiley Periodicals, Inc.

  19. Expandable LED array interconnect

    Science.gov (United States)

    Yuan, Thomas Cheng-Hsin; Keller, Bernd

    2011-03-01

    A light emitting device that can function as an array element in an expandable array of such devices. The light emitting device comprises a substrate that has a top surface and a plurality of edges. Input and output terminals are mounted to the top surface of the substrate. Both terminals comprise a plurality of contact pads disposed proximate to the edges of the substrate, allowing for easy access to both terminals from multiple edges of the substrate. A lighting element is mounted to the top surface of the substrate. The lighting element is connected between the input and output terminals. The contact pads provide multiple access points to the terminals which allow for greater flexibility in design when the devices are used as array elements in an expandable array.

  20. Grazing incidence beam expander

    Energy Technology Data Exchange (ETDEWEB)

    Akkapeddi, P.R.; Glenn, P.; Fuschetto, A.; Appert, Q.; Viswanathan, V.K.

    1985-01-01

    A Grazing Incidence Beam Expander (GIBE) telescope is being designed and fabricated to be used as an equivalent end mirror in a long laser resonator cavity. The design requirements for this GIBE flow down from a generic Free Electron Laser (FEL) resonator. The nature of the FEL gain volume (a thin, pencil-like, on-axis region) dictates that the output beam be very small. Such a thin beam with the high power levels characteristic of FELs would have to travel perhaps hundreds of meters or more before expanding enough to allow reflection from cooled mirrors. A GIBE, on the other hand, would allow placing these optics closer to the gain region and thus reduces the cavity lengths substantially. Results are presented relating to optical and mechanical design, alignment sensitivity analysis, radius of curvature analysis, laser cavity stability analysis of a linear stable concentric laser cavity with a GIBE. Fabrication details of the GIBE are also given.

  1. Expanding the HAWC Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Johanna [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-17

    The High Altitude Water Cherenkov Gamma-Ray Observatory is expanding its current array of 300 water tanks to include 350 outrigger tanks to increase sensitivity to gamma rays above 10 TeV. This involves creating and testing hardware with which to build the new tanks, including photomultiplier tubes, high voltage supply units, and flash analog to digital converters. My responsibilities this summer included preparing, testing and calibrating that equipment.

  2. In-depth characterization of viral isolates from plasma and cells compared with plasma circulating quasispecies in early HIV-1 infection.

    Directory of Open Access Journals (Sweden)

    Judith Dalmau

    Full Text Available BACKGROUND: The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep Pyrosequencing (DPS technology in combination with phenotypic experiments to analyze and compare with unprecedented detail the composition of viral isolates and in vivo quasispecies. METHODOLOGY/PRINCIPAL FINDINGS: We amplified by DPS HIV-1 genomic regions covering gag, protease, integrase and env-V3 to characterize paired isolates from plasma and peripheral blood mononuclear cells and compare them with total plasma viral RNA in four recently HIV-1 infected subjects. Our study demonstrated the presence of unique haplotypes scattered between sample types with conservation of major variants. In addition, no differences in intra- and inter-population encoded protein variability were found between the different types of isolates or when these were compared to plasma viral RNA within subjects. Additionally, in vitro experiments demonstrated phenotypic similarities in terms of replicative capacity and co-receptor usage between viral isolates and plasma viral RNA. CONCLUSION: This study is the first in-depth comparison and characterization of viral isolates from different sources and plasma circulating quasispecies using DPS in recently HIV-1 infected subjects. Our data supports the use of primary isolates regardless of their plasma or cellular origin to define

  3. Clonal forestry, heterosis and advanced-generation breeding

    Energy Technology Data Exchange (ETDEWEB)

    Tuskan, G.A.

    1997-08-01

    This report discusses the clonal planting stock offers many advantages to the forest products industry. Advanced-generation breeding strategies should be designed to maximize within-family variance and at the same time allow the capture of heterosis. Certainly there may be a conflict in the choice of breeding strategy based on the trait of interest. It may be that the majority of the traits express heterosis due to overdominance. Alternatively, disease resistance is expressed as the lack of a specific metabolite or infection court then the homozygous recessive genotype may be the most desirable. Nonetheless, as the forest products industry begins to utilize the economic advantages of clonal forestry, breeding strategies will have to be optimized for these commercial plant materials. Here, molecular markers can be used to characterize the nature of heterosis and therefore define the appropriate breeding strategy.

  4. Clonal tests of new cottonwood selections from the southeast

    Science.gov (United States)

    Jonathan Paul Jeffreys; Samuel B. Land; Emily B. Schultz; Andrew J. Londo

    2006-01-01

    One hundred “new” clones and 20 “check” clones were established with unrooted cuttings during March-April 2003 in a second-stage clonal trial in Missouri and Georgia. The new clones had been selected for 2-year superiority in Melampsora leaf rust resistance, height growth, and diameter growth during first-stage rooted cutting trials. All 120 clones were vegetatively...

  5. Genetic Barcodes Facilitate Competitive Clonal Analyses In Vivo.

    Science.gov (United States)

    Aranyossy, Tim; Thielecke, Lars; Glauche, Ingmar; Fehse, Boris; Cornils, Kerstin

    2017-10-01

    Monitoring the fate of individual cell clones is an important task to better understand normal tissue regeneration, for example after hematopoietic stem cell (HSC) transplantation, but also cancerogenesis. Based on their integration into the host cell's genome, retroviral vectors are commonly used to stably mark target cells and their progeny. The development of genetic barcoding techniques has opened new possibilities to determine clonal composition and dynamics in great detail. A modular genetic barcode was recently introduced consisting of 32 variable positions (BC32) with a customized backbone, and its advantages were demonstrated with regard to barcode calling and quantification. The study presented applied the BC32 system in a complex in vivo situation, namely to analyze clonal reconstitution dynamics for HSC grafts consisting of up to three cell populations with distinguishable barcodes using different alpha- and lentiviral vectors. In a competitive transplantation setup, it was possible to follow the differently marked cell populations within individual animals. This enabled the clonal contribution of the different BC32 constructs during reconstitution and long-term hematopoiesis in the peripheral blood and the spatial distribution in bone marrow and spleen to be identified. Thus, it was demonstrated that the system allows the output of individually marked cells to be tracked in vivo and their influence on clonal dynamics to be analyzed. Successful application of the BC32 system in a complex, competitive in vivo situation provided proof-of-principle that its high complexity and the large Hamming distance between individual barcodes, combined with the easy customization, facilitate efficient and precise quantification, even without prior knowledge of individual barcode sequences. Importantly, simultaneous high-sensitivity analyses of different cell populations in single animals may significantly reduce numbers of animals required to investigate specific

  6. Clonal analysis of the microbiota of severe early childhood caries.

    Science.gov (United States)

    Kanasi, E; Dewhirst, F E; Chalmers, N I; Kent, R; Moore, A; Hughes, C V; Pradhan, N; Loo, C Y; Tanner, A C R

    2010-01-01

    Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the microbiota of severe early childhood caries. Dental plaque samples from 2- to 6-year-old children were analyzed using 16S rRNA gene cloning and sequencing, and by specific PCR amplification for Streptococcus mutans and Bifidobacteriaceae species. Children with severe caries (n = 39) had more dental plaque and gingival inflammation than caries-free children (n = 41). Analysis of phylotypes from operational taxonomic unit analysis of 16S rRNA clonal metalibraries from severe caries and caries-free children indicated that while libraries differed significantly (p children included Capnocytophaga gingivalis (p severe caries. Clonal analysis of 80 children identified a diverse microbiota that differed between severe caries and caries-free children, but the association of S. mutans with caries was from specific PCR analysis, not from clonal analysis, of samples. Copyright © 2010 S. Karger AG, Basel.

  7. A computational clonal analysis of the developing mouse limb bud.

    Directory of Open Access Journals (Sweden)

    Luciano Marcon

    Full Text Available A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study tissue movement during morphogenesis. Such experiments allow cell populations to be labeled at an early stage of development and to follow their spatial evolution over time. However, disentangling the cumulative effects of the multiple events responsible for the expansion of the labeled cell population is not always straightforward. To overcome this problem, we develop a novel computational method that combines accurate quantification of 2D limb bud morphologies and growth modeling to analyze mouse clonal data of early limb development. Firstly, we explore various tissue movements that match experimental limb bud shape changes. Secondly, by comparing computational clones with newly generated mouse clonal data we are able to choose and characterize the tissue movement map that better matches experimental data. Our computational analysis produces for the first time a two dimensional model of limb growth based on experimental data that can be used to better characterize limb tissue movement in space and time. The model shows that the distribution and shapes of clones can be described as a combination of anisotropic growth with isotropic cell mixing, without the need for lineage compartmentalization along the AP and PD axis. Lastly, we show that this comprehensive description can be used to reassess spatio-temporal gene regulations taking tissue movement into account and to investigate PD patterning hypothesis.

  8. Clonal Analysis of the Microbiota of Severe Early Childhood Caries

    Science.gov (United States)

    Kanasi, E.; Dewhirst, F.E.; Chalmers, N.I.; Kent, R.; Moore, A.; Hughes, C.V.; Pradhan, N.; Loo, C.Y.; Tanner, A.C.R.

    2010-01-01

    Background/Aims Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the microbiota of severe early childhood caries. Methods Dental plaque samples from 2- to 6-year-old children were analyzed using 16S rRNA gene cloning and sequencing, and by specific PCR amplification for Streptococcus mutans and Bifidobacteriaceae species. Results Children with severe caries (n = 39) had more dental plaque and gingival inflammation than caries-free children (n = 41). Analysis of phylotypes from operational taxonomic unit analysis of 16S rRNA clonal metalibraries from severe caries and caries-free children indicated that while libraries differed significantly (p caries-associated taxa included Granulicatella elegans (p caries-free children included Capnocytophaga gingivalis (p Streptococcus sanguinis (p Streptococcus cristatus (p mutans (p caries. Conclusion Clonal analysis of 80 children identified a diverse microbiota that differed between severe caries and caries-free children, but the association of S. mutans with caries was from specific PCR analysis, not from clonal analysis, of samples. PMID:20861633

  9. Competitive equivalence maintains persistent inter-clonal boundaries.

    Science.gov (United States)

    Ferrell, David L

    2005-01-01

    Clear boundaries often separate adjacent conspecific competitors. These boundaries may reflect bordering animal territories or regions of inter-organism contact in mobile and non-mobile organisms, respectively. Sessile, clonal organisms often form persistent inter-clonal boundaries despite great variation in competitive ability among genotypes within a population. I show that neighboring clones in the sea anemone Anthopleura elegantissima and three species of the marine hydroid genus Hydractinia are more evenly matched in terms of competitive ability than expected by chance. Hypotheses of genetic relatedness or similar environmental regime shared by neighboring clones are inconsistent with the observed similarities between adjacent competitors in one or both taxa. Instead, inter-clonal borders evidently persist as standoffs between evenly matched competitors. Large differences in competitive ability between bordering clones were rarely observed, suggesting that dominant clones quickly displace or eliminate others in competitive mismatches. This ecological parallel between taxa (i.e., competitive equivalence) exists despite several fundamental differences (e.g., geographical distribution, habitat, body size, longevity), suggesting that competitive equivalence may be a widespread determinant of boundary persistence between adjacent competitors.

  10. Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring.

    Science.gov (United States)

    Becheler, R; Benkara, E; Moalic, Y; Hily, C; Arnaud-Haond, S

    2014-02-01

    Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time.

  11. The preservation of genetic resources of the vine requires cohabitation between institutional clonal selection, mass selection and private clonal selection

    Directory of Open Access Journals (Sweden)

    Roby Jean-Philippe

    2014-01-01

    Full Text Available Clonal selection allows control of virus diseases and selection of genotypes on agronomic, viticultural or enological criteria. Clonal selection has the major drawback that it impoverishes genetic diversity and exposes growers to environmental instability of clones (genotype X environment interaction. Clonal selection has become the almost unique way of propagating plant material for vineyards, hence threatening the genetic diversity of the grapevine. For major grapevine varieties, some genetic diversity is maintained in institutional collections. However, this way of conservation is insufficiently developed, it is expensive and remains fragile. A cost effective way to preserve intra-varietal diversity is to maintain a limited proportion of mass selection in vine propagation. Private clonal selection can also contribute, in a more limited way, in maintaining genetic resources. Another approach to carry out conservation and selection of grapevine is the methodology followed in Portugal. This strategy is exemplified with the conservation/selection of an ancient Portuguese variety. The work begins with the “ex situ” conservation of a representative sample of the intravarietal diversity of the variety, which, in practice, corresponds to a large field trial with hundreds of clones under an experimental design suitable for reducing random variation of quantitative traits. From evaluating those traits (yield and must quality traits, the intravarietal diversity is quantified and the range of the predicted genotypic effects for each of those traits is analyzed. Different mass selections (polyclonal selections are carried out for distribution and planting of new vineyards. These different mass selections provide high economic gains and also the preservation of diversity in a complementary manner to that which started the work on-farm conservation.

  12. The expanding universe

    CERN Document Server

    Lew, Kristi

    2011-01-01

    People have always been fascinated with the stars above and the universe that contains them. Over the years, astronomers have developed numerous theories to explain how the universe began, how it works, and what its ultimate fate will be. But all of the scientists' questions are far from answered. The Expanding Universe goes beyond the creation of the universe to explain how scientists think the universe works, grows, and changes, including what great thinkers Isaac Newton and Albert Einstein had to say about its fate. Readers will also learn about how researchers are slowly shedding light on

  13. Expanding Your Horizon 2015

    CERN Multimedia

    Kaltenhauser, Kristin

    2015-01-01

    Expanding your horizons is a bi-annual “Science Day” for girls aged 11 to 14, held at the University of Geneva on 14 November. The girls had the opportunity to take part in hands-on workshops held by local professional women in the field of science, mathematics, engineering and technology. For the fourth time, CERN was part of this event, offering three workshops as well as a booth at the Discovery Fair, including Higgnite, an interactive visualization of the Higgs Field.

  14. Whole body clonality analysis in an aggressive STLV-1 associated leukemia (ATLL) reveals an unexpected clonal complexity.

    Science.gov (United States)

    Turpin, Jocelyn; Alais, Sandrine; Marçais, Ambroise; Bruneau, Julie; Melamed, Anat; Gadot, Nicolas; Tanaka, Yuetsu; Hermine, Olivier; Melot, Sandrine; Lacoste, Romain; Bangham, Charles R; Mahieux, Renaud

    2017-03-28

    HTLV-1 causes Adult T cell Leukemia/Lymphoma (ATLL) in humans. We describe an ATL-like disease in a 9 year-old female baboon naturally infected with STLV-1 (the simian counterpart of HTLV-1), with a lymphocyte count over 10(10)/L, lymphocytes with abnormal nuclear morphology, and pulmonary and skin lesions. The animal was treated with a combination of AZT and alpha interferon. Proviral load (PVL) was measured every week. Because the disease continued to progress, the animal was euthanized. Abnormal infiltrates of CD3(+)CD25(+) lymphocytes and Tax-positive cells were found by histological analyses in both lymphoid and non-lymphoid organs. PVL was measured and clonal diversity was assessed by LM-PCR (Ligation-Mediated Polymerase Chain Reaction) and high throughput sequencing, in blood during treatment and in 14 different organs. The highest PVL was found in lymph nodes, spleen and lungs. One major clone and a number of intermediate abundance clones were present in blood throughout the course of treatment, and in organs. These results represent the first multi-organ clonality study in ATLL. We demonstrate a previously undescribed clonal complexity in ATLL. Our data reinforce the usefulness of natural STLV-1 infection as a model of ATLL. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Integración clonal en una palma tropical

    Directory of Open Access Journals (Sweden)

    1992-01-01

    Full Text Available INTEGRATION CLONALE D'UN PALMIER TROPICAL. Reinhardtia gracilis est un palmier clonal du sous-bois d’une forêt tropicale pluvieuse de Veracruz, Mexico. Cette espèce forme des clones. Pendant les deux années qui ont suivi l’application des traitements, on a enregistré les réponses des plantes dans la production, l’abscission et le changement net des feuilles. L’étude du degré d’intégration physiologique des axes composant le clone procède par un traitement combiné de défeuillage, de séparation physique des axes et de fertilisation du sol. Il en résulte un gain net de production foliaire chez les axes qui n’ont pas été séparés, alors que les axes séparés témoins s’avèrent être les plus affectés par le traitement. Ces résultats suggèrent que l’intégration clonale de ce palmier lui permet de supporter les perturbations fréquentes dues à la chute de branches et de feuilles de la canopée. Reinhardtia gracilis es una palma clonal que habita en el sotobosque de una selva tropical lluviosa en Veracruz, México. Con el objeto de investigar el grado de integración fisiológica de los ramets de esta especie, se diseñó un experimento que combina tratamientos de defoliación, separación física de las conexiones entre ramets y fertilización del suelo. Las respuestas de las plantas en la producción, abscisión y cambio neto de hojas se registraron durante los dos años posteriores a la aplicación de los tratamientos. La separación física de los ramets, la defoliación y la fertilización del suelo incrementaron la ganancia neta de hojas en los ramets de las palmas a las que no se les cortaron las conexiones. El tratamiento más severo se encontró en las palmas desconectadas que no fueron ni defoliadas ni fertilizadas. Estos resultados sugieren que la integración clonal en esta palma permite soportar las frecuentes perturbaciones producidas por la caída de ramas y hojas del dosel superior. CLONAL INTEGRATION IN A

  16. Self-mating in the definitive host potentiates clonal outbreaks of the apicomplexan parasites Sarcocystis neurona and Toxoplasma gondii.

    Directory of Open Access Journals (Sweden)

    Jered M Wendte

    2010-12-01

    Full Text Available Tissue-encysting coccidia, including Toxoplasma gondii and Sarcocystis neurona, are heterogamous parasites with sexual and asexual life stages in definitive and intermediate hosts, respectively. During its sexual life stage, T. gondii reproduces either by genetic out-crossing or via clonal amplification of a single strain through self-mating. Out-crossing has been experimentally verified as a potent mechanism capable of producing offspring possessing a range of adaptive and virulence potentials. In contrast, selfing and other life history traits, such as asexual expansion of tissue-cysts by oral transmission among intermediate hosts, have been proposed to explain the genetic basis for the clonal population structure of T. gondii. In this study, we investigated the contributing roles self-mating and sexual recombination play in nature to maintain clonal population structures and produce or expand parasite clones capable of causing disease epidemics for two tissue encysting parasites. We applied high-resolution genotyping against strains isolated from a T. gondii waterborne outbreak that caused symptomatic disease in 155 immune-competent people in Brazil and a S. neurona outbreak that resulted in a mass mortality event in Southern sea otters. In both cases, a single, genetically distinct clone was found infecting outbreak-exposed individuals. Furthermore, the T. gondii outbreak clone was one of several apparently recombinant progeny recovered from the local environment. Since oocysts or sporocysts were the infectious form implicated in each outbreak, the expansion of the epidemic clone can be explained by self-mating. The results also show that out-crossing preceded selfing to produce the virulent T. gondii clone. For the tissue encysting coccidia, self-mating exists as a key adaptation potentiating the epidemic expansion and transmission of newly emerged parasite clones that can profoundly shape parasite population genetic structures or cause

  17. Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins

    NARCIS (Netherlands)

    Izdebski, R.; Fiett, J.; Urbanowicz, P.; Baraniak, A.; Derde, L. P G; Bonten, M. J M; Carmeli, Y.; Goossens, H.; Hryniewicz, W.; Brun-Buisson, C.; Brisse, S.; Gniadkowski, M.; Herda, M.; Dautzenberg, M. J.; Adler, A.; Kazma, M.; Navon-Venezia, S.; Malhotra-Kumar, S.; Lammens, C.; Legrand, P.; Chalfine, A.; Giamarellou, H.; Petrikkos, G. L.; Balode, A.; Dumpis, U.; Stammet, P.; Aragăo, I.; Esteves, F.; Torres Martí, A.; Lawrence, C.; Salomon, J.; Paul, M.; Lerman, Y.; Rossini, A.; Salvia, A.; Vidal Samso, J.; Fierro, J.

    2015-01-01

    Objectives: The objective of this study was to examine Klebsiella oxytoca clonal and phylogenetic diversity, based on an international collection of carriage isolates non-susceptible to expanded-spectrum cephalosporins (ESCs). Methods: The study material comprised 68 rectal carriage K. oxytoca

  18. Clonal Immune Responses of Mycobacterium-Specific γδ T Cells in Tuberculous and Non-Tuberculous Tissues during M. tuberculosis Infection

    Science.gov (United States)

    Qiu, Liyou; Shen, Yun; Du, George; Zhou, Keyuan; Wang, Richard; Chen, Zheng W.

    2012-01-01

    Background We previously demonstrated that unvaccinated macaques infected with large-dose M.tuberculosis(Mtb) exhibited delays for pulmonary trafficking of Ag-specific αβ and γδ T effector cells, and developed severe lung tuberculosis(TB) and “secondary” Mtb infection in remote organs such as liver and kidney. Despite delays in lungs, local immunity in remote organs may accumulate since progressive immune activation after pulmonary Mtb infection may allow IFNγ-producing γδ T cells to adequately develop and traffic to lately-infected remote organs. As initial efforts to test this hypothesis, we comparatively examined TCR repertoire/clonality, tissue trafficking and effector function of Vγ2Vδ2 T cells in lung with severe TB and in liver/kidney without apparent TB. Methodology/Principal Findings We utilized conventional infection-immunity approaches in macaque TB model, and employed our decades-long expertise for TCR repertoire analyses. TCR repertoires in Vγ2Vδ2 T-cell subpopulation were broad during primary Mtb infection as most TCR clones found in lymphoid system, lung, kidney and liver were distinct. Polyclonally-expanded Vγ2Vδ2 T-cell clones from lymphoid tissues appeared to distribute and localize in lung TB granuloms at the endpoint after Mtb infection by aerosol. Interestingly, some TCR clones appeared to be more predominant than others in lymphocytes from liver or kidney without apparent TB lesions. TCR CDR3 spetratyping revealed such clonal dominance, and the clonal dominance of expanded Vγ2Vδ2 T cells in kidney/liver tissues was associated with undetectable or low-level TB burdens. Furthermore, Vγ2Vδ2 T cells from tissue compartments could mount effector function for producing anti-mycobacterium cytokine. Conclusion We were the first to demonstrate clonal immune responses of mycobacterium-specific Vγ2Vδ2 T cells in the lymphoid system, heavily-infected lungs and lately subtly-infected kidneys or livers during primary Mtb infection

  19. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

    Science.gov (United States)

    Mathers, Thomas C; Chen, Yazhou; Kaithakottil, Gemy; Legeai, Fabrice; Mugford, Sam T; Baa-Puyoulet, Patrice; Bretaudeau, Anthony; Clavijo, Bernardo; Colella, Stefano; Collin, Olivier; Dalmay, Tamas; Derrien, Thomas; Feng, Honglin; Gabaldón, Toni; Jordan, Anna; Julca, Irene; Kettles, Graeme J; Kowitwanich, Krissana; Lavenier, Dominique; Lenzi, Paolo; Lopez-Gomollon, Sara; Loska, Damian; Mapleson, Daniel; Maumus, Florian; Moxon, Simon; Price, Daniel R G; Sugio, Akiko; van Munster, Manuella; Uzest, Marilyne; Waite, Darren; Jander, Georg; Tagu, Denis; Wilson, Alex C C; van Oosterhout, Cock; Swarbreck, David; Hogenhout, Saskia A

    2017-02-13

    The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

  20. Clonal integration of Fragaria orientalis in reciprocal and coincident patchiness resources: cost-benefit analysis.

    Directory of Open Access Journals (Sweden)

    Yunchun Zhang

    Full Text Available Clonal growth allows plants to spread horizontally and to experience different levels of resources. If ramets remain physiologically integrated, clonal plants can reciprocally translocate resources between ramets in heterogeneous environments. But little is known about the interaction between benefits of clonal integration and patterns of resource heterogeneity in different patches, i.e., coincident patchiness or reciprocal patchiness. We hypothesized that clonal integration will show different effects on ramets in different patches and more benefit to ramets under reciprocal patchiness than to those under coincident patchiness, as well as that the benefit from clonal integration is affected by the position of proximal and distal ramets under reciprocal or coincident patchiness. A pot experiment was conducted with clonal fragments consisting of two interconnected ramets (proximal and distal ramet of Fragaria orientalis. In the experiment, proximal and distal ramets were grown in high or low availability of resources, i.e., light and water. Resource limitation was applied either simultaneously to both ramets of a clonal fragment (coincident resource limitation or separately to different ramets of the same clonal fragment (reciprocal resource limitation. Half of the clonal fragments were connected while the other half were severed. From the experiment, clonal fragments growing under coincident resource limitation accumulated more biomass than those under reciprocal resource limitation. Based on a cost-benefit analysis, the support from proximal ramets to distal ramets was stronger than that from distal ramets to proximal ramets. Through division of labour, clonal fragments of F. orientalis benefited more in reciprocal patchiness than in coincident patchiness. While considering biomass accumulation and ramets production, coincident patchiness were more favourable to clonal plant F. orientalis.

  1. Population dynamics of a long-lived alpine plant with sexual and clonal reproduction

    OpenAIRE

    Weppler, Tina

    2006-01-01

    This thesis focuses on the demography, reproduction, and pre-dispersal seed predation of the alpine clonal plant Geum reptans. In chapter 2, I studied the population dynamics of G. reptans, thereby I particularly addressed the relative importance of sexual vs. clonal reproduction for population growth in this longlived species. In chapter 3, the balance between sexual and clonal reproduction in plants of different sizes and the frequency of life-cycle stages i...

  2. Disturbance Is an Important Driver of Clonal Richness in Tropical Seagrasses.

    Science.gov (United States)

    McMahon, Kathryn M; Evans, Richard D; van Dijk, Kor-Jent; Hernawan, Udhi; Kendrick, Gary A; Lavery, Paul S; Lowe, Ryan; Puotinen, Marji; Waycott, Michelle

    2017-01-01

    Clonality is common in many aquatic plant species, including seagrasses, where populations are maintained through a combination of asexual and sexual reproduction. One common measure used to describe the clonal structure of populations is clonal richness. Clonal richness is strongly dependent on the biological characteristics of the species, and how these interact with the environment but can also reflect evolutionary scale processes especially at the edge of species ranges. However, little is known about the spatial patterns and drivers of clonal richness in tropical seagrasses. This study assessed the spatial patterns of clonal richness in meadows of three tropical seagrass species, Thalassia hemprichii, Halodule uninervis, and Halophila ovalis, spanning a range of life-history strategies and spatial scales (2.5-4,711 km) in Indonesia and NW Australia. We further investigated the drivers of clonal richness using general additive mixed models for two of the species, H. uninervis and H. ovalis, over 8° latitude. No significant patterns were observed in clonal richness with latitude, yet disturbance combined with sea surface temperature strongly predicted spatial patterns of clonal richness. Sites with a high probability of cyclone disturbance had low clonal richness, whereas an intermediate probability of cyclone disturbance and the presence of dugong grazing combined with higher sea surface temperatures resulted in higher levels of clonal richness. We propose potential mechanisms for these patterns related to the recruitment and mortality rates of individuals as well as reproductive effort. Under a changing climate, increased severity of tropical cyclones and the decline in populations of mega-grazers have the potential to reduce clonal richness leading to less genetically diverse populations.

  3. Disturbance Is an Important Driver of Clonal Richness in Tropical Seagrasses

    Directory of Open Access Journals (Sweden)

    Kathryn M. McMahon

    2017-12-01

    Full Text Available Clonality is common in many aquatic plant species, including seagrasses, where populations are maintained through a combination of asexual and sexual reproduction. One common measure used to describe the clonal structure of populations is clonal richness. Clonal richness is strongly dependent on the biological characteristics of the species, and how these interact with the environment but can also reflect evolutionary scale processes especially at the edge of species ranges. However, little is known about the spatial patterns and drivers of clonal richness in tropical seagrasses. This study assessed the spatial patterns of clonal richness in meadows of three tropical seagrass species, Thalassia hemprichii, Halodule uninervis, and Halophila ovalis, spanning a range of life-history strategies and spatial scales (2.5–4,711 km in Indonesia and NW Australia. We further investigated the drivers of clonal richness using general additive mixed models for two of the species, H. uninervis and H. ovalis, over 8° latitude. No significant patterns were observed in clonal richness with latitude, yet disturbance combined with sea surface temperature strongly predicted spatial patterns of clonal richness. Sites with a high probability of cyclone disturbance had low clonal richness, whereas an intermediate probability of cyclone disturbance and the presence of dugong grazing combined with higher sea surface temperatures resulted in higher levels of clonal richness. We propose potential mechanisms for these patterns related to the recruitment and mortality rates of individuals as well as reproductive effort. Under a changing climate, increased severity of tropical cyclones and the decline in populations of mega-grazers have the potential to reduce clonal richness leading to less genetically diverse populations.

  4. Expanding hollow metal rings

    Science.gov (United States)

    Peacock, Harold B [Evans, GA; Imrich, Kenneth J [Grovetown, GA

    2009-03-17

    A sealing device that may expand more planar dimensions due to internal thermal expansion of a filler material. The sealing material is of a composition such that when desired environment temperatures and internal actuating pressures are reached, the sealing materials undergoes a permanent deformation. For metallic compounds, this permanent deformation occurs when the material enters the plastic deformation phase. Polymers, and other materials, may be using a sealing mechanism depending on the temperatures and corrosivity of the use. Internal pressures are generated by either rapid thermal expansion or material phase change and may include either liquid or solid to gas phase change, or in the gaseous state with significant pressure generation in accordance with the gas laws. Sealing material thickness and material composition may be used to selectively control geometric expansion of the seal such that expansion is limited to a specific facing and or geometric plane.

  5. Invasive clonal plant species have a greater root-foraging plasticity than non-invasive ones.

    Science.gov (United States)

    Keser, Lidewij H; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

    2014-03-01

    Clonality is frequently positively correlated with plant invasiveness, but which aspects of clonality make some clonal species more invasive than others is not known. Due to their spreading growth form, clonal plants are likely to experience spatial heterogeneity in nutrient availability. Plasticity in allocation of biomass to clonal growth organs and roots may allow these plants to forage for high-nutrient patches. We investigated whether this foraging response is stronger in species that have become invasive than in species that have not. We used six confamilial pairs of native European clonal plant species differing in invasion success in the USA. We grew all species in large pots under homogeneous or heterogeneous nutrient conditions in a greenhouse, and compared their nutrient-foraging response and performance. Neither invasive nor non-invasive species showed significant foraging responses to heterogeneity in clonal growth organ biomass or in aboveground biomass of clonal offspring. Invasive species had, however, a greater positive foraging response in terms of root and belowground biomass than non-invasive species. Invasive species also produced more total biomass. Our results suggest that the ability for strong root foraging is among the characteristics promoting invasiveness in clonal plants.

  6. How past and present influence the foraging of clonal plants?

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    Philipe Louâpre

    Full Text Available Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information and the resource variability sampled by the older ramets (i.e. the past information. We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.

  7. Feline gastrointestinal lymphoma: mucosal architecture, immunophenotype, and molecular clonality.

    Science.gov (United States)

    Moore, P F; Rodriguez-Bertos, A; Kass, P H

    2012-07-01

    Gastrointestinal lymphomas were identified in 120 cats between 1995 and 2006. Lymphomas were classified according to the World Health Organization (WHO) scheme. Cats with mucosal T-cell lymphoma (n = 84) predominated and had a median survival of 29 months. Mucosal T-cell lymphoma matched WHO enteropathy-associated T-cell lymphoma (EATCL) type II. Epitheliotropic T-cell infiltrates were present in 62% of cats and occurred as clusters or diffuse infiltrates of small to intermediate-sized T cells in villous and/or crypt epithelium. Similar lymphocytes infiltrated the lamina propria in distinctive patterns. Cats with transmural T-cell lymphoma (n = 19) had a median survival of 1.5 months. Transmural T-cell lymphoma matched WHO EATCL type I. Epitheliotropic T-cell infiltrates were present in 58% of cats. Large lymphocytes (n = 11), mostly with cytoplasmic granules (LGL-granzyme B+) (n = 9) predominated. Transmural extension across the muscularis propria characterized the lesion. Both mucosal and transmural T-cell lymphomas were largely confined to the small intestine, and molecular clonality analysis revealed clonal or oligoclonal rearrangements of T-cell receptor-γ in 90% of cats. Cats with B-cell lymphoma (n = 19) had a median survival of 3.5 months. B-cell lymphomas occurred as transmural lesions in stomach, jejunum, and ileo-cecal-colic junction. The majority were diffuse, large B-cell lymphomas of centroblastic type. In conclusion, T-cell lymphomas characterized by distinctive mucosal architecture, CD3 expression, and clonal expansion predominated in the feline gastrointestinal tract.

  8. Clonal architectures and driver mutations in metastatic melanomas.

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    Li Ding

    Full Text Available To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1, protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT, as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2. Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9 with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma.

  9. How past and present influence the foraging of clonal plants?

    Science.gov (United States)

    Louâpre, Philipe; Bittebière, Anne-Kristel; Clément, Bernard; Pierre, Jean-Sébastien; Mony, Cendrine

    2012-01-01

    Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.

  10. Clonal origins of ETV6-RUNX1+ acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Alpar, D.; Wren, D.; Ermini, Luca

    2015-01-01

    Studies on twins with concordant acute lymphoblastic leukemia (ALL) have revealed that ETV6-RUNX1 gene fusion is a common, prenatal genetic event with other driver aberrations occurring subclonally and probably postnatally. The fetal cell type that is transformed by ETV6-RUNX1 is not identified...... by such studies or by the analysis of early B-cell lineage phenotype of derived progeny. Ongoing, clonal immunoglobulin (IG) and cross-lineage T-cell receptor (TCR) gene rearrangements are features of B-cell precursor leukemia and commence at the pro-B-cell stage of normal B-cell lineage development. We reasoned...

  11. Clonal human fetal ventral mesencephalic dopaminergic neuron precursors for cell therapy research.

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    Tania Ramos-Moreno

    Full Text Available A major challenge for further development of drug screening procedures, cell replacement therapies and developmental studies is the identification of expandable human stem cells able to generate the cell types needed. We have previously reported the generation of an immortalized polyclonal neural stem cell (NSC line derived from the human fetal ventral mesencephalon (hVM1. This line has been biochemically, genetically, immunocytochemically and electrophysiologically characterized to document its usefulness as a model system for the generation of A9 dopaminergic neurons (DAn. Long-term in vivo transplantation studies in parkinsonian rats showed that the grafts do not mature evenly. We reasoned that diverse clones in the hVM1 line might have different abilities to differentiate. In the present study, we have analyzed 9 hVM1 clones selected on the basis of their TH generation potential and, based on the number of v-myc copies, v-myc down-regulation after in vitro differentiation, in vivo cell cycle exit, TH⁺ neuron generation and expression of a neuronal mature marker (hNSE, we selected two clones for further in vivo PD cell replacement studies. The conclusion is that homogeneity and clonality of characterized NSCs allow transplantation of cells with controlled properties, which should help in the design of long-term in vivo experiments.

  12. Autoimmunity since the 1957 clonal selection theory: a little acorn to a large oak.

    Science.gov (United States)

    Mackay, Ian R

    2008-01-01

    Knowledge on autoimmunity is examined from the launch of clonal selection theory 1957-1959. Crucial elements then were 'forbidden clones' of immunocytes as agents of tissue damage, somatic mutations that generated such clones and 'homeostatic mechanisms' that controlled them. The understanding of autoimmunity over the succeeding 50 years has expanded immensely, and many more diseases now come under this rubric. Examined here are current problems of definition including 'adaptive' and 'innate' types of autoimmunity, estimations of population burdens of autoimmune diseases, the nature of autoepitopes in the context of the diabetes autoantigen GAD65, and the complexities of immune tolerance and the genetic influences thereon, leading to the nomination of multiple 'tolerance/autoimmunity' genes as critical components of pathogenesis. Burnet's concept of mutagenesis as a basic feature of various pathologies including autoimmunity is given a contemporary focus, his views on deletional tolerance have been well vindicated, his 'forbidden clones' remain as unphysiological as before albeit phenotypically resembling normal lymphocytes, and his 'homeostatic mechanisms' can be now interpreted in terms of immunoregulatory networks.

  13. Ex-vivo Clonally Expanded B Lymphocytes Infiltrating Colorectal Carcinoma Are of Mature Immunophenotype and Produce Functional IgG

    OpenAIRE

    Claudia Maletzki; Annika Jahnke; Christiane Ostwald; Ernst Klar; Friedrich Prall; Michael Linnebacher

    2012-01-01

    BACKGROUND: Tumor infiltrating B cells (TiBc) have not yet been investigated in detail. This may at least in part be due to technical difficulties. Here we describe a straightforward and reproducible method to isolate and culture TiBc from primary colorectal carcinomas (CRC). METHODS/RESULTS: TiBc cultures were generated by Epstein-Barr virus (EBV) immortalization. With this method, monoclonal TiBc cultures were obtained for 14/19 CRCs. As assessed by flow cytometry and ELISA, TiBc showed an ...

  14. Ex-vivo clonally expanded B lymphocytes infiltrating colorectal carcinoma are of mature immunophenotype and produce functional IgG.

    Science.gov (United States)

    Maletzki, Claudia; Jahnke, Annika; Ostwald, Christiane; Klar, Ernst; Prall, Friedrich; Linnebacher, Michael

    2012-01-01

    Tumor infiltrating B cells (TiBc) have not yet been investigated in detail. This may at least in part be due to technical difficulties. Here we describe a straightforward and reproducible method to isolate and culture TiBc from primary colorectal carcinomas (CRC). TiBc cultures were generated by Epstein-Barr virus (EBV) immortalization. With this method, monoclonal TiBc cultures were obtained for 14/19 CRCs. As assessed by flow cytometry and ELISA, TiBc showed an activated immunophenotype (CD23(+), CD80(+)) and produced immunoglobulin (Ig; IgG secretion in 55% of the cultures). In functional in vitro analysis, most of the IgGs specifically bound to allogeneic CRC target cells. These data suggest that TiBc are antigen-experienced and thus may exhibit functionality in situ. Additionally, mini-cultures generated from 12 further CRCs revealed TiBc outgrowth exclusively in the presence of EBV. In summary, this simple method provides a cellular tool and our data set the stage for analysing the bivalent role of TiBc; being antigen-presenting cells on the one hand and tumor-specific antibody producers on the other. Additionally, the generation of long-term TiBc cultures and their monoclonal Ig may serve to identify novel tumor-specific antigens.

  15. Ex-vivo clonally expanded B lymphocytes infiltrating colorectal carcinoma are of mature immunophenotype and produce functional IgG.

    Directory of Open Access Journals (Sweden)

    Claudia Maletzki

    Full Text Available BACKGROUND: Tumor infiltrating B cells (TiBc have not yet been investigated in detail. This may at least in part be due to technical difficulties. Here we describe a straightforward and reproducible method to isolate and culture TiBc from primary colorectal carcinomas (CRC. METHODS/RESULTS: TiBc cultures were generated by Epstein-Barr virus (EBV immortalization. With this method, monoclonal TiBc cultures were obtained for 14/19 CRCs. As assessed by flow cytometry and ELISA, TiBc showed an activated immunophenotype (CD23(+, CD80(+ and produced immunoglobulin (Ig; IgG secretion in 55% of the cultures. In functional in vitro analysis, most of the IgGs specifically bound to allogeneic CRC target cells. These data suggest that TiBc are antigen-experienced and thus may exhibit functionality in situ. Additionally, mini-cultures generated from 12 further CRCs revealed TiBc outgrowth exclusively in the presence of EBV. CONCLUSION: In summary, this simple method provides a cellular tool and our data set the stage for analysing the bivalent role of TiBc; being antigen-presenting cells on the one hand and tumor-specific antibody producers on the other. Additionally, the generation of long-term TiBc cultures and their monoclonal Ig may serve to identify novel tumor-specific antigens.

  16. Expander chunked codes

    Science.gov (United States)

    Tang, Bin; Yang, Shenghao; Ye, Baoliu; Yin, Yitong; Lu, Sanglu

    2015-12-01

    Chunked codes are efficient random linear network coding (RLNC) schemes with low computational cost, where the input packets are encoded into small chunks (i.e., subsets of the coded packets). During the network transmission, RLNC is performed within each chunk. In this paper, we first introduce a simple transfer matrix model to characterize the transmission of chunks and derive some basic properties of the model to facilitate the performance analysis. We then focus on the design of overlapped chunked codes, a class of chunked codes whose chunks are non-disjoint subsets of input packets, which are of special interest since they can be encoded with negligible computational cost and in a causal fashion. We propose expander chunked (EC) codes, the first class of overlapped chunked codes that have an analyzable performance, where the construction of the chunks makes use of regular graphs. Numerical and simulation results show that in some practical settings, EC codes can achieve rates within 91 to 97 % of the optimum and outperform the state-of-the-art overlapped chunked codes significantly.

  17. Clonal diversity and structure within a population of the pondweed Potamogeton pectinatus foraged by Bewick's swans.

    Science.gov (United States)

    Hangelbroek, H H; Ouborg, N J; Santamaría, L; Schwenk, K

    2002-10-01

    Clonal diversity within plant populations is affected by factors that influence genet (clone) survival and seed recruitment, such as resource availability, disturbance, seed dispersal mechanism, propagule predation and the age of the population. Here we studied a population of Potamogeton pectinatus, a pseudo-annual aquatic macrophyte. Within populations reproduction appears to be mainly asexually through subterranean propagules (tubers), while recruitment via seeds is believed to be relatively unimportant. RAPD markers were used to analyse clonal diversity and genetic variation within the population. Ninety-seven genets were identified among 128 samples taken from eight plots. The proportion of distinguishable genets (0.76) and Simpson's diversity index (0.99) exhibited high levels of clonal diversity compared to other clonal plants. According to an analysis of molecular variance (amova) most genetic variation occurred between individuals within plots (93-97%) rather than between plots (8-3%). These results imply that sexual reproduction plays an unexpectedly important role within the population. Nevertheless, autocorrelation statistics revealed a spatial genetic structure resulting from clonal growth. In contrast to genetic variation, clonal diversity was affected by several ecological factors. Water depth and silt content had direct negative effects on clonal diversity. Tuber predation by Bewick's swans had an unexpected indirect negative effect on clonal diversity through reducing the tuber-bank biomass in spring, which on its turn was positively correlated to clonal diversity. The disturbance by swans, therefore, did not enhance seed recruitment and thus clonal diversity; on the contrary, heavily foraged areas are probably more prone to stochastic loss of genets leading to reduced clonal diversity.

  18. Plant traits and ecosystem effects of clonality: a new research agenda.

    Science.gov (United States)

    Cornelissen, Johannes H C; Song, Yao-Bin; Yu, Fei-Hai; Dong, Ming

    2014-08-01

    Clonal plants spread laterally by spacers between their ramets (shoot-root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling. The response-effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal 'response traits' that promote plant fitness and interspecific variation in 'effect traits', which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention. This review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on ecosystem functions. © The Author 2014

  19. The Use of Auxin Quantification for Understanding Clonal Tree Propagation

    Directory of Open Access Journals (Sweden)

    Carlos A. Stuepp

    2017-01-01

    Full Text Available Qualitative and quantitative hormone analyses have been essential for understanding the metabolic, physiological, and morphological processes that are influenced by plant hormones. Auxins are key hormones in the control of many aspects of plant growth and development and their endogenous levels are considered critical in the process of adventitious root induction. Exogenous auxins are used extensively in the clonal propagation of tree species by cuttings or tissue culture. Understanding of auxin effects has advanced with the development of increasingly accurate methods for auxin quantification. However, auxin analysis has been challenging because auxins typically occur at low concentrations, while compounds that interfere with their detection often occur at high concentrations, in plant tissues. Interference from other compounds has been addressed by extensive purification of plant extracts prior to auxin analysis, although this means that quantification methods have been limited by their expense. This review explores the extraction, purification, and quantification of auxins and the application of these techniques in developing improved methods for the clonal propagation of forestry trees.

  20. AMPELOGRAPHIC CHARACTERIZATION OF SOME CHASSELAS DORÉ ELITE CLONAL ACCESSIONS

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    Elena Brînduse

    2017-07-01

    Full Text Available Four elite clonal accessions of Vitis vinifera L., Chasselas doré variety were identified in a very old plantation, of 110 years, located in Valea Cãlugãreascã, on the St. Nicolas Monastery vineyard. The vines, grafted on the SO4 (Selection Oppenheim 4 rootstock, were planted in 2007 in the germplasm collection belonging to the Research and Development Institute for Viticulture and Enology, Valea Cãlugãreascã. The present study aimed to evaluate these elite clonal accessions from ampelographic point of view, in comparison with Chasselas doré variety. Ampelographic characterization of genotypes was performed according to the descriptors ampelographic methodology, based on the specifications made in the OIV Descriptor List for Grape Varieties and Vitis species, Second Edition (2009. The shoot tips descriptions were made when they were approximately 10 to 30 cm in height and, in this stage, also, the first four distal leaves of young leaves were evaluated. Mature leaf descriptions were carried out between berry set and veraison. The clusters and berry characteristics were evaluated at maturity and woody shoots were analyzed after fall of the leaves. Ampelographic characterization was performed based on 59 descriptors, of which 43 for morphological characters and 16 for agro-biological attributes.

  1. Clonal Heterogeneity Influences the Fate of New Adaptive Mutations

    Directory of Open Access Journals (Sweden)

    Ignacio Vázquez-García

    2017-10-01

    Full Text Available The joint contribution of pre-existing and de novo genetic variation to clonal adaptation is poorly understood but essential to designing successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast, S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven by de novo mutations but remain genetically and phenotypically diverse. The clones exhibit widespread genomic instability, rendering recessive de novo mutations homozygous and refining pre-existing variation. Finally, we decompose the fitness contributions of pre-existing and de novo mutations by creating a large recombinant library of adaptive mutations in an ensemble of genetic backgrounds. Both pre-existing and de novo mutations substantially contribute to fitness, and the relative fitness of pre-existing variants sets a selective threshold for new adaptive mutations.

  2. Escherichia coli ST131, an intriguing clonal group.

    Science.gov (United States)

    Nicolas-Chanoine, Marie-Hélène; Bertrand, Xavier; Madec, Jean-Yves

    2014-07-01

    In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  3. Preventing clonal evolutionary processes in cancer: Insights from mathematical models.

    Science.gov (United States)

    Rodriguez-Brenes, Ignacio A; Wodarz, Dominik

    2015-07-21

    Clonal evolutionary processes can drive pathogenesis in human diseases, with cancer being a prominent example. To prevent or treat cancer, mechanisms that can potentially interfere with clonal evolutionary processes need to be understood better. Mathematical modeling is an important research tool that plays an ever-increasing role in cancer research. This paper discusses how mathematical models can be useful to gain insights into mechanisms that can prevent disease initiation, help analyze treatment responses, and aid in the design of treatment strategies to combat the emergence of drug-resistant cells. The discussion will be done in the context of specific examples. Among defense mechanisms, we explore how replicative limits and cellular senescence induced by telomere shortening can influence the emergence and evolution of tumors. Among treatment approaches, we consider the targeted treatment of chronic lymphocytic leukemia (CLL) with tyrosine kinase inhibitors. We illustrate how basic evolutionary mathematical models have the potential to make patient-specific predictions about disease and treatment outcome, and argue that evolutionary models could become important clinical tools in the field of personalized medicine.

  4. Somatic clonal evolution: A selection-centric perspective.

    Science.gov (United States)

    Scott, Jacob; Marusyk, Andriy

    2017-04-01

    It is generally accepted that the initiation and progression of cancers is the result of somatic clonal evolution. Despite many peculiarities, evolution within populations of somatic cells should obey the same Darwinian principles as evolution within natural populations, i.e. variability of heritable phenotypes provides the substrate for context-specific selection forces leading to increased population frequencies of phenotypes, which are better adapted to their environment. Yet, within cancer biology, the more prevalent way to view evolution is as being entirely driven by the accumulation of "driver" mutations. Context-specific selection forces are either ignored, or viewed as constraints from which tumor cells liberate themselves during the course of malignant progression. In this review, we will argue that explicitly focusing on selection forces acting on the populations of neoplastic cells as the driving force of somatic clonal evolution might provide for a more accurate conceptual framework compared to the mutation-centric driver gene paradigm. Whereas little can be done to counteract the "bad luck" of stochastic occurrences of cancer-related mutations, changes in selective pressures and the phenotypic adaptations they induce can, in principle, be exploited to limit the incidence of cancers and to increase the efficiency of existing and future therapies. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Clonality and intracellular polyploidy in virus evolution and pathogenesis

    Science.gov (United States)

    Perales, Celia; Moreno, Elena; Domingo, Esteban

    2015-01-01

    In the present article we examine clonality in virus evolution. Most viruses retain an active recombination machinery as a potential means to initiate new levels of genetic exploration that go beyond those attainable solely by point mutations. However, despite abundant recombination that may be linked to molecular events essential for genome replication, herein we provide evidence that generation of recombinants with altered biological properties is not essential for the completion of the replication cycles of viruses, and that viral lineages (near-clades) can be defined. We distinguish mechanistically active but inconsequential recombination from evolutionarily relevant recombination, illustrated by episodes in the field and during experimental evolution. In the field, recombination has been at the origin of new viral pathogens, and has conferred fitness advantages to some viruses once the parental viruses have attained a sufficient degree of diversification by point mutations. In the laboratory, recombination mediated a salient genome segmentation of foot-and-mouth disease virus, an important animal pathogen whose genome in nature has always been characterized as unsegmented. We propose a model of continuous mutation and recombination, with punctuated, biologically relevant recombination events for the survival of viruses, both as disease agents and as promoters of cellular evolution. Thus, clonality is the standard evolutionary mode for viruses because recombination is largely inconsequential, since the decisive events for virus replication and survival are not dependent on the exchange of genetic material and formation of recombinant (mosaic) genomes. PMID:26195777

  6. Age-related cancer mutations associated with clonal hematopoietic expansion

    Science.gov (United States)

    Xie, Mingchao; Lu, Charles; Wang, Jiayin; McLellan, Michael D.; Johnson, Kimberly J.; Wendl, Michael C.; McMichael, Joshua F.; Schmidt, Heather K.; Yellapantula, Venkata; Miller, Christopher A.; Ozenberger, Bradley A.; Welch, John S.; Link, Daniel C.; Walter, Matthew J.; Mardis, Elaine R.; Dipersio, John F.; Chen, Feng; Wilson, Richard K.; Ley, Timothy J.; Ding, Li

    2015-01-01

    Several genetic alterations characteristic of leukemia and lymphoma have been detected in the blood of individuals without apparent hematological malignancies. We analyzed blood-derived sequence data from 2,728 individuals within The Cancer Genome Atlas, and discovered 77 blood-specific mutations in cancer-associated genes, the majority being associated with advanced age. Remarkably, 83% of these mutations were from 19 leukemia/lymphoma-associated genes, and nine were recurrently mutated (DNMT3A, TET2, JAK2, ASXL1, TP53, GNAS, PPM1D, BCORL1 and SF3B1). We identified 14 additional mutations in a very small fraction of blood cells, possibly representing the earliest stages of clonal expansion in hematopoietic stem cells. Comparison of these findings to mutations in hematological malignancies identified several recurrently mutated genes that may be disease initiators. Our analyses show that the blood cells of more than 2% of individuals (5–6% of people older than 70 years) contain mutations that may represent premalignant, initiating events that cause clonal hematopoietic expansion. PMID:25326804

  7. Clonal analysis of stable chromosome rearrangements in Bloom's syndrome fibroblasts.

    Science.gov (United States)

    Hoehn, H; Salk, D

    1984-04-01

    In situ cytogenetic analysis was performed on colonies derived from single cells of cultured skin fibroblast-like strains from two patients with Bloom's syndrome (GM 1492 and GM 2520). Metaphases in all of the colonies displayed structural chromosome rearrangements. Among 212 metaphases from 24 colonies of GM 1492, only 16% were pseudodiploid, and there was a high incidence of de novo rearrangements within individual colonies. There were two "families" of 16 and five colonies, respectively, each containing identical or related aneusomies, and these could be arranged into pedigrees showing clonal evolution. The heterochromatic region of chromosome #1 and the telomeric regions of chromosome arms 2q, 3q, 4p, and 11q were most frequently involved in the rearrangements. In contrast, strain GM 2520 showed less intraclonal variation, was primarily pseudodiploid, and displayed only three clonal types, one of which had extensive subclonal variation (19 of 24 clones). A remarkable finding in GM 2520 was that, in some clones, extra copies of specific chromosome segments were present as translocations. These results caution against the use of strain GM 1492 as a prototype Bloom's syndrome strain for cell biological studies.

  8. Escherichia coli ST131, an Intriguing Clonal Group

    Science.gov (United States)

    Bertrand, Xavier; Madec, Jean-Yves

    2014-01-01

    SUMMARY In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131. PMID:24982321

  9. The Artful Universe Expanded

    Science.gov (United States)

    Barrow, John D.

    2005-07-01

    Our love of art, writes John Barrow, is the end product of millions of years of evolution. How we react to a beautiful painting or symphony draws upon instincts laid down long before humans existed. Now, in this enhanced edition of the highly popular The Artful Universe , Barrow further explores the close ties between our aesthetic appreciation and the basic nature of the Universe. Barrow argues that the laws of the Universe have imprinted themselves upon our thoughts and actions in subtle and unexpected ways. Why do we like certain types of art or music? What games and puzzles do we find challenging? Why do so many myths and legends have common elements? In this eclectic and entertaining survey, Barrow answers these questions and more as he explains how the landscape of the Universe has influenced the development of philosophy and mythology, and how millions of years of evolutionary history have fashioned our attraction to certain patterns of sound and color. Barrow casts the story of human creativity and thought in a fascinating light, considering such diverse topics as our instinct for language, the origins and uses of color in nature, why we divide time into intervals as we do, the sources of our appreciation of landscape painting, and whether computer-generated fractal art is really art. Drawing on a wide variety of examples, from the theological questions raised by St. Augustine and C.S. Lewis to the relationship between the pure math of Pythagoras and the music of the Beatles, The Artful Universe Expanded covers new ground and enters a wide-ranging debate about the meaning and significance of the links between art and science.

  10. Clonal plasticity of aquatic plant species submitted to mechanical stress: escape versus resistance strategy

    NARCIS (Netherlands)

    Puijalon, S.; Bouma, T.J.; Van Groenendael, J.M.; Bornette, G.

    2008-01-01

    Background and Aims: The plastic alterations of clonal architecture are likely to have functional consequences, as they affect the spatial distribution of ramets over patchy environments. However, little is known about the effect of mechanical stresses on the clonal growth. The aim of the present

  11. Growth and stem form quality of clonal Pinus taeda following fertilization in the Virginia Piedmont

    Science.gov (United States)

    Jeremy P. Stovall; Colleen A. Carlson; John R. Seiler; Thomas R. Fox

    2013-01-01

    Clonal forestry offers the opportunity to increase yields, enhance uniformity, and improve wood characteristics. Intensive silvicultural practices, including fertilization, will be required to capture the full growth potential of clonal plantations. However, variation in nutrient use efficiency that exists among clones could affect growth responses. Our research...

  12. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

    DEFF Research Database (Denmark)

    McGranahan, Nicholas; Furness, Andrew J S; Rosenthal, Rachel

    2016-01-01

    demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4...

  13. Genetic and clonal diversity of the endemic ant-plant Humboldtia ...

    Indian Academy of Sciences (India)

    A combination of clonality and short-distance pollen movement by small pollinating bees (Braunsapis puangensis) coupled with primary ballistic seed dispersal, and possible secondary seed dispersal by rodents, may contribute to spatial genetic structure at such small scales. The clonality of H. brunonis may be a factor that ...

  14. Genotype-by-temperature interactions may help to maintain clonal diversity in Asterionella formosa (Bacillariophyceae)

    NARCIS (Netherlands)

    Gsell, A.S.; De Senerpont Domis, L.N.; Przytulska-Bartosiewicz, A.; Mooij, W.M.; Van Donk, E.; Ibelings, B.W.

    2012-01-01

    Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity.

  15. Genotype-by-temperature interactions may help to maintain clonal diversity in asterionella formosa (Bacillariophyceae)

    NARCIS (Netherlands)

    Gsell, A.S.; Domis, L.N.D.; Przytulska-Bartosiewicz, A.; Mooij, W.M.; Donk, van E.; Ibelings, B.W.

    2012-01-01

    Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity.

  16. Clonal relation in a case of CLL, ALCL, and Hodgkin composite lymphoma

    NARCIS (Netherlands)

    van den Berg, Anke; Maggio, Ewerton; Rust, R; Kooistra, K; Diepstra, A; Poppema, S

    2002-01-01

    Large cell lymphomas and Hodgkin disease may develop during the course of chronic lymphocytic leukemia (CLL). In some cases the transformed cells are Epstein-Barr virus (EBV)-positive and not clonally related to the CLL cells. In other cases the transformed cells have the same clonal rearrangements

  17. SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis

    Science.gov (United States)

    Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic ...

  18. Three Clonal Lineages of Phytophthora cinnamomi in Australia Revealed by Microsatellites.

    Science.gov (United States)

    Dobrowolski, M P; Tommerup, I C; Shearer, B L; O'Brien, P A

    2003-06-01

    ABSTRACT The genetic structure of populations of Phytophthora cinnamomi, a pathogen of an enormous variety of woody plants, was investigated using microsatellites. Three intensively sampled disease sites in southwest Australia were analyzed along with a large culture collection of Austra-lian isolates and some isolates from elsewhere in the world. The mutation in the four microsatellite loci analyzed revealed spatial patterns at the disease sites that correlated with the age of the infestation. Only three clonal lineages were identified in Australian populations and these same clonal lineages were present in worldwide populations, where it is suggested that a limited number of clonal lineages have spread in most regions. No evidence for sexual reproduction between these clonal lineages in Australia has been found even though the pathogen has the opportunity. Instead, mitotic recombination is frequent within the clonal lineages. The implications of this are discussed.

  19. Uncovering the Number and Clonal Dynamics of Mesp1 Progenitors during Heart Morphogenesis

    Directory of Open Access Journals (Sweden)

    Samira Chabab

    2016-01-01

    Full Text Available The heart arises from distinct sources of cardiac progenitors that independently express Mesp1 during gastrulation. The precise number of Mesp1 progenitors that are specified during the early stage of gastrulation, and their clonal behavior during heart morphogenesis, is currently unknown. Here, we used clonal and mosaic tracing of Mesp1-expressing cells combined with quantitative biophysical analysis of the clonal data to define the number of cardiac progenitors and their mode of growth during heart development. Our data indicate that the myocardial layer of the heart derive from ∼250 Mesp1-expressing cardiac progenitors born during gastrulation. Despite arising at different time points and contributing to different heart regions, the temporally distinct cardiac progenitors present very similar clonal dynamics. These results provide insights into the number of cardiac progenitors and their mode of growth and open up avenues to decipher the clonal dynamics of progenitors in other organs and tissues.

  20. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa.

    Science.gov (United States)

    Tibayrenc, Michel; Ayala, Francisco J

    2012-11-27

    We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.

  1. Endothelial progenitor cells display clonal restriction in multiple myeloma

    Directory of Open Access Journals (Sweden)

    Dai Kezhi

    2006-06-01

    Full Text Available Abstract Background In multiple myeloma (MM, increased neoangiogenesis contributes to tumor growth and disease progression. Increased levels of endothelial progenitor cells (EPCs contribute to neoangiogenesis in MM, and, importantly, covary with disease activity and response to treatment. In order to understand the mechanisms responsible for increased EPC levels and neoangiogenic function in MM, we investigated whether these cells were clonal by determining X-chromosome inactivation (XCI patterns in female patients by a human androgen receptor assay (HUMARA. In addition, EPCs and bone marrow cells were studied for the presence of clonotypic immunoglobulin heavy-chain (IGH gene rearrangement, which indicates clonality in B cells; thus, its presence in EPCs would indicate a close genetic link between tumor cells in MM and endothelial cells that provide tumor neovascularization. Methods A total of twenty-three consecutive patients who had not received chemotherapy were studied. Screening in 18 patients found that 11 displayed allelic AR in peripheral blood mononuclear cells, and these patients were further studied for XCI patterns in EPCs and hair root cells by HUMARA. In 2 patients whose EPCs were clonal by HUMARA, and in an additional 5 new patients, EPCs were studied for IGH gene rearrangement using PCR with family-specific primers for IGH variable genes (VH. Results In 11 patients, analysis of EPCs by HUMARA revealed significant skewing (≥ 77% expression of a single allele in 64% (n = 7. In 4 of these patients, XCI skewing was extreme (≥ 90% expression of a single allele. In contrast, XCI in hair root cells was random. Furthermore, PCR amplification with VH primers resulted in amplification of the same product in EPCs and bone marrow cells in 71% (n = 5 of 7 patients, while no IGH rearrangement was found in EPCs from healthy controls. In addition, in patients with XCI skewing in EPCs, advanced age was associated with poorer clinical status

  2. The Expanding Universe: Dark Energy

    Energy Technology Data Exchange (ETDEWEB)

    Lincoln, Don [Fermilab; Nord, Brian [Fermilab

    2014-09-01

    In 1998, observations of distant supernovae led physicists that not only was the universe expanding, but the expansion was speeding up. In this article, we describe the evidence for an expanding universe and describe what physicists and cosmologists have learned in the intervening years. The target audience for this article is high school physics teachers and college physics professors at teaching institutions.

  3. Transcriptomic variation in a coral reveals pathways of clonal organisation

    DEFF Research Database (Denmark)

    K Bay, Line; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard

    2009-01-01

    A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base......) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with energy...... of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels...

  4. Aging, Clonality, and Rejuvenation of Hematopoietic Stem Cells.

    Science.gov (United States)

    Akunuru, Shailaja; Geiger, Hartmut

    2016-08-01

    Aging is associated with reduced organ function and increased disease incidence. Hematopoietic stem cell (HSC) aging driven by both cell intrinsic and extrinsic factors is linked to impaired HSC self-renewal and regeneration, aging-associated immune remodeling, and increased leukemia incidence. Compromised DNA damage responses and the increased production of reactive oxygen species (ROS) have been previously causatively attributed to HSC aging. However, recent paradigm-shifting concepts, such as global epigenetic and cytoskeletal polarity shifts, cellular senescence, as well as the clonal selection of HSCs upon aging, provide new insights into HSC aging mechanisms. Rejuvenating agents that can reprogram the epigenetic status of aged HSCs or senolytic drugs that selectively deplete senescent cells provide promising translational avenues for attenuating hematopoietic aging and, potentially, alleviating aging-associated immune remodeling and myeloid malignancies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Two Distinct Broadly Neutralizing Antibody Specificities of Different Clonal Lineages in a Single HIV-1-Infected Donor: Implications for Vaccine Design

    Science.gov (United States)

    Montefiori, David C.; Wu, Xueling; Chen, Xi; Hwang, Kwan-Ki; Tsao, Chun-Yen; Kozink, Daniel M.; Parks, Robert J.; Tomaras, Georgia D.; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Kwong, Peter D.; Kepler, Thomas B.; Liao, Hua-Xin; Mascola, John R.

    2012-01-01

    Plasma from a small subset of subjects chronically infected with HIV-1 shows remarkable magnitude and breadth of neutralizing activity. From one of these individuals (CH0219), we isolated two broadly neutralizing antibodies (bnAbs), CH01 and VRC-CH31, from two clonal lineages of memory B cells with distinct specificities (variable loop 1 and 2 [V1V2] conformational specificity and CD4-binding site specificity, respectively) that recapitulate 95% of CH0219 serum neutralization breadth. These data provide proof of concept for an HIV-1 vaccine that aims to elicit bnAbs of multiple specificities. PMID:22301150

  6. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    Directory of Open Access Journals (Sweden)

    Suzanna M. Evans

    2016-02-01

    Full Text Available Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of

  7. Plasma-chemical reactions: low pressure acetylene plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Benedikt, J [Faculty for Physics and Astronomy, Research Group Reactive Plasmas, Ruhr-Universitaet Bochum, Universitaetsstr. 150, 44780 Bochum (Germany)

    2010-02-03

    Reactive plasmas are a well-known tool for material synthesis and surface modification. They offer a unique combination of non-equilibrium electron and ion driven plasma chemistry, energetic ions accelerated in the plasma sheath at the plasma-surface interface, high fluxes of reactive species towards surfaces and a friendly environment for thermolabile objects. Additionally, small negatively charged clusters can be generated, because they are confined in the positive plasma potential. Plasmas in hydrocarbon gases, and especially in acetylene, are a good example for the discussion of different plasma-chemical processes. These plasmas are involved in a plethora of possible applications ranging from fuel conversion to formation of single wall carbon nanotubes. This paper provides a concise overview of plasma-chemical reactions (PCRs) in low pressure reactive plasmas and discusses possible experimental and theoretical methods for the investigation of their plasma chemistry. An up-to-date summary of the knowledge about low pressure acetylene plasmas is given and two particular examples are discussed in detail: (a) Ar/C{sub 2}H{sub 2} expanding thermal plasmas with electron temperatures below 0.3 eV and with a plasma chemistry initiated by charge transfer reactions and (b) radio frequency C{sub 2}H{sub 2} plasmas, in which the energetic electrons mainly control PCRs. (topical review)

  8. The use of Hardy-Weinberg Equilibrium in clonal plant systems.

    Science.gov (United States)

    Douhovnikoff, Vladimir; Leventhal, Matthew

    2016-02-01

    Traditionally population genetics precludes the use of the same genetic individual more than once in Hardy-Weinberg (HW) based calculations due to the model's explicit assumptions. However, when applied to clonal plant populations this can be difficult to do, and in some circumstances, it may be ecologically informative to use the ramet as the data unit. In fact, ecologists have varied the definition of the individual from a strict adherence to a single data point per genotype to a more inclusive approach of one data point per ramet. With the advent of molecular tools, the list of facultatively clonal plants and the recognition of their ecological relevance grows. There is an important risk of misinterpretation when HW calculations are applied to a clonal plant not recognized as clonal, as well as when the definition of the individual for those calculations is not clearly stated in a known clonal species. Focusing on heterozygosity values, we investigate cases that demonstrate the extreme range of potential modeling outcomes and describe the different contexts where a particular definition could better meet ecological modeling goals. We emphasize that the HW model can be ecologically relevant when applied to clonal plants, but caution is necessary in how it is used, reported, and interpreted. We propose that in known clonal plants, both genotype (GHet) and ramet (RHet) based calculations are reported to define the full range of potential values and better facilitate cross-study comparisons.

  9. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China

    Science.gov (United States)

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K.; Dong, Ming; Cornelissen, Johannes H. C.

    2016-06-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients.

  10. Detecting truly clonal alterations from multi-region profiling of tumours

    Science.gov (United States)

    Werner, Benjamin; Traulsen, Arne; Sottoriva, Andrea; Dingli, David

    2017-03-01

    Modern cancer therapies aim at targeting tumour-specific alterations, such as mutations or neo-antigens, and maximal treatment efficacy requires that targeted alterations are present in all tumour cells. Currently, treatment decisions are based on one or a few samples per tumour, creating uncertainty on whether alterations found in those samples are actually present in all tumour cells. The probability of classifying clonal versus sub-clonal alterations from multi-region profiling of tumours depends on the earliest phylogenetic branching event during tumour growth. By analysing 181 samples from 10 renal carcinoma and 11 colorectal cancers we demonstrate that the information gain from additional sampling falls onto a simple universal curve. We found that in colorectal cancers, 30% of alterations identified as clonal with one biopsy proved sub-clonal when 8 samples were considered. The probability to overestimate clonal alterations fell below 1% in 7/11 patients with 8 samples per tumour. In renal cell carcinoma, 8 samples reduced the list of clonal alterations by 40% with respect to a single biopsy. The probability to overestimate clonal alterations remained as high as 92% in 7/10 renal cancer patients. Furthermore, treatment was associated with more unbalanced tumour phylogenetic trees, suggesting the need of denser sampling of tumours at relapse.

  11. Helical plasma thruster

    Energy Technology Data Exchange (ETDEWEB)

    Beklemishev, A. D., E-mail: bekl@bk.ru [Budker Institute of Nuclear Physics SB RAS, Novosibirsk (Russian Federation)

    2015-10-15

    A new scheme of plasma thruster is proposed. It is based on axial acceleration of rotating magnetized plasmas in magnetic field with helical corrugation. The idea is that the propellant ionization zone can be placed into the local magnetic well, so that initially the ions are trapped. The E × B rotation is provided by an applied radial electric field that makes the setup similar to a magnetron discharge. Then, from the rotating plasma viewpoint, the magnetic wells of the helically corrugated field look like axially moving mirror traps. Specific shaping of the corrugation can allow continuous acceleration of trapped plasma ions along the magnetic field by diamagnetic forces. The accelerated propellant is expelled through the expanding field of magnetic nozzle. By features of the acceleration principle, the helical plasma thruster may operate at high energy densities but requires a rather high axial magnetic field, which places it in the same class as the VASIMR{sup ®} rocket engine.

  12. Clonal Plasticity of Aquatic Plant Species Submitted to Mechanical Stress: Escape versus Resistance Strategy

    Science.gov (United States)

    Puijalon, Sara; Bouma, Tjeerd J.; Van Groenendael, Jan; Bornette, Gudrun

    2008-01-01

    Background and Aims The plastic alterations of clonal architecture are likely to have functional consequences, as they affect the spatial distribution of ramets over patchy environments. However, little is known about the effect of mechanical stresses on the clonal growth. The aim of the present study was to investigate the clonal plasticity induced by mechanical stress consisting of continuous water current encountered by aquatic plants. More particularly, the aim was to test the capacity of the plants to escape this stress through clonal plastic responses. Methods The transplantation of ramets of the same clone in two contrasting flow velocity conditions was carried out for two species (Potamogeton coloratus and Mentha aquatica) which have contrasting clonal growth forms. Relative allocation to clonal growth, to creeping stems in the clonal biomass, number and total length of creeping stems, spacer length and main creeping stem direction were measured. Key Results For P. coloratus, plants exposed to water current displayed increased total length of creeping stems, increased relative allocation to creeping stems within the clonal dry mass and increased spacer length. For M. aquatica, plants exposed to current displayed increased number and total length of creeping stems. Exposure to current induced for both species a significant increase of the proportion of creeping stems in the downstream direction to the detriment of creeping stems perpendicular to flow. Conclusions This study demonstrates that mechanical stress from current flow induced plastic variation in clonal traits for both species. The responses of P. coloratus could lead to an escape strategy, with low benefits with respect to sheltering and anchorage. The responses of M. aquatica that may result in a denser canopy and enhancement of anchorage efficiency could lead to a resistance strategy. PMID:18854376

  13. Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps.

    Science.gov (United States)

    Geremew, Addisie; Stiers, Iris; Sierens, Tim; Kefalew, Alemayehu; Triest, Ludwig

    2018-01-01

    Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m) in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low) were sampled for two years. We found that ramets under the high sedimentation regime (HSR) were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR). The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR) to phalanx (in HSR). Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80) as compared to the LSR (R = 0.48). Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.

  14. Clonal integration facilitates spread of Paspalum paspaloides from terrestrial to cadmium-contaminated aquatic habitats.

    Science.gov (United States)

    Luo, F-L; Xing, Y-P; Wei, G-W; Li, C-Y; Yu, F-H

    2017-11-01

    Cadmium (Cd) is a hazardous environmental pollutant with high toxicity to plants, which has been detected in many wetlands. Clonal integration (resource translocation) between connected ramets of clonal plants can increase their tolerance to stress. We hypothesised that clonal integration facilitates spread of amphibious clonal plants from terrestrial to Cd-contaminated aquatic habitats. The spread of an amphibious grass Paspalum paspaloides was simulated by growing basal older ramets in uncontaminated soil connected (allowing integration) or not connected (preventing integration) to apical younger ramets of the same fragments in Cd-contaminated water. Cd contamination of apical ramets of P. paspaloides markedly decreased growth and photosynthetic capacity of the apical ramets without connection to the basal ramets, but did not decrease these properties with connection. Cd contamination did not affect growth of the basal ramets without connection to the apical ramets, but Cd contamination of 4 and 12 mg·l -1 significantly increased growth with connection. Consequently, clonal integration increased growth of the apical ramets, basal ramets and whole clones when the apical ramets were grown in Cd-contaminated water of 4 and 12 mg·l -1 . Cd was detected in the basal ramets with connection to the apical ramets, suggesting Cd could be translocated due to clonal integration. Clonal integration, most likely through translocation of photosynthates, can support P. paspaloides to spread from terrestrial to Cd-contaminated aquatic habitats. Amphibious clonal plants with a high ability for clonal integration are particularly useful for re-vegetation of degraded aquatic habitats caused by Cd contamination. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  15. Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps.

    Directory of Open Access Journals (Sweden)

    Addisie Geremew

    Full Text Available Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus, in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low were sampled for two years. We found that ramets under the high sedimentation regime (HSR were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR. The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR to phalanx (in HSR. Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80 as compared to the LSR (R = 0.48. Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.

  16. The opportunistic pathogen Propionibacterium acnes: insights into typing, human disease, clonal diversification and CAMP factor evolution.

    Directory of Open Access Journals (Sweden)

    Andrew McDowell

    Full Text Available We previously described a Multilocus Sequence Typing (MLST scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA and two putative virulence (tly; camp2 genes (MLST4 that correctly predicted the phylogroup (IA1, IA2, IB, IC, II, III, clonal complex (CC and sequence type (ST (novel or described status for 91% isolates (n = 372 via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/. Even in the small number of cases where specific STs were not completely resolved, the MLST4 method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated 'virulence' factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal

  17. Preleukaemic clonal haemopoiesis and risk of therapy-related myeloid neoplasms: a case-control study.

    Science.gov (United States)

    Takahashi, Koichi; Wang, Feng; Kantarjian, Hagop; Doss, Denaha; Khanna, Kanhav; Thompson, Erika; Zhao, Li; Patel, Keyur; Neelapu, Sattva; Gumbs, Curtis; Bueso-Ramos, Carlos; DiNardo, Courtney D; Colla, Simona; Ravandi, Farhad; Zhang, Jianhua; Huang, Xuelin; Wu, Xifeng; Samaniego, Felipe; Garcia-Manero, Guillermo; Futreal, P Andrew

    2017-01-01

    Therapy-related myeloid neoplasms are secondary malignancies that are often fatal, but their risk factors are not well understood. Evidence suggests that individuals with clonal haemopoiesis have increased risk of developing haematological malignancies. We aimed to identify whether patients with cancer who have clonal haemopoiesis are at an increased risk of developing therapy-related myeloid neoplasms. We did this retrospective case-control study to compare the prevalence of clonal haemopoiesis between patients treated for cancer who later developed therapy-related myeloid neoplasms (cases) and patients who did not develop these neoplasms (controls). All patients in both case and control groups were treated at MD Anderson Cancer Center (Houston, TX, USA) from 1997 to 2015. We used the institutional medical database to locate these patients. Patients were included as cases if they were treated for a primary cancer, subsequently developed therapy-related myeloid neoplasms, and had available paired samples of bone marrow from the time of therapy-related myeloid neoplasm diagnosis and peripheral blood from the time of primary cancer diagnosis. Patients were eligible for inclusion as age-matched controls if they were treated for lymphoma, received combination chemotherapy, and did not develop therapy-related myeloid neoplasms after at least 5 years of follow-up. We used molecular barcode sequencing of 32 genes on the pretreatment peripheral blood samples to detect clonal haemopoiesis. For cases, we also used targeted gene sequencing on bone marrow samples and investigated clonal evolution from clonal haemopoiesis to the development of therapy-related myeloid neoplasms. To further clarify the association between clonal haemopoiesis and therapy-related myeloid neoplasm development, we also analysed the prevalence of clonal haemopoiesis in an external cohort of patients with lymphoma who were treated in a randomised trial of front-line chemotherapy with cyclophosphamide

  18. Next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue.

    Science.gov (United States)

    Ishikawa, Tetsuya

    2017-05-26

    To investigate genotype variation among induced pluripotent stem cell (iPSC) lines that were clonally generated from heterogeneous colon cancer tissues using next-generation sequencing. Human iPSC lines were clonally established by selecting independent single colonies expanded from heterogeneous primary cells of S-shaped colon cancer tissues by retroviral gene transfer (OCT3/4, SOX2, and KLF4). The ten iPSC lines, their starting cancer tissues, and the matched adjacent non-cancerous tissues were analyzed using next-generation sequencing and bioinformatics analysis using the human reference genome hg19. Non-synonymous single-nucleotide variants (SNVs) (missense, nonsense, and read-through) were identified within the target region of 612 genes related to cancer and the human kinome. All SNVs were annotated using dbSNP135, CCDS, RefSeq, GENCODE, and 1000 Genomes. The SNVs of the iPSC lines were compared with the genotypes of the cancerous and non-cancerous tissues. The putative genotypes were validated using allelic depth and genotype quality. For final confirmation, mutated genotypes were manually curated using the Integrative Genomics Viewer. In eight of the ten iPSC lines, one or two non-synonymous SNVs in EIF2AK2, TTN, ULK4, TSSK1B, FLT4, STK19, STK31, TRRAP, WNK1, PLK1 or PIK3R5 were identified as novel SNVs and were not identical to the genotypes found in the cancer and non-cancerous tissues. This result suggests that the SNVs were de novo or pre-existing mutations that originated from minor populations, such as multifocal pre-cancer (stem) cells or pre-metastatic cancer cells from multiple, different clonal evolutions, present within the heterogeneous cancer tissue. The genotypes of all ten iPSC lines were different from the mutated ERBB2 and MKNK2 genotypes of the cancer tissues and were identical to those of the non-cancerous tissues and that found in the human reference genome hg19. Furthermore, two of the ten iPSC lines did not have any confirmed mutated

  19. Clonal expansion of T cells in abdominal aortic aneurysm: a role for doxycycline as drug of choice?

    Science.gov (United States)

    Kroon, Albert M; Taanman, Jan-Willem

    2015-05-18

    Most reported studies with animal models of abdominal aortic aneurysm (AAA) and several studies with patients have suggested that doxycycline favourably modifies AAA; however, a recent large long-term clinical trial found that doxycycline did not limit aneurysm growth. Thus, there is currently no convincing evidence that doxycycline reduces AAA expansion. Here, we critically review the available experimental and clinical information about the effects of doxycycline when used as a pharmacological treatment for AAA. The view that AAA can be considered an autoimmune disease and the observation that AAA tissue shows clonal expansion of T cells is placed in the light of the well-known inhibition of mitochondrial protein synthesis by doxycycline. In T cell leukaemia animal models, this inhibitory effect of the antibiotic has been shown to impede T cell proliferation, resulting in complete tumour eradication. We suggest that the available evidence of doxycycline action on AAA is erroneously ascribed to its inhibition of matrix metalloproteinases (MMPs) by competitive binding of the zinc ion co-factor. Although competitive binding may explain the inhibition of proteolytic activity, it does not explain the observed decreases of MMP mRNA levels. We propose that the observed effects of doxycycline are secondary to inhibition of mitochondrial protein synthesis. Provided that serum doxycycline levels are kept at adequate levels, the inhibition will result in a proliferation arrest, especially of clonally expanding T cells. This, in turn, leads to the decrease of proinflammatory cytokines that are normally generated by these cells. The drastic change in cell type composition may explain the changes in MMP mRNA and protein levels in the tissue samples.

  20. Clonality in myeloproliferative disorders: Analysis by means of polymerase chain reaction

    Energy Technology Data Exchange (ETDEWEB)

    Gilliland, D.G.; Blanchard, K.L.; Levy, J.; Perrin, S.; Bunn, H.F. (Harvard Medical School, Boston, MA (United States))

    1991-08-01

    The myeloproliferative syndromes are acquired disorders of hematopoiesis that provide insights into the transition from somatic cell mutation to neoplasia. The clonal origin of specific blood cells can be assessed in patients with X chromosome-linked polymorphisms, taking advantage of random inactivation of the X chromosome. The authors have adapted the PCR for determination of clonality on as few as 100 cells, including individual colonies grown in culture. Amplifying a polymorphic portion of the X chromosome-linked phosphoglycerate kinase (PGK) gene after selective digestion of the active X chromosome with a methylation-sensitive restriction enzyme gave results fully concordant with standard Southern blotting of DNA samples form normal (polyclonal) polymorphonuclear cells (PMN) as well as clonal PMN from patients with myelodysplastic syndrome and polycythemia vera (PCV). They have used this technique to demonstrate heterogeneity of lineage involvement in patients with PCV. The same clinical phenotype may arise from clonal proliferation of different hematopoietic progenitors.

  1. Directional growth of a clonal bromeliad species in response to spatial habitat heterogeneity

    NARCIS (Netherlands)

    Sampaio, M.C.; Araujo, T.F.; Scarano, F.R.; Stuefer, J.F.

    2004-01-01

    Habitat selection by directional growth of plants has previously been investigated but field evidence for this phenomenon is extremely scarce. In this study we demonstrate directional clonal growth in Aechmea nudicaulis, a monocarpic, perennial bromeliad native to spatially heterogeneous sandy

  2. Clonal diversity and structure within a population of the pondweed Potamogeton pectinatus foraged by Bewick's swans

    NARCIS (Netherlands)

    Hangelbroek, H.H.; Ouborg, N.J.; Santamaría, L.; Schwenk, K.

    2002-01-01

    Clonal diversity within plant populations is affected by factors that influence genet (clone) survival and seed recruitment, such as resource availability, disturbance, seed dispersal mechanism, propagule predation and the age of the population. Here we studied a population of Potamogeton

  3. Epigenetic Memory as a Basis for Intelligent Behavior in Clonal Plants.

    Science.gov (United States)

    Latzel, Vít; Rendina González, Alejandra P; Rosenthal, Jonathan

    2016-01-01

    Environmentally induced epigenetic change enables plants to remember past environmental interactions. If this memory capability is exploited to prepare plants for future challenges, it can provide a basis for highly sophisticated behavior, considered intelligent by some. Against the backdrop of an overview of plant intelligence, we hypothesize: (1) that the capability of plants to engage in such intelligent behavior increases with the additional level of complexity afforded by clonality, and; (2) that more faithful inheritance of epigenetic information in clonal plants, in conjunction with information exchange and coordination between connected ramets, is likely to enable especially advanced intelligent behavior in this group. We therefore further hypothesize that this behavior provides ecological and evolutionary advantages to clonal plants, possibly explaining, at least in part, their widespread success. Finally, we suggest avenues of inquiry to enable assessing intelligent behavior and the role of epigenetic memory in clonal species.

  4. An atlas of B-cell clonal distribution in the human body.

    Science.gov (United States)

    Meng, Wenzhao; Zhang, Bochao; Schwartz, Gregory W; Rosenfeld, Aaron M; Ren, Daqiu; Thome, Joseph J C; Carpenter, Dustin J; Matsuoka, Nobuhide; Lerner, Harvey; Friedman, Amy L; Granot, Tomer; Farber, Donna L; Shlomchik, Mark J; Hershberg, Uri; Luning Prak, Eline T

    2017-09-01

    B-cell responses result in clonal expansion, and can occur in a variety of tissues. To define how B-cell clones are distributed in the body, we sequenced 933,427 B-cell clonal lineages and mapped them to eight different anatomic compartments in six human organ donors. We show that large B-cell clones partition into two broad networks-one spans the blood, bone marrow, spleen and lung, while the other is restricted to tissues within the gastrointestinal (GI) tract (jejunum, ileum and colon). Notably, GI tract clones display extensive sharing of sequence variants among different portions of the tract and have higher frequencies of somatic hypermutation, suggesting extensive and serial rounds of clonal expansion and selection. Our findings provide an anatomic atlas of B-cell clonal lineages, their properties and tissue connections. This resource serves as a foundation for studies of tissue-based immunity, including vaccine responses, infections, autoimmunity and cancer.

  5. Diverse cellular architecture of atherosclerotic plaque derives from clonal expansion of a few medial SMCs

    DEFF Research Database (Denmark)

    Jacobsen, Kevin; Lund, Marie Bek; Shim, Jeong

    2017-01-01

    Fibrous cap smooth muscle cells (SMCs) protect atherosclerotic lesions from rupturing and causing thrombosis, while other plaque SMCs may have detrimental roles in plaque development. To gain insight into recruitment of different plaque SMCs, we mapped their clonal architecture in aggregation...... of either eGFP+ or nonfluorescent SMCs, indicating substantial clonal expansion of a few cells. Similarly, plaques in mice with SMC-restricted Confetti expression showed oligoclonal SMC populations with little intermixing between the progeny of different medial SMCs. Phenotypes comprised both ACTA2+ SMCs...... in the cap and heterogeneous ACTA2– SMCs in the plaque interior, including chondrocyte-like cells and cells with intracellular lipid and crystalline material. Fibrous cap SMCs were invariably arranged in endothelium-aligned clonal sheets, confirming results in the aggregation chimeras. Analysis of the clonal...

  6. The reproductive biology of Polytrichum formosum : clonal structure and paternity revealed by microsatellites

    NARCIS (Netherlands)

    Van der Velde, M; During, HJ; Van de Zande, L; Bijlsma, R

    2001-01-01

    Using highly polymorphic microsatellite markers, we assessed clonal structure and paternity in a population of the bryophyte species Polytrichum formosum. Identical multilocus genotypes of individual shoots were almost never observed in spatially separated cushions, but were found to be highly

  7. Factors influencing rapid clonal propagation of Chlorophytum arundinaceum , an endangered medicinal plant

    National Research Council Canada - National Science Library

    Samantaray, Sanghamitra; Maiti, Satyabrata

    2011-01-01

    ... de cosecharla, asociado con una mala germinacion y pobre multiplicacion vegetativa. Para contribuir con sus sistemas de produccion, se desarrollo un protocolo eficiente para la propagacion clonal in vitro a traves del cultivo de brotes...

  8. Filters for cathodic arc plasmas

    Science.gov (United States)

    Anders, Andre; MacGill, Robert A.; Bilek, Marcela M. M.; Brown, Ian G.

    2002-01-01

    Cathodic arc plasmas are contaminated with macroparticles. A variety of magnetic plasma filters has been used with various success in removing the macroparticles from the plasma. An open-architecture, bent solenoid filter, with additional field coils at the filter entrance and exit, improves macroparticle filtering. In particular, a double-bent filter that is twisted out of plane forms a very compact and efficient filter. The coil turns further have a flat cross-section to promote macroparticle reflection out of the filter volume. An output conditioning system formed of an expander coil, a straightener coil, and a homogenizer, may be used with the magnetic filter for expanding the filtered plasma beam to cover a larger area of the target. A cathodic arc plasma deposition system using this filter can be used for the deposition of ultrathin amorphous hard carbon (a-C) films for the magnetic storage industry.

  9. Environmental gradients structure Daphnia pulex × pulicaria clonal distribution.

    Science.gov (United States)

    Pantel, J H; Juenger, T E; Leibold, M A

    2011-04-01

    The rarity of eukaryotic asexual reproduction is frequently attributed to the disadvantage of reduced genetic variation relative to sexual reproduction. However, parthenogenetic lineages that evolved repeatedly from sexual ancestors can generate regional pools of phenotypically diverse clones. Various theories to explain the maintenance of this genetic diversity as a result of environmental and spatial heterogeneity [frozen niche variation (FNV), general-purpose genotype] are conceptually similar to community ecological explanations for the maintenance of regional species diversity. We employed multivariate statistics common in community ecological research to study population genetic structure in the freshwater crustacean, Daphnia pulex × pulicaria. This parthenogenetic hybrid arose repeatedly from sexual ancestors. Daphnia pulex × pulicaria populations harboured substantial genetic variation among populations and the clonal composition at each pond corresponded to nutrient levels and invertebrate predator densities. The interclonal selection process described by the FNV hypothesis likely structured our D. pulex × pulicaria populations. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  10. Clonal cell populations unresponsive to radiosensitization induced by telomerase inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Ju, Yeun-Jin; Shin, Hyun-Jin; Park, Jeong-Eun; Juhn, Kyoung-Mi; Woo, Seon Rang; Kim, Hee-Young; Han, Young-Hoon; Hwang, Sang-Gu; Hong, Sung-Hee; Kang, Chang-Mo [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of); Yoo, Young-Do [Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul 136-705 (Korea, Republic of); Park, Won-Bong [Division of Natural Science, Seoul Women' s University, Seoul 139-774 (Korea, Republic of); Cho, Myung-Haing [Laboratory of Toxicology, College of Veterinary Medicine, Seoul National University, Seoul (Korea, Republic of); Park, Gil Hong, E-mail: ghpark@korea.ac.kr [Department of Biochemistry, College of Medicine, Korea University, Seoul (Korea, Republic of); Lee, Kee-Ho, E-mail: khlee@kirams.re.kr [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)

    2010-11-12

    Research highlights: {yields} In our present manuscript, we have clearly showed an interesting but problematic obstacle of a radiosensitization strategy based on telomerase inhibition by showing that: Clonal population unresponsive to this radiosensitization occasionally arise. {yields} The telomere length of unsensitized clones was reduced, as was that of most sensitized clones. {yields} The unsensitized clones did not show chromosome end fusion which was noted in all sensitized clones. {yields} P53 status is not associated with the occurrence of unsensitized clone. {yields} Telomere end capping in unsensitized clone is operative even under telomerase deficiency. -- Abstract: A combination of a radiotherapeutic regimen with telomerase inhibition is valuable when tumor cells are to be sensitized to radiation. Here, we describe cell clones unresponsive to radiosensitization after telomere shortening. After extensive division of individual transformed clones of mTERC{sup -/-} cells, about 22% of clones were unresponsive to radiosensitization even though telomerase action was inhibited. The telomere lengths of unsensitized mTERC{sup -/-} clones were reduced, as were those of most sensitized clones. However, the unsensitized clones did not exhibit chromosomal end-to-end fusion to the extent noted in all sensitized clones. Thus, a defense mechanism preventing telomere erosion is operative even when telomeres become shorter under conditions of telomerase deficiency, and results in unresponsiveness to the radiosensitization generally mediated by telomere shortening.

  11. Adapting populations in space: clonal interference and genetic diversity

    Science.gov (United States)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  12. Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution

    Science.gov (United States)

    Bozic, Ivana; Gerold, Jeffrey M.; Nowak, Martin A.

    2016-01-01

    The vast majority of mutations in the exome of cancer cells are passengers, which do not affect the reproductive rate of the cell. Passengers can provide important information about the evolutionary history of an individual cancer, and serve as a molecular clock. Passengers can also become targets for immunotherapy or confer resistance to treatment. We study the stochastic expansion of a population of cancer cells describing the growth of primary tumors or metastatic lesions. We first analyze the process by looking forward in time and calculate the fixation probabilities and frequencies of successive passenger mutations ordered by their time of appearance. We compute the likelihood of specific evolutionary trees, thereby informing the phylogenetic reconstruction of cancer evolution in individual patients. Next, we derive results looking backward in time: for a given subclonal mutation we estimate the number of cancer cells that were present at the time when that mutation arose. We derive exact formulas for the expected numbers of subclonal mutations of any frequency. Fitting this formula to cancer sequencing data leads to an estimate for the ratio of birth and death rates of cancer cells during the early stages of clonal expansion. PMID:26828429

  13. Clonal propagation of Cyclamen persicum via somatic embryogenesis.

    Science.gov (United States)

    Winkelmann, Traud

    2010-01-01

    Cyclamen (Cyclamen persicum) is an economically important ornamental pot plant with local use as cut flower as well. Traditionally, it is propagated via seeds, but interest is given in vegetative propagation of parental lines as well as superior single plants. Somatic embryogenesis is an efficient in vitro propagation method for many cyclamen cultivars. Starting from ovules of unpollinated flowers, callus is induced and propagated in a medium containing 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-(gamma,gamma-dimethylallylamino)purine (2iP). Transfer to hormone-free medium results in the differentiation of somatic embryos, which afterwards germinate on the same medium. These first culture stages take about 6-7 months and are carried out in complete darkness. Two to four months after the transfer to light, plantlets develop which can be acclimatized in the greenhouse. The regenerated plants are characterized by low percentages of somaclonal variation. This protocol has proven useful not only for clonal propagation, but also for artificial seed preparation, cryopreservation, genetic transformation and protoplast regeneration.

  14. Parameter Identification of PMSM Using Immune Clonal Selection Differential Evolution Algorithm

    OpenAIRE

    Guohan Lin; Jing Zhang; Zhaohua Liu

    2014-01-01

    Permanent magnet synchronous motor (PMSM) models with accurate parameters are crucial to high performance PMSM control system designs. As the estimation of PMSM parameters is very difficult due to the nonlinear model complexity, a novel immune clonal differential evolution algorithm (ICDEA) is proposed to identify the electrical parameters of nonsalient pole PMSM. Clonal selection and receptor editing mechanism are introduced to ICDEA to increase the diversity of the population and improve se...

  15. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors.

    Directory of Open Access Journals (Sweden)

    Lei Bao

    Full Text Available Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC mutations/ # total HC mutations.Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48 and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value 0.99, supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.

  16. Clonal analysis reveals a common origin between nonsomite-derived neck muscles and heart myocardium

    Science.gov (United States)

    Lescroart, Fabienne; Hamou, Wissam; Francou, Alexandre; Théveniau-Ruissy, Magali; Kelly, Robert G.; Buckingham, Margaret

    2015-01-01

    Neck muscles constitute a transition zone between somite-derived skeletal muscles of the trunk and limbs, and muscles of the head, which derive from cranial mesoderm. The trapezius and sternocleidomastoid neck muscles are formed from progenitor cells that have expressed markers of cranial pharyngeal mesoderm, whereas other muscles in the neck arise from Pax3-expressing cells in the somites. Mef2c-AHF-Cre genetic tracing experiments and Tbx1 mutant analysis show that nonsomitic neck muscles share a gene regulatory network with cardiac progenitor cells in pharyngeal mesoderm of the second heart field (SHF) and branchial arch-derived head muscles. Retrospective clonal analysis shows that this group of neck muscles includes laryngeal muscles and a component of the splenius muscle, of mixed somitic and nonsomitic origin. We demonstrate that the trapezius muscle group is clonally related to myocardium at the venous pole of the heart, which derives from the posterior SHF. The left clonal sublineage includes myocardium of the pulmonary trunk at the arterial pole of the heart. Although muscles derived from the first and second branchial arches also share a clonal relationship with different SHF-derived parts of the heart, neck muscles are clonally distinct from these muscles and define a third clonal population of common skeletal and cardiac muscle progenitor cells within cardiopharyngeal mesoderm. By linking neck muscle and heart development, our findings highlight the importance of cardiopharyngeal mesoderm in the evolution of the vertebrate heart and neck and in the pathophysiology of human congenital disease. PMID:25605943

  17. Chromosome aberrations of clonal origin are present in astronauts' blood lymphocytes

    Science.gov (United States)

    George, K.; Durante, M.; Willingham, V.; Cucinotta, F. A.

    2004-01-01

    Radiation-induced chromosome translocations remain in peripheral blood cells over many years, and can potentially be used to measure retrospective doses or prolonged low-dose rate exposures. However, several recent studies have indicated that some individuals possess clones of cells with balanced chromosome abnormalities, which can result in an overestimation of damage and, therefore, influence the accuracy of dose calculations. We carefully examined the patterns of chromosome damage found in the blood lymphocytes of twelve astronauts, and also applied statistical methods to screen for the presence of potential clones. Cells with clonal aberrations were identified in three of the twelve individuals. These clonal cells were present in samples collected both before and after space flight, and yields are higher than previously reported for healthy individuals in this age range (40-52 years of age). The frequency of clonal damage appears to be even greater in chromosomes prematurely condensed in interphase, when compared with equivalent analysis in metaphase cells. The individuals with clonal aberrations were followed-up over several months and the yields of all clones decreased during this period. Since clonal aberrations may be associated with increased risk of tumorigenesis, it is important to accurately identify cells containing clonal rearrangements for risk assessment as well as biodosimetry. Copyright 2003 S. Karger AG, Basel.

  18. Geographic clonal tracking in macaques provides insights into HSPC migration and differentiation.

    Science.gov (United States)

    Wu, Chuanfeng; Espinoza, Diego A; Koelle, Samson J; Potter, E Lake; Lu, Rong; Li, Brian; Yang, Di; Fan, Xing; Donahue, Robert E; Roederer, Mario; Dunbar, Cynthia E

    2018-01-02

    The geographic distribution of hematopoiesis at a clonal level is of interest in understanding how hematopoietic stem and progenitor cells (HSPCs) and their progeny interact with bone marrow (BM) niches during regeneration. We tagged rhesus macaque autologous HSPCs with genetic barcodes, allowing clonal tracking over time and space after transplantation. We found marked geographic segregation of CD34+ HSPCs for at least 6 mo posttransplantation, followed by very gradual clonal mixing at different BM sites over subsequent months to years. Clonal mapping was used to document local production of granulocytes, monocytes, B cells, and CD56+ natural killer (NK) cells. In contrast, CD16+CD56- NK cells were not produced in the BM, and in fact were clonally distinct from multipotent progenitors producing all other lineages. Most surprisingly, we documented local BM production of CD3+ T cells early after transplantation, using both clonal mapping and intravascular versus tissue-resident T cell staining, suggesting a thymus-independent T cell developmental pathway operating during BM regeneration, perhaps before thymic recovery. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

  19. Clonal expansion of renal cell carcinoma-infiltrating T lymphocytes

    DEFF Research Database (Denmark)

    Sittig, Simone; Køllgaard, Tania; Grønbæk, Kirsten

    2013-01-01

    in the range of 1-17 (median = 5), and in several patients, the number of clonotypes expanded within tumor lesions resembled that observed among autologous peripheral blood mononuclear cells. Moreover, several of these clonotypes were identical in TILs and PBMCs. Flow cytometry data demonstrated...

  20. Expanding the Game Design Space

    DEFF Research Database (Denmark)

    Larsen, Lasse Juel; Majgaard, Gunver

    2016-01-01

    . It encapsulates the entire development process from the first ideas to the final game with emphasis on game design thinking. Our model of expanded game design space consists of four separate – yet interconnected – layers in the process of game development. The first layer addresses the importance of framing...... as a guideline for evaluating game design thinking and for measuring solutions made in the development process. To strengthen our model of expanded design space, we will present examples from our game design courses.......This article considers game design research in educational settings. Its focus is on how undergraduate students – particularly engineering students – learn computer game design. From observations conducted during our game design courses we have developed a model of expanded game design space...

  1. Flow boiling in expanding microchannels

    CERN Document Server

    Alam, Tamanna

    2017-01-01

    This Brief presents an up to date summary of details of the flow boiling heat transfer, pressure drop and instability characteristics; two phase flow patterns of expanding microchannels. Results obtained from the different expanding microscale geometries are presented for comparison and addition to that, comparison with literatures is also performed. Finally, parametric studies are performed and presented in the brief. The findings from this study could help in understanding the complex microscale flow boiling behavior and aid in the design and implementation of reliable compact heat sinks for practical applications.

  2. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and and pyrosequencing for the characterisation of the caries-associated microbiome

    Directory of Open Access Journals (Sweden)

    Kathrin eSchulze-Schweifing

    2014-11-01

    Full Text Available Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture.

  3. Expanding nail or expanding femur? An adverse event with the expandable intramedullary nail.

    Science.gov (United States)

    Gangopadhyay, Soham; Riley, Nicholas D; Sivaji, Chellappan K

    2010-01-01

    The expandable intramedullary nail is self-locking and has the advantage of reducing operating time and exposure to ionizing radiation. The nail is recommended for simple diaphyseal fractures involving the middle third of long bones, where the nail can bypass the fracture site by at least 5 cm. We encountered a unique complication with the expandable nail in a simple transverse shaft fracture at the junction of the middle and distal third of the left femur in an otherwise healthy 57-year-old man. The fracture was reduced and a 12-mm expandable nail was inserted. Following full expansion, intraoperative radiographs were obtained prior to closure. After six postoperative weeks, it was noted that the nail expanded the femoral canal, converting a simple fracture to a distally progressing comminuted fracture with a butterfly fragment. A review of the intraoperative radiographs showed slight widening of the medullary canal at the level of the fracture. As the alignment was satisfactory and callus was present, no further surgical intervention was considered. The patient was advised not to bear weight and was provided with a locked knee brace in extension to wear for six weeks. Radiographs at 12 weeks demonstrated good progress of healing with adequate callus and the patient was permitted to bear weight as tolerated and commence knee flexion. The fracture united satisfactorily at four months. This adverse experience emphasizes that caution should be exercised when expanding the nail, with close observation of the medullary canal diameter during the later stages of expansion.

  4. Probing the importance of clonality: Single cell subcloning of clonally derived CHO cell lines yields widely diverse clones differing in growth, productivity, and product quality.

    Science.gov (United States)

    Ko, Peggy; Misaghi, Shahram; Hu, Zhilan; Zhan, Dejin; Tsukuda, Joni; Yim, Mandy; Sanford, Mark; Shaw, David; Shiratori, Masaru; Snedecor, Brad; Laird, Michael; Shen, Amy

    2017-12-11

    In the past few decades, a large variety of therapeutic antibodies and proteins have been expressed in Chinese hamster ovary (CHO) cells. This mammalian expression system is robust, scalable, relatively inexpensive, and importantly allows for post-translational modifications that are important for some therapeutic proteins. Historically, CHO cell lines were derived from colonies of cells grown in semi-solid or liquid plates using either serum-containing or serum-free media. Current advancements in cell sorting and imaging technologies have allowed for isolating and imaging single cell progenitors at the seeding step, significantly increasing the probability of isolating clonally derived cell lines. However, it is debatable how much population heterogeneity can be eliminated when clonally derived cell lines, originated from a single cell progenitor, are scaled up. To further investigate this phenomenon, we subcloned two different clonally derived (day 0 imaged and visually inspected) cell lines expressing antibody-X. The results showed that when six randomly chosen subclones of each line were evaluated in a production assay, these subclones displayed a range of variation in titer, specific productivity, growth, and product quality attributes. Some subclones displayed variations in transgene copy numbers. Additionally, clonal derivation did not assure stability of the derived cell lines. Our findings show that cell heterogeneity exists in a population even when derived from a single cell progenitor. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 2017. © 2017 American Institute of Chemical Engineers.

  5. Ultracold neutral plasmas

    Science.gov (United States)

    Lyon, M.; Rolston, S. L.

    2017-01-01

    By photoionizing samples of laser-cooled atoms with laser light tuned just above the ionization limit, plasmas can be created with electron and ion temperatures below 10 K. These ultracold neutral plasmas have extended the temperature bounds of plasma physics by two orders of magnitude. Table-top experiments, using many of the tools from atomic physics, allow for the study of plasma phenomena in this new regime with independent control over the density and temperature of the plasma through the excitation process. Characteristic of these systems is an inhomogeneous density profile, inherited from the density distribution of the laser-cooled neutral atom sample. Most work has dealt with unconfined plasmas in vacuum, which expand outward at velocities of order 100 m/s, governed by electron pressure, and with lifetimes of order 100 μs, limited by stray electric fields. Using detection of charged particles and optical detection techniques, a wide variety of properties and phenomena have been observed, including expansion dynamics, collective excitations in both the electrons and ions, and collisional properties. Through three-body recombination collisions, the plasmas rapidly form Rydberg atoms, and clouds of cold Rydberg atoms have been observed to spontaneously avalanche ionize to form plasmas. Of particular interest is the possibility of the formation of strongly coupled plasmas, where Coulomb forces dominate thermal motion and correlations become important. The strongest impediment to strong coupling is disorder-induced heating, a process in which Coulomb energy from an initially disordered sample is converted into thermal energy. This restricts electrons to a weakly coupled regime and leaves the ions barely within the strongly coupled regime. This review will give an overview of the field of ultracold neutral plasmas, from its inception in 1999 to current work, including efforts to increase strong coupling and effects on plasma properties due to strong coupling.

  6. Ultracold neutral plasmas.

    Science.gov (United States)

    Lyon, M; Rolston, S L

    2017-01-01

    By photoionizing samples of laser-cooled atoms with laser light tuned just above the ionization limit, plasmas can be created with electron and ion temperatures below 10 K. These ultracold neutral plasmas have extended the temperature bounds of plasma physics by two orders of magnitude. Table-top experiments, using many of the tools from atomic physics, allow for the study of plasma phenomena in this new regime with independent control over the density and temperature of the plasma through the excitation process. Characteristic of these systems is an inhomogeneous density profile, inherited from the density distribution of the laser-cooled neutral atom sample. Most work has dealt with unconfined plasmas in vacuum, which expand outward at velocities of order 100 m/s, governed by electron pressure, and with lifetimes of order 100 μs, limited by stray electric fields. Using detection of charged particles and optical detection techniques, a wide variety of properties and phenomena have been observed, including expansion dynamics, collective excitations in both the electrons and ions, and collisional properties. Through three-body recombination collisions, the plasmas rapidly form Rydberg atoms, and clouds of cold Rydberg atoms have been observed to spontaneously avalanche ionize to form plasmas. Of particular interest is the possibility of the formation of strongly coupled plasmas, where Coulomb forces dominate thermal motion and correlations become important. The strongest impediment to strong coupling is disorder-induced heating, a process in which Coulomb energy from an initially disordered sample is converted into thermal energy. This restricts electrons to a weakly coupled regime and leaves the ions barely within the strongly coupled regime. This review will give an overview of the field of ultracold neutral plasmas, from its inception in 1999 to current work, including efforts to increase strong coupling and effects on plasma properties due to strong coupling.

  7. Plasmid and clonal interference during post horizontal gene transfer evolution.

    Science.gov (United States)

    Bedhomme, S; Perez Pantoja, D; Bravo, I G

    2017-04-01

    Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions. This conflict between cellular fitness and plasmid spread sets the scene for multilevel selection processes. We have engineered a system to study the short-term evolutionary impact of different synonymous versions of a plasmid-encoded antibiotic resistance gene. Applying experimental evolution under different selection conditions and deep sequencing allowed us to show rapid local adaptation to the presence of antibiotic and to the specific version of the resistance gene transferred. We describe the presence of clonal interference at two different levels: at the within-cell level, because a single cell can carry several plasmids, and at the between-cell level, because a bacterial population may contain several clones carrying different plasmids and displaying different fitness in the presence/absence of antibiotic. Understanding the within-cell and between-cell dynamics of plasmids after horizontal gene transfer is essential to unravel the dense network of mobile elements underlying the worldwide threat to public health of antibiotic resistance. © 2017 John Wiley & Sons Ltd.

  8. Clonality analysis of neuroendocrine cells in gastric adenocarcinoma

    Science.gov (United States)

    Wang, Ling-Ling; Yao, Gen-You; Zhao, Zhong-Sheng; Wei, Xiao-Li; Xu, Ru-Jun

    2013-01-01

    AIM: To achieve a better understanding of the origination of neuroendocrine (NE) cells in gastric adenocarcinoma. METHODS: In this study, 120 cases of gastric adenocarcinoma were obtained. First, frozen section-immunohistochemistrical samples were selected from a large quantity of neuroendocrine cells. Second, laser capture microdissection was used to get target cells from gastric adenocarcinoma and whole genome amplification was applied to get a large quantity of DNA for further study. Third, genome-wide microsatellite abnormalities [microsatellite instability (MSI), loss of heterozygosity (LOH)] and p53 mutation were detected by polymerase chain reaction (PCR)-single-strand conformation polymer- phism-silver staining and PCR-sequencing in order to identify the clonality of NE cells. RESULTS: The total incidence rate of MSI was 27.4%, while LOH was 17.9%. Ten cases had a highest concordance for the two types of cells. The other samples had similar microsatellite changes, except for cases 7 and 10. Concordant p53 mutations exhibited in sample 4, 14, 21 and 27, and there were different mutations between two kinds of cells in case 7. In case 17, mutation took place only in adenocarcinoma cells. p53 mutation was closely related with degree of differentiation, tumor-node-metastasis stage, vessel invasion and lymph node metastasis. In brief, NE and adenocarcinoma cells showed the same MSI, LOH or p53 mutation in most cases (27/30). In the other three cases, different MSI, LOH or p53 mutation occurred. CONCLUSION: NE and the gastric adenocarcinoma cells may mainly derive from the same stem cells, but the remaining cases showing different origin needs further investigation. PMID:23983439

  9. Stability of stagnation via an expanding accretion shock wave

    CERN Document Server

    Velikovich, A L; Taylor, B D; Giuliani, J L; Zalesak, S T; Iwamoto, Y

    2016-01-01

    Stagnation of a cold plasma streaming to the center or axis of symmetry via an expanding accretion shock wave is ubiquitous in inertial confinement fusion (ICF) and high-energy-density plasma physics, the examples ranging from plasma flows in x-ray-generating Z pinches [Y. Maron et al., Phys. Rev. Lett. 111, 035001 (2013)] to the experiments in support of the recently suggested concept of impact ignition in ICF [H. Azechi et al., Phys. Rev. Lett. 102, 235002 (2009); M. Murakami et al., Nucl. Fusion 54, 054007 (2014)]. Some experimental evidence indicates that stagnation via an expanding shock wave is stable, but its stability has never been studied theoretically. We present such analysis for the stagnation that does not involve a rarefaction wave behind the expanding shock front and is described by the classic ideal-gas Noh solution in spherical and cylindrical geometry. In either case the stagnated flow has been demonstrated to be stable, initial perturbations exhibiting a power-law, oscillatory or monotonic...

  10. Stability of stagnation via an expanding accretion shock wave

    Energy Technology Data Exchange (ETDEWEB)

    Velikovich, A. L.; Giuliani, J. L. [Plasma Physics Division, Naval Research Laboratory, Washington, DC 20375 (United States); Murakami, M. [Institute of Laser Engineering, Osaka University, Osaka 565-0871 (Japan); Taylor, B. D. [Laboratory for Computational Physics and Fluid Dynamics, Naval Research Laboratory, Washington, DC 20375 (United States); Zalesak, S. T. [Berkeley Research Associates, Beltsville, Maryland 20705 (United States); Iwamoto, Y. [Ehime University, Matsuyama, Ehime Pref. 790-8577 (Japan)

    2016-05-15

    Stagnation of a cold plasma streaming to the center or axis of symmetry via an expanding accretion shock wave is ubiquitous in inertial confinement fusion (ICF) and high-energy-density plasma physics, the examples ranging from plasma flows in x-ray-generating Z pinches [Maron et al., Phys. Rev. Lett. 111, 035001 (2013)] to the experiments in support of the recently suggested concept of impact ignition in ICF [Azechi et al., Phys. Rev. Lett. 102, 235002 (2009); Murakami et al., Nucl. Fusion 54, 054007 (2014)]. Some experimental evidence indicates that stagnation via an expanding shock wave is stable, but its stability has never been studied theoretically. We present such analysis for the stagnation that does not involve a rarefaction wave behind the expanding shock front and is described by the classic ideal-gas Noh solution in spherical and cylindrical geometry. In either case, the stagnated flow has been demonstrated to be stable, initial perturbations exhibiting a power-law, oscillatory or monotonic, decay with time for all the eigenmodes. This conclusion has been supported by our simulations done both on a Cartesian grid and on a curvilinear grid in spherical coordinates. Dispersion equation determining the eigenvalues of the problem and explicit formulas for the eigenfunction profiles corresponding to these eigenvalues are presented, making it possible to use the theory for hydrocode verification in two and three dimensions.

  11. EFFECT OF INCORPORATING EXPANDED POLYSTYRENE ...

    African Journals Online (AJOL)

    2012-11-03

    Nov 3, 2012 ... Abstract. Incorporating expanded polystyrene granules in concrete matrix can produce lightweight polystyrene aggregate concrete of various densities. Workability which is an important property of concrete, affects the rate of placement and the degree of compaction of concrete. Inadequate compaction.

  12. Expanding the eukaryotic genetic code

    Science.gov (United States)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2013-01-22

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  13. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2017-02-28

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  14. Barrett's metaplasia glands are clonal, contain multiple stem cells and share a common squamous progenitor.

    Science.gov (United States)

    Nicholson, Anna M; Graham, Trevor A; Simpson, Ashley; Humphries, Adam; Burch, Nicola; Rodriguez-Justo, Manuel; Novelli, Marco; Harrison, Rebecca; Wright, Nicholas A; McDonald, Stuart A C; Jankowski, Janusz A

    2012-10-01

    Little is known about the stem cell organisation of the normal oesophagus or Barrett's metaplastic oesophagus. Using non-pathogenic mitochondrial DNA mutations as clonal markers, the authors reveal the stem cell organisation of the human squamous oesophagus and of Barrett's metaplasia and determine the mechanism of clonal expansion of mutations. Mutated cells were identified using enzyme histochemistry to detect activity of cytochrome c oxidase (CCO). CCO-deficient cells were laser-captured and mutations confirmed by PCR sequencing. Cell lineages were identified using immunohistochemistry. The normal squamous oesophagus contained CCO-deficient patches varying in size from around 30 μm up to about 1 mm. These patches were clonal as each area within a CCO-deficient patch contained an identical mitochondrial DNA mutation. In Barrett's metaplasia partially CCO-deficient glands indicate that glands are maintained by multiple stem cells. Wholly mutated Barrett's metaplasia glands containing all the expected differentiated cell lineages were seen, demonstrating multilineage differentiation from a clonal population of Barrett's metaplasia stem cells. Patches of clonally mutated Barrett's metaplasia glands were observed, indicating glands can divide to form patches. In one patient, both the regenerating squamous epithelium and the underlying glandular tissue shared a clonal mutation, indicating that they are derived from a common progenitor cell. In normal oesophageal squamous epithelium, a single stem cell clone can populate large areas of epithelium. Barrett's metaplasia glands are clonal units, contain multiple multipotential stem cells and most likely divide by fission. Furthermore, a single cell of origin can give rise to both squamous and glandular epithelium suggesting oesophageal plasticity.

  15. Clonal analysis and virulent traits of pathogenic extraintestinal Escherichia coli isolates from swine in China

    Directory of Open Access Journals (Sweden)

    Ding Yi

    2012-08-01

    Full Text Available Abstract Background Extraintestinal pathogenic Escherichia coli (ExPEC can cause a variety of infections outside the gastrointestinal tract in humans and animals. Infections due to swine ExPECs have been occurring with increasing frequency in China. These ExPECs may now be considered a new food-borne pathogen that causes cross-infections between humans and pigs. Knowledge of the clonal structure and virulence genes is needed as a framework to improve the understanding of phylogenetic traits of porcine ExPECs. Results Multilocus sequence typing (MLST data showed that the isolates investigated in this study could be placed into four main clonal complexes, designated as CC10, CC1687, CC88 and CC58. Strains within CC10 were classified as phylogroup A, and these accounted for most of our porcine ExPEC isolates. Isolates in the CC1687 clonal complex, formed by new sequence types (STs, was classified as phylogroup D, with CC88 isolates considered as B2 and CC58 isolates as B1. Porcine ExPECs in these four clonal complexes demonstrated significantly different virulence gene patterns. A few porcine ExPECs were indentified in phylogroup B2, the phylogroup in which human ExPECs mainly exist. However some STs in the four clonal groups of porcine ExPECs were reported to cause extraintestinal infections in human, based on data in the MLST database. Conclusion Porcine ExPECs have different virulence gene patterns for different clonal complexes. However, these strains are mostly fell in phylogenentic phylogroup A, B1 and D, which is different from human ExPECs that concentrate in phylogroup B2. Our findings provide a better understanding relating to the clonal structure of ExPECs in diseased pigs and indicate a need to re-evaluate their contribution to human ExPEC diseases.

  16. Phylogenetic meta-analysis of the functional traits of clonal plants foraging in changing environments.

    Science.gov (United States)

    Xie, Xiu-Fang; Song, Yao-Bin; Zhang, Ya-Lin; Pan, Xu; Dong, Ming

    2014-01-01

    Foraging behavior, one of the adaptive strategies of clonal plants, has stimulated a tremendous amount of research. However, it is a matter of debate whether there is any general pattern in the foraging traits (functional traits related to foraging behavior) of clonal plants in response to diverse environments. We collected data from 97 published papers concerning the relationships between foraging traits (e.g., spacer length, specific spacer length, branch intensity and branch angle) of clonal plants and essential resources (e.g., light, nutrients and water) for plant growth and reproduction. We incorporated the phylogenetic information of 85 plant species to examine the universality of foraging hypotheses using phylogenetic meta-analysis. The trends toward forming longer spacers and fewer branches in shaded environments were detected in clonal plants, but no evidence for a relation between foraging traits and nutrient availability was detected, except that there was a positive correlation between branch intensity and nutrient availability in stoloniferous plants. The response of the foraging traits of clonal plants to water availability was also not obvious. Additionally, our results indicated that the foraging traits of stoloniferous plants were more sensitive to resource availability than those of rhizomatous plants. In consideration of plant phylogeny, these results implied that the foraging traits of clonal plants (notably stoloniferous plants) only responded to light intensity in a general pattern but did not respond to nutrient or water availability. In conclusion, our findings on the effects of the environment on the foraging traits of clonal plants avoided the confounding effects of phylogeny because we incorporated phylogeny into the meta-analysis.

  17. Assessment of various strategies for the preservation of clonal genetic resources in oil palm (Elaeis guineensis Jacq.)

    OpenAIRE

    Konan, K.E.; Rival, A.; Kouadio, Y. J.; Duval, Yves; FLORI, A.; Adon, B.; Pene, C.; Gasselin, T.D.

    2006-01-01

    Three different approaches for the preservation of oil palm (Elaeis guineensis Jacq.) clonal genetic resources and their impacts on the induction of the « mantled » somaclonal variation were assessed. In vitro long term preservation of somatic embryos stock-cultures was studied : after a 5 year cultivation period, 75 % of clonal lines were still normal. Between 8 and 13 years of embryo cultures, half of the considered clonal lines were found to be « mantled ». Finally, 40 % were found t...

  18. Low clonal propagation in Atlantic and Mediterranean populations of the red gorgonian Paramuricea clavata (Octocorallia

    Directory of Open Access Journals (Sweden)

    Joanna Pilczynska

    2017-03-01

    Full Text Available Clonal propagation is a common feature of benthic marine organisms. In the present study, we investigated the contribution of clonal reproduction in the red gorgonian Paramuricea clavata. Mediterranean populations of P. clavata were severely affected by mass mortality events caused by increased water temperature in 1999 and 2003. The populations are characterized by slow growth and episodic recruitment, but after the observed mortalities, an unexpectedly high recovery rate was observed in the severely affected populations from the Ligurian Sea, NW Mediterranean. Ten years after the last mortality event, we investigated the contribution of clonal propagation in populations from the Ligurian Sea, where some populations were highly affected by mass mortality events, and from the Atlantic, where mortality was never observed. All individuals were genotyped for nine microsatellite loci. The contribution of clonal reproduction varied from 0% to 13% and did not differ significantly between affected and unaffected populations. We confirm by using genetic markers that clonal propagation in P. clavata is not common, and that the contribution of clones is too low to play an important role in red gorgonian reproduction and cannot contribute to population recovery at sites that have been affected by mass mortality events.

  19. Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing.

    Directory of Open Access Journals (Sweden)

    Andrew E O Hughes

    2014-07-01

    Full Text Available Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions-the population frequency of individual clones, their genetic composition, and their evolutionary relationships-which we set out to test by sequencing individual cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples. Single-cell mutation profiling strongly supported the clonal architecture implied by the analysis of bulk material. In addition, it resolved the clonal assignment of single nucleotide variants that had been initially ambiguous and identified areas of previously unappreciated complexity. Accordingly, we find that many of the key assumptions underlying the analysis of tumor clonality by deep sequencing of unfractionated material are valid. Furthermore, we illustrate a single-cell sequencing strategy for interrogating the clonal relationships among known variants that is cost-effective, scalable, and adaptable to the analysis of both hematopoietic and solid tumors, or any heterogeneous population of cells.

  20. Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome.

    Directory of Open Access Journals (Sweden)

    Claude Pasquier

    Full Text Available Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.

  1. Expanding the Game Design Space

    DEFF Research Database (Denmark)

    Larsen, Lasse Juel; Majgaard, Gunver

    2016-01-01

    layer establishes correspondence between formal elements of computer games and the structure of problem-based creativity. It addresses how game design challenges should be formulated and how creative solutions can be measured. The fourth and final layer demonstrates how clear framing can act......This article considers game design research in educational settings. Its focus is on how undergraduate students – particularly engineering students – learn computer game design. From observations conducted during our game design courses we have developed a model of expanded game design space....... It encapsulates the entire development process from the first ideas to the final game with emphasis on game design thinking. Our model of expanded game design space consists of four separate – yet interconnected – layers in the process of game development. The first layer addresses the importance of framing...

  2. Clonal expansions of CD8+ T cells with IL-10 secreting capacity occur during chronic Mycobacterium tuberculosis infection.

    Directory of Open Access Journals (Sweden)

    Joshua C Cyktor

    Full Text Available The exact role of CD8(+ T cells during Mycobacterium tuberculosis (Mtb infection has been heavily debated, yet it is generally accepted that CD8(+ T cells contribute to protection against Mtb. In this study, however, we show that the Mtb-susceptible CBA/J mouse strain accumulates large numbers of CD8(+ T cells in the lung as infection progresses, and that these cells display a dysfunctional and immunosuppressive phenotype (PD-1(+, Tim-3(+, CD122(+. CD8(+ T cell expansions from the lungs of Mtb-infected CBA/J mice were also capable of secreting the immunosuppressive cytokine interleukin-10 (IL-10, although in vivo CD8(+ T cell depletion did not significantly alter Mtb burden. Further analysis revealed that pulmonary CD8(+ T cells from Mtb-infected CBA/J mice were clonally expanded, preferentially expressing T cell receptor (TcR Vβ chain 8 (8.2, 8.3 or Vβ 14. Although Vβ8(+ CD8(+ T cells were responsible for the majority of IL-10 production, in vivo depletion of Vβ8(+ did not significantly change the outcome of Mtb infection, which we hypothesize was a consequence of their dual IL-10/IFN-γ secreting profiles. Our data demonstrate that IL-10-secreting CD8(+ T cells can arise during chronic Mtb infection, although the significance of this T cell population in tuberculosis pathogenesis remains unclear.

  3. Plasma harmonics

    CERN Document Server

    Ganeev, Rashid A

    2014-01-01

    Preface; Why plasma harmonics? A very brief introduction Early stage of plasma harmonic studies - hopes and frustrations New developments in plasma harmonics studies: first successes Improvements of plasma harmonics; Theoretical basics of plasma harmonics; Basics of HHG Harmonic generation in fullerenes using few-cycle pulsesVarious approaches for description of observed peculiarities of resonant enhancement of a single harmonic in laser plasmaTwo-colour pump resonance-induced enhancement of odd and even harmonics from a tin plasmaCalculations of single harmonic generation from Mn plasma;Low-o

  4. Epigenetic memory as a basis for intelligent behaviour in clonal plants

    Directory of Open Access Journals (Sweden)

    Vit Latzel

    2016-08-01

    Full Text Available Environmentally induced epigenetic change enables plants to remember past environmental interactions. If this memory capability is exploited to prepare plants for future challenges, it can provide a basis for highly sophisticated behaviour, considered intelligent by some. Against the backdrop of an overview of plant intelligence, we hypothesise: 1 that the capability of plants to engage in such intelligent behaviour increases with increasing modularity, and; 2 that more faithful inheritance of epigenetic information in clonal plants, in conjunction with information exchange and coordination between connected ramets, is likely to enable especially advanced intelligent behaviour in this group. We therefore further hypothesise that this behaviour provides ecological and evolutionary advantages to clonal plants, possibly explaining, at least in part, their widespread success. Finally, we suggest experiments that could allow for assessing intelligent behaviour and the role of epigenetic memory in clonal species.

  5. Malignant Phyllodes Tumor and Acute Megakaryoblastic Leukemia Sharing a Common Clonal Origin

    Directory of Open Access Journals (Sweden)

    Yngvar Fløisand

    2013-01-01

    Full Text Available There is a well-known association in male patients between mediastinal germ cell tumors (GCT and hematologic malignancies, with a propensity towards acute megakaryoblastic leukemia. These rare malignancies have been shown to share a common clonal origin, often deduced from the finding of isochromosome 12p, i(12p, in cells from both the solid tumor and the leukemia, and thus are now known to represent different manifestations of the same clonal process. We treated a young female patient with a malignant phyllodes tumor followed by an acute megakaryoblastic leukemia and found several of the same marker chromosomes by karyotype analysis of cells from both the tumor and the leukemia implying a common clonal origin of the two. To the best of our knowledge, this has not been demonstrated in phyllodes tumors before, but indicates that the same type of leukemization may occur of this tumor as has been described in mediastinal GCT.

  6. Invasion strategies in clonal aquatic plants: Are phenotypic differences caused by phenotypic plasticity or local adaptation?

    DEFF Research Database (Denmark)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit

    2010-01-01

    populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis...... and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained by local nutrient conditions. All together this strongly suggests that invasive clonal aquatic plants adapt to a wide......Background and Aims: The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important...

  7. Clonal reproduction with androgenesis and somatic recombination: the case of the ant Cardiocondyla kagutsuchi

    Science.gov (United States)

    Okita, Ichiro; Tsuchida, Koji

    2016-04-01

    In haplodiploid insects such as ants, male sexuals develop from unfertilised haploid eggs, while female sexuals and workers develop from fertilized diploid eggs. However, some ant species do not exchange their gene pool between sexes; both male and female sexuals are clonally produced, while workers are sexually produced. To date, three ant species, Wasmannia auropunctata, Vollenhovia emeryi, and Paratrechina longicornis, have been reported to reproduce using such reproductive systems. In this study, we reveal that in one lineage of the ant Cardiocondyla kagutsuchi, male and female sexuals are also clonally produced. In contrast to the abovementioned three species, the workers were not only sexually produced but had recombinant sequences in their nuclear internal transcribed spacer regions, although the recombinant sequences were not detected in male or female sexuals. These results suggest that the lineage likely possesses a mechanism to compensate for the reduction in genetic variation due to clonal reproduction with somatic recombination that occurs within the workers.

  8. Different growth promoting effects of endophytic bacteria on invasive and native clonal plants

    Directory of Open Access Journals (Sweden)

    Zhi-Cong eDai

    2016-05-01

    Full Text Available The role of the interactions between endophytes and alien plants has been unclear yet in plant invasion. We used a completely germ-free culture system to quantify the plant growth-promoting (PGP effects of endophytic bacteria Bacillus sp. on aseptic seedlings of W. trilobata and of its native clonal congener W. chinensis. The endophytic bacteria did not affect the growth of W. chinensis, but they significantly promoted the growth of W. trilobata. With the PGP effects of endophytic bacteria, relative change ratios of the clonal traits and the ramets' growth traits of W. trilobata were significantly greater than those of W. chinensis. Our results indicate that the growth-promoting effects of endophytes may differ between invasive and native clonal plants, and the endophytes of invasive plant may be host-specific to facilitate plant invasion.

  9. Genetic Heterogeneity and Clonal Evolution of Tumor Cells and their Impact on Precision Cancer Medicine.

    Science.gov (United States)

    Sabaawy, Hatem E

    2013-11-18

    The efficacy of targeted therapies in leukemias and solid tumors depends upon the accurate detection and sustained targeting of initial and evolving driver mutations and/or aberrations in cancer cells. Tumor clonal evolution of the diverse populations of cancer cells during cancer progression contributes to the longitudinal variations of clonal, morphological, anatomical, and molecular heterogeneity of tumors. Moreover, drug-resistant subclones present at initiation of therapy or emerging as a result of targeted therapies represent major challenges for achieving success of personalized therapies in providing meaningful improvement in cancer survival rates. Here, I briefly portray tumor cell clonal evolution at the cellular and molecular levels, and present the multiple types of genetic heterogeneity in tumors, with a focus on their impact on the implementation of personalized or precision cancer medicine.

  10. Intracavernous delivery of clonal mesenchymal stem cells restores erectile function in a mouse model of cavernous nerve injury.

    Science.gov (United States)

    Ryu, Ji-Kan; Kim, Da-Ham; Song, Kang Moon; Yi, Tacghee; Suh, Jun-Kyu; Song, Sun U

    2014-02-01

    Recently, much attention has focused on stem cell therapy; bone marrow-derived stem cells (BMSCs) are one of the most studied mesenchymal stem cells used in the field of erectile dysfunction (ED). However, a major limitation for the clinical application of stem cell therapy is the heterogeneous nature of the isolated cells, which may cause different treatment outcomes. We investigated the effectiveness of mouse clonal BMSCs obtained from a single colony by using subfractionation culturing method (SCM) for erectile function in a mouse model of cavernous nerve injury (CNI). Twelve-week-old C57BL/6J mice were divided into four groups: sham operation group, bilateral CNI group receiving a single intracavernous (IC) injection of phosphate-buffered saline (20 μL) or clonal BMSCs (3 × 10(5) cells/20 μL), and receiving a single intraperitoneal (IP) injection of clonal BMSCs (3 × 10(5) cells/20 μL). The clonal BMSC line was analyzed for cell-surface epitopes by using fluorescence-activated cell sorting and for differentiation potential. Two weeks after CNI and treatment, erectile function was measured by electrically stimulating the cavernous nerve. The penis was harvested for histologic examinations and Western blot analysis. Clonal BMSCs expressed cell surface markers for mesenchymal stem cells and were capable of differentiating into several lineages, including adipogenic, osteogenic, and chondrogenic cells. Both IC and IP injections of clonal BMSCs significantly restored cavernous endothelial and smooth muscle content, and penile nNOS and neurofilament content in CNI mice. IC injection of clonal BMSCs induced significant recovery of erectile function, which reached 90-100% of the sham control values, whereas IP injection of clonal BMSCs partially restored erectile function. We established a homogeneous population of mouse clonal BMSCs using SCM; clonal BMSCs successfully restored erectile function in CNI mice. The homogeneous nature of clonal mesenchymal stem cells

  11. Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions

    Science.gov (United States)

    2012-01-01

    Introduction Lobular carcinoma in situ (LCIS) has been accepted as a marker of risk for the development of invasive breast cancer, yet modern models of breast carcinogenesis include LCIS as a precursor of low-grade carcinomas. We provide evidence favoring a clonal origin for LCIS and synchronous estrogen receptor-positive malignant lesions of the ductal and lobular phenotype. Methods Patients with prior LCIS undergoing mastectomy were identified preoperatively from 2003 to 2008. Specimens were widely sampled, and frozen blocks were screened for LCIS and co-existing malignant lesions, and were subject to microdissection. Samples from 65 patients were hybridized to the Affymetrix SNP 6.0 array platform. Cases with both an LCIS sample and an associated ductal carcinoma in situ (DCIS) or invasive tumor sample were evaluated for patterns of somatic copy number changes to assess evidence of clonal relatedness. Results LCIS was identified in 44 of the cases, and among these a DCIS and/or invasive lesion was also identified in 21 cases. A total of 17 tumor pairs had adequate DNA/array data for analysis, including nine pairs of LCIS/invasive lobular cancer, four pairs of LCIS/DCIS, and four pairs of LCIS/invasive ductal cancer. Overall, seven pairs (41%) were judged to be clonally related; in five (29%) evidence suggested clonality but was equivocal, and five (29%) were considered independent. Clonal pairs were observed with all matched lesion types and low and high histological grades. We also show anecdotal evidence of clonality between a patient-matched triplet of LCIS, DCIS, and invasive ductal cancer. Conclusion Our results support the role of LCIS as a precursor in the development of both high-grade and low-grade ductal and lobular cancers. PMID:22776144

  12. Features of active-medium formation for lasers with a sectioned plasma source of metal vapor

    Energy Technology Data Exchange (ETDEWEB)

    Apollonov, V.V.; Derzhavin, S.I.; Prokhorov, A.M.; Sirotkin, A.A.

    1988-06-01

    Experimental results are presented on active-medium formation mechanisms in a laser with a sectioned plasma source of metal vapor (a SPER laser). The following processes were observed in the laser active medium: buffer-gas preionization; mixing of metal vapor and buffer gas during plasma expansion; plasma-chemical reactions in the expanding plasma; and a collisional mechanism of plasma cooling.

  13. Characteristic of a triple-cathode vacuum arc plasma source.

    Science.gov (United States)

    Xiang, W; Li, M; Chen, L

    2012-02-01

    In order to generate a better ion beam, a triple-cathode vacuum arc plasma source has been developed. Three plasma generators in the vacuum arc plasma source are equally located on a circle. Each generator initiated by means of a high-voltage breakdown between the cathode and the anode could be operated separately or simultaneously. The arc plasma expands from the cathode spot region in vacuum. In order to study the behaviors of expanding plasma plume generated in the vacuum arc plasma source, a Langmuir probe array is employed to measure the saturated ion current of the vacuum arc plasma source. The time-dependence profiles of the saturated current density of the triple vacuum arc plasma source operated separately and simultaneously are given. Furthermore, the plasma characteristic of this vacuum arc plasma source is also presented in the paper.

  14. Cold plasma processing to improve food safety

    Science.gov (United States)

    Cold plasma is an antimicrobial process being developed for application as a food processing technology. This novel intervention is the subject of an expanding research effort by groups around the world. A variety of devices can be used to generate cold plasma and apply it to the food commodity bein...

  15. Large contribution of clonal reproduction to the distribution of deciduous liana species (Wisteria floribunda) in an old-growth cool temperate forest: evidence from genetic analysis.

    Science.gov (United States)

    Mori, Hideki; Ueno, Saneyoshi; Matsumoto, Asako; Kamijo, Takashi; Tsumura, Yoshihiko; Masaki, Takashi

    2017-12-25

    Extensive clonal (vegetative) reproduction in lianas is a common and important life history strategy for regeneration and colonization success. However, few studies have evaluated the contribution of clonal reproduction to stand-level distribution of lianas in their natural habitat using genetic tools. The objectives of the present study were to investigate (1) the contribution of clonal reproduction to the distribution of Wisteria floribunda, (2) the size of clonal patches and (3) how the distribution patterns of W. floribunda clones are affected by micro-topography. The contribution of clonal reproduction to the distribution of the deciduous liana species W. floribunda was evaluated using genetic analysis across a 6-ha plot of an old-growth temperate forest in Japan and preference in landform between clonal ramets and non-clonal ramets was assessed. Of the 391 ramets sampled, clonal reproduction contributed to 71 and 62 % of the total abundance and basal area, respectively, or 57 and 31 % when the largest ramet within a genet was excluded. The large contribution of clonal reproduction to the density and basal area of W. floribunda was consistent with previous observational studies. The largest genet included a patch size of 0.47 ha and ranged over 180 m. Preferred landforms of clonal and non-clonal ramets were significantly different when evaluated by both abundance and basal area. Non-clonal ramets distributed more on lower part of the slope than other landforms in comparison with clonal ramets and trees, possibly reflecting the limitation of clonal growth by stolons. Using genetic analysis, the present study found evidence of a large contribution of clonal reproduction on the distribution of W. floribunda in its natural habitat. The results indicate that clonal reproduction plays an important role not only in the formation of populations but also in determining the distribution patterns of liana species.

  16. Fatal septicemia linked to transmission of MRSA clonal complex 398 in hospital and nursing home, Denmark

    DEFF Research Database (Denmark)

    Nielsen, Rikke Thoft; Kemp, Michael; Holm, Anette

    2016-01-01

    We describe 2 fatal cases of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 septicemia in persons who had no contact with livestock. Whole-genome sequencing of the isolated MRSA strains strongly suggest that both were of animal origin and that the patients had been infected...

  17. Drug hypersensitivity in clonal mast cell disorders : ENDA/EAACI position paper

    NARCIS (Netherlands)

    Bonadonna, P.; Pagani, M.; Aberer, W.; Bilo, M. B.; Brockow, K.; Elberink, H. Oude; Garvey, L.; Mosbech, H.; Romano, A.; Zanotti, R.; Torres, M. J.

    Mastocytosis is a clonal disorder characterized by the proliferation and accumulation of mast cells (MC) in different tissues, with a preferential localization in skin and bone marrow (BM). The excess of MC in mastocytosis as well as the increased releasability of MC may lead to a higher frequency

  18. Genetic and clonal diversity of the endemic ant-plant Humboldtia ...

    Indian Academy of Sciences (India)

    Prakash

    Dev S A, Shenoy M and Borges R M 2010 Genetic and clonal diversity of the endemic ant-plant Humboldtia brunonis (Fabaceae) in the Western. Ghats of India; J. ...... 503–520. Levin D A 1984 Inbreeding depression and proximity dependent.

  19. On numbers of clones needed for managing risks in clonal forestry

    Science.gov (United States)

    J. Bishir; J.H. Roberds

    1999-01-01

    An important question in clonal forestry concerns the number of clones needed in plantations to protect against catastrophic failure while at the same time achieving the uniform stands, high yields, and ease of management associated with this management system. This paper looks at how the required number of clones needed to achieve a predetermined maximum acceptable...

  20. Clonal reproduction by males and females in the little fire ant.

    Science.gov (United States)

    Fournier, Denis; Estoup, Arnaud; Orivel, Jérôme; Foucaud, Julien; Jourdan, Hervé; Le Breton, Julien; Keller, Laurent

    2005-06-30

    Sexual reproduction can lead to major conflicts between sexes and within genomes. Here we report an extreme case of such conflicts in the little fire ant Wasmannia auropunctata. We found that sterile workers are produced by normal sexual reproduction, whereas daughter queens are invariably clonally produced. Because males usually develop from unfertilized maternal eggs in ants and other haplodiploid species, they normally achieve direct fitness only through diploid female offspring. Hence, although the clonal production of queens increases the queen's relatedness to reproductive daughters, it potentially reduces male reproductive success to zero. In an apparent response to this conflict between sexes, genetic analyses reveal that males reproduce clonally, most likely by eliminating the maternal half of the genome in diploid eggs. As a result, all sons have nuclear genomes identical to those of their father. The obligate clonal production of males and queens from individuals of the same sex effectively results in a complete separation of the male and female gene pools. These findings show that the haplodiploid sex-determination system provides grounds for the evolution of extraordinary genetic systems and new types of sexual conflict.

  1. Application of microfluidic technology to the BIOMED-2 protocol for detection of B-cell clonality.

    NARCIS (Netherlands)

    Zamo, A.; Bertolaso, A.; Raaij, A.W. van; Mancini, F.; Scardoni, M.; Montresor, M.; Menestrina, F.; Krieken, J.H.J.M. van; Chilosi, M.; Groenen, P.J.T.A.; Scarpa, A.

    2012-01-01

    The BIOMED-2 protocol is widely used for detecting clonality in lymphoproliferative disorders. The protocol requires multiple PCR reactions, which are analyzed by either capillary electrophoresis (GeneScan analysis) or heteroduplex PAGE analysis. We tested a microfluidic chip-based electrophoresis

  2. Fatal septicemia linked to transmission of MRSA clonal complex 398 in hospital and nursing home, Denmark

    DEFF Research Database (Denmark)

    Nielsen, Rikke Thoft; Kemp, Michael; Holm, Anette

    2016-01-01

    We describe 2 fatal cases of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 septicemia in persons who had no contact with livestock. Whole-genome sequencing of the isolated MRSA strains strongly suggest that both were of animal origin and that the patients had been infected...... through 2 independent person-to-person transmission chains....

  3. Physiological integration of the clonal plant Carex arenaria and its response to soil-borne pathogens

    NARCIS (Netherlands)

    D'Hertefeldt, T.; Van der Putten, W.H.

    1998-01-01

    We test the hypothesis that the expansive horizontal clonal growth of Carex arenaria may provide a method of escape from soil-borne pathogens (fungi and nematodes) by growing away from the site of infection. Plants were grown in non-sterilized or sterilized dune sand, i.e., with or without

  4. Clonality and Micro-Diversity of a Nationwide Spreading Genotype of Mycobacterium tuberculosis in Japan

    Science.gov (United States)

    Wada, Takayuki; Iwamoto, Tomotada; Tamaru, Aki; Seto, Junji; Ahiko, Tadayuki; Yamamoto, Kaori; Hase, Atushi; Maeda, Shinji; Yamamoto, Taro

    2015-01-01

    Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as ‘M-strain’ has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB. PMID:25734518

  5. Clonal Analysis of Cells with Cellular Barcoding : When Numbers and Sizes Matter

    NARCIS (Netherlands)

    Bystrykh, Leonid V; Belderbos, Mirjam E; Turksen, Kursad

    2016-01-01

    Cellular barcoding is a recently rediscovered tool to trace the clonal output of individual cells with genetically distinct and heritable DNA sequences. Each year a few dozens of papers are published using the cellular barcoding technique. Those publications largely focus on mutually related issues,

  6. Bacteria associated with toxic clonal cultures of the dinoflagellate Ostreopsis lenticularis.

    Science.gov (United States)

    Pérez-Guzmán, Lumarie; Pérez-Matos, Ana E; Rosado, William; Tosteson, Thomas R; Govind, Nadathur S

    2008-01-01

    The marine toxic dinoflagellate Ostreopsis lenticularis has been implicated as the major vector in ciguatera seafood poisoning on the southwest coast of Puerto Rico. Studies have demonstrated that associated bacteria play a role in the ciguatoxin production and that different clonal cultures of O. lenticularis harbor different culturable bacteria. In this study, more than 125 associated bacteria from two toxic clonal cultures of O. lenticularis (no. 302 and no. 303) were analyzed utilizing polymerase chain reaction amplification of the partial small subunit ribosomal DNA (rRNA), denaturing gradient gel electrophoresis, and DNA sequencing. Approximately 50% of total bacteria identified in both cultures were a single species belonging to the Cytophaga-Flavobacter-Bacteroides complex. This bacterium was also found in six new O. lenticularis clonal cultures established 10 years after the original cultures used in this study and absent from a clonal culture of a different dinoflagellate species. The data presented here indicate a persistent and apparently specific association of this bacterium with O. lenticularis, which makes it a candidate involved in ciguatoxin production.

  7. Clonal vs leaf-height-seed (LHS) traits: which are filtered more strongly across habitats?

    Czech Academy of Sciences Publication Activity Database

    E.-Vojtkó, A.; Freitag, M.; Bricca, A.; Martello, F.; Compañ, J. M.; Küttim, M.; Kun, R.; de Bello, Francesco; Klimešová, Jitka; Götzenberger, Lars

    2017-01-01

    Roč. 52, 3-4 (2017), s. 269-281 ISSN 1211-9520 R&D Projects: GA ČR(CZ) GA16-15012S Institutional support: RVO:67985939 Keywords : environmental filtering * functional diversity * clonal traits Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.017, year: 2016

  8. Integration Site and Clonal Expansion in Human Chronic Retroviral Infection and Gene Therapy

    Science.gov (United States)

    Niederer, Heather A.; Bangham, Charles R. M.

    2014-01-01

    Retroviral vectors have been successfully used therapeutically to restore expression of genes in a range of single-gene diseases, including several primary immunodeficiency disorders. Although clinical trials have shown remarkable results, there have also been a number of severe adverse events involving malignant outgrowth of a transformed clonal population. This clonal expansion is influenced by the integration site profile of the viral integrase, the transgene expressed, and the effect of the viral promoters on the neighbouring host genome. Infection with the pathogenic human retrovirus HTLV-1 also causes clonal expansion of cells containing an integrated HTLV-1 provirus. Although the majority of HTLV-1-infected people remain asymptomatic, up to 5% develop an aggressive T cell malignancy. In this review we discuss recent findings on the role of the genomic integration site in determining the clonality and the potential for malignant transformation of cells carrying integrated HTLV-1 or gene therapy vectors, and how these results have contributed to the understanding of HTLV-1 pathogenesis and to improvements in gene therapy vector safety. PMID:25365582

  9. “Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups

    Science.gov (United States)

    Cantinelli, Thomas; Chenal-Francisque, Viviane; Diancourt, Laure; Frezal, Lise; Leclercq, Alexandre; Wirth, Thierry

    2013-01-01

    The food-borne pathogen Listeria monocytogenes is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how “epidemic clones” should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define L. monocytogenes clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the “epidemic clone” denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space. PMID:24006010

  10. Propagacion clonal in vitro y enraizamiento de estacas de algodon nativo (Gossypium barbadense L.)

    National Research Council Canada - National Science Library

    Guillermo Eduardo Delgado Paredes; Consuelo Rojas Idrogo; Carola Cuzquen Cabrejos

    2013-01-01

      En este trabajo se evalúo el efecto de reguladores de crecimiento en la propagación clonal in vitro y el efecto de diferentes soluciones nutritivas y reguladores de crecimiento en el enraizamiento de estacas de algodón...

  11. Flower production on clonal orchards at Oconto River Seed Orchard in Wisconsin

    Science.gov (United States)

    J.G. Murphy; R.G. Miller

    1977-01-01

    The Eastern Region, USDA Forest Service has been establishing and managing seed orchards to produce improved seed for the National Forests in the Lake States since 1969. This paper presents a review of the female flower production for the past 4 years in the white pine, white spruce, and black spruce clonal seed orchards.

  12. Ephemeral clonal integration in Calathea marantifolia (Marantaceae): Evidence of diminished integration over time.

    Science.gov (United States)

    Matlaga, David P; da S L Sternberg, Leonel

    2009-02-01

    A major advantage of clonal growth forms is the intergenerational transfer of resources through vascular connections (clonal integration). Connections linking ramets can be persistent or ephemeral. For species with ephemeral connections, whether the extent of clonal integration changes over time is unclear. To address this issue, we tracked water movement using an isotopic label and assessed the demographic performance of parent and offspring ramets over time in a severing experiment. Our study system was the understory herb Calathea marantifolia, which has parent ramets that produce vegetative bulbils (clonal offspring) that pass through distinct pre- and post-rooting stages. Little water was transported between parents and offspring, and the direction of movement was primarily from parent to pre-rooting offspring. Anatomical observations of inter-ramet connections showed that vascular bundles were twice as abundant in parent stems compared to inter-ramet connections. Severing inter-ramet connections reduced the growth of offspring ramets but not parents. Survival of pre-rooting offspring was reduced by 10% due to severing, but post-rooting offspring were not affected. Our results suggest that offspring ramets of C. marantifolia are weaned from their parent as they progress from pre- to post-rooting stages.

  13. The effect of herbivores on genotypic diversity in a clonal aquatic plant

    NARCIS (Netherlands)

    Hidding, B.; Meirmans, P.G.; Klaassen, M.; de Boer, T.; Ouborg, N.J.; Wagemaker, C.A.M.; Nolet, B.A.

    2014-01-01

    In clonal plants, vegetative parts may outcompete seeds in the absence of disturbance, limiting the build-up of genotypic diversity through repeated seedling recruitment (RSR). Herbivory may provide disturbance and trigger establishment of strong colonizers (seeds) at the expense of strong

  14. Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine.

    Directory of Open Access Journals (Sweden)

    Nicholas J Loman

    Full Text Available Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7 is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15 and disease (n = 4 states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST clonal complex 395 (CC395. A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design.

  15. Detectable clonal mosaicism from birth to old age and its relationship to cancer

    Science.gov (United States)

    Laurie, Cathy C.; Laurie, Cecelia A.; Rice, Kenneth; Doheny, Kimberly F.; Zelnick, Leila R.; McHugh, Caitlin P.; Ling, Hua; Hetrick, Kurt N.; Pugh, Elizabeth W.; Amos, Chris; Wei, Qingyi; Wang, Li-e; Lee, Jeffrey E.; Barnes, Kathleen C.; Hansel, Nadia N.; Mathias, Rasika; Daley, Denise; Beaty, Terri H.; Scott, Alan F.; Ruczinski, Ingo; Scharpf, Rob B.; Bierut, Laura J.; Hartz, Sarah M.; Landi, Maria Teresa; Freedman, Neal D.; Goldin, Lynn R.; Ginsburg, David; Li, Jun; Desch, Karl C.; Strom, Sara S.; Blot, William J.; Signorello, Lisa B.; Ingles, Sue A.; Chanock, Stephen J.; Berndt, Sonja I.; Le Marchand, Loic; Henderson, Brian E.; Monroe, Kristine R; Heit, John A.; de Andrade, Mariza; Armasu, Sebastian M.; Regnier, Cynthia; Lowe, William L.; Hayes, M. Geoffrey; Marazita, Mary L.; Feingold, Eleanor; Murray, Jeffrey C.; Melbye, Mads; Feenstra, Bjarke; Kang, Jae H.; Wiggs, Janey L.; Jarvik, Gail P.; McDavid, Andrew N.; Seshan, Venkatraman E.; Mirel, Daniel B.; Crenshaw, Andrew; Sharopova, Nataliya; Wise, Anastasia; Shen, Jess; Crosslin, David R.; Levine, David M.; Zheng, Xiuwen; Udren, Jenna I; Bennett, Siiri; Nelson, Sarah C.; Gogarten, Stephanie M.; Conomos, Matthew P.; Heagerty, Patrick; Manolio, Teri; Pasquale, Louis R.; Haiman, Christopher A.; Caporaso, Neil; Weir, Bruce S.

    2012-01-01

    Clonal mosaicism for large chromosomal anomalies (duplications, deletions and uniparental disomy) was detected using SNP microarray data from over 50,000 subjects recruited for genome-wide association studies. This detection method requires a relatively high frequency of cells (>5–10%) with the same abnormal karyotype (presumably of clonal origin) in the presence of normal cells. The frequency of detectable clonal mosaicism in peripheral blood is low (<0.5%) from birth until 50 years of age, after which it rises rapidly to 2–3% in the elderly. Many of the mosaic anomalies are characteristic of those found in hematological cancers and identify common deleted regions that pinpoint the locations of genes previously associated with hematological cancers. Although only 3% of subjects with detectable clonal mosaicism had any record of hematological cancer prior to DNA sampling, those without a prior diagnosis have an estimated 10-fold higher risk of a subsequent hematological cancer (95% confidence interval = 6–18). PMID:22561516

  16. Analyzing clonal fidelity of micropropagated Psidium guajava L. plants using simple sequence repeat markers

    Science.gov (United States)

    Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planti...

  17. Biased competition between Lgr5 intestinal stem cells driven by oncogenic mutation induces clonal expansion

    NARCIS (Netherlands)

    Snippert, Hugo J; Schepers, Arnout G; van Es, Johan H; Simons, Benjamin D; Clevers, Hans

    The concept of 'field cancerization' describes the clonal expansion of genetically altered, but morphologically normal cells that predisposes a tissue to cancer development. Here, we demonstrate that biased stem cell competition in the mouse small intestine can initiate the expansion of such clones.

  18. Prevalence, serotype, virulence characteristics, clonality and antibiotic susceptibility of pathogenic Yersinia enterocolitica from swine feces

    Science.gov (United States)

    Introduction: Swine are the only known animal reservoir of Yersinia enterocolitica (YE), a human pathogen. Since YE is a fecal organism of swine, the primary goal of this study was to evaluate the prevalence, serotype, virulence plasmid (pYV)-associated characteristics, clonality, and antibiotic su...

  19. Clonal structure through space and time: High stability in the holothurianStichopus chloronotus(Echinodermata).

    Science.gov (United States)

    Pirog, Agathe; Gélin, Pauline; Bédier, Alexandre; Bianchetti, Grégoire; Georget, Stéphane; Frouin, Patrick; Magalon, Hélène

    2017-09-01

    Sea cucumbers are increasingly exploited for human consumption and for their curative properties, and many wild populations are now depleted or in danger of extinction. While aquaculture is seen as an alternative to fisheries and as a mean to restore wild populations, more knowledge is needed on their reproductive strategies to render this practice efficient, notably for fissiparous holothurians, which are some of the mobile animals able of asexual reproduction by transverse fission. Little information is available on their population genetic diversity and structure. Here, the clonal structure of populations of the fissiparous sea cucumber Stichopus chloronotus has been investigated using nine microsatellite loci and a random sampling, at different spatial (intra-reef and inter-reef) and temporal (inter-season and inter-year) scales. Our findings highlight the importance of asexual reproduction in maintaining these populations, and the prevalence of the "initial seedling recruitment" strategy (ISR), leading to a high stability of clonal composition over seasons and years. It also seemed that clonal propagation was limited to the reef scale (<10 km) while reefs were connected by sexual dispersal. This is the first time that clonal structure in sea cucumbers has been studied at such a fine scale, with a specific sampling strategy. It provides key findings on the genetic diversity and structure of fissiparous sea cucumbers, which will be useful for the management of wild populations and aquaculture.

  20. Reverse Transcriptase Mechanism of Somatic Hypermutation: 60 Years of Clonal Selection Theory

    Directory of Open Access Journals (Sweden)

    Edward J. Steele

    2017-11-01

    Full Text Available The evidence for the reverse transcriptase mechanism of somatic hypermutation is substantial and multifactorial. In this 60th anniversary year of the publication of Sir MacFarlane Burnet’s Clonal Selection Theory, the evidence is briefly reviewed and updated.

  1. Clonal analysis of cells with cellular barcoding : When numbers and sizes matter

    NARCIS (Netherlands)

    Bystrykh, Leonid V.; Belderbos, Mirjam E.

    2016-01-01

    Cellular barcoding is a recently rediscovered tool to trace the clonal output of individual cells with genetically distinct and heritable DNA sequences. Each year a few dozens of papers are published using the cellular barcoding technique. Those publications largely focus on mutually related issues,

  2. Hunner-Type (Classic Interstitial Cystitis: A Distinct Inflammatory Disorder Characterized by Pancystitis, with Frequent Expansion of Clonal B-Cells and Epithelial Denudation.

    Directory of Open Access Journals (Sweden)

    Daichi Maeda

    Full Text Available Interstitial cystitis (IC is a chronic bladder disease with urinary frequency, bladder discomfort or bladder pain of unknown etiology. Based on cystoscopic findings, patients with IC are classified as either Hunner-type/classic IC (HIC, presenting with a specific Hunner lesion, or non-Hunner-type IC (NHIC, presenting with no Hunner lesion, but post-hydrodistension mucosal bleeding. Inflammatory cell infiltration, composed predominantly of lymphocytes, plasma cells and epithelial denudation, has in the past been documented as a major pathological IC finding. However, the significance of the pathological evaluation of IC, especially with regard to the difference between HIC and NHIC, has been downplayed in recent years. In this study, we performed immunohistochemical quantification of infiltrating T-lymphocytes, B-lymphocytes and plasma cells, and measured the amount of residual epithelium in urinary bladder biopsy specimens taken from patients with HIC and NHIC, and those with no IC, using image analysis software. In addition, in situ hybridization of the light chains was performed to examine clonal B-cell expansion. Lymphoplasmacytic infiltration was significantly more severe in HIC specimens than in NHIC specimens (P <0.0001. Substantial lymphoplasmacytic inflammation (≥200 cells/mm2 was observed in 93% of HIC specimens, whereas only 8% of NHIC specimens were inflamed. Plasmacytic infiltration was more prominent in HIC specimens compared with NHIC and non-IC cystitis specimens (P <0.005. Furthermore, expansion of light-chain-restricted B-cells was observed in 31% of cases of HIC. The amount of residual epithelium was decreased in HIC specimens compared with NHIC specimens and non-IC cystitis specimens (P <0.0001. These results suggest that NHIC and HIC are distinct pathological entities, with the latter characterized by pancystitis, frequent clonal B-cell expansion and epithelial denudation. An abnormality in the B-cell population may be

  3. OCT Expanded Clinical Data Analysis

    Science.gov (United States)

    Van Baalen, Mary; Tafreshi, Ali; Patel, Nimesh; Young, Millennia; Mason, Sara; Otto, Christian; Samuels, Brian; Koslovsky, Matthew; Schaefer, Caroline; Taiym, Wafa; hide

    2017-01-01

    Vision changes identified in long duration space fliers has led to a more comprehensive clinical monitoring protocol. Optical Coherence Tomography (OCT) was recently implemented on board the International Space Station in 2013. NASA is collaborating with Heidelberg Engineering to expand our current OCT data analysis capability by implementing a volumetric approach. Volumetric maps will be created by combining the circle scan, the disc block scan, and the radial scan. This assessment may provide additional information about the optic nerve and further characterize changes related microgravity exposure. We will discuss challenges with collection and analysis of OCT data, present the results of this reanalysis and outline the potential benefits and limitations of the additional data.

  4. Preventive Ethics Through Expanding Education.

    Science.gov (United States)

    Ho, Anita; MacDonald, Lisa Mei-Hwa; Unger, David

    2016-03-01

    Healthcare institutions have been making increasing efforts to standardize consultation methodology and to accredit both bioethics training programs and the consultants accordingly. The focus has traditionally been on the ethics consultation as the relevant unit of ethics intervention. Outcome measures are studied in relation to consultations, and the hidden assumption is that consultations are the preferred or best way to address day-to-day ethical dilemmas. Reflecting on the data from an internal quality improvement survey and the literature, we argue that having general ethics education as a key function of ethics services may be more important in meeting the contemporaneous needs of acute care settings. An expanded and varied ethics education, with attention to the time constraints of healthcare workers' schedules, was a key recommendation brought forward by survey respondents. Promoting ethical reflection and creating a culture of ethics may serve to prevent ethical dilemmas or mitigate their effects.

  5. Expanding Human Cognition and Communication

    Energy Technology Data Exchange (ETDEWEB)

    Spohrer, Jim [IBM, North Castle, NY (United States); Pierce, Brian M. [Raytheon Co., Waltham, MA (United States); Murray, Cherry A. [Lucent Technologies, Murray Hill, NJ (United States); Golledge, Reginald G. [Univ. of California, Santa Barbara, CA (United States); Horn, Robert E. [Stanford Univ., CA (United States); Turkle, Sherry [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Yonas, Gerold [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Glicken Turnley, Jessica [Galisteo Consulting Group, Inc., Albuquerque, NM (United States); Pollack, Jordan [Brandeis Univ., Waltham, MA (United States); Burger, Rudy [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Robinett, Warren; Wilson, Larry Todd [Inst. of Electrical and Electronics Engineers (IEEE), Piscataway, NJ (United States); Bainbridge, W. S.; Canton, J.; Kuekes, P.; Loomis, J.; Penz, P.

    2013-01-01

    To be able to chart the most profitable future directions for societal transformation and corresponding scientific research, five multidisciplinary themes focused on major goals have been identified to fulfill the overall motivating vision of convergence described in the previous pages. The first, “Expanding Human Cognition and Communication,” is devoted to technological breakthroughs that have the potential to enhance individuals’ mental and interaction abilities. Throughout the twentieth century, a number of purely psychological techniques were offered for strengthening human character and personality, but evaluation research has generally failed to confirm the alleged benefits of these methods (Druckman and Bjork 1992; 1994). Today, there is good reason to believe that a combination of methods, drawing upon varied branches of converging science and technology, would be more effective than attempts that rely upon mental training alone.

  6. Cytokines can reduce clonal, CD34-positive cells in acute myeloid leukemia in vitro.

    Science.gov (United States)

    Braun, S; Gerhartz, H H; Schmetzer, H M

    2000-07-01

    We studied the influence of cytokine mixes on the survival of acute myeloid leukemia (AML) bone-marrow (BM) cells in a 14-day culture assay in vitro. Southern-blot analysis using a panel of different probes in combination with densitometry and flow cytometry were used to detect and compare the amount of clonal or CD34-positive BM cells before and after the culturing procedure. A significant reduction of CD34-positive cells after incubation with a cytokine mix [interleukin (IL)-1beta, IL-3, IL-6, stem cell factor (SCF), erythropoietin (EP) with granulocyte macrophage/colony-stimulating factor (GM-CSF, Cytok1) could be achieved in all 16 cases with a CD34-positive blast phenotype studied at diagnosis (PVitality of BM cells was not influenced by 14-day cytokine treatment; however, the total cell count could be increased by Cytok1 and Cytok2 by 55-174%, but not by the control medium. Our data show that: (1) clonal cell populations can be regularly detected at diagnosis, during complete remission, and at relapse; (2) CD34-positive cells in AML can be demonstrated to be clonal, gene-rearranged cells; (3) incubation of AML BM-cells with Cytokl leads to a reduction of the CD34-positive, clonal cell load in all cases at diagnosis and in 78% of the cases in complete remission of AML, but in only 25% of the cases at relapse; (4) in all healthy BM samples, proportions of 'healthy' CD34-positive cells were increased. Moreover, absolute cell counts were increased by cytokine incubation of cells obtained at diagnosis, relapse, or complete remission of AML and from healthy donors indicating a selective stimulation of healthy, but not of leukemic CD34-positive cells; (5) cytokine cocktails containing GM-CSF are more efficient in reducing leukemic cells than cocktails without GM-CSF; and (6) in vitro reactivity of clonal or CD34-positive BM cells against Cytokl has clinical relevance. We conclude, that Southern-blot analysis and flow cytometry are suitable methods to detect and

  7. Expanding the Trilinos developer community.

    Energy Technology Data Exchange (ETDEWEB)

    Heroux, Michael Allen

    2010-10-01

    The Trilinos Project started approximately nine years ago as a small effort to enable research, development and ongoing support of small, related solver software efforts. The 'Tri' in Trilinos was intended to indicate the eventual three packages we planned to develop. In 2007 the project expanded its scope to include any package that was an enabling technology for technical computing. Presently the Trilinos repository contains over 55 packages covering a broad spectrum of reusable tools for constructing full-featured scalable scientific and engineering applications. Trilinos usage is now worldwide, and many applications have an explicit dependence on Trilinos for essential capabilities. Users come from other US laboratories, universities, industry and international research groups. Awareness and use of Trilinos is growing rapidly outside of Sandia. Members of the external research community are becoming more familiar with Trilinos, its design and collaborative nature. As a result, the Trilinos project is receiving an increasing number of requests from external community members who want to contribute to Trilinos as developers. To-date we have worked with external developers in an ad hoc fashion. Going forward, we want to develop a set of policies, procedures, tools and infrastructure to simplify interactions with external developers. As we go forward with multi-laboratory efforts such as CASL and X-Stack, and international projects such as IESP, we will need a more streamlined and explicit process for making external developers 'first-class citizens' in the Trilinos development community. This document is intended to frame the discussion for expanding the Trilinos community to all strategically important external members, while at the same time preserving Sandia's primary leadership role in the project.

  8. Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh.

    Science.gov (United States)

    Chattaway, Marie Anne; Day, Michaela; Mtwale, Julia; White, Emma; Rogers, James; Day, Martin; Powell, David; Ahmad, Marwa; Harris, Ross; Talukder, Kaisar Ali; Wain, John; Jenkins, Claire; Cravioto, Alejandro

    2017-10-01

    This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative virulence genes and/or antimicrobial resistance. The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007-2011 in the rural setting of Mirzapur, Bangladesh (Kotloff KL, Blackwelder WC, Nasrin D, Nataro JP, Farag TH et al.Clin Infect Dis 2012;55:S232-S245). These data were then analysed in the context of previously determined serotypes and clonal complexes defined by multi-locus sequence typing. Overall there was no association between the presence of virulence or antimicrobial resistance genes in isolates of EAEC from cases versus controls. However, when stratified by clonal complex (CC) one CC associated with cases harboured more virulence factors (CC40) and one CC harboured more resistance genes (CC38) than the average. There was no direct link between the virulence gene content and antibiotic resistance. Strains within a single CC had variable virulence and resistance gene content indicating independent and multiple gene acquisitions over time. In Bangladesh, there are multiple clonal complexes of EAEC harbouring a variety of virulence and resistance genes. The emergence of two of the most successful clones appeared to be linked to either increased virulence (CC40) or antimicrobial resistance (CC38), but increased resistance and virulence were not found in the same clonal complexes.

  9. Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

    Science.gov (United States)

    Tchesnokova, Veronika; Avagyan, Hovhannes; Rechkina, Elena; Chan, Diana; Muradova, Mariya; Haile, Helen Ghirmai; Radey, Matthew; Weissman, Scott; Riddell, Kim; Scholes, Delia; Johnson, James R; Sokurenko, Evgeni V

    2017-01-01

    Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients' urine within 25-35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care.

  10. Demonstration of the cell clonality in canine hematopoietic tumors by X-chromosome inactivation pattern analysis.

    Science.gov (United States)

    Mochizuki, H; Goto-Koshino, Y; Takahashi, M; Fujino, Y; Ohno, K; Tsujimoto, H

    2015-01-01

    X-chromosome inactivation pattern (XCIP) analysis has been widely used to assess cell clonality in various types of human neoplasms. In this study, a polymerase chain reaction-based canine XCIP analysis of the androgen receptor (AR) gene was applied for the assessment of cell clonality in canine hematopoietic tumors. This XCIP analysis is based on the polymorphic CAG repeats in the AR gene and the difference of methylation status between active and inactive X chromosomes. We first examined the polymorphisms of 2 CAG tandem repeats in the AR gene in 52 male and 150 female dogs of various breeds. The 2 polymorphic CAG repeats contained 9 to 12 and 10 to 14 CAGs in the first and second CAG repeats, respectively. Of the 150 female dogs, 74 (49.3%) were heterozygous for the first and/or second polymorphic CAG tandem repeats, indicating the utility of XCIP analysis in these dogs. Canine XCIP analysis was then applied to clinical samples from female dogs with canine high-grade lymphoma, chronic myelogenous leukemia, acute myelogenous leukemia, and benign lymph node hyperplasia. Of 10 lymphoma cell samples, 9 (90%) showed skewed XCIPs, indicating their clonal origins, whereas all the nonneoplastic lymph node samples showed balanced XCIPs. Moreover, bone marrow specimen from a dog with acute myelogenous leukemia and peripheral leukocyte specimens from 2 dogs with chronic myelogenous leukemia showed skewed XCIPs. XCIP analysis was successfully employed to demonstrate the cell clonality of canine hematopoietic tumors in this study and will be applicable to evaluate the clonality in various proliferative disorders in dogs. © The Author(s) 2014.

  11. Floral variation and environmental heterogeneity in a tristylous clonal aquatic of the Pantanal wetlands of Brazil

    Science.gov (United States)

    Leme da Cunha, Nicolay; Fischer, Erich; Lorenz-Lemke, Aline P.; Barrett, Spencer C. H.

    2014-01-01

    Background and Aims The balance between stochastic forces and frequency-dependent mating largely governs style morph frequencies in heterostylous populations. In clonal species, deviations from equal morph ratios often result from founder events and unfavourable conditions for sexual reproduction. The aim of this study was to investigate whether different flooding regimes, because of their influence on sexual vs. clonal reproduction, are associated with regional variation in morph frequencies and floral trait differentiation in populations of the clonal, tristylous, aquatic Eichhornia azurea (Pontederiaceae) in the Pantanal wetlands of Brazil. Methods Style morph frequencies were sampled from 73 populations distributed across four flooding regimes differing in depth and duration. Measurements of flower size, sex-organ dimension, pollen size and pollen production were made in selected populations, and pollinator assemblages and their functional traits were recorded. Key Results Most populations of E. azurea were tristylous (78 %), but the majority exhibited uneven morph ratios. The frequency of the mid-styled morph was significantly lower than that of the long- and short-styled morphs. Morph evenness was positively associated with population size but not with flooding regime. There were significant phenotypic differences among flooding regimes for all floral traits, including populations with reduced flower size, sex-organ length and smaller pollen. Pollinator assemblages varied with flood duration. Conclusions The similar morph structure and evenness of populations, regardless of flooding regime, suggest that sexual reproduction and clonal dispersal are sufficiently common to prevent the signature of founder events from dominating in a region. However, the pervasive occurrence of biased morph ratios in most populations suggests that many are in a non-equilibrium state. The reduced frequency of the mid-styled morph in trimorphic and dimorphic populations may be

  12. Plasma astrophysics

    CERN Document Server

    Kaplan, S A; ter Haar, D

    2013-01-01

    Plasma Astrophysics is a translation from the Russian language; the topics discussed are based on lectures given by V.N. Tsytovich at several universities. The book describes the physics of the various phenomena and their mathematical formulation connected with plasma astrophysics. This book also explains the theory of the interaction of fast particles plasma, their radiation activities, as well as the plasma behavior when exposed to a very strong magnetic field. The text describes the nature of collective plasma processes and of plasma turbulence. One author explains the method of elementary

  13. Plasma waves

    CERN Document Server

    Swanson, DG

    1989-01-01

    Plasma Waves discusses the basic development and equations for the many aspects of plasma waves. The book is organized into two major parts, examining both linear and nonlinear plasma waves in the eight chapters it encompasses. After briefly discussing the properties and applications of plasma wave, the book goes on examining the wave types in a cold, magnetized plasma and the general forms of the dispersion relation that characterize the waves and label the various types of solutions. Chapters 3 and 4 analyze the acoustic phenomena through the fluid model of plasma and the kinetic effects. Th

  14. Interpenetration and stagnation in colliding laser plasmas

    Science.gov (United States)

    Al-Shboul, K. F.; Harilal, S. S.; Hassan, S. M.; Hassanein, A.; Costello, J. T.; Yabuuchi, T.; Tanaka, K. A.; Hirooka, Y.

    2014-01-01

    We have investigated plasma stagnation and interaction effects in colliding laser-produced plasmas. For generating colliding plasmas, two split laser beams were line-focused onto a hemi-circular target and the seed plasmas so produced were allowed to expand in mutually orthogonal directions. This experimental setup forced the expanding seed plasmas to come to a focus at the center of the chamber. The interpenetration and stagnation of plasmas of candidate fusion wall materials, viz., carbon and tungsten, and other materials, viz., aluminum, and molybdenum were investigated in this study. Fast-gated imaging, Faraday cup ion analysis, and optical emission spectroscopy were used for diagnosing seed and colliding plasma plumes. Our results show that high-Z target (W, Mo) plasma ions interpenetrate each other, while low-Z (C, Al) plasmas stagnate at the collision plane. For carbon seed plasmas, an intense stagnation was observed resulting in longer plasma lifetime; in addition, the stagnation layer was found to be rich with C2 dimers.

  15. Interpenetration and stagnation in colliding laser plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Al-Shboul, K. F. [Center for Materials Under eXtreme Environment, School of Nuclear Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Department of Nuclear Engineering, Jordan University of Science and Technology, Irbid 22110 (Jordan); Harilal, S. S., E-mail: hari@purdue.edu; Hassan, S. M.; Hassanein, A. [Center for Materials Under eXtreme Environment, School of Nuclear Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Costello, J. T. [School of Physical Sciences and NCPST, Dublin City University, Dublin 9 (Ireland); Yabuuchi, T.; Tanaka, K. A. [Graduate School of Engineering, Osaka University, Yamada-oka 2-1, Suita, Osaka 5650871 (Japan); Hirooka, Y. [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu (Japan)

    2014-01-15

    We have investigated plasma stagnation and interaction effects in colliding laser-produced plasmas. For generating colliding plasmas, two split laser beams were line-focused onto a hemi-circular target and the seed plasmas so produced were allowed to expand in mutually orthogonal directions. This experimental setup forced the expanding seed plasmas to come to a focus at the center of the chamber. The interpenetration and stagnation of plasmas of candidate fusion wall materials, viz., carbon and tungsten, and other materials, viz., aluminum, and molybdenum were investigated in this study. Fast-gated imaging, Faraday cup ion analysis, and optical emission spectroscopy were used for diagnosing seed and colliding plasma plumes. Our results show that high-Z target (W, Mo) plasma ions interpenetrate each other, while low-Z (C, Al) plasmas stagnate at the collision plane. For carbon seed plasmas, an intense stagnation was observed resulting in longer plasma lifetime; in addition, the stagnation layer was found to be rich with C{sub 2} dimers.

  16. Microbial Biofilms and Breast Tissue Expanders

    Directory of Open Access Journals (Sweden)

    Melissa J. Karau

    2013-01-01

    Full Text Available We previously developed and validated a vortexing-sonication technique for detection of biofilm bacteria on the surface of explanted prosthetic joints. Herein, we evaluated this technique for diagnosis of infected breast tissue expanders and used it to assess colonization of breast tissue expanders. From April 2008 to December 2011, we studied 328 breast tissue expanders at Mayo Clinic, Rochester, MN, USA. Of seven clinically infected breast tissue expanders, six (85.7% had positive cultures, one of which grew Propionibacterium species. Fifty-two of 321 breast tissue expanders (16.2%, 95% CI, 12.3–20.7% without clinical evidence of infection also had positive cultures, 45 growing Propionibacterium species and ten coagulase-negative staphylococci. While vortexing-sonication can detect clinically infected breast tissue expanders, 16 percent of breast tissue expanders appear to be asymptomatically colonized with normal skin flora, most commonly, Propionibacterium species.

  17. Discovery of Uniformly Expanding Universe

    Directory of Open Access Journals (Sweden)

    Cahill R. T.

    2012-01-01

    Full Text Available Saul Perlmutter and the Brian Schmidt – Adam Riess teams reported that their Friedmann-model GR-based analysis of their supernovae magnitude-redshift data re- vealed a new phenomenon of “dark energy” which, it is claimed, forms 73% of the energy / matter density of the present-epoch universe, and which is linked to the further claim of an accelerating expansion of the universe. In 2011 Perlmutter, Schmidt and Riess received the Nobel Prize in Physics “for the discovery of the accelerating ex- pansion of the Universe through observations of distant supernovae”. Here it is shown that (i a generic model-independent analysis of this data reveals a uniformly expanding universe, (ii their analysis actually used Newtonian gravity, and finally (iii the data, as well as the CMB fluctuation data, does not require “dark energy” nor “dark matter”, but instead reveals the phenomenon of a dynamical space, which is absent from the Friedmann model.

  18. Expanding cosmic horizons of life

    Science.gov (United States)

    Wickramasinghe, Nalin C.; Narlikar, J. V.; Wickramasinghe, J. T.; Wainwright, Milton

    2003-02-01

    The conceptual boundaries of life are rapidly expanding far beyond the confines of our planet to encompass an ever-widening region of the universe. Complex organic molecules in interstellar dust and comets appear most plausibly to be biologically derived, or at least closely related spectroscopically and structurally to such material. A de novo origin of life from non-living material is reckoned to have so minuscule a probability that its occurrence once in the universe can be considered miracle enough. The widespread distribution of similar material (e.g with the characteristics of the diffuse infrared bands and 2175 absorption features) throughout the galaxy and in external galaxies adds weight to the theory of panspermia, where it is supposed that the components of life at a generic level are readily transferred from one place to another. Spectroscopic evidence consistent with life extends to redshifts z=0.5, and from elemental abundance studies alone (e.g, of C, O and metals) in distant galaxies the possibility of cosmic life extends to redshifts as high as z=3.

  19. Clonal Structure and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and Genetic Markers.

    Science.gov (United States)

    Ilczyszyn, Weronika M; Sabat, Artur J; Akkerboom, Viktoria; Szkarlat, Anna; Klepacka, Joanna; Sowa-Sierant, Iwona; Wasik, Barbara; Kosecka-Strojek, Maja; Buda, Aneta; Miedzobrodzki, Jacek; Friedrich, Alexander W

    2016-01-01

    The aim of current study was to examine clonal structure and genetic profile of invasive Staphylococcus aureus isolates recovered from infants and children treated at the Jagiellonian University Children's Hospital of Krakow, Poland. The 107 invasive S. aureus isolates, collected between February 2012 and August 2014, were analysed retrospectively. Antimicrobial susceptibility testing, spa typing and DNA microarray analysis were performed to determine clonal distribution, diversity and gene content in regard to patients characteristics. In total, 107 isolates were recovered from 88 patients with clinical symptoms of invasive bacterial infection. The final set of 92 non-duplicate samples included 38 MRSA isolates. Additionally, a set of 54 S. aureus isolates collected during epidemiological screening was genotyped and analysed. There were 72 healthcare-associated (HCA) and 20 community-onset (CO) infection events caused by 33 and 5 MRSA isolates, respectively. The majority of isolates were affiliated with the major European clonal complexes CC5 (t003, spa-CC 002), CC45 (spa-CC 015), CC7 or CC15 (t084, t091, spa-CC 084). Two epidemic clones (CC5-MRSA-II or CC45-MRSA-IV) dominated among MRSA isolates, while MSSA population contained 15 different CCs. The epidemiological screening isolates belonged to similar genetic lineages as those collected from invasive infection cases. The HCA infection events, spa types t003, t2642 or CC5 were significantly associated with infections occurring in neonates and children under 5 years of age. Moreover, carriage of several genetic markers, including erm(A), sea (N315), egc-cluster, chp was significantly higher in isolates obtained from children in this age group. The spa types t091 and t008 were underrepresented among patients aged 5 years or younger, whereas spa type t008, CC8 and presence of splE was associated with infection in children aged 10 years or older. The HCA-MRSA strains were most frequently found in children under 5

  20. Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.

    Directory of Open Access Journals (Sweden)

    Robert Kridel

    2016-12-01

    Full Text Available Follicular lymphoma (FL is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease. We contend that detailed knowledge of the expansion patterns of specific cell populations plus their associated mutations would provide insight into therapeutic strategies and disease biology over the time course of FL clinical histories.Using a combination of whole genome sequencing, targeted deep sequencing, and digital droplet PCR on matched diagnostic and relapse specimens, we deciphered the constituent clonal populations in 15 transformation cases and 6 progression cases, and measured the change in clonal population abundance over time. We observed widely divergent patterns of clonal dynamics in transformed cases relative to progressed cases. Transformation specimens were generally composed of clones that were rare or absent in diagnostic specimens, consistent with dramatic clonal expansions that came to dominate the transformation specimens. This pattern was independent of time to transformation and treatment modality. By contrast, early progression specimens were composed of clones that were already present in the diagnostic specimens and exhibited only moderate clonal dynamics, even in the presence of immunochemotherapy. Analysis of somatic mutations impacting 94 genes was undertaken in an extension cohort consisting of 395 samples from 277 patients in order to decipher disrupted biology in the two clinical end points. We found 12 genes that were more commonly mutated in transformed samples than in the preceding FL tumors, including TP53, B2M, CCND3, GNA

  1. Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models.

    Science.gov (United States)

    Sepúlveda, Nuno; Paulino, Carlos Daniel; Carneiro, Jorge

    2010-02-28

    The answer to many fundamental questions in Immunology requires the quantitative characterization of the T-cell repertoire, namely T cell receptor (TCR) diversity and clonal size distribution. An increasing number of repertoire studies are based on sequencing of the TCR variable regions in T-cell samples from which one tries to estimate the diversity of the original T-cell populations. Hitherto, estimation of TCR diversity was tackled either by a "standard" method that assumes a homogeneous clonal size distribution, or by non-parametric methods, such as the abundance-coverage and incidence-coverage estimators. However, both methods show caveats. On the one hand, the samples exhibit clonal size distributions with heavy right tails, a feature that is incompatible with the assumption of an equal frequency of every TCR sequence in the repertoire. Thus, this "standard" method produces inaccurate estimates. On the other hand, non-parametric estimators are robust in a wide range of situations, but per se provide no information about the clonal size distribution. This paper redeploys Poisson abundance models from Ecology to overcome the limitations of the above inferential procedures. These models assume that each TCR variant is sampled according to a Poisson distribution with a specific sampling rate, itself varying according to some Exponential, Gamma, or Lognormal distribution, or still an appropriate mixture of Exponential distributions. With these models, one can estimate the clonal size distribution in addition to TCR diversity of the repertoire. A procedure is suggested to evaluate robustness of diversity estimates with respect to the most abundant sampled TCR sequences. For illustrative purposes, previously published data on mice with limited TCR diversity are analyzed. Two of the presented models are more consistent with the data and give the most robust TCR diversity estimates. They suggest that clonal sizes follow either a Lognormal or an appropriate mixture of

  2. Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances of each individual bacteria.

    Science.gov (United States)

    Loyola, David E; Navarro, Cristell; Uribe, Paulina; García, Katherine; Mella, Claudia; Díaz, Diego; Valdes, Natalia; Martínez-Urtaza, Jaime; Espejo, Romilio T

    2015-03-13

    New strains of Vibrio parahaemolyticus that cause diarrhea in humans by seafood ingestion periodically emerge through continuous evolution in the ocean. Influx and expansion in the Southern Chilean ocean of a highly clonal V. parahaemolyticus (serotype O3:K6) population from South East Asia caused one of the largest seafood-related diarrhea outbreaks in the world. Here, genomics analyses of isolates from this rapidly expanding clonal population offered an opportunity to observe the molecular evolutionary changes often obscured in more diverse populations. Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from different years) was performed. Differences of 1366 to 217,729 bp genome length and 13 to 164 bp single nucleotide variants (SNVs) were found. Most genomic differences corresponded to the presence of regions unique to only one or two isolates, and were probably acquired by horizontal gene transfer (HGT). Some DNA gain was chromosomal but most was in plasmids. One isolate had a large region (8,644 bp) missing, which was probably caused by excision of a prophage. Genome innovation by the presence of unique DNA, attributable to HGT from related bacteria, varied greatly among the isolates, with values of 1,366 (ten times the number of highest number of SNVs) to 217,729 (a thousand times more than the number of highest number of SNVs). The evolutionary forces (SNVs, HGT) acting on each isolate of the same population were found to differ to an extent that probably depended on the ecological scenario and life circumstances of each bacterium.

  3. Expanding the knowledge translation metaphor.

    Science.gov (United States)

    Engebretsen, Eivind; Sandset, Tony Joakim; Ødemark, John

    2017-03-13

    Knowledge translation (KT) is a buzzword in modern medical science. However, there has been little theoretical reflection on translation as a process of meaning production in KT. In this paper, we argue that KT will benefit from the incorporation of a more theoretical notion of translation as an entangled material, textual and cultural process. We discuss and challenge fundamental assumptions in KT, drawing on theories of translation from the human sciences. We show that the current construal of KT as separate from and secondary to the original scientific message is close to the now deeply compromised literary view of translation as the simple act of copying the original. Inspired by recent theories of translation, we claim that KT can be more adequately understood in terms of a 'double supplement' - on the one hand, KT offers new approaches to the communication of scientific knowledge to different groups in the healthcare system with the aim of supplementing a lack of knowledge among clinicians (and patients). On the other, it demonstrates that a textual and cultural supplement, namely a concern with target audiences (clinicians and patients), is inevitable in the creation of an 'autonomous' science. Hence, the division between science and its translation is unproductive and impossible to maintain. We discuss some possible implications of our suggested shift in concept by drawing on pharmaceutical interventions for the prevention of HIV as a case. We argue that such interventions are based on a supplementary and paradoxical relation to the target audiences, both presupposing and denying their existence. More sophisticated theories of translation can lay the foundation for an expanded model of KT that incorporates a more adequate and reflective description of the interdependency of scientific, cultural, textual and material practices.

  4. Improving and expanding NGO programmes.

    Science.gov (United States)

    Mukhopadhyay, A

    1993-06-01

    India has massive problems and is in need of improving and expanding non governmental organization (NGO) programs by broadening the scope of NGO activities, identifying successful NGO activities, and by moving closer to the community to participate in their activities. The problems and experience in the last few decades indicate that with expansion bureaucratization takes place. The institution begins to depend on donors and follows donor-driven agendas. As more money is given by the government, many more so called GONGO or Government-NGO projects materialize. Another problem is that the government almost always approaches the NGOs for the implementation of a project, and there is complete lack of cooperation at the planning stage. The government is considering a loan from the World Bank and UNICEF to launch a mother and child health program, but there has not been any discussion with the dozens of people who have worked on issues concerning mother and child health issues for many years. There is a need to be more demanding of the government about the various programs that are implemented for the government. Very few NGO health and family welfare projects are run by ordinary nurses or ordinary Ayurvedic doctors under ordinary conditions. Since successful NGO work has to be extended to other parts of the country, they will have to be run by ordinary people with very ordinary resources. Over the years, the NGO community has become preoccupied with its own agenda. Today, despite very sophisticated equipment and infrastructure, they are not able to reach the 60,000-70,000 workers and employees. Some of the ideas with respect to the strengthens and weaknesses of community participation have to be shared. NGOs should include all the existing non governmental organizations throughout the country, and have a dialogue with other nongovernmental bodies such as trade unions. The challenge is to adjust the current agenda, prevailing style, and present way of operating and move

  5. Expanding the Interaction Equivalency Theorem

    Directory of Open Access Journals (Sweden)

    Brenda Cecilia Padilla Rodriguez

    2015-06-01

    Full Text Available Although interaction is recognised as a key element for learning, its incorporation in online courses can be challenging. The interaction equivalency theorem provides guidelines: Meaningful learning can be supported as long as one of three types of interactions (learner-content, learner-teacher and learner-learner is present at a high level. This study sought to apply this theorem to the corporate sector, and to expand it to include other indicators of course effectiveness: satisfaction, knowledge transfer, business results and return on expectations. A large Mexican organisation participated in this research, with 146 learners, 30 teachers and 3 academic assistants. Three versions of an online course were designed, each emphasising a different type of interaction. Data were collected through surveys, exams, observations, activity logs, think aloud protocols and sales records. All course versions yielded high levels of effectiveness, in terms of satisfaction, learning and return on expectations. Yet, course design did not dictate the types of interactions in which students engaged within the courses. Findings suggest that the interaction equivalency theorem can be reformulated as follows: In corporate settings, an online course can be effective in terms of satisfaction, learning, knowledge transfer, business results and return on expectations, as long as (a at least one of three types of interaction (learner-content, learner-teacher or learner-learner features prominently in the design of the course, and (b course delivery is consistent with the chosen type of interaction. Focusing on only one type of interaction carries a high risk of confusion, disengagement or missed learning opportunities, which can be managed by incorporating other forms of interactions.

  6. Parameter Identification of PMSM Using Immune Clonal Selection Differential Evolution Algorithm

    Directory of Open Access Journals (Sweden)

    Guohan Lin

    2014-01-01

    Full Text Available Permanent magnet synchronous motor (PMSM models with accurate parameters are crucial to high performance PMSM control system designs. As the estimation of PMSM parameters is very difficult due to the nonlinear model complexity, a novel immune clonal differential evolution algorithm (ICDEA is proposed to identify the electrical parameters of nonsalient pole PMSM. Clonal selection and receptor editing mechanism are introduced to ICDEA to increase the diversity of the population and improve searching capability. The effectiveness of the proposed identification method is verified by both simulation and experiment. The results show that the proposed algorithm has good convergence in simultaneously estimating stator resistance, dq-axis inductances, and rotor flux linkage. In addition, the convergence speed of ICDEA is compared with other differential evolution (DE algorithms, which verifies that the ICDEA has better performances in global searching.

  7. Escherichia coli clonal group A causing bacteraemia of urinary tract origin

    DEFF Research Database (Denmark)

    Skjøt-Rasmussen, L; Olsen, S S; Jakobsen, L

    2013-01-01

    Clin Microbiol Infect ABSTRACT: Escherichia coli clonal group A (CgA) causes disease in humans. This is the first study investigating the prevalence of CgA among E. coli from non-urine, extraintestinal infections in a northern European country. E. coli blood (n = 196) and paired urine (n = 195...... practice and a CgA isolate from a community-dwelling human reported previously, was found, suggesting a community origin of CgA. The finding of CgA strains in 15% of the E. coli bloodstream infections with a urinary tract origin in Denmark suggests that CgA constitutes an important clonal lineage among...... extraintestinal pathogenic E. coli. A reservoir of this pathogenic E. coli group in the community causing not only UTI but also more severe infections such as bacteraemia has implications for public health....

  8. Assessing T cell clonal size distribution: a non-parametric approach.

    Science.gov (United States)

    Bolkhovskaya, Olesya V; Zorin, Daniil Yu; Ivanchenko, Mikhail V

    2014-01-01

    Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.

  9. Assessing T cell clonal size distribution: a non-parametric approach.

    Directory of Open Access Journals (Sweden)

    Olesya V Bolkhovskaya

    Full Text Available Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.

  10. Fusion of remote sensing images based on pyramid decomposition with Baldwinian Clonal Selection Optimization

    Science.gov (United States)

    Jin, Haiyan; Xing, Bei; Wang, Lei; Wang, Yanyan

    2015-11-01

    In this paper, we put forward a novel fusion method for remote sensing images based on the contrast pyramid (CP) using the Baldwinian Clonal Selection Algorithm (BCSA), referred to as CPBCSA. Compared with classical methods based on the transform domain, the method proposed in this paper adopts an improved heuristic evolutionary algorithm, wherein the clonal selection algorithm includes Baldwinian learning. In the process of image fusion, BCSA automatically adjusts the fusion coefficients of different sub-bands decomposed by CP according to the value of the fitness function. BCSA also adaptively controls the optimal search direction of the coefficients and accelerates the convergence rate of the algorithm. Finally, the fusion images are obtained via weighted integration of the optimal fusion coefficients and CP reconstruction. Our experiments show that the proposed method outperforms existing methods in terms of both visual effect and objective evaluation criteria, and the fused images are more suitable for human visual or machine perception.

  11. Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh

    DEFF Research Database (Denmark)

    Chattaway, Marie Anne; Day, Michaela; Mtwale, Julia

    2017-01-01

    Purpose. This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative...... virulence genes and/or antimicrobial resistance.Methodology. The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007-2011 in the rural setting...... of Mirzapur, Bangladesh (Kotloff KL, Blackwelder WC, Nasrin D, Nataro JP, Farag TH et al. Clin Infect Dis 2012; 55: S232-S245). These data were then analysed in the context of previously determined serotypes and clonal complexes defined by multi-locus sequence typing.Results. Overall there was no association...

  12. Staphylococcus aureus clonal dynamics and virulence factors in children with atopic dermatitis

    DEFF Research Database (Denmark)

    Lomholt, Hans Bredsted; Andersen, KE; Kilian, Mogens

    2005-01-01

    A prospective cohort study was undertaken to determine the clonal dynamics of Staphylococcus aureus colonization and infection during 1 y in children with atopic dermatitis, and to correlate specific clones, accessory gene regulator (agr) groups, and production of virulence factors with eczema...... activity. Eleven children were examined every 6 wk with swaps taken from active eczema, anterior nose, axillae and perineum, and scoring of eczema activity by severity scoring of atopic dermatitis (SCORAD). Individual S. aureus clonal types were identified and examined for production of superantigens...... SCORAD value. In 11 of 12 cases with two different clones co-colonizing a child the clones belonged to the same agr group. In conclusion, this limited group of children with atopic dermatitis showed highly variable colonization patterns of S. aureus, and communication between strains by use of agr...

  13. Solving Multi Objective ORPD Problem Using AIS Based Clonal Selection Algorithm with UPFC

    Directory of Open Access Journals (Sweden)

    B. Srinivasa Rao

    2017-03-01

    Full Text Available In this paper, a solution for the multi objective optimal reactive power dispatch problem by using an artificial immune system (AIS based clonal selection algorithm was presented. The proposed AIS based clonal selection algorithm uses cloning of antibodies and followed by hyper maturation to minimize the voltage stability index (L-index, voltage deviations at all load buses and the transmission real power losses by incorporating the multi type FACTS device namely the UPFC. The proposed algorithm also uses concepts of non dominated sorting and crowding distance comparison procedures to solve the multi objective optimization problem. Finally, a fuzzy decision maker strategy is applied to find the best compromise solution. The algorithm was implemented and tested on two standard IEEE 30-bus and 57-bus test systems with UPFC. The proposed results are compared with and without placing the UPFC by considering two objectives for optimization.

  14. Antipredator behavior QTL: differences in rainbow trout clonal lines derived from wild and hatchery populations.

    Science.gov (United States)

    Christensen, Kris A; Brunelli, Joseph P; Wheeler, Paul A; Thorgaard, Gary H

    2014-09-01

    Variation in antipredator behavior may partially explain the survival differences seen between wild and hatchery trout and salmon. Antipredator behavior is thought to change during the domestication process, along with other traits. Investigations of antipredator behavior could benefit conservation efforts and supplementation programs. Our goal was to characterize the antipredator behavior in clonal rainbow trout lines derived from either wild or hatchery populations and identify genetic loci associated with variation between lines. We identified several behaviors that varied between clonal lines and QTL for several behavioral and size traits. Characterizing genetic variation underlying these behaviors may prove valuable in future conservation efforts by enabling monitoring of allele frequencies of loci affecting predation in wild populations.

  15. Demographic variability and heterogeneity among individuals within and among clonal bacteria strains

    DEFF Research Database (Denmark)

    Jouvet, Lionel; Rodriguez-Rojas, Alexandro; Steiner, Ulrich

    2018-01-01

    to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high...... control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction...... is dominating at about 82–88%, over the 12–18% genetically (adaptive fixed) driven differences. The genetic differences among the clonal strains still lead to substantial variability in population growth rates (fitness), but, as well understood based on foundational work in population genetics, the within...

  16. Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia

    DEFF Research Database (Denmark)

    Jethwa, Alexander; Hüllein, Jennifer; Stolz, Tatjana

    2013-01-01

    Recurrent gene mutations contribute to the pathogenesis of chronic lymphocytic leukaemia (CLL). We developed a next-generation sequencing (NGS) platform to determine the genetic profile, intratumoural heterogeneity, and clonal structure of two independent CLL cohorts. TP53, SF3B1, and NOTCH1 were...... most frequently mutated (16.3%, 16.9%, 10.7%). We found evidence for subclonal mutations in 67.5% of CLL cases with mutations of cancer consensus genes. We observed selection of subclones and found initial evidence for convergent mutations in CLL. Our data suggest that assessment of (sub......)clonal structure may need to be integrated into analysis of the mutational profile in CLL....

  17. Plasma radiation in tokamak disruption simulation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Arkhipov, N.; Bakhtin, V.; Safronov, V.; Toporkov, D.; Vasenin, S.; Zhitlukhin, A. [Troitsk Inst. for Innovation and Fusion Research (Russian Federation); Wuerz, H. [Forschungszentrum Karlsruhe (Germany)

    1995-12-31

    Plasma impact results in sudden evaporation of divertor plate material and produces a plasma cloud which acts as a protective shield. The incoming energy flux is absorbed in the plasma shield and is converted mainly into radiation. Thus the radiative characteristics of the target plasma determine the dissipation of the incoming energy and the heat load at the target. Radiation of target plasma is studied at the two plasma gun facility 2MK-200 at Troitsk. Space- and time-resolved spectroscopy and time-integrated space-resolved calorimetry are employed as diagnostics. Graphite and tungsten samples are exposed to deuterium plasma streams. It is found that the radiative characteristics depend strongly on the target material. Tungsten plasma arises within 1 {micro}s close to the surface and shows continuum radiation only. Expansion of tungsten plasma is restricted. For a graphite target the plasma shield is a mixture of carbon and deuterium. It expands along the magnetic field lines with a velocity of v = (3--4) 10{sub 6} cm/s. The plasma shield is a two zone plasma with a hot low dense corona and a cold dense layer close to the target. The plasma corona emits intense soft x-ray (SXR) line radiation in the frequency range from 300--380 eV mainly from CV ions. It acts as effective dissipation system and converts volumetrically the incoming energy flux into SXR radiation.

  18. Spin quantum plasmas - new aspects of collective dynamics

    CERN Document Server

    Marklund, M

    2008-01-01

    Quantum plasmas is a rapidly expanding field of research, with applications ranging from nanoelectronics, nanoscale devices and ultracold plasmas, to inertial confinement fusion and astrophysics. Here we give a short systematic overview of quantum plasmas. In particular, we analyze the collective effects due to spin using fluid models. The introduction of an intrinsic magnetization due to the plasma electron (or positron) spin properties in the magnetohydrodynamic limit is discussed. Finally, a discussion of the theory and examples of applications is given.

  19. Genetic variation for clonal propagation and trait association with field performance in sainfoin

    Directory of Open Access Journals (Sweden)

    Sayareh Irani

    2016-01-01

    Full Text Available Clonal plant materials with identical genotypes may be used to precisely detect environmental effects and genotype x environment interactions resulting in a more accurate estimate of genetic parameters in plant genetic analysis. In sainfoin (Onobrychis viciifolia, knowledge on genetic variation for clonal propagation and its association with field performance is limited. Eleven natural ecotypes of sainfoin from wide geographical areas of Iran were used to evaluate genetic variation for clonal propagation and its association with related traits. From each ecotype 11‒21 genotypes were cloned via cuttings. Then, clones of a hundred genotypes from 10 ecotypes were transplanted to the field. High genetic variation was found between ecotypes of sainfoin for producing viable clones. The mean values for viable clones varied from 50% (Borujen ecotype to 97% (Najafabad ecotype. The values of within-ecotype coefficient of variation were higher than the genetic coefficient of variation. The highest heritability estimates were obtained for sensitivity to powdery mildew, plant height and number of stems per plant. Dry matter yield (DMY in the field was significantly and positively correlated with plant height and number of stems per plant, inflorescence length and growth score. An association between DMY and percent of viable clones was found indicating the possibility of selection during the early stages of clonal propagation. According to principal component analysis, Baft and Fereydunshahr ecotypes have potential for improving production of sainfoin if introduced into breeding programs. These issues warrant further study.Keywords: Clone viability, genetic variability, Onobrychis viciifolia, phenotypic  correlation, principal component analysis.DOI: 10.17138/TGFT(438-46

  20. A novel artificial immune clonal selection classification and rule mining with swarm learning model

    Science.gov (United States)

    Al-Sheshtawi, Khaled A.; Abdul-Kader, Hatem M.; Elsisi, Ashraf B.

    2013-06-01

    Metaheuristic optimisation algorithms have become popular choice for solving complex problems. By integrating Artificial Immune clonal selection algorithm (CSA) and particle swarm optimisation (PSO) algorithm, a novel hybrid Clonal Selection Classification and Rule Mining with Swarm Learning Algorithm (CS2) is proposed. The main goal of the approach is to exploit and explore the parallel computation merit of Clonal Selection and the speed and self-organisation merits of Particle Swarm by sharing information between clonal selection population and particle swarm. Hence, we employed the advantages of PSO to improve the mutation mechanism of the artificial immune CSA and to mine classification rules within datasets. Consequently, our proposed algorithm required less training time and memory cells in comparison to other AIS algorithms. In this paper, classification rule mining has been modelled as a miltiobjective optimisation problem with predictive accuracy. The multiobjective approach is intended to allow the PSO algorithm to return an approximation to the accuracy and comprehensibility border, containing solutions that are spread across the border. We compared our proposed algorithm classification accuracy CS2 with five commonly used CSAs, namely: AIRS1, AIRS2, AIRS-Parallel, CLONALG, and CSCA using eight benchmark datasets. We also compared our proposed algorithm classification accuracy CS2 with other five methods, namely: Naïve Bayes, SVM, MLP, CART, and RFB. The results show that the proposed algorithm is comparable to the 10 studied algorithms. As a result, the hybridisation, built of CSA and PSO, can develop respective merit, compensate opponent defect, and make search-optimal effect and speed better.

  1. Prevalence of clonal complexes and virulence genes among commensal and invasive Staphylococcus aureus isolates in Sweden.

    Directory of Open Access Journals (Sweden)

    Gunlög Rasmussen

    Full Text Available Staphylococcus aureus encodes a remarkable number of virulence factors which may contribute to its pathogenicity and ability to cause invasive disease. The main objective of this study was to evaluate the association between S. aureus invasiveness and bacterial genotype, in terms of the presence of virulence genes and affiliation to clonal complexes. Also, the significance of different virulence genes, mainly adhesins, for the development of infective endocarditis was investigated. DNA microarray technology was used to analyze 134 S. aureus isolates, all methicillin-susceptible, derived from three groups of clinically well-characterized patients: nasal carriers (n=46, bacteremia (n=55, and bacteremia with infective endocarditis (n=33. Invasive isolates were dominant in four of the major clonal complexes: 5, 8, 15, and 25. Of the 170 virulence genes examined, those encoding accessory gene regulator group II (agr II, capsule polysaccharide serotype 5 (cap5, and adhesins such as S. aureus surface protein G (sasG and fibronectin-binding protein B (fnbB were found to be associated with invasive disease. The same was shown for the leukocidin genes lukD/lukE, as well as the genes encoding serine protease A and B (splA/splB, staphylococcal complement inhibitor (scn and the staphylococcal exotoxin-like protein (setC or selX. In addition, there was a trend of higher prevalence of certain genes or gene clusters (sasG, agr II, cap5 among isolates causing infective endocarditis compared to other invasive isolates. In most cases, the presence of virulence genes was linked to clonal complex affiliation. In conclusion, certain S. aureus clonal lineages harboring specific sets of virulence genes seem to be more successful in causing invasive disease.

  2. Against the odds: complete outcrossing in a monoecious clonal seagrass Posidonia australis (Posidoniaceae).

    Science.gov (United States)

    Sinclair, Elizabeth A; Gecan, Ilena; Krauss, Siegfried L; Kendrick, Gary A

    2014-06-01

    Seagrasses are marine, flowering plants with a hydrophilous pollination strategy. In these plants, successful mating requires dispersal of filamentous pollen grains through the water column to receptive stigmas. Approximately 40 % of seagrass species are monoecious, and therefore little pollen movement is required if inbreeding is tolerated. Outcrossing in these species is further impacted by clonality, which is variable, but can be extensive in large, dense meadows. Despite this, little is known about the interaction between clonal structure, genetic diversity and mating systems in hydrophilous taxa. Polymorphic microsatellite DNA markers were used to characterize genetic diversity, clonal structure, mating system and realized pollen dispersal in two meadows of the temperate, monoecious seagrass, Posidonia australis, in Cockburn Sound, Western Australia. Within the two sampled meadows, genetic diversity was moderate among the maternal shoots (R = 0·45 and 0·64) and extremely high in the embryos (R = 0·93-0·97). Both meadows exhibited a highly clumping (or phalanx) structure among clones, with spatial autocorrelation analysis showing significant genetic structure among shoots and embryos up to 10-15 m. Outcrossing rates were not significantly different from one. Pollen dispersal distances inferred from paternity assignment averaged 30·8 and 26·8 m, which was larger than the mean clone size (12·8 and 13·8 m). These results suggest highly effective movement of pollen in the water column. Despite strong clonal structure and moderate genetic diversity within meadows, hydrophilous pollination is an effective vector for completely outcrossed offspring. The different localized water conditions at each site (highly exposed conditions vs. weak directional flow) appear to have little influence on the success and pattern of successful pollination in the two meadows. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All

  3. Light limitation and litter of an invasive clonal plant, Wedelia trilobata, inhibit its seedling recruitment.

    Science.gov (United States)

    Qi, Shan-Shan; Dai, Zhi-Cong; Miao, Shi-Li; Zhai, De-Li; Si, Chun-Can; Huang, Ping; Wang, Rui-Ping; Du, Dao-Lin

    2014-08-01

    Invasive clonal plants have two reproduction patterns, namely sexual and vegetative propagation. However, seedling recruitment of invasive clonal plants can decline as the invasion process proceeds. For example, although the invasive clonal Wedelia trilobata (Asteraceae) produces numerous seeds, few seedlings emerge under its dense population canopy in the field. In this study it is hypothesized that light limitation and the presence of a thick layer of its own litter may be the primary factors causing the failure of seedling recruitment for this invasive weed in the field. A field survey was conducted to determine the allocation of resources to sexual reproduction and seedling recruitment in W. trilobata. Seed germination was also determined in the field. Effects of light and W. trilobata leaf extracts on seed germination and seedling growth were tested in the laboratory. Wedelia trilobata blooms profusely and produces copious viable seeds in the field. However, seedlings of W. trilobata were not detected under mother ramets and few emerged seedlings were found in the bare ground near to populations. In laboratory experiments, low light significantly inhibited seed germination. Leaf extracts also decreased seed germination and inhibited seedling growth, and significant interactions were found between low light and leaf extracts on seed germination. However, seeds were found to germinate in an invaded field after removal of the W. trilobata plant canopy. The results indicate that lack of light and the presence of its own litter might be two major factors responsible for the low numbers of W. trilobata seedlings found in the field. New populations will establish from seeds once the limiting factors are eliminated, and seeds can be the agents of long-distance dispersal; therefore, prevention of seed production remains an important component in controlling the spread of this invasive clonal plant. © The Author 2014. Published by Oxford University Press on behalf of

  4. Clonal micropropagation of peppermint (Mentha piperita L. varieties of Ukrainian breeding

    Directory of Open Access Journals (Sweden)

    Т. Є. Таланкова-Середа

    2016-05-01

    Full Text Available Purpose. Developing technology for clonal micropropagation of peppermint (Mentha piperita L. plants of Ukrainian breeding based on the complex of methods of isolated tissue and organ culture in vitro. Methods. During the experiment, such methods as isolated tissue and organ culture in vitro, clonal micropropagation, detached scion grafting, chemotherapy with adding of virucide Ribavirin to the nutrient medium, biometric and statistical ones were used. Results. The stepped procedure of sterilization that we have developed allows to receive 88–100% of sterile explants. For M. piperita L. introduction into culture and clonal micropropagation, Murashige and Skoog (MS nut­rient medium appeared to be optimal supplemented with 6-benzylaminopurine (0.75 mg/l, adenine (0.05 mg/l, indole-3-acetic acid (IAA (0.05 mg/l and gibberellic acid (0.5 mg/l on which the reproduction ratio on the 28th day ranged between 1:7 and 1:15. For recovery of plants from viral infection, virucide Ribavirin at concentration of 10 mg/l was added to the nutrient medium. The proposed nutrient medium for rhizogenesis, that contained IAA (0.5 mg/l and indole butyric acid (IBA (0.5 mg/l, allows to obtain the frequency of rhizogenesis up to 84–100%. Regenerated plants were adapted to the conditions in vivo on substrate peat : universal soil : perlite : sand in the ratio 2:1:1:1. The survival rate for peppermint varieties amounted to 96–100%. Conclusions. Biotechnological scheme was developed that permits to get healthy, purebred planting material and intensively propagate plants for supplying breeding programs of the Experimental Station for Medicinal Plants of the Institute of Agroecology and Environmental Management of the National Academy of Agrarian Sciences of Ukraine, among which such varieties as ‘Lebedyna pisnia’ and ‘Ukrainska pertseva’ were selected as the most promising for clonal micropropagation.

  5. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

    Directory of Open Access Journals (Sweden)

    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  6. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations

    OpenAIRE

    Lee, U.; Skinner, J.J.; Reinitz, J.; Rosner, M.R.; Kim, E-J.

    2015-01-01

    There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with fi...

  7. Clonality and virulence traits of Escherichia coli associated with hemorrhagic septicaemia in turkeys

    OpenAIRE

    Olsen, Rikke Heidemann; Chadfield, Mark; Christensen, Jens Peter; Scheutz, Flemming; Christensen, Henrik; Bisgaard, Magne

    2011-01-01

    Abstract Fifty-five clinical isolates of avian pathogenic Escherichia coli (APEC) from seven outbreaks of acute hemorrhagic septicaemia in turkeys were characterised by serotyping, plasmid profiling including restriction analysis with HindIII, ribotyping with EcoRI and HindIII, multilocus sequence typing (MLST) and virulence profiling. A clonal relationship was demonstrated for each outbreak according to serotype, plasmid profiling, ribotyping, and MLST.In addition, isolates demons...

  8. Heterogeneity of clonal patterns among patches of kudzu, Pueraria montana var. lobata, an invasive plant

    OpenAIRE

    Kartzinel, Tyler R.; Hamrick, J. L.; Wang, Chongyun; Bowsher, Alan W.; Quigley, Bryan G. P.

    2015-01-01

    Background and Aims Viny species are among the most serious invasive plants, and better knowledge of how vines grow to dominate landscapes is needed. Patches may contain a single genotype (i.e. genet), a competitively dominant genet or many independent but interacting genets, yet the clonal structure of vining species is often not apparent. Molecular markers can discriminate among the genetic identities of entwined vines to reveal the number and spatial distribution of genets. This study inve...

  9. Network intrusion detection by the coevolutionary immune algorithm of artificial immune systems with clonal selection

    Science.gov (United States)

    Salamatova, T.; Zhukov, V.

    2017-02-01

    The paper presents the application of the artificial immune systems apparatus as a heuristic method of network intrusion detection for algorithmic provision of intrusion detection systems. The coevolutionary immune algorithm of artificial immune systems with clonal selection was elaborated. In testing different datasets the empirical results of evaluation of the algorithm effectiveness were achieved. To identify the degree of efficiency the algorithm was compared with analogs. The fundamental rules based of solutions generated by this algorithm are described in the article.

  10. Plasma contactor research, 1990

    Science.gov (United States)

    Williams, John D.; Wilbur, Paul J.

    1991-01-01

    Emissive and Langmuir probes were used to measure plasma potential profiles, plasma densities, electron energy distributions, and plasma noise levels near a hollow cathode-based plasma contactor emitting electrons. The effects of electron emission current (100 to 1500 mA) and contactor flowrate (2 to 10 sccm (Xenon)) on these data are examined. Retarding potential analyzer (RPA) measurements showing that high energy ions generally stream from a contactor along with the electrons being emitted are also presented, and a mechanism by which this occurs is postulated. This mechanism, which involves a high rate of ionization induced between electrons and atoms flowing together from the hollow cathode orifice, results in a region of high positive space charge and high positive potential. Langmuir and RPA probe data suggests that both electrons and ions expand spherically from this potential hill region. In addition to experimental observations, a simple one-dimensional model which describes the electron emission process and predicts the phenomena just mentioned is presented and is shown to agree qualitatively with these observations. Experimental results of the first stage of bilateral cooperation with the Italian Institute of Interplanetary Space Physics (IFSI CNR) are presented. Sharp, well-defined double layers were observed downstream of a contactor collecting electrons from an ambient plasma created in the IFSI Facility. The voltage drop across these double layers was observed to increase with the current drawn from the ambient plasma. This observation, which was not as clear in previous IFSI tests conducted at higher neutral pressures, is in agreement with previous experimental observations made at both Colorado State University and NASA Lewis Research Center. Greater double layer voltage drops, multiple double layers, and higher noise levels in the region near the double layers were also observed when a magnetic field was imposed and oriented perpendicular to the

  11. The clinicopathologic observation, c-KIT gene mutation and clonal status of gastrointestinal stromal tumor in the sacrum

    OpenAIRE

    Gong, Li; Li, Yan-Hong; Zhao, Hua-Dong; Zhao, Jian-Ye; Zhang, Wei

    2009-01-01

    Abstract Background It is very rare that gastrointestinal stromal tumor (GIST) occurs in the sacrum. Only one case of GIST occuring in the sacral region, with intracranial metastasis, has been reported in the literature. Moreover, only few cases have been published in literature about its clonal origin. Case presentation In this report, we present a rare case of GIST occuring in the sacrum and describe its clinicopathologic features, c-KIT gene mutation and clonal status. Microscopically, the...

  12. Subpopulations of Staphylococcus aureus clonal complex 121 are associated with distinct clinical entities.

    Directory of Open Access Journals (Sweden)

    Kevin Kurt

    Full Text Available We investigated the population structure of Staphylococcus aureus clonal complex CC121 by mutation discovery at 115 genetic housekeeping loci from each of 154 isolates, sampled on five continents between 1953 and 2009. In addition, we pyro-sequenced the genomes from ten representative isolates. The genome-wide SNPs that were ascertained revealed the evolutionary history of CC121, indicating at least six major clades (A to F within the clonal complex and dating its most recent common ancestor to the pre-antibiotic era. The toxin gene complement of CC121 isolates was correlated with their SNP-based phylogeny. Moreover, we found a highly significant association of clinical phenotypes with phylogenetic affiliations, which is unusual for S. aureus. All isolates evidently sampled from superficial infections (including staphylococcal scalded skin syndrome, bullous impetigo, exfoliative dermatitis, conjunctivitis clustered in clade F, which included the European epidemic fusidic-acid resistant impetigo clone (EEFIC. In comparison, isolates from deep-seated infections (abscess, furuncle, pyomyositis, necrotizing pneumonia were disseminated in several clades, but not in clade F. Our results demonstrate that phylogenetic lineages with distinct clinical properties exist within an S. aureus clonal complex, and that SNPs serve as powerful discriminatory markers, able to identify these lineages. All CC121 genomes harboured a 41-kilobase prophage that was dissimilar to S. aureus phages sequenced previously. Community-associated MRSA and MSSA from Cambodia were extremely closely related, suggesting this MRSA arose in the region.

  13. Genetic and clonal diversity of two cattail species, Typha latifolia and T. angustifolia (Typhaceae), from Ukraine.

    Science.gov (United States)

    Tsyusko, Olga V; Smith, Michael H; Sharitz, Rebecca R; Glenn, Travis C

    2005-07-01

    Genetic and clonal diversity vary between two closely related cattail species (Typha angustifolia and T. latifolia) from Ukraine. This diversity was calculated from microsatellite data. Forty-eight percent of the total variation was partitioned between species, which formed distinct clusters in a dendrogram with no indication of hybrid populations. Typha angustifolia had higher heterozygosity at the species (H(es) = 0.66) and population (H(ep) = 0.49) levels than did T. latifolia (H(es) = 0.37 and H(ep) = 0.29, respectively). The higher number of alleles in T. angustifolia may be indicative of larger effective population sizes due to its higher seed production. Clonal diversity of T. angustifolia was lower than that of T. latifolia (N(g)/N(r) = 0.40 and 0.61, Simpson's D = 0.82 and 0.94, respectively). Correlations between clonal and genetic diversity were higher for T. latifolia than T. angustifolia, suggesting that the importance of factors and their interactions affecting this relationship are different for the two species. Latitudinal and longitudinal trends were not observed in either species despite the large sampling area. Population differentiation was relatively high with F(ST) of 0.24 and 0.29 for T. angustifolia and T. latifolia, respectively. Weak isolation by distance was observed for T. latifolia but not for T. angustifolia.

  14. X-chromosome inactivation pattern analysis for the assessment of cell clonality in cats.

    Science.gov (United States)

    Mochizuki, H; Goto-Koshino, Y; Takahashi, M; Fujino, Y; Ohno, K; Tsujimoto, H

    2012-11-01

    X-chromosome inactivation pattern (XCIP) analysis has been widely used to assess cell clonality in various types of neoplasms in humans. In the present study, a polymerase chain reaction-based feline XCIP analysis using the feline androgen receptor gene was developed. To construct the system of the analysis, polymorphism in CAG tandem repeats within the feline androgen receptor gene was explored using somatic DNAs from 50 male and 103 female cats. CAG tandem repeats in exon 1 of the feline androgen receptor gene were found to be polymorphic, containing 15 to 22 CAG repeats. Of the 103 female cats, 70 (68%) were heterozygous for the number of CAG repeats, indicating the possible usefulness of XCIP analysis in cats. Application of the feline XCIP analysis to 3 feline mammary gland adenocarcinoma cell lines revealed distinctly skewed XCIPs in these cell lines, indicating their clonal origins. Twelve (80%) of the 15 primary tissue/cell samples obtained from cats with various neoplastic diseases showed skewed XCIPs. Moreover, bone marrow samples from 3 cats with myelodysplastic syndrome were also found to have skewed XCIPs. The polymerase chain reaction-based XCIP analysis developed in this study can provide information on cell clonality in female cats, potentially facilitating the differential diagnosis of various disorders in cats.

  15. Consequences of multiple inflorescences and clonality for pollinator behavior and plant mating.

    Science.gov (United States)

    Liao, Wan-Jin; Harder, Lawrence D

    2014-11-01

    Angiosperms engage in distributed reproduction, producing sex organs in multiple flowers on one or more inflorescences, including on different physical individuals of clonal plants. We investigated the effects of alternative deployments of artificial flowers for pollinator behavior and simulated pollen dispersal. Plants presented 18 flowers on either one inflorescence (1-I plants) or three inflorescences (3-I plants) spaced either closely or widely. Bees often skipped inflorescences on 3-I plants, visiting an average of 1.5 fewer flowers overall than on 1-I plants. In simulations with all flowers receiving and donating pollen, this behavior caused 7% less geitonogamy for 3-I plants, contradicting a common supposition that clonality increases geitonogamy. Bees generally moved upward within inflorescences and downward between inflorescences. Consequently, in simulations, segregation of pollen receipt to lower flowers and pollen donation to upper flowers reduced self-pollination and enhanced pollen export much more for 1-I plants. Nectar volume per flower had little relevant influence on bee behavior. The observed bee responses and simulated mating results suggest that production of multiple inflorescences and clonality promote pollination quality when flowers simultaneously receive and donate pollen, whereas a single large inflorescence is advantageous when segregation of sex roles among flowers reduces geitonogamy effectively.

  16. PROPAGAÇÃO CLONAL DE GUANANDI (Calophyllum brasiliense POR MINIESTAQUIA

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    Rogério Luiz da Silva

    2010-01-01

    Full Text Available El objetivo de este trabajo fue evaluar la eficiencia de la técnica de miniestaca para la propagación clonal de la especie forestal guanandi (Calophyllum brasiliense. Para esto, se estableció un minijardín clonal en cajas de arena, del cual se obtuvo brotes para utilizar como miniestacas, buscando hacer 2 experimentos: en un ensayo se evaluó 2 tipos de miniestacas (apical e intermedia tratadas con diferentes dosis de acido indolbutírico (0, 2000, 4000 y 8000 mg.l-1; en el otro, las miniestacas fueros sembradas en 3 tipos de sustrato (vermiculita, cascarilla de arroz quemada y sustrato agrícola (corteza de pino compostada. Los índices de enraizamiento no variaron en el primer ensayo; en el segundo, hubo una reducción en el tiempo de permanencia en invernadero usando vermiculita como sustrato. De manera general, la técnica de miniestaca es una eficiente estrategia para la propagación clonal de guanandi.

  17. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.

    Directory of Open Access Journals (Sweden)

    UnJin Lee

    Full Text Available There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with finite auto-correlation time, where a randomly fluctuating growth rate with a negative average is shown to result in exponential growth for sufficiently large fluctuations in growth rate. We then present a non-linear stochastic self-regulation model where the loss of coherent self-regulation and an increase in noise can induce a shift from bounded to unbounded growth. An important consequence of these models is that while the average change in phenotype may not differ for various parameter sets, the variance of the resulting distributions may considerably change. This demonstrates the necessity of understanding the influence of variance and heterogeneity within seemingly identical clonal populations, while providing a mechanism for varying functional consequences of such heterogeneity. Our results highlight the importance of a paradigm shift from a deterministic to a probabilistic view of clonality in understanding selection as an optimization problem on noise-driven processes, resulting in a wide range of biological implications, from robustness to environmental stress to the development of drug resistance.

  18. Correspondence between performance of Eucalyptus spp trees selected from family and clonal tests.

    Science.gov (United States)

    Reis, C A F; Gonçalves, F M A; Rosse, L N; Costa, R R G F; Ramalho, M A P

    2011-06-21

    We examined the correspondence in performance between trees selected from a family test and their respective clones from a clonal test of Eucalyptus. Full-sib families were obtained from controlled pollination among individuals of Eucalyptus grandis and between E. grandis and E. urophylla. The hybridizations did not follow a factorial scheme. The family tests were carried out at three locations in Eunápolis and Itabela counties, in Bahia, Brazil, in 2003. Four hundred and ninety-seven high-performance trees were selected, by the individual BLUP procedure, in the family tests at two years of age, based on wood volume. The clones from these trees and 14 checks were evaluated in clonal tests carried out in the same region in 2006. The wood volume of the clones was evaluated at two years of age. Trait correlation between the trees selected from the family and clonal tests was low. The estimate of the coincidence between the best trees and the best clones using an average of the different intensities of selection was only 27%. These results demonstrate that the selection of trees in the family test should not be too drastic; otherwise the chance plus clones may be overlooked.

  19. Clonal multiplication of Cymbidiums through tissue culture of the shoot meristem

    Energy Technology Data Exchange (ETDEWEB)

    Wimber, Donald E.

    1963-09-01

    The propagation of clonal varieties of some orchids is at times exasperatingly slow and occasionally an almost futile effort. Clonal multiplication is generally confined to dlvidlng mature plants and to starting plants from pseudobulbs. There is, of course, the specialized technique for obtaining Phalaenopsis plantlets from the aseptic culture of inflorescence nodes, but this is basically the same thing as propagating plants from pseudobulbs. In certain cases it is highly desirable to rapidly multiply certain clones of orchids. Awarded varieties could thereby be dispersed with great rapidity where now it may take decades for some clones to became fairly common. Commercial flower production would be very much enhanced if certain desirable clones could be multiplied ad infinitum within a short time. Orchid flower production could then be placed more on a par with many of the other cut flowers and the clonal peculiarities of some fo the current hybrids could be pampered instead of ignored. This paper describes a tissue culture method for the rapid propagation of Cymbidium clones.

  20. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.

    Science.gov (United States)

    Lee, UnJin; Skinner, John J; Reinitz, John; Rosner, Marsha Rich; Kim, Eun-Jin

    2015-01-01

    There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with finite auto-correlation time, where a randomly fluctuating growth rate with a negative average is shown to result in exponential growth for sufficiently large fluctuations in growth rate. We then present a non-linear stochastic self-regulation model where the loss of coherent self-regulation and an increase in noise can induce a shift from bounded to unbounded growth. An important consequence of these models is that while the average change in phenotype may not differ for various parameter sets, the variance of the resulting distributions may considerably change. This demonstrates the necessity of understanding the influence of variance and heterogeneity within seemingly identical clonal populations, while providing a mechanism for varying functional consequences of such heterogeneity. Our results highlight the importance of a paradigm shift from a deterministic to a probabilistic view of clonality in understanding selection as an optimization problem on noise-driven processes, resulting in a wide range of biological implications, from robustness to environmental stress to the development of drug resistance.

  1. Spatial heterogeneity in light supply affects intraspecific competition of a stoloniferous clonal plant.

    Directory of Open Access Journals (Sweden)

    Pu Wang

    Full Text Available Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition or nine ramets (with intraspecific competition of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensity and two heterogeneous ones differing in patch size (large and small patch treatments. The total light in the two heterogeneous treatments was the same as that in the homogeneous medium light treatment. Both decreasing light intensity and intraspecific competition significantly decreased the growth (biomass, number of ramets and total stolon length of D. indica. As compared with the homogeneous medium light treatment, the large patch treatment significantly increased the growth of D. indica without intraspecific competition. However, the growth of D. indica with competition did not differ among the homogeneous medium light, the large and the small patch treatments. Consequently, light heterogeneity significantly increased intraspecific competition intensity, as measured by the decreased log response ratio. These results suggest that spatial heterogeneity in light supply can alter intraspecific interactions of clonal plants.

  2. Genotyping the clonal structure of a gorgonian coral, Junceella juncea (Anthozoa: Octocorallia), using microsatellite loci

    Science.gov (United States)

    Liu, Shang-Yin Vanson; Yu, Hon-Tsen; Fan, Tung-Yung; Dai, Chang-Feng

    2005-11-01

    The identification of different clones is fundamental to the study of population structure among organisms with mixed reproductive modes such as cnidarians. However, due to the low genetic variation of coral mtDNA and contamination by zooxanthellate DNA, very few molecular markers are available for studying the clonal structure of cnidarians. Herein we used four polymorphic loci of microsatellite DNA isolated from a zooxanthellae-free octocoral, Junceella juncea, to study its clonal structure in seven populations collected from three localities in Taiwan. In total, 40 multilocus genotypes were found among 152 colonies, and the number of genotypes (clones) identified in the seven populations ranged from 2 to 16. Each of the 40 multilocus genotypes was restricted to a single population, even where adjacent populations were only 100 m distant. The ratio of observed to expected genotypic diversity (Go:Ge) ranged from 0.217 to 0.650, and Go showed a significant departure from Ge ( p<0.05) at each site indicating that asexual fragmentation may play a major role in the maintenance of established populations. Mean relatedness ( R) values showed that genotypes within reefs were more closely related than those between regions. The results indicate that microsatellites are useful for discerning the clonal structures among and within populations at different spatial scales.

  3. Mutated nucleophosmin detects clonal multilineage involvement in acute myeloid leukemia: Impact on WHO classification.

    Science.gov (United States)

    Pasqualucci, Laura; Liso, Arcangelo; Martelli, Maria Paola; Bolli, Niccolò; Pacini, Roberta; Tabarrini, Alessia; Carini, Manola; Bigerna, Barbara; Pucciarini, Alessandra; Mannucci, Roberta; Nicoletti, Ildo; Tiacci, Enrico; Meloni, Giovanna; Specchia, Giorgina; Cantore, Nicola; Di Raimondo, Francesco; Pileri, Stefano; Mecucci, Cristina; Mandelli, Franco; Martelli, Massimo Fabrizio; Falini, Brunangelo

    2006-12-15

    Because of a lack of specific clonality markers, information on lineage involvement and cell of origin of acute myeloid leukemia with normal karyotype (AML-NK), is missing. Because Nucleophosmin (NPM) gene is frequently mutated in AML-NK and causes aberrant NPM cytoplasmic localization (NPMc+), it was used as an AML lineage clonality marker. Clonal NPM exon 12 mutations were detected in myeloid, monocytic, erythroid, and megakaryocytic cells but not in fibroblasts or endothelia that were laser-microdissected from 3 patients with NPMc+ AML. Aberrant cytoplasmic expression of mutated NPM proteins was identified with anti-NPM antibodies in 2 or more myeloid hemopoietic cell lineages in 99 (61.5%) of 161 of NPMc+ AML paraffin-embedded bone marrow biopsies; lymphoid involvement was excluded in 3 investigated cases. These findings suggest that NPMc+ AML derives from either a common myeloid or earlier progenitor. Immunohistochemical studies show that varying combinations and ratios of NPMc+ leukemic cells from distinct lineages are responsible for heterogeneity within each French-American-British (FAB) classification type and for NPMc+ AML falling into different FAB categories. These findings question the value of FAB criteria in subdividing the WHO category of "AML not otherwise characterized" and suggest that, for clinical use, NPMc+ AML be provisionally regarded as a separate AML with prognostic significance.

  4. Loss of heterozygosity drives clonal diversity of Phytophthora capsici in China.

    Directory of Open Access Journals (Sweden)

    Jian Hu

    Full Text Available Phytophthora capsici causes significant loss to pepper (Capsicum annum in China and our goal was to develop single nucleotide polymorphism (SNP markers for P. capsici and characterize genetic diversity nationwide. Eighteen isolates of P. capsici from locations worldwide were re-sequenced and candidate nuclear and mitochondrial SNPs identified. From 2006 to 2012, 276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH. Analysis of SNPs directly from infected peppers confirmed LOH in field populations. One clonal lineage is dominant throughout much of the country. The overall implications for long-lived genetically diverse clonal lineages amidst a widely dispersed sexual population are discussed.

  5. AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species.

    Science.gov (United States)

    de Witte, Lucienne C; Armbruster, Georg F J; Gielly, Ludovic; Taberlet, Pierre; Stöcklin, Jürg

    2012-03-01

    We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change. © 2011 Blackwell Publishing Ltd.

  6. EVOLUÇÃO DA SILVICULTURA CLONAL DE eucalyptus NO BRASIL

    Directory of Open Access Journals (Sweden)

    Aloisio Xavier

    2010-01-01

    Full Text Available En los últimos años, en Brasil, hubo un aumento en el interés por la silvicultura clonal de Eucalyptus, debido principalmente a las ventajas del proceso en cuanto a la posibilidad de resolver problemas de enfermedades, heterogeneidad y productividad de las plantaciones forestales. El creciente uso de clones, tanto por las grandes empresas como por pequeños inversionistas, inclusive productores rurales, generó considerables avances tecnológicos en las últimas décadas, con relación a procesos de selección de árboles, rescate de individuos superiores, evaluación de clones, producción comercial de plantas (estaquilla, miniestaquilla y microestaquilla y en las prácticas silviculturales adoptadas en la siembra y conducción de plantaciones forestales clonales. En este sentido, se busca enfocar los principales temas relacionados al proceso de clonación de Eucalyptus, involucarados en un programa clonal de esta especie.

  7. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae

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    Keith D. Gaddis

    2014-08-01

    Full Text Available The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in Northeastern Costa Rica dominated by the species Pentaclethra macroloba, which sprouts from the root mass of fallen trees and from snapped trunks. We examined the population structure of juvenile P. macroloba growing in different soil types and across an elevational gradient. Using seven molecular markers, we genotyped 173 juvenile P. macroloba from 18 plots (six plots in seasonally inundated swamps, and 12 plots in upland non-swamp spanning 50-300m in elevation at La Selva Biological Station and the adjacent Reserva Ecológica Bijagual in Northeastern Costa Rica. We answered two specific questions: (1 How extensive is clonal reproduction? and (2 what is the distribution of genetic diversity and structure?. We found that clonal reproduction occurred exclusively within inundated swamp areas. However, there was no significant difference between genetic diversity measures in swamp and non-swamp plots, which were both generally low when compared with other tropical forest species. Genetic structure was significant across all plots (F ST=0.109. However, genetic structure among swamp plots (F ST=0.128 was higher than among non-swamp upland plots (F ST=0.093. Additionally, spatial autocorrelation among individuals within non-swamp upland plots was significant from the 25 to 100m spatial scale, but not within swamp plots. The degree of overall genetic structure we found in P. macroloba is high for a tropical forest tree. The incidence of clonal reproduction is a

  8. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant.

    Science.gov (United States)

    Mason, William S; Gill, Upkar S; Litwin, Samuel; Zhou, Yan; Peri, Suraj; Pop, Oltin; Hong, Michelle L W; Naik, Sandhia; Quaglia, Alberto; Bertoletti, Antonio; Kennedy, Patrick T F

    2016-11-01

    Chronic infection with hepatitis B virus (HBV) progresses through different phases. The first, called the immune-tolerant phase, has been associated with a lack of disease activity. We examined HBV-DNA integration, clonal hepatocyte expansion, HBV antigen expression, and HBV-specific immune responses in patients in the immune-tolerant phase to assess whether this designation is appropriate or if there is evidence of disease activity. We studied HBV-DNA integration, clonal hepatocyte expansion, and expression of hepatitis B surface antigen and core antigen in liver tissues from 26 patients with chronic HBV infection (ages, 14-39 y); 9 patients were positive for hepatitis B e antigen (HBeAg) in the immune-tolerant phase and were matched for age with 10 HBeAg-positive patients with active disease and 7 HBeAg-negative patients with active disease. Peripheral blood samples were collected and HBV-specific T cells were quantified for each group. Detection of HBV antigens differed among groups. However, unexpectedly high numbers of HBV-DNA integrations, randomly distributed among chromosomes, were detected in all groups. Clonal hepatocyte expansion in patients considered immune tolerant also was greater than expected, potentially in response to hepatocyte turnover mediated by HBV-specific T cells, which were detected in peripheral blood cells from patients in all phases of infection. We measured HBV-specific T cells, HBV-DNA integration, and clonal hepatocyte expansion in different disease phases of young patients with chronic hepatitis B, with emphasis on the so-called immune-tolerant phase. A high level of HBV-DNA integration and clonal hepatocyte expansion in patients considered immune tolerant indicated that hepatocarcinogenesis could be underway-even in patients with early stage chronic HBV infection. Our findings do not support the concepts that this phase is devoid of markers of disease progression or that an immune response has not been initiated. We propose that

  9. Effects of sediment burial on tropical ruderal seagrasses are moderated by clonal integration

    Science.gov (United States)

    Ooi, Jillian Lean Sim; Kendrick, Gary A.; Van Niel, Kimberly P.

    2011-12-01

    Seagrasses are clonal plants that grow submerged in dynamic sedimentary environments where burial is a common occurrence. Clonal organisms may respond to burial in very different ways depending on how strongly integrated they are through horizontal rhizomes, but the effect of clonal integration under conditions of stress such as burial is poorly studied for seagrasses. We test the effect of burial on tropical seagrasses that occur in multispecific meadows by subjecting plants in mixed stands to burial of 0, 2, 4, 8 and 16 cm for 27 days. Treatments were divided into those where rhizomes were severed and those where rhizomes were left intact. We hypothesize that species withstand burial better if clonal integration is maintained (intact rhizomes). Results showed that all species tolerated burial of up to 4 cm without adverse effects but significant reductions in shoot density and biomass become evident at 8 cm of burial. Furthermore, Cymodocea serrulata and Syringodium isoetifolium were strong integrators, i.e. they provide support for buried shoots, whereas Halophila ovalis and Halodule uninervis were weak integrators that did not show evidence of subsidizing buried shoots. Vertical elongation was observed for C. serrulata and H. uninervis as a response to burial only when rhizomes were severed, leading us to speculate on whether species rely on vertical elongation as an escape strategy only in the absence of resource translocation. Our distinction between the responses of treatments with intact rhizomes from those with severed rhizomes may be extended to an interpretation of burial scale (intact rhizomes=broad spatial-scale burial; severed rhizomes=fine spatial-scale burial). We concluded that broad spatial-scale burial exceeding 4 cm leads to rapid loss or reduction of all species. However, fine spatial-scale burial exceeding 4 cm, such as those caused by shrimp mounds (bioturbation), is expected to favor C. serrulata and S. isoetifolium, while H. ovalis and H

  10. Plasma physics

    CERN Document Server

    Drummond, James E

    2013-01-01

    A historic snapshot of the field of plasma physics, this fifty-year-old volume offers an edited collection of papers by pioneering experts in the field. In addition to assisting students in their understanding of the foundations of classical plasma physics, it provides a source of historic context for modern physicists. Highly successful upon its initial publication, this book was the standard text on plasma physics throughout the 1960s and 70s.Hailed by Science magazine as a ""well executed venture,"" the three-part treatment ranges from basic plasma theory to magnetohydrodynamics and microwa

  11. Human umbilical cord blood plasma can replace fetal bovine serum for in vitro expansion of functional human endothelial colony-forming cells.

    Science.gov (United States)

    Huang, Lan; Critser, Paul J; Grimes, Brenda R; Yoder, Mervin C

    2011-07-01

    A hierarchy of endothelial colony-forming cells (ECFC) with different levels of proliferative potential has been identified in human circulating blood and blood vessels. ECFC has recently become an attractive target for new vascular regenerative therapies; however, in vitro expansion of ECFC typically depends on the presence of fetal bovine serum (FBS) or fetal calf serum (FCS) in the culture medium, which is not appropriate for its therapeutic application. To identify optimal conditions for in vitro expansion of ECFC, the effects of human endothelial serum-free medium (SFM) supplemented with six pro-angiogenic cytokines and human umbilical cord blood plasma (HCP) were investigated. The in vitro morphology, proliferation, surface antigen expression and in vivo vessel-forming ability were utilized for examining the effects of medium on ECFC. This novel formulation of endothelial cell culture medium allows us, for the first time, to isolate and expand human ECFC efficiently in vitro with a low concentration of HCP (1.5%) and without bovine serum additives. In this serum-reduced medium (SRM), human ECFC colony yields remained quantitatively similar to those cultured in a high concentration (10%) of bovine serum-supplemented medium. SRM-cultured ECFC displayed a robust clonal proliferative ability in vitro and human vessel-forming capacity in vivo. The present study provides a novel method for the expansion of human ECFC in vitro and will help to advance approaches for using the cells in human therapeutic trials.

  12. A comparison of skin expansion and contraction between one expander and two expanders: a preliminary study.

    Science.gov (United States)

    Zhang, Gan-lin; Zhang, Jin-ming; Ji, Chen-yang; Meng, Hong; Huang, Jian-hua; Luo, He-yuan; Zhang, Hua-sheng; Liu, Xiao-tao; Hong, Xiao-fang

    2013-12-01

    This study aimed to compare the difference between the skin expansion and contraction rates for an expanded flap with one versus two expanders. The study cohort comprised 24 cases of two overlapping expanders and 15 cases of a single implanted expander involving 22 patients. The method of "wet-cloth sampling" was applied to measure the expanded flap area and the initial unexpanded area and to calculate the skin expansion rate. Two points 5 cm apart in the center of the expanded flap were selected before the second surgical stage. After removal of the expander, the distance between the two fixed points was measured and recorded. The contraction rate of the expanded flap then was calculated. During the same period of expansion in the two groups (p = 0.06, >0.01), the skin expansion rate was 3.5 ± 0.9 % in the group with two overlapping expanders and 2.6 ± 0.6 % in the control group. The difference between the two groups was statistically significant (p = 0.002, 0.05). We fitted a linear regression model that was Y = 0.533 − 0.003X, where Y was the contraction rate of the expanded flap and X was the period of expansion. The contraction rate of the expanded flap was negatively correlated with the period of expansion. Compared with the traditional method of implanting a single expander, the new method of overlapping two expanders in a single cavity increased the skin expansion rate. The instantly expanded flap contraction rate did not differ significantly between the two groups, so the amount of expanded skin area absolutely increased. The clinical application of the new method is worth promoting. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

  13. Plasma spectroscopy

    CERN Document Server

    Fujimoto, Takashi

    2004-01-01

    Plasma is ubiquitous, whether it occurs in cooking gas flames, fluorescent lamps or in the sun and the stars. This book deals with the light that these plasmas emit, the characteristics of the light, and why it occurs. The author provides a framework from which a coherent account of this phenomena can be made.

  14. PLASMA ENERGIZATION

    Science.gov (United States)

    Furth, H.P.; Chambers, E.S.

    1962-03-01

    BS>A method is given for ion cyclotron resonance heatthg of a magnetically confined plasma by an applied radio-frequency field. In accordance with the invention, the radiofrequency energy is transferred to the plasma without the usual attendent self-shielding effect of plasma polarlzatlon, whereby the energy transfer is accomplished with superior efficiency. More explicitly, the invention includes means for applying a radio-frequency electric field radially to an end of a plasma column confined in a magnetic mirror field configuration. The radio-frequency field propagates hydromagnetic waves axially through the column with the waves diminishing in an intermediate region of the column at ion cyclotron resonance with the fleld frequency. In such region the wave energy is converted by viscous damping to rotational energy of the plasma ions. (AEC)

  15. Expanding Scope of Practice for Ontario Optometrists

    National Research Council Canada - National Science Library

    Emily Bray; Ivy Bourgault

    2017-01-01

    In 2011, The Optometry Act, 1991 was amended to include The Designated Drugs and Standards of Practice Regulation which expanded the scope of practice for Ontario optometrists to include prescribing...

  16. Efficacy of Nickel-Titanium Palatal Expanders

    Directory of Open Access Journals (Sweden)

    Rahul Paul

    2011-01-01

    Conclusion : To conclude, a Ni-Ti expander brings about expansion by a combination of orthodontic and orthopedic effects by an increase in maxillary intermolar, maxillary intercanine and mandibular intercanine widths as also the opening of the midpalatal suture.

  17. Cutaneous basal cell carcinosarcomas: evidence of clonality and recurrent chromosomal losses.

    Science.gov (United States)

    Harms, Paul W; Fullen, Douglas R; Patel, Rajiv M; Chang, Dannie; Shalin, Sara C; Ma, Linglei; Wood, Benjamin; Beer, Trevor W; Siddiqui, Javed; Carskadon, Shannon; Wang, Min; Palanisamy, Nallasivam; Fisher, Gary J; Andea, Aleodor

    2015-05-01

    Cutaneous carcinosarcomas are heterogeneous group of tumors composed of malignant epithelial and mesenchymal components. Although mutation analyses have identified clonal changes between these morphologically disparate components in some subtypes of cutaneous carcinosarcoma, few cases have been analyzed thus far. To our knowledge, copy number variations (CNVs) and copy-neutral loss of heterozygosity (CN-LOH) have not been investigated in cutaneous carcinosarcomas. We analyzed 4 carcinosarcomas with basal cell carcinoma and osteosarcomatous components for CNVs/CN-LOH by comparative genomic hybridization/single-nucleotide polymorphism array, TP53 hot spot mutations by polymerase chain reaction and Sanger sequencing, and TP53 genomic rearrangements by fluorescence in situ hybridization. All tumors displayed multiple CNV/CN-LOH events (median, 7.5 per tumor). Three of 4 tumors displayed similar CNV/CN-LOH patterns between the epithelial and mesenchymal components within each tumor, supporting a common clonal origin. Recurrent changes included allelic loss at 9p21 (CDKN2A), 9q (PTCH1), and 17p (TP53). Allelic losses of chromosome 16 including CDH1 (E-cadherin) were present in 2 tumors and were restricted to the sarcomatous component. TP53 mutation analysis revealed an R248L mutation in both epithelial and mesenchymal components of 1 tumor. No TP53 rearrangements were identified. Our findings indicate that basal cell carcinosarcomas harbor CNV/CN-LOH changes similar to conventional basal cell carcinoma, with additional changes including recurrent 9p21 losses and a relatively high burden of copy number changes. In addition, most cutaneous carcinosarcomas show evidence of clonality between epithelial and mesenchymal components. Published by Elsevier Inc.

  18. Physiological integration ameliorates negative effects of drought stress in the clonal herb Fragaria orientalis.

    Directory of Open Access Journals (Sweden)

    Yunchun Zhang

    Full Text Available Clonal growth allows plants to spread horizontally and to establish ramets in sites of contrasting resource status. If ramets remain physiologically integrated, clones in heterogeneous environments can act as cooperative systems--effects of stress on one ramet can be ameliorated by another connected ramet inhabiting benign conditions. But little is known about the effects of patch contrast on physiological integration of clonal plants and no study has addressed its effects on physiological traits like osmolytes, reactive oxygen intermediates and antioxidant enzymes. We examined the effect of physiological integration on survival, growth and stress indicators such as osmolytes, reactive oxygen intermediates (ROIs and antioxidant enzymes in a clonal plant, Fragaria orientalis, growing in homogenous and heterogeneous environments differing in patch contrast of water availability (1 homogeneous (no contrast group; 2 low contrast group; 3 high contrast group. Drought stress markedly reduced the survival and growth of the severed ramets of F. orientalis, especially in high contrast treatments. Support from a ramet growing in benign patch considerably reduced drought stress and enhanced growth of ramets in dry patches. The larger the contrast between water availability, the larger the amount of support the depending ramet received from the supporting one. This support strongly affected the growth of the supporting ramet, but not to an extent to cause increase in stress indicators. We also found indication of costs related to maintenance of physiological connection between ramets. Thus, the net benefit of physiological integration depends on the environment and integration between ramets of F. orientalis could be advantageous only in heterogeneous conditions with a high contrast.

  19. Clonal mutations in primary human glial tumors: evidence in support of the mutator hypothesis

    Directory of Open Access Journals (Sweden)

    Sarkar Chitra

    2007-10-01

    Full Text Available Abstract Background A verifiable consequence of the mutator hypothesis is that even low grade neoplasms would accumulate a large number of mutations that do not influence the tumor phenotype (clonal mutations. In this study, we have attempted to quantify the number of clonal mutations in primary human gliomas of astrocytic cell origin. These alterations were identified in tumor tissue, microscopically confirmed to have over 70% neoplastic cells. Methods Random Amplified Polymorphic DNA (RAPD analysis was performed using a set of fifteen 10-mer primers of arbitrary but definite sequences in 17 WHO grade II astrocytomas (low grade diffuse astrocytoma or DA and 16 WHO grade IV astrocytomas (Glioblastoma Multiforme or GBM. The RAPD profile of the tumor tissue was compared with that of the leucocyte DNA of the same patient and alteration(s scored. A quantitative estimate of the overall genomic changes in these tumors was obtained by 2 different modes of calculation. Results The overall change in the tumors was estimated to be 4.24% in DA and 2.29% in GBM by one method and 11.96% and 6.03% in DA and GBM respectively by the other. The difference between high and lower grade tumors was statistically significant by both methods. Conclusion This study demonstrates the presence of extensive clonal mutations in gliomas, more in lower grade. This is consistent with our earlier work demonstrating that technique like RAPD analysis, unbiased for locus, is able to demonstrate more intra-tumor genetic heterogeneity in lower grade gliomas compared to higher grade. The results support the mutator hypothesis proposed by Loeb.

  20. Clonal types of Toxoplasma gondii among immune compromised and immune competent individuals in Accra, Ghana.

    Science.gov (United States)

    Ayi, Irene; Kwofie, Kofi Dadzie; Blay, Emmanuel Awusah; Osei, Joseph Harold Nyarko; Frempong, Kwadwo Kyeremeh; Koku, Roberta; Ghansah, Anita; Lartey, Margaret; Suzuki, Takashi; Boakye, Daniel Adjei; Koram, Kwadwo Ansah; Ohta, Nobuo

    2016-06-01

    There are three major clonal lineages, types I, II, and III, of Toxoplasma gondii known to cause human toxoplasmosis worldwide. Toxoplasma gondii infections have, however, not been genotyped in Ghana. This study detected the clonal types infecting immune compromised and immune competent individuals in Accra, Ghana. Blood samples were obtained from 148 HIV seropositive pre-antiretroviral therapy individuals (0 ≤ CD4(+) T-cell count/μl blood ≤ 200) at the Fevers Unit and 149 HIV seronegative apparently healthy blood donors at the blood bank, all of the Korle-Bu Teaching Hospital. Genomic DNA was extracted and multilocus genotyping conducted by nested PCR-RFLP analysis using GRA6, SAG3, and BTUB gene markers. Among the HIV seropositive participants, 54.7% (81/148) were T. gondii DNA positive for any of the markers. Out of the 81, 42.0% (34) were positive for SAG3 only, 30.9% (25) for GRA6 only, 24.7% (20) for both SAG3 and GRA6, and 2.5% (2) for SAG3, GRA6, and BTUB. Overall, 93.8% of the positives were of clonal type II, 1.2% type I, while 4.9% (4) were atypical or mixed types (I and II). In the healthy blood donors, prevalence of T. gondii DNA positivity was 3.4% (5/149) by SAG3 and/or GRA6; among them, 60.0% (3/5) were type I, and the remaining 40.0%, type II. This study showed a relatively high prevalence of active T. gondii infections in immune compromised patients and low prevalence in immune competent individuals in Accra. Type II was highly prevalent. Detection of T. gondii in blood donors raises public health concerns and screening for T. gondii should be considered. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds.

    Science.gov (United States)

    Getz, Wayne M; Salter, Richard; Lyons, Andrew J; Sippl-Swezey, Nicolas

    2015-01-01

    We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals' foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual's biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1.) within-patch consumer-resource dynamics, 2.) within-generation movement and competition mitigation processes, 3.) across-generation evolutionary processes, and 4.) multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among individuals

  2. Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds.

    Directory of Open Access Journals (Sweden)

    Wayne M Getz

    Full Text Available We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals' foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual's biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1. within-patch consumer-resource dynamics, 2. within-generation movement and competition mitigation processes, 3. across-generation evolutionary processes, and 4. multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among

  3. Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina.

    Science.gov (United States)

    Garcia-Cisneros, A; Pérez-Portela, R; Almroth, B C; Degerman, S; Palacín, C; Sköld, H Nilsson

    2015-11-01

    Telomeres usually shorten during an organism's lifespan and have thus been used as an aging and health marker. When telomeres become sufficiently short, senescence is induced. The most common method of restoring telomere length is via telomerase reverse transcriptase activity, highly expressed during embryogenesis. However, although asexual reproduction from adult tissues has an important role in the life cycles of certain species, its effect on the aging and fitness of wild populations, as well as its implications for the long-term survival of populations with limited genetic variation, is largely unknown. Here we compare relative telomere length of 58 individuals from four populations of the asexually reproducing starfish Coscinasterias tenuispina. Additionally, 12 individuals were used to compare telomere lengths in regenerating and non-regenerating arms, in two different tissues (tube feet and pyloric cecum). The level of clonality was assessed by genotyping the populations based on 12 specific microsatellite loci and relative telomere length was measured via quantitative PCR. The results revealed significantly longer telomeres in Mediterranean populations than Atlantic ones as demonstrated by the Kruskal-Wallis test (K=24.17, significant value: P-value<0.001), with the former also characterized by higher levels of clonality derived from asexual reproduction. Telomeres were furthermore significantly longer in regenerating arms than in non-regenerating arms within individuals (pyloric cecum tissue: Mann-Whitney test, V=299, P-value<10(-6); and tube feet tissue Student's t=2.28, P-value=0.029). Our study suggests that one of the mechanisms responsible for the long-term somatic maintenance and persistence of clonal populations is telomere elongation.

  4. Effect of lenalidomide treatment on clonal architecture of myelodysplastic syndromes without 5q deletion.

    Science.gov (United States)

    Chesnais, Virginie; Renneville, Aline; Toma, Andrea; Lambert, Jérôme; Passet, Marie; Dumont, Florent; Chevret, Sylvie; Lejeune, Julie; Raimbault, Anna; Stamatoullas, Aspasia; Rose, Christian; Beyne-Rauzy, Odile; Delaunay, Jacques; Solary, Eric; Fenaux, Pierre; Dreyfus, François; Preudhomme, Claude; Kosmider, Olivier; Fontenay, Michaela

    2016-02-11

    Non-del(5q) transfusion-dependent low/intermediate-1 myelodysplastic syndrome (MDS) patients achieve an erythroid response with lenalidomide in 25% of cases. Addition of an erythropoiesis-stimulating agent could improve response rate. The impact of recurrent somatic mutations identified in the diseased clone in response to lenalidomide and the drug's effects on clonal evolution remain unknown. We investigated recurrent mutations by next-generation sequencing in 94 non-del(5q) MDS patients randomized in the GFM-Len-Epo-08 clinical trial to lenalidomide or lenalidomide plus epoetin β. Clonal evolution was analyzed after 4 cycles of treatment in 42 cases and reanalyzed at later time points in 18 cases. The fate of clonal architecture of single CD34(+)CD38(-) hematopoietic stem cells was also determined in 5 cases. Mutation frequency was >10%: SF3B1 (74.5%), TET2 (45.7%), DNMT3A (20.2%), and ASXL1 (19.1%). Analysis of variant allele frequencies indicated a decrease of major mutations in 15 of 20 responders compared with 10 of 22 nonresponders after 4 cycles. The decrease in the variant allele frequency of major mutations was more significant in responders than in nonresponders (P < .001). Genotyping of single CD34(+)CD38(-) cell-derived colonies showed that the decrease in the size of dominant subclones could be associated with the rise of founding clones or of hematopoietic stem cells devoid of recurrent mutations. These effects remained transient, and disease escape was associated with the re-emergence of the dominant subclones. In conclusion, we show that, although the drug initially modulates the distribution of subclones, loss of treatment efficacy coincides with the re-expansion of the dominant subclone. This trial was registered at www.clinicaltrials.gov as #NCT01718379. © 2016 by The American Society of Hematology.

  5. Defense signaling among interconnected ramets of a rhizomatous clonal plant, induced by jasmonic-acid application

    Science.gov (United States)

    Chen, Jin-Song; Lei, Ning-Fei; Liu, Qing

    2011-07-01

    Resource sharing between ramets of clonal plants is a well-known phenomenon that allows stoloniferous and rhizomatous species to internally transport water, mineral nutrients and carbohydrates from sites of high supply to sites of high demand. Moreover, vascular ramet connections are likely to provide an excellent means to share substances other than resources, such as defense signals. In a greenhouse experiment, the rhizomatous sedge Carex alrofusca, consisting of integrated ramets of different ages, was used to study the transmission of defense signals through belowground rhizome connections in response to local spray with jasmonic-acid. A feeding preference test with the caterpillar Gynaephora rnenyuanensis was employed to assess benefits of rhizome connections on defense signaling. Young ramets were more responsive to jasmonic-acid treatment than middle-aged or old ramets. Condensed tannin content in the foliage of young ramets showed a significant increase and soluble carbohydrate and nitrogen content showed marginally significant decreases in the 1 mM jasmonic-acid treatment but not in control and/or 0.0001 mM jasmonic-acid treatments. The caterpillar G. rnenyuanensis preferentially grazed young ramets. After a localized spray of 1 mM jasmonic-acid, the leaf area of young ramets consumed by herbivores was greatly reduced. We propose that defense signals may be transmitted through physical connections (stolon or rhizome) among interconnected ramets of clonal plants. Induced resistance to herbivory may selectively enhance the protection of more vulnerable and valuable plant tissues and confer a significant benefit to clonal plants by a modular risk-spreading strategy, equalizing ontogenetic differences of unevenly-aged ramets in chemical defense compounds and nutritional properties of tissue.

  6. NetF-producing Clostridium perfringens: Clonality and plasmid pathogenicity loci analysis.

    Science.gov (United States)

    Mehdizadeh Gohari, Iman; Kropinski, Andrew M; Weese, Scott J; Whitehead, Ashley E; Parreira, Valeria R; Boerlin, Patrick; Prescott, John F

    2017-04-01

    Clostridium perfringens is an important cause of foal necrotizing enteritis and canine acute hemorrhagic diarrhea. A major virulence determinant of the strains associated with these diseases appears to be a beta-sheet pore-forming toxin, NetF, encoded within a pathogenicity locus (NetF locus) on a large tcp-conjugative plasmid. Strains producing NetF also produce the putative toxin NetE, encoded within the same pathogenicity locus, as well as CPE enterotoxin and CPB2 on a second plasmid, and sometimes the putative toxin NetG within a pathogenicity locus (NetG locus) on another separate large conjugative plasmid. Previous genome sequences of two netF-positive C. perfringens showed that they both shared three similar plasmids, including the NetF/NetE and CPE/CPB2 toxins-encoding plasmids mentioned above and a putative bacteriocin-encoding plasmid. The main purpose of this study was to determine whether all NetF-producing strains share this common plasmid profile and whether their distinct NetF and CPE pathogenicity loci are conserved. To answer this question, 15 equine and 15 canine netF-positive isolates of C. perfringens were sequenced using Illumina Hiseq2000 technology. In addition, the clonal relationships among the NetF-producing strains were evaluated by core genome multilocus sequence typing (cgMLST). The data obtained showed that all NetF-producing strains have a common plasmid profile and that the defined pathogenicity loci on the plasmids are conserved in all these strains. cgMLST analysis showed that the NetF-producing C. perfringens strains belong to two distinct clonal complexes. The pNetG plasmid was absent from isolates of one of the clonal complexes, and there were minor but consistent differences in the NetF/NetE and CPE/CPB2 plasmids between the two clonal complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Clonal diversity of Staphylococcus aureus originating from the small ruminants goats and sheep

    DEFF Research Database (Denmark)

    Concepción Porrero, M.; Hasman, Henrik; Vela, Ana I.

    2012-01-01

    Staphylococcus aureus is an important pathogen in humans and many animal species. The prevalence of different clonal types in animal species remains largely unknown. We analyzed 267 S. aureus from intramammary infections in goats (47) and sheep (220) by spa typing, multi-locus sequence typing (MLST......) and antimicrobial susceptibility. The most frequent spa types in goats were t337 (N = 9), t759 (N = 6) and t1534 (N = 5). Sheep isolates mainly belonged to spa types t1534 (N = 72), t2678 (N = 29) and t3576 (N = 20). Eighteen novel spa-types were observed; two from goat strains, 13 from sheep and three in both...

  8. Identification of uropathogenic Escherichia coli clonal group A (CgA) in hospitalised patients.

    Science.gov (United States)

    Dias, Rubens C S; Marangoni, Denise V; Riley, Lee W; Moreira, Beatriz M

    2009-08-01

    This study provides the first description of healthcare-associated infections with Escherichia coli clonal group A (CgA) isolates in Latin America. Isolates were typed by enterobacterial repetitive intergenic consensus-PCR, pulsed-field gel electrophoresis, E. coli phylogenetic grouping, multilocus sequence typing and fimH single nucleotide polymorphism analysis. Out of 42 E. coli hospital isolates studied, three belonged to E. coli phylogenetic group D and ST69 and had fimH sequences identical to that of the CgA reference strain ATCC BAA-457. E. coli CgA is another potential source of resistant infections in hospitals.

  9. Identification of uropathogenic Escherichia coli clonal group A (CgA in hospitalised patients

    Directory of Open Access Journals (Sweden)

    Rubens CS Dias

    2009-08-01

    Full Text Available This study provides the first description of healthcare-associated infections with Escherichia coli clonal group A (CgA isolates in Latin America. Isolates were typed by enterobacterial repetitive intergenic consensus-PCR, pulsed-field gel electrophoresis, E. coli phylogenetic grouping, multilocus sequence typing and fimH single nucleotide polymorphism analysis. Out of 42 E. coli hospital isolates studied, three belonged to E. coli phylogenetic group D and ST69 and had fimH sequences identical to that of the CgA reference strain ATCC BAA-457. E. coli CgA is another potential source of resistant infections in hospitals.

  10. Clonal dominance between subpopulations of mixed small cell lung cancer xenografts implanted ectopically in nude mice

    DEFF Research Database (Denmark)

    Aabo, K; Vindeløv, L L; Spang-Thomsen, M

    1995-01-01

    Clonal evolution of neoplastic cells during solid tumour growth leads to the emergence of new tumour cell subpopulations with diverging phenotypic characteristics which may alter the behaviour of a malignant disease. Cellular interaction was studied in mixed xenografts in nude mice and during...... in vitro growth of two sets of small cell lung cancer (SCLC) subpopulations (54A, 54B and NYH, NYH2). The tumour cell lines differed in cellular DNA content enabling flow cytometric DNA analysis (FCM) to be used to monitor changes in the fractional composition of the mixed cell populations. The progeny...

  11. Rare sexual reproduction events in the clonal reproduction system of introduced populations of the little fire ant.

    Science.gov (United States)

    Foucaud, Julien; Jourdan, Hervé; Le Breton, Julien; Loiseau, Anne; Konghouleux, Djoël; Estoup, Arnaud

    2006-08-01

    A unique reproductive system has previously been described in Wasmannia auropunctata, a widespread invasive ant species, where males are produced clonally, female queens are parthenogens, and female workers are produced sexually. However, these findings were mostly based on samples originating from only a limited part of the native range of the species in South America. We used microsatellite markers to uncover the reproductive modes displayed by a large number of nests collected in various invasive W. auropunctata populations introduced 40 years ago into New Caledonia, where the species now forms a single 450-km-long supercolony. Although the main reproduction system in New Caledonia remained clonality for both male and female reproductives, we found evidence of rare sexual reproduction events that led to the production of both new queen and male clonal lineages. All clonal lineages observed in New Caledonia potentially derived from sexual reproduction, recombination, and mutation events from a single female and a single male genotype. Hence, the male and female gene pools are not strictly separated in New Caledonia and the two sexes do not follow independent evolutionary trajectories. Our results also suggest genetic determination for both parthenogenesis and caste. We discuss the evolutionary implications of the emergence of sex in the clonal reproduction system of introduced populations of W. auropunctata.

  12. Clonal dissemination of multilocus sequence type 11 Klebsiella pneumoniae carbapenemase - producing K. pneumoniae in a Chinese teaching hospital.

    Science.gov (United States)

    Sun, Kangde; Chen, Xu; Li, Chunsheng; Yu, Zhongmin; Zhou, Qi; Yan, Yuzhong

    2015-02-01

    Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae has disseminated rapidly in China. We aimed to analyze the molecular epidemiology of four KPC-producing K. pneumoniae strains isolated from a suspected clonal outbreak during a 3-month period and to track the dissemination of KPC-producing K. pneumonia retrospectively. We created antimicrobial susceptibility profiles using an automated broth microdilution system and broth microdilution methods. We screened carbapenemase and KPC phenotypes using the modified Hodge test and meropenem-boronic acid (BA) disk test, respectively. We identified β-lactamase genes with PCR and sequencing. We investigated clonal relatedness for epidemiological comparison using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). All isolates expressed multidrug resistance and yielded positive results for the modified Hodge and meropenem-BA disk tests. The isolates all carried blaKPC -2 , and coproduced CTX-M-type extended-spectrum β-lactamase. PFGE and MLST showed that the isolates were clonally related. The PFGE patterns of these isolates had ≥90% similarity. We found a single clone, sequence type (ST) 11, and its typical dissemination mode resembled clonal spread. The dissemination of KPC-producing K. pneumoniae is clonally related and there is probable local transmission of a successful ST11 clone. © 2014 APMIS. Published by John Wiley & Sons Ltd.

  13. Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population.

    Science.gov (United States)

    Clark, Clifford G; Berry, Chrystal; Walker, Matthew; Petkau, Aaron; Barker, Dillon O R; Guan, Cai; Reimer, Aleisha; Taboada, Eduardo N

    2016-12-03

    Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates. Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain. The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression

  14. The first dose of a Haemophilus influenzae type b conjugate vaccine reactivates memory B cells: evidence for extensive clonal selection, intraclonal affinity maturation, and multiple isotype switches to IgA2

    DEFF Research Database (Denmark)

    Hougs, L; Juul, L; Ditzel, H J

    1999-01-01

    The Ab response of a healthy adult to the first dose of a Haemophilus influenzae type b capsular polysaccharide (HibCP) conjugate vaccine was studied at the level of Ig gene usage by circulating Ab-secreting cells. Forty-one IgA and 17 IgG mRNA sequences were obtained. The major part...... selected, and expanded population of cells existing before vaccination, i.e., memory B cells. The dominating heavy and light chains of the response were combined in a Fab that bound HibCP. It was shown that the shared heavy and light chain mutations increased the affinity for HibCP considerably, indicating...... that the clonal selection had been driven by affinity. Pre-existing memory cells in unvaccinated adults may explain several features of Ab responses to polysaccharide vaccines and may play a role in acquiring the ability to respond to pure polysaccharides during infancy....

  15. Plasma chromograninx

    DEFF Research Database (Denmark)

    Goetze, Jens P; Hilsted, Linda M; Rehfeld, Jens F

    2014-01-01

    Cardiovascular risk assessment remains difficult in elderly patients. We examined whether chromogranin A (CgA) measurement in plasma may be valuable in assessing risk of death in elderly patients with symptoms of heart failure in a primary care setting. A total of 470 patients (mean age 73 years......) were followed for 10 years. For CgA plasma measurement, we used a two-step method including a screening test and a confirmative test with plasma pre-treatment with trypsin. Cox multivariable proportional regression and receiver-operating curve (ROC) analyses were used to assess mortality risk...... of follow-up showed significant additive value of CgA confirm measurements compared with NT-proBNP and clinical variables. CgA measurement in the plasma of elderly patients with symptoms of heart failure can identify those at increased risk of short- and long-term mortality....

  16. Plasma Cleaning

    Science.gov (United States)

    Hintze, Paul E.

    2016-01-01

    NASA's Kennedy Space Center has developed two solvent-free precision cleaning techniques: plasma cleaning and supercritical carbon dioxide (SCCO2), that has equal performance, cost parity, and no environmental liability, as compared to existing solvent cleaning methods.

  17. Plasma confinement

    CERN Document Server

    Hazeltine, R D

    2003-01-01

    Detailed and authoritative, this volume examines the essential physics underlying international research in magnetic confinement fusion. It offers readable, thorough accounts of the fundamental concepts behind methods of confining plasma at or near thermonuclear conditions. Designed for a one- or two-semester graduate-level course in plasma physics, it also represents a valuable reference for professional physicists in controlled fusion and related disciplines.

  18. FLOCK cluster analysis of plasma cell flow cytometry data predicts bone marrow involvement by plasma cell neoplasia.

    Science.gov (United States)

    Dorfman, David M; LaPlante, Charlotte D; Li, Betty

    2016-09-01

    We analyzed plasma cell populations in bone marrow samples from 353 patients with possible bone marrow involvement by a plasma cell neoplasm, using FLOCK (FLOw Clustering without K), an unbiased, automated, computational approach to identify cell subsets in multidimensional flow cytometry data. FLOCK identified discrete plasma cell populations in the majority of bone marrow specimens found by standard histologic and immunophenotypic criteria to be involved by a plasma cell neoplasm (202/208 cases; 97%), including 34 cases that were negative by standard flow cytometric analysis that included clonality assessment. FLOCK identified discrete plasma cell populations in only a minority of cases negative for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria (38/145 cases; 26%). Interestingly, 55% of the cases negative by standard analysis, but containing a FLOCK-identified discrete plasma cell population, were positive for monoclonal gammopathy by serum protein electrophoresis and immunofixation. FLOCK-identified and quantitated plasma cell populations accounted for 3.05% of total cells on average in cases positive for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria, and 0.27% of total cells on average in cases negative for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria (pflow cytometric analysis, and had specificity of 74%, PPV of 84% and NPV of 95%. FLOCK analysis, which has been shown to provide useful diagnostic information for evaluating patients with suspected systemic mastocytosis, is able to identify neoplastic plasma cell populations analyzed by flow cytometry, and may be helpful in the diagnostic evaluation of bone marrow samples for involvement by plasma cell neoplasia. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Clonal Propagation of Khaya senegalensis: The Effects of Stem Length, Leaf Area, Auxins, Smoke Solution, and Stockplant Age

    Directory of Open Access Journals (Sweden)

    Catherine Ky-Dembele

    2011-01-01

    Full Text Available Khaya senegalensis is a multipurpose African timber species. The development of clonal propagation could improve plantation establishment, which is currently impeded by mahogany shoot borer. To examine its potential for clonal propagation, the effects of cutting length, leaf area, stockplant maturation, auxin, and smoke solution treatments were investigated. Leafy cuttings rooted well (up to 80% compared to leafless cuttings (0%. Cuttings taken from seedlings rooted well (at least 95%, but cuttings obtained from older trees rooted poorly (5% maximum. The rooting ability of cuttings collected from older trees was improved (16% maximum by pollarding. Auxin application enhanced root length and the number of roots while smoke solution did not improve cuttings' rooting ability. These results indicate that juvenile K. senegalensis is amenable to clonal propagation, but further work is required to improve the rooting of cuttings from mature trees.

  20. The Physics of Ion Decoupling in Magnetized Plasma Explosions

    Energy Technology Data Exchange (ETDEWEB)

    Hewett, D; Larson, D; Brecht, S

    2011-02-08

    When a finite pulse of plasma expands into a magnetized background plasma, MHD predicts the pulse expel background plasma and its B-field - i.e. cause a magnetic 'bubble'. The expanding plasma is confined within the bubble, later to escape down the B-field lines. MHD suggests that the debris energy goes to expelling the B-field from the bubble volume and kinetic energy of the displaced background. For HANEs, this is far from the complete story. For many realistic HANE regimes, the long mean-free-path for collisions necessitates a Kinetic Ion Simulation Model (KISM). The most obvious effect is that the debris plasma can decouple and slip through the background plasma. The implications are: (1) the magnetic bubble is not as large as expected and (2) the debris is no longer confined within the magnetic bubble.

  1. Multidisciplinary insight into clonal expansion of HTLV-1-infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing.

    Science.gov (United States)

    Farmanbar, Amir; Firouzi, Sanaz; Park, Sung-Joon; Nakai, Kenta; Uchimaru, Kaoru; Watanabe, Toshiki

    2017-01-31

    Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the direct cause of ATL onset, and integration of HTLV-1 into the human genome is essential for clonal expansion of leukemic cells. Therefore, monitoring clonal expansion of HTLV-1-infected cells via isolation of integration sites assists in analyzing infected individuals from early infection to the final stage of ATL development. However, because of the complex nature of clonal expansion, the underlying mechanisms have yet to be clarified. Combining computational/mathematical modeling with experimental and clinical data of integration site-based clonality analysis derived from next generation sequencing technologies provides an appropriate strategy to achieve a better understanding of ATL development. As a comprehensively interdisciplinary project, this study combined three main aspects: wet laboratory experiments, in silico analysis and empirical modeling. We analyzed clinical samples from HTLV-1-infected individuals with a broad range of proviral loads using a high-throughput methodology that enables isolation of HTLV-1 integration sites and accurate measurement of the size of infected clones. We categorized clones into four size groups, "very small", "small", "big", and "very big", based on the patterns of clonal growth and observed clone sizes. We propose an empirical formal model based on deterministic finite state automata (DFA) analysis of real clinical samples to illustrate patterns of clonal expansion. Through the developed model, we have translated biological data of clonal expansion into the formal language of mathematics and represented the observed clonality data with DFA. Our data suggest that combining experimental data (absolute size of clones) with DFA can describe the clonality status of patients. This kind of modeling provides a basic

  2. Limpeza clonal de mudas de videira infectadas por Xanthomonas campestris pv. viticola Clonal cleaning of grapevine plants infected by Xanthomonas campestris pv. viticola

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    Adriano Márcio Freire Silva

    2013-03-01

    Full Text Available O cancro bacteriano da videira é causado por Xanthomonas campestris pv. viticola (Xcv. Visando à limpeza clonal de mudas de 'Red Globe', foram estudados: tamanho ideal de ápices e gemas axilares para cultivo em meio de Galzy modificado (MGM; efeito da termoterapia (38ºC/30 dias; e ação de antibióticos na eliminação de Xcv em videiras infectadas. Os percentuais de contaminação por Xcv e de regeneração foram analisados, e as plantas obtidas foram indexadas em meio ágar nutritivo-dextrose-extrato de levedura-ampicilina (NYDAM, seguindo-se teste de patogenicidade. O cultivo de explantes com 3 mm possibilitou a obtenção de plantas livres da bactéria, com regeneração 14,3 vezes maior que explantes com 1 mm. A termoterapia de mudas infectadas, associada ao cultivo in vitro, não eliminou o patógeno. O cultivo de explantes com 10 mm, durante 40 dias em MGM + cefotaxima (300 mg L-1, proporcionou limpeza clonal das mudas. A indexação de plantas de videira regeneradas in vitro, quanto à infecção por Xcv utilizando NYDAM, seguida de teste de patogenicidade, é uma alternativa econômica e eficiente para produção de mudas de alta qualidade fitossanitária.Bacterial canker is caused by Xanthomonas campestris pv. viticola (Xcv. In order to eliminate Xcv from 'Red Globe' plants it was studied: optimal size of meristem tips and axillary buds for cultivation in modified Galzy's medium (MGM; effects of thermotherapy (38ºC/30 days; and action of antibiotics in the elimination of Xcv in infected grapevines. The percentages of contamination by Xcv and regeneration were analyzed and plants obtained were indexed using the semi-selective culture medium nutrient agar-dextrose-yeast extract-ampicilin (NYDAM followed by a pathogenicity test. The cultivation of 3 mm explants permitted to obtain plants free of bacteria with regeneration 14.3 times higher than 1 mm explants. The thermotherapy of infected plants associated to the in vitro culture

  3. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

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    Rachel Daniels

    Full Text Available Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs, use of rapid diagnostic tests (RDTs for malaria detection, and deployment of artemisinin combination therapy (ACT. Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.

  4. Clonal relatedness and resistance patterns of Salmonella Corvallis from poultry carcasses in a Brazilian slaughterhouse.

    Science.gov (United States)

    Yamatogi, Ricardo S; Oliveira, Heverton C; Camargo, Carlos H; Fernandes, Sueli A; Hernandes, Rodrigo T; Pinto, José Pan; Rall, Vera Lm; Araújo, João P

    2015-10-29

    Salmonella is a major cause of foodborne disease, and poultry products are important contributors to the transmission of this zoonotic pathogen. Although considered to be rare in most countries, Salmonella Corvallis has been reported in specific geographic areas isolated from both human and non-human sources. The aim of this study was to report the occurrence, the antimicrobial resistance profiles including the extended-spectrum beta-lactamase (ESBL) production, and the clonal relatedness of S. Corvallis strains. A total of 132 fragments of poultry carcasses from a slaughterhouse in São Paulo State, Brazil, were collected at different stages of the manufacturing process (post-bleeding, post-plucking, and post-chilling) and analyzed for the presence of Salmonella. Antimicrobial resistance was determined by disc diffusion method and Etest. Clonal relatedness was determined by pulsed-field gel electrophoresis (PFGE). Among the 272 Salmonella strains recovered, fourteen were S. Corvallis. Ten (71.4%) showed ESBL production and resistance to at least three antimicrobial agents. Nalidixic acid resistance and reduced ciprofloxacin susceptibility was verified in four (28.6%) strains. PFGE analyses showed that all the S. Corvallis strains belonged to the same pulsotype. This study identified genetically related S. Corvallis strains exhibiting ESBL production and reduced susceptibility to quinolone. The results suggest the need to improve the sanitary conditions in the slaughterhouse. Moreover, from a public health perspective, continuous surveillance on Salmonella is needed to control the dissemination of this important zoonotic pathogen and its resistance determinants.

  5. Characterization of virulence factors and clonal diversity of Enterococcus faecalis isolates from treated dental root canals.

    Science.gov (United States)

    Zoletti, Gustavo O; Pereira, Eliezer M; Schuenck, Ricardo P; Teixeira, Lúcia M; Siqueira, José F; dos Santos, Kátia Regina N

    2011-01-01

    The high prevalence of Enterococcus faecalis in root canal treated teeth with post-treatment disease, as evidenced by both molecular and traditional culturing methods, suggests that this species may be a key player in endodontic treatment failure. This study aimed to detect virulence factors by phenotypic and western blotting tests, and virulence genes by PCR from 20 clinical strains of E. faecalis isolated from treated root canals of teeth with (10) or without (10) apical periodontitis. Moreover, genomic diversity of these strains was assessed by pulsed-field gel electrophoresis (PFGE) and rep-PCR. All 20 strains presented the gelE gene (gelatinase), but 10 of them did not hydrolyze gelatin. Seven of the 10 gelatinase-producing isolates were recovered from root canals with lesions, which suggests a role for this virulence factor in the pathogenesis of post-treatment disease. The esp gene was expressed only in cases where gelatinase production was negative. The other virulence genes were found in 90% (efaA and ace genes), 45% (agg gene) and 95% (cpd gene) of the E. faecalis isolates. As for PFGE and rep-PCR, no specific clonal type of E. faecalis was found in association with teeth with or without disease, revealing the interindividual clonal diversity of endodontic infections. Copyright © 2010 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

  6. Clonal persistence of Salmonella enterica serovars Montevideo, Tennessee, and Infantis in feed factories.

    Science.gov (United States)

    Prunić, Bojana; Milanov, Dubravka; Velhner, Maja; Pajić, Marko; Pavlović, Ljiljana; Mišić, Dušan

    2016-06-30

    Novel molecular techniques applied in biotechnology research have provided sound evidence on clonal persistence of distinct serovars of Salmonella in feed factory environments, over long periods of time (months, even years), which can be responsible for repeated in-house contamination of final products. In this study, we examined the possibility of clonal persistence of isolates of three Salmonella serovars that have been repeatedly identified in animal feed samples from three feed factories throughout a two-year period. The isolates Salmonella enterica serovars Tennessee (n = 7), Montevideo (n = 8), and Infantis (n = 4) were tested for genetic diversity using pulsed-field gel electrophoresis (PFGE) and multicellular behavior patterns by applying the Congo red agar test. SpeI and XbaI macro-restriction profiles indicated that isolates S. Montevideo and S. Infantis were identical, whereas isolates of S. Tennessee demonstrated greater genetic diversity, although the genetic differences did not exceed 10%. All Salmonella serovars demonstrated the ability to produce predominant matrix compounds essential for biofilm formation, curli fimbriae and cellulose. The identification of identical clones of S. Montevideo and S. Infantis, as well as the minor genetic diversity of S. Tennessee, which have been repeatedly isolated from animal feed in three production plants throughout a two-year period, indirectly suggests the possibility of their persistence in feed factory environments. Their ability to express the key biofilm matrix components further supports this hypothesis.

  7. Brake fault diagnosis using Clonal Selection Classification Algorithm (CSCA – A statistical learning approach

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    R. Jegadeeshwaran

    2015-03-01

    Full Text Available In automobile, brake system is an essential part responsible for control of the vehicle. Any failure in the brake system impacts the vehicle's motion. It will generate frequent catastrophic effects on the vehicle cum passenger's safety. Thus the brake system plays a vital role in an automobile and hence condition monitoring of the brake system is essential. Vibration based condition monitoring using machine learning techniques are gaining momentum. This study is one such attempt to perform the condition monitoring of a hydraulic brake system through vibration analysis. In this research, the performance of a Clonal Selection Classification Algorithm (CSCA for brake fault diagnosis has been reported. A hydraulic brake system test rig was fabricated. Under good and faulty conditions of a brake system, the vibration signals were acquired using a piezoelectric transducer. The statistical parameters were extracted from the vibration signal. The best feature set was identified for classification using attribute evaluator. The selected features were then classified using CSCA. The classification accuracy of such artificial intelligence technique has been compared with other machine learning approaches and discussed. The Clonal Selection Classification Algorithm performs better and gives the maximum classification accuracy (96% for the fault diagnosis of a hydraulic brake system.

  8. Limpeza clonal de mudas de videira infectadas por Xanthomonas campestris pv. viticola

    Directory of Open Access Journals (Sweden)

    Adriano Márcio Freire Silva

    2013-03-01

    Full Text Available O cancro bacteriano da videira é causado por Xanthomonas campestris pv. viticola (Xcv. Visando à limpeza clonal de mudas de 'Red Globe', foram estudados: tamanho ideal de ápices e gemas axilares para cultivo em meio de Galzy modificado (MGM; efeito da termoterapia (38ºC/30 dias; e ação de antibióticos na eliminação de Xcv em videiras infectadas. Os percentuais de contaminação por Xcv e de regeneração foram analisados, e as plantas obtidas foram indexadas em meio ágar nutritivo-dextrose-extrato de levedura-ampicilina (NYDAM, seguindo-se teste de patogenicidade. O cultivo de explantes com 3 mm possibilitou a obtenção de plantas livres da bactéria, com regeneração 14,3 vezes maior que explantes com 1 mm. A termoterapia de mudas infectadas, associada ao cultivo in vitro, não eliminou o patógeno. O cultivo de explantes com 10 mm, durante 40 dias em MGM + cefotaxima (300 mg L-1, proporcionou limpeza clonal das mudas. A indexação de plantas de videira regeneradas in vitro, quanto à infecção por Xcv utilizando NYDAM, seguida de teste de patogenicidade, é uma alternativa econômica e eficiente para produção de mudas de alta qualidade fitossanitária.

  9. Unexpected heterogeneity derived from Cas9 ribonucleoprotein-introduced clonal cells at the HPRT1 locus.

    Science.gov (United States)

    Sakuma, Tetsushi; Mochida, Keiji; Nakade, Shota; Ezure, Toru; Minagawa, Sachi; Yamamoto, Takashi

    2018-02-09

    Single-cell cloning is an essential technique for establishing genome-edited cell clones mediated by programmable nucleases such as CRISPR-Cas9. However, residual genome-editing activity after single-cell cloning may cause heterogeneity in the clonal cells. Previous studies showed efficient mutagenesis and rapid degradation of CRISPR-Cas9 components in cultured cells by introducing Cas9 ribonucleoproteins (RNPs). In this study, we investigated how the timing for single-cell cloning of Cas9 RNP-transfected cells affected the heterogeneity of the resultant clones. We carried out transfection of Cas9 RNPs targeting several loci in the HPRT1 gene in HCT116 cells, followed by single-cell cloning at 24, 48, 72 hr and 1 week post-transfection. After approximately 3 weeks of incubation, the clonal cells were collected and genotyped by high-resolution microchip electrophoresis and Sanger sequencing. Unexpectedly, long-term incubation before single-cell cloning resulted in highly heterogeneous clones. We used a lipofection method for transfection, and the media containing transfectable RNPs were not removed before single-cell cloning. Therefore, the active Cas9 RNPs were considered to be continuously incorporated into cells during the precloning incubation. Our findings provide a warning that lipofection of Cas9 RNPs may cause continuous introduction of gene mutations depending on the experimental procedures. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  10. Reproductive strategies and isolation-by-demography in a marine clonal plant along an eutrophication gradient.

    Science.gov (United States)

    Oliva, Silvia; Romero, Javier; Pérez, Marta; Manent, Pablo; Mascaró, Oriol; Serrão, Ester A; Coelho, Nelson; Alberto, Filipe

    2014-12-01

    Genetic diversity in clonal organisms includes two distinct components, (i) the diversity of genotypes or clones (i.e. genotypic richness) in a population and (ii) that of the alleles (i.e. allelic and gene diversity within populations, and differentiation between populations). We investigated how population differentiation and genotypic components are associated across a gradient of eutrophication in a clonal marine plant. To that end, we combined direct measurements of sexual allocation (i.e. flower and seed counts) and genotypic analyses, which are used as an estimator of effective sexual reproduction across multiple generations. Genetic differentiation across sites was also modelled according to a hypothesis here defined as isolation-by-demography, in which we use population-specific factors, genotypic richness and eutrophication that are hypothesized to affect the source-sink dynamics and thus influence the genetic differentiation between a pair of populations. Eutrophic populations exhibited lower genotypic richness, in agreement with lower direct measurements of sexual allocation and contemporaneous gene flow. Genetic differentiation, while not explained by distance, was best predicted by genotypic richness and habitat quality. A multiple regression model using these two predictors was considered the best model (R(2) = 0.43). In this study, the relationship between environment and effective sexual-asexual balance is not simply (linearly) predicted by direct measurements of sexual allocation. Our results indicate that population-specific factors and the isolation-by-demography model should be used more often to understand genetic differentiation. © 2014 John Wiley & Sons Ltd.

  11. A Novel Hybrid Clonal Selection Algorithm with Combinatorial Recombination and Modified Hypermutation Operators for Global Optimization.

    Science.gov (United States)

    Zhang, Weiwei; Lin, Jingjing; Jing, Honglei; Zhang, Qiuwen

    2016-01-01

    Artificial immune system is one of the most recently introduced intelligence methods which was inspired by biological immune system. Most immune system inspired algorithms are based on the clonal selection principle, known as clonal selection algorithms (CSAs). When coping with complex optimization problems with the characteristics of multimodality, high dimension, rotation, and composition, the traditional CSAs often suffer from the premature convergence and unsatisfied accuracy. To address these concerning issues, a recombination operator inspired by the biological combinatorial recombination is proposed at first. The recombination operator could generate the promising candidate solution to enhance search ability of the CSA by fusing the information from random chosen parents. Furthermore, a modified hypermutation operator is introduced to construct more promising and efficient candidate solutions. A set of 16 common used benchmark functions are adopted to test the effectiveness and efficiency of the recombination and hypermutation operators. The comparisons with classic CSA, CSA with recombination operator (RCSA), and CSA with recombination and modified hypermutation operator (RHCSA) demonstrate that the proposed algorithm significantly improves the performance of classic CSA. Moreover, comparison with the state-of-the-art algorithms shows that the proposed algorithm is quite competitive.

  12. A Novel Hybrid Clonal Selection Algorithm with Combinatorial Recombination and Modified Hypermutation Operators for Global Optimization

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    Weiwei Zhang

    2016-01-01

    Full Text Available Artificial immune system is one of the most recently introduced intelligence methods which was inspired by biological immune system. Most immune system inspired algorithms are based on the clonal selection principle, known as clonal selection algorithms (CSAs. When coping with complex optimization problems with the characteristics of multimodality, high dimension, rotation, and composition, the traditional CSAs often suffer from the premature convergence and unsatisfied accuracy. To address these concerning issues, a recombination operator inspired by the biological combinatorial recombination is proposed at first. The recombination operator could generate the promising candidate solution to enhance search ability of the CSA by fusing the information from random chosen parents. Furthermore, a modified hypermutation operator is introduced to construct more promising and efficient candidate solutions. A set of 16 common used benchmark functions are adopted to test the effectiveness and efficiency of the recombination and hypermutation operators. The comparisons with classic CSA, CSA with recombination operator (RCSA, and CSA with recombination and modified hypermutation operator (RHCSA demonstrate that the proposed algorithm significantly improves the performance of classic CSA. Moreover, comparison with the state-of-the-art algorithms shows that the proposed algorithm is quite competitive.

  13. Amplified fragment length polymorphism versus random amplified polymorphic DNA markers: clonal diversity in Saxifraga cernua.

    Science.gov (United States)

    Kjølner, S; Såstad, S M; Taberlet, P; Brochmann, C

    2004-01-01

    Random amplified polymorphic DNA (RAPD) markers are sensitive to changes in reaction conditions and may express polymorphisms of nongenetic origin. Taxa with variable chromosome numbers are particularly challenging cases, as differences in DNA content may also influence marker reproducibility. We addressed these problems by comparing RAPD and amplified fragment length polymorphism (AFLP) analyses of clonal identity and relationships in a chromosomally variable arctic plant, the polyploid Saxifraga cernua, which has been thought to be monoclonal over large geographical distances. Fifty-seven plants from four Greenland populations were analysed using a conservative scoring approach. In total, 26 AFLP and 32 RAPD multilocus phenotypes (putative clones) were identified, of which 21 were identical and each of the remaining five AFLP clones was split into two to three very similar RAPD clones. This minor difference can be explained by sampling error and stochastic variation. The pattern observed in Greenland corroborates our previous results from Svalbard, suggesting that rare sexual events in S. cernua are sufficient to maintain high levels of clonal diversity even at small spatial scales. We conclude that although AFLP analysis is superior in terms of efficiency, RAPDs may still be used as reliable markers in small low-tech laboratories.

  14. Influence of clonal growth on selfing rate in Vaccinium myrtillus L.

    Science.gov (United States)

    Albert, T; Raspé, O; Jacquemart, A-L

    2008-09-01

    Clonal growth, which allows the multiplication of flowering shoots of the same genet, can lead to a large floral display and may thus increase the rate of selfing through geitonogamy as a consequence of an increase in the number of successively visited flowers. The aim of the present research was to analyse the combined effect of the diversity and intermingling of clones on the rate of selfing in Vaccinium myrtillus. Four mother plants were selected within patches characterised by contrasting clonal structure (low versus high number and intermingling of clones). The selfing rate was significantly lower for plants situated within patches characterised by a high number of intermingled clones (3%) than for plants situated in patches with a low number of clones (50%). Therefore, for this species suffering from inbreeding depression, an increase in the number or the intermingling of the clones could reduce the rate and the cost of geitonogamy and allow a large floral display to attract pollinators. We also found that the main pollinators, bumblebee queens, presented a foraging behaviour favouring geitonogamy, as their successive visits to flowers were quite short (89% of flights were 40 cm or less).

  15. Mutational landscape and clonal architecture in grade II and III gliomas.

    Science.gov (United States)

    Suzuki, Hiromichi; Aoki, Kosuke; Chiba, Kenichi; Sato, Yusuke; Shiozawa, Yusuke; Shiraishi, Yuichi; Shimamura, Teppei; Niida, Atsushi; Motomura, Kazuya; Ohka, Fumiharu; Yamamoto, Takashi; Tanahashi, Kuniaki; Ranjit, Melissa; Wakabayashi, Toshihiko; Yoshizato, Tetsuichi; Kataoka, Keisuke; Yoshida, Kenichi; Nagata, Yasunobu; Sato-Otsubo, Aiko; Tanaka, Hiroko; Sanada, Masashi; Kondo, Yutaka; Nakamura, Hideo; Mizoguchi, Masahiro; Abe, Tatsuya; Muragaki, Yoshihiro; Watanabe, Reiko; Ito, Ichiro; Miyano, Satoru; Natsume, Atsushi; Ogawa, Seishi

    2015-05-01

    Grade II and III gliomas are generally slowly progressing brain cancers, many of which eventually transform into more aggressive tumors. Despite recent findings of frequent mutations in IDH1 and other genes, knowledge about their pathogenesis is still incomplete. Here, combining two large sets of high-throughput sequencing data, we delineate the entire picture of genetic alterations and affected pathways in these glioma types, with sensitive detection of driver genes. Grade II and III gliomas comprise three distinct subtypes characterized by discrete sets of mutations and distinct clinical behaviors. Mutations showed significant positive and negative correlations and a chronological hierarchy, as inferred from different allelic burdens among coexisting mutations, suggesting that there is functional interplay between the mutations that drive clonal selection. Extensive serial and multi-regional sampling analyses further supported this finding and also identified a high degree of temporal and spatial heterogeneity generated during tumor expansion and relapse, which is likely shaped by the complex but ordered processes of multiple clonal selection and evolutionary events.

  16. Multi-locus sequence typing confirms the clonality of Trichomonas gallinae isolates circulating in European finches.

    Science.gov (United States)

    Ganas, Petra; Jaskulska, Barbara; Lawson, Becki; Zadravec, Marko; Hess, Michael; Bilic, Ivana

    2014-04-01

    In recent years, Trichomonas gallinae emerged as the causative agent of an infectious disease of passerine birds in Europe leading to epidemic mortality of especially greenfinches Chloris chloris and chaffinches Fringilla coelebs. After the appearance of finch trichomonosis in the UK and Fennoscandia, the disease spread to Central Europe. Finch trichomonosis first reached Austria and Slovenia in 2012. In the present study the genetic heterogeneity of T. gallinae isolates from incidents in Austria and Slovenia were investigated and compared with British isolates. For this purpose comparative sequence analyses of the four genomic loci ITS1-5.8S-ITS2, 18S rRNA, rpb1 and Fe-hydrogenase were performed. The results corroborate that one clonal T. gallinae strain caused the emerging infectious disease within passerine birds and that the disease is continuing to spread in Europe. The same clonal strain was also found in a columbid bird from Austria. Additionally, the present study demonstrates clearly the importance of multi-locus sequence typing for discrimination of circulating T. gallinae strains.

  17. Performance of clonal olive tree gardens in successive cuts aiming cutting propagation

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    João Vieira Neto

    2011-03-01

    Full Text Available This work evaluated the performance of clonal olive tree gardens in successive cuts aiming cutting propagation. The clonal garden was installed in March 2006, in grooves 40 cm deep. Two cultivars (Ascolano 315 and Arbequina were evaluated and cut in 2007, 2008 and 2009. The test was carried out in split plot in time in a randomized block design with five replications. The plots were composed of three lines, one meter spaced between them, three plants in each line, spaced 0,5 m from each other, totaling nine plants per plot, being evaluated only the three most vigorous plants. For evaluation, three plants were pruned 20 cm height above soil, after 12 months of cultivation, it was evaluated the yield of cuttings with four knots and two pairs of leaves; plants height (m, torso diameter the 20 cm height of the soil (cm; branches length (m; and total green mass accumulated (kg. In most features evaluated, the best results were observed in the ‘Ascolano 315’. The successive cuts may be extended over a three year period. The parameter estimates indicate that plants of both cultivars y responded satisfactorily to regrowth.

  18. Clonal evolution of a case of treatment refractory maxillary sinus carcinoma.

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    Shilpi Arora

    Full Text Available Maxillary sinus carcinoma (MSC is a rare cancer of the head and neck region. Patients are treated with surgery, radiation therapy, and chemotherapy and the treatment regimen is based on patient's age, general health condition, disease stage, and its extent of spread. There is very little information available on the genetics of this disease. DNA content based flow sorting of tumor cells followed by array comparative genomic hybridization allows for high definition global assessment of distinct clonal changes within tumor populations.We applied this technique to primary and metastatic samples collected from a patient with radio- and chemotherapy refractory maxillary sinus carcinoma to gauge the progression of this disease.A clonal KIT amplicon was present in aneuploid populations sorted from the primary tumor and in divergent subclones arising in metastatic foci found in the brain, lung, and jejunum. The evolution of these subclones was associated with distinct genetic aberrations and DNA ploidies.The information presented here paves the path to understanding the development and progression of this disease.

  19. Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular.

    Science.gov (United States)

    Regenberg, Birgitte; Hanghøj, Kristian Ebbesen; Andersen, Kaj Scherz; Boomsma, Jacobus J

    2016-11-16

    How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11+ and Flo11- cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11+/- colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11- colonies do. Flo11+/- colonies maintain their structure and differentiated state by switching non-adhesive cells to adhesive cells with predictable probability. Mixtures of Flo11+ and Flo11- cells from mutant strains that are unable to use this epigenetic switch mechanism produced neither integrated colonies nor growth advantages, so the condition-dependent selective advantages of differentiated FLO11 expression can only be reaped by clone-mate cells. Our results show that selection for cell differentiation in clonal eukaryotes can evolve before the establishment of obligate undifferentiated multicellularity, and without necessarily leading to more advanced organizational complexity. © 2016 The Author(s).

  20. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

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    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  1. Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica.

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    Osamu Nishimura

    Full Text Available We established a laboratory clonal strain of freshwater planarian (Dugesia japonica that was derived from a single individual and that continued to undergo autotomous asexual reproduction for more than 20 years, and we performed large-scale genome sequencing and transcriptome analysis on it. Despite the fact that a completely clonal strain of the planarian was used, an unusually large number of mutations were detected. To enable quantitative genetic analysis of such a unique organism, we developed a new model called the Reference Gene Model, and used it to conduct large-scale transcriptome analysis. The results revealed large numbers of mutations not only outside but also inside gene-coding regions. Non-synonymous SNPs were detected in 74% of the genes for which valid ORFs were predicted. Interestingly, the high-mutation genes, such as metabolism- and defense-related genes, were correlated with genes that were previously identified as diverse genes among different planarian species. Although a large number of amino acid substitutions were apparently accumulated during asexual reproduction over this long period of time, the planarian maintained normal body-shape, behaviors, and physiological functions. The results of the present study reveal a unique aspect of asexual reproduction.

  2. Genotypic diversity and clonal structure of Erigeron annuus (Asteraceae in Lithuania

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    Tunaitienė, Virginija

    2014-02-01

    Full Text Available This study was conducted to assess the clonal structure and genetic diversity of alien herbaceous plant species Erigeron annuus. The global warming and changes in agriculture practice in the past few decades were favourable for the expansion of this species in Lithuania. We used RAPD and ISSR assays to assess genetic variation within and among 29 populations of E. annuus. A total of 278 molecular markers were revealed. Our study detected reduced level of genetic diversity of invasive populations of E. annuus. Significant differences in DNA polymorphism among populations of E. annuus were also found. Some populations of this species are composed of genetically identical plants, while others were polymorphic. Clonal diversity of study populations ranged from 0.083 to 0.4 for both DNA marker systems. The Simpsons diversity index values ranged from 0.0 to 0.636. The average number of genotypes per population established using both assays was about 1.7. Out of 328 E. annuus individuals only 16 showed unique RAPD and 14 unique ISSR banding patterns. The remaining plants were clones of different size. The most common genotype of E. annuus identified in our study was represented by predominate in nine populations.

  3. Genetic composition of replication competent clonal HIV-1 variants isolated from peripheral blood mononuclear cells (PBMC), HIV-1 proviral DNA from PBMC and HIV-1 RNA in serum in the course of HIV-1 infection.

    Science.gov (United States)

    Edo-Matas, Diana; van Gils, Marit J; Bowles, Emma J; Navis, Marjon; Rachinger, Andrea; Boeser-Nunnink, Brigitte; Stewart-Jones, Guillaume B; Kootstra, Neeltje A; van 't Wout, Angélique B; Schuitemaker, Hanneke

    2010-09-30

    The HIV-1 quasispecies in peripheral blood mononuclear cells (PBMC) is considered to be a mix of actively replicating, latent, and archived viruses and may be genetically distinct from HIV-1 variants in plasma that are considered to be recently produced. Here we analyzed the genetic relationship between gp160 env sequences from replication competent clonal HIV-1 variants that were isolated from PBMC and from contemporaneous HIV-1 RNA in serum and HIV-1 proviral DNA in PBMC of four longitudinally studied therapy naïve HIV-1 infected individuals. Replication competent clonal HIV-1 variants, HIV-1 RNA from serum, and HIV-1 proviral DNA from PBMC formed a single virus population at most time points analyzed. However, an under-representation in serum of HIV-1 sequences with predicted CXCR4 usage was sometimes observed implying that the analysis of viral sequences from different sources may provide a more complete assessment of the viral quasispecies in peripheral blood in vivo. Copyright 2010 Elsevier Inc. All rights reserved.

  4. Emergence of MHD structures in a collisionless PIC simulation plasma

    Science.gov (United States)

    Dieckmann, M. E.; Folini, D.; Walder, R.; Romagnani, L.; d'Humieres, E.; Bret, A.; Karlsson, T.; Ynnerman, A.

    2017-09-01

    The expansion of a dense plasma into a dilute plasma across an initially uniform perpendicular magnetic field is followed with a one-dimensional particle-in-cell simulation over magnetohydrodynamics time scales. The dense plasma expands in the form of a fast rarefaction wave. The accelerated dilute plasma becomes separated from the dense plasma by a tangential discontinuity at its back. A fast magnetosonic shock with the Mach number 1.5 forms at its front. Our simulation demonstrates how wave dispersion widens the shock transition layer into a train of nonlinear fast magnetosonic waves.

  5. Acoustic and optical emission during laser-induced plasma formation

    Energy Technology Data Exchange (ETDEWEB)

    Conesa, S.; Palanco, S.; Laserna, J.J. E-mail: laserna@uma.es

    2004-09-20

    Laser ablation is widely used in laser processing and analysis of materials. The laser beam evaporates and ionizes material, creating a plasma plume that expands to variable extent and morphology depending on both the sample and its surrounding gas properties. At ambient pressure a shock wave front appears, traveling at variable velocities which are related to the own plasma formation mechanism. Plasma images as well as the acoustic spectral content of the emission within the aural perception range are related to the plasma formation and evolution dynamics. These results are discussed on the basis of different plasma expansion mechanisms.

  6. Effects of lead contamination on the clonal propagative ability of Phragmites australis (common reed) grown in wet and dry environments.

    Science.gov (United States)

    Zhang, N; Zhang, J W; Yang, Y H; Li, X Y; Lin, J X; Li, Z L; Cheng, L Y; Wang, J F; Mu, C S; Wang, A X

    2015-07-01

    Clonal propagation is important for the survival and maintenance of the common reed Phragmites australis. Pot culture experiments were conducted to investigate the effects of lead (Pb) concentration (0, 500, 1500, 3000, 4500 mg·kg(-1) ) and water stress on the clonal reproductive ability of this species. The Pb concentration found in plant organs, in decreasing order, was roots >shoots >rhizomes. There was a negative relationship between the growth of clonal propagative modules (excluding axillary shoot buds) and Pb concentrations, which caused a decrease in biomass, rhizome growth and number of axillary and apical rhizome buds. Daughter axillary shoots exhibited a tolerance strategy, with no significant change in their number; the axillary and apical rhizome buds, daughter apical rhizome shoots and rhizomes exhibited compensatory growth during the late stage of Pb (excluding 4500 mg·kg(-1) ) treatment in a wet environment. Pb applications above 500 mg·kg(-1) reduced these parameters significantly in the drought treatment, except for the number of axillary shoot buds, which did not change. Our results indicate that clonal propagative resistance to Pb contamination can occur via tolerance strategies, compensatory growth and a Pb allocation strategy, enabling these reeds to maintain population stability in wet environments. However, clonal modular growth and reproductive ability were inhibited significantly by the interaction between drought and Pb, which would cause a decline in P. australis populations in a dry environment. Lead concentrations of 4500 and 500 mg·kg(-1) in soils might meet or exceed the Pb tolerance threshold of clonally propagated reeds in wet and dry environments, respectively. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  7. A Monomorphic Haplotype of Chromosome Ia Is Associated with Widespread Success in Clonal and Nonclonal Populations of Toxoplasma gondii

    Science.gov (United States)

    Khan, Asis; Miller, Natalie; Roos, David S.; Dubey, J. P.; Ajzenberg, Daniel; Dardé, Marie Laure; Ajioka, James W.; Rosenthal, Benjamin; Sibley, L. David

    2011-01-01

    ABSTRACT Toxoplasma gondii is a common parasite of animals that also causes a zoonotic infection in humans. Previous studies have revealed a strongly clonal population structure that is shared between North America and Europe, while South American strains show greater genetic diversity and evidence of sexual recombination. The common inheritance of a monomorphic version of chromosome Ia (referred to as ChrIa*) among three clonal lineages from North America and Europe suggests that inheritance of this chromosome might underlie their recent clonal expansion. To further examine the diversity and distribution of ChrIa, we have analyzed additional strains with greater geographic diversity. Our findings reveal that the same haplotype of ChrIa* is found in the clonal lineages from North America and Europe and in older lineages in South America, where sexual recombination is more common. Although lineages from all three continents harbor the same conserved ChrIa* haplotype, strains from North America and Europe are genetically separate from those in South America, and these respective geographic regions show limited evidence of recent mixing. Genome-wide, array-based profiling of polymorphisms provided evidence for an ancestral flow from particular older southern lineages that gave rise to the clonal lineages now dominant in the north. Collectively, these data indicate that ChrIa* is widespread among nonclonal strains in South America and has more recently been associated with clonal expansion of specific lineages in North America and Europe. These findings have significant implications for the spread of genetic loci influencing transmission and virulence in pathogen populations. PMID:22068979

  8. Differential roles for Bim and Nur77 in thymocyte clonal deletion induced by ubiquitous self-antigen.

    Science.gov (United States)

    Hu, Qian Nancy; Baldwin, Troy A

    2015-03-15

    Negative selection, primarily mediated through clonal deletion of self-reactive thymocytes, is critical for establishing self-tolerance and preventing autoimmunity. Recent studies suggest that the molecular mechanisms of negative selection differ depending on the thymic compartment and developmental stage at which thymocytes are deleted. Using the physiological HY(cd4) TCR transgenic model of negative selection against ubiquitous self-antigen, we previously found that one of the principal mediators implicated in clonal deletion, Bim, is required for caspase-3 activation but is ultimately dispensable for negative selection. On the basis of these data, we hypothesized that Nur77, another molecule thought to be a key mediator of clonal deletion, could be responsible for Bim-independent deletion. Despite comparable Nur77 induction in thymocytes during negative selection, Bim deficiency resulted in an accumulation of high-affinity-signaled thymocytes as well as impairment in caspase-mediated and caspase-independent cell death. Although these data suggested that Bim may be required for Nur77-mediated cell death, we found that transgenic Nur77 expression was sufficient to induce apoptosis independently of Bim. However, transgenic Nur77-induced apoptosis was significantly inhibited in the context of TCR signaling, suggesting that endogenous Nur77 could be similarly regulated during negative selection. Although Nur77 deficiency alone did not alter positive or negative selection, combined deficiency in Bim and Nur77 impaired clonal deletion efficiency and significantly increased positive selection efficiency. Collectively, these data shed light on the different roles for Bim and Nur77 during ubiquitous Ag-mediated clonal deletion and highlight potential differences from their reported roles in tissue-restricted Ag-mediated clonal deletion. Copyright © 2015 by The American Association of Immunologists, Inc.

  9. Design of laser afocal zoom expander system

    Science.gov (United States)

    Jiang, Lian; Zeng, Chun-Mei; Hu, Tian-Tian

    2018-01-01

    Laser afocal zoom expander system due to the beam diameter variable, can be used in the light sheet illumination microscope to observe the samples of different sizes. Based on the principle of afocal zoom system, the laser collimation and beam expander system with a total length of less than 110mm, 6 pieces of spherical lens and a beam expander ratio of 10 is designed by using Zemax software. The system is focused on laser with a wavelength of 532nm, divergence angle of less than 4mrad and incident diameter of 4mm. With the combination of 6 spherical lens, the beam divergence angle is 0.4mrad at the maximum magnification ratio, and the RMS values at different rates are less than λ/4. This design is simple in structure and easy to process and adjust. It has certain practical value.

  10. Bank Directors’ Perceptions of Expanded Auditor's Reports

    DEFF Research Database (Denmark)

    Boolaky, Pran Krishansing; Quick, Reiner

    2016-01-01

    of expanded audit reports, namely information on the assurance level, materiality levels and key audit matters (KAM), on bank director perceptions of the quality of the financial statements, the audit and the audit report, as well as on their credit approval decisions. We conduct an experiment involving......Subsequent to the financial crisis, standard setters developed suggestions for enhancing the audit function, in order to increase financial stability. One related idea is to expand the audit report disclosed to the public, to ensure that it is fit for purpose. This study investigates the impact...... the materiality level or KAM. As a consequence, standard setters should carefully analyse the effect of additional information before making decisions on expanding the content of the audit report. Such expansions are not necessarily perceived as useful by stakeholders. © 2016 John Wiley & Sons Ltd...

  11. Plasma metallization

    CERN Document Server

    Crowther, J M

    1997-01-01

    Many methods are currently used for the production of thin metal films. However, all of these have drawbacks associated with them, for example the need for UHV conditions, high temperatures, exotic metal precursors, or the inability to coat complex shaped objects. Reduction of supported metal salts by non-isothermal plasma treatment does not suffer from these drawbacks. In order to produce and analyse metal films before they become contaminated, a plasma chamber which could be attached directly to a UHV chamber with XPS capability was designed and built. This allowed plasma treatment of supported metal salts and surface analysis by XPS to be performed without exposure of the metal film to the atmosphere. Non-equilibrium plasma treatment of Nylon 66 supported gold(lll) chloride using hydrogen as the feed gas resulted in a 95% pure gold film, the remaining 5% of the film being carbon. If argon or helium were used as the feed gases during plasma treatment the resultant gold films were 100% pure. Some degree of s...

  12. Occurrence of the Plasmid-Mediated Fluoroquinolone Resistance qepA1 Gene in Two Clonal Clinical Isolates of CTX-M-15-Producing Escherichia coli from Algeria.

    Science.gov (United States)

    Yanat, Betitera; Dali Yahia, Radia; Yazi, Leila; Machuca, Jesús; Díaz-De-Alba, Paula; Touati, Abdelaziz; Pascual, Álvaro; Rodríguez-Martínez, José-Manuel

    2017-06-01

    QepA is a plasmid-mediated quinolone resistance determinant of low prevalence described worldwide, mainly in Enterobacteriaceae. This study describes, for the first time in Algeria, two clonally related, QepA-producing Escherichia coli clinical isolates positive for CTX-M-15. The clonal spread of these multidrug-resistant isolates is a major public health concern.

  13. Replicating an expanded genetic alphabet in cells.

    Science.gov (United States)

    Chaput, John C

    2014-09-05

    Recent advances in synthetic biology have made it possible to replicate an unnatural base pair in living cells. This study highlights the technologies developed to create a semisynthetic organism with an expanded genetic alphabet and the potential challenges of moving forward. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Expanding the Focus of Career Assessment.

    Science.gov (United States)

    Lock, Jared D.; Hogan, Robert

    2000-01-01

    Issues affecting career assessment include change in the focus and definition of career, emphasis on quality of work life, expansion of career paths, increased amount of career information available on the Internet, and questionable quality of online assessment. An expanded model of career assessment now includes technical fit, personal fit,…

  15. Expanding CTE Opportunities through Blended Learning

    Science.gov (United States)

    McKinstry, Elizabeth

    2012-01-01

    The global economy, 21st century skills, knowledge society, college and career readiness, digital and project-based learning are all common terms to educators who are expanding their learning environments beyond the classroom to meet the needs of all students. It is common knowledge that the rapid technological advances of this century have…

  16. Expanding the Reader Landscape of Histone Acylation.

    Science.gov (United States)

    Khan, Abid; Bridgers, Joseph B; Strahl, Brian D

    2017-04-04

    In this issue of Structure,Klein et al. (2017) expand our understanding of what reader domains bind to by showing that MORF, a double PHD domain containing lysine acetyltransferase, is a preferential reader of histone lysine acylation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Sulfonated graphenes catalyzed synthesis of expanded porphyrins ...

    Indian Academy of Sciences (India)

    A newer synthesis of sulfonic acid functionalized graphenes have been developed, which have been characterized, examined as heterogeneous solid acid carbocatalyst in the synthesis of selected expanded porphyrins in different reaction conditions. This environment-friendly catalyst avoids the use of toxic catalysts and ...

  18. Expanding Your Horizons Conference in Geneva

    CERN Multimedia

    Chromek-Burckhart, Doris

    2011-01-01

    CERN and its experiments participated in Expanding Your Horizons (EYH) in Science and Mathematics conference in Geneva on 12th November. EYH nurture girls' interest in science and math courses to encourage them to consider careers in science, technology, engineering, and math.

  19. Sulfonated graphenes catalyzed synthesis of expanded porphyrins ...

    Indian Academy of Sciences (India)

    Abstract. A newer synthesis of sulfonic acid functionalized graphenes have been developed, which have been characterized, examined as heterogeneous solid acid carbocatalyst in the synthesis of selected expanded porphyrins in different reaction conditions. This environment-friendly catalyst avoids the use of toxic ...

  20. Technical Note: Effect of Incorporating Expanded Polystyrene ...

    African Journals Online (AJOL)

    Incorporating expanded polystyrene granules in concrete matrix can produce lightweight polystyrene aggregate concrete of various densities. Workability which is an important property of concrete, aects the rate of placement and the degree of compaction of concrete. Inadequate compaction leads to reduction in both ...

  1. Hubble, Hubble's Law and the Expanding Universe

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 3. Hubble, Hubble's Law and the Expanding Universe. J S Bagla. General Article Volume 14 Issue 3 March 2009 pp 216-225. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/014/03/0216-0225 ...

  2. Expanding the collaboration between CERN and Pakistan

    CERN Multimedia

    2002-01-01

    Parvez Butt, chairman of the Pakistan Atomic Energy Commission, and CERN Director General, Luciano Maiani, signed a letter of intent last week to expand collaboration. Through an agreement which should be formalized within a few months, Pakistan would make a substantial contribution to the LHC and its detectors, coordinated by the Pakistani National Centre of Physics.

  3. Circle diffeomorphisms forced by expanding circle maps

    NARCIS (Netherlands)

    Homburg, A.J.

    2012-01-01

    We discuss the dynamics of skew product maps defined by circle diffeomorphisms forced by expanding circle maps. We construct an open class of such systems that are robustly topologically mixing and for which almost all points in the same fiber converge under iteration. This property follows from the

  4. Discrete Groups, Expanding Graphs and Invariant Measures

    CERN Document Server

    Lubotzky, Alexander

    2009-01-01

    Presents the solutions to two problems: the first is the construction of expanding graphs - graphs which are of fundamental importance for communication networks and computer science, and the second is the Ruziewicz problem concerning the finitely additive invariant measures on spheres

  5. Expanding Educational Excellence: The Power of Schools

    Science.gov (United States)

    Coleman, Mary Ruth; Winn, Donna-Marie; Harradine, Christine

    2012-01-01

    In this paper, the authors explore four major barriers to academic success that must be addressed, briefly describe two projects that have worked to address these barriers, and make recommendations for moving forward as they work to expand educational excellence for all students. They provide examples of the myriad ways in which schools have the…

  6. Expanded Core Curriculum: 12 Years Later

    Science.gov (United States)

    Lohmeier, Keri; Blankenship, Karen; Hatlen, Phil

    2009-01-01

    This study investigated changes in teachers' and parents' understanding and implementation of or philosophy on the implementation of the content areas of the expanded core curriculum for students who are visually impaired. The results demonstrated some changes since the original survey results were reported in 1998 and a discrepancy between the…

  7. CLASSICS WHY THE UNIVERSE IS EXPANDING

    Indian Academy of Sciences (India)

    (H. G. Wells, The Time Machine and other Stories). WHY IS THE UNIVERSE EXPANDING? Chemical Explosion and Astrophysical Explosion Similarities and Differences. The expansion of the Universe is a reliably established fact. There was the “Big Bang” about 15 billion years ago. But why did it happen? What are the ...

  8. Hubble, Hubble's Law and the Expanding Universe

    Indian Academy of Sciences (India)

    Srimath

    H ubble's nam e is associated closely w ith the idea of an expanding universe as he discovered the relation between the recession velocity and the distances of galaxies. H ubble also did a lot of pioneering w ork on the distribution of galaxies in the universe. In this article we take a look at H ubble's law and discuss how it ...

  9. Women Engineering Faculty: Expanding the Pipeline

    Science.gov (United States)

    Greni, Nadene Deiterman

    2006-01-01

    The purpose for this case study was to explore the features of undergraduate engineering departmental and college support that influenced the persistence of women students. Women engineering faculty members were among the participants at three Land Grant universities in the Midwest. The data revealed the theme, Expanding the Pipeline, and…

  10. Expanded austenite, crystallography and residual stress

    DEFF Research Database (Denmark)

    Christiansen, Thomas; Hummelshøj, Thomas Strabo; Somers, Marcel A. J.

    2010-01-01

    compositions and (b) unravelling of the contributions of stress-depth and composition-depth profiles in expanded austenite layers are summarised and discussed. It is shown through simulation of line profiles that the combined effects of composition gradients, stress gradients and stacking fault gradients can...

  11. Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity.

    Science.gov (United States)

    Dahdouh, Elias; Hajjar, Micheline; Suarez, Monica; Daoud, Ziad

    2016-01-01

    Introduction:Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence. Materials and Methods:A. baumannii clinical isolates (n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of blaOXA-51-like were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations. Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored blaOXA-23-like including two that also harbored blaOXA-24-like. 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between motility, siderophore

  12. Reactivity zones around an atmospheric pressure plasma jet

    Energy Technology Data Exchange (ETDEWEB)

    Birer, Özgür, E-mail: obirer@ku.edu.tr

    2015-11-01

    Highlights: • Polyethylene surfaces were treated with atmospheric pressure cold plasma jet. • The effect of plasma extends beyond the physical jet diameter. • Moieties of –NO, –COO, –CO and –NO{sub 3} as expanding ring patterns were detected. • Active species in the plasma are identified for specific surface moieties. - Abstract: The reactivity zones around an atmospheric pressure plasma jet are revealed by XPS mapping of chemical moieties on a polyethylene surface treated with a 3-mm plasma jet. The area directly hit by the helium plasma jet initially oxidizes and later etches away as the plasma treatment continues. The oxidation initially starts at the center and expands outwards as a ring pattern with different spatial potency. At the end of 10 min plasma jet treatment, distinct ring patterns for –NO, –COO, –CO and –NO{sub 3} species can be detected with respectively increasing diameters. The plasma jet can cause chemical changes at locations several millimeters away from the center. The spatial distribution of oxidized species suggests presence of chemical reactivity zones. Introduction of nitrogen into the helium plasma jet, not only increases the type of nitrogen moieties, but enriches the reactivity zones by generating nitrogen molecular ions within the plasma jet. The complex competing reaction mechanisms among the radicals, ions, metastable atoms and UV photons lead to unusual etching patterns on the surfaces.

  13. Refrigeration generation using expander-generator units

    Science.gov (United States)

    Klimenko, A. V.; Agababov, V. S.; Koryagin, A. V.; Baidakova, Yu. O.

    2016-05-01

    The problems of using the expander-generator unit (EGU) to generate refrigeration, along with electricity were considered. It is shown that, on the level of the temperatures of refrigeration flows using the EGU, one can provide the refrigeration supply of the different consumers: ventilation and air conditioning plants and industrial refrigerators and freezers. The analysis of influence of process parameters on the cooling power of the EGU, which depends on the parameters of the gas expansion process in the expander and temperatures of cooled environment, was carried out. The schematic diagram of refrigeration generation plant based on EGU is presented. The features and advantages of EGU to generate refrigeration compared with thermotransformer of steam compressive and absorption types were shown, namely: there is no need to use the energy generated by burning fuel to operate the EGU; beneficial use of the heat delivered to gas from the flow being cooled in equipment operating on gas; energy production along with refrigeration generation, which makes it possible to create, using EGU, the trigeneration plants without using the energy power equipment. It is shown that the level of the temperatures of refrigeration flows, which can be obtained by using the EGU on existing technological decompression stations of the transported gas, allows providing the refrigeration supply of various consumers. The information that the refrigeration capacity of an expander-generator unit not only depends on the parameters of the process of expansion of gas flowing in the expander (flow rate, temperatures and pressures at the inlet and outlet) but it is also determined by the temperature needed for a consumer and the initial temperature of the flow of the refrigeration-carrier being cooled. The conclusion was made that the expander-generator units can be used to create trigeneration plants both at major power plants and at small energy.

  14. Radiation phenomena in plasmas

    National Research Council Canada - National Science Library

    Ohnuma, Toshiro; Ohnuma, T

    1994-01-01

    ... electromagnetic and electrostatic waves can propagate. In the development of space sciences, processing plasmas and fusion plasmas etc., plasmas have been investigated in many problems and practic...

  15. Plasma physics and engineering

    CERN Document Server

    Fridman, Alexander

    2011-01-01

    Part I: Fundamentals of Plasma Physics and Plasma ChemistryPlasma in Nature, in the Laboratory, and in IndustryOccurrence of Plasma: Natural and Man MadeGas DischargesPlasma Applications, Plasmas in IndustryPlasma Applications for Environmental ControlPlasma Applications in Energy ConversionPlasma Application for Material ProcessingBreakthrough Plasma Applications in Modern TechnologyElementary Processes of Charged Species in PlasmaElementary Charged Particles in Plasma and Their Elastic and Inelastic CollisionsIonization ProcessesMechanisms of Electron Losses: The Electron-Ion RecombinationEl

  16. PLASMA SPECTROSCOPY

    NARCIS (Netherlands)

    Jaspers, R. J. E.

    2010-01-01

    A brief introduction into the spectroscopy of fusion plasmas is presented. Basic principles of the emission of ionic, atomic and molecular radiation is explained and a survey of the effects, which lead to the population of the respective excited levels, is given. Line radiation, continuum radiation,

  17. Letter to the Editor : Standardizing the nomenclature for clonal lineages of the sudden oak death pathogen, Phytophthora ramorum

    NARCIS (Netherlands)

    Grünwald, N.J.; Goss, E.M.; Ivors, K.; Garbelotto, M.; Martin, F.N.; Prospero, S.; Hansen, E.; Bonants, P.J.M.; Hamelin, R.C.; Chastagner, M.; Werres, S.; Rizzo, D.M.; Abad, G.; Beales, P.; Bilodeau, G.J.; Blomquist, C.L.; Brasier, C.; Brière, S.C.; Chandelier, A.; Davidson, J.M.; Denman, S.; Elliott, M.; Frankel, S.J.; Goheen, E.M.; Gruyter, de H.; Heungens, K.; James, D.; Kanaskie, A.; McWilliams, M.G.; Man in't Veld, W.; Moralejo, E.; Osterbauer, N.K.; Palm, M.E.; Parke, J.L.; Perez Sierra, A.M.; Shamoun, S.F.; Shishkoff, N.; Tooley, P.W.; Vettraino, A.M.; Webber, J.; Widmer, T.L.

    2009-01-01

    Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages.

  18. Application of biomarkers in cancer risk management: evaluation from stochastic clonal evolutionary and dynamic system optimization points of view.

    Directory of Open Access Journals (Sweden)

    Xiaohong Li

    2011-02-01

    Full Text Available Aside from primary prevention, early detection remains the most effective way to decrease mortality associated with the majority of solid cancers. Previous cancer screening models are largely based on classification of at-risk populations into three conceptually defined groups (normal, cancer without symptoms, and cancer with symptoms. Unfortunately, this approach has achieved limited successes in reducing cancer mortality. With advances in molecular biology and genomic technologies, many candidate somatic genetic and epigenetic "biomarkers" have been identified as potential predictors of cancer risk. However, none have yet been validated as robust predictors of progression to cancer or shown to reduce cancer mortality. In this Perspective, we first define the necessary and sufficient conditions for precise prediction of future cancer development and early cancer detection within a simple physical model framework. We then evaluate cancer risk prediction and early detection from a dynamic clonal evolution point of view, examining the implications of dynamic clonal evolution of biomarkers and the application of clonal evolution for cancer risk management in clinical practice. Finally, we propose a framework to guide future collaborative research between mathematical modelers and biomarker researchers to design studies to investigate and model dynamic clonal evolution. This approach will allow optimization of available resources for cancer control and intervention timing based on molecular biomarkers in predicting cancer among various risk subsets that dynamically evolve over time.

  19. Thelytokous parthenogenesis, male clonality and genetic caste determination in the little fire ant: new evidence and insights from the lab.

    Science.gov (United States)

    Foucaud, J; Estoup, A; Loiseau, A; Rey, O; Orivel, J

    2010-08-01

    Previous studies indicate that some populations of the little fire ant, Wasmannia auropunctata, display an unusual reproduction system polymorphism. Although some populations have a classical haplodiploid reproduction system, in other populations queens are produced by thelytokous parthenogenesis, males are produced by a male clonality system and workers are produced sexually. An atypical genetic caste determination system was also suggested. However, these conclusions were indirectly inferred from genetic studies on field population samples. Here we set up experimental laboratory nests that allow the control of the parental relationships between individuals. The queens heading those nests originated from either putatively clonal or sexual populations. We characterized the male, queen and worker offspring they produced at 12 microsatellite loci. Our results unambiguously confirm the unique reproduction system polymorphism mentioned above and that male clonality is strictly associated with thelytokous parthenogenesis. We also observed direct evidence of the rare production of sexual gynes and arrhenotokous males in clonal populations. Finally, we obtained evidence of a genetic basis for caste determination. The evolutionary significance of the reproduction system polymorphism and genetic caste determination as well as future research opportunities are discussed.

  20. In vivo clonal analysis reveals lineage-restricted progenitor characteristics in mammalian kidney development, maintenance, and regeneration

    NARCIS (Netherlands)

    Rinkevich, Y.; Montoro, D.T.; Contreras-Trujillo, H.; Harari-Steinberg, O.; Newman, A.M.; Tsai, J.M.; Lim, X.; van Amerongen, R.; Bowman, A.; Januszyk, M.; Pleniceanu, O.; Nusse, R.; Longaker, M.T.; Weissman, I.L.; Dekel, B.

    2014-01-01

    The mechanism and magnitude by which the mammalian kidney generates and maintains its proximal tubules, distal tubules, and collecting ducts remain controversial. Here, we use long-term in vivo genetic lineage tracing and clonal analysis of individual cells from kidneys undergoing development,

  1. Implications of extreme life span in clonal organisms: millenary clones in meadows of the threatened seagrass Posidonia oceanica.

    Science.gov (United States)

    Arnaud-Haond, Sophie; Duarte, Carlos M; Diaz-Almela, Elena; Marbà, Núria; Sintes, Tomas; Serrão, Ester A

    2012-01-01

    The maximum size and age that clonal organisms can reach remains poorly known, although we do know that the largest natural clones can extend over hundreds or thousands of metres and potentially live for centuries. We made a review of findings to date, which reveal that the maximum clone age and size estimates reported in the literature are typically limited by the scale of sampling, and may grossly underestimate the maximum age and size of clonal organisms. A case study presented here shows the occurrence of clones of slow-growing marine angiosperm Posidonia oceanica at spatial scales ranging from metres to hundreds of kilometres, using microsatellites on 1544 sampling units from a total of 40 locations across the Mediterranean Sea. This analysis revealed the presence, with a prevalence of 3.5 to 8.9%, of very large clones spreading over one to several (up to 15) kilometres at the different locations. Using estimates from field studies and models of the clonal growth of P. oceanica, we estimated these large clones to be hundreds to thousands of years old, suggesting the evolution of general purpose genotypes with large phenotypic plasticity in this species. These results, obtained combining genetics, demography and model-based calculations, question present knowledge and understanding of the spreading capacity and life span of plant clones. These findings call for further research on these life history traits associated with clonality, considering their possible ecological and evolutionary implications.

  2. Effects of artemisinin and Artemisia annua extracts on xenic bacteria isolated from clonal cultures of Histomonas meleagridis

    DEFF Research Database (Denmark)

    Thøfner, Ida; Hess, Claudia; Liebhart, Dieter

    nutrient supply due to their appearance in parasitic food vacuoles. However, the relationship of the parasite and the bacteria is not fully clear. Six previously established clonal cultures of H. meleagridis were used to evaluate the effect of five Artemisia annua derived materials (i.e. dry leaves...

  3. Implications of extreme life span in clonal organisms: millenary clones in meadows of the threatened seagrass Posidonia oceanica.

    Directory of Open Access Journals (Sweden)

    Sophie Arnaud-Haond

    Full Text Available The maximum size and age that clonal organisms can reach remains poorly known, although we do know that the largest natural clones can extend over hundreds or thousands of metres and potentially live for centuries. We made a review of findings to date, which reveal that the maximum clone age and size estimates reported in the literature are typically limited by the scale of sampling, and may grossly underestimate the maximum age and size of clonal organisms. A case study presented here shows the occurrence of clones of slow-growing marine angiosperm Posidonia oceanica at spatial scales ranging from metres to hundreds of kilometres, using microsatellites on 1544 sampling units from a total of 40 locations across the Mediterranean Sea. This analysis revealed the presence, with a prevalence of 3.5 to 8.9%, of very large clones spreading over one to several (up to 15 kilometres at the different locations. Using estimates from field studies and models of the clonal growth of P. oceanica, we estimated these large clones to be hundreds to thousands of years old, suggesting the evolution of general purpose genotypes with large phenotypic plasticity in this species. These results, obtained combining genetics, demography and model-based calculations, question present knowledge and understanding of the spreading capacity and life span of plant clones. These findings call for further research on these life history traits associated with clonality, considering their possible ecological and evolutionary implications.

  4. Trampling, defoliation and physiological integration affect growth, morphological and mechanical properties of a root-suckering clonal tree

    NARCIS (Netherlands)

    Xu, L.; Yu, F.H.; Drunen, van E.; Schieving, F.; Dong, M.; Anten, N.P.R.

    2012-01-01

    Background and Aims Grazing is a complex process involving the simultaneous occurrence of both trampling and defoliation. Clonal plants are a common feature of heavily grazed ecosystems where large herbivores inflict the simultaneous pressures of trampling and defoliation on the vegetation. We test

  5. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

    Science.gov (United States)

    Bowers, Jolene R; Kitchel, Brandon; Driebe, Elizabeth M; MacCannell, Duncan R; Roe, Chandler; Lemmer, Darrin; de Man, Tom; Rasheed, J Kamile; Engelthaler, David M; Keim, Paul; Limbago, Brandi M

    2015-01-01

    Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.

  6. ERRATUM to: Taxonomy, chromosome numbers, clonal diversity and population dynamics of Phragmites australis (vol 64, pg 185, 1999)

    NARCIS (Netherlands)

    Clevering, O.A.; Lissner, J.

    2000-01-01

    Phragmites australis (Cav.) Trin. ex Steud. (common reed) is one of the most widespread plant species in the world. The species has a high phenotypic variation in morphology and life-history traits. This high phenotypic variation can be related to variance in chromosome numbers, clonal diversity,

  7. Analysis of clonal expansions through the normal and premalignant human breast epithelium reveals the presence of luminal stem cells

    NARCIS (Netherlands)

    Cereser, B. (Biancastella); M. Jansen (Marnix); Austin, E. (Emily); Elia, G. (George); Mcfarlane, T. (Taneisha); C.H.M. van Deurzen (Carolien); A.M. Sieuwerts (Anieta); M.G. Daidone (Maria Grazia); Tadrous, P.J. (Paul J); Wright, N.A. (Nicholas A); L. Jones (Louise); Mcdonald, S.A. (Stuart Ac)

    2017-01-01

    textabstractIt is widely accepted that the cell of origin of breast cancer is the adult mammary epithelial stem cell; however, demonstrating the presence and location of tissue stem cells in the human breast has proved difficult. Furthermore, we do not know the clonal architecture of the normal and

  8. Males are here to stay: fertilization enhances viable egg production by clonal queens of the little fire ant ( Wasmannia auropunctata)

    Science.gov (United States)

    Miyakawa, Misato O.; Mikheyev, Alexander S.

    2015-04-01

    Evolution of reproduction strategies is affected by both phylogenetic and physiological constraints. Although clonality may benefit females, it may not be selected if a male contribution is necessary to start egg laying and embryo development. In little fire ant, Wasmannia auropunctata, sexual populations employ a typical Hymenopteran system of reproduction. In clonal populations, however, queens and males are produced with only maternal and paternal genomes, respectively, whereas sterile workers are produced sexually. Although this system requires both sexes for worker production, previous work has shown that workers may also be produced clonally by the queens. If so, why are males maintained in this species? Our data suggest that fertilization is necessary to increase the hatching rate of eggs. Although clonal queens can indeed produce both workers and queens without mating, the hatching rate is far below the level necessary to maintain functional colonies. On the other hand, virgin queens from populations exhibiting the original Hymenopteran reproduction system also show low hatching rates, but produce only haploid male eggs. Reasons for the existence of W. auropunctata males have been disputed. However, our data suggest that physiological constraints, such as the requirement for insemination, must be considered in regard to evolution of reproduction systems, in addition to ecological data and theoretical considerations of fitness.

  9. Identification of a Novel Genomic Island Specific to Hospital-Acquired Clonal Complex 17 Enterococcus faecium Isolates

    NARCIS (Netherlands)

    Heikens, Esther; van Schaik, Willem; Leavis, Helen L.; Bonten, Marc J. M.; Willems, Rob J. L.

    2008-01-01

    Hospital-acquired clonal complex 17 (CC17) Enterococcus faecium strains are genetically distinct from indigenous strains and are enriched with resistance genes and virulence genes. We identified a genomic island in CC17 E. faecium tentatively encoding a metabolic pathway involved in carbohydrate

  10. The effects of fine-scale disturbances on demography and population dynamics of the clonal moss Hylocomium splendens

    NARCIS (Netherlands)

    Rydgren, K.; Kroon, de H.; Okland, R.H.; Groenendael, van J.

    2001-01-01

    1. The boreal forest is subject to disturbance but the effects on population dynamics are poorly understood. We investigated how a prominent species of the forest floor, the clonal moss Hylocomium splendens, responded to different types of fine-scale disturbance. 2. Canopy gap formation was

  11. The T963C mutation of TP53 gene does not participate in the clonal origin of canine TVT.

    Science.gov (United States)

    Vázquez-Mota, N; Simón-Martínez, J; Córdova-Alarcon, E; Lagunes, L; Fajardo, R

    2008-02-01

    In dogs, the canine transmissible venereal tumor (CTVT) is the only neoplasm which is not produced by neoplastic transformation of normal cells; the tumor is transmitted from the affected dog to healthy dogs by implantation of one or various clones of cancer cells. Thus, the CTVT of dogs analyzed in various countries reveals similar genetic characteristics and consequently CTVT is considered to have a clonal origin. The CTVTs obtained from dogs in Korea showed the T963C mutation on TP53 gene; this mutation was thought to be a molecular alteration which participates in the origin of the ancestral clone, CTVT. Nonetheless, this supposed mutation has not been identified in other studies which were carried out for the purpose of clarifying the clonal origin of CTVT. Thus we have considered it important to identify the role of the T963C mutation of the TP53 gene in the clonal origin of CTVT in dogs. Consequently the region which includes the mutation of the TP53 gene in twenty samples of CTVT obtained from various canine breeds was PCR amplified and afterwards its sequence of nucleotides was determined. We conclude that this mutation did not participate in the clonal origin of the tumor, but was acquired at a later stage.

  12. A Robust Single Primate Neuroepithelial Cell Clonal Expansion System for Neural Tube Development and Disease Studies

    Directory of Open Access Journals (Sweden)

    Xiaoqing Zhu

    2016-02-01

    Full Text Available Developing a model of primate neural tube (NT development is important to promote many NT disorder studies in model organisms. Here, we report a robust and stable system to allow for clonal expansion of single monkey neuroepithelial stem cells (NESCs to develop into miniature NT-like structures. Single NESCs can produce functional neurons in vitro, survive, and extensively regenerate neuron axons in monkey brain. NT formation and NESC maintenance depend on high metabolism activity and Wnt signaling. NESCs are regionally restricted to a telencephalic fate. Moreover, single NESCs can turn into radial glial progenitors (RGPCs. The transition is accurately regulated by Wnt signaling through regulation of Notch signaling and adhesion molecules. Finally, using the “NESC-TO-NTs” system, we model the functions of folic acid (FA on NT closure and demonstrate that FA can regulate multiple mechanisms to prevent NT defects. Our system is ideal for studying NT development and diseases.

  13. Clonal Occurrence of Salmonella Weltevreden in Cultured Shrimp in the Mekong Delta, Vietnam

    Science.gov (United States)

    Noor Uddin, Gazi Md.; Larsen, Marianne Halberg; Barco, Lisa; Minh Phu, Tran; Dalsgaard, Anders

    2015-01-01

    This study investigated the occurrence, serovar and antimicrobial resistance of Salmonella spp. in shrimp samples from intensive and extensive farms located in three different provinces in the Mekong Delta, Vietnam. Shrimp from 11 of the 48 farms all contained S. Weltevreden, except for one farm yielding S. Agona, with no difference in Salmonella occurrence between the two production systems. Pulsed field gel electrophoresis (PFGE) of S. Weltevreden showed closely related XbaI pulse types, suggesting a clonal relationship despite the farms and shrimp samples being epidemiologically unrelated. S. Weltevreden was susceptible to most antimicrobials tested, with a few strains being resistant to florfenicol, chloramphenicol, sulfamethoxazole or trimethoprim. Future studies of the ecology of S. Weltevreden should establish if this serovar may survive better and even multiply in warm-water shrimp farm environments compared to other Salmonella serovars. PMID:26222547

  14. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer

    DEFF Research Database (Denmark)

    Brocks, David; Assenov, Yassen; Minner, Sarah

    2014-01-01

    Despite much evidence on epigenetic abnormalities in cancer, it is currently unclear to what extent epigenetic alterations can be associated with tumors' clonal genetic origins. Here, we show that the prostate intratumor heterogeneity in DNA methylation and copy-number patterns can be explained...... by a unified evolutionary process. By assaying multiple topographically distinct tumor sites, premalignant lesions, and lymph node metastases within five cases of prostate cancer, we demonstrate that both DNA methylation and copy-number heterogeneity consistently reflect the life history of the tumors....... Furthermore, we show cases of genetic or epigenetic convergent evolution and highlight the diversity in the evolutionary origins and aberration spectrum between tumor and metastatic subclones. Importantly, DNA methylation can complement genetic data by serving as a proxy for activity at regulatory domains...

  15. Ampicillin-resistant Enterococcus faecium clonal complex 17 is widespread in healthy dogs: anthropozoonosis or zooanthroponosis?

    DEFF Research Database (Denmark)

    Damborg, Peter Panduro; Williams, Nicola J; Willems, Rob

    2008-01-01

    to the spread of this AREfm genetic lineage in the human population. The unexpected and widespread occurrence of hospital-adapted clones in dogs raises an important question concerning the evolution of this clonal complex: does CC17 originate from humans (anthropozoonosis) or from dogs (zooanthroponosis......). In this study, we investigated the occurrence of AREfm CC17 in faecal samples collected from healthy dogs in Denmark and in England. Methods: 210 healthy dogs were screened for the occurrence of AREfm using a selective isolation procedure, i.e. plating on Slanetz Bartley agar containing 32 µg/ml ampicillin....... Presumptive AREfm were confirmed by a species-specific PCR and their resistance patterns were determined according to CLSI guidelines. The purK gene was sequenced in all isolates and a subset of 15 isolates was further analysed by MLST analysis. Results: AREfm was detected in 59 (28%) dogs. Based on MLST...

  16. Factors influencing rapid clonal propagation of Chlorophytum arundinaceum (Liliales: Liliaceae, an endangered medicinal plant

    Directory of Open Access Journals (Sweden)

    Sanghamitra Samantaray

    2011-03-01

    Full Text Available Chlorophytum arundinaceum is an important medicinal plant and its tuberous roots are used for various health ailment treatments. It has become an endangered species in the Eastern Ghats, and a rare medicinal herb in India, due to its excessive collection from its natural habitat and its destructive harvesting techniques, coupled with poor seed germination and low vegetative multiplication ratio. In order to contribute to its production systems, an efficient protocol was developed for in vitro clonal propagation through shoot bud culture. For this, multiple shoots were induced from shoot bud explants on Murashige and Skoog’s medium supplemented with 2.5-3.0mg/L BAP, 0.01-0.1mg/L NAA and 3% (w/v sucrose. Inclusion of Adenine Sulphate (25mg/L in the culture medium improved the frequency of multiple shoot production and recovered the chlorotic symptoms of the leaves. Media having pH 5.9 and 4% sucrose showed significant improvement on shoot bud multiplication and growth. In vitro flowering was observed when the subcultures were carried out for over four months in the same multiplication media. Rooting was readily achieved upon transferring the shoots on to half- strength MS medium supplemented with 0.1mg/L IBA and 2% (w/v sucrose. Micropropagated plantlets were hardened in the green house, successfully established, and flowered in the field. This method could effectively be applied for the conservation and clonal propagation to meet the demand of planting materials. Rev. Biol. Trop. 59 (1: 435-445. Epub 2011 March 01.Chlorophytum arundinaceum es una planta medicinal importante y sus raíces se utilizan en diversos tratamientos contra enfermedades. Se ha convertido en una especie en peligro de extinción en el Ghats Oriental y una hierba medicinal rara en la India, debido a la recolecta excesiva en su hábitat natural y la manera destructiva de cosecharla, asociado con una mala germinación y pobre multiplicación vegetativa. Para contribuir con

  17. Immune complex formation and in situ B-cell clonal expansion in human cerebral cavernous malformations.

    Science.gov (United States)

    Shi, Changbin; Shenkar, Robert; Kinloch, Andrew; Henderson, Scott G; Shaaya, Mark; Chong, Anita S; Clark, Marcus R; Awad, Issam A

    2014-07-15

    Cerebral cavernous malformations (CCMs) represent clusters of dilated vascular channels, predisposing to hemorrhagic stroke and seizures. They are associated with defective blood brain barrier, hemorrhages of different ages and a robust inflammatory cell infiltrate. We report for the first time evidence of co-localized IgG and complement membrane attack complexes in CCM lesions. CD4(+) and CD8(+) T-cells are aggregated with CD20(+) B-cells. And IgG repertoire analyses demonstrate in situ B-cell clonal expansion and antigen-driven affinity maturation in CCMs. These results suggest an organ-intrinsic adaptive immune response in CCMs that should be further characterized as a potential therapeutic target. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. ROOT HYDRAULIC CONDUCTIVITY AND PHOTOSYNTHETIC CAPACITY OF EUCALYPT CLONAL CUTTINGS WITH ROOT MALFORMATION INDUCTIONS

    Directory of Open Access Journals (Sweden)

    Fábio Afonso Mazzei Moura de Assis Figueiredo

    2014-06-01

    Full Text Available http://dx.doi.org/10.5902/1980509814566The gain reduction of wood biomass in trees has been assigned to root deformations even in the nursery phase. The objective of this work was the evaluation of the root system hydraulic conductivity, gas exchanges and photochemical efficiency of eucalypt clonal cuttings with and without root deformation inductions. The treatments were: 1 operational cuttings without root malformation inductions (grown according to the used methodology of Fibria Cellulose S.A.; 2 root deformation inductions. These inductions did not promote decrease in the root volume. However, the deformations brought reduction of the root system hydraulic conductivity. Lower photosynthetic rates were also observed along the day in the cuttings in the root deformed cuttings. This decreasing rate is connected to stomatal and non stomatal factors.

  19. A new fate mapping system reveals context-dependent random or clonal expansion of microglia.

    Science.gov (United States)

    Tay, Tuan Leng; Mai, Dominic; Dautzenberg, Jana; Fernández-Klett, Francisco; Lin, Gen; Sagar; Datta, Moumita; Drougard, Anne; Stempfl, Thomas; Ardura-Fabregat, Alberto; Staszewski, Ori; Margineanu, Anca; Sporbert, Anje; Steinmetz, Lars M; Pospisilik, J Andrew; Jung, Steffen; Priller, Josef; Grün, Dominic; Ronneberger, Olaf; Prinz, Marco

    2017-06-01

    Microglia constitute a highly specialized network of tissue-resident immune cells that is important for the control of tissue homeostasis and the resolution of diseases of the CNS. Little is known about how their spatial distribution is established and maintained in vivo. Here we establish a new multicolor fluorescence fate mapping system to monitor microglial dynamics during steady state and disease. Our findings suggest that microglia establish a dense network with regional differences, and the high regional turnover rates found challenge the universal concept of microglial longevity. Microglial self-renewal under steady state conditions constitutes a stochastic process. During pathology this randomness shifts to selected clonal microglial expansion. In the resolution phase, excess disease-associated microglia are removed by a dual mechanism of cell egress and apoptosis to re-establish the stable microglial network. This study unravels the dynamic yet discrete self-organization of mature microglia in the healthy and diseased CNS.

  20. A clonal strain of Trichomonas gallinae is the aetiologic agent of an emerging avian epidemic disease.

    Science.gov (United States)

    Lawson, Becki; Cunningham, Andrew A; Chantrey, Julian; Hughes, Laura A; John, Shinto K; Bunbury, Nancy; Bell, Diana J; Tyler, Kevin M

    2011-10-01

    Trichomonas gallinae is a protozoan parasite that is well characterised as a cause of trichomonosis in columbid and raptor species world-wide. The parasite emerged as a novel infection of British passerines in 2005, leading to epidemic mortality associated with significant declines of breeding populations of greenfinches (Carduelis chloris) and chaffinches (Fringilla coelebs). We characterised the extent of T. gallinae genotypic heterogeneity within the affected wild British avifauna by analysing individual isolates from 17 of the species affected. To do so, we employed improved platform-based multilocus typing tools as well as the hydrogenosomal Fe-hydrogenase gene as a single marker locus for fine-typing. We found no evidence of heterogeneity amongst the parasites infecting British passerines, indicating that a clonal strain of T. gallinae is the causative agent of this emerging infectious disease. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Axenization and optimization of in vitro growth of clonal cultures of Tetratrichomonas gallinarum and Trichomonas gallinae.

    Science.gov (United States)

    Amin, Aziza; Neubauer, Claudia; Liebhart, Dieter; Grabensteiner, Elvira; Hess, Michael

    2010-02-01

    A rapid and simple procedure was established to obtain clonal axenic cultures of Tetratrichomonas gallinarum and Trichomonas gallinae and to optimize their in vitro growth conditions. Medium 199 was used for axenization of two genetically different clones of T. gallinarum and T. gallinae. Six different media were used to optimize the growth behaviour of axenically grown parasites: Medium 199, TYM, TYI-S-33, Hollander fluid (HF), Trichomonas vaginalis (TV) and modified TV media. The highest cell yields for both axenic clones of T. gallinarum were obtained in modified TV medium without antibiotics. The maximum numbers of trophozoites of T. gallinae were obtained in an optimized HF medium. This study demonstrated that axenic cultures for T. gallinarum and T. gallinae could be obtained avoiding the migration technique through a V-tube. Following axenization and optimization, both clones of T. gallinarum and T. gallinae could be propagated both aerobically and anaerobically. Copyright 2009 Elsevier Inc. All rights reserved.

  2. Clonal Occurrence of Salmonella Weltevreden in Cultured Shrimp in the Mekong Delta, Vietnam.

    Directory of Open Access Journals (Sweden)

    Gazi Md Noor Uddin

    Full Text Available This study investigated the occurrence, serovar and antimicrobial resistance of Salmonella spp. in shrimp samples from intensive and extensive farms located in three different provinces in the Mekong Delta, Vietnam. Shrimp from 11 of the 48 farms all contained S. Weltevreden, except for one farm yielding S. Agona, with no difference in Salmonella occurrence between the two production systems. Pulsed field gel electrophoresis (PFGE of S. Weltevreden showed closely related XbaI pulse types, suggesting a clonal relationship despite the farms and shrimp samples being epidemiologically unrelated. S. Weltevreden was susceptible to most antimicrobials tested, with a few strains being resistant to florfenicol, chloramphenicol, sulfamethoxazole or trimethoprim. Future studies of the ecology of S. Weltevreden should establish if this serovar may survive better and even multiply in warm-water shrimp farm environments compared to other Salmonella serovars.

  3. Nanocarbon materials fabricated using plasmas

    Science.gov (United States)

    Hatakeyama, Rikizo

    2017-12-01

    Since the discovery of fullerenes more than three decades ago, new kinds of nanoscale materials of carbon allotropes called "nanocarbons" have so far been discovered or synthesized at successive intervals as cases such as carbon nanotubes, carbon nanohorns, graphene, carbon nanowalls, and a carbon nanobelt, while nanodiamonds were actually discovered before then. Their attractively excellent mechanical, physical, and chemical properties have driven researchers to continuously create one of the hottest frontiers in materials science and technology. While plasma states have often been involved in their discovery, on the other hand, plasma-based approaches to this exciting field originally hold promising and enormous potentials for advancing and expanding industrial/biomedical applications of nanocarbons of great diversity. This article provides an extensive overview on plasma-fabricated nanocarbon materials, where the term "fabrication" is defined as synthesis, functionalization, and assembly of devices to cover a wide range of issues associated with the step-by-step plasma processes. Specific attention has been paid to the comparative examination between plasma-based and non-plasma methods for fabricating the nanocarobons with an emphasis on the advantages of plasma processing, such as low-temperature/large-scale fabrication and diversity-carrying structure controllability. The review ends with current challenges and prospects including a ripple effect of the nanocarbon studies on the development of related novel nanomaterials such as transition metal dichalcogenides. It contains not only the latest progress in the field for cutting-edge scientists and engineers, but also the introductory guidance to non-specialists such as lower-class graduate students.

  4. The relationship of patient age to the pathobiology of the clonal myeloid diseases.

    Science.gov (United States)

    Lichtman, Marshall A; Rowe, Jacob M

    2004-04-01

    The incidence of the major clonal myeloid diseases, clonal cytopenias, acute, subacute (oligoblastic), and chronic myelogenous leukemia, polycythemia vera, thrombocythemia, and idiopathic myelofibrosis increases in a log-linear manner from young adulthood through advanced age. In older patients, diseases requiring cytotoxic treatment are more difficult and less successful to manage because comorbid conditions and poor performance status are more prevalent, decreasing the tolerance to therapy and increasing the frequency of side effects. This age effect is highlighted by the dramatically less favorable outcome in older than younger patients with acute myeloid leukemia with similar "favorable" cytogenetic changes. In addition, in acute and subacute myeloid leukemia in older patients, the disease is intrinsically more resistant to therapy. Overexpression of drug resistance genes and unfavorable genetic mutations are more prevalent in older patients and provide evidence that acute myeloid leukemia is often qualitatively different in these patients. The gradient of age effects is continuous; the frequency of poor outcome increasing by decade (or less). The decline in survival becomes especially steep as quinquagenarians (50-year-olds) age to nonagenarians (90-year-olds). Although improved drug schedules have led to significant improvements in event-free survival in younger patients, these improvements have been far less evident in older patients. New approaches, especially the development of drugs aimed at new targets, will be required to obtain a high frequency of long-term remissions in older patients. Agents that reverse inherent cellular drug resistance, farnesyltransferase inhibitors, BCL-2 inhibitors, and FLT3 inhibitors are early examples of such approaches.

  5. Clonal Expansion of the Macrolide Resistant ST386 within Pneumococcal Serotype 6C in France

    Science.gov (United States)

    Janoir, Claire; Cohen, Robert; Levy, Corinne; Bingen, Edouard; Lepoutre, Agnès; Gutmann, Laurent; Varon, Emmanuelle

    2014-01-01

    In France, the use of the 7-valent pneumococcal conjugate vaccine (PCV7) lead to an overall significant decrease in PCV7 invasive pneumococcal disease (IPD) incidence. However, the decrease in vaccine serotype prevalence was partially counterbalanced by the serotype replacement phenomenon. In this study, we analyzed the role of the newly described serotype 6C as one of the replacement serotypes. This work was conducted on a large time scale from the early PCV7 era (2002–2003) to the PCV13 era (2010–2011), both on IPD strains recovered from the whole population and nasopharyngeal colonizing strains isolated in infant less than two years, who are known to be the main reservoir for pneumococci. Serotype 6C took advantage over 6A and 6B serotypes, which both decreased over time. A continuous and significant increase in 6C IPD was observed in adults along the study period; in contrast, in children less than two years, only an increase in 6C nasopharyngeal carriage was found, the prevalence of serotype 6C in IPD remaining very low over time. Among 101 6C invasive and colonizing strains studied by MLST, 24 STs were found to be related to three major clonal complexes, CC395, CC176, and CC315. STs related to CC176 tend to disappear after 2009 and were essentially replaced by ST386 (CC315), which dramatically increased over time. This clonal expansion may be explained by the erythromycin and tetracycline resistances associated with this clone. Finally, the decrease observed in nasopharyngeal 6C carriage since 2010, likely related to the PCV13 introduction in the French immunization schedule, is expected to lead to a decrease in 6C IPD in adults thereafter. PMID:24603763

  6. Soil biota effects on clonal growth and flowering in the forest herb Stachys sylvatica

    Science.gov (United States)

    de la Peña, Eduardo; Bonte, Dries

    2011-03-01

    The composition of a soil community can vary drastically at extremely short distances. Therefore, plants from any given population can be expected to experience strong differences in belowground biotic interactions. Although it is well recognized that the soil biota plays a significant role in the structure and dynamics of plant communities, plastic responses in growth strategies as a function of soil biotic interactions have received little attention. In this study, we question whether the biotic soil context from two forest associated contrasting environments (the forest understory and the hedgerows) determines the balance between clonal growth and flowering of the perennial Stachys sylvatica. Using artificial soils, we compared the growth responses of this species following inoculation with the mycorrhizal and microbial community extracted either from rhizospheric soil of the forest understory or from the hedgerows. The microbial context had a strong effect on plant functional traits, determining the production of runners and inflorescences. Plants inoculated with the hedgerow community had a greater biomass, larger number of runners, and lower resource investment in flower production than was seen in plants inoculated with the understory microbial community. The obtained results illustrate that belowground biotic interactions are essential to understand basic plastic growth responses determinant for plant establishment and survival. The interactions with microbial communities from two contrasting habitats resulted in two different, and presumably adaptive, growth strategies that were optimal for the conditions prevalent in the environments compared; and they are as such an essential factor to understand plant-plant, plant-animal interactions and the dispersal capacities of clonal plants.

  7. Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis

    Directory of Open Access Journals (Sweden)

    Franz Silvio

    2011-06-01

    Full Text Available Abstract Background Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC, the etiological agent of tuberculosis (TB, experts have first identified several groups according to their pattern at repetitive sequences, especially at the CRISPR locus (spoligotyping, and to their epidemiological relevance. Most groups such as "Beijing" found good support when tested with other loci. However, other groups such as T family and T1 subfamily (belonging to the "Euro-American" lineage correspond to non-monophyletic groups and still need to be refined. Here, we propose to use a method called Affinity Propagation that has been successfully used in image categorization to identify relevant patterns at the CRISPR locus in MTC. Results To adequately infer the relative divergence time between strains, we used a distance method inspired by the recent evolutionary model by Reyes et al. We first confirm that this method performs better than the Jaccard index commonly used to compare spoligotype patterns. Second, we document the support of each spoligotype family among the previous classification using affinity propagation on the international spoligotyping database SpolDB4. This allowed us to propose a consensus assignation for all SpolDB4 spoligotypes. Third, we propose new signatures to subclassify the T family. Conclusion Altogether, this study shows how the new clustering algorithm Affinity Propagation can help building or refining clonal organims classifications. It also describes well-supported families and subfamilies among M. tuberculosis complex, especially inside the modern "Euro-American" lineage.

  8. The Resistance Mechanism and Clonal Distribution of Tigecycline-Nonsusceptible Klebsiella pneumoniae Isolates in Korea.

    Science.gov (United States)

    Ahn, Chulsoo; Yoon, Sang Sun; Yong, Tae Soon; Jeong, Seok Hoon; Lee, Kyungwon

    2016-05-01

    Tigecycline is one of the drugs used to treat multi-drug resistant Klebsiella pneumoniae (K. pneumoniae) infections, including complicated skin and soft tissue infections, complicated intra-abdominal infection, and community-acquired pneumonia in the Republic of Korea. However, since its commercial release, K. pneumoniae resistance against tigecycline has been reported, and there is a serious concern about the spread of tigecycline resistant bacteria. In this study, we collected and analyzed 342 isolates from 23 hospitals in the Republic of Korea to determine the mechanisms of tigecycline susceptibility and their clonal types. The hospitals include several from each province in the Republic of Korea, except Jeju, an island province, and nonsusceptibility among the isolates was tested by the disk diffusion method. In our lab, susceptibility was checked again using the broth dilution method, and clonal types were determined using the multilocus sequence typing protocol. Real-time PCR was performed to measure the ramR mutation in the isolates nonsusceptible to tigecycline, which would suggest an increased expression of the AcrAB multidrug pump. Fifty-six K. pneumoniae isolates were found to be nonsusceptible, 16% of the 342 collected. Twenty-seven and nine isolates of the tigecycline nonsusceptible isolates had mutations in the ramR and rpsJ genes, respectively; while 18 nonsusceptible isolates harbored the tetA gene. Comparison of isolates with and without ramR mutation showed a significant statistical difference (ppneumoniae, including ST11, ST768, ST15, ST23, ST48, and ST307. There does not seem to be a transferrable medium, such as plasmid, for the resistance yet, although mutation of the ramR gene may be a common event, accounting for 48% of the nonsusceptibility in this study.

  9. MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance.

    Science.gov (United States)

    Kwok, Brian; Hall, Jeff M; Witte, John S; Xu, Yin; Reddy, Prashanti; Lin, Keming; Flamholz, Rachel; Dabbas, Bashar; Yung, Aine; Al-Hafidh, Jenan; Balmert, Emily; Vaupel, Christine; El Hader, Carlos; McGinniss, Matthew J; Nahas, Shareef A; Kines, Julie; Bejar, Rafael

    2015-11-19

    Establishing a diagnosis in patients suspected of having a myelodysplastic syndrome (MDS) can be challenging and could be informed by the identification of somatic mutations. We performed a prospective study to examine the frequency and types of mutations encountered in 144 patients with unexplained cytopenias. Based on bone marrow findings, 17% were diagnosed with MDS, 15% with idiopathic cytopenias of undetermined significance (ICUS) and some evidence of dysplasia, and 69% with ICUS and no dysplasia. Bone marrow DNA was sequenced for mutations in 22 frequently mutated myeloid malignancy genes. Somatic mutations were identified in 71% of MDS patients, 62% of patients with ICUS and some dysplasia, and 20% of ICUS patients and no dysplasia. In total, 35% of ICUS patients carried a somatic mutation or chromosomal abnormality indicative of clonal hematopoiesis. We validated these results in a cohort of 91 lower-risk MDS and 249 ICUS cases identified over a 6-month interval. Mutations were found in 79% of those with MDS, in 45% of those with ICUS with dysplasia, and in 17% of those with ICUS without dysplasia. The spectrum of mutated genes was similar with the exception of SF3B1 which was rarely mutated in patients without dysplasia. Variant allele fractions were comparable between clonal ICUS (CCUS) and MDS as were mean age and blood counts. We demonstrate that CCUS is a more frequent diagnosis than MDS in cytopenic patients. Clinical and mutational features are similar in these groups and may have diagnostic utility once outcomes in CCUS patients are better understood. © 2015 by The American Society of Hematology.

  10. Clonal chromosomal abnormalities appearing in Philadelphia chromosome-negative metaphases during CML treatment.

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    Issa, Ghayas C; Kantarjian, Hagop M; Gonzalez, Graciela Nogueras; Borthakur, Gautam; Tang, Guilin; Wierda, William; Sasaki, Koji; Short, Nicholas J; Ravandi, Farhad; Kadia, Tapan; Patel, Keyur; Luthra, Raja; Ferrajoli, Alessandra; Garcia-Manero, Guillermo; Rios, Mary Beth; Dellasala, Sara; Jabbour, Elias; Cortes, Jorge E

    2017-11-09

    Clonal chromosomal abnormalities in Philadelphia chromosome-negative (CCA/Ph-) metaphases emerge as patients with chronic phase chronic myeloid leukemia (CP-CML) are treated with tyrosine kinase inhibitors (TKIs). We assessed the characteristics and prognostic impact of 598 patients with CP-CML treated on clinical trials with various TKIs. CCA/Ph- occurred in 58 patients (10%); the most common were -Y in 25 (43%) and trisomy 8 in 7 patients (12%). Response to TKI therapy was similar for patients with CCA/Ph- and those without additional chromosomal abnormalities (ACAs). We further categorized CCA/Ph- into those in which -Y was the only clonal abnormality, and all others. We found that patients with non -Y CCA/Ph- had worse failure-free survival (FFS), event-free survival (EFS), transformation-free survival (TFS), and overall survival (OS) compared with those without ACAs with the following 5-year rates: FFS (52% vs 70%, P = .02), EFS (68% vs 86%, P = .02), TFS (76% vs 94%, P < .01), and OS (79% vs 94%, P = .03). In a multivariate analysis, non -Y CCA/Ph- increased the risk of transformation or death when baseline characteristics were considered with a hazard ratio of 2.81 (95% confidence interval, 1.15-6.89; P = .02). However, this prognostic impact was not statistically significant when achieving BCR-ABL <10% at 3 months was included in the analysis. In conclusion, non -Y CCA/Ph- are associated with decreased survival when emerging in patients with chronic-phase CML across various TKIs. This trial was registered at www.clinicaltrials.gov as #NCT00048672, #NCT00038649, and #NCT00050531 (imatinib); #NCT00254423 (dasatinib); #NCT00129740 (nilotinib); and NCT01570868 (ponatinib). © 2017 by The American Society of Hematology.

  11. LOH detected by microsatellite markers reveals the clonal origin of recurrent laryngeal squamous cell carcinoma.

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    Zhaoyang Cui

    Full Text Available The question of whether "recurrent" laryngeal carcinoma is truly a new tumour with a clonal origin that differs from that of the primary tumour has remained unanswered. The objective of this study was to determine whether recurrent tumours have the same genetic basis as primary tumours, as the answer to this question is important for the development of treatment strategies.Matched samples consisting of primary tumour, recurrent tumour and normal tissue were obtained from the same patient. A total of 37 patients with laryngeal cancer were examined for loss of heterozygosity (LOH on the 3p, 5p, 7q, 8p, 9p, 13p, 17p and 18q chromosomal arms using PCR to amplify microsatellite markers. All patients were routinely followed up and 5-year survival rates were calculated using directly calculating method and Kaplan-Meier's method.A total of 28 out of 37 (75.6% patients showed LOH at a minimum of one locus, and 19 out of 37 (51.3% patients showed LOH at two loci. Primary and recurrent tumours in each patient showed identical allelic loss patterns and incidence rates. Patients without LOH had a longer average time to recurrence than patients with LOH (P<0.05. Additionally, patients with LOH had a longer average smoking duration prior to surgery than patients without LOH (P<0.05. The 5-year survival rates were 32.14%in patients with LOH versus 44.4% in patients without LOH.The data indicate that primary and recurrent tumours have the same clonal origin. This result implies that we failed to radically resect the primary tumours and/or micrometastases in these patients. Consequently, some form of adjunctive therapy may be necessary. Additionally, the data indicate that the recurrence of laryngeal squamous cell carcinoma is closely related to chromosomal aberrations (specifically LOH.

  12. Clonal expansion during Staphylococcus aureus infection dynamics reveals the effect of antibiotic intervention.

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    Gareth McVicker

    2014-02-01

    Full Text Available To slow the inexorable rise of antibiotic resistance we must understand how drugs impact on pathogenesis and influence the selection of resistant clones. Staphylococcus aureus is an important human pathogen with populations of antibiotic-resistant bacteria in hospitals and the community. Host phagocytes play a crucial role in controlling S. aureus infection, which can lead to a population "bottleneck" whereby clonal expansion of a small fraction of the initial inoculum founds a systemic infection. Such population dynamics may have important consequences on the effect of antibiotic intervention. Low doses of antibiotics have been shown to affect in vitro growth and the generation of resistant mutants over the long term, however whether this has any in vivo relevance is unknown. In this work, the population dynamics of S. aureus pathogenesis were studied in vivo using antibiotic-resistant strains constructed in an isogenic background, coupled with systemic models of infection in both the mouse and zebrafish embryo. Murine experiments revealed unexpected and complex bacterial population kinetics arising from clonal expansion during infection in particular organs. We subsequently elucidated the effect of antibiotic intervention within the host using mixed inocula of resistant and sensitive bacteria. Sub-curative tetracycline doses support the preferential expansion of resistant microorganisms, importantly unrelated to effects on growth rate or de novo resistance acquisition. This novel phenomenon is generic, occurring with methicillin-resistant S. aureus (MRSA in the presence of β-lactams and with the unrelated human pathogen Pseudomonas aeruginosa. The selection of resistant clones at low antibiotic levels can result in a rapid increase in their prevalence under conditions that would previously not be thought to favor them. Our results have key implications for the design of effective treatment regimes to limit the spread of antimicrobial

  13. Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate.

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    Münzbergová, Zuzana; Hadincová, Věroslava

    2017-07-01

    In spite of the increasing number of studies on the importance of transgenerational plasticity for species response to novel environments, its effects on species ability to respond to climate change are still largely unexplored. We study the importance of transgenerational plasticity for response of a clonal species Festuca rubra. Individuals from four natural populations representing two levels of temperature and two levels of precipitation were cultivated in four growth chambers that simulate the temperature and precipitation of origin of the populations (maternal phase). Each population was represented in each growth chamber. After 6 months, single young ramets of these plants were reshuffled among the growth chambers and let to grow for additional 2 months (offspring phase). The results show that transgenerational effects (i.e., maternal phase conditions) significantly modify species response to novel climates, and the direction and intensity of the response depend on the climate of origin of the plants. For traits related to recourse acquisition, the conditions of maternal phase, either alone or in interaction mainly with climate of origin, had stronger effect than the conditions of cultivation. Overall, the maternal climate interacted more intensively with the climate of origin than with the offspring climate. The direction of the effect of the maternal climate was of different directions and intensities depending on plant origin and trait studied. The data demonstrated strong significant effects of conditions during maternal phase on species response to novel climates. These transgenerational affects were, however, not adaptive. Still, transgenerational plasticity may be an important driver of species response to novel conditions across clonal generations. These effects thus need to be carefully considered in future studies exploring species response to novel climates. This will also have strong effects on species performance under increasingly variable

  14. Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis.

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    Tiago Dos Vultos

    Full Text Available BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP analysis of DNA repair, recombination and replication (3R genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly high levels of polymorphisms as compared to house-keeping genes, making it possible to distinguish between 80% of clinical isolates analyzed in this study. Bioinformatics analysis suggests that a large number of these polymorphisms are potentially deleterious. Site frequency spectrum comparison of synonymous and non-synonymous variants and Ka/Ks ratio analysis suggest a general negative/purifying selection acting on these sets of genes that may lead to suboptimal 3R system activity. In turn, the relaxed fidelity of 3R genes may allow the occurrence of adaptive variants, some of which will survive. Furthermore, 3R-based phylogenetic trees are a new tool for distinguishing between M. tuberculosis complex strains. CONCLUSIONS/SIGNIFICANCE: This situation, and the consequent lack of fidelity in genome maintenance, may serve as a starting point for the evolution of antibiotic resistance, fitness for survival and pathogenicity, possibly conferring a selective advantage in certain stressful situations. These findings suggest that 3R genes may play an important role in the evolution of highly clonal bacteria, such as M. tuberculosis. They also facilitate further epidemiological studies of these bacteria, through the development of high-resolution tools. With many more microbial genomes being sequenced, our results open the door to 3R gene-based studies of adaptation and evolution of other, highly clonal bacteria.

  15. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma.

    Science.gov (United States)

    Russo, Mariano; Broach, James; Sheldon, Kathryn; Houser, Kenneth R; Liu, Dajiang J; Kesterson, Joshua; Phaeton, Rebecca; Hossler, Carrie; Hempel, Nadine; Baker, Maria; Newell, Jordan M; Zaino, Richard; Warrick, Joshua I

    2017-09-01

    Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar to those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next-generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma. In evaluating all samples, EIN/AH and carcinoma did not differ in mutational burden, CNA burden, or specific genes mutated (all P>.1). All paired EIN/AH and carcinoma samples shared at least one identical somatic mutation, frequently in PI(3)K pathway members. Large CNAs (>10 genes in length) were identified in 83% of cases; paired EIN/AH and carcinoma samples shared at least one identical CNA in these cases. Mismatch repair protein expression matched in all paired EIN/AH and carcinoma samples. All paired EIN/AH and carcinoma samples had identical The Cancer Genome Atlas subtype, with 3 classified as "copy number low endometrioid" and 3 classified as "microsatellite instability hypermutated." Although paired EIN/AH and carcinoma samples were clonal, private mutations (ie, present in only one sample) were identified in EIN/AH and carcinoma in all cases, frequently in established cancer-driving genes. These findings indicate that EIN/AH gives rise to endometrioid adenocarcinoma by a complex process of subclone evolution, not a linear accumulation of molecular events. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Clonal replacement of epidemic KPC-producing Klebsiella pneumoniae in a hospital in China.

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    Liang, Yuying; Yin, Xiuyun; Zeng, Lijun; Chen, Shuiping

    2017-05-23

    Klebsiella pneumoniae is a frequent nosocomial pathogen causing difficult-to-treat infections worldwide. The prevalence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-KP) is increasing in China. The aim of this study was to investigate the molecular epidemiology of KPC-KP in a nosocomial outbreak. Fifty-four KPC-KP isolates were consecutively collected between November 2013 and August 2014 during a KPC-KP outbreak in a tertiary care hospital in Beijing, China. Antimicrobial susceptibility was determined by agar dilution. Carbapenemase, extended-spectrum β-lactamase, 16S rRNA methylase, AmpC β-lactamase, and plasmid-mediated quinolone resistance determinants were detected by PCR amplification. The genetic relatedness of isolates was analyzed by pulsed-field gel electrophoresis and multi-locus sequence typing. All isolates belonged to ST11 except one isolate which was identified as a new sequence type (ST2040). PFGE profile of genomic DNA revealed seven clusters, of which cluster A and C dominated the KPC-KP outbreak and cluster A was replaced by cluster C during the outbreak. PFGE of genomic DNA, S1-PFGE of plasmids, replicon typing, and drug resistant characteristics showed that clonal spread occurred during the outbreak. When compared with isolates within cluster A, all isolates in cluster C harbored rmtB and showed higher level of resistance to cefepime, amikacin, tobramycin, and tigecycline. We reported a nosocomial outbreak of KPC-KP with clonal replacement and a new sequence type (ST2040) of KP. High degree of awareness and surveillance of KPC-KP should be given to avoid potential outbreaks, especially in ICU wards.

  17. Novel features of computer-simulated clonal life of Paramecium caudatum.

    Science.gov (United States)

    Uezu, Tatsuya; Kakutani, Sae; Yoshida, Mika; Nakajima, Akino; Asao, Takeshi; Takagi, Yoshiomi

    2009-05-21

    The clone of the ciliated protozoan Paramecium caudatum has the immaturity period of about 60 fissions and the lifespan of about 600 fissions. These life cycle figures have been depicted through laboratory experiments that allow continuous cell divisions for hundreds, which never occur in nature. We here constructed the nature-mimicking model culture that alternated the log- and stationary phases to allow conjugation, and computer-simulated the age structure modifying parameters such as cell distributions to start the culture, fission rates, death rates, immaturity periods, probabilities of conjugation, proportions of transplantation and so on. The average and maximum ages in the culture after thousands of alternations were converged to 43+/-2 and 140+/-5 fissions, respectively, when parameters for the immaturity period and the maximum clonal lifespan were set at 60 and 600 fissions. This result explains why cells collected in nature are usually young and vigorous. The average and maximum ages proportionally prolonged as the immaturity period was prolonged, as reported true for species of the ciliate. These results indicate the validity of our simulation. The average and maximum ages remained unchanged when the initial condition for starting the culture was changed from two complementary mating-type cells to a population with a quadratic-function distribution, and when the fission rate at the log-phase and the death rate at the stationary phase were modified for older ages. The average and maximum ages changed slightly when either the conjugation rate or the proportion of transplantation was somewhat lowered. Although they changed considerably when such parameters as the immaturity period, conjugation rate and death rate were extremely modified, no clones with the age over 230 fissions appeared in any simulations. These results indicate the robustness of the model, which provides us with fresh insight into the structural system of the clonal lifespan of P. caudatum

  18. Significance of clonal rearrangements of lymphocyte antigen receptor genes on the prognosis of chronic enteropathy in 22 Shiba dogs.

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    Ohmi, Aki; Ohno, Koichi; Uchida, Kazuyuki; Goto-Koshino, Yuko; Tomiyasu, Hirotaka; Kanemoto, Hideyuki; Fukushima, Kenjiro; Tsujimoto, Hajime

    2017-09-29

    Shiba dogs are predisposed to chronic enteropathy (CE) and have poorer prognosis than other dog breeds. The objective of this study was to investigate the significance of polymerase chain reaction for antigen receptor rearrangement (PARR) results on clinical findings and prognosis of Shiba dogs with CE. We retrospectively collected data on 22 Shiba dogs diagnosed as having CE. Fifty-nine percent of the dogs had clonality-positive results on PARR analysis. Furthermore, on histopathology, epitheliotropic behavior of small lymphocytes of the intestinal mucosa was observed significantly more frequently in dogs with clonal rearrangement of antigen receptor genes (P=0.027). The median overall survival time of clonality-positive dogs was 48 days (range, 4-239 days), compared to 271 days (range, 45-1,316+ days) in clonality-negative dogs. The median overall survival time of epitheliotropism-positive dogs was 76 days (range, 30-349 days) compared to 239 days (range, 4-1,316+ days) for epitheliotropism-negative dogs. Statistical analysis revealed that the clonality-positive result was associated with significantly shorter survival time (P=0.036). In contrast, presence or absence of epitheliotropism had no statistically significant effect on survival time (P=0.223). These cases might appropriately be diagnosed as small T-cell intestinal lymphoma; there are some common clinical and pathogenic features with human enteropathy-associated T-cell lymphoma type 2. The pathogenesis and poor prognosis for Shiba dogs with CE seem to be associated with this type of lymphoma, although further investigation is warranted.

  19. Genetic characterisation of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type

    Science.gov (United States)

    Dubey, J.P.; Velmurugan, G.V.; Ragendran, C.; Yabsley, M.J.; Thomas, N.J.; Beckmen, K.B.; Sinnett, D.; Ruid, D.; Hart, J.; Fair, P.A.; McFee, W.E.; Shearn-Bochsler, V.; Kwok, O.C.H.; Ferreira, L.R.; Choudhary, S.; Faria, E.B.; Zhou, H.; Felix, T.A.; Su, C.

    2011-01-01

    Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study wild animals, from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. gondii was isolated from 31 animals including, to our knowledge for the first time, from a bald eagle (Haliaeetus leucocephalus), five gray wolves (Canis lupus), a woodrat (Neotoma micropus), and five Arctic foxes (Alopex lagopus). Additionally, 66 T. gondii isolates obtained previously, but not genetically characterised, were revived in mice. Toxoplasma gondii DNA isolated from these 97 samples (31+66) was characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers (SAG1, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). A total of 95 isolates were successfully genotyped. In addition to clonal Types II, and III, 12 different genotypes were found. These genotype data were combined with 74 T. gondii isolates previously characterised from wildlife from North America and a composite data set of 169 isolates comprised 22 genotypes, including clonal Types II, III and 20 atypical genotypes. Phylogenetic network analysis showed limited diversity with dominance of a recently designated fourth clonal type (Type 12) in North America, followed by the Type II and III lineages. These three major lineages together accounted for 85% of strains in North America. The Type 12 lineage includes previously identified Type A and X strains from sea otters. This study revealed that the Type 12 lineage accounts for 46.7% (79/169) of isolates and is dominant in wildlife of North America. No clonal Type I strain was identified among these wildlife isolates. These results suggest that T. gondii strains in wildlife from North America have limited diversity, with the occurrence of only a few major clonal types.

  20. Vibrio parahaemolyticus isolates from southeastern Chinese coast are genetically diverse with circulation of clonal complex 3 strains since 2002.

    Science.gov (United States)

    Yu, Ying; Hu, Weizhao; Wu, Beibei; Zhang, Peipei; Chen, Jianshun; Wang, Shuna; Fang, Weihuan

    2011-11-01

    Multilocus sequence typing (MLST) was used to examine the clonal relationship and genetic diversity of 71 Vibrio parahaemolyticus isolates from clinical and seafood-related sources in southeastern Chinese coast between 2002 and 2009. The tested isolates fell into 61 sequence types (STs). Of 17 clinical isolates, 7 belonged to ST3 of the pandemic clonal complex 3, with 3 strains isolated in 2002. Although there was no apparent clonal relationship found between clinical strains and those from seafood-related sources positive with pathogenic markers, there were clonal relationships between clinical strains from this study and those from environmental sources in other parts of China. Phylogenetic analysis showed that strains of 112 STs (61 STs from this study and 51 retrieved from PUBMLST database covering different continents) could be divided into four branches. The vast majority of our isolates and those from other countries were genetically diverse and clustered into two major branches of mixed distribution (of geographic origins and sample sources), whereas five STs representing six isolates split as two minor branches because of divergence of their recA genes, which had 80%-82% nucleotide identity to typical V. parahaemolyticus strains and 73.3%-76.9% identity to the CDS24 of a Vibrio sp. plasmid p23023, indicating that the recA gene might have recombined by lateral gene transfer. This was further supported by a high ratio of recombination to mutation (3.038) for recA. In conclusion, MLST with fully extractable database is a powerful system for analysis of clonal relationship for strains of a particular region in a national or global scale as well as between clinical and environmental or food-related strains.