WorldWideScience

Sample records for clonally expanded plasma

  1. The expanding plasma jet

    International Nuclear Information System (INIS)

    Sanden, M.C.M. van den.

    1991-01-01

    This thesis concerns the fundamental aspects of an argon plasma expanding from a cascaded arc. This type of plasma is not only used for fundamental research but also for technologically orientated research on plasma deposition and plasma sources. The important characteristics of the plasma are a strong supersonic expansion in which the neutral particle and ion densities decrease three orders of magnitude, followed by a stationary shock front. After the shock front the plasma expands further subsonically. A part of this thesis is devoted to the discussion of a newly constructed combined Thomson-Rayleigh scattering set up. With this set up the electron density, the electron temperature and the neutral particle density are measured locally in the plasma for different conditions. In the analysis of the measured spectra weak coherent effects and the measured apparatus profile are included. The inaccuracies are small, ranging from 1 to 4 percent for the electron density and 2 to 6 percent for the electron temperature, depending on the plasma conditions. The inaccuracy of the neutral particle density determination is larger and ranges from 10 to 50 percent. The detection limits for the electron and neutral particle density are 7.10 17 m -3 and 1.10 20 m -3 respectively. A side path in this thesis is the derivation of the Saha equation for a two-temperature plasma. The reason for this derivation was the dispute in the literature about the correct form of this equation. In this thesis it is shown, from the correct extension of the second law of thermodynamics and from the non-equilibrium formalism of Zubarev, That in the limit of m e /m h ->0 the generalized Saha equation depends on the electron temperature only. (author). 221 refs.; 54 figs.; 13 tabs

  2. Stability of expanded plasma focus

    International Nuclear Information System (INIS)

    Soliman, H.M.

    1994-01-01

    In this study, the stabilization of the expanded plasma focus formed by 4.5 kJ plasma focus device of Mather type by magnetic field is presented. The experimental results of the induced axial magnetic field and electric probe measurements of the expanded plasma focus show that, the plasma consists of three plasmoids, electron temperature measurements off the plasmoids at a point close to the muzzle are 26 eV, 30 eV and 27 eV respectively and the electron densities are 6.6 x 10 14 , 6.1 x 10 14 / cm 3 respectively. The presence of external axial magnetic field (B 2 = 1.6 kg) at the mid distance between the breech and the muzzle has a less effect on the stability of expanded focus and it causes a restriction for the plasma motion. the electron temperature of the three plasmoids are found to increase in that case by 23%, 18.5% respectively. When this axial magnetic field is applied at the muzzle end, it leads to a more stable expanded plasma focus which consists mainly of one plasmoid with electron temperature of 39 eV and density of 3.4 x 10 14 / cm 3 . 5 figs

  3. Clonally Expanding Thymocytes Having Lineage Capability in Gamma-Ray-Induced Mouse Atrophic Thymus

    International Nuclear Information System (INIS)

    Yamamoto, Takashi; Morita, Shin-ichi; Go, Rieka; Obata, Miki; Katsuragi, Yoshinori; Fujita, Yukari; Maeda, Yoshitaka; Yokoyama, Minesuke; Aoyagi, Yutaka; Ichikawa, Hitoshi; Mishima, Yukio; Kominami, Ryo

    2010-01-01

    Purpose: To characterize, in the setting of γ-ray-induced atrophic thymus, probable prelymphoma cells showing clonal growth and changes in signaling, including DNA damage checkpoint. Methods and Materials: A total of 111 and 45 mouse atrophic thymuses at 40 and 80 days, respectively, after γ-irradiation were analyzed with polymerase chain reaction for D-J rearrangements at the TCRβ locus, flow cytometry for cell cycle, and Western blotting for the activation of DNA damage checkpoints. Results: Limited D-J rearrangement patterns distinct from normal thymus were detected at high frequencies (43 of 111 for 40-day thymus and 21 of 45 for 80-day thymus). Those clonally expanded thymocytes mostly consisted of CD4 + CD8 + double-positive cells, indicating the retention of lineage capability. They exhibited pausing at a late G1 phase of cell cycle progression but did not show the activation of DNA damage checkpoints such as γH2AX, Chk1/2, or p53. Of interest is that 17 of the 52 thymuses showing normal D-J rearrangement patterns at 40 days after irradiation showed allelic loss at the Bcl11b tumor suppressor locus, also indicating clonal expansion. Conclusion: The thymocytes of clonal growth detected resemble human chronic myeloid leukemia in possessing self-renewal and lineage capability, and therefore they can be a candidate of the lymphoma-initiating cells.

  4. Secondary immunization generates clonally related antigen-specific plasma cells and memory B cells.

    Science.gov (United States)

    Frölich, Daniela; Giesecke, Claudia; Mei, Henrik E; Reiter, Karin; Daridon, Capucine; Lipsky, Peter E; Dörner, Thomas

    2010-09-01

    Rechallenge with T cell-dependent Ags induces memory B cells to re-enter germinal centers (GCs) and undergo further expansion and differentiation into plasma cells (PCs) and secondary memory B cells. It is currently not known whether the expanded population of memory B cells and PCs generated in secondary GCs are clonally related, nor has the extent of proliferation and somatic hypermutation of their precursors been delineated. In this study, after secondary tetanus toxoid (TT) immunization, TT-specific PCs increased 17- to 80-fold on days 6-7, whereas TT-specific memory B cells peaked (delayed) on day 14 with a 2- to 22-fold increase. Molecular analyses of V(H)DJ(H) rearrangements of individual cells revealed no major differences of gene usage and CDR3 length between TT-specific PCs and memory B cells, and both contained extensive evidence of somatic hypermutation with a pattern consistent with GC reactions. This analysis identified clonally related TT-specific memory B cells and PCs. Within clusters of clonally related cells, sequences shared a number of mutations but also could contain additional base pair changes. The data indicate that although following secondary immunization PCs can derive from memory B cells without further somatic hypermutation, in some circumstances, likely within GC reactions, asymmetric mutation can occur. These results suggest that after the fate decision to differentiate into secondary memory B cells or PCs, some committed precursors continue to proliferate and mutate their V(H) genes.

  5. Expanding plasma jet in a vacuum vessel

    International Nuclear Information System (INIS)

    Chutov, Yu.I.; Kravchenko, A.Yu.; Yakovetskij, V.S.

    1998-01-01

    The paper deals with numerical calculations of parameters of a supersonic quasi-neutral argon plasma jet expanding into a cylindrical vacuum vessel and interacting with its inner surface. A modified method of large particles was used, the complex set of hydrodynamic equations being broken into simpler components, each of which describes a separate physical process. Spatial distributions of the main parameters of the argon plasma jet were simulated at various times after the jet entering the vacuum vessel, the parameters being the jet velocity field, the full plasma pressure, the electron temperature, the temperature of heavy particles, and the degree of ionization. The results show a significant effect of plasma jet interaction on the plasma parameters. The jet interaction with the vessel walls may result e.g. in excitation of shock waves and rotational plasma motions. (J.U.)

  6. 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 inexpen...... was characterized in human colon carcinoma xenograft bearing nude mice. A tumor specific accumulation of HES 450 was observed, which proves it’s potential as carrier for passive tumor targeting....

  7. Short wavelength striations on expanding plasma clouds

    International Nuclear Information System (INIS)

    Winske, D.; Gary, S.P.

    1989-01-01

    The growth and evolution of short wavelength (< ion gyroradius) flute modes on a plasma expanding across an ambient magnetic field have been actively studied in recent years, both by means of experiments in the laboratory as well as in space and through numerical simulations. We review the relevant observations and simulations results, discuss the instability mechanism and related linear theory, and describe recent work to bring experiments and theory into better agreement. 30 refs., 6 figs

  8. Clonally expanded cytotoxic CD4+ T cells and the pathogenesis of IgG4-related disease.

    Science.gov (United States)

    Mattoo, Hamid; Stone, John H; Pillai, Shiv

    2017-02-01

    IgG4-related disease (IgG4-RD) is a systemic condition of unknown cause characterized by highly fibrotic lesions, with dense lymphoplasmacytic infiltrates containing a preponderance of IgG4-expressing plasma cells. CD4 + T cells and B cells constitute the major inflammatory cell populations in IgG4-RD lesions. IgG4-RD patients with active, untreated disease show a marked expansion of plasmablasts in the circulation. Although the therapeutic depletion of B cells suggests a role for these cells in the disease, a direct role for B cells or IgG4 in the pathogenesis of IgG4-RD is yet to be demonstrated. Among the CD4 + T-cell subsets, Th2 cells were initially thought to contribute to IgG4-RD pathogenesis, but many previous studies were confounded by the concomitant history of allergic diseases in the patients studied and the failure to use multi-color staining to definitively identify T-cell subsets in tissue samples. More recently, using an unbiased approach to characterize CD4 + T-cell subsets in patients with IgG4-RD - based on their clonal expansion and ability to infiltrate affected tissue sites - CD4 + CTLs have been identified as the major CD4 + T-cell subset in disease lesions as well as in the circulation. CD4 + CTLs in affected tissues secrete pro-fibrotic cytokines including IL-1β, TGF-β1, and IFN-γ as well as cytolytic molecules such as perforin and granzymes A and B. In this review, we examine possible mechanisms by which activated B cells and plasmablasts may collaborate with the expanded CD4 + CTLs in driving the fibrotic pathology of the disease and describe the lacunae in the field and in our understanding of IgG4-RD pathogenesis.

  9. Measuring the Plasma Density of a Ferroelectric Plasma Source in an Expanding Plasma

    International Nuclear Information System (INIS)

    Dunaevsky, A.; Fisch, N.J.

    2003-01-01

    The initial density and electron temperature at the surface of a ferroelectric plasma source were deduced from floating probe measurements in an expanding plasma. The method exploits negative charging of the floating probe capacitance by fast flows before the expanding plasma reaches the probe. The temporal profiles of the plasma density can be obtained from the voltage traces of the discharge of the charged probe capacitance by the ion current from the expanding plasma. The temporal profiles of the plasma density, at two different distances from the surface of the ferroelectric plasma source, could be further fitted by using the density profiles for the expanding plasma. This gives the initial values of the plasma density and electron temperature at the surface. The method could be useful for any pulsed discharge, which is accompanied by considerable electromagnetic noise, if the initial plasma parameters might be deduced from measurements in expanding plasma

  10. Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy.

    Science.gov (United States)

    Page, David B; Yuan, Jianda; Redmond, David; Wen, Y Hanna; Durack, Jeremy C; Emerson, Ryan; Solomon, Stephen; Dong, Zhiwan; Wong, Phillip; Comstock, Christopher; Diab, Adi; Sung, Janice; Maybody, Majid; Morris, Elizabeth; Brogi, Edi; Morrow, Monica; Sacchini, Virgilio; Elemento, Olivier; Robins, Harlan; Patil, Sujata; Allison, James P; Wolchok, Jedd D; Hudis, Clifford; Norton, Larry; McArthur, Heather L

    2016-10-01

    In early-stage breast cancer, the degree of tumor-infiltrating lymphocytes (TIL) predicts response to chemotherapy and overall survival. Combination immunotherapy with immune checkpoint antibody plus tumor cryoablation can induce lymphocytic infiltrates and improve survival in mice. We used T-cell receptor (TCR) DNA sequencing to evaluate both the effect of cryoimmunotherapy in humans and the feasibility of TCR sequencing in early-stage breast cancer. In a pilot clinical trial, 18 women with early-stage breast cancer were treated preoperatively with cryoablation, single-dose anti-CTLA-4 (ipilimumab), or cryoablation + ipilimumab. TCRs within serially collected peripheral blood and tumor tissue were sequenced. In baseline tumor tissues, T-cell density as measured by TCR sequencing correlated with TIL scores obtained by hematoxylin and eosin (H&E) staining. However, tumors with little or no lymphocytes by H&E contained up to 3.6 × 10 6 TCR DNA sequences, highlighting the sensitivity of the ImmunoSEQ platform. In this dataset, ipilimumab increased intratumoral T-cell density over time, whereas cryoablation ± ipilimumab diversified and remodeled the intratumoral T-cell clonal repertoire. Compared with monotherapy, cryoablation plus ipilimumab was associated with numerically greater numbers of peripheral blood and intratumoral T-cell clones expanding robustly following therapy. In conclusion, TCR sequencing correlates with H&E lymphocyte scoring and provides additional information on clonal diversity. These findings support further study of the use of TCR sequencing as a biomarker for T-cell responses to therapy and for the study of cryoimmunotherapy in early-stage breast cancer. Cancer Immunol Res; 4(10); 835-44. ©2016 AACR. ©2016 American Association for Cancer Research.

  11. Recombination of a fast expanding plasma

    International Nuclear Information System (INIS)

    Salvat, M.

    1979-05-01

    The goal of the following calculations is to determine numerically the recombination of dense plasmas (for instance of laser-produced plasmas). The recombination is computed for plasmas with initial densities of 10 24 27 [m -3 ] and with initial temperatures >= 50 eV. The ionization of the plasma remains essentially constant during the early phase of expansion. The time for which the ionization is 'frozen-in' grows with decreasing initial density and with increasing initial temperature. (orig.) [de

  12. Industrial implementation of plasma deposition using the expanding thermal plasma technique

    NARCIS (Netherlands)

    Sanden, van de M.C.M.; Oever, van den P.J.; Creatore, M.; Schaepkens, M.; Miebach, T.; Iacovangelo, C.D.; Bosch, R.C.M.; Bijker, M.D.; Evers, M.F.J.; Schram, D.C.; Kessels, W.M.M.

    2004-01-01

    Two successful industrial implementations of the expanding thermal plasma setup, a novel plasma source, obtaining high deposition rate are discussed. The Ar/O2/hexamethyldisiloxane and Ar/O2/octamethyl-cyclosiloxane-fed expanding thermal plasma setup is used to deposit scratch resistant silicone

  13. 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.

  14. Bremsstrahlung radiation of a plasma expanding into vacuum

    International Nuclear Information System (INIS)

    Grigor'ev, V.G.; Silakov, V.P.; Fetisov, V.S.

    1978-01-01

    Bremsstrahlung of a flat layer of a dense hot homogeneous plasma expanding to vacuum is considered. The spread of plasma is assumed to be adiabatic, and the plasma density and temperature are considered as known functions of coordinates and time in the radiation transport equation. Formulae for radiation intensity have been obtained in cases when the plasma layer covered by the rarefaction wave are optically thin and optically thick. The dependences of radiation intensity on the parameter α characterizing the optical thickness of the plasma layer and the spectrum of radiation of the spreading layer are presented graphically. It is shown that spread has an essential effect on the heat transfer and the spectral composition of the bremsstrahlung of a dense high-temperature plasma

  15. Planar cell polarity signaling coordinates oriented cell division and cell rearrangement in clonally expanding growth plate cartilage

    OpenAIRE

    Li, Yuwei; Li, Ang; Junge, Jason; Bronner, Marianne

    2017-01-01

    Both oriented cell divisions and cell rearrangements are critical for proper embryogenesis and organogenesis. However, little is known about how these two cellular events are integrated. Here we examine the linkage between these processes in chick limb cartilage. By combining retroviral-based multicolor clonal analysis with live imaging, the results show that single chondrocyte precursors can generate both single-column and multi-column clones through oriented division followed by cell rearra...

  16. 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.

  17. The presence of lytic HSV-1 transcripts and clonally expanded T cells with a memory effector phenotype in human sensory ganglia.

    Science.gov (United States)

    Derfuss, Tobias; Arbusow, Viktor; Strupp, Michael; Brandt, Thomas; Theil, Diethilde

    2009-05-01

    Herpes simplex virus type 1 (HSV-1) latent persistence in human trigeminal ganglia (TG) is accompanied by a chronic CD8 T-cell infiltration. Thus far, during HSV-1 latency only a single transcript, namely the latency-associated transcript (LAT), has been identified to be synthesized but not translated into a protein. In contrast, the chronic CD8 T-cell infiltration suggests that an antigen trigger must be present. The focus of the current work was to look for HSV-1 transcription activity as a potential trigger of the immune response and to demonstrate whether the immune cells are clonally expanded and have a phenotype that suggests that they have been triggered by viral antigen. By combining in situ hybridization, laser cutting microscopy, and single-cell real time RT-PCR, we demonstrated expression of the HSV-1 immediate early (IE) genes ICP0 and ICP4 in human trigeminal neurons. Using CDR3 spectratyping, we showed that the infiltrating T cells are clonally expanded, indicating an antigen-driven immune response. Moreover, the persisting CD8(+) T cells had prominent features of the memory effector phenotype. Chemokines CCL5 and CXCL10 were expressed by a subpopulation of infiltrating cells and the corresponding chemokine receptors CCR5 and CXCR3 were co-expressed on virtually all T cells bearing the CD8 phenotype. Thus, HSV-1 IE genes are expressed in human TG, and the infiltrating T cells bear several characteristics that suggest viral antigenic stimulation.

  18. Debye's length in expanding quark-gluon plasma

    International Nuclear Information System (INIS)

    Bialas, A.

    1988-06-01

    The screening properties of an abelian quark-gluon plasma and boost invariantly expanding in a given direction, are discussed. The expansion results in anisotropic screening. At early stages of the process, the Debye length along the direction of the expansion is reduced by a factor of about 2, relative to static calculations. This may have important consequences for the J/ψ production rate. 12 refs., 2 figs., 1 tab. (author)

  19. Plasma processes and film growth of expanding thermal plasma deposited textured zinc oxide

    NARCIS (Netherlands)

    Groenen, R.; Linden, J.L.; Sanden, van de M.C.M.

    2005-01-01

    Plasma processes and film growth of textured zinc oxide deposited from oxygen and diethyl zinc utilizing expanding thermal argon plasma created by a cascaded arc is discussed. In all conditions explored, an excess of argon ions and low temperature electrons is available, which represent the

  20. On the electric and magnetic field generation in expanding plasmas

    International Nuclear Information System (INIS)

    Gielen, H.J.G.

    1989-01-01

    This thesis deals with the generation of electric and magnetic fields in expanding plasmas. The theoretical model used to calculate the different field quantities in such plasmas is discussed in part 1 and is in fact an analysis of Ohm's law. A general method is given that decomposes each of the forces terms in Ohm's law in a component that induces a charge separation in the plasma and in a component that can drive current. This decomposition is unambiguous and depends upon the boundary conditions for the electric potential. It is shown that in calculating the electromagnetic field quantities in a plasma that is located in the vicinity of a boundary that imposes constraints on the electric potential, Ohm's law should be analyzed instead of the so-called induction equation. Three applications of the model are presented. A description is given of the unipolar arc discharge where both plasma and sheath effects have been taken into account. Secondly a description is presented of the plasma effects of a cathode spot. The third application of the model deals with the generation of magnetic fields in laser-produced plasmas. The second part of this thesis describes the experiments on a magnetized argon plasma expanding from a cascaded arc. With the use of spectroscopic techniques the electron density, ion temperature and the rotation velocity profiles of the ion gas have been determined. The magnetic field generated by the plasma has been measured with the use of the Zeeman effect. Depending on the channel diameter of the nozzle of the cascaded arc, self-generated magnetic fields with axial components of the order of 1% of the externally applied mangetic field have been observed. From the measured ion rotation it has been concluded that this magnetic field is mainly generated by azimuthal electron currents. The corresponding azimuthal current density is of the order of 15% of the axial current density. The observed ion rotation is caused by electron-ion friction. (author

  1. Plane and hemispherical potential structures in magnetically expanding plasmas

    International Nuclear Information System (INIS)

    Takahashi, Kazunori; Igarashi, Yuichi; Fujiwara, Tamiya

    2010-01-01

    Two-dimensional potential structures are measured for different gas pressure in expanding argon plasma using permanent magnets, where the magnetic field is about 100 G in the source and several gauss in the diffusion chamber. The plane potential drop is observed near the source exit for 0.35 mTorr, while the potential structure becomes hemispherical when increasing up to 1 mTorr; the hemispherical structure results in the radial divergence of the ion beam. It is found that the trajectories of the accelerated ions and the electrons overcoming the potential drop are dominated by the potential structure and magnetic-field lines, respectively.

  2. 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.)

  3. Expanding plasmas from anti de Sitter black holes

    International Nuclear Information System (INIS)

    Camilo, Giancarlo

    2016-01-01

    We introduce a new foliation of AdS_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.)

  4. Planar cell polarity signaling coordinates oriented cell division and cell rearrangement in clonally expanding growth plate cartilage.

    Science.gov (United States)

    Li, Yuwei; Li, Ang; Junge, Jason; Bronner, Marianne

    2017-10-10

    Both oriented cell divisions and cell rearrangements are critical for proper embryogenesis and organogenesis. However, little is known about how these two cellular events are integrated. Here we examine the linkage between these processes in chick limb cartilage. By combining retroviral-based multicolor clonal analysis with live imaging, the results show that single chondrocyte precursors can generate both single-column and multi-column clones through oriented division followed by cell rearrangements. Focusing on single column formation, we show that this stereotypical tissue architecture is established by a pivot-like process between sister cells. After mediolateral cell division, N-cadherin is enriched in the post-cleavage furrow; then one cell pivots around the other, resulting in stacking into a column. Perturbation analyses demonstrate that planar cell polarity signaling enables cells to pivot in the direction of limb elongation via this N-cadherin-mediated coupling. Our work provides new insights into the mechanisms generating appropriate tissue architecture of limb skeleton.

  5. Nonequilibrium quark production in the expanding QCD plasma

    Science.gov (United States)

    Tanji, Naoto; Berges, Jürgen

    2018-02-01

    We perform real-time lattice simulations of nonequilibrium quark production in the longitudinally expanding QCD plasma. Starting from a highly occupied gluonic state with vacuum quark sector, we extract the time evolution of quark and gluon number densities per unit transverse area and rapidity. The total quark number shows after an initial rapid increase an almost linear growth with time. Remarkably, this growth rate appears to be consistent with a simple kinetic theory estimate involving only two-to-two scattering processes in small-angle approximation. This extends previous findings about the role of two-to-two scatterings for purely gluonic dynamics in accordance with the early stages of the bottom-up thermalization scenario.

  6. The volume-expanding effects of autologous liquid stored plasma following hemorrhage

    DEFF Research Database (Denmark)

    Bentzer, Peter; Thomas, Owain D; Westborg, Johan

    2012-01-01

    of plasma transfusion on plasma volume. We report a prospective interventional study in which the plasma volume-expanding effect of autologous plasma was investigated after a controlled hemorrhage. Methods. Plasma obtained by plasmapheresis from nine healthy regular blood donors was stored at 2-6°C. Five...

  7. Frequency threshold for ion beam formation in expanding RF plasma

    Science.gov (United States)

    Chakraborty Thakur, Saikat; Harvey, Zane; Biloiu, Ioana; Hansen, Alex; Hardin, Robert; Przybysz, William; Scime, Earl

    2008-11-01

    We observe a threshold frequency for ion beam formation in expanding, low pressure, argon helicon plasma. Mutually consistent measurements of ion beam energy and density relative to the background ion density obtained with a retarding field energy analyzer and laser induced fluorescence indicate that a stable ion beam of 15 eV appears for source frequencies above 11.5 MHz. Reducing the frequency increases the upstream beam amplitude. Downstream of the expansion region, a clear ion beam is seen only for the higher frequencies. At lower frequencies, large electrostatic instabilities appear and an ion beam is not observed. The upstream plasma density increases sharply at the same threshold frequency that leads to the appearance of a stable double layer. The observations are consistent with the theoretical prediction that downstream electrons accelerated into the source by the double layer lead to increased ionization, thus balancing the higher loss rates upstream [1]. 1. M. A. Lieberman, C. Charles and R. W. Boswell, J. Phys. D: Appl. Phys. 39 (2006) 3294-3304

  8. Competition between clonal plasma cells and normal cells for potentially overlapping bone marrow niches is associated with a progressively altered cellular distribution in MGUS vs myeloma.

    Science.gov (United States)

    Paiva, B; Pérez-Andrés, M; Vídriales, M-B; Almeida, J; de las Heras, N; Mateos, M-V; López-Corral, L; Gutiérrez, N C; Blanco, J; Oriol, A; Hernández, M T; de Arriba, F; de Coca, A G; Terol, M-J; de la Rubia, J; González, Y; Martín, A; Sureda, A; Schmidt-Hieber, M; Schmitz, A; Johnsen, H E; Lahuerta, J-J; Bladé, J; San-Miguel, J F; Orfao, A

    2011-04-01

    Disappearance of normal bone marrow (BM) plasma cells (PC) predicts malignant transformation of monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM) into symptomatic multiple myeloma (MM). The homing, behavior and survival of normal PC, but also CD34(+) hematopoietic stem cells (HSC), B-cell precursors, and clonal PC largely depends on their interaction with stromal cell-derived factor-1 (SDF-1) expressing, potentially overlapping BM stromal cell niches. Here, we investigate the distribution, phenotypic characteristics and competitive migration capacity of these cell populations in patients with MGUS, SMM and MM vs healthy adults (HA) aged >60 years. Our results show that BM and peripheral blood (PB) clonal PC progressively increase from MGUS to MM, the latter showing a slightly more immature immunophenotype. Of note, such increased number of clonal PC is associated with progressive depletion of normal PC, B-cell precursors and CD34(+) HSC in the BM, also with a parallel increase in PB. In an ex vivo model, normal PC, B-cell precursors and CD34(+) HSC from MGUS and SMM, but not MM patients, were able to abrogate the migration of clonal PC into serial concentrations of SDF-1. Overall, our results show that progressive competition and replacement of normal BM cells by clonal PC is associated with more advanced disease in patients with MGUS, SMM and MM.

  9. Magnetic field in expanding quark-gluon plasma

    Science.gov (United States)

    Stewart, Evan; Tuchin, Kirill

    2018-04-01

    Intense electromagnetic fields are created in the quark-gluon plasma by the external ultrarelativistic valence charges. The time evolution and the strength of this field are strongly affected by the electrical conductivity of the plasma. Yet, it has recently been observed that the effect of the magnetic field on the plasma flow is small. We compute the effect of plasma flow on magnetic field and demonstrate that it is less than 10%. These observations indicate that the plasma hydrodynamics and the dynamics of electromagnetic field decouple. Thus, it is a very good approximation, on the one hand, to study QGP in the background electromagnetic field generated by external sources and, on the other hand, to investigate the dynamics of magnetic field in the background plasma. We also argue that the wake induced by the magnetic field in plasma is negligible.

  10. Emission spectroscopy on a supersonically expanding argon/silane plasma

    NARCIS (Netherlands)

    Meeusen, G.J.; Ershov-Pavlov, E.A.; Meulenbroeks, R.F.G.; Sanden, van de M.C.M.; Schram, D.C.

    1992-01-01

    Results from emission spectroscopy measurements on an Ar/SiH/sub 4/ plasma jet which is used for fast deposition of amorphous hydrogenated silicon are presented. The jet is produced by allowing a thermal cascaded arc plasma in argon (I=60 A, V=80 V, Ar flow=60 scc/s and pressure 4*10/sup 4/ Pa) to

  11. Energy spectra of gold and silver ions jointly expanding in multielement laser plasma

    International Nuclear Information System (INIS)

    Bedilov, M.R.; Kuramatov, D.; Tsoj, T.G.; Kholbaev, A.; Khaitbaev, K.

    1986-01-01

    The results of the investigations on energy distribution of Au and Ag ions jointly expanding in multielement paser plasma are presented. It is denonstrated, that on the stages of formation and expanding of multielement plasma multucharged ions considerable contribution is made by collision processes between electrons and ions and between ions of light and heavy elements. The results are discussed on the basis of existing theoretical models

  12. Non Equilbrium Vibrational Kinetics in Expanding Plasma Flows

    International Nuclear Information System (INIS)

    Colonna, Gianpiero

    2008-01-01

    The supersonic expansion of a plasma is a system of interest for aerospace applications, ranging from propulsion to hypersonic wind tunnels. Under these conditions the plasma shows significant departures from chemical and thermal equilibrium, similarly to post-discharge conditions. The multitemperature description is not adequate because the internal level distributions show tails overpopulated with respect to a Boltzmann distribution. The state-to-state approach has to be used, including the interaction with free electrons which follow non-maxwellian distributions.

  13. Two-dimensional model of a freely expanding plasma

    International Nuclear Information System (INIS)

    Khalid, Q.

    1975-01-01

    The free expansion of an initially confined plasma is studied by the computer experiment technique. The research is an extension to two dimensions of earlier work on the free expansion of a collisionless plasma in one dimension. In the two-dimensional rod model, developed in this research, the plasma particles, electrons and ions are modeled as infinitely long line charges or rods. The line charges move freely in two dimensions normal to their parallel axes, subject only to a self-consistent electric field. Two approximations, the grid approximation and the periodic boundary condition are made in order to reduce the computation time. In the grid approximation, the space occupied by the plasma at a given time is divided into boxes. The particles are subject to an average electric field calculated for that box assuming that the total charge within each box is located at the center of the box. However, the motion of each particle is exactly followed. The periodic boundary condition allows us to consider only one-fourth of the total number of particles of the plasma, representing the remaining three-fourths of the particles as symmetrically placed images of those whose positions are calculated. This approximation follows from the expected azimuthal symmetry of the plasma. The dynamics of the expansion are analyzed in terms of average ion and electron positions, average velocities, oscillation frequencies and relative distribution of energy between thermal, flow and electric field energies. Comparison is made with previous calculations of one-dimensional models which employed plane, spherical or cylindrical sheets as charged particles. In order to analyze the effect of the grid approximation, the model is solved for two different grid sizes and for each grid size the plasma dynamics is determined. For the initial phase of expansion, the agreement for the two grid sizes is found to be good

  14. Fibrinogen estimates are influenced by methods of measurement and hemodilution with colloid plasma expanders.

    Science.gov (United States)

    Fenger-Eriksen, Christian; Moore, Gary W; Rangarajan, Savita; Ingerslev, Jørgen; Sørensen, Benny

    2010-12-01

    Measurement of plasma fibrinogen is often required in critically ill patients or massively bleeding patients being resuscitated with colloid plasma expander. This study aimed at evaluating different assays of plasma fibrinogen after in vitro dilution with commonly used plasma expanders and challenged the hypothesis that levels of fibrinogen are estimated significantly higher in plasma diluted with colloid plasma expander compared with isotonic saline. Fibrinogen measurements were established in plasma samples each diluted in vitro to 30 or 50% with isotonic saline, hydroxyethyl starch (HES) 130/0.4, and human albumin. Fibrinogen levels were assessed using an antigen determination, three photo-optical Clauss methods, one mechanical Clauss method, a prothrombin-derived method, and viscoelastic measurement through thromboelastometry. Measurement of fibrinogen levels was significantly different when performed on alternate analytical platforms. By 30 and 50% dilution with HES 130/0.4 coagulation analyzers using the photo-optical Clauss methods significantly overestimated levels of fibrinogen. Dilution with human albumin did not affect fibrinogen levels except from one analyzer by 50% dilution level. Viscoelastic measurement of fibrin polymerization was reduced at both dilution levels and appeared to reflect the impairment of fibrin polymerization induced by HES 130/0.4 and to a lesser extent human albumin. This study demonstrated that different automated coagulation analyzers revealed significantly different levels of fibrinogen. The presence of colloid plasma expander gave rise to erroneous high levels of fibrinogen returned from some coagulation analyzers employing the method of Clauss. © 2010 American Association of Blood Banks.

  15. Analysis of the expanding thermal argon-oxygen plasma gas phase

    NARCIS (Netherlands)

    Hest, van M.F.A.M.; Haartsen, J.R.; Weert, van M.H.M.; Schram, D.C.; Sanden, van de M.C.M.

    2003-01-01

    An expanding thermal argon plasma into which oxygen is injected has been analyzed by means of Langmuir and Pitot probe measurements. Information is obtained on the ion d. profile and the flow pattern in the downstream plasma. A combination of Langmuir and Pitot probe measurements provide information

  16. Screening in an expanding quark-gluon plasma

    International Nuclear Information System (INIS)

    Broniowski, W.

    1988-12-01

    Effects of expansion on the Debye length in quark-gluon plasma are calculated in an abelian, boost invariant model. It is found that for early times the screening is significantly more efficient than what follows from naive static considerations. 11 refs., 1 fig., 1 tab. (author)

  17. Double-layer ion acceleration triggered by ion magnetization in expanding radiofrequency plasma sources

    International Nuclear Information System (INIS)

    Takahashi, Kazunori; Charles, Christine; Boswell, Rod W.; Fujiwara, Tamiya

    2010-01-01

    Ion energy distribution functions downstream of the source exit in magnetically expanding low-pressure plasmas are experimentally investigated for four source tube diameters ranging from about 5 to 15 cm. The magnetic-field threshold corresponding to a transition from a simple expanding plasma to a double layer-containing plasma is observed to increase with a decrease in the source tube diameter. The results demonstrate that for the four geometries, the double layer and the accelerated ion beam form when the ion Larmour radius in the source becomes smaller than the source tube radius, i.e., when the ions become magnetized in the source tube.

  18. Diagnostic study of multiple double layer formation in expanding RF plasma

    Science.gov (United States)

    Chakraborty, Shamik; Paul, Manash Kumar; Roy, Jitendra Nath; Nath, Aparna

    2018-03-01

    Intensely luminous double layers develop and then expand in size in a visibly glowing RF discharge produced using a plasma source consisting of a semi-transparent cylindrical mesh with a central electrode, in a linear plasma chamber. Although RF discharge is known to be independent of device geometry in the absence of magnetic field, the initiation of RF discharge using such a plasma source results in electron drift and further expansion of the plasma in the vessel. The dynamics of complex plasma structures are studied through electric probe diagnostics in the expanding RF plasma. The measurements made to study the parametric dependence of evolution of double layer structures are analyzed and presented here. The plasma parameter measurements suggest that the complex potential structures initially form with low potential difference between the layers and then gradually expand producing burst oscillations. The present study provides interesting information about the stability of plasma sheath and charge particle dynamics in it that are important to understand the underlying basic sheath physics along with applications in plasma acceleration and propulsion.

  19. 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

  20. Optoelectronic properties of expanding thermal plasma deposited textured zinc oxide : effect of aluminum doping

    NARCIS (Netherlands)

    Groenen, R.; Kieft, E.R.; Linden, J.L.; Sanden, van de M.C.M.

    2006-01-01

    Aluminum-doped zinc oxide films exhibiting a rough surface morphol. are deposited on glass substrates utilizing expanding thermal plasma. Spectroscopic ellipsometry is used to evaluate optical and electronic film properties. The presence of aluminum donors in doped films is confirmed by a shift in

  1. High throughput deposition of hydrogenated amorphous carbon coatings on rubber with expanding thermal plasma

    NARCIS (Netherlands)

    Pei, Y.T.; Eivani, A.R.; Zaharia, T.; Kazantis, A.V.; Sanden, van de M.C.M.; De Hosson, J.T.M.

    2014-01-01

    Flexible hydrogenated amorphous carbon (a-C:H) thin film coated on rubbers has shown outstanding protection of rubber seals from friction and wear. This work concentrates on the potential advances of expanding thermal plasma (ETP) process for a high throughput deposition of a-C:H thin films in

  2. Carbon deposition using an expanding cascaded arc d.c. plasma

    NARCIS (Netherlands)

    Beulens, J.J.; Buuron, A.J.M.; Schram, D.C.

    1991-01-01

    In this work a strongly flowing cascaded arc burning on an argon-hydrogen mixture is used to dissociate and ionize hydrocarbons which are injected inside a nozzle which is mounted in the anode of the arc. The thermal plasma (T ˜ 10 000 K, p ˜ 0.5 bar) will then expand supersonically into a vessel

  3. Experimental study of CF4 conical theta pinch plasma expanding into vacuum

    International Nuclear Information System (INIS)

    Pedrow, P.D.; Nasiruddin, A.M.

    1989-01-01

    Langmuir probe, photodiode, and optical multichannel analyzer (OMA) measurements have been made on a pulsed CF 4 conical theta pinch plasma. A cloud of CF 4 gas was puffed into a conical theta pinch coil, converted to plasma, and propelled into the vacuum region ahead of the expanding gas cloud. At a position 67 cm away from the conical theta pinch coil, the plasma arrived in separate packets that were about 20 μs in duration. The average drift velocity of these packets corresponded to an energy of about 3 eV. The OMA measurements showed that the second packet contained neutral atomic fluorine as well as charged particles

  4. Ion acoustic waves and double-layers in electronegative expanding plasmas

    International Nuclear Information System (INIS)

    Plihon, Nicolas; Chabert, Pascal

    2011-01-01

    Ion acoustic waves and double-layers are observed in expanding plasmas in electronegative gases, i.e., plasmas containing an appreciable fraction of negative ions. The reported experiments are performed in argon gas with a variable amount of SF 6 . When varying the amount of SF 6 , the negative ion fraction increases and three main regimes were identified previously: (i) the plasma smoothly expands at low negative ion fraction, (ii) a static double-layer (associated with an abrupt potential drop and ion acceleration) forms at intermediate negative ion fraction, (iii) double-layers periodically form and propagate (in the plasma expansion direction) at high negative ion fraction. In this paper, we show that transition phases exist in between these regimes, where fluctuations are observed. These fluctuations are unstable slow ion acoustic waves, propagating in the direction opposite to the plasma expansion. These fluctuations are excited by the most unstable eigenmodes and display turbulent features. It is suggested that the static double layer forms when the ion acoustic fluctuations become non-linearly unstable: the double layer regime being a bifurcated state of the smoothly expanding regime. For the highest negative ion fraction, a coexistence of (upstream propagating) slow ion acoustic fluctuations and (downstream) propagating double layers was observed.

  5. Analysis of the expanding thermal argon-oxygen plasma gas phase

    International Nuclear Information System (INIS)

    Hest, M F A M van; Haartsen, J R; Weert, M H M van; Schram, D C; Sanden, M C M van de

    2003-01-01

    An expanding thermal argon plasma into which oxygen is injected has been analysed by means of Langmuir and Pitot probe measurements. Information is obtained on the ion density profile and the flow pattern in the downstream plasma. A combination of Langmuir and Pitot probe measurements provide information on the total ion flux generated by the plasma source (cascaded arc). It has been found that the ion diffusion is mainly determined by the background pressure in the expansion vessel and the arc current. The ion density is determined by the total power input into the plasma as well as the gas flow in the plasma source. There is an optimum in the power transfer used for ionization from plasma source to the feed gas. Interaction of oxygen with the plasma results in a decrease in the argon ion density and the plasma beam radius. The recirculation pattern of the downstream plasma has been investigated experimentally using the Pitot probe. Due to the low downstream pressure (10-30 Pa), the conventional compressible Pitot probe theory no longer applies. It is concluded that viscous effects start to play an important role at these low pressures and should be taken into account in the analysis of the Pitot probe measurements

  6. High spatial resolution in laser-induced breakdown spectroscopy of expanding plasmas

    International Nuclear Information System (INIS)

    Siegel, J.; Epurescu, G.; Perea, A.; Gordillo-Vazquez, F.J.; Gonzalo, J.; Afonso, C.N.

    2005-01-01

    We report a technique that is able to achieve high spatial resolution in the measurement of the temporal and spectral emission characteristics of laser-induced expanding plasmas. The plasma is imaged directly onto the slit of an imaging spectrograph coupled to a time-gated intensified camera, with the plasma expansion direction being parallel to the slit extension. In this way, a single hybrid detection system is used to acquire the spatial, spectral and temporal characteristics of the laser induced plasma. The parallel acquisition approach of this technique ensures a much better spatial resolution in the expansion direction, reproducibility and data acquisition speed than commonly obtained by sequential measurements at different distances from the target. We have applied this technique to study the laser-induced plasma in LiNbO 3 and Bi 12 Ge 1 O 20 , revealing phenomena not seen in such detail with standard instruments. These include extreme line broadening up to a few nanometers accompanied by self-absorption near the target surface, as well as different ablation and expansion dynamics for the different species ejected. Overall, the high precision and wealth of quantitative information accessible with this technique open up new possibilities for the study of fundamental plasma expansion processes during pulsed laser ablation

  7. Heating and Acceleration of Solar Wind Ions by Turbulent Wave Spectrum in Inhomogeneous Expanding Plasma

    Science.gov (United States)

    Ofman, Leon; Ozak, Nataly; Vinas, Adolfo F.

    2016-01-01

    Near the Sun (plasma. The heating and the acceleration of the solar wind ions by turbulent wave spectrum in inhomogeneous plasma is studied using a 2.5D hybrid model. The hybrid model describes the kinetics of the ions, while the electrons are modeled as massless neutralizing fluid in an expanding box approach. Turbulent magnetic fluctuations dominated by power-law frequency spectra, which are evident from in-situ as well as remote sensing measurements, are used in our models. The effects of background density inhomogeneity across the magnetic field on the resonant ion heating are studied. The effect of super- Alfvenic ion drift on the ion heating is investigated. It is found that the turbulent wave spectrum of initially parallel propagating waves cascades to oblique modes, and leads to enhanced resonant ion heating due to the inhomogeneity. The acceleration of the solar wind ions is achieved by the parametric instability of large amplitude waves in the spectrum, and is also affected by the inhomogeneity. The results of the study provide the ion temperature anisotropy and drift velocity temporal evolution due to relaxation of the instability. The non-Maxwellian velocity distribution functions (VDFs) of the ions are modeled in the inhomogeneous solar wind plasma in the acceleration region close to the Sun.

  8. Heating and acceleration of solar wind ions by turbulent wave spectrum in inhomogeneous expanding plasma

    Energy Technology Data Exchange (ETDEWEB)

    Ofman, Leon, E-mail: Leon.Ofman@nasa.gov [Department of Physics, The Catholic University of America, Washington, DC (United States); NASA Goddard Space Flight Center, Greenbelt, MD (United States); Visiting, Department of Geosciences, Tel Aviv University, Tel Aviv (Israel); Ozak, Nataly [Centre for mathematical Plasma Astrophysics, KU Leuven, Celestijnenlaan 200B, 3001 Leuven (Belgium); Viñas, Adolfo F. [NASA Goddard Space Flight Center, Greenbelt, MD (United States)

    2016-03-25

    Near the Sun (< 10R{sub s}) the acceleration, heating, and propagation of the solar wind are likely affected by the background inhomogeneities of the magnetized plasma. The heating and the acceleration of the solar wind ions by turbulent wave spectrum in inhomogeneous plasma is studied using a 2.5D hybrid model. The hybrid model describes the kinetics of the ions, while the electrons are modeled as massless neutralizing fluid in an expanding box approach. Turbulent magnetic fluctuations dominated by power-law frequency spectra, which are evident from in-situ as well as remote sensing measurements, are used in our models. The effects of background density inhomogeneity across the magnetic field on the resonant ion heating are studied. The effect of super-Alfvénic ion drift on the ion heating is investigated. It is found that the turbulent wave spectrum of initially parallel propagating waves cascades to oblique modes, and leads to enhanced resonant ion heating due to the inhomogeneity. The acceleration of the solar wind ions is achieved by the parametric instability of large amplitude waves in the spectrum, and is also affected by the inhomogeneity. The results of the study provide the ion temperature anisotropy and drift velocity temporal evolution due to relaxation of the instability. The non-Maxwellian velocity distribution functions (VDFs) of the ions are modeled in the inhomogeneous solar wind plasma in the acceleration region close to the Sun.

  9. Photon production in an expanding and chemically equilibrating gluon-enriched plasma

    International Nuclear Information System (INIS)

    Kaempfer, B.; Technische Univ. Dresden; Pavlenko, O.P.; AN Ukrainskoj SSR, Kiev

    1993-12-01

    Photon production in a longitudinally and transversely expanding gluon plasma with initially little quark admixture is considered. Chemical equilibration of quarks and gluons is followed by rate equations. The yields of hard photons with E ≥ 2 GeV are insensitive to chemical equilibration and depend mainly on the initial thermalized state. Medium-energy photons with E ∼ 1 GeV are more frequently produced in case of faster equilibration, despite of faster cooling. For an assumed fast equilibration we follow the evolution of matter through mixed and hadron phases. The transverse momentum kick, due to transverse expansion, of photons from hadron matter is shown to be reduced for an equation of state with reduced latent heat. The photon yield in the region E > 1 GeV from deconfined matter dominates for conditions, estimated to be achieved at RHIC, in case of a weakly first-order confinement transition. (orig.)

  10. Plasma treatment of expanded PTFE offers a way to a biofunctionalization of its surface

    International Nuclear Information System (INIS)

    Baquey, Ch.; Palumbo, F.; Porte-Durrieu, M.C.; Legeay, G.; Tressaud, A.; D'Agostino, R.

    1999-01-01

    Biointegration is the ideal outcome which is expected for an artificial implant. That means that the phenomena which seats at the interface between the implant and the host tissues does not induce neither any deleterious effect, such as chronic inflammatory response, nor the formation of unusual tissues. Thus it is of paramount importance to design biomaterials, used for the fabrication of implants, with the best appropriate surface properties. At the same time these biomaterials must feature bulk properties which meet other requirements, especially mechanical properties, deriving from the intended function of the implant in which they are involved. As it is quite impossible to design biomaterials which fulfil at the same time both types of requirements, it is commonly agreed that the solution to this issue goes through the selection or the design of biomaterials with adequate bulk properties, and a further treatment of the surface which would improve the properties of the latter. In this respect ionizing radiations and plasma based treatments, offer a wide panel of possibilities; as an example we describe here how the surface of expanded poly(tetrafluoroethylene) samples can be activated using cold plasma, in order to open a way to chemical modifications of such a surface. Subsequently, Radio Frequency Glow Discharge (RFGD) containing oligopeptides, known for their role in mediating the adhesion of cells to the extracellular matrix, were bound to the modified surface, and the affinity of endothelial cells for the latter was investigated

  11. Absorption and stimulated emission between the electronic states of C and C_2 radicals in an expanding thermal plasma

    NARCIS (Netherlands)

    Otorbaev, D.K.; Sanden, van de M.C.M.; Buuron, A.J.M.; Schram, D.C.

    1995-01-01

    Using the method of reabsorption the absolute densities of argon, atomic and molecular carbon are determined during the deposition of amorphous hydrogenated (diamond-like) carbon coatings by an expanding thermal are plasma. Depending on the gas mixture argon/methane or argon/acetylene and the manner

  12. 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.

  13. Kinetic evolution and correlation of fluctuations in an expanding quark gluon plasma

    Science.gov (United States)

    Sarwar, Golam; Alam, Jan-E.

    2018-03-01

    Evolution of spatially anisotropic perturbation created in the system formed after Relativistic Heavy Ion Collisions has been studied. The microscopic evolution of the fluctuations has been examined within the ambit of Boltzmann Transport Equation (BTE) in a hydrodynamically expanding background. The expansion of the background composed of quark gluon plasma (QGP) is treated within the framework of relativistic hydrodynamics. Spatial anisotropic fluctuations with different geometries have been evolved through Boltzmann equation. It is observed that the trace of such fluctuation survives the evolution. Within the relaxation time approximation, analytical results have been obtained for the evolution of these anisotropies. Explicit relations between fluctuations and transport coefficients have been derived. The mixing of various Fourier (or k) modes of the perturbations during the evolution of the system has been explicitly demonstrated. This study is very useful in understanding the presumption that the measured anisotropies in the data from heavy ion collisions at relativistic energies imitate the initial state effects. The evolution of correlation function for the perturbation in pressure has been studied and shows that the initial correlation between two neighbouring points in real space evolves to a constant value at later time which gives rise to Dirac delta function for the correlation function in Fourier space. The power spectrum of the fluctuation in thermodynamic quantities (like temperature estimated in this work) can be connected to the fluctuation in transverse momentum of the thermal hadrons measured experimentally. The bulk viscous coefficient of the QGP has been estimated by using correlations of pressure fluctuation with the help of Green-Kubo relation. Angular power spectrum of the anisotropies has been estimated in the appendix.

  14. 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.

  15. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

    Science.gov (United States)

    Laskey, Sarah B.; Pohlmeyer, Christopher W.; Bruner, Katherine M.; Siliciano, Robert F.

    2016-01-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  16. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.

    Directory of Open Access Journals (Sweden)

    Sarah B Laskey

    2016-08-01

    Full Text Available In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.

  17. Populations in clonal plants

    Directory of Open Access Journals (Sweden)

    Jussi Tammisola

    1986-12-01

    Full Text Available Population phenomena in higher plants are reviewed critically, particularly in relation to clonality. An array of concepts used in the field are discussed. In contrast to animals, higher plants are modular in structure. Plant populations show hierarchy at two levels: ramets and genets. In addition, their demography is far more complicated, since even the direction of development of a ramet may change by rejuvenation. Therefore, formulae concerning animal populations often require modification for plants. Furthermore, at the zygotic stage, higher plants are generally less mobile than animals. Accordingly, their population processes tend to be more local. Most populations of plants have a genetic structure: alleles and genotypes are spatially aggregated. Due to the short-ranged foraging behaviour of pollinators, genetically non-random pollination prevails. A generalized formula for parent-offspring dispersal variance is derived. It is used to analyze the effect of clonality on genetic patchiness in populations. In self-compatible species, an increase in clonality will tend to increase the degree of patchiness, while in self-incompatible species a decrease may result. Examples of population structure studies in different species are presented. A considerable degree of genetic variation appears to be found also in the populations of species with a strong allocation of resources to clonal growth or apomictic seed production. Some consequences of clonality are considered from the point of view of genetic conservation and plant breeding.

  18. Characteristics of an under-expanded supersonic flow in arcjet plasmas

    Science.gov (United States)

    Namba, Shinichi; Shikama, Taiichi; Sasano, Wataru; Tamura, Naoki; Endo, Takuma

    2018-06-01

    A compact apparatus to produce arcjet plasma was fabricated to investigate supersonic flow dynamics. Periodic bright–dark emission structures were formed in the arcjets, depending on the plasma source and ambient gas pressures in the vacuum chamber. A directional Langmuir probe (DLP) and emission spectroscopy were employed to characterize plasma parameters such as the Mach number of plasma flows and clarify the mechanism for the generation of the emission pattern. In particular, in order to investigate the influence of the Mach number on probe size, we used two DLPs of different probe size. The results indicated that the arcjets could be classified into shock-free expansion and under-expansion, and the behavior of plasma flow could be described by compressible fluid dynamics. Comparison of the Langmuir probe results with emission and laser absorption spectroscopy showed that the small diameter probe was reliable to determine the Mach number, even for the supersonic jet.

  19. Potential and electron density calculated for freely expanding plasma by an electron beam

    International Nuclear Information System (INIS)

    Ho, C. Y.; Tsai, Y. H.; Ma, C.; Wen, M. Y.

    2011-01-01

    This paper investigates the radial distributions of potential and electron density in free expansion plasma induced by an electron beam irradiating on the plate. The region of plasma production is assumed to be cylindrical, and the plasma expansion is assumed to be from a cylindrical source. Therefore, the one-dimensional model in cylindrical coordinates is employed in order to analyze the radial distributions of the potential and electron density. The Runge-Kutta method and the perturbation method are utilized in order to obtain the numerical and approximate solutions, respectively. The results reveal that the decrease in the initial ion energy makes most of the ions gather near the plasma production region and reduces the distribution of the average positive potential, electron, and ion density along the radial direction. The oscillation of steady-state plasma along the radial direction is also presented in this paper. The ions induce a larger amplitude of oscillation along the radial direction than do electrons because the electrons oscillate around slowly moving ions due to a far smaller electron mass than ion mass. The radial distributions of the positive potential and electron density predicted from this study are compared with the available experimental data.

  20. Stimulated Brillouin scattering reduction induced by self-focusing for a single laser speckle interacting with an expanding plasma

    International Nuclear Information System (INIS)

    Masson-Laborde, P. E.; Depierreux, S.; Loiseau, P.; Hüller, S.; Pesme, D.; Labaune, Ch.; Bandulet, H.

    2014-01-01

    The origin of the low level of stimulated Brillouin scattering (SBS) observed in laser-plasma experiments carried out with a single laser speckle is investigated by means of three-dimensional simulations and modeling in the limit when the laser beam power P is well above the critical power for ponderomotive self-focusing We find that the order of magnitude of the time averaged reflectivities, together with the temporal and spatial SBS localization observed in our simulations, are correctly reproduced by our modeling. It is observed that, after a short transient stage, SBS reaches a significant level only (i) as long as the incident laser pulse is increasing in amplitude and (ii) in a single self-focused speckle located in the low-density front part of the plasma. In order to describe self-focusing in an inhomogeneous expanding plasma, we have derived a new Lagrangian density describing this process. Using then a variational approach, our model reproduces the position and the peak intensity of the self-focusing hot spot in the front part of the plasma density profile as well as the local density depletion in this hot spot. The knowledge of these parameters then makes it possible to estimate the spatial amplification of SBS as a function of the laser beam power and consequently to explain the experimentally observed SBS reflectivity, considerably reduced with respect to standard theory in the regime of large laser beam power

  1. Stability of an expanding cylindrical plasma envelope: Rayleigh--Taylor instability

    International Nuclear Information System (INIS)

    Han, S.J.

    1982-01-01

    The stability of a cylindrically symmetric plasma envelope driven outward by blast waves is considered. The plasma fluid is assumed to be a compressible, isentropic gas describable as an ideal gas ( p = arho/sup γ/, γ>1). The stability problem of such an envelope undergoing self-similar motion is solved by considering the initial-value problem. It is shown that in the early phase of an expansion, the envelope is unstable to Rayleigh--Taylor modes which develop at the inner surface. In the later phase of the expansion, the Rayleigh--Taylor modes are weakened due to the geometrical divergence effect. The implications of the time-dependent behavior of the Rayleigh--Taylor instability for plasma switches are discussed

  2. 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...... and the magnitude of the ion flux, at the time when the ion flux is maximised, agree with the predictions of the self-similar isentropic model of the plasma expansion by Anisimov et al. (C) 2002 Elsevier Science B.V. All rights reserved....

  3. 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.

  4. High-speed interferometry of expanding and collapsing laser produced plasma

    International Nuclear Information System (INIS)

    Basov, N.G.; Boiko, V.A.; Gribkov, V.A.; Zakharov, S.M.; Krokhin, O.N.; Nikulin, V.Ya.; Sklizkov, G.V.

    An installation with a good time and space resolution for the interferometric investigation of dense non-stationary plasma is described. The installation consists of a Mach-Zender interferometer, an electro-optical image converter camera and a ruby laser with an impulse of variable duration of 1nsec to 150nsec

  5. Stationary Population Inversion in an Expanding Argon Plasma Jet by Helium Puffing

    International Nuclear Information System (INIS)

    Akatsuka, H.; Kano, K.

    2005-01-01

    An experiment of He gas-contact for generating population inversion in a recombining Ar plasma jet is carried out. Population inversion between Ar I excited states 5s' → 4p'[1/2]1 and 5s' → 4p[3/2]1,2, [5/2]2,3 is created by helium gas-contact cooling of electrons, whereas it is not created without gas-contact. Ar I lines 1.14 μm, 1.34 μm, and 1.09 μm are strongly enhanced due to the He gas cooling. It is experimentally found that helium gas contact effectively lowers electron temperature of the Ar plasma jet. The mechanisms giving rise to population inversion are discussed in terms of atomic collisional processes of the recombining plasma. The experimental results of electron temperature and population densities are discussed by simple numerical analysis which we previously developed. It is shown that the experimental results are well explained by our modeling quantitatively for the case without gas contact, except that the agreement of number densities of lower lying non-LTE levels is qualitative for the case with the gas contact

  6. The effect of radio-frequency self bias on ion acceleration in expanding argon plasmas in helicon sources

    Science.gov (United States)

    Wiebold, Matthew D.

    Time-averaged plasma potential differences up to ˜ 165 V over several hundred Debye lengths are observed in low pressure (pn floating potential for argon (Vp ≈ 5kTe/e). In the capacitive mode, the ion acceleration is not well described by an ambipolar relation. The accelerated population decay is consistent with that predicted by charge-exchange collisions. Grounding the upstream endplate increases the self-bias voltage compared to a floating endplate. In the inductive and helicon modes, the ion acceleration more closely follows an ambipolar relation, a result of decreased capacitive coupling due to the decreased RF skin depth. The scaling of the potential gradient with the argon flow rate, magnetic field and RF power are investigated, with the highest potential gradients observed for the lowest flow rates in the capacitive mode. The magnitude of the self-bias voltage agrees well with that predicted for RF sheaths. Use of the self-bias effect in a plasma thruster is explored, possibly for a low thrust, high specific impulse mode in a multi-mode helicon thruster. This work could also explain similar potential gradients in expanding helicon plasmas that are ascribed to double layer formation in the literature.

  7. Transport of energetic electrons in a magnetically expanding helicon double layer plasma

    International Nuclear Information System (INIS)

    Takahashi, Kazunori; Charles, Christine; Boswell, Rod; Cox, Wes; Hatakeyama, Rikizo

    2009-01-01

    Peripheral magnetic field lines extending from the plasma source into the diffusion chamber are found to separate two regions of Maxwellian electron energy probability functions: the central, ion-beam containing region with an electron temperature of 5 eV, and region near the chamber walls with electrons at 3 eV. Along the peripheral field lines a bi-Maxwellian population with a hot tail at 9 eV is shown to both originate from electrons in the source traveling downstream across the double layer and correspond to a local maximum in ion and electron densities.

  8. Soft x-ray emission from postpulse expanding laser-produced plasmas

    International Nuclear Information System (INIS)

    Weaver, J.L.; Feldman, U.; Mostovych, A.N.; Seely, J.F.; Colombant, D.; Holland, G.

    2003-01-01

    A diagnostic spectrometer has been developed at the Naval Research Laboratory to measure the time resolved absolute intensity of radiation emitted from targets irradiated by the Nike laser. The spectrometer consists of a dispersive transmission grating of 2500 lines/mm or 5000 lines/mm and a detection system consisting of an absolutely calibrated Si photodiode array and a charge coupled device camera. In this article, this spectrometer was used to study the spatial distribution of soft x-ray radiation from low Z elements (primarily carbon) that lasted tens of nanoseconds after the main laser illumination was over. We recorded soft x-ray emission as a function of the target material and target orientation with respect to the incoming laser beam and the spectrometer line of sight. While a number of spectral features have been identified in the data, the instrument's combined temporal and spatial resolution allowed observation of the plasma expansion from CH targets for up to ∼25 ns after the cessation of the main laser pulse. The inferred plasma expansion velocities are slightly higher than those previously reported

  9. Soft x-ray emission from postpulse expanding laser-produced plasmas

    Science.gov (United States)

    Weaver, J. L.; Feldman, U.; Mostovych, A. N.; Seely, J. F.; Colombant, D.; Holland, G.

    2003-12-01

    A diagnostic spectrometer has been developed at the Naval Research Laboratory to measure the time resolved absolute intensity of radiation emitted from targets irradiated by the Nike laser. The spectrometer consists of a dispersive transmission grating of 2500 lines/mm or 5000 lines/mm and a detection system consisting of an absolutely calibrated Si photodiode array and a charge coupled device camera. In this article, this spectrometer was used to study the spatial distribution of soft x-ray radiation from low Z elements (primarily carbon) that lasted tens of nanoseconds after the main laser illumination was over. We recorded soft x-ray emission as a function of the target material and target orientation with respect to the incoming laser beam and the spectrometer line of sight. While a number of spectral features have been identified in the data, the instrument's combined temporal and spatial resolution allowed observation of the plasma expansion from CH targets for up to ˜25 ns after the cessation of the main laser pulse. The inferred plasma expansion velocities are slightly higher than those previously reported.

  10. Simulating time-dependent energy transfer between crossed laser beams in an expanding plasma

    International Nuclear Information System (INIS)

    Hittinger, J.A.F.; Dorr, M.R.; Berger, R.L.; Williams, E.A.

    2005-01-01

    A coupled mode system is derived to investigate a three-wave parametric instability leading to energy transfer between co-propagating laser beams crossing in a plasma flow. The model includes beams of finite width refracting in a prescribed transverse plasma flow with spatial and temporal gradients in velocity and density. The resulting paraxial light equations are discretized spatially with a Crank-Nicholson-type scheme, and these algebraic constraints are nonlinearly coupled with ordinary differential equations in time that describe the ion acoustic response. The entire nonlinear differential-algebraic system is solved using an adaptive, backward-differencing method coupled with Newton's method. A numerical study is conducted in two dimensions that compares the intensity gain of the fully time-dependent coupled mode system with the gain computed under the further assumption of a strongly damped ion acoustic response. The results demonstrate a time-dependent gain suppression when the beam diameter is commensurate with the velocity gradient scale length. The gain suppression is shown to depend on time-dependent beam refraction and is interpreted as a time-dependent frequency shift

  11. Jet quenching parameter in an expanding QCD plasma arXiv

    CERN Document Server

    Iancu, Edmond; Wu, Bin

    We study the phenomenon of transverse momentum broadening for a high-$p_T$ parton propagating through a weakly-coupled quark-gluon plasma undergoing boost-invariant longitudinal expansion. We propose a boost-invariant description for this phenomenon, in which the broadening refers to the angular variables $\\eta$ (the pseudo-rapidity) and $\\phi$ (the azimuthal angle). The jet quenching parameter $\\hat{q}$ which enters this description depends upon the proper time alone. We furthermore consider radiative corrections to $\\hat q$. As in the case of a static medium, we find potentially large corrections enhanced by a double logarithm. But unlike for the static medium, these corrections are now local in time: they depend upon the local (proper) time characterizing the expansion, and not upon the overall path length. We resum such corrections to all orders into a renormalized jet quenching parameter. The main effect of this resummation is to slow down the decrease of $\\hat q$ with increasing proper time.

  12. 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.

  13. Novel recurrent chromosomal aberrations detected in clonal plasma cells of light chain amyloidosis patients show potential adverse prognostic effect: first results from a genome-wide copy number array analysis.

    Science.gov (United States)

    Granzow, Martin; Hegenbart, Ute; Hinderhofer, Katrin; Hose, Dirk; Seckinger, Anja; Bochtler, Tilmann; Hemminki, Kari; Goldschmidt, Hartmut; Schönland, Stefan O; Jauch, Anna

    2017-07-01

    Immunoglobulin light chain (AL) amyloidosis is a rare plasma cell dyscrasia characterized by the deposition of abnormal amyloid fibrils in multiple organs, thus impairing their function. In the largest cohort studied up to now of 118 CD138-purified plasma cell samples from previously untreated immunoglobulin light chain amyloidosis patients, we assessed in parallel copy number alterations using high-density copy number arrays and interphase fluorescence in situ hybridization (iFISH). We used fluorescence in situ hybridization probes for the IgH translocations t(11;14), t(4;14), and t(14;16) or any other IgH rearrangement as well as numerical aberrations of the chromosome loci 1q21, 8p21, 5p15/5q35, 11q22.3 or 11q23, 13q14, 15q22, 17p13, and 19q13. Recurrent gains included chromosomes 1q (36%), 9 (24%), 11q (24%), as well as 19 (15%). Recurrent losses affected chromosome 13 (29% monosomy) and partial losses of 14q (19%), 16q (14%) and 13q (12%), respectively. In 88% of patients with translocation t(11;14), the hallmark chromosomal aberration in AL amyloidosis, a concomitant gain of 11q22.3/11q23 detected by iFISH was part of the unbalanced translocation der(14)t(11;14)(q13;q32) with the breakpoint in the CCND1/MYEOV gene region. Partial loss of chromosome regions 14q and 16q were significantly associated to gain 1q. Gain 1q21 detected by iFISH almost always resulted from a gain of the long arm of chromosome 1 and not from trisomy 1, whereas deletions on chromosome 1p were rarely found. Overall and event-free survival analysis found a potential adverse prognostic effect of concomitant gain 1q and deletion 14q as well as of deletion 1p. In conclusion, in the first whole genome report of clonal plasma cells in AL amyloidosis, novel aberrations and hitherto unknown potential adverse prognostic effects were uncovered. Copyright© 2017 Ferrata Storti Foundation.

  14. 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.

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

    DEFF Research Database (Denmark)

    Sittig, Simone; Køllgaard, Tania; Grønbæk, Kirsten

    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 indic......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 indication of ongoing HLA-restricted T cell-mediated immune responses. Multiple tumors, including renal cell carcinomas (RCCs), are often infiltrated by significant amounts of T cells, the so-called tumor-infiltrating lymphocytes (TILs). In the present study, we analyzed RCC lesions (n = 13) for the presence...... of expanded T-cell clonotypes using T-cell receptor clonotype mapping. Surprisingly, we found that RCCs comprise relatively low numbers of distinct expanded T-cell clonotypes as compared with melanoma lesions. The numbers of different T-cell clonotypes detected among RCC-infiltrating lymphocytes were...

  16. 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

  17. Identification of lysophosphatidylcholine, γ-stearoyl (LPCD) as an endogenous Na+, K+-ATPase inhibitor in volume-expanded hog plasma

    International Nuclear Information System (INIS)

    Tamura, M.; Inagami, T.

    1986-01-01

    We have shown that the Na + , K + -ATPase inhibitory activities in the plasma of volume-expanded hog consist of multiple components. One group of the major inhibitory activities induced by intravascular saline infusion was identified as unsaturated free fatty acids. The present study was undertaken to determine the identity of the remaining Na + , K + -ATPase inhibitory activity in the plasma of volume-expanded hogs. Three peaks with ouabain displacing activity (ODA) were separated by HPLC on a reversed phase octadecyl column. The slowest eluting material which showed good solubility in water and recognizable optical absorbance at 214 nm was purified further by three additional steps of reverse phase HPLC. FAB mass spectrometry and 1 H NMR spectroscopy identified this substance as lysophosphatidylcholine, γ-stearoyl. Both purified and synthetic LPCS showed dose-dependent inhibition of Na + , K + -ATPase and displacement of [ 3 H] ouabain from the ATPase. Lysophosphatidylcholines containing either palmitoyl or myristoyl groups also exhibited the Na + , K + -ATPase inhibitory activity and the ODA. The ODA in the LPCS containing fraction increased during the saline infusion. These results indicate that LPCS is an endogenous Na + , K + -ATPase inhibitor which is induced by the expansion of plasma volume

  18. Transgenerational plasticity in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Latzel, Vít; Klimešová, Jitka

    2010-01-01

    Roč. 24, č. 6 (2010), s. 1537-1543 ISSN 0269-7653 R&D Projects: GA ČR GD206/08/H044; GA ČR GA526/09/0963; GA ČR GPP505/10/P173 Institutional research plan: CEZ:AV0Z60050516 Keywords : maternal effect * evolution * clonal plants Subject RIV: EF - Botanics Impact factor: 2.398, year: 2010

  19. ION HEATING IN INHOMOGENEOUS EXPANDING SOLAR WIND PLASMA: THE ROLE OF PARALLEL AND OBLIQUE ION-CYCLOTRON WAVES

    International Nuclear Information System (INIS)

    Ozak, N.; Ofman, L.; Viñas, A.-F.

    2015-01-01

    Remote sensing observations of coronal holes show that heavy ions are hotter than protons and their temperature is anisotropic. In-situ observations of fast solar wind streams provide direct evidence for turbulent Alfvén wave spectrum, left-hand polarized ion-cyclotron waves, and He ++ - proton drift in the solar wind plasma, which can produce temperature anisotropies by resonant absorption and perpendicular heating of the ions. Furthermore, the solar wind is expected to be inhomogeneous on decreasing scales approaching the Sun. We study the heating of solar wind ions in inhomogeneous plasma with a 2.5D hybrid code. We include the expansion of the solar wind in an inhomogeneous plasma background, combined with the effects of a turbulent wave spectrum of Alfvénic fluctuations and initial ion-proton drifts. We study the influence of these effects on the perpendicular ion heating and cooling and on the spectrum of the magnetic fluctuations in the inhomogeneous background wind. We find that inhomogeneities in the plasma lead to enhanced heating compared to the homogenous solar wind, and the generation of significant power of oblique waves in the solar wind plasma. The cooling effect due to the expansion is not significant for super-Alfvénic drifts, and is diminished further when we include an inhomogeneous background density. We reproduce the ion temperature anisotropy seen in observations and previous models, which is present regardless of the perpendicular cooling due to solar wind expansion. We conclude that small scale inhomogeneities in the inner heliosphere can significantly affect resonant wave ion heating

  20. Expanded Stem Cells, Stromal-Vascular Fraction, and Platelet-Rich Plasma Enriched Fat: Comparing Results of Different Facial Rejuvenation Approaches in a Clinical Trial.

    Science.gov (United States)

    Rigotti, Gino; Charles-de-Sá, Luiz; Gontijo-de-Amorim, Natale Ferreira; Takiya, Christina Maeda; Amable, Paola Romina; Borojevic, Radovan; Benati, Donatella; Bernardi, Paolo; Sbarbati, Andrea

    2016-03-01

    In a previous study, the authors demonstrated that treatment with expanded adipose-derived stem cells or stromal vascular fraction (SVF)-enriched fat modify the pattern of the dermis in human beings, representing a skin rejuvenation effect. Considering that expanded stem cells require a cell factor, the authors wanted to assess similar results by replacing them with platelet-rich plasma (PRP), which is easier to obtain and for which an empirical regenerative effect has been already described. To determine if PRP injection could replace the cutaneous regenerative effect of adipose-derived stem cells. This study was performed in 13 patients who were candidates for facelift. The patients underwent sampling of fat by liposuction from the abdomen and submitted to one of three protocols: injection of SVF-enriched fat or expanded adipose-derived stem cells or fat plus PRP in the preauricular areas. Fragments of skin were removed before and 3 months after treatment and analyzed by optical and electron microscopy. The use of fat plus PRP led to the presence of more pronounced inflammatory infiltrates and a greater vascular reactivity, increasing in vascular permeability and a certain reactivity of the nervous component. The addition of PRP did not improve the regenerative effect. The use of PRP did not have significant advantages in skin rejuvenation over the use of expanded adipose-derived stem cells or SVF-enriched fat. The effect of increased vascular reactivity may be useful in pathological situations in which an intense angiogenesis is desirable, such as tissular ischemia. © 2016 The American Society for Aesthetic Plastic Surgery, Inc. Reprints and permission: journals.permissions@oup.com.

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

    International Nuclear Information System (INIS)

    Hairapetian, G.; Stenzel, R.L.

    1991-01-01

    The expansion of a two-electron-population, collisionless plasma into vacuum is investigated experimentally. Detailed in situ measurements of plasma density, plasma potential, electric field, and particle distribution functions are performed. At the source, the electron population consists of a high-density, cold (kT e congruent 4 eV) Maxwellian, and a sparse, energetic ( (1)/(2) mv 2 e congruent 80 eV) tail. During the expansion of plasma, space-charge effects self-consistently produce an ambipolar electric field whose amplitude is controlled by the energy of tail electrons. The ambipolar electric field accelerates a small number (∼1%) of ions to streaming energies which exceed and scale linearly with the energy of tail electrons. As the expansion proceeds, the energetic tail electrons electrostatically trap the colder Maxwellian electrons and prevent them from reaching the expansion front. A potential double layer develops at the position of the cold electron front. Upstream of the double layer both electron populations exist; but downstream, only the tail electrons do. Hence, the expansion front is dominated by retarded tail electrons. Initially, the double layer propagates away from the source with a speed approximately equal to the ion sound speed in the cold electron population. The propagation speed is independent of the tail electron energy. At later times, the propagating double layer slows down and eventually stagnates. The final position and amplitude of the double layer are controlled by the relative densities of the two electron populations in the source. The steady-state double layer persists till the end of the discharge (Δt congruent 1 msec), much longer than the ion transit time through the device (t congruent 150 μsec)

  2. Role of ion magnetization in formation of radial density profile in magnetically expanding plasma produced by helicon antenna

    Science.gov (United States)

    Yadav, Sonu; Ghosh, Soumen; Bose, Sayak; Barada, Kshitish K.; Pal, Rabindranath; Chattopadhyay, Prabal K.

    2018-04-01

    Experimentally, the density profile in the magnetic nozzle of a helicon antenna based plasma device is seen to be modified from being centrally peaked to that of hollow nature as the external magnetic field is increased. It occurs above a characteristic field value when the ions become magnetized in the expansion chamber. The density profile in the source chamber behind the nozzle, however, remains peaked on-axis irrespective of the magnetic field. The electron temperature there is observed to be hollow and this nature is carried to the expansion chamber along the field line. In the electron energy distribution near the off axis peak location, a high energy tail exists. Rotation of these tail electrons in the azimuthal direction due to the gradient-B drift in the expansion chamber leads to an additional off-axis ionization and forms the hollow density profile. It seems that if the ions are not magnetized, then the off-axially produced additional plasma is not confined and the density profile retains the on-axis peak nature. The present experiment successfully demonstrates how the knowledge of the ion magnetization together with tail electrons significantly contributes to the design of an efficient helicon plasma based thruster.

  3. Clonal hematopoiesis in acquired aplastic anemia

    OpenAIRE

    Ogawa, Seishi

    2016-01-01

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolut...

  4. Clonal sets of a binary relation

    Science.gov (United States)

    Zedam, Lemnaouar; Pérez-Fernández, Raúl; Bouremel, Hassane; De Baets, Bernard

    2018-05-01

    In a recent paper, we have introduced the notion of clone relation of a given binary relation. Intuitively, two elements are said to be "clones" if they are related in the same way w.r.t. every other element. In this paper, we generalize this notion from pairs of elements to sets of elements of any cardinality, resulting in the introduction of clonal sets. We investigate the most important properties of clonal sets, paying particular attention to the introduction of the clonal closure operator, to the analysis of the (lattice) structure of the set of clonal sets and to a distance metric expressing how close two elements are to being clones.

  5. Intra-articular injections of expanded mesenchymal stem cells with and without addition of platelet-rich plasma are safe and effective for knee osteoarthritis.

    Science.gov (United States)

    Bastos, Ricardo; Mathias, Marcelo; Andrade, Renato; Bastos, Raquel; Balduino, Alex; Schott, Vinicius; Rodeo, Scott; Espregueira-Mendes, João

    2018-03-06

    To compare the effectiveness and safety of intra-articular injections of autologous expanded mesenchymal stromal stem cells alone (MSCs), or in combination with platelet-rich plasma (MSCs + PRP), in patients with knee osteoarthritis. Eighteen patients (57.6 ± 9.6 years) with radiographic symptomatic knee osteoarthritis (Dejour grades II-IV) were randomized to receive intra-articular injections of MSCs (n = 9) or MSCs + PRP (n = 9). Injections were performed 2-3 weeks after bone marrow aspiration (± 80-100 ml) which was obtained from both posterior iliac crests. The Knee Injury and Osteoarthritis Outcome Score (KOOS) improved significantly throughout the 12 months for both groups (p injections of expanded MSCs alone or in combination with PRP are safe and have a beneficial effect on symptoms in patients with symptomatic knee osteoarthritis. Adding PRP to the MSCs injections did not provide additional benefit. These results are encouraging and support the recommendation of this minimally invasive procedure in patients with knee osteoarthritis, without requiring hospitalization. The CFU-F results may be used as reference for future research. Prospective cohort study, Level II.

  6. 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......-Saxon and continental traditions, this special issue provides examples of the use of researcher subjectivity, informed by psychoanalytic thinking, in expanding research understanding....

  7. Emergence of clonal hematopoiesis in the majority of patients with acquired aplastic anemia.

    Science.gov (United States)

    Babushok, Daria V; Perdigones, Nieves; Perin, Juan C; Olson, Timothy S; Ye, Wenda; Roth, Jacquelyn J; Lind, Curt; Cattier, Carine; Li, Yimei; Hartung, Helge; Paessler, Michele E; Frank, Dale M; Xie, Hongbo M; Cross, Shanna; Cockroft, Joshua D; Podsakoff, Gregory M; Monos, Dimitrios; Biegel, Jaclyn A; Mason, Philip J; Bessler, Monica

    2015-04-01

    Acquired aplastic anemia (aAA) is a nonmalignant disease caused by autoimmune destruction of early hematopoietic cells. Clonal hematopoiesis is a late complication, seen in 20-25% of older patients. We hypothesized that clonal hematopoiesis in aAA is a more general phenomenon, which can arise early in disease, even in younger patients. To evaluate clonal hematopoiesis in aAA, we used comparative whole exome sequencing of paired bone marrow and skin samples in 22 patients. We found somatic mutations in 16 patients (72.7%) with a median disease duration of 1 year; of these, 12 (66.7%) were patients with pediatric-onset aAA. Fifty-eight mutations in 51 unique genes were found primarily in pathways of immunity and transcriptional regulation. Most frequently mutated was PIGA, with seven mutations. Only two mutations were in genes recurrently mutated in myelodysplastic syndrome. Two patients had oligoclonal loss of the HLA alleles, linking immune escape to clone emergence. Two patients had activating mutations in key signaling pathways (STAT5B (p.N642H) and CAMK2G (p.T306M)). Our results suggest that clonal hematopoiesis in aAA is common, with two mechanisms emerging-immune escape and increased proliferation. Our findings expand conceptual understanding of this nonneoplastic blood disorder. Future prospective studies of clonal hematopoiesis in aAA will be critical for understanding outcomes and for designing personalized treatment strategies. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. 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.

  9. Clonal growth and plant species abundance.

    Science.gov (United States)

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-08-01

    Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf-height-seed) traits and by actual performance in the botanical garden. Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area - height - seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden

  10. 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.

  11. Expandable stents.

    Science.gov (United States)

    Nesbitt, J C; Carrasco, H

    1996-05-01

    Expandable metallic stents are effective in selected patients with malignant or benign airway stenoses. When used for malignant lesions, the primary purpose of the stent is to improve the quality of life; stents are usually chosen for palliation of symptoms in recognition of the low likelihood of success for other therapy. For patients with benign stenoses, the stents provide a permanent source of structural support to alleviate the narrowed segment. The advantages of the expandable metallic stents are as follows: (1) they can be inserted through an endotracheal tube or under local anesthesia with relative simplicity under fluoroscopic guidance; (2) they do not impair the drainage of sputum because ciliary movement is not interrupted; (3) over a period of a few weeks, the meshwork is gradually covered with mucosa as the stent becomes incorporated into the airway wall; (4) ventilation usually is not impaired if the metallic mesh stent covers another nonstenosed bronchus, because the interstices of the stent are nonobstructive; and (5) they are dynamic and continue to expand over time, particularly if concurrent treatment achieves an effect on the lesion that caused stenosis. Disadvantages of the expandable stent include (1) they often are only temporarily effective for tracheobronchial stenosis due to intraluminal tumor or granulation tissue, both of which can grow between the wires; (2) they are considered permanent stents because removal is difficult; and (3) they can be poorly positioned during placement or can become displaced by progressive migration after placement, and they cannot be repositioned. A relative contraindication to insertion is an inflammatory process or infection that can predispose to granulation formation, particularly at the points of maximal contact pressure of the stent to the airway mucosa. In the presence of inflammation, it may be better to use a silicone prosthesis until the inflammatory process subsides and fibrosis occurs. Granulation

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Distribution of clonal growth forms in wetlands

    Czech Academy of Sciences Publication Activity Database

    Sosnová, Monika; van Diggelen, R.; Klimešová, Jitka

    2010-01-01

    Roč. 92, č. 1 (2010), s. 33-39 ISSN 0304-3770 R&D Projects: GA ČR GD206/08/H044 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal growth organ * the Netherlands * wetland plant community Subject RIV: EF - Botanics Impact factor: 2.087, year: 2010

  17. Quality improvement in Vignoles through clonal selection

    Science.gov (United States)

    Our goal is to select an improved, loose-clustered clone of Vignoles that will contribute to an integrated approach to disease control. Clonal selection has historically proven useful in reducing cluster compactness through a variety of mechanisms, including decreased berry size, lengthening of the ...

  18. Clonal growth and plant species abundance

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Nováková, Z.; Klimešová, Jitka

    2014-01-01

    Roč. 114, č. 2 (2014), s. 377-388 ISSN 0305-7364 R&D Projects: GA ČR GA526/09/0963 Institutional support: RVO:67985939 Keywords : clonal plants * frequency * plant communities of Central Europe Subject RIV: EF - Botanics Impact factor: 3.654, year: 2014

  19. 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 OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.645, year: 2016 http://link.springer.com/article/10.1007%2Fs00224-016-9738-5

  20. Clonality analysis of lymphoid proliferations using the BIOMED-2 clonality assays: a single institution experience

    Science.gov (United States)

    Kokovic, Ira; Novakovic, Barbara Jezersek; Cerkovnik, Petra; Novakovic, Srdjan

    2014-01-01

    Background Clonality determination in patients with lymphoproliferative disorders can improve the final diagnosis. The aim of our study was to evaluate the applicative value of standardized BIOMED-2 gene clonality assay protocols for the analysis of clonality of lymphocytes in a group of different lymphoid proliferations. Materials and methods. With this purpose, 121 specimens from 91 patients with suspected lymphoproliferations submitted for routine diagnostics from January to December 2011 were retrospectively analyzed. According to the final diagnosis, our series comprised 32 cases of B-cell lymphomas, 38 cases of non-Hodgkin’s T-cell lymphomas and 51 cases of reactive lymphoid proliferations. Clonality testing was performed using the BIOMED-2 clonality assays. Results The determined sensitivity of the TCR assay was 91.9%, while the sensitivity of the IGH assay was 74.2%. The determined specificity of the IGH assay was 73.3% in the group of lymphomas and 87.2% in the group of reactive lesions. The determined specificity of the TCR assay was 62.5% in the group of lymphomas and 54.3% in the group of reactive lesions. Conclusions In the present study, we confirmed the utility of standardized BIOMED-2 clonality assays for the detection of clonality in a routine diagnostical setting of non-Hodgkin’s lymphomas. Reactions for the detection of the complete IGH rearrangements and reactions for the detection of the TCR rearrangements are a good choice for clonality testing of a wide range of lymphoid proliferations and specimen types while the reactions for the detection of incomplete IGH rearrangements have not shown any additional diagnostic value. PMID:24991205

  1. Clonal hematopoiesis in acquired aplastic anemia.

    Science.gov (United States)

    Ogawa, Seishi

    2016-07-21

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolution. Genetic abnormalities are found in ∼50% of patients with AA and, except for PIGA mutations and copy-neutral loss-of-heterozygosity, or uniparental disomy (UPD) in 6p (6pUPD), are most frequently represented by mutations involving genes commonly mutated in myeloid malignancies, including DNMT3A, ASXL1, and BCOR/BCORL1 Mutations exhibit distinct chronological profiles and clinical impacts. BCOR/BCORL1 and PIGA mutations tend to disappear or show stable clone size and predict a better response to IST and a significantly better clinical outcome compared with mutations in DNMT3A, ASXL1, and other genes, which are likely to increase their clone size, are associated with a faster progression to MDS/AML, and predict an unfavorable survival. High frequency of 6pUPD and overrepresentation of PIGA and BCOR/BCORL1 mutations are unique to AA, suggesting the role of autoimmunity in clonal selection. By contrast, DNMT3A and ASXL1 mutations, also commonly seen in CH in the general population, indicate a close link to CH in the aged bone marrow, in terms of the mechanism for selection. Detection and close monitoring of somatic mutations/evolution may help with prediction and diagnosis of clonal evolution of MDS/AML and better management of patients with AA. © 2016 by The American Society of Hematology.

  2. Clonal expansion of CD4+ Cytotoxic T Lymphocytes in IgG4-related disease

    Science.gov (United States)

    Mattoo, Hamid; Mahajan, Vinay S.; Maehara, Takashi; Deshpande, Vikram; Della-Torre, Emanuel; Wallace, Zachary S.; Kulikova, Maria; Drijvers, Jefte M.; Daccache, Joe; Carruthers, Mollie N.; Castellino, Flavia; Stone, James R.; Stone, John H.; Pillai, Shiv

    2016-01-01

    Background IgG4-related disease (IgG4-RD) is a systemic condition of unknown etiology, characterized by highly fibrotic lesions with dense lymphoplasmacytic infiltrates. CD4+ T cells constitute the major inflammatory cell population in IgG4-RD lesions. Objective We used an unbiased approach to characterize CD4+ T cell subsets in IgG4-RD subjects based on their clonal expansion and their ability to infiltrate affected tissue sites. Methods We used flow cytometry to identify CD4+ effector/memory T cells (TEM) in a cohort of 101 IgG4-related disease (IgG4-RD) patients. These expanded cells were characterized by gene expression analysis and flow cytometry. Next-generation sequencing of the T cell receptor β chain gene was performed on CD4+SLAMF7+ CTLs and CD4+GATA3+ TH2 cells in a subset of patients to identify their clonality. Tissue infiltration by specific T cells was examined using quantitative multi-color imaging. Results CD4+ effector/memory T cells with a cytolytic phenotype were expanded in IgG4-RD patients. Next-generation sequencing revealed prominent clonal expansions of these CD4+CTLs but not CD4+GATA3+ memory TH2 cells in subjects with IgG4-RD. The dominant T cells infiltrating a range of inflamed IgG4-RD tissue sites were clonally-expanded CD4+CTLs that expressed SLAMF7, granzyme A, IL-1β, and TGF-β1. Clinical remission induced by rituximab-mediated B cell depletion was associated with a reduction in disease-associated CD4+ CTLs Conclusions IgG4-RD is prominently linked to clonally-expanded, IL-1β, and TGF- β1 secreting, CD4+ CTLs in peripheral blood as well as in inflammatory tissue lesions. These active, terminally-differentiated, cytokine-secreting effector CD4+ T cells are now linked to a human disease characterized by chronic inflammation and fibrosis. PMID:26971690

  3. 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......, 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...... 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...

  4. Big Bang Tumor Growth and Clonal Evolution.

    Science.gov (United States)

    Sun, Ruping; Hu, Zheng; Curtis, Christina

    2018-05-01

    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 © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  5. Metabolic heterogeneity in clonal microbial populations.

    Science.gov (United States)

    Takhaveev, Vakil; Heinemann, Matthias

    2018-02-21

    In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in constant environments to molecular noise in gene expression that propagates into metabolism. Furthermore, we provide an overview of current methods to quantify the levels of metabolites and biomass components in single cells. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Clonal integration supports the expansion from terrestrial to aquatic environments of the amphibious stoloniferous herb Alternanthera philoxeroides.

    Science.gov (United States)

    Wang, N; Yu, F-H; Li, P-X; He, W-M; Liu, J; Yu, G-L; Song, Y-B; Dong, M

    2009-05-01

    Effects of clonal integration on land plants have been extensively studied, but little is known about the role in amphibious plants that expand from terrestrial to aquatic conditions. We simulated expansion from terrestrial to aquatic habitats in the amphibious stoloniferous alien invasive alligator weed (Alternanthera philoxeroides) by growing basal ramets of clonal fragments in soils connected (allowing integration) or disconnected (preventing integration) to the apical ramets of the same fragments submerged in water to a depth of 0, 5, 10 or 15 cm. Clonal integration significantly increased growth and clonal reproduction of the apical ramets, but decreased both of these characteristics in basal ramets. Consequently, integration did not affect the performance of whole clonal fragments. We propose that alligator weed possesses a double-edged mechanism during population expansion: apical ramets in aquatic habitats can increase growth through connected basal parts in terrestrial habitats; however, once stolon connections with apical ramets are lost by external disturbance, the basal ramets in terrestrial habitats increase stolon and ramet production for rapid spreading. This may contribute greatly to the invasiveness of alligator weed and also make it very adaptable to habitats with heavy disturbance and/or highly heterogeneous resource supply.

  7. Recent advances in understanding clonal haematopoiesis in aplastic anaemia.

    Science.gov (United States)

    Stanley, Natasha; Olson, Timothy S; Babushok, Daria V

    2017-05-01

    Acquired aplastic anaemia (AA) is an immune-mediated bone marrow failure disorder inextricably linked to clonal haematopoiesis. The majority of AA patients have somatic mutations and/or structural chromosomal abnormalities detected as early as at diagnosis. In contrast to other conditions linked to clonal haematopoiesis, the clonal signature of AA reflects its immune pathophysiology. The most common alterations are clonal expansions of cells lacking glycophosphotidylinositol-anchored proteins, loss of human leucocyte antigen alleles, and mutations in BCOR/BCORL1, ASXL1 and DNMT3A. Here, we present the current knowledge of clonal haematopoiesis in AA as it relates to aging, inherited bone marrow failure, and the grey-zone overlap of AA and myelodysplastic syndrome (MDS). We conclude by discussing the significance of clonal haematopoiesis both for improved diagnosis of AA, as well as for a more precise, personalized approach to prognostication of outcomes and therapy choices. © 2017 John Wiley & Sons Ltd.

  8. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma.

    Science.gov (United States)

    Doucet-O'Hare, Tara T; Sharma, Reema; Rodić, Nemanja; Anders, Robert A; Burns, Kathleen H; Kazazian, Haig H

    2016-09-01

    Squamous cell carcinoma of the esophagus (SCC) is the most common form of esophageal cancer in the world and is typically diagnosed at an advanced stage when successful treatment is challenging. Understanding the mutational profile of this cancer may identify new treatment strategies. Because somatic retrotransposition has been shown in tumors of the gastrointestinal system, we focused on LINE-1 (L1) mobilization as a source of genetic instability in this cancer. We hypothesized that retrotransposition is ongoing in SCC patients. The expression of L1 encoded proteins is necessary for retrotransposition to occur; therefore, we evaluated the expression of L1 open reading frame 1 protein (ORF1p). Using immunohistochemistry, we detected ORF1p expression in all four SCC cases evaluated. Using L1-seq, we identified and validated 74 somatic insertions in eight tumors of the nine evaluated. Of these, 12 insertions appeared to be somatic, not genetically inherited, and sub-clonal (i.e., present in less than one copy per genome equivalent) in the adjacent normal esophagus (NE), while clonal in the tumor. Our results indicate that L1 retrotransposition is active in SCC of the esophagus and that insertion events are present in histologically NE that expands clonally in the subsequent tumor. © 2016 WILEY PERIODICALS, INC.

  9. Clonal dominance among T-lymphocyte infiltrates in arthritis

    International Nuclear Information System (INIS)

    Stamenkovic, I.; Stegagno, M.; Wright, K.A.; Krane, S.M.; Amento, E.P.; Colvin, R.B.; Duquesnoy, R.J.; Kurnick, J.T.

    1988-01-01

    Synovial membranes in patients with rheumatoid arthritis as well as other types of chronic destructive inflammatory arthritis contain infiltrates of activated T lymphocytes that probably contribute to the pathogenesis of the disease. In an effort to elucidate the nature of these infiltrates, interleukin 2 (IL-2)-responsive T lymphocytes were grown out of synovial fragments from 14 patients undergoing surgery for advanced destructive inflammatory joint disease. Eleven of the samples examined were from patients with classical rheumatoid arthritis, while three others were obtained from individuals with clinical osteoarthritis. Southern blot analysis of T-cell receptor (TCR) β-chain genes in 13 of 14 cultures showed distinct rearrangements, indicating that each culture was characterized by the predominance of a limited number of clones. T-cell populations from peripheral blood stimulated with a variety of activators and expanded with IL-2 did not demonstrate evidence of similar clonality in long-term culture. These results suggest that a limited number of activated T-cell clones predominate at the site of tissue injury in rheumatoid synovial membranes as well as in other types of destructive inflammatory joint disease. Further characterization of these T-cell clones may aid our understanding of the pathogenesis of these rheumatic disorders

  10. 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.

  11. 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.

  12. 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

    2018-07-01

    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

  13. On the ecological genetics of the clonal perennial Agrostis stolonifera

    NARCIS (Netherlands)

    Kik, Christoffel

    1987-01-01

    There have to date been few studies specifically addressed to the evolution of clonal organisms. The present study attempts to fill this gap and aims to analyse the distribution pattern of a clonal plant species, using the wide-spread grass Agrostis stolonifera L.(Creeping Bent) as a model species.

  14. 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

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

    African Journals Online (AJOL)

    This study describes the stomatal response occurring during water stress and subsequent recovery of three Eucalyptus grandis clonal hybrids. 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.

  16. Insights in Anaphylaxis and Clonal Mast Cell Disorders

    Directory of Open Access Journals (Sweden)

    David González-de-Olano

    2017-07-01

    Full Text Available The prevalence of anaphylaxis among patients with clonal mast cell disorders (MCD is clearly higher comparing to the general population. Due to a lower frequency of symptoms outside of acute episodes, clonal MCD in the absence of skin lesions might sometimes be difficult to identify which may lead to underdiagnosis, and anaphylaxis is commonly the presenting symptom in these patients. Although the release of mast cell (MC mediators upon MC activation might present with a wide variety of symptoms, particular clinical features typically characterize MC mediator release episodes in patients with clonal MCD without skin involvement. Final diagnosis requires a bone marrow study, and it is recommended that this should be done in reference centers. In this article, we address the main triggers for anaphylaxis, risk factors, clinical presentation, diagnosis, and management of patients with MC activation syndromes (MCASs, with special emphasis on clonal MCAS [systemic mastocytosis and mono(clonal MC activations syndromes].

  17. Identification and clonal characterisation of a progenitor cell sub-population in normal human articular cartilage.

    Directory of Open Access Journals (Sweden)

    Rebecca Williams

    Full Text Available BACKGROUND: Articular cartilage displays a poor repair capacity. The aim of cell-based therapies for cartilage defects is to repair damaged joint surfaces with a functional replacement tissue. Currently, chondrocytes removed from a healthy region of the cartilage are used but they are unable to retain their phenotype in expanded culture. The resulting repair tissue is fibrocartilaginous rather than hyaline, potentially compromising long-term repair. Mesenchymal stem cells, particularly bone marrow stromal cells (BMSC, are of interest for cartilage repair due to their inherent replicative potential. However, chondrocyte differentiated BMSCs display an endochondral phenotype, that is, can terminally differentiate and form a calcified matrix, leading to failure in long-term defect repair. Here, we investigate the isolation and characterisation of a human cartilage progenitor population that is resident within permanent adult articular cartilage. METHODS AND FINDINGS: Human articular cartilage samples were digested and clonal populations isolated using a differential adhesion assay to fibronectin. Clonal cell lines were expanded in growth media to high population doublings and karyotype analysis performed. We present data to show that this cell population demonstrates a restricted differential potential during chondrogenic induction in a 3D pellet culture system. Furthermore, evidence of high telomerase activity and maintenance of telomere length, characteristic of a mesenchymal stem cell population, were observed in this clonal cell population. Lastly, as proof of principle, we carried out a pilot repair study in a goat in vivo model demonstrating the ability of goat cartilage progenitors to form a cartilage-like repair tissue in a chondral defect. CONCLUSIONS: In conclusion, we propose that we have identified and characterised a novel cartilage progenitor population resident in human articular cartilage which will greatly benefit future cell

  18. Divergent clonal selection dominates medulloblastoma at recurrence

    Science.gov (United States)

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  19. 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.

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

    Science.gov (United States)

    Ruan, Zhi; Yang, Ting; Shi, Xinyan; Kong, Yingying; Xie, Xinyou; Zhang, Jun

    2017-01-01

    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 Ureaplasma spp. The present study also attained excellent agreement of the identification of both Ureaplasma species between paired urine and semen specimens from the male partners (k > 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.

  1. Plasma membrane profiling defines an expanded class of cell surface proteins selectively targeted for degradation by HCMV US2 in cooperation with UL141.

    Directory of Open Access Journals (Sweden)

    Jye-Lin Hsu

    2015-04-01

    Full Text Available Human cytomegalovirus (HCMV US2, US3, US6 and US11 act in concert to prevent immune recognition of virally infected cells by CD8+ T-lymphocytes through downregulation of MHC class I molecules (MHC-I. Here we show that US2 function goes far beyond MHC-I degradation. A systematic proteomic study using Plasma Membrane Profiling revealed US2 was unique in downregulating additional cellular targets, including: five distinct integrin α-chains, CD112, the interleukin-12 receptor, PTPRJ and thrombomodulin. US2 recruited the cellular E3 ligase TRC8 to direct the proteasomal degradation of all its targets, reminiscent of its degradation of MHC-I. Whereas integrin α-chains were selectively degraded, their integrin β1 binding partner accumulated in the ER. Consequently integrin signaling, cell adhesion and migration were strongly suppressed. US2 was necessary and sufficient for degradation of the majority of its substrates, but remarkably, the HCMV NK cell evasion function UL141 requisitioned US2 to enhance downregulation of the NK cell ligand CD112. UL141 retained CD112 in the ER from where US2 promoted its TRC8-dependent retrotranslocation and degradation. These findings redefine US2 as a multifunctional degradation hub which, through recruitment of the cellular E3 ligase TRC8, modulates diverse immune pathways involved in antigen presentation, NK cell activation, migration and coagulation; and highlight US2's impact on HCMV pathogenesis.

  2. Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

    Science.gov (United States)

    Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

    2017-10-01

    Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

  3. ClonEvol: clonal ordering and visualization in cancer sequencing.

    Science.gov (United States)

    Dang, H X; White, B S; Foltz, S M; Miller, C A; Luo, J; Fields, R C; Maher, C A

    2017-12-01

    Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones

  4. Clonal expansion of CD4(+) cytotoxic T lymphocytes in patients with IgG4-related disease.

    Science.gov (United States)

    Mattoo, Hamid; Mahajan, Vinay S; Maehara, Takashi; Deshpande, Vikram; Della-Torre, Emanuel; Wallace, Zachary S; Kulikova, Maria; Drijvers, Jefte M; Daccache, Joe; Carruthers, Mollie N; Castelino, Flavia V; Stone, James R; Stone, John H; Pillai, Shiv

    2016-09-01

    IgG4-related disease (IgG4-RD) is a systemic condition of unknown cause characterized by highly fibrotic lesions with dense lymphoplasmacytic infiltrates. CD4(+) T cells constitute the major inflammatory cell population in IgG4-RD lesions. We used an unbiased approach to characterize CD4(+) T-cell subsets in patients with IgG4-RD based on their clonal expansion and ability to infiltrate affected tissue sites. We used flow cytometry to identify CD4(+) effector/memory T cells in a cohort of 101 patients with IgG4-RD. These expanded cells were characterized by means of gene expression analysis and flow cytometry. Next-generation sequencing of the T-cell receptor β chain gene was performed on CD4(+)SLAMF7(+) cytotoxic T lymphocytes (CTLs) and CD4(+)GATA3(+) TH2 cells in a subset of patients to identify their clonality. Tissue infiltration by specific T cells was examined by using quantitative multicolor imaging. CD4(+) effector/memory T cells with a cytolytic phenotype were expanded in patients with IgG4-RD. Next-generation sequencing revealed prominent clonal expansions of these CD4(+) CTLs but not CD4(+)GATA3(+) memory TH2 cells in patients with IgG4-RD. The dominant T cells infiltrating a range of inflamed IgG4-RD tissue sites were clonally expanded CD4(+) CTLs that expressed SLAMF7, granzyme A, IL-1β, and TGF-β1. Clinical remission induced by rituximab-mediated B-cell depletion was associated with a reduction in numbers of disease-associated CD4(+) CTLs. IgG4-RD is prominently linked to clonally expanded IL-1β- and TGF-β1-secreting CD4(+) CTLs in both peripheral blood and inflammatory tissue lesions. These active, terminally differentiated, cytokine-secreting effector CD4(+) T cells are now linked to a human disease characterized by chronic inflammation and fibrosis. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  5. NSAIDs modulate clonal evolution in Barrett's esophagus.

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    Rumen L Kostadinov

    2013-06-01

    Full Text Available Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs. Non-steroidal anti-inflammatory drugs (NSAIDs have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE to esophageal adenocarcinoma (EA. However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5-8 time points over 6.4-19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1-8.6 off-NSAIDs and 0.6 (95% SI 0.3-1.5 on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs.

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

    Indian Academy of Sciences (India)

    study was to assess the clinical benefits of clonality testing with previously evaluated .... with the samples, negative controls containing no DNA were ..... 2003 Standardization and quality con- ... In Molecular cloning, a laboratory manual (ed.

  7. 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.

  8. An Invasive Clonal Plant Benefits from Clonal Integration More than a Co-Occurring Native Plant in Nutrient-Patchy and Competitive Environments

    Science.gov (United States)

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

  9. Propagule pressure, habitat conditions and clonal integration influence the establishment and growth of an invasive clonal plant, Alternanthera philoxeroides

    Directory of Open Access Journals (Sweden)

    Wen-Hua eYou

    2016-05-01

    Full Text Available Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules may affect the establishment, growth and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments or low (one fragment propagule pressure was established either in bare soil (open habitat or dense native vegetation of Jussiaea repens (vegetative habitat, with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions.

  10. What Expands in an Expanding Universe?

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    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.

  11. 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.

  12. Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells.

    Science.gov (United States)

    Lee, Guinevere Q; Orlova-Fink, Nina; Einkauf, Kevin; Chowdhury, Fatema Z; Sun, Xiaoming; Harrington, Sean; Kuo, Hsiao-Hsuan; Hua, Stephane; Chen, Hsiao-Rong; Ouyang, Zhengyu; Reddy, Kavidha; Dong, Krista; Ndung'u, Thumbi; Walker, Bruce D; Rosenberg, Eric S; Yu, Xu G; Lichterfeld, Mathias

    2017-06-30

    HIV-1 causes a chronic, incurable disease due to its persistence in CD4+ T cells that contain replication-competent provirus, but exhibit little or no active viral gene expression and effectively resist combination antiretroviral therapy (cART). These latently infected T cells represent an extremely small proportion of all circulating CD4+ T cells but possess a remarkable long-term stability and typically persist throughout life, for reasons that are not fully understood. Here we performed massive single-genome, near-full-length next-generation sequencing of HIV-1 DNA derived from unfractionated peripheral blood mononuclear cells, ex vivo-isolated CD4+ T cells, and subsets of functionally polarized memory CD4+ T cells. This approach identified multiple sets of independent, near-full-length proviral sequences from cART-treated individuals that were completely identical, consistent with clonal expansion of CD4+ T cells harboring intact HIV-1. Intact, near-full-genome HIV-1 DNA sequences that were derived from such clonally expanded CD4+ T cells constituted 62% of all analyzed genome-intact sequences in memory CD4 T cells, were preferentially observed in Th1-polarized cells, were longitudinally detected over a duration of up to 5 years, and were fully replication- and infection-competent. Together, these data suggest that clonal proliferation of Th1-polarized CD4+ T cells encoding for intact HIV-1 represents a driving force for stabilizing the pool of latently infected CD4+ T cells.

  13. Clonal selection versus clonal cooperation: the integrated perception of immune objects [version 1; referees: 2 approved

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    Serge Nataf

    2016-09-01

    Full Text Available Analogies between the immune and nervous systems were first envisioned by the immunologist Niels Jerne who introduced the concepts of antigen "recognition" and immune "memory". However, since then, it appears that only the cognitive immunology paradigm proposed by Irun Cohen, attempted to further theorize the immune system functions through the prism of neurosciences. The present paper is aimed at revisiting this analogy-based reasoning. In particular, a parallel is drawn between the brain pathways of visual perception and the processes allowing the global perception of an "immune object". Thus, in the visual system, distinct features of a visual object (shape, color, motion are perceived separately by distinct neuronal populations during a primary perception task. The output signals generated during this first step instruct then an integrated perception task performed by other neuronal networks. Such a higher order perception step is by essence a cooperative task that is mandatory for the global perception of visual objects. Based on a re-interpretation of recent experimental data, it is suggested that similar general principles drive the integrated perception of immune objects in secondary lymphoid organs (SLOs. In this scheme, the four main categories of signals characterizing an immune object (antigenic, contextual, temporal and localization signals are first perceived separately by distinct networks of immunocompetent cells.  Then, in a multitude of SLO niches, the output signals generated during this primary perception step are integrated by TH-cells at the single cell level. This process eventually generates a multitude of T-cell and B-cell clones that perform, at the scale of SLOs, an integrated perception of immune objects. Overall, this new framework proposes that integrated immune perception and, consequently, integrated immune responses, rely essentially on clonal cooperation rather than clonal selection.

  14. Clonal analysis of stem cells in differentiation and disease.

    Science.gov (United States)

    Colom, Bartomeu; Jones, Philip H

    2016-12-01

    Tracking the fate of individual cells and their progeny by clonal analysis has redefined the concept of stem cells and their role in health and disease. The maintenance of cell turnover in adult tissues is achieved by the collective action of populations of stem cells with an equal likelihood of self-renewal or differentiation. Following injury stem cells exhibit striking plasticity, switching from homeostatic behavior in order to repair damaged tissues. The effects of disease states on stem cells are also being uncovered, with new insights into how somatic mutations trigger clonal expansion in early neoplasia. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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

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    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.

  16. Effect of environmental stress on clonal structure of Eucypris virens (Crustacea, Ostracoda)

    OpenAIRE

    Martins M. J. F.; Vandekerkhove J.; Adolfsson S.; Rossetti G.; Namiotko T.; Jokela J.

    2010-01-01

    Environmental stress imposes strong natural selection on clonal populations, promoting evolutionary change in clonal structure. Environmental stress may also lead to reduction in population size, which together with clonal selection may reduce genotypic diversity of the local populations. We examined how clonal structure in wild-collected samples of two parthenogenetic populations of the freshwater ostracod Eucypris virens responded to hypersalinity and starvation, and the combination of the ...

  17. Aging in a long-lived clonal tree.

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    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.

  18. 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

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

    African Journals Online (AJOL)

    Productivity gains by fertilisation in Eucalyptus urophylla clonal plantations across gradients in site and stand conditions. ... The control plot may typically be a permanent plot of an inventory network, providing representative information for a company's decisionmaking. The paired twin-plot receives intensive management ...

  20. 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

  1. 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 ...

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

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

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

    African Journals Online (AJOL)

    Clonal conformity of ramets resulting from the re-cloning of somaplants depended, on one hand, on the floral status of the mother plant at the time of sampling and, on the other hand, on its origin. Re-cloning of abnormal regenerants led, in all cases, to 100 % abnormal offspring. The age of the ramet used as mother palm at ...

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

    NARCIS (Netherlands)

    Langerak, A. W.; Groenen, P. J. T. A.; Brüggemann, 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. S.; Gameiro, P.; Garcia Sanz, R.; Gonzalez, D.; Grand, D.; Håkansson, A.; Hummel, M.; Liu, H.; Lombardia, L.; Macintyre, E. A.; Milner, B. J.; Montes-Moreno, S.; Schuuring, E.; Spaargaren, M.; Hodges, E.; van Dongen, J. J. M.

    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. Standardization of the pre-analytical and post-analytical phases is now essential to

  5. Functional specialization of ramets in a clonal plant network functional specialization of ramets in a clonal plant network

    NARCIS (Netherlands)

    Ikegami, M.

    2004-01-01

    Functional specialization of ramets and co-operation between interconnected ramets in heterogeneous environments are studied in this thesis. Since clonal plants can spread horizontally by vegetative growth, a genet has the potential to grow across a heterogeneous environment. Therefore, ramets can

  6. 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.

  7. Proton fire hose instabilities in the expanding solar wind

    Czech Academy of Sciences Publication Activity Database

    Hellinger, Petr

    2017-01-01

    Roč. 83, č. 1 (2017), č. článku 705830105. ISSN 0022-3778 Institutional support: RVO:68378289 Keywords : astrophysicals plasmas * plasma expansion * plasma simulation Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics) Impact factor: 1.160, year: 2016 https://www.cambridge.org/ core /journals/journal-of-plasma-physics/article/proton-fire-hose-instabilities-in-the-expanding-solar-wind/6BA70378B25728533588A1A68073AC2F

  8. Expanded-boundary approach to impurity control in tokamaks

    International Nuclear Information System (INIS)

    Ohyabu, N.

    1981-01-01

    It is proposed to expand the outermost flux surfaces in tokamaks to divert the heat flux emerging from the plasma core. The expanded flux surfaces provide a large volume for radiative cooling. The radiative power at the boundary is enhanced by the effects of plasma flow as well as by a volumetric factor, and the resultant edge cooling and reduced heat load on the limiter may significantly retard impurity generation. Furthermore, it seems to be compatible with reactor engineering requirements. (author)

  9. Comparative drug susceptibility study of five clonal strains of Trichomonas vaginalis in vitro

    Institute of Scientific and Technical Information of China (English)

    Hemantkumar Somabhai Chaudhari; Prati Pal Singh

    2011-01-01

    Objective: To produce comparative data on a group of Trichomonas vaginalis clonal strains with varied drug responses using identical methods and materials. Methods: Five clonal strains of Trichomonas vaginalis were isolated from reference strain using agar plate technique. The variability of growth kinetic and susceptibility of clonal strain to metronidazole, tinidazole, satranidazole and nitazoxanide were observed in 96 well microtitre plate. Results: Among these clonal strains there was a good correlation between rates of growth with the relative susceptibility of the strains to drugs in vitro. Regarding metronidazole, tinidazole and satranidazole susceptibility, different degrees of susceptibility were determined. However, no difference in nitazoxanide susceptibility was found between the clonal strain tested and a reference strain.Conclusions: This is the first description of biological variability in clonal stock of Trichomonas vaginalis. Different degrees of drug susceptibility were determined among clonal strains tested. Further studies will be necessary to ascertain the importance of this variability in clinical infection.

  10. 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.

  11. Clonal multiplication of guava through softwood cuttings under mist conditions

    International Nuclear Information System (INIS)

    Kareem, A.; Jaskkani, M.J.; Fatima, B.; Sadia, B.

    2012-01-01

    Guava (psidium guajava l.) is a luscious and important tropical fruit crop. the objective of the study was to develop vegetative propagation system to avoid clonal degradation in guava fruit plants. softwood cuttings from five year old gola accession were prepared from the shoot tops of current season growth, measuring 12 cm in length and carrying 2 to 4 nodes. iba and naa (0, 2000, 4000, 6000, 8000 ppm) were selected to treat cuttings for root induction. cuttings were planted under mist conditions by maintaining temperature at 25 degree c and 85% relative humidity for 25 days. maximum survival percentage (92.17%) of plants at transplanting was noted with 4000 ppm concentration followed by 2000 ppm (85.50%). In general iba 4000 ppm concentration performed better as compared to naa for all parameters studied. This study revealed the potential of clonal propagation of guava through softwood cuttings treated with auxins. (author)

  12. Dynamics of Tumor Heterogeneity Derived from Clonal Karyotypic Evolution

    Directory of Open Access Journals (Sweden)

    Ashley M. Laughney

    2015-08-01

    Full Text Available Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution.

  13. Clonal and bud bank traits: patterns across temperate plant communities

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Herben, Tomáš

    2015-01-01

    Roč. 26, č. 2 (2015), s. 243-253 ISSN 1100-9233 R&D Projects: GA ČR GB14-36079G; GA ČR GA13-17118S; GA ČR GAP505/12/1007 Institutional support: RVO:67985939 Keywords : clonal and bud bank traits * vegetation * central Europe Subject RIV: EH - Ecology, Behaviour Impact factor: 3.151, year: 2015

  14. Nutrient leaching under zero tension in a subtropical clonal eucalypt ...

    African Journals Online (AJOL)

    Little is known about the effects of residue burning or retention on nutrient leaching during the inter-rotation of clonal Eucalyptus grown on the sandy soils of subtropical Zululand, South Africa. A study compared zero-tension nutrient leaching through the top metre of soil at depths of 0.15, 0.5 and 1.0 m in an undisturbed crop ...

  15. Silicon microfabricated beam expander

    International Nuclear Information System (INIS)

    Othman, A.; Ibrahim, M. N.; Hamzah, I. H.; Sulaiman, A. A.; Ain, M. F.

    2015-01-01

    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

  16. Silicon microfabricated beam expander

    Science.gov (United States)

    Othman, A.; Ibrahim, M. N.; Hamzah, I. H.; Sulaiman, A. A.; Ain, M. F.

    2015-03-01

    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.

  17. 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.

  18. Clonal status and clinicopathological observation of cervical minimal deviation adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Lan Miao

    2010-04-01

    Full Text Available Abstract Background Minimal deviation adenocarcinoma (MDA of the uterine cervix is defined as an extremely well differentiated variant of cervical adenocarcinoma, with well-formed glands that resemble benign glands but show distinct nuclear anaplasia or evidence of stromal invasion. Thus, MDA is difficult to differentiate from other cervical hyperplastic lesions. Monoclonality is a major characteristic of most tumors, whereas normal tissue and reactive hyperplasia are polyclonal. Methods The clinicopathological features and clonality of MDA were investigated using laser microdissection and a clonality assay based on the polymorphism of androgen receptor (AR and X-chromosomal inactivation mosaicism in female somatic tissues. Results The results demonstrated that the glands were positive for CEA, Ki-67, and p53 and negative for estrogen receptor (ER, progesterone receptor (PR, and high-risk human papilloma virus (HPV DNA. The index of proliferation for Ki-67 was more than 50%. However, the stromal cells were positive for ER, PR, vimentin, and SM-actin. The clonal assay showed that MDA was monoclonal. Thus, our findings indicate that MDA is a true neoplasm but is not associated with high-risk HPV. Conclusions Diagnosis of MDA depends mainly on its clinical manifestations, the pathological feature that MDA glands are located deeper than the lower level of normal endocervical glands, and immunostaining.

  19. Multiplexing clonality: combining RGB marking and genetic barcoding

    Science.gov (United States)

    Cornils, Kerstin; Thielecke, Lars; Hüser, Svenja; Forgber, Michael; Thomaschewski, Michael; Kleist, Nadja; Hussein, Kais; Riecken, Kristoffer; Volz, Tassilo; Gerdes, Sebastian; Glauche, Ingmar; Dahl, Andreas; Dandri, Maura; Roeder, Ingo; Fehse, Boris

    2014-01-01

    RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies. PMID:24476916

  20. Likelihood-Based Inference of B Cell Clonal Families.

    Directory of Open Access Journals (Sweden)

    Duncan K Ralph

    2016-10-01

    Full Text Available The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets.

  1. 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.

  2. 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

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

    Science.gov (United States)

    Wendte, Jered M; Miller, Melissa A; Lambourn, Dyanna M; Magargal, Spencer L; Jessup, David A; Grigg, Michael E

    2010-12-23

    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 devastating disease

  4. ExpandED Options: Learning beyond High School Walls

    Science.gov (United States)

    ExpandED Schools, 2014

    2014-01-01

    Through ExpandED Options by TASC, New York City high school students get academic credit for learning career-related skills that lead to paid summer jobs. Too many high school students--including those most likely to drop out--are bored or see classroom learning as irrelevant. ExpandED Options students live the connection between mastering new…

  5. 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.

  6. 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.

  7. 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.

  8. Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia.

    Science.gov (United States)

    Yoshizato, Tetsuichi; Dumitriu, Bogdan; Hosokawa, Kohei; Makishima, Hideki; Yoshida, Kenichi; Townsley, Danielle; Sato-Otsubo, Aiko; Sato, Yusuke; Liu, Delong; Suzuki, Hiromichi; Wu, Colin O; Shiraishi, Yuichi; Clemente, Michael J; Kataoka, Keisuke; Shiozawa, Yusuke; Okuno, Yusuke; Chiba, Kenichi; Tanaka, Hiroko; Nagata, Yasunobu; Katagiri, Takamasa; Kon, Ayana; Sanada, Masashi; Scheinberg, Phillip; Miyano, Satoru; Maciejewski, Jaroslaw P; Nakao, Shinji; Young, Neal S; Ogawa, Seishi

    2015-07-02

    In patients with acquired aplastic anemia, destruction of hematopoietic cells by the immune system leads to pancytopenia. Patients have a response to immunosuppressive therapy, but myelodysplastic syndromes and acute myeloid leukemia develop in about 15% of the patients, usually many months to years after the diagnosis of aplastic anemia. We performed next-generation sequencing and array-based karyotyping using 668 blood samples obtained from 439 patients with aplastic anemia. We analyzed serial samples obtained from 82 patients. Somatic mutations in myeloid cancer candidate genes were present in one third of the patients, in a limited number of genes and at low initial variant allele frequency. Clonal hematopoiesis was detected in 47% of the patients, most frequently as acquired mutations. The prevalence of the mutations increased with age, and mutations had an age-related signature. DNMT3A-mutated and ASXL1-mutated clones tended to increase in size over time; the size of BCOR- and BCORL1-mutated and PIGA-mutated clones decreased or remained stable. Mutations in PIGA and BCOR and BCORL1 correlated with a better response to immunosuppressive therapy and longer and a higher rate of overall and progression-free survival; mutations in a subgroup of genes that included DNMT3A and ASXL1 were associated with worse outcomes. However, clonal dynamics were highly variable and might not necessarily have predicted the response to therapy and long-term survival among individual patients. Clonal hematopoiesis was prevalent in aplastic anemia. Some mutations were related to clinical outcomes. A highly biased set of mutations is evidence of Darwinian selection in the failed bone marrow environment. The pattern of somatic clones in individual patients over time was variable and frequently unpredictable. (Funded by Grant-in-Aid for Scientific Research and others.).

  9. Clonal architectures and driver mutations in metastatic melanomas.

    Directory of Open Access Journals (Sweden)

    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.

  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. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

    Directory of Open Access Journals (Sweden)

    Meng Yang

    2017-05-01

    Full Text Available Abstract Background Solid tumors residing in tissues and organs leave footprints in circulation through circulating tumor cells (CTCs and circulating tumor DNAs (ctDNA. Characterization of the ctDNA portraits and comparison with tumor DNA mutational portraits may reveal clinically actionable information on solid tumors that is traditionally achieved through more invasive approaches. Methods We isolated ctDNAs from plasma of patients of 103 lung cancer and 74 other solid tumors of different tissue origins. Deep sequencing using the Guardant360 test was performed to identify mutations in 73 clinically actionable genes, and the results were associated with clinical characteristics of the patient. The mutation profiles of 37 lung cancer cases with paired ctDNA and tumor genomic DNA sequencing were used to evaluate clonal representation of tumor in circulation. Five lung cancer cases with longitudinal ctDNA sampling were monitored for cancer progression or response to treatments. Results Mutations in TP53, EGFR, and KRAS genes are most prevalent in our cohort. Mutation rates of ctDNA are similar in early (I and II and late stage (III and IV cancers. Mutation in DNA repair genes BRCA1, BRCA2, and ATM are found in 18.1% (32/177 of cases. Patients with higher mutation rates had significantly higher mortality rates. Lung cancer of never smokers exhibited significantly higher ctDNA mutation rates as well as higher EGFR and ERBB2 mutations than ever smokers. Comparative analysis of ctDNA and tumor DNA mutation data from the same patients showed that key driver mutations could be detected in plasma even when they were present at a minor clonal population in the tumor. Mutations of key genes found in the tumor tissue could remain in circulation even after frontline radiotherapy and chemotherapy suggesting these mutations represented resistance mechanisms. Longitudinal sampling of five lung cancer cases showed distinct changes in ctDNA mutation portraits that

  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. 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

  15. 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

  16. Clonal variation in proliferation rate of cultures of GPK cells.

    Science.gov (United States)

    Riley, P A; Hola, M

    1981-09-01

    Pedigrees of twenty-six clones of a line of keratocytes derived from guinea-pig ear epidermis (GPK cells) were analysed from time-lapse film. The mean interdivision time (IDT) for the culture was 1143 +/- 215 (SD) min. The mean generation rates (mean reciprocal interdivision times) of clones varied over a range of 3.93--10.2 x 10(-4)/min and the standard deviation of the clonal mean generation rates was 16.8% of the average value. Transient intraclonal variations in IDT due to mitoses in a plane perpendicular to the substratum were observed. The data were also analysed on the basis of cell location in sixteen equal zones (quadrats) of the filmed area. The mean generation rate of quadrats was 8.73 x 10(-4)/min (SD = 4.9%). The spatial distribution showed some clustering of cells. The mean local density of the clones (2.25 +/- 0.62 cells/10(-4) cm2) was significantly higher than the quadrat density (1.76 +/- 0.8 cells/10(-4) cm2). There was no significant correlation between clonal density and mean generation rates, whereas for quadrats a significant negative correlation was found (P = 2.7%). The results support the proposition that cell lineage is the major determinant of the proliferation rate of subconfluent cultures.

  17. Competition, salinity, and clonal growth in native and introduced irises.

    Science.gov (United States)

    Mopper, Susan; Wiens, Karen C; Goranova, Greta A

    2016-09-01

    Iris pseudacorus spread rapidly into North America after introduction from Europe in the 1800s and now co-occurs with native I. hexagona in freshwater Louisiana wetlands. Native irises support and interact with multiple trophic levels, whereas I. pseudacorus is classified an invasive pest because it grows aggressively, reduces biodiversity, and displaces native vegetation. Salinity levels are increasing in coastal wetlands worldwide. We examined how salt-stress affects competitive interactions between these conspecifics. We established a three-way full-factorial common-garden experiment that included species (I. pseudacorus, I. hexagona), competition (no competition, intraspecific competition, and interspecific competition), and salinity (0, 4, 8 parts per thousand NaCl), with six replicates per treatment. After 18 mo, Iris pseudacorus produced much more biomass than the native species did (F1, 92 = 71.5, P Interspecific competition did not affect the introduced iris, but biomass of the native was strongly reduced (competition × species interaction: F2, 95 = 76.7, P = 0.002). Salinity significantly reduced biomass of both species (F2, 92 = 21.8, P competitive advantage over the native, regardless of environmental salinity levels. Based on patterns in clonal reproduction, the introduced iris could potentially threaten native iris populations. We are currently investigating seed production and mortality during competition and stress because both clonal and sexual reproduction must be considered when predicting long-term population dynamics. © 2016 Botanical Society of America.

  18. Clonal Spread in Second Growth Stands of Coast Redwood, Sequoia sempervirens

    Science.gov (United States)

    Vladimir Douhovnikoff; Richard S. Dodd

    2007-01-01

    Coast redwood (Sequoia sempervirens) is one of the rare conifers to reproduce successfully through clonal spread. The importance of this mode of reproduction in stand development is largely unknown. Understanding the importance of clonal spread and the spatial structure of clones is crucial for stand management strategies that would aim to maximize...

  19. Virulence, sporulation, and elicitin production in three clonal lineages of Phytophthora ramorum

    Science.gov (United States)

    Phytophthora ramorum populations are clonal and consist of three lineages. Recent studies have shown that the clonal lineages may have varying degrees of aggressiveness on some host species, such as Quercus rubra. In this study, we examined virulence, sporulation and elicitin production of five P. ...

  20. 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

  1. 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...

  2. 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...

  3. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    Science.gov (United States)

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytica...

  4. Clonal Growth Forms in Eastern Ladakh, Western Himalayas: Classification and Habitat Preferences

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Doležal, Jiří; Dvorský, Miroslav; de Bello, Francesco; Klimeš, Leoš

    2011-01-01

    Roč. 46, 2-3 (2011), 191-217 ISSN 1211-9520 R&D Projects: GA AV ČR IAA600050802 Institutional research plan: CEZ:AV0Z60050516 Keywords : Clonal growth form * Clonal space occupancy strategies * Habitat types Subject RIV: EF - Botanics Impact factor: 1.500, year: 2011

  5. Bigelow Expandable Activity Module Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Bigelow Expandable Activity Module (BEAM) project is a NASA-industry partnership with Bigelow Aerospace (BA) that has developing the first human-rated expandable...

  6. Tissue expander infections in children: look beyond the expander pocket.

    Science.gov (United States)

    Mason, A C; Davison, S P; Manders, E K

    1999-11-01

    Infection of the expander pocket is the most common complication encountered with soft-tissue expansion. It is usually due to direct inoculation with skin flora either at the time of expander insertion or from extrusion of the device. The authors report two cases of infection of tissue expanders in which the children had concomitant infected sites distant from the prosthesis. Etiological bacteria of common pediatric infections like otitis media and pharyngitis were cultured from the infected expander pocket, raising suspicion that translocation of the organism to the expander had occurred. Aggressive antibiotic treatment, removal of the prosthesis, and flap advancement is advocated.

  7. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

    Science.gov (United States)

    Reinius, Björn; Mold, Jeff E; Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

    2016-11-01

    Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8 + T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

  8. 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.

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

    Science.gov (United States)

    McGranahan, Nicholas; Furness, Andrew J. S.; Rosenthal, Rachel; Ramskov, Sofie; Lyngaa, Rikke; Saini, Sunil Kumar; Jamal-Hanjani, Mariam; Wilson, Gareth A.; Birkbak, Nicolai J.; Hiley, Crispin T.; Watkins, Thomas B. K.; Shafi, Seema; Murugaesu, Nirupa; Mitter, Richard; Akarca, Ayse U.; Linares, Joseph; Marafioti, Teresa; Henry, Jake Y.; Van Allen, Eliezer M.; Miao, Diana; Schilling, Bastian; Schadendorf, Dirk; Garraway, Levi A.; Makarov, Vladimir; Rizvi, Naiyer A.; Snyder, Alexandra; Hellmann, Matthew D.; Merghoub, Taha; Wolchok, Jedd D.; Shukla, Sachet A.; Wu, Catherine J.; Peggs, Karl S.; Chan, Timothy A.; Hadrup, Sine R.; Quezada, Sergio A.; Swanton, Charles

    2016-01-01

    As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we 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 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy–induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens. PMID:26940869

  10. Plasma expansion: fundamentals and applications

    International Nuclear Information System (INIS)

    Engeln, R; Mazouffre, S; Vankan, P; Bakker, I; Schram, D C

    2002-01-01

    The study of plasma expansion is interesting from a fundamental point of view as well as from a more applied point of view. We here give a short overview of the way properties like density, velocity and temperature behave in an expanding thermal plasma. Experimental data show that the basic phenomena of plasma expansion are to some extent similar to those of the expansion of a hot neutral gas. From the application point of view, we present first results on the use of an expanding thermal plasma in the plasma-activated catalysis of ammonia, from N 2 -H 2 mixtures

  11. Ambipolar ion acceleration in an expanding magnetic nozzle

    Energy Technology Data Exchange (ETDEWEB)

    Longmier, Benjamin W; Carter, Mark D; Cassady, Leonard D; Chancery, William J; Diaz, Franklin R Chang; Glover, Tim W; Ilin, Andrew V; McCaskill, Greg E; Olsen, Chris S; Squire, Jared P [Ad Astra Rocket Company, 141 W. Bay Area Blvd, Webster, TX (United States); Bering, Edgar A III [Department of Physics and Department of Electrical and Computer Engineering, University of Houston, 617 Science and Research Building 1, Houston, TX (United States); Hershkowitz, Noah [Department of Engineering Physics, University of Wisconsin, 1500 Engineering Dr., Madison, WI (United States)

    2011-02-15

    The helicon plasma stage in the Variable Specific Impulse Magnetoplasma Rocket (VASIMR (registered)) VX-200i device was used to characterize an axial plasma potential profile within an expanding magnetic nozzle region of the laboratory based device. The ion acceleration mechanism is identified as an ambipolar electric field produced by an electron pressure gradient, resulting in a local axial ion speed of Mach 4 downstream of the magnetic nozzle. A 20 eV argon ion kinetic energy was measured in the helicon source, which had a peak magnetic field strength of 0.17 T. The helicon plasma source was operated with 25 mg s{sup -1} argon propellant and 30 kW of RF power. The maximum measured values of plasma density and electron temperature within the exhaust plume were 1 x 10{sup 20} m{sup -3} and 9 eV, respectively. The measured plasma density is nearly an order of magnitude larger than previously reported steady-state helicon plasma sources. The exhaust plume also exhibits a 95% to 100% ionization fraction. The size scale and spatial location of the plasma potential structure in the expanding magnetic nozzle region appear to follow the size scale and spatial location of the expanding magnetic field. The thickness of the potential structure was found to be 10{sup 4} to 10{sup 5} {lambda}{sub De} depending on the local electron temperature in the magnetic nozzle, many orders of magnitude larger than typical laboratory double layer structures. The background plasma density and neutral argon pressure were 10{sup 15} m{sup -3} and 2 x 10{sup -5} Torr, respectively, in a 150 m{sup 3} vacuum chamber during operation of the helicon plasma source. The agreement between the measured plasma potential and plasma potential that was calculated from an ambipolar ion acceleration analysis over the bulk of the axial distance where the potential drop was located is a strong confirmation of the ambipolar acceleration process.

  12. The expanding EU

    DEFF Research Database (Denmark)

    Zank, Wolfgang

    In this paper I try to explore whether the EU can go on expanding and thereby become culturally ever more diversified, and at the same retain its stability. The answer is, in principle, affirmative. Europe has always been much diversified, and therefore it is not possible to define a European...... identity in terms of particular cultural traditions. However, in spite of their diversity, the EU-member countries are united by their adherence to the principles of democracy, rule by law and human rights. Countries which do not share this basic consensus would not be accepted as members, nor is it likely...... that they would apply for it. An essential part is the willingness of member states to accept a reduction of national sovereignty on some important policy fields. The EU project is basically about lifting the principles of democracy and rule by law on the international level, most and foremost among the member...

  13. 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.

  14. Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis.

    Science.gov (United States)

    Lin, Chia-Hua; Miriti, Maria N; Goodell, Karen

    2016-06-01

    Clonality is a widespread life history trait in flowering plants that may be essential for population persistence, especially in environments where sexual reproduction is unpredictable. Frequent clonal reproduction, however, could hinder sexual reproduction by spatially aggregating ramets that compete with seedlings and reduce inter-genet pollination. Nevertheless, the role of clonality in relation to variable sexual reproduction in population dynamics is often overlooked. We combined population matrix models and pollination experiments to compare the demographic contributions of clonal and sexual reproduction in three Dicentra canadensis populations, one in a well-forested landscape and two in isolated forest remnants. We constructed stage-based transition matrices from 3 years of census data to evaluate annual population growth rates, λ. We used loop analysis to evaluate the relative contribution of different reproductive pathways to λ. Despite strong temporal and spatial variation in seed set, populations generally showed stable growth rates. Although we detected some pollen limitation of seed set, manipulative pollination treatments did not affect population growth rates. Clonal reproduction contributed significantly more than sexual reproduction to population growth in the forest remnants. Only at the well-forested site did sexual reproduction contribute as much as clonal reproduction to population growth. Flowering plants were more likely to transition to a smaller size class with reduced reproductive potential in the following year than similarly sized nonflowering plants, suggesting energy trade-offs between sexual and clonal reproduction at the individual level. Seed production had negligible effects on growth and tuber production of individual plants. Our results demonstrate that clonal reproduction is vital for population persistence in a system where sexual reproduction is unpredictable. The bias toward clonality may be driven by low fitness returns

  15. Early circulating tumor DNA dynamics and clonal selection with palbociclib and fulvestrant for breast cancer.

    Science.gov (United States)

    O'Leary, Ben; Hrebien, Sarah; Morden, James P; Beaney, Matthew; Fribbens, Charlotte; Huang, Xin; Liu, Yuan; Bartlett, Cynthia Huang; Koehler, Maria; Cristofanilli, Massimo; Garcia-Murillas, Isaac; Bliss, Judith M; Turner, Nicholas C

    2018-03-01

    CDK4/6 inhibition substantially improves progression-free survival (PFS) for women with advanced estrogen receptor-positive breast cancer, although there are no predictive biomarkers. Early changes in circulating tumor DNA (ctDNA) level may provide early response prediction, but the impact of tumor heterogeneity is unknown. Here we use plasma samples from patients in the randomized phase III PALOMA-3 study of CDK4/6 inhibitor palbociclib and fulvestrant for women with advanced breast cancer and show that relative change in PIK3CA ctDNA level after 15 days treatment strongly predicts PFS on palbociclib and fulvestrant (hazard ratio 3.94, log-rank p = 0.0013). ESR1 mutations selected by prior hormone therapy are shown to be frequently sub clonal, with ESR1 ctDNA dynamics offering limited prediction of clinical outcome. These results suggest that early ctDNA dynamics may provide a robust biomarker for CDK4/6 inhibitors, with early ctDNA dynamics demonstrating divergent response of tumor sub clones to treatment.

  16. Endothelial progenitor cells display clonal restriction in multiple myeloma

    International Nuclear Information System (INIS)

    Braunstein, Marc; Özçelik, Tayfun; Bağişlar, Sevgi; Vakil, Varsha; Smith, Eric LP; Dai, Kezhi; Akyerli, Cemaliye B; Batuman, Olcay A

    2006-01-01

    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. 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 (V H ). 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 V H 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, unlike patients whose EPCs had random XCI

  17. The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence

    Science.gov (United States)

    Murray, Alexandra J.; Kwon, Kyungyoon J.; Farber, Donna L.; Siliciano, Robert F.

    2016-01-01

    Combination antiretroviral therapy (ART) for HIV-1 infection reduces plasma virus levels to below the limit of detection of clinical assays. However, even with prolonged suppression of viral replication with ART, viremia rebounds rapidly after treatment interruption. Thus ART is not curative. The principal barrier to cure is a remarkably stable reservoir of latent HIV-1 in resting memory CD4+ T cells. Here we consider explanations for the remarkable stability of the latent reservoir. Stability does not appear to reflect replenishment from new infection events but rather normal physiologic processes that provide for immunologic memory. Of particular importance are proliferative processes that drive clonal expansion of infected cells. Recent evidence suggests that in some infected cells, proliferation is a consequence of proviral integration into host genes associated with cell growth. Efforts to cure HIV-1 infection by targeting the latent reservoir may need to consider the potential of latently infected cells to proliferate. PMID:27382129

  18. Aging, Clonality and Rejuvenation of Hematopoietic Stem Cells

    Science.gov (United States)

    Akunuru, Shailaja; Geiger, Hartmut

    2016-01-01

    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 increased production of reactive oxygen species 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 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. PMID:27380967

  19. Atherosclerosis and clonal hematopoyesis: A new risk factor.

    Science.gov (United States)

    Páramo Fernández, José A

    Recent research has revealed that clonal hematopoyesis of indeterminate potential (CHIP) characterized by the acquisition of somatic mutations in hematopoietic stem cells, is not only a common age-related disorder and a premalignant condition, but it is also associated with the development of atherosclerotic vascular diseases. Mutations in DNMT3A, TET2 and ASXL1 were each individually associated with coronary heart disease, stroke and coronary calcification. Therefore, CHIP emerges as a new risk factor for atherosclerotic vascular pathologies and its detection may be relevant as a new therapeutic target in order to modify the natural course of the disease. Copyright © 2018 Sociedad Española de Arteriosclerosis. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. Clonal proliferation of cultured nonmalignant and malignant human breast epithelia

    International Nuclear Information System (INIS)

    Smith, H.S.; Lan, S.; Ceriani, R.; Hackett, A.J.; Stampfer, M.R.

    1981-01-01

    We have developed a method for clonal growth of human mammary epithelial cells of both nonmalignant and malignant origin. Plating efficiencies of 1 to 50% were obtained by seeding second-passage mammary epithelial cells on fibroblast feeder layers in an enriched medium composed of various hormones and growth factors, as well as conditioned media from three specific human cell lines. Single mammary epithelial cells seeded sparsely onto the fibroblasts underwent at least eight population doublings to form large, readily visible colonies. Optimal colony formation required both feeder cells and the enriched medium. Epithelial colonies containing at least 16 cells were visible 5 days postseeding, and these colonies continued to grow progressively. Plating efficiency and colony size were similar on ultraviolet-irradiated or nonirradiated fibroblasts. The number of colonies formed was proportional to the number of epithelial cells plated. The colonies were identified as epithelial by the presence of human mammary epithelial antigens

  1. Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

    Science.gov (United States)

    Deshwar, Amit G; Vembu, Shankar; Morris, Quaid

    2015-01-01

    Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor…

  2. 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...

  3. The Artful Universe Expanded

    International Nuclear Information System (INIS)

    Bassett, B A

    2005-01-01

    The cosmos is an awfully big place and there is no better guide to its vast expanse and fascinating nooks and crannies than John Barrow. A professor of mathematical sciences at Cambridge University, Barrow embodies that rare combination of highly polished writer and expert scientist. His deft touch brings together the disparate threads of human knowledge and weaves them into a tapestry as rich and interesting for the expert as it is for the layperson. The Artful Universe Expanded is an updated edition of this popular book first published in 1995. It explores the deeply profound manner in which natural law and the nature of the cosmos have moulded and shaped us, our cultures and the very form of our arts and music-a new type of 'cosmic' anthropology. The main themes Barrow chooses for revealing this new anthropology are the subjects of evolution, the size of things, the heavens and the nature of music. The book is a large, eclectic repository of knowledge often unavailable to the layperson, hidden in esoteric libraries around the world. It rivals The Da Vinci Code for entertainment value and insights, but this time it is Nature's code that is revealed. It is rare indeed to find common threads drawn through topics as diverse as The Beetles, Bach and Beethoven or between Jackson Pollock, the Aztecs, Kant, Picasso, Byzantine mosaics, uranium-235 and the helix nebula. Barrow unerringly binds them together, presenting them in a stimulating, conversational style that belies the amount of time that must have gone into researching this book. Dip into it at random, or read it from cover to cover, but do read it. The Artful Universe Expanded is an entertaining antidote to the oft-lamented pressures to know more and more about less and less and the apparently inexorable march of specialization. On reading this book one can, for a short time at least, hold in one's mind a vision that unifies science, art and culture and glimpse a universal tapestry of great beauty. (book review)

  4. The Artful Universe Expanded

    Energy Technology Data Exchange (ETDEWEB)

    Bassett, B A [Institute of Cosmology and Gravitation, University of Portsmouth (United Kingdom)

    2005-07-29

    The cosmos is an awfully big place and there is no better guide to its vast expanse and fascinating nooks and crannies than John Barrow. A professor of mathematical sciences at Cambridge University, Barrow embodies that rare combination of highly polished writer and expert scientist. His deft touch brings together the disparate threads of human knowledge and weaves them into a tapestry as rich and interesting for the expert as it is for the layperson. The Artful Universe Expanded is an updated edition of this popular book first published in 1995. It explores the deeply profound manner in which natural law and the nature of the cosmos have moulded and shaped us, our cultures and the very form of our arts and music-a new type of 'cosmic' anthropology. The main themes Barrow chooses for revealing this new anthropology are the subjects of evolution, the size of things, the heavens and the nature of music. The book is a large, eclectic repository of knowledge often unavailable to the layperson, hidden in esoteric libraries around the world. It rivals The Da Vinci Code for entertainment value and insights, but this time it is Nature's code that is revealed. It is rare indeed to find common threads drawn through topics as diverse as The Beetles, Bach and Beethoven or between Jackson Pollock, the Aztecs, Kant, Picasso, Byzantine mosaics, uranium-235 and the helix nebula. Barrow unerringly binds them together, presenting them in a stimulating, conversational style that belies the amount of time that must have gone into researching this book. Dip into it at random, or read it from cover to cover, but do read it. The Artful Universe Expanded is an entertaining antidote to the oft-lamented pressures to know more and more about less and less and the apparently inexorable march of specialization. On reading this book one can, for a short time at least, hold in one's mind a vision that unifies science, art and culture and glimpse a universal tapestry of great

  5. Selective Inhibition of Tumor Growth by Clonal NK Cells Expressing an ErbB2/HER2-Specific Chimeric Antigen Receptor

    Science.gov (United States)

    Schönfeld, Kurt; Sahm, Christiane; Zhang, Congcong; Naundorf, Sonja; Brendel, Christian; Odendahl, Marcus; Nowakowska, Paulina; Bönig, Halvard; Köhl, Ulrike; Kloess, Stephan; Köhler, Sylvia; Holtgreve-Grez, Heidi; Jauch, Anna; Schmidt, Manfred; Schubert, Ralf; Kühlcke, Klaus; Seifried, Erhard; Klingemann, Hans G; Rieger, Michael A; Tonn, Torsten; Grez, Manuel; Wels, Winfried S

    2015-01-01

    Natural killer (NK) cells are an important effector cell type for adoptive cancer immunotherapy. Similar to T cells, NK cells can be modified to express chimeric antigen receptors (CARs) to enhance antitumor activity, but experience with CAR-engineered NK cells and their clinical development is still limited. Here, we redirected continuously expanding and clinically usable established human NK-92 cells to the tumor-associated ErbB2 (HER2) antigen. Following GMP-compliant procedures, we generated a stable clonal cell line expressing a humanized CAR based on ErbB2-specific antibody FRP5 harboring CD28 and CD3ζ signaling domains (CAR 5.28.z). These NK-92/5.28.z cells efficiently lysed ErbB2-expressing tumor cells in vitro and exhibited serial target cell killing. Specific recognition of tumor cells and antitumor activity were retained in vivo, resulting in selective enrichment of NK-92/5.28.z cells in orthotopic breast carcinoma xenografts, and reduction of pulmonary metastasis in a renal cell carcinoma model, respectively. γ-irradiation as a potential safety measure for clinical application prevented NK cell replication, while antitumor activity was preserved. Our data demonstrate that it is feasible to engineer CAR-expressing NK cells as a clonal, molecularly and functionally well-defined and continuously expandable cell therapeutic agent, and suggest NK-92/5.28.z cells as a promising candidate for use in adoptive cancer immunotherapy. PMID:25373520

  6. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

    Science.gov (United States)

    Scarcelli, Nora; Couderc, Marie; Baco, Mohamed N; Egah, Janvier; Vigouroux, Yves

    2013-11-13

    Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.

  7. 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.

  8. 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.

  9. Prediction for the occurrence of clonal chromosome aberrations in human blood lymphocytes

    International Nuclear Information System (INIS)

    Nakano, M.; Kadama, Y.; Ohtaki, K.; Itoh, M.; Awa, A.; Cologne, J.; Nakamura, N.

    2003-01-01

    Full text: Identical chromosome aberrations among multiple blood lymphocytes in a blood sample (clonal aberrations) are encountered occasionally during cytogenetic examination of radiation-exposed people. Clonal aberrations are found primarily among high-dose exposed people but no systematic surveys were ever conducted. Therefore, the underlying mechanism is unknown. Here we conducted a large-scale screening for detecting clonal aberrations using FISH followed by Q-banding. Examinations of 500 cells from each of 513 A-bomb survivors led us to detect 96 clones. The clonal cell fraction (Cf) varied from 0.6% to 20% among the 500 cells. As the number of clonal event was inversely proportional to Cf, we hypothesized that the progenitor cells vary extensively in the number of offspring that they can produce and relative number of progenitor cells decreases as the increase of treatment, while other genes such as DNA repair proteinsnumber of progenitor cells capable to form clones (Cf >=0.6%) to be 2 (1 to 3) in non-exposed individuals. The number increased to up to 7 among the high-dose exposed survivors. Further, our preliminary results for the origins of 10 clones indicated that both hematopoietic stem cells (HSCs) and mature T cells contributed to the clone formation roughly equally. Thus, the estimated number of 2 in non-exposed individuals is shared as one HSC and one mature T cells. The model could neatly explain the frequency of clones in two reports. Our model predicts that clonal aberrations are rarely found but clonal expansion of T lymphocytes occurs commonly. In fact, clonal expansions of non-aberrant cells are reported using TCR gene rearrangement patterns as a marker. We now understand the rough structure of lymphocyte pool in humans and can predict the probability of detecting a clone if the individual frequency of non-clonal translocations and the number of cells scored are given

  10. A steady-state fluid model of the coaxial plasma gun

    International Nuclear Information System (INIS)

    Herziger, G.; Krompholz, H.; Schneider, W.; Schoenbach, K.

    1979-01-01

    The plasma layer in a coaxial plasma gun is considered as a shock front driven by expanding magnetic fields. Analytical steady-state solutions of the fluid equations yield the plasma properties, allowing the scaling of plasma focus devices. (Auth.)

  11. 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.

  12. 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...... 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...

  13. Clonal structure of Streptococcus sanguinis strains isolated from endocarditis cases and the oral cavity.

    Science.gov (United States)

    Do, T; Gilbert, S C; Klein, J; Warren, S; Wade, W G; Beighton, D

    2011-10-01

    A collection of Streptococcus sanguinis strains from patients with endocarditis (n = 21) and from the oral cavity (n = 34) was subjected to a multi-locus sequence typing analysis using seven housekeeping genes, carbamoyl-phosphate synthetase (carB), Co/Zn/Cd efflux system component (czcD), d-alanyl-d-alanine ligase (ddl), DNA polymerase III (dnaX), glucose-6-phosphate dehydrogenase (gdh), DNA-directed RNA polymerase, beta subunit (rpoB) and superoxide dismutase (sodA). The scheme was expanded by the inclusion of two the putative virulence genes, bacitracin-resistance protein (bacA) and saliva-binding protein (ssaB), to increase strain discrimination. Extensive intra-species recombination was apparent in all genes but inter-species recombination was also apparent with strains apparently harbouring gdh and ddl from unidentified sources and one isolate harboured a sodA allele apparently derived from Streptococcus oralis. The recombination/mutation ratio for the concatenated housekeeping gene sequences was 1.67 (95% confidence limits 1.25-2.72) and for the two virulence genes the r/m ratio was 3.99 (95% confidence limits 1.61-8.72); recombination was the major driver for genetic variation. All isolates were distinct and the endocarditis strains did not form distinct sub-clusters when the data were analysed using ClonalFrame. These data support the widely held opinion that infecting S. sanguinis strains are opportunistic human pathogens. © 2011 John Wiley & Sons A/S.

  14. Measurement of Debye length in laser-produced plasma.

    Science.gov (United States)

    Ehler, W.

    1973-01-01

    The Debye length of an expanded plasma created by placing an evacuated chamber with an entrance slit in the path of a freely expanding laser produced plasma was measured, using the slab geometry. An independent measurement of electron density together with the observed value for the Debye length also provided a means for evaluating the plasma electron temperature. This temperature has applications in ascertaining plasma conductivity and magnetic field necessary for confinement of the laser produced plasma. Also, the temperature obtained would be useful in analyzing electron-ion recombination rates in the expanded plasma and the dynamics of the cooling process of the plasma expansion.

  15. 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

  16. Screening of clonal chromosome aberrations present in A-bomb survivors by FISH method

    International Nuclear Information System (INIS)

    Nakano, Mimako; Kodama, Yoshiaki; Ito, Masahiro; Otaki, Kazuo; Nakamura, Nori

    1997-01-01

    Significance of FISH method for detection of clonal chromosome aberration was reviewed. A clonal chromosome aberration is derived from one abnormal cell clone and gives the influence on the frequency of the aberration. As well, the size and frequency of the aberration give an important information concerning lymphocyte kinetics. FISH method is meaningful for detection of the clonal aberration. Fifteen kinds of clonal aberrations were detected in A-bomb survivors, of which 10 were specifically detected by the method, indicating that its detection rate was 2-3 time as high as the ordinary method. The results were those on the DNA probe on no.1, no.2 and no.3 chromosomes, which consisting of about 23% of the genome. (K.H.)

  17. Implementation of Microfluidic Chip Electrophoresis for the Detection of B-cell Clonality

    Directory of Open Access Journals (Sweden)

    Vazan M

    2016-04-01

    Full Text Available Introduction: A clonal population of B-cells is defined as those cells arising from the mitotic division of a single somatic cell with the same rearrangement of immunoglobulin genes. This gives rise to DNA markers for each individual lymphoid cell and its progenies and enables us to study clonality in different B-cell malignancies using multiplex polymerase chain reaction - PCR. The BIOMED-2 protocol has been implemented for clonality detection in lymphoproliferative diseases and exploits multiplex PCR reaction, subsequently analyzed by heteroduplex analysis (HDA using polyacrylamide gel electrophoresis (PAGE. With the advent of miniaturization and automation of molecular biology methods, lab-on-chip technologies were developed and replace partially the conventional approaches. We tested device for microfluidic chip, which is used for B-cells clonality analysis, using a PCR reaction for three subregions called frameworks (FR of the immunoglobulin heavy locus (IGH gene.

  18. 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.

  19. The expanding universe: an introduction

    OpenAIRE

    Pössel, Markus

    2017-01-01

    An introduction to the physics and mathematics of the expanding universe, using no more than high-school level / undergraduate mathematics. Covered are the basics of scale factor expansion, the dynamics of the expanding universe, various distance concepts and the generalized redshift-luminosity relation, among other topics.

  20. Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia.

    Science.gov (United States)

    Zhang, Linsheng; Znoyko, Iya; Costa, Luciano J; Conlin, Laura K; Daber, Robert D; Self, Sally E; Wolff, Daynna J

    2011-12-01

    Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease. The methods currently used for monitoring CLL and determining conditions for treatment are limited in their ability to predict disease progression, patient survival, and response to therapy. Although clonal diversity and the acquisition of new chromosomal abnormalities during the disease course (clonal evolution) have been associated with disease progression, their prognostic potential has been underappreciated because cytogenetic and fluorescence in situ hybridization (FISH) studies have a restricted ability to detect genomic abnormalities and clonal evolution. We hypothesized that whole genome analysis using high resolution single nucleotide polymorphism (SNP) microarrays would be useful to detect diversity and infer clonal evolution to offer prognostic information. In this study, we used the Infinium Omni1 BeadChip (Illumina, San Diego, CA) array for the analysis of genetic variation and percent mosaicism in 25 non-selected CLL patients to explore the prognostic value of the assessment of clonal diversity in patients with CLL. We calculated the percentage of mosaicism for each abnormality by applying a mathematical algorithm to the genotype frequency data and by manual determination using the Simulated DNA Copy Number (SiDCoN) tool, which was developed from a computer model of mosaicism. At least one genetic abnormality was identified in each case, and the SNP data was 98% concordant with FISH results. Clonal diversity, defined as the presence of two or more genetic abnormalities with differing percentages of mosaicism, was observed in 12 patients (48%), and the diversity correlated with the disease stage. Clonal diversity was present in most cases of advanced disease (Rai stages III and IV) or those with previous treatment, whereas 9 of 13 patients without detected clonal diversity were asymptomatic or clinically stable. In conclusion, SNP microarray studies with simultaneous evaluation

  1. Clonal diversity and fine-scale genetic structure in a high andean treeline population

    Czech Academy of Sciences Publication Activity Database

    Peng, Y.; Macek, P.; Macková, Jana; Romoleroux, K.; Hensen, I.

    2015-01-01

    Roč. 47, č. 1 (2015), s. 59-65 ISSN 0006-3606 Grant - others:GA AV ČR(CZ) IAA601110702; GA MŠk(CZ) LM2010009 Program:IA Institutional support: RVO:60077344 Keywords : AFLP * clonal diversity * clonal propagation * fine-scale genetic structure * Polylepis reticulata * treeline Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.944, year: 2015

  2. Clonal Evaluation of Prostate Cancer by ERG/SPINK1 Status to Improve Prognosis Prediction

    Science.gov (United States)

    2017-12-01

    19 NIH Exploiting drivers of androgen receptor signaling negative prostate cancer for precision medicine Goal(s): Identify novel potential drivers...AWARD NUMBER: W81XWH-14-1-0466 TITLE: Clonal evaluation of prostate cancer by ERG/SPINK1 status to improve prognosis prediction PRINCIPAL...Sept 2017 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Clonal Evaluation of Prostate Cancer by ERG/SPINK1 Status to Improve Prognosis Prediction 5b

  3. 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.

  4. Detectable clonal mosaicism and its relationship to aging and cancer

    Science.gov (United States)

    Jacobs, Kevin B; Yeager, Meredith; Zhou, Weiyin; Wacholder, Sholom; Wang, Zhaoming; Rodriguez-Santiago, Benjamin; Hutchinson, Amy; Deng, Xiang; Liu, Chenwei; Horner, Marie-Josephe; Cullen, Michael; Epstein, Caroline G; Burdett, Laurie; Dean, Michael C; Chatterjee, Nilanjan; Sampson, Joshua; Chung, Charles C; Kovaks, Joseph; Gapstur, Susan M; Stevens, Victoria L; Teras, Lauren T; Gaudet, Mia M; Albanes, Demetrius; Weinstein, Stephanie J; Virtamo, Jarmo; Taylor, Philip R; Freedman, Neal D; Abnet, Christian C; Goldstein, Alisa M; Hu, Nan; Yu, Kai; Yuan, Jian-Min; Liao, Linda; Ding, Ti; Qiao, You-Lin; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Aldrich, Melinda C; Amos, Christopher; Blot, William J; Bock, Cathryn H; Gillanders, Elizabeth M; Harris, Curtis C; Haiman, Christopher A; Henderson, Brian E; Kolonel, Laurence N; Le Marchand, Loic; McNeill, Lorna H; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret R; Wiencke, John K; Wrensch, Margaret; Wu, Xifeng; Zanetti, Krista A; Ziegler, Regina G; Figueroa, Jonine D; Garcia-Closas, Montserrat; Malats, Nuria; Marenne, Gaelle; Prokunina-Olsson, Ludmila; Baris, Dalsu; Schwenn, Molly; Johnson, Alison; Landi, Maria Teresa; Goldin, Lynn; Consonni, Dario; Bertazzi, Pier Alberto; Rotunno, Melissa; Rajaraman, Preetha; Andersson, Ulrika; Freeman, Laura E Beane; Berg, Christine D; Buring, Julie E; Butler, Mary A; Carreon, Tania; Feychting, Maria; Ahlbom, Anders; Gaziano, J Michael; Giles, Graham G; Hallmans, Goran; Hankinson, Susan E; Hartge, Patricia; Henriksson, Roger; Inskip, Peter D; Johansen, Christoffer; Landgren, Annelie; McKean-Cowdin, Roberta; Michaud, Dominique S; Melin, Beatrice S; Peters, Ulrike; Ruder, Avima M; Sesso, Howard D; Severi, Gianluca; Shu, Xiao-Ou; Visvanathan, Kala; White, Emily; Wolk, Alicja; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Silverman, Debra T; Kogevinas, Manolis; Gonzalez, Juan R; Villa, Olaya; Li, Donghui; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Kooperberg, Charles; Wolpin, Brian M; Jiao, Li; Hassan, Manal; Wheeler, William; Arslan, Alan A; Bas Bueno-de-Mesquita, H; Fuchs, Charles S; Gallinger, Steven; Gross, Myron D; Holly, Elizabeth A; Klein, Alison P; LaCroix, Andrea; Mandelson, Margaret T; Petersen, Gloria; Boutron-Ruault, Marie-Christine; Bracci, Paige M; Canzian, Federico; Chang, Kenneth; Cotterchio, Michelle; Giovannucci, Edward L; Goggins, Michael; Bolton, Judith A Hoffman; Jenab, Mazda; Khaw, Kay-Tee; Krogh, Vittorio; Kurtz, Robert C; McWilliams, Robert R; Mendelsohn, Julie B; Rabe, Kari G; Riboli, Elio; Tjønneland, Anne; Tobias, Geoffrey S; Trichopoulos, Dimitrios; Elena, Joanne W; Yu, Herbert; Amundadottir, Laufey; Stolzenberg-Solomon, Rachael Z; Kraft, Peter; Schumacher, Fredrick; Stram, Daniel; Savage, Sharon A; Mirabello, Lisa; Andrulis, Irene L; Wunder, Jay S; García, Ana Patiño; Sierrasesúmaga, Luis; Barkauskas, Donald A; Gorlick, Richard G; Purdue, Mark; Chow, Wong-Ho; Moore, Lee E; Schwartz, Kendra L; Davis, Faith G; Hsing, Ann W; Berndt, Sonja I; Black, Amanda; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Peplonska, Beata; McGlynn, Katherine A; Cook, Michael B; Graubard, Barry I; Kratz, Christian P; Greene, Mark H; Erickson, Ralph L; Hunter, David J; Thomas, Gilles; Hoover, Robert N; Real, Francisco X; Fraumeni, Joseph F; Caporaso, Neil E; Tucker, Margaret; Rothman, Nathaniel; Pérez-Jurado, Luis A; Chanock, Stephen J

    2012-01-01

    In an analysis of 31,717 cancer cases and 26,136 cancer-free controls drawn from 13 genome-wide association studies (GWAS), we observed large chromosomal abnormalities in a subset of clones from DNA obtained from blood or buccal samples. Mosaic chromosomal abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of size >2 Mb were observed in autosomes of 517 individuals (0.89%) with abnormal cell proportions between 7% and 95%. In cancer-free individuals, the frequency increased with age; 0.23% under 50 and 1.91% between 75 and 79 (p=4.8×10−8). Mosaic abnormalities were more frequent in individuals with solid-tumors (0.97% versus 0.74% in cancer-free individuals, OR=1.25, p=0.016), with a stronger association for cases who had DNA collected prior to diagnosis or treatment (OR=1.45, p=0.0005). Detectable clonal mosaicism was common in individuals for whom DNA was collected at least one year prior to diagnosis of leukemia compared to cancer-free individuals (OR=35.4, p=3.8×10−11). These findings underscore the importance of the role and time-dependent nature of somatic events in the etiology of cancer and other late-onset diseases. PMID:22561519

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

    International Nuclear Information System (INIS)

    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; Yoo, Young-Do; Park, Won-Bong; Cho, Myung-Haing; Park, Gil Hong; Lee, Kee-Ho

    2010-01-01

    Research highlights: → 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. → The telomere length of unsensitized clones was reduced, as was that of most sensitized clones. → The unsensitized clones did not show chromosome end fusion which was noted in all sensitized clones. → P53 status is not associated with the occurrence of unsensitized clone. → 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 -/- cells, about 22% of clones were unresponsive to radiosensitization even though telomerase action was inhibited. The telomere lengths of unsensitized mTERC -/- 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.

  6. High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies

    Directory of Open Access Journals (Sweden)

    Frank A Giordano

    Full Text Available Gene transfer to hematopoietic stem cells with integrating vectors not only allows sustained correction of monogenic diseases but also tracking of individual clones in vivo. Quantitative real-time PCR (qPCR has been shown to be an accurate method to quantify individual stem cell clones, yet due to frequently limited amounts of target material (especially in clinical studies, it is not useful for large-scale analyses. To explore whether vector integration site (IS recovery techniques may be suitable to describe clonal contributions if combined with next-generation sequencing techniques, we designed artificial ISs of different sizes which were mixed to simulate defined clonal situations in clinical settings. We subjected all mixes to either linear amplification–mediated PCR (LAM-PCR or nonrestrictive LAM-PCR (nrLAM-PCR, both combined with 454 sequencing. We showed that nrLAM-PCR/454-detected clonality allows estimating qPCR-detected clonality in vitro. We then followed the kinetics of two clones detected in a patient enrolled in a clinical gene therapy trial using both, nrLAM-PCR/454 and qPCR and also saw nrLAM-PCR/454 to correlate to qPCR-measured clonal contributions. The method presented here displays a feasible high-throughput strategy to monitor clonality in clinical gene therapy trials is at hand.

  7. Plant Clonal Integration Mediates the Horizontal Redistribution of Soil Resources, Benefiting Neighboring Plants.

    Science.gov (United States)

    Ye, Xue-Hua; Zhang, Ya-Lin; Liu, Zhi-Lan; Gao, Shu-Qin; Song, Yao-Bin; Liu, Feng-Hong; Dong, Ming

    2016-01-01

    Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor) microsite could be translocated within a clonal network, released into different (recipient) microsites and subsequently used by neighbor plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbors. The isotopes [(15)N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighboring A. ordosica, which increased growth of the neighboring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighboring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes.

  8. Plant clonal integration mediates the horizontal redistribution of soil resources, benefiting neighbouring plants

    Directory of Open Access Journals (Sweden)

    Xuehua eYe

    2016-02-01

    Full Text Available Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor microsite could be translocated within a clonal network, released into different (recipient microsites and subsequently used by neighbour plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbours. The isotopes [15N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighbouring A. ordosica, which increased growth of the neighbouring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighbouring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes.

  9. 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.

  10. New generation expandable sand screens

    OpenAIRE

    Syltøy, Christer

    2014-01-01

    Master's thesis in Petroleum engineering This thesis aims to give a general insight into sand control and various sorts of sand control measures and applications of sand control tools. Special focus will be given to expandable sand screens – a technology which came about in the late 1990’s through the use of flexible, expandable tubulars as base pipe in sand screens. More specifically Darcy’s Hydraulic Endurance Screens, a compliant sand screen system using hydraulic activation, and the fu...

  11. Neutrinos in an expanding Universe

    International Nuclear Information System (INIS)

    Wigmans, Richard

    2015-01-01

    The Universe contains several billion neutrinos for each nucleon. In this paper, we follow the history of these relic neutrinos as the Universe expanded. At present, their typical velocity is a few hundred km/s and, therefore, their spectra are affected by gravitational forces. This may have led to a phenomenon that could explain two of todays great mysteries: The large-scale structure of the Universe and the increasing rate at which it expands. (paper)

  12. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    OpenAIRE

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

  13. Production and Characterization of Femtosecond-Laser-Induced Air Plasma

    National Research Council Canada - National Science Library

    Armbruster, David R

    2008-01-01

    .... A beam expander was used to expand the beam to a diameter of approximately 6.5 mm, and the beam was focused through a 25 mm focal length achromatic lens to produce laser-induced plasma in ambient air...

  14. [Lymphocytic Clonal Expansion in Adult Patients with Epstein-Barr Virus-Associated Lymphoproliferative Disease].

    Science.gov (United States)

    Zhong, Feng-Luan; Zhang, Hong-Yu; Zhang, Qian; Feng, Jia; Zhang, Wen-Li; Xu, Lei; Xu, Hai-Chan; Wen, Juan-Juan; Meng, Qing-Xiang

    2017-12-01

    To explore the lymphocytic clonal expansion in adult patients with Epstein-Barr virus-associated lymphoproliferative diseases (EBV+LPD), and to investigate the experimental methods for EBV+LPD cells so as to provide a more objective measure for the diagnosis, classification and prognosis in the early stage of this disease. Peripheral blood samples from 5 patients with EBV+LPD, 4 patients with adult infectious mononucleosis(IM) as negative control and 3 patients with acute NK-cell leukemia(ANKL) as positive control were collected. Prior to immunochemotherapy, viral loads and clonality were analysed by flow cytometry (FCM), T cell receptor gene rearrangement (TCR) was detected by real-time polymerase chain reaction (RT-PCR), and diversity of EB virus terminal repeat (EBV-TR) was detected by Southern blot. FCM showed only 1 case with clonal TCRVβ in 5 patients with EBV+LPD, TCR clonal expansion could be detected both in patients with IM(4 of 4) and 4 patients with EBV+LPD(4 of 5), Out of patients with EBV+LPD, 1 patient displayed a monoclonal band and 2 patients showed oligoclonal bands when detecting EBV-TR by southen blot. Detecting the diversity of EBV-TR by Southern blot may be the most objective way to reflex clonal transformation of EBV+LPD, which is of great benefit to the diagnosis, classification and prognosis in the early stage of this disease.

  15. 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.

  16. Plasmatron with expanding channel of outlet electrode and its applications

    International Nuclear Information System (INIS)

    Chinnov, V.F.; Isakajev, E.Kh.; Ivanov, P.P.; Sinkevich, O.A.; Tyuftyaev, A.S.

    2000-01-01

    A serious industrial application is found for the plasmatron with expanding channel of outlet electrode - hardening and nitriding surface treatment of railway wheels. Several plasma installations are under operation at the engine houses of Moscow Railways. More than 12 000 wheel sets have been treated up to now. Results are evident: wheel life doubles due to plasma treatment. The plasmatron developed essentially in an empiric way is now under heavy investigation both theoretically and experimentally. High precision measurements of nitrogen emission spectra are expected to be used directly for accurate calculation of radiation heat loss term in a quasi-one dimensional flow code. (Authors)

  17. Variation of functional clonal traits along elevation in two fern species

    International Nuclear Information System (INIS)

    Song, Y.B.; Chen, L.Y.; Xiong, W.

    2015-01-01

    Phenotypical plasticity is generally considered among adaptive strategies by which plants can cope with environmental variation in space and time. Although much is known about plasticity in seed plants in terms of functional clonal traits while little is known about ferns. Variation of functional clonal traits of two ferns Dicranopteris dichotoma and Diplopterygium glaucum among plots differing in elevation in a subtropical evergreen broad-leaved forest in southern China was investigated. Along with elevation increasing the two fern species showed similar variation pattern of functional clonal traits: stable spacer length, increasing specific spacer length and decreasing spacer weight per ramet and specific spacer weight. The two ferns species had similar variation pattern of ramet performance traits but different variation pattern of ramet population properties. These results suggest an evolutionary trade-off between functions of foraging for and storing of resources in the two ferns, with a functional preference for the foraging in response to environmental change. (author)

  18. Usefullness of IGH/TCR PCR studies in lymphoproliferative disorders with inconclusive clonality by flow cytometry.

    Science.gov (United States)

    Ribera, Jordi; Zamora, Lurdes; Juncà, Jordi; Rodríguez, Inés; Marcé, Silvia; Cabezón, Marta; Millá, Fuensanta

    2013-07-25

    In up to 5-15% of studies of lymphoproliferative disorders (LPD) flow cytometry (FCM) or immunomorphologic methods cannot discriminate malignant from reactive processes. The aim of this work was to determine the usefulness of PCR for solving these diagnostic uncertainties. We analyzed IGH and TCRγ genes by PCR in 106 samples with inconclusive FCM results. A clonal result was registered in 36/106 studies, with a LPD being confirmed in 27 (75%) of these cases. Specifically, 9/9 IGH clonal and 16/25 TCRγ clonal results were finally diagnosed with LPD. Additionally, 2 clonal TCRγ samples with suspicion of undefined LPD were finally diagnosed with T LPD. Although polyclonal results were obtained in 47 of the cases studied (38 IGH and 9 TCRγ), hematologic neoplasms were diagnosed in 4/38 IGH polyclonal and in 1/9 TCRγ polyclonal studies. There were also 14 PCR polyclonal results (4 IGH, 10 TCRγ), albeit non-conclusive. Of these, 2/4 were eventually diagnosed with B-cell lymphoma and 3/10 with T-cell LPD. In 8 IGH samples the results of PCR techniques were non-informative but in 3/8 cases a B lymphoma was finally confirmed. We concluded that PCR is a useful technique to identify LPD when FCM is inconclusive. A PCR clonal B result is indicative of malignancy but IGH polyclonal and non-conclusive results do not exclude lymphoid neoplasms. Interpretation of T-cell clonality should be based on all the available clinical and analytical data. © 2013 Clinical Cytometry Society. Copyright © 2013 Clinical Cytometry Society.

  19. 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

  20. PPARγ ligand production is tightly linked to clonal expansion during initiation of adipocyte differentiation

    DEFF Research Database (Denmark)

    Hallenborg, Philip; Petersen, Rasmus Koefoed; Feddersen, Søren

    2014-01-01

    of differentiation. Concomitant with agonist production, murine fibroblasts undergo two rounds of mitosis referred to as mitotic clonal expansion. Here we show that mouse embryonic fibroblasts deficient in either of two cell cycle inhibitors, the transcription factor p53 or its target gene encoding the cyclin...... cycle inhibitory compounds decreased PPAR ligand production in differentiating 3T3-L1 preadipocytes. Furthermore, these inhibitors abolished the release of arachidonic acid induced by the hormonal cocktail initiating adipogenesis. Collectively, our results suggest that murine fibroblasts require clonal...... expansion for PPAR ligand production at the onset of adipocyte differentiation....

  1. 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

    chimeras of eGFP+Apoe-/- and Apoe-/- mouse embryos and in mice with a mosaic expression of fluorescent proteins in medial SMCs that were rendered atherosclerotic by PCSK9-induced hypercholesterolemia. Fibrous caps in aggregation chimeras were found constructed from large, endothelial-aligned layers...... 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...

  2. 'In situ' expanded graphite extinguishant

    International Nuclear Information System (INIS)

    Cao Qixin; Shou Yuemei; He Bangrong

    1987-01-01

    This report is concerning the development of the extinguishant for sodium fire and the investigation of its extinguishing property. The experiment result shows that 'in situ' expanded graphite developed by the authors is a kind of extinguishant which extinguishes sodium fire quickly and effectively and has no environment pollution during use and the amount of usage is little

  3. EFFECT OF INCORPORATING EXPANDED POLYSTYRENE ...

    African Journals Online (AJOL)

    2012-11-03

    Nov 3, 2012 ... Incorporating expanded polystyrene granules in concrete matrix can produce lightweight polystyrene aggregate concrete of ... structure. [1] reported that the standard workability tests are not suitable for the polystyrene aggregate concrete since they are sensitive to the unit weight of concrete. [2] made ...

  4. Expanding the Universe of Education.

    Science.gov (United States)

    Parsons, Elizabeth

    1996-01-01

    Definitions of "education" and "rural" are debunked and expanded. The three major tasks of rural education are educating people to understand their own needs, the unavoidable changes that will transform rural Australia within their lifetimes, and the range of technologies that can enhance their well-being. Presents a strategy…

  5. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

    NARCIS (Netherlands)

    Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

    2015-01-01

    We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

  6. Clinical significance of T-cell clonality in mycosis fungoides and other cutaneous T-cell lymphomas

    NARCIS (Netherlands)

    Muche, Joachim Marcus

    2010-01-01

    The purpose of this thesis was to obtain more insight into T-cell clonality in blood of mycosis fungoides (MF) patients. Investigation of the frequency of blood T-cell clonality clearly indicated early dissemination of neoplastic T-cells into skin and blood as a sign of physiological recirculation.

  7. Stability of stagnation via an expanding accretion shock wave

    International Nuclear Information System (INIS)

    Velikovich, A. L.; Giuliani, J. L.; Murakami, M.; Taylor, B. D.; 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 [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.

  8. 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.

  9. Stability of stagnation via an expanding accretion shock wave

    Science.gov (United States)

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

    2016-05-01

    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 [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.

  10. Langerhans cell sarcoma following marginal zone lymphoma: expanding the knowledge on mature B cell plasticity.

    Science.gov (United States)

    Ambrosio, Maria Raffaella; De Falco, Giulia; Rocca, Bruno Jim; Barone, Aurora; Amato, Teresa; Bellan, Cristiana; Lazzi, Stefano; Leoncini, Lorenzo

    2015-10-01

    The concept of unidirectional differentiation of the haematopoietic stem cell has been challenged after recent findings that human B cell progenitors and even mature B cells can be reprogrammed into histiocytic/dendritic cells by altering expression of lineage-associated transcription factors. The conversion of mature B cell lymphomas to Langerhans cell neoplasms is not well documented. Three previous reports have described clonally related follicular lymphoma and Langerhans cell tumours, whereas no case has been published of clonally related marginal zone lymphoma and Langerhans cell sarcoma. We describe the case of a 77-year-old patient who developed a Langerhans cell sarcoma and 6 years later a nodal marginal zone lymphoma. Mutation status examination showed 100 % gene identity to the germline sequence, suggesting direct trans-differentiation or dedifferentiation of the nodal marginal zone lymphoma to the Langerhans cell sarcoma rather than a common progenitor. We found inactivation of paired box 5 (PAX-5) in the lymphoma cells by methylation, along with duplication of part of the long arm of chromosomes 16 and 17 in the sarcoma cells. The absence of PAX-5 could have triggered B cells to differentiate into macrophages and dendritic cells. On the other hand, chromosomal imbalances might have activated genes involved in myeloid lineage maturation, transcription activation and oncogenesis. We hypothesize that this occurred because of previous therapies for nodal marginal zone lymphoma. Better understanding of this phenomenon may help in unravelling the molecular interplay between transcription factors during haematopoietic lineage commitment and may expand the spectrum of clonally related mature B cell neoplasms and Langerhans cell tumours.

  11. Expanding the Game Design Space

    DEFF Research Database (Denmark)

    Larsen, Lasse Juel; Majgaard, Gunver

    2016-01-01

    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...... 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....... 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...

  12. Seal-less cryogenic expander

    International Nuclear Information System (INIS)

    Faria, L.E.; Christopher, E.H.

    1987-01-01

    In an expander for use in a split Stirling cycle refrigeration system of the type wherein a displacer moves with reciprocating motion inside an expander housing, and wherein a plunger force and a regenerator force are formed on the displacer, the plunger force cyclically varying and having a time of minimum and maximum plunger force amplitude, and the regenerator force cyclically varying and having a time of minimum and maximum regenerator force amplitude, the improvement is described comprising: (a) means for maintaining displacer forces, such that the maximum plunger force amplitude is substantially equal to the maximum regenerator force amplitude; and (b) means for adjusting a time difference, the time difference being the time between the time of maximum plunger force and the time of maximum regenerator force such that a measure of the cooling power of the refrigeration system is maximized

  13. In vitro clonal propagation of the neem tree ( Azadirachta indica A ...

    African Journals Online (AJOL)

    In vitro clonal propagation of the neem tree (Azadirachta indica A. Juss.) M Shahin-uz-zaman, M Ashrafuzzaman, MS Haque, LN Luna. Abstract. A study was conducted with root and shoot tip explants of neem to develop an efficient protocol of regeneration. Shoot tips and root tips from 10 - 20 days old seedlings of neem ...

  14. [Chronologic analysis of clonal evolution in acquired aplastic anemia and sMDS].

    Science.gov (United States)

    Yoshizato, Tetsuichi

    2016-04-01

    Acquired aplastic anemia (AA) is a prototype of idiopathic bone marrow failure, which is caused by immune-mediated destruction of hematopoietic progenitors but is also characterized by frequent evolution to clonal myeloid disorders, such as myelodysplastic syndromes or acute myeloid leukemia. However, the chronological behavior of the clonality and its link to myelodysplastic syndrome or acute myeloid leukemia has not been fully explored. To define the clonality and its chronological behavior in AA, we performed targeted sequencing (N=439) in cases with AA. Somatic mutations were detected in 1/3 of our cases. Mutations were most frequently found in DNMT3A, followed by BCOR, PIGA and ASXL1. The prevalence of mutations increased with age. The clone sizes in DNMT3A and ASXL1 were prone to increase, whereas those of BCOR and PIGA were more likely to decrease or remain stable. Mutations in PIGA, BCOR and BCORL1 correlated with a better response to immunosuppressive therapy and more favorable survival. On the other hand, other mutations were associated with worse outcomes. The chronological dynamics of clonality showed marked variability and were not necessarily associated with prognosis.

  15. Epigenetic memory as a basis for intelligent behavior in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Latzel, Vít; González, Alejandra Pilar Rendina; Rosenthal, J.

    2016-01-01

    Roč. 7, AUG 31 (2016), s. 1-7, č. článku 1354. ISSN 1664-462X R&D Projects: GA ČR(CZ) GA14-06802S Institutional support: RVO:67985939 Keywords : epigenetic variability * memory * clonal plant s Subject RIV: EF - Botanics Impact factor: 4.298, year: 2016

  16. Descriptions of new varieties recently distributed from the Citrus Clonal Protection Program

    Science.gov (United States)

    The Citrus Clonal Protection Program (CCPP) is operated through the Department of Plant Pathology and Microbiology at University of California (UC) Riverside and is funded in large part by The California Citrus Research Board (CRB). The CCPP processes citrus propagative material in two phases. First...

  17. Clonal genotype of Geomyces destructans among bats with White Nose Syndrome, New York, USA.

    Science.gov (United States)

    Rajkumar, Sunanda S; Li, Xiaojiang; Rudd, Robert J; Okoniewski, Joseph C; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2011-07-01

    The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008-2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

  18. Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA

    OpenAIRE

    Rajkumar, Sunanda S.; Li, Xiaojiang; Rudd, Robert J.; Okoniewski, Joseph C.; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2011-01-01

    The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008–2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

  19. 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...

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

    Science.gov (United States)

    Jacobsen, Kevin; Lund, Marie Bek; Shim, Jeong; Gunnersen, Stine; Füchtbauer, Ernst-Martin; Kjolby, Mads; Carramolino, Laura; Bentzon, Jacob Fog

    2017-10-05

    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 chimeras of eGFP+Apoe-/- and Apoe-/- mouse embryos and in mice with a mosaic expression of fluorescent proteins in medial SMCs that were rendered atherosclerotic by PCSK9-induced hypercholesterolemia. Fibrous caps in aggregation chimeras were found constructed from large, endothelial-aligned layers 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 structure showed that a low number of local medial SMCs partake in atherosclerosis and that single medial SMCs can produce several different SMC phenotypes in plaque. The combined results show that few medial SMCs proliferate to form the entire phenotypically heterogeneous plaque SMC population in murine atherosclerosis.

  1. CLO-PLA: the database of clonal and bud bank traits of Central European flora

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; de Bello, F.

    2009-01-01

    Roč. 20, č. 3 (2009), s. 511-516 ISSN 1100-9233 R&D Projects: GA ČR(CZ) GA526/06/0723 Institutional research plan: CEZ:AV0Z60050516 Keywords : bud bank * clonal traits * database Subject RIV: EF - Botanics Impact factor: 2.376, year: 2009

  2. Clonal splitters and integrators in harsh environments of the Trans-Himalaya

    Czech Academy of Sciences Publication Activity Database

    Klimeš, Leoš

    2008-01-01

    Roč. 22, č. 3 (2008), s. 351-367 ISSN 0269-7653 R&D Projects: GA ČR GA206/03/1219 Institutional research plan: CEZ:AV0Z60050516 Keywords : Ladakh * altitude * clonal growth Subject RIV: EF - Botanics Impact factor: 3.448, year: 2008

  3. Analysis of the clonal repertoire of gene-corrected cells in gene therapy.

    Science.gov (United States)

    Paruzynski, Anna; Glimm, Hanno; Schmidt, Manfred; Kalle, Christof von

    2012-01-01

    Gene therapy-based clinical phase I/II studies using integrating retroviral vectors could successfully treat different monogenetic inherited diseases. However, with increased efficiency of this therapy, severe side effects occurred in various gene therapy trials. In all cases, integration of the vector close to or within a proto-oncogene contributed substantially to the development of the malignancies. Thus, the in-depth analysis of integration site patterns is of high importance to uncover potential clonal outgrowth and to assess the safety of gene transfer vectors and gene therapy protocols. The standard and nonrestrictive linear amplification-mediated PCR (nrLAM-PCR) in combination with high-throughput sequencing exhibits technologies that allow to comprehensively analyze the clonal repertoire of gene-corrected cells and to assess the safety of the used vector system at an early stage on the molecular level. It enables clarifying the biological consequences of the vector system on the fate of the transduced cell. Furthermore, the downstream performance of real-time PCR allows a quantitative estimation of the clonality of individual cells and their clonal progeny. Here, we present a guideline that should allow researchers to perform comprehensive integration site analysis in preclinical and clinical studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Production and carbon allocation in a clonal Eucalyptus plantation with water and nutrient manipulations

    Science.gov (United States)

    Jose Luiz Stape; Dan Binkley; Michael G. Ryan

    2008-01-01

    We examined resource limitations on growth and carbon allocation in a fast-growing, clonal plantation of Eucalyptus grandis urophylla in Brazil by characterizing responses to annual rainfall, and response to irrigation and fertililization for 2 years. Productivity measures included gross primary production (GPP), total belowground carbon allocation (...

  5. 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

  6. 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...

  7. Searching for the relevance of clonal and bud bank traits across floras and communities

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; de Bello, Francesco; Herben, Tomáš

    2011-01-01

    Roč. 46, 2-3 (2011), 109-115 ISSN 1211-9520 R&D Projects: GA ČR GA526/09/0963; GA ČR GA526/07/0808 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal growth * bud bank * database Subject RIV: EF - Botanics Impact factor: 1.500, year: 2011

  8. Age and distribution of an evergreen clonal shrub in the Coweeta basin: Rhododendron maximum L

    Science.gov (United States)

    Katherine J. Elliott; James M. Vose

    2012-01-01

    Rhododendron maximum L. is an evergreen, clonal shrub that forms a dominant sub-canopy layer and is a key species in southern Appalachian forests. We investigated the age and distribution of R. maximum across the Coweeta Basin, a 1626 ha watershed in western North Carolina. We selected 16 perennial, second-order streams and used a Global Positioning System to establish...

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

    NARCIS (Netherlands)

    Jethwa, Alexander; Hüllein, Jennifer; Stolz, Tatjana; Blume, Carolin; Sellner, Leopold; Jauch, Anna; Sill, Martin; Kater, Arnon P.; te Raa, G. Doreen; Geisler, Christian; van Oers, Marinus; Dietrich, Sascha; Dreger, Peter; Ho, Anthony D.; Paruzynski, Anna; Schmidt, Manfred; von Kalle, Christof; Glimm, Hanno; Zenz, Thorsten

    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

  10. 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

  11. 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.

  12. Rapid clonal analysis of recurrent tuberculosis by direct MIRU-VNTR typing on stored isolates

    Directory of Open Access Journals (Sweden)

    de Viedma Darío

    2007-07-01

    Full Text Available Abstract Background The application of molecular tools to the analysis of tuberculosis has revealed examples of clonal complexity, such as exogenous reinfection, coinfection, microevolution or compartmentalization. The detection of clonal heterogeneity by standard genotyping approaches is laborious and often requires expertise. This restricts the rapid availability of Mycobacterium tuberculosis (MTB genotypes for clinical or therapeutic decision-making. A new PCR-based technique, MIRU-VNTR, has made it possible to genotype MTB in a time frame close to real-time fingerprinting. Our purpose was to evaluate the capacity of this technique to provide clinicians with a rapid discrimination between reactivation and exogenous reinfection and whether MIRU-VNTR makes it possible to obtain data directly from stored MTB isolates from recurrent episodes. Results We detected differences, between the MIRUtypes of recurrent isolates in 38.5% (5/13 of the cases studied. These included cases of i exogenous reinfection, often with more resistant strains, ii likely examples of microevolution, leading to the appearance of new clonal variants and iii a combination of microevolution, coinfection and competition. Conclusion MIRU-VNTR rapidly obtained clinically useful genotyping data in a challenging situation, directly from stored MTB isolates without subculturing them or purifying their DNA. Our results also mean that MIRU-VNTR could be applied for easy, rapid and affordable massive screening of collections of stored MTB isolates, which could establish the real dimension of clonal heterogeneity in MTB infection.

  13. 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

  14. 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 (ML...

  15. 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...

  16. Implications of self/non-self discrimination for spatial patterning of clonal plants

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Novoplansky, A.

    2008-01-01

    Roč. 22, č. 3 (2008), s. 337-350 ISSN 0269-7653 R&D Projects: GA ČR GA206/06/0098 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal plants * clustering * competition * facilitation Subject RIV: EF - Botanics Impact factor: 3.448, year: 2008

  17. Physiological integration affects growth form and competitive ability in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš

    2004-01-01

    Roč. 18, - (2004), s. 493-520 ISSN 0269-7653 R&D Projects: GA ČR(CZ) GA206/02/0953 Institutional research plan: CEZ:AV0Z6005908 Keywords : competitive ability * Physiological integration * clonal plants Subject RIV: EF - Botanics Impact factor: 3.215, year: 2004

  18. Clonal diversity and genetic differentiation of Maianthemum bifolium among forest fragments of different age

    NARCIS (Netherlands)

    Arens, P.F.P.; Grashof-Bokdam, C.J.; Sluis, van der T.; Smulders, M.J.M.

    2005-01-01

    Maianthemum bifolium Schmidt (May Lily) is a woodland species with low colonisation ability and high demands for seedling establishment conditions. To study the colonisation process, we analysed the clonal organisation and population structure of Maianthemum bifolium populations in a number of

  19. OCCURRENCE OF ANTIBIOTIC-RESISTANT UROPATHOGENIC ESCHERICHIA COLI CLONAL GROUP A IN WASTEWATER EFFLUENTS

    Science.gov (United States)

    Isolates of Escherichia coli belonging to clonal group A (CGA), a recently described disseminated cause of drug-resistant urinary tract infections in humans, were present in four of seven sewage effluents collected from geographically dispersed areas of the United States. ...

  20. Reproduction by seed and clonality in plants: correlated syndromes or independent strategies?

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Tackenberg, O.; Klimešová, Jitka

    2016-01-01

    Roč. 104, č. 6 (2016), s. 1696-1706 ISSN 0022-0477 R&D Projects: GA ČR(CZ) GA16-19245S; GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : bud bank traits * clonal traits * CLOPLA database * dispersal * phylogenetic regressions Subject RIV: EF - Botanics Impact factor: 5.813, year: 2016

  1. Clonal growth forms in Arctic plants and their habitat preferences: a study from Petuniabukta, Spitsbergen

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Doležal, Jiří; Prach, Karel; Košnar, J.

    2012-01-01

    Roč. 33, č. 4 (2012), 421-442 ISSN 0138-0338 R&D Projects: GA MŠk LA341; GA AV ČR IAA600050802 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : clonality * plants * Arctic Subject RIV: EH - Ecology, Behaviour Impact factor: 0.745, year: 2012

  2. 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...

  3. DISRUPTIVE TECHNOLOGIES: AN EXPANDED VIEW

    OpenAIRE

    JAMES M. UTTERBACK; HAPPY J. ACEE

    2005-01-01

    The term "disruptive technology" as coined by Christensen (1997, The Innovator's Dilemma; How New Technologies Cause Great Firms to Fail. Harvard Business School Press) refers to a new technology having lower cost and performance measured by traditional criteria, but having higher ancillary performance. Christensen finds that disruptive technologies may enter and expand emerging market niches, improving with time and ultimately attacking established products in their traditional markets. This...

  4. Entropy in an expanding universe

    International Nuclear Information System (INIS)

    Frautschi, S.

    1982-01-01

    The question of how the observed evolution of organized structures from initial chaos in the expanding universe can be reconciled with the laws of statistical mechanics is studied, with emphasis on effects of the expansion and gravity. Some major sources of entropy increase are listed. An expanding causal region is defined in which the entropy, though increasing, tends to fall further and further behind its maximum possible value, thus allowing for the development of order. The related questions of whether entropy will continue increasing without limit in the future, and whether such increase in the form of Hawking radiation or radiation from positronium might enable life to maintain itself permanently, are considered. Attempts to find a scheme for preserving life based on solid structures fail because events such as quantum tunneling recurrently disorganize matter on a very long but fixed time scale, whereas all energy sources slow down progressively in an expanding universe. However, there remains hope that other modes of life capable of maintaining themselves permanently can be found

  5. Multifragment disintegrations of expanding nuclear systems

    International Nuclear Information System (INIS)

    Gelbke, K.

    1993-01-01

    Two phase transitions are expected to exist in bulk nuclear matter: a liquid-gas phase transition and a deconfinement transition to a quark-gluon plasma. In studies of nucleus-nucleus collisions, conditions similar to those pertaining to phase transitions in infinite systems can be created, but the fundamental problem yet to be solved is the identification of remnant signatures uniquely related to either of these phase transitions. Nuclear systems at densities and temperatures corresponding to the liquid-gas coexistence region can be produced in intermediate energy nucleus-nucleus collisions; they are expected to decay into many intermediate mass fragments (IMF's: Z=3-20). Recent investigations with low-threshold electronic 4π detector arrays have firmly established the occurrence of multifragment disintegrations of hot nuclear systems and allowed to challenge various theoretical approaches. In this talk, an overview of pertinent experimental results on multifragmentation will be presented and discussed. it will be shown that current microscopic transport theories designed to treat the growth of density fluctuations predict fragment multiplicities much smaller than observed experimentally. Measurements of the time scales of fragment formation are consistent with statistical model calculations for expanding hot nuclear system which indicate that fragments may form during a rather narrow time interval after the system has cooled and expanded to a density below that of normal nuclear matter. The expansion rate (and hence the fragment multiplicity) is sensitive to the equation of state (EOS). However, a number of recent results provide increasing evidence that current theoretical treatments need to be refined to allow an experimental determination of the EOS

  6. High density plasma gun generates plasmas at 190 kilometers per second

    Science.gov (United States)

    Espy, P. N.

    1971-01-01

    Gun has thin metal foil disc which positions or localizes gas to be ionized during electrical discharge cycle, overcoming major limiting factor in obtaining such plasmas. Expanding plasma front travels at 190 km/sec, compared to plasmas of 50 to 60 km/sec previously achieved.

  7. 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.

  8. High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas.

    Science.gov (United States)

    Henrich, Manfred; Scheffold, Svenja; Hecht, Werner; Reinacher, Manfred

    2018-06-01

    Analysis of clonality is gaining importance in diagnosing lymphomas in veterinary medicine. Usually, PCR for the analysis of antigen receptor rearrangement (PARR) is followed by electrophoretic separation of the PCR products. Aim of this study was to test the feasibility of HRM for the assessment of clonality in B-cell lymphomas of cats. High resolution melting analysis differentiates PCR products by their different melting point using the decrease in fluorescence of an intercalating dye during melting of the PCR product. Additionally, the method is easy to use with no post-PCR manipulation of the samples. Forty-seven feline B-cell lymphomas and 31 reactive lymphatic proliferations of cats were investigated by PARR followed either by capillary electrophoresis or an HRM assay. To objectify the interpretation of the HRM results a recently published mathematical approach was applied to the melting curve. To overcome discrepancies between the visual interpretation and the mathematical approach, the latter was modified to include testing of reproducibility and recognition of pseudoclonality. In 11 of 47 lymphoma cases clonal populations were detectable by HRM assay compared to 14 of 47 lymphomas in which clonal populations were detected by capillary electrophoresis assay. Neither of the methods showed a clonal pattern in any of the reactive samples. However, the HRM assay showed a unique pattern in cases of follicular lymphatic hyperplasia that had no corresponding pattern in capillary electrophoresis. The capillary electrophoresis assay could identify 3 lymphomas that were not detected by the HRM assay and is therefore regarded superior to the HRM assay. The comparison however, was hampered by the overall bad performance of the PARR, that might be the consequence of insufficient primer binding due to somatic hypermutation of the binding sites during antigen stimulated proliferation of the B lymphocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Veronika Tchesnokova

    Full Text Available 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. 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.

  11. 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

  12. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

    Science.gov (United States)

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

    2016-10-15

    Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

  13. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  14. Plasma Physics Applied (New Book)

    Science.gov (United States)

    Grabbe, Crockett

    2007-03-01

    0.5cm Plasma physics applications are one of the most rapidly growing fields in engineering & applied science today. The last decade alone has seen the rapid emergence of new applications such as dusty plasmas in the semiconductor and microchip industries, and plasma TVs. In addition, this last decade saw the achievement of the 50-year Lawson breakeven condition for fusion. With new discoveries in space plasma physics and applications to spacecraft for worldwide communication and space weather, as well as new applications being discovered, this diversity is always expanding. The new book Plasma Physics Applied reviews developments in several of these areas. Chapter 1 reviews the content and its authors, and is followed by a more comprehensive review of plasma physics applications in general in Chapter 2. Plasma applications in combustion and environmental uses are presented in Chapter 3. Lightning effects in planetary magnetospheres and potential application are described in Chapter 4. The area of dusty plasmas in both industrial and space plasmas and their applications are reviewed in Chapter 5. The particular area of Coulomb clusters in dusty plasmas is presented in Chapter 6. The variety of approaches to plasma confinement in magnetic devices for fusion are laid out in Chapter 7. Finally, an overview of plasma accelerator developments and their applications are presented in Chapter 8.

  15. Wiggler magnetic field assisted third harmonic generation in expanding clusters

    Science.gov (United States)

    Vij, Shivani

    2018-04-01

    A simple theoretical model is constructed to study the wiggler magnetic field assisted third harmonic generation of intense short pulse laser in a cluster in its expanding phase. The ponderomotive force of laser causes density perturbations in cluster electron density which couples with wiggler magnetic field to produce a nonlinear current that generates transverse third harmonic. An intense short pulse laser propagating through a gas embedded with atomic clusters, converts it into hot plasma balls via tunnel ionization. Initially, the electron plasma frequency inside the clusters ω pe > \\sqrt{3}{ω }1 (with ω 1 being the frequency of the laser). As the cluster expands under Coulomb force and hydrodynamic pressure, ω pe decreases to \\sqrt{3}{ω }1. At this time, there is resonant enhancement in the efficiency of the third harmonic generation. The efficiency of third harmonic generation is enhanced due to cluster plasmon resonance and by phase matching due to wiggler magnetic field. The effect of cluster size on the expansion rate is studied to observe that the clusters of different radii would expand differently. The impact of laser intensity and wiggler magnetic field on the efficiency of third harmonic generation is also explored.

  16. CONTRIBUTIONS OF SEXUAL AND ASEXUAL REPRODUCTION TO POPULATION STRUCTURE IN THE CLONAL SOFT CORAL, ALCYONIUM RUDYI.

    Science.gov (United States)

    McFadden, Catherine S

    1997-02-01

    Numerous studies of population structure in sessile clonal marine invertebrates have demonstrated low genotypic diversity and nonequilibrium genotype frequencies within local populations that are monopolized by relatively few, highly replicated genets. All of the species studied to date produce planktonic sexual propagules capable of dispersing long distances; despite local genotypic disequilibria, populations are often panmictic over large geographic areas. The population structure paradigm these species represent may not be typical of the majority of clonal invertebrate groups, however, which are believed to produce highly philopatric sexual propagules. I used allozyme variation to examine the population structure of the temperate soft coral, Alcyonium rudyi, a typical clonal species whose sexually produced larvae and asexually produced ramets both have very low dispersal capabilities. Like other clonal plants and invertebrates, the local population dynamics of A. rudyi are dominated by asexual reproduction, and recruitment of new sexually produced genets occurs infrequently. As expected from its philopatric larval stage, estimates of genetic differentiation among populations of A. rudyi were highly significant at all spatial scales examined (mean θ = 0.300 among 20 populations spanning a 1100-km range), suggesting that genetic exchange seldom occurs among populations separated by as little as a few hundred meters. Mapping of multilocus allozyme genotypes within a dense aggregation of A. rudyi ramets confirmed that dispersal of asexual propagules is also very limited: members of the same genet usually remain within invertebrates, populations of A. rudyi do not appear to be dominated by a few widespread genets: estimates of genotypic diversity (G o ) within 20 geographically distinct populations did not differ from expectations for outcrossing, sexual populations. Despite theoretical suggestions that philopatric dispersal combined with typically small effective

  17. Clonal expansion of T-cell receptor beta gene segment in the retrocochlear lesions of EAE mice.

    Science.gov (United States)

    Cheng, K C; Lee, K M; Yoo, T J

    1998-01-01

    It has been reported that the T cell receptor V beta 8.2 (TcrbV8.2) gene segment is predominantly expressed in encephalomyelitic T cells responding to myelin basic protein (MBP) in experimental allergic encephalomyelitis (EAE) mice. We have demonstrated retrocochlear hearing loss in EAE mice in previous studies. Administration of a monoclonal antibody specific to the T cell receptor V beta 8 (TcrbV8) subfamily prevented both this type of hearing loss and the central nerve disease. In this study, we examined the role of the TcrbV8.2 gene segment in the retrocochlear lesions of EAE mice. A clonal expression of T cell receptor beta chain gene segment (TcrbV8.2-TcrbD2-TcrbJ2.7) was identified in the retrocochlear lesions. The TcrbV8.2 gene segment appears to recombine only with TcrbJ2.1 (32.1%) and TcrbJ2.7 (67.9%) gene segments. The TcrbJ2.7 gene segment has also been previously identified as the dominant TcrbJ gene in the lymph nodes of EAE mice. Only TcrbD2, with a length of 4 amino acids, was observed recombining with these TcrbV8.2 sequences. G and C nucleotides are predominantly expressed at the N regions between the V-D and D-J junctions. This dominant TcrbV gene segment (TcrbV8.2-TcrbD2-TcrbJ2.7) observed in the retrocochlear lesions has been identified in the MBP-specific T cells from the lymph nodes of EAE mice. These results suggest that a small subset of antigen-specific T cells migrate to, and expand at, the retrocochlear lesions, which leads to hearing loss.

  18. Expander for Thin-Wall Tubing

    Science.gov (United States)

    Pessin, R.

    1983-01-01

    Tool locally expands small-diameter tubes. Tube expander locally expands and deforms tube: Compressive lateral stress induced in elastomeric sleeve by squeezing axially between two metal tool parts. Adaptable to situations in which tube must have small bulge for mechanical support or flow control.

  19. Plasma turbulence

    International Nuclear Information System (INIS)

    Horton, W.

    1998-07-01

    The origin of plasma turbulence from currents and spatial gradients in plasmas is described and shown to lead to the dominant transport mechanism in many plasma regimes. A wide variety of turbulent transport mechanism exists in plasmas. In this survey the authors summarize some of the universally observed plasma transport rates

  20. Prevalence and clonal analysis of Porphyromonas gingivalis in primary endodontic infections.

    Science.gov (United States)

    Siqueira, José F; Rôças, Isabela N; Silva, Marlei G

    2008-11-01

    This study investigated the prevalence of Porphyromonas gingivalis in 62 teeth with primary endodontic infections by using a species-specific 16S rRNA gene-based nested polymerase chain reaction assay. P. gingivalis isolates recovered from 2 infected root canals were also analyzed for clonal diversity by using arbitrarily primed PCR. Overall, P. gingivalis was found in 48% of the samples. This species was specifically detected in 36% of canals of teeth with chronic apical periodontitis, in 46% of the cases of acute apical periodontitis, and in 67% of acute apical abscesses. P. gingivalis was significantly more frequent in abscess aspirates than in canals of teeth with chronic apical periodontitis (P abscesses, and demonstrated that different clonal types of this species can colonize the root canal in the same individual.

  1. 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......, toxins, and were assigned to agr groups. S. aureus colonization patterns ranged from rare colonization over transient colonization to persistent colonization by a single clone or a dynamic exchange of up to five clones. Production of no single virulence factor including superantigens and toxins...... 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...

  2. 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.

  3. 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.

  4. 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...... 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...

  5. 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.

  6. Instability of expanding bacterial droplets.

    Science.gov (United States)

    Sokolov, Andrey; Rubio, Leonardo Dominguez; Brady, John F; Aranson, Igor S

    2018-04-03

    Suspensions of motile bacteria or synthetic microswimmers, termed active matter, manifest a remarkable propensity for self-organization, and formation of large-scale coherent structures. Most active matter research deals with almost homogeneous in space systems and little is known about the dynamics of strongly heterogeneous active matter. Here we report on experimental and theoretical studies on the expansion of highly concentrated bacterial droplets into an ambient bacteria-free fluid. The droplet is formed beneath a rapidly rotating solid macroscopic particle inserted in the suspension. We observe vigorous instability of the droplet reminiscent of a violent explosion. The phenomenon is explained in terms of continuum first-principle theory based on the swim pressure concept. Our findings provide insights into the dynamics of active matter with strong density gradients and significantly expand the scope of experimental and analytic tools for control and manipulation of active systems.

  7. 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.

  8. SHEAR ACCELERATION IN EXPANDING FLOWS

    Energy Technology Data Exchange (ETDEWEB)

    Rieger, F. M. [ZAH, Institut für Theoretische Astrophysik, Universität Heidelberg, Philosophenweg 12, D-69120 Heidelberg (Germany); Duffy, P., E-mail: frank.rieger@mpi-hd.mpg.de, E-mail: peter.duffy@ucd.ie [University College Dublin, Belfield, Dublin 4 (Ireland)

    2016-12-10

    Shear flows are naturally expected to occur in astrophysical environments and potential sites of continuous non-thermal Fermi-type particle acceleration. Here we investigate the efficiency of expanding relativistic outflows to facilitate the acceleration of energetic charged particles to higher energies. To this end, the gradual shear acceleration coefficient is derived based on an analytical treatment. The results are applied to the context of the relativistic jets from active galactic nuclei. The inferred acceleration timescale is investigated for a variety of conical flow profiles (i.e., power law, Gaussian, Fermi–Dirac) and compared to the relevant radiative and non-radiative loss timescales. The results exemplify that relativistic shear flows are capable of boosting cosmic-rays to extreme energies. Efficient electron acceleration, on the other hand, requires weak magnetic fields and may thus be accompanied by a delayed onset of particle energization and affect the overall jet appearance (e.g., core, ridge line, and limb-brightening).

  9. Nonlinear beam expander for ESNIT

    International Nuclear Information System (INIS)

    Rusthoi, D.P.; Blind, B.; Garnett, R.W.; Hanna, D.S.; Jason, A.J.; Kraus, R.H. Jr.; Neri, F.

    1994-01-01

    We describe the design of a beam-redistribution and expansion system for the Japanese Atomic Energy Research Institute (JAERI) Energy Selective Neutron Irradiation Test Facility (ESNIT). The system tailors the beam exiting a deuteron accelerator at energies from 20 to 35 MeV for deposition on a lithium neutron-production target. A uniform beam-intensity distribution in a well-defined irradiation area is inquired at the target and is achieved by the use of nonlinear elements. The design of the high-energy beam transport (HEBT) for ESNIT includes a 90 degree achromatic bend, a matching section with an energy-compacting cavity, a nonlinear beam expander, a target imager, a shielding dipole, and an rf-cavity system to add energy spread to the beam before it impinges on the target. The system meets performance requirements at multiple energies and currents, and for different spot sizes on target

  10. Establishment of dna fingerprinting in clonal tea improved cultivars from yunnan of china using issr markers

    International Nuclear Information System (INIS)

    Liu, B.Y.; Zhao, C.M.; Sun, X.M.; Jiang, H.B.

    2015-01-01

    In this study, DNA fingerprints were constructed by using ISSR markers for 20 clonal improved varieties developed by two breeding institutes in Yunnan province. Seven core ISSR primers were selected from 15 primers. A total of 110 bands were generated by PAGE with seven core primers, 93 of which were polymorphic bands, the percentage of polymorphic band (PPB) was 84.54%, and the mean value of polymorphism information content (PIC) reached 0.417; the genetic similarity coefficient of the cultivars was 0.574-0.854. The two primers, UBC835 and ISSR2, had high PIC values, and could be used to distinguish all cultivars, presenting the most efficient single primers. Among the all of primer combinations from the seven core primers, the three combinations, UBC835/UBC811, UBC835/ISSR2, and UBC835/ISSR3 showed lower similar coefficients, and more efficient in identifying the 20 improved varieties than the other primer combinations. Then these three primer combinations were further scored in 15 traditional cultivars. The results showed that UBC835/ISSR2 was the optimal primer combination, which could be used to distinguish each material among the 20 clonal improved varieties and 15 traditional cultivals. Finally, the DNA fingerprints of the 20 clonal improved varieties were constructed based on country and region code, breeding institute, core primer name and ISSR marker data. The established fingerprints could provide reliable scientific base for the protection of intellectual property right for these clonal improved varieties, and the important molecular information contained in these fingerprints would be useful for the authenticity identification and genetic relationship analysis of tea varieties. (author)

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

    Science.gov (United States)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.

    2010-01-01

    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. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between 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

  12. Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate

    OpenAIRE

    M?nzbergov?, Zuzana; Hadincov?, V?roslava

    2017-01-01

    Abstract 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 th...

  13. MIRU-VNTR allelic variability depends on Mycobacterium bovis clonal group identity.

    Science.gov (United States)

    Hauer, Amandine; Michelet, Lorraine; De Cruz, Krystel; Cochard, Thierry; Branger, Maxime; Karoui, Claudine; Henault, Sylvie; Biet, Franck; Boschiroli, María Laura

    2016-11-01

    The description of the population of M. bovis strains circulating in France from 1978 to 2013 has highlighted the discriminating power of the MLVA among predominant spoligotype groups. In the present study we aimed to characterize clonal groups via MLVA and to better understand the strain's population structure. MLVA was performed with eight MIRU-VNTR loci, most of them defined by the Venomyc European consortium. The discriminatory index of each MLVA loci was calculated for SB0120, SB0134, SB0121 and the "F4-family", the main spoligotype groups in France. Differences in global DI per spoligotype, but also by locus within each spoligotype, were observed, which strongly suggest the clonal complex nature of these major groups. These MLVA results were compared to those of other European countries where strain collections had been characterized (Spain, Portugal, Italy, Northern Ireland and Belgium). Overall, QUB 3232 and ETR D are respectively the most and the least discriminative loci, regardless of the strains geographical origin. However, marked DI differences are observed in the rest of the MIRU-VNTR loci, again highlighting that strain genetic variability in a country depends on the dominant existing clonal complexes. A web application for M. bovis, including spoligotyping and MIRU-VNTR typing data, was developed to allow inter-laboratory comparison of field isolates. In conclusion, combination of typing methods is required for M. bovis optimum discrimination and differentiation of groups of strains. Thus, the loci employed for MLVA in a country should be those which are the most discriminative for the clonal complexes which characterize their M. bovis population. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae)

    OpenAIRE

    Gaddis, Keith D.; Zukin, Helen L.; Dieterich, Inca A.; Braker, Elizabeth; Sork, Victoria L.

    2014-01-01

    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 North...

  15. 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

  16. Clonal differences in generation times of GPK epithelial cells in monolayer culture.

    Science.gov (United States)

    Riley, P A; Hola, M

    1980-01-01

    Pedigrees of cells in eight clones of guinea pig keratocyte (GPK) cells in monolayer culture were analyzed from a time-lapse film. The generation times and the position in the field of observation were recorded up to the sixth generation when the cultures were still subconfluent. Statistical analysis of the results indicates that the position in the culture has less significance than the clonal origin of the cell in determining the interval between successive mitoses.

  17. Clonal structure and variable fertilization success in Florida Keys broadcast-spawning corals

    Science.gov (United States)

    Miller, M. W.; Baums, I. B.; Pausch, R. E.; Bright, A. J.; Cameron, C. M.; Williams, D. E.; Moffitt, Z. J.; Woodley, C. M.

    2018-03-01

    Keystone reef-building corals in the Caribbean are predominantly self-incompatible broadcast spawners and a majority are threatened due to both acute adult mortality and poor recruitment. As population densities decline, concerns about fertilization limitation and effective population size in these species increase and would be further exacerbated by either high clonality or gametic incompatibility of parental genotypes. This study begins to address these concerns for two Caribbean broadcasting species by characterizing clonal structure and quantifying experimental pairwise fertilization success. Orbicella faveolata showed surprisingly high and contrasting levels of clonality between two sampled sites; Acropora palmata was previously known to be highly clonal. Individual pairwise crosses of synchronously spawning genotypes of each species were conducted by combining aliquots of gamete bundles immediately after spawning, and showed high and significant variability in fertilization success. Over half of the individual crosses of O. faveolata and about one-third of A. palmata crosses yielded ≤ 40% fertilization. Total sperm concentration was quantified in only a subset of O. faveolata crosses (range of 1-6 × 107 mL-1), but showed no correlation with fertilization success. We interpret that both parental incompatibility and individual genotypes with low-quality gametes are likely to have contributed to the variable fertilization observed with important implications for conservation. Differential fertilization success implies effective population size may be considerably smaller than hoped and population enhancement efforts need to incorporate many more parental genotypes at the patch scale to ensure successful larval production than indicated by estimates based simply on preserving levels of standing genetic diversity.

  18. The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells.

    Science.gov (United States)

    Ndifon, Wilfred; Dushoff, Jonathan

    2016-06-15

    Having a large number of sufficiently abundant T cell clones is important for adequate protection against diseases. However, as shown in this paper and elsewhere, between young adulthood and >70 y of age the effective clonal diversity of naive CD4/CD8 T cells found in human blood declines by a factor of >10. (Effective clonal diversity accounts for both the number and the abundance of T cell clones.) The causes of this observation are incompletely understood. A previous study proposed that it might result from the emergence of certain rare, replication-enhancing mutations in T cells. In this paper, we propose an even simpler explanation: that it results from the loss of T cells that have attained replicative senescence (i.e., the Hayflick limit). Stochastic numerical simulations of naive T cell population dynamics, based on experimental parameters, show that the rate of homeostatic T cell proliferation increases after the age of ∼60 y because naive T cells collectively approach replicative senescence. This leads to a sharp decline of effective clonal diversity after ∼70 y, in agreement with empirical data. A mathematical analysis predicts that, without an increase in the naive T cell proliferation rate, this decline will occur >50 yr later than empirically observed. These results are consistent with a model in which exhaustion of the proliferative capacity of naive T cells causes a sharp decline of their effective clonal diversity and imply that therapeutic potentiation of thymopoiesis might either prevent or reverse this outcome. Copyright © 2016 by The American Association of Immunologists, Inc.

  19. 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.

  20. 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.

  1. A novel genetic tool for clonal analysis of fourth chromosome mutations

    OpenAIRE

    Sousa-Neves, Rui; Schinaman, Joseph M.

    2012-01-01

    The fourth chromosome of Drosophila remains one of the most intractable regions of the fly genome to genetic analysis. The main difficulty posed to the genetic analyses of mutations on this chromosome arises from the fact that it does not undergo meiotic recombination, which makes recombination mapping impossible, and also prevents clonal analysis of mutations, a technique which relies on recombination to introduce the prerequisite recessive markers and FLP-recombinase recognition targets (FR...

  2. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  3. Genetic diversity of a clonal angiosperm near its range limit: The case of Cymodocea nodosa at the Canary Islands

    OpenAIRE

    Alberto, Filipe; Arnaud-Haond, Sophie; Duarte, Carlos M.; Serrao, Ester Álvares

    2006-01-01

    The seagrass Cymodocea nodosa forms a unique community in the Canary Islands, where it is classified as an endangered species. Biogeographic theory predicts that clonal species on islands near their distributional limits might show lower proportions of sexual (versus clonal) reproduction, lower genetic diversity, and higher differentiation. We addressed these hypotheses by comparing the genetic structure of C. nodosa from 10 meadows in the 4 main Canary Islands with 2 Iberian sites (Atlantic ...

  4. Age-related mutations associated with clonal hematopoietic expansion and malignancies.

    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

    2014-12-01

    Several genetic alterations characteristic of leukemia and lymphoma have been detected in the blood of individuals without apparent hematological malignancies. The Cancer Genome Atlas (TCGA) provides a unique resource for comprehensive discovery of mutations and genes in blood that may contribute to the clonal expansion of hematopoietic stem/progenitor cells. Here, we analyzed blood-derived sequence data from 2,728 individuals from TCGA 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 and/or 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 events that cause clonal hematopoietic expansion.

  5. Genetic diversity in three invasive clonal aquatic species in New Zealand

    Directory of Open Access Journals (Sweden)

    Sorrell Brian K

    2010-06-01

    Full Text Available Abstract Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946 and L. major (1950. Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient.

  6. Ribosomal DNA sequence analysis of different geographically distributed Aloe Vera plants: Comparison with clonally regenerated plants

    International Nuclear Information System (INIS)

    Yagi, A.; Sato, Y.; Miwa, Y.; Kabbash, A.; Moustafa, S.; Shimomura, K.; El-Bassuony, A.

    2006-01-01

    A comparison of the sequences in an internally transcribed spacer (ITS) 1 region of rDNA between clonally regenerated A.vera and same species in Japan, USA and Egypt revealed the presence of two types of nucleotide sequences, 252 and 254 bps. Based on the findings in the ITS 1 region, A.vera having 252 and 254 bps clearly showed a stable sequence similarity, suggesting high conversation of the base peak sequence in the ITS 1 region. However, frequent base substitutions in the 252 bps samples leaves that came from callus tissue and micropropagated plants were observed around the regions of nucleotide positions 66, 99 and 199-201. The minor deviation in clonally regenerated A.vera may be due to the stage of regeneration and cell specification in cases of the callus tissue. In the present study, the base peak sequence of the Its 1 region of rDNA was adopted as a molecular marker for differentiating A.vera plants from geographically distributed and clonally regenerated A.vera plants and it was suggested that the base peak substitutions in the ITS 1 region may arise from the different nutritional and environmental factors in cultivation and plant growth stages. (author)

  7. 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.

  8. 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.

  9. Different rates of defense evolution and niche preferences in clonal and nonclonal milkweeds (Asclepias spp.).

    Science.gov (United States)

    Pellissier, Loïc; Litsios, Glenn; Fishbein, Mark; Salamin, Nicolas; Agrawal, Anurag A; Rasmann, Sergio

    2016-02-01

    Given the dual role of many plant traits to tolerate both herbivore attack and abiotic stress, the climatic niche of a species should be integrated into the study of plant defense strategies. Here we investigate the impact of plant reproductive strategy and components of species' climatic niche on the rate of chemical defense evolution in the milkweeds using a common garden experiment of 49 species. We found that across Asclepias species, clonal reproduction repeatedly evolved in lower temperature conditions, in species generally producing low concentrations of a toxic defense (cardenolides). Additionally, we found that rates of cardenolide evolution were lower for clonal than for nonclonal species. We thus conclude that because the clonal strategy is based on survival, long generation times, and is associated with tolerance of herbivory, it may be an alternative to toxicity in colder ecosystems. Taken together, these results indicate that the rate of chemical defense evolution is influenced by the intersection of life-history strategy and climatic niches into which plants radiate. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  10. 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.

  11. Genetic diversity in three invasive clonal aquatic species in New Zealand

    Science.gov (United States)

    2010-01-01

    Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946) and L. major (1950). Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient. PMID:20565861

  12. A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals.

    Science.gov (United States)

    Edel-Hermann, Véronique; Sautour, Marc; Gautheron, Nadine; Laurent, Julie; Aho, Serge; Bonnin, Alain; Sixt, Nathalie; Hartemann, Philippe; Dalle, Frédéric; Steinberg, Christian

    2016-11-01

    Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Clonal stability of latex yield in eleven clones of Hevea brasiliensis Muell. Arg.

    Directory of Open Access Journals (Sweden)

    K.O. Omokhafe

    2003-01-01

    Full Text Available Eleven Hevea brasiliensis clones were evaluated for clonal stability of latex yield. A randomized complete block design was used with four replicates, two locations, seven years and three periods per year. Stability analysis was based on clone x year and clone x year x location interactions. Five stability parameters viz environmental variance, shukla's stability variance, regression of clonal latex yield on environmental index, variance due to regression and variance due to deviation from regression were applied. There was significant clone x environment effect at the two levels of interaction. Among the eleven clones, C 162 was outstanding for clonal stability and it can serve as donor parent for stability alleles. Three clones (C 76, C 150 and C 154 were also stable. The four stable clones (C 76, C 150, C 154 and C 162 are suitable for broad-spectrum recommendation for latex yield. Five clones (C 83, C 143, C 163, C 202 and RRIM 600 will require environment-specific recommendation because of their unstable phenotype. The stability feature of two clones (C 145 and C 159 was not clear and this will be investigated in subsequent studies.

  14. Gamma irradiation effect on the formation of Clonal variation from catharantus roseus plant

    International Nuclear Information System (INIS)

    Syukur, Sumaryati

    2000-01-01

    Clonal variation have been found in Catharantus roseus plant after gamma irradiation. Several doses have been used to produce clonal variation. The most effective doses used to perform better clonal variation was 20 krad. About 103 seeds irradiated for every radiation treatment, but only several clones were grown better than wild type. We have success to get (M) seeds the expected mutant. The seeds from selected mutant are bigger when compare to the wild type and growth better on medium containing 5-methyl Tryptophan (5-MT). The chlorophyll content is higher (almost twice) as compared to the wild type. Fulther experiment continue to do in vitro culture in order to develop embryonic callus from leaf tip and leaf base. Several manipulation of auxin and cytokini have been used to differentiate the callus formation. Modified MS medium with kinetin and cytokinin (10:1) can induce globular embryo like structure. Dragendrof alkaloid reagent were used to determine high alkaloid clones from the expected mutant. TLC analysis from callus mutant shows 3 clear bands with subsequence Rf about 0.22, 0.58 while control shows two smearing bands at 0.21 and 0.52

  15. Morphological response to competition for light in the clonal Trifolium repens (Fabaceae).

    Science.gov (United States)

    Bittebiere, Anne-Kristel; Renaud, Nolwenn; Clément, Bernard; Mony, Cendrine

    2012-04-01

    Plant communities in temperate zones are dominated by clonal plants that can plastically modify their growth characteristics in response to competition. Given that plants compete with one another, and the implications this has for species coexistence, we conducted a study to assess how clonal species morphologically respond to competition for light depending on its intensity and heterogeneity, which are determined by the competitor species. We assessed the morphological response to competition for light of the clonal species Trifolium repens L. by measuring its growth performance, and vertical and horizontal growth traits. We used five competitive environments, i.e., one without competitor and four differing by their competitor species creating different conditions of competition intensity and heterogeneity. The morphological response of Trifolium repens to competition for light depended on the competitor identity. Competition intensity and heterogeneity, determined by competitor identity, had an interactive effect on most traits. The increase in petiole elongation and specific leaf area due to increased competition intensity was observed only at low to intermediate competition heterogeneity. Competition heterogeneity promoted the elongation of clone connections allowing space exploration. Our results demonstrated that the intensity and heterogeneity of competition, which depended on competitor identity, are of primary importance in determining the plastic response of Trifolium repens. This emphasizes that it is important to consider the fine-scale spatial distribution of individuals when studying their interactions within plant communities.

  16. 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.

  17. Large-scale structuring of a rotating plasma due to plasma macroinstabilities

    International Nuclear Information System (INIS)

    Kikuchi, Toshinori; Ikehata, Takashi; Sato, Naoyuki; Watahiki, Takeshi; Tanabe, Toshio; Mase, Hiroshi

    1995-01-01

    The formation of coherent structures during plasma macroinstabilities have been of interest in view of the nonlinear plasma physics. In the present paper, we have investigated in detail, the mechanism and specific features of large-scale structuring of a rotating plasma. In the case of weak magnetic field, the plasma ejected from a plasma gun has a high beta value (β > 1) so that it expands rapidly across the magnetic field excluding a magnetic flux from its interior. Then, the boundary between the expanding plasma and the magnetic field becomes unstable against Rayleigh-Taylor instability. This instability has the higher growth rate at the shorter wavelength and the mode appears as flute. These features of the instability are confirmed by the observation of radial plasma jets with the azimuthal mode number m=20-40 in the early time of the plasma expansion. In the case of strong magnetic field, on the other hand, the plasma little expands and rotates at two times the ion sound speed. Especially, we observe spiral jets of m=2 instead of short-wavelength radial jets. This mode appears only when a glass target is installed or a dense neutral gas is introduced around the plasma to give the plasma a frictional force. From these results and with reference to the theory of plasma instabilities, the centrifugal instability caused by a combination of the velocity shear and centrifugal force is concluded to be responsible for the formation of spiral jets. (author)

  18. Plasma properties

    International Nuclear Information System (INIS)

    Weitzner, H.

    1990-06-01

    This paper discusses the following topics: MHD plasma activity: equilibrium, stability and transport; statistical analysis; transport studies; edge physics studies; wave propagation analysis; basic plasma physics and fluid dynamics; space plasma; and numerical methods

  19. Plasma accelerators

    International Nuclear Information System (INIS)

    Bingham, R.; Angelis, U. de; Johnston, T.W.

    1991-01-01

    Recently attention has focused on charged particle acceleration in a plasma by a fast, large amplitude, longitudinal electron plasma wave. The plasma beat wave and plasma wakefield accelerators are two efficient ways of producing ultra-high accelerating gradients. Starting with the plasma beat wave accelerator (PBWA) and laser wakefield accelerator (LWFA) schemes and the plasma wakefield accelerator (PWFA) steady progress has been made in theory, simulations and experiments. Computations are presented for the study of LWFA. (author)

  20. 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.

  1. Extreme hydrogen plasma densities achieved in a linear plasma generator

    NARCIS (Netherlands)

    Rooij, van G.J.; Veremiyenko, V.P.; Goedheer, W.J.; Groot, de B.; Kleyn, A.W.; Smeets, P.H.M.; Versloot, T.W.; Whyte, D.G.; Engeln, R.A.H.; Schram, D.C.; Lopes Cardozo, N.J.

    2007-01-01

    A magnetized hydrogen plasma beam was generated with a cascaded arc, expanding in a vacuum vessel at an axial magnetic field of up to 1.6 T. Its characteristics were measured at a distance of 4 cm from the nozzle: up to a 2 cm beam diameter, 7.5×1020 m-3 electron density, ~2 eV electron and ion

  2. Microscopic analysis of nanostructured plasma coatings

    Science.gov (United States)

    Ageev, E. V.; Altukhov, A. Yu; Ageeva, E. V.; Khardikov, S. V.

    2018-03-01

    In the course of the study, it was found that plasma nanocomposite coating obtained from a mixture of powders of BRS, VK8 and nichrome with a portable plasma device “ALPES-02M” has high performance properties, which significantly expands the scope of its application.

  3. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae).

    Science.gov (United States)

    Gaddis, Keith D; Zukin, Helen L; Dieterich, Inca A; Braker, Elizabeth; Sork, Victoria L

    2014-06-01

    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 contributing

  4. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae

    Directory of Open Access Journals (Sweden)

    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

  5. Expanding the grid in Alberta

    Energy Technology Data Exchange (ETDEWEB)

    Horner, M. [AltaLink Management Ltd., Calgary, AB (Canada)

    2010-07-01

    This PowerPoint presentation discussed some of the changes and strategies that are currently being adopted by AltaLink to expand Alberta's electricity grid in relation to wind power development. The company is Alberta's largest transmission facility operator. Wind power currently accounts for approximately 5 percent of the province's generation mix. Applications for new wind farms will increase Alberta's 629 MW of wind power generation capacity to 5530 MW. Alberta's transmission regulation requires that 100 percent of in-merit generation can occur when transmission facilities are in service, and that 95 percent of in-merit generation can occur under abnormal operating conditions. A new transmission line is being constructed in the Pincher Creek and Lethbridge region as part of a southern Alberta transmission reinforcement project. The Alberta Electric System Operator (AESO) and Canadian Wind Energy Association (CanWEA) are working together to ensure that adequate resources are available while system reliability is maintained. The Ardenville wind farm is the first wind power project to be energized under the new connection model launched by the AESO. The connection model was developed to identify, connect, and construct new energy projects. The project will also identify connection routes with the lowest overall impact on the province. Alberta will also continue to implement technologies that ensure the development of a smart grid. tabs., figs.

  6. Attitudes toward expanding nurses' authority.

    Science.gov (United States)

    Kerzman, Hana; Van Dijk, Dina; Eizenberg, Limor; Khaikin, Rut; Phridman, Shoshi; Siman-Tov, Maya; Goldberg, Shoshi

    2015-01-01

    In recent years, an increasing number of care procedures previously under the physician's authority have been placed in the hands of registered nurses. The purpose of this study was to examine the attitudes of nurses towards expanding nurses' authority and the relationships between these attitudes and job satisfaction facets, professional characteristics, and demographics. A cross-sectional study was conducted between 2010 and 2011 in three major medical centers in Israel. Participants included 833 nurses working in 89 departments. Attitudes toward the expansion of nurses' authority were assessed by self-report questionnaire, as well as job satisfaction facets including perception of professional autonomy, nurse-physician working relations, workload and burnout, perceptions of quality of care, and nursing staff satisfaction at work. Nurses reported positive attitudes toward the expansion of nurses' authority and moderate attitudes for interpretation of diagnostic tests in selected situations. The results of multivariate regression analyses demonstrate that the nurses' satisfaction from professional autonomy and work relations were the most influential factors in explaining their attitudes toward the expansion of nurses' authority. In addition, professionally young nurses tend to be more positive regarding changes in nurses' authority. In the Israeli reality of a nurse's shortage, we are witnessing professional transitions toward expansion of the scope of nurses' accountability and decision-making authority. The current research contributes to our understanding of attitudes toward the expansion of nurses' authority among the nursing staffs. The findings indicate the necessity of redefining the scope of nursing practice within the current professional context.

  7. 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.

  8. Studies of intense-laser plasma instabilities

    Czech Academy of Sciences Publication Activity Database

    Láska, Leoš; Krása, Josef; Badziak, J.; Jungwirth, Karel; Krouský, Eduard; Margarone, Daniele; Parys, P.

    2013-01-01

    Roč. 272, May (2013), 94-98 ISSN 0169-4332 R&D Projects: GA MŠk(CZ) 7E09092; GA MŠk(CZ) LC528; GA AV ČR IAA100100715 Institutional research plan: CEZ:AV0Z10100523 Keywords : laser plasma instabilities * self-generated magnetic field * longitudinal structure of the expanding plasma Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 2.538, year: 2013

  9. Plasma device

    International Nuclear Information System (INIS)

    Thode, L.E.

    1981-01-01

    A method is described for electron beam heating of a high-density plasma to drive a fast liner. An annular or solid relativistic electron beam is used to heat a plasma to kilovolt temperatures through streaming instabilities in the plasma. Energy deposited in the plasma then converges on a fast liner to explosively or ablatively drive the liner to implosion. (U.K.)

  10. 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.

  11. Gene surfing in expanding populations.

    Science.gov (United States)

    Hallatschek, Oskar; Nelson, David R

    2008-02-01

    Large scale genomic surveys are partly motivated by the idea that the neutral genetic variation of a population may be used to reconstruct its migration history. However, our ability to trace back the colonization pathways of a species from their genetic footprints is limited by our understanding of the genetic consequences of a range expansion. Here, we study, by means of simulations and analytical methods, the neutral dynamics of gene frequencies in an asexual population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds, C.A., Lillie, A.S., Cavalli-Sforza, L.L., 2004. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. 101, 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our stochastic simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in the presence of cooperation between individuals ("pushed waves") than when individuals proliferate independently ("pulled waves"), and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics. Our analytical theory compares well with the simulation results for pushed waves, but is less accurate in the case of pulled waves when stochastic fluctuations in the tip of the wave are important.

  12. 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.

  13. Plasma Modes

    Science.gov (United States)

    Dubin, D. H. E.

    This chapter explores several aspects of the linear electrostatic normal modes of oscillation for a single-species non-neutral plasma in a Penning trap. Linearized fluid equations of motion are developed, assuming the plasma is cold but collisionless, which allow derivation of the cold plasma dielectric tensor and the electrostatic wave equation. Upper hybrid and magnetized plasma waves in an infinite uniform plasma are described. The effect of the plasma surface in a bounded plasma system is considered, and the properties of surface plasma waves are characterized. The normal modes of a cylindrical plasma column are discussed, and finally, modes of spheroidal plasmas, and finite temperature effects on the modes, are briefly described.

  14. Geothermal ORC Systems Using Large Screw Expanders

    OpenAIRE

    Biederman, Tim R.; Brasz, Joost J.

    2014-01-01

    Geothermal ORC Systems using Large Screw Expanders Tim Biederman Cyrq Energy Abstract This paper describes a low-temperature Organic Rankine Cycle Power Recovery system with a screw expander a derivative of developed of Kaishan's line of screw compressors, as its power unit. The screw expander design is a modified version of its existing refrigeration compressor used on water-cooled chillers. Starting the ORC development program with existing refrigeration screw compre...

  15. Identification of genuine primary pulmonary NK cell lymphoma via clinicopathologic observation and clonality assay.

    Science.gov (United States)

    Gong, Li; Wei, Long-Xiao; Huang, Gao-Sheng; Zhang, Wen-Dong; Wang, Lu; Zhu, Shao-Jun; Han, Xiu-Juan; Yao, Li; Lan, Miao; Li, Yan-Hong; Zhang, Wei

    2013-08-19

    Extranodal natural killer (NK)/T-cell lymphoma, nasal type, is an uncommon lymphoma associated with the Epstein-Barr virus (EBV). It most commonly involves the nasal cavity and upper respiratory tract. Primary pulmonary NK/T cell lymphoma is extremely rare. If a patient with a NK or T-cell tumor has an unusual reaction to treatment or an unusual prognosis, it is wise to differentiate NK from T-cell tumors. The clinicopathologic characteristics, immunophenotype, EBV in situ hybridization, and T cell receptor (TCR) gene rearrangement of primary pulmonary NK cell lymphoma from a 73-year-old Chinese woman were investigated and the clonal status was determined using female X-chromosomal inactivation mosaicism and polymorphisms at the phosphoglycerate kinase (PGK) gene. The lesion showed the typical histopathologic characteristics and immunohistochemical features of NK/T cell lymphoma. However, the sample was negative for TCR gene rearrangement. A clonality assay demonstrated that the lesion was monoclonal. It is concluded that this is the first recorded case of genuine primary pulmonary NK cell lymphoma. The purpose of the present work is to recommend that pathologists carefully investigate the whole lesion to reduce the likelihood that primary pulmonary NK cell lymphoma will be misdiagnosed as an infectious lesion. In addition, TCR gene rearrangement and clonal analysis, which is based on female X-chromosomal inactivation mosaicism and polymorphisms at PGK and androgen receptor (AR) loci, were found to play important roles in differentiating NK cell lymphoma from T cell lymphoma. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5205300349457729.

  16. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

    Science.gov (United States)

    Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

    2011-12-01

    Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics

  17. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

    Directory of Open Access Journals (Sweden)

    Julia Dale

    2011-12-01

    Full Text Available Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST. These populations correlate with the major foci of endemicity (Australia and Southeast Asia. Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs. Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic

  18. 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.

  19. Clonal mutations in primary human glial tumors: evidence in support of the mutator hypothesis

    International Nuclear Information System (INIS)

    Misra, Anjan; Chattopadhyay, Parthaprasad; Chosdol, Kunzang; Sarkar, Chitra; Mahapatra, Ashok K; Sinha, Subrata

    2007-01-01

    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. 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. 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. 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. Self-expandable nitinol stent placement in homocysteinemic porcine aorta

    Directory of Open Access Journals (Sweden)

    Luís Henrique Gil França

    2008-01-01

    Full Text Available PURPOSE: To compare aortic intimal thickening of normal and hyperhomocysteinemic pigs (induced with a methionine-rich diet following placement of a self-expanding nitinol stent. METHODS: Eighteen Macau pigs were used. They were older than eight weeks in age and had an average weight of 30 kg. Pigs were randomly divided into two groups. The first, Group C (control, was fed a regular diet, and the second group, Group M, was fed a methionine-rich diet for 30 days to induce hyperhomocysteinemia. The self-expandable nitinol stents were 25mm in length and 8 mm in diameter after expansion. Blood samples were collected to measure total cholesterol, triglycerides, HDL and homocysteine concentrations. All animals were subjected to angiography. Thirty days after the procedure, the animals were sacrificed, and the abdominal aorta was removed for histological and digital morphometry analysis. RESULTS: Under microscopic evaluation, the intima was significantly thicker in Group C than in Group M. When groups were compared by digital morphometric analysis, intimal thickening of the vessel wall was higher in Group C than in Group M. There was no significant change in total cholesterol, triglycerides or HDL concentrations in either group. In group C the levels of plasma homocysteine ranged from 14,40 to 16,73µmol/l; in Group M, plasma homocysteine levels ranged from 17.47 to 59.80 µmol/l after 30 days of a methionine-rich diet. CONCLUSION: Compared to normal pigs, less intimal hyperplasia was observed in the abdominal aortas of hyperhomocysteinemic pigs thirty days after the insertion of a self-expandable nitinol stent.

  1. Confirmation of the reported association of clonal chromosomal mosaicism with an increased risk of incident hematologic cancer.

    Directory of Open Access Journals (Sweden)

    Ursula M Schick

    Full Text Available Chromosomal abnormalities provide clinical utility in the diagnosis and treatment of hematologic malignancies, and may be predictive of malignant transformation in individuals without apparent clinical presentation of a hematologic cancer. In an effort to confirm previous reports of an association between clonal mosaicism and incident hematologic cancer, we applied the anomDetectBAF algorithm to call chromosomal anomalies in genotype data from previously conducted Genome Wide Association Studies (GWAS. The genotypes were initially collected from DNA derived from peripheral blood of 12,176 participants in the Group Health electronic Medical Records and Genomics study (eMERGE and the Women's Health Initiative (WHI. We detected clonal mosaicism in 169 individuals (1.4% and large clonal mosaic events (>2 mb in 117 (1.0% individuals. Though only 9.5% of clonal mosaic carriers had an incident diagnosis of hematologic cancer (multiple myeloma, myelodysplastic syndrome, lymphoma, or leukemia, the carriers had a 5.5-fold increased risk (95% CI: 3.3-9.3; p-value = 7.5×10(-11 of developing these cancers subsequently. Carriers of large mosaic anomalies showed particularly pronounced risk of subsequent leukemia (HR = 19.2, 95% CI: 8.9-41.6; p-value = 7.3×10(-14. Thus we independently confirm the association between detectable clonal mosaicism and hematologic cancer found previously in two recent publications.

  2. Clonal relationship among Vibrio cholerae O1 El Tor strains isolated in Somalia.

    Science.gov (United States)

    Scrascia, Maria; Pugliese, Nicola; Maimone, Francesco; Mohamud, Kadigia A; Grimont, Patrick A D; Materu, Sadiki F; Pazzani, Carlo

    2009-03-01

    One hundred and three Vibrio cholerae O1 strains, selected to represent the cholera outbreaks which occurred in Somalia in 1998-1999, were characterized by random amplified polymorphic DNA patterns, ribotyping, and antimicrobial susceptibility. All strains showed a unique amplified DNA pattern and 2 closely related ribotypes (B5a and B8a), among which B5a was the more frequently identified. Ninety-one strains were resistant to ampicillin, chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim, conferred, except for spectinomycin, by a conjugative plasmid IncC. These findings indicated that the group of strains active in Somalia in the late 1990s had a clonal origin.

  3. Clonal propagation of Stevia rebaudiana Bertoni by stem-tip culture.

    Science.gov (United States)

    Tamura, Y; Nakamura, S; Fukui, H; Tabata, M

    1984-10-01

    Clonal propagation of Stevia rebaudiana has been established by culturing stem-tips with a few leaf primordia on an agar medium supplemented with a high concentration (10 mg/l) of kinetin. Anatomical examination has suggested that these multiple shoots originate from a number of adventitious buds formed on the margin of the leaf. Innumerable shoots can be obtained by repeating the cycle of multiple-shoot formation from a single stem-tip of Stevia. These shoots produce roots when transferred to a medium containing NAA (0.1 mg/l) without kinetin. The regenerated plantlets can be transplanted to soil.

  4. 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...

  5. Clonal outbreaks of [ Pasteurella] pneumotropica biovar Heyl in two mouse colonies

    DEFF Research Database (Denmark)

    Adhikary, Sadhana; Bisgaard, Magne; Dagnæs-Hansen, Frederik

    2017-01-01

    The aim of this study was to document the pathogenic role of biovar Heyl of [Pasteurella] pneumotropica in mouse colonies. Fifty-three isolates associated with mastitis and orbital, cutaneous and vaginal abscesses as well as isolates from the nose and vagina of healthy mice were investigated...... strains with the same rpoB sequence type, as shown by the PFGE profiles. The investigation documented that members of biovar Heyl of [P.] pneumotropica caused disease outbreaks in mouse colonies since the clonality indicated a primary role of [P.] pneumotropica biovar Heyl in the infections observed....

  6. Probable clonal origin of acute myeloblastic leukemia following radiation and chemotherapy of colon cancer

    International Nuclear Information System (INIS)

    Wiggans, R.G.; Jacobson, R.J.; Fialkow, P.J.; Woolley, P.V. III; Macdonald, J.S.; Schein, P.S.

    1978-01-01

    A 64-yr-old female developed acute myeloblastic leukemia following radiation and drug therapy for colon carcinoma. The patient was heterozygous for glucose-6-phosphate dehydrogenase [G-6-PD) and displayed types A and B isoenzymes in nonhematopoietic tissue. In contrast, only type B G-6-PD was observed in peripheral blood white cells. In addition, a karyotypic abnormality was found in peripheral blood and marrow cells but not in skin fibroblasts. The data are consistent with a clonal origin of this leukemia

  7. Expanding/Extending English: Interdisciplinarity and Internationalism.

    Science.gov (United States)

    Fleishman, Avrom

    1994-01-01

    Discusses the recent efforts to expand literary studies into numerous allied fields and the possible effects that such attempts toward interdisciplinarity and internationalism might have. Warns against possible negative consequences of interdisciplinary approaches. Calls for an expanded view of English as a field of study. (HB)

  8. Plasma centrifuges

    International Nuclear Information System (INIS)

    Karchevskij, A.I.; Potanin, E.P.

    2000-01-01

    The review of the most important studies on the isotope separation processes in the rotating plasma is presented. The device is described and the characteristics of operation of the pulse plasma centrifuges with weakly and strongly ionized plasma as well as the stationary plasma centrifuges with the medium weak ionization and devices, applying the stationary vacuum arc with the high ionization rate and the stationary beam-plasma discharge with complete ionization, are presented. The possible mechanisms of the isotope separation in plasma centrifuges are considered. The specific energy consumption for isotope separation in these devices is discussed [ru

  9. 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

  10. 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

  11. Screw expander for light duty diesel engines

    Science.gov (United States)

    1983-01-01

    Preliminary selection and sizing of a positive displacement screw compressor-expander subsystem for a light-duty adiabatic diesel engine; development of a mathematical model to describe overall efficiencies for the screw compressor and expander; simulation of operation to establish overall efficiency for a range of design parameters and at given engine operating points; simulation to establish potential net power output at light-duty diesel operating points; analytical determination of mass moments of inertia for the rotors and inertia of the compressor-expander subsystem; and preparation of engineering layout drawings of the compressor and expander are discussed. As a result of this work, it was concluded that the screw compressor and expander designed for light-duty diesel engine applications are viable alternatives to turbo-compound systems, with acceptable efficiencies for both units, and only a moderate effect on the transient response.

  12. Protracted Clonal Trajectory of a JAK2 V617F-Positive Myeloproliferative Neoplasm Developing during Long-Term Remission from Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Stephen E. Langabeer

    2018-01-01

    Full Text Available Although transformation of the myeloproliferative neoplasms (MPNs to acute myeloid leukemia (AML is well documented, development of an MPN in patients previously treated for, and in remission from, AML is exceedingly rare. A case is described in which a patient was successfully treated for AML and in whom a JAK2 V617F-positive MPN was diagnosed after seven years in remission. Retrospective evaluation of the JAK2 V617F detected a low allele burden at AML diagnosis and following one course of induction chemotherapy. This putative chemoresistant clone subsequently expanded over the intervening seven years, resulting in a hematologically overt MPN. As AML relapse has not occurred, the MPN may have arose in a separate initiating cell from that of the AML. Alternatively, both malignancies possibly evolved from a common precursor defined by a predisposition mutation with divergent evolution into MPN through acquisition of the JAK2 V617F and AML through acquisition of different mutations. This case emphasizes the protracted time frame from acquisition of a disease-driving mutation to overt MPN and further underscores the clonal complexity in MPN evolution.

  13. Shifts in the Antibiotic Susceptibility, Serogroups, and Clonal Complexes of Neisseria meningitidis in Shanghai, China: A Time Trend Analysis of the Pre-Quinolone and Quinolone Eras.

    Science.gov (United States)

    Chen, Mingliang; Guo, Qinglan; Wang, Ye; Zou, Ying; Wang, Gangyi; Zhang, Xi; Xu, Xiaogang; Zhao, Miao; Hu, Fupin; Qu, Di; Chen, Min; Wang, Minggui

    2015-06-01

    Fluoroquinolones have been used broadly since the end of the 1980s and have been recommended for Neisseria meningitidis prophylaxis since 2005 in China. The aim of this study was to determine whether and how N. meningitidis antimicrobial susceptibility, serogroup prevalence, and clonal complex (CC) prevalence shifted in association with the introduction and expanding use of quinolones in Shanghai, a region with a traditionally high incidence of invasive disease due to N. meningitidis. A total of 374 N. meningitidis isolates collected by the Shanghai Municipal Center for Disease Control and Prevention between 1965 and 2013 were studied. Shifts in the serogroups and CCs were observed, from predominantly serogroup A CC5 (84%) in 1965-1973 to serogroup A CC1 (58%) in 1974-1985, then to serogroup C or B CC4821 (62%) in 2005-2013. The rates of ciprofloxacin nonsusceptibility in N. meningitidis disease isolates increased from 0% in 1965-1985 to 84% (31/37) in 2005-2013 (p convenience isolates from 1965-1985 were available. The increasing prevalence of ciprofloxacin resistance since 2005 in Shanghai was associated with the spread of hypervirulent lineages CC4821 and CC5. Two resistant meningococcal clones ChinaCC4821-R1-C/B and ChinaCC5-R14-A have emerged in Shanghai during the quinolone era. Ciprofloxacin should be utilized with caution for the chemoprophylaxis of N. meningitidis in China.

  14. Clonal Propagation of Khaya senegalensis: The Effects of Stem Length, Leaf Area, Auxins, Smoke Solution, and Stockplant Age

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    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.

  15. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

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    Kiwako S Araki

    Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

  16. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Science.gov (United States)

    Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

    2017-01-01

    In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

  17. Effects of Cu Pollution on the Expansion of an Amphibious Clonal Herb in Aquatic-Terrestrial Ecotones.

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    Liang Xu

    Full Text Available Physiological integration can enhance the performance of clonal plants in aquatic and terrestrial heterogeneous habitats and associated ecotones. Similar to nutrients, pollutants may be transported among connected ramets via physiological integration. Few studies have examined the expansion of amphibious clonal plants from terrestrial to aquatic environments, particularly when the local water supply is polluted with heavy metals. A greenhouse experiment was conducted using the amphibious plant Alternanthera philoxeroides to determine whether Cu can spread among clonal plants and examine the corresponding effects of this pollution on the expansion of clonal plants in aquatic-terrestrial ecotones. Ramets from the same clonal fragments were rooted in unpolluted soil and polluted water at five different levels. The responses of the ramets in terrestrial and aquatic habitats were quantified via traits associated with growth, morphology and Cu accumulation. The results indicated that ramets in soil and water significantly differed in nearly all of these traits. The expansion of populations from terrestrial to polluted aquatic habitats was facilitated by stem elongation rather than new ramet production. The accumulated Cu in polluted ramets can be horizontally transported to other ramets in soil via connected stolons. In terms of clonal growth patterns, variations in Cu pollution intensity were negatively correlated with variations in the morphological and growth traits of ramets in polluted aquatic habitats and unpolluted soil. We concluded that Cu ions are distributed among the clones and accumulated in different ramet tissues in heterogeneous habitats. Therefore, we suggest that Cu pollution of aquatic-terrestrial ecotones, especially at high levels, can affect the growth and expansion of the whole clones because Cu ions are shared between integrated ramets.

  18. Effects of Cu Pollution on the Expansion of an Amphibious Clonal Herb in Aquatic-Terrestrial Ecotones.

    Science.gov (United States)

    Xu, Liang; Zhou, Zhen-Feng

    2016-01-01

    Physiological integration can enhance the performance of clonal plants in aquatic and terrestrial heterogeneous habitats and associated ecotones. Similar to nutrients, pollutants may be transported among connected ramets via physiological integration. Few studies have examined the expansion of amphibious clonal plants from terrestrial to aquatic environments, particularly when the local water supply is polluted with heavy metals. A greenhouse experiment was conducted using the amphibious plant Alternanthera philoxeroides to determine whether Cu can spread among clonal plants and examine the corresponding effects of this pollution on the expansion of clonal plants in aquatic-terrestrial ecotones. Ramets from the same clonal fragments were rooted in unpolluted soil and polluted water at five different levels. The responses of the ramets in terrestrial and aquatic habitats were quantified via traits associated with growth, morphology and Cu accumulation. The results indicated that ramets in soil and water significantly differed in nearly all of these traits. The expansion of populations from terrestrial to polluted aquatic habitats was facilitated by stem elongation rather than new ramet production. The accumulated Cu in polluted ramets can be horizontally transported to other ramets in soil via connected stolons. In terms of clonal growth patterns, variations in Cu pollution intensity were negatively correlated with variations in the morphological and growth traits of ramets in polluted aquatic habitats and unpolluted soil. We concluded that Cu ions are distributed among the clones and accumulated in different ramet tissues in heterogeneous habitats. Therefore, we suggest that Cu pollution of aquatic-terrestrial ecotones, especially at high levels, can affect the growth and expansion of the whole clones because Cu ions are shared between integrated ramets.

  19. 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

    2018-04-01

    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.

  20. Wind power forecast using wavelet neural network trained by improved Clonal selection algorithm

    International Nuclear Information System (INIS)

    Chitsaz, Hamed; Amjady, Nima; Zareipour, Hamidreza

    2015-01-01

    Highlights: • Presenting a Morlet wavelet neural network for wind power forecasting. • Proposing improved Clonal selection algorithm for training the model. • Applying Maximum Correntropy Criterion to evaluate the training performance. • Extensive testing of the proposed wind power forecast method on real-world data. - Abstract: With the integration of wind farms into electric power grids, an accurate wind power prediction is becoming increasingly important for the operation of these power plants. In this paper, a new forecasting engine for wind power prediction is proposed. The proposed engine has the structure of Wavelet Neural Network (WNN) with the activation functions of the hidden neurons constructed based on multi-dimensional Morlet wavelets. This forecast engine is trained by a new improved Clonal selection algorithm, which optimizes the free parameters of the WNN for wind power prediction. Furthermore, Maximum Correntropy Criterion (MCC) has been utilized instead of Mean Squared Error as the error measure in training phase of the forecasting model. The proposed wind power forecaster is tested with real-world hourly data of system level wind power generation in Alberta, Canada. In order to demonstrate the efficiency of the proposed method, it is compared with several other wind power forecast techniques. The obtained results confirm the validity of the developed approach

  1. Limpeza clonal de mudas de videira infectadas por 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.

  2. 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.

  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. Using BOX-PCR to exclude a clonal outbreak of melioidosis

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    Ward Linda

    2007-06-01

    Full Text Available Abstract Background Although melioidosis in endemic regions is usually caused by a diverse range of Burkholderia pseudomallei strains, clonal outbreaks from contaminated potable water have been described. Furthermore B. pseudomallei is classified as a CDC Group B bioterrorism agent. Ribotyping, pulsed-field gel electrophoresis (PFGE and multilocus sequence typing (MLST have been used to identify genetically related B. pseudomallei isolates, but they are time consuming and technically challenging for many laboratories. Methods We have adapted repetitive sequence typing using a BOX A1R primer for typing B. pseudomallei and compared BOX-PCR fingerprinting results on a wide range of well-characterized B. pseudomallei isolates with MLST and PFGE performed on the same isolates. Results BOX-PCR typing compared favourably with MLST and PFGE performed on the same isolates, both discriminating between the majority of multilocus sequence types and showing relatedness between epidemiologically linked isolates from various outbreak clusters. Conclusion Our results suggest that BOX-PCR can be used to exclude a clonal outbreak of melioidosis within 10 hours of receiving the bacterial strains.

  5. Clonal heterogeneity and chromosomal instability at disease presentation in high hyperdiploid acute lymphoblastic leukemia.

    Science.gov (United States)

    Talamo, Anna; Chalandon, Yves; Marazzi, Alfio; Jotterand, Martine

    2010-12-01

    Although aneuploidy has many possible causes, it often results from underlying chromosomal instability (CIN) leading to an unstable karyotype with cell-to-cell variation and multiple subclones. To test for the presence of CIN in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) at diagnosis, we investigated 20 patients (10 HeH ALL and 10 non-HeH ALL), using automated four-color interphase fluorescence in situ hybridization (I-FISH) with centromeric probes for chromosomes 4, 6, 10, and 17. In HeH ALL, the proportion of abnormal cells ranged from 36.3% to 92.4%, and a variety of aneuploid populations were identified. Compared with conventional cytogenetics, I-FISH revealed numerous additional clones, some of them very small. To investigate the nature and origin of this clonal heterogeneity, we determined average numerical CIN values for all four chromosomes together and for each chromosome and patient group. The CIN values in HeH ALL were relatively high (range, 22.2-44.7%), compared with those in non-HeH ALL (3.2-6.4%), thus accounting for the presence of numerical CIN in HeH ALL at diagnosis. We conclude that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by I-FISH in HeH ALL at presentation, which would corroborate the potential role of CIN in tumor pathogenesis. Copyright © 2010 Elsevier Inc. All rights reserved.

  6. How old are you? Genet age estimates in a clonal animal.

    Science.gov (United States)

    Devlin-Durante, M K; Miller, M W; Precht, W F; Baums, I B

    2016-11-01

    Foundation species such as redwoods, seagrasses and corals are often long-lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral, Acropora palmata (n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195 -04 per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542 -05 per locus per year based on sea level changes to habitat availability. Long-lived A. palmata genets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events in A. palmata suggest that capacity is now being frequently exceeded. © 2016 John Wiley & Sons Ltd.

  7. Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome.

    Science.gov (United States)

    Saida, Satoshi; Watanabe, Ken-ichiro; Sato-Otsubo, Aiko; Terui, Kiminori; Yoshida, Kenichi; Okuno, Yusuke; Toki, Tsutomu; Wang, RuNan; Shiraishi, Yuichi; Miyano, Satoru; Kato, Itaru; Morishima, Tatsuya; Fujino, Hisanori; Umeda, Katsutsugu; Hiramatsu, Hidefumi; Adachi, Souichi; Ito, Etsuro; Ogawa, Seishi; Ito, Mamoru; Nakahata, Tatsutoshi; Heike, Toshio

    2013-05-23

    Transient abnormal myelopoiesis (TAM) is a clonal preleukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, interleukin (IL)-2Rγ(null) mice. Serial engraftment after transplantation of cells from a TAM patient who developed ML-DS a year later demonstrated their self-renewal capacity. A GATA1 mutation and no copy number alterations (CNAs) were detected in the primary patient sample by conventional genomic sequencing and CNA profiling. However, in serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. Detailed genomic analysis identified minor subclones with a 16q deletion or this distinct GATA1 mutation in the primary patient sample. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Our xenograft model of TAM may provide unique insight into the evolutionary process of leukemia.

  8. BRAF inhibition is associated with increased clonality in tumor-infiltrating lymphocytes

    Science.gov (United States)

    Cooper, Zachary A; Frederick, Dennie T; Juneja, Vikram R; Sullivan, Ryan J; Lawrence, Donald P; Piris, Adriano; Sharpe, Arlene H; Fisher, David E; Flaherty, Keith T; Wargo, Jennifer A

    2013-01-01

    There have been significant advances with regard to BRAF-targeted therapies against metastatic melanoma. However, the majority of patients receiving BRAF inhibitors (BRAFi) manifest disease progression within a year. We have recently shown that melanoma patients treated with BRAFi exhibit an increase in melanoma-associated antigens and in CD8+ tumor-infiltrating lymphocytes in response to therapy. To characterize such a T-cell infiltrate, we analyzed the complementarity-determining region 3 (CDR3) of rearranged T-cell receptor (TCR) β chain-coding genes in tumor biopsies obtained before the initiation of BRAFi and 10–14 d later. We observed an increase in the clonality of tumor-infiltrating lymphocytes in 7 of 8 patients receiving BRAFi, with a statistically significant 21% aggregate increase in clonality. Over 80% of individual T-cell clones detected after initiation of BRAFi treatment were new clones. Interestingly, the comparison of tumor infiltrates with clinical responses revealed that patients who had a high proportion of pre-existing dominant clones after the administration of BRAFi responded better to therapy than patients who had a low proportion of such pre-existing dominant clones following BRAFi. These data suggest that although the inhibition of BRAF in melanoma patients results in tumor infiltration by new lymphocytes, the response to treatment appears to be related to the presence of a pre-existing population of tumor-infiltrating T-cell clones. PMID:24251082

  9. 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.

  10. Clonal deletion: A mechanism of tolerance in mixed bone marrow chimeras

    International Nuclear Information System (INIS)

    Yu, J.C.; Webster, M.; Fox, I.J.

    1990-01-01

    The mechanism of antigen-specific immunologic unresponsiveness which results from lethal irradiation and mixed (syngeneic-allogeneic) bone marrow cell (BMC) reconstitution is unknown. To determine whether clonal deletion is the mechanism of tolerance in this model, monoclonal antibody (Mab) RR-4-4, specific for a T-cell receptor (V beta 6) reactive against the minor alloantigen MLsa, was employed. Six-week-old B10 mice (H-2b, Mlsb, Thyl.2) were tolerized to AKR antigens (H-2k, Mlsa, Thyl.1) by whole body irradiation (950 R) and iv infusion of T-cell-depleted (TCD) B10 BMC + non-TCD AKR BMC. Chimerism and antigen-specific tolerance were documented by flow microfluorometry (FMF), skin grafting, mixed lymphocyte reaction, and cell-mediated lympholysis. When tolerant B10 mice (n = 15) had accepted AKR skin grafts for greater than 100 days, these animals were studied for the presence of host V beta 6+ T cells using Mab RR-4-4. FMF revealed that 0-5% of host (B10) lymph node and spleen cells from chimeras were V beta 6+ while 15-20% of lymph node and spleen cells from control B10 mice expressed V beta 6. These data demonstrate that clonal deletion occurs in the lethal irradiation-mixed reconstitution model as evidenced by the near total elimination of Mlsa-reactive V beta 6+ T cells and suggest that it maybe a mechanism responsible for tolerance in adult mice

  11. Unforeseen clonal evolution of tumor cell population in recurrent and metastatic dermatofibrosarcoma protuberans.

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    Ensel Oh

    Full Text Available Dermatofibrosarcoma protuberans (DFSP is a very rare soft tissue sarcoma, generally of low-grade malignancy. DFSP is locally aggressive with a high recurrence rate, but metastasis occurs rarely. To investigate the mechanism of metastasis in DFSP, we analyzed the whole exome sequencing data of serial tumor samples obtained from a patient who had a 10-year history of recurrent and metastatic DFSP. Tracking various genomic alterations, namely somatic mutations, copy number variations, and chromosomal rearrangements, we observed a dramatic change in tumor cell population during the occurrence of metastasis in this DFSP case. The new subclone that emerged in metastatic DFSP harbored a completely different set of somatic mutations and new focal amplifications, which had not been observed in the primary clone before metastasis. The COL1A1-PDGFB fusion, characteristic of DFSP, was found in all of the serial samples. Moreover, the break position on the fusion gene was identical in all samples. Based on these observations, we suggest a clonal evolution model to explain the mechanism underlying metastasis in DFSP and identified several candidate target genes responsible for metastatic DFSP by utilizing The Cancer Genome Atlas database. This is the first study to observe clonal evolution in metastatic DFSP and provide insight for a possible therapeutic strategy for imatinib-resistant or metastatic DFSP.

  12. Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

    Science.gov (United States)

    Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

    2008-08-19

    Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.

  13. 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.

  14. Clonal origins of cells in the pigmented retina of the zebrafish eye

    International Nuclear Information System (INIS)

    Streisinger, G.; Coale, F.; Taggart, C.; Walker, C.; Grunwald, D.J.

    1989-01-01

    Mosaic analysis has been used to study the clonal basis of the development of the pigmented retina of the zebrafish, Brachydanio rerio. Zebrafish embryos heterozygous for a recessive mutation at the gol-1 locus were exposed to gamma-irradiation at various developmental stages to create mosaic individuals consisting of wild-type pigmented cells and a clone of pigmentless (golden) cells in the eye. The contribution of individual embryonic cells to the pigmented retina was measured and the total number of cells in the embryo that contributed descendants to this tissue was determined. Until the 32-cell stage, almost every blastomere has some descendants that participate in the formation of the pigmented retina of the zebrafish. During subsequent cell divisions, up to the several thousand-cell stage, the number of ancestral cells is constant: approximately 40 cells are present that will give rise to progeny in the pigmented retina. Analysis of the size of clones in the pigmented retina indicates that the cells of this tissue do not arise through a rigid series of cell divisions originating in the early embryo. The findings that each cleavage stage cell contributes to the pigmented retina and yet the contribution of such cells is highly variable are consistent with the interpretation that clonal descendants of different blastomeres normally intermix extensively prior to formation of the pigmented retina

  15. Effects of clonal fragmentation on intraspecific competition of a stoloniferous floating plant.

    Science.gov (United States)

    Wang, P; Xu, Y-S; Dong, B-C; Xue, W; Yu, F-H

    2014-11-01

    Disturbance is common and can fragment clones of plants. Clonal fragmentation may affect the density and growth of ramets so that it could alter intraspecific competition. To test this hypothesis, we grew one (low density), five (medium density) or nine (high density) parent ramets of the floating invasive plant Pistia stratiotes in buckets, and newly produced offspring ramets were either severed (with fragmentation) or remained connected to parent ramets (no fragmentation). Increasing density reduced biomass of the whole clone (i.e. parent ramet plus its offspring ramets), showing intense intraspecific competition. Fragmentation decreased biomass of offspring ramets, but increased biomass of parent ramets and the whole clone, suggesting significant resource translocation from parent to offspring ramets when clones were not fragmented. There was no interaction effect of density x fragmentation on biomass of the whole clone, and fragmentation did not affect competition intensity index. We conclude that clonal fragmentation does not alter intraspecific competition between clones of P. stratiotes, but increases biomass production of the whole clone. Thus, fragmentation may contribute to its interspecific competitive ability and invasiveness, and intentional fragmentation should not be recommended as a measure to stop the rapid growth of this invasive species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  16. Multiplex polymerase chain reaction on FTA cards vs. flow cytometry for B-lymphocyte clonality.

    Science.gov (United States)

    Dictor, Michael; Skogvall, Ingela; Warenholt, Janina; Rambech, Eva

    2007-01-01

    Two-colour flow cytometry was compared with multiplex PCR with capillary electrophoresis for clonality determination in specific categories of B-cell lymphoma. FTA cards were evaluated for preserving DNA from node imprints and expediting molecular analysis. A single-tube multiplex PCR targeted IGH and lymphoma-specific translocations in DNA extracted from 180 frozen lymphoid tissues and DNA bound to FTA cards from 192 fresh tissues and 137 aspirates. PCR results were compared with flow cytometry in the extracted and aspirated samples. Overall, single-tube multiplex PCR sensitivity was equivalent in the sample groups (intergroup range 79%-91%). False negatives were associated with tumour origin in the follicle centre. Multiplex PCR and flow cytometry were equally sensitive and together detected 98% of B-cell lymphomas. Additional two-tube targeting of IGK suggested an overall molecular sensitivity >90%. False positive (pseudoclonal) single-tube multiplex PCR was associated with necrosis and sparse lymphocytes. Multiplex PCR using template DNA bound to an FTA card effectively detects B-lymphocyte clonality, obviates DNA extraction and refrigeration, and can be used without diminished sensitivity in fine needle aspirates or node imprints as a replacement for or complement to flow cytometry at any point in the diagnostic work-up.

  17. Clonal diversity and clone formation in the parthenogenetic Caucasian rock Lizard Darevskia dahli [corrected].

    Science.gov (United States)

    Vergun, Andrey A; Martirosyan, Irena A; Semyenova, Seraphima K; Omelchenko, Andrey V; Petrosyan, Varos G; Lazebny, Oleg E; Tokarskaya, Olga N; Korchagin, Vitaly I; Ryskov, Alexey P

    2014-01-01

    The all-female Caucasian rock lizard species Darevskia dahli and other parthenogenetic species of this genus reproduce normally via true parthenogenesis. Previously, the genetic diversity of this species was analyzed using allozymes, mitochondrial DNA, and DNA fingerprint markers. In the present study, variation at three microsatellite loci was studied in 111 specimens of D. dahli from five populations from Armenia, and new information regarding clonal diversity and clone formation in D. dahli was obtained that suggests a multiple hybridization origin. All individuals but one were heterozygous at the loci studied. Based on specific allele combinations, 11 genotypes were identified among the individuals studied. Individuals with the same genotypes formed distinct clonal lineages: one major clone was represented by 72 individuals, an intermediate clone was represented by 21 individuals, and nine other clones were rare and represented by one or several individuals. A new approach based on the detection and comparison of genotype-specific markers formed by combinations of parental-specific markers was developed and used to identify at least three hybridization founder events that resulted in the initial formation of one major and two rare clones. All other clones, including the intermediate and seven rare clones, probably arose through postformation microsatellite mutations of the major clone. This approach can be used to identify hybridization founder events and to study clone formation in other unisexual taxa.

  18. Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies.

    Science.gov (United States)

    Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

    2013-04-19

    Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis.

  19. Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies

    International Nuclear Information System (INIS)

    Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

    2013-01-01

    Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis

  20. Limpeza clonal de mudas de videira infectadas por Xanthomonas campestris pv. viticola Clonal cleaning of grapevine plants infected by 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.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

  1. Plasma device

    International Nuclear Information System (INIS)

    Thode, L.E.

    1981-01-01

    A method is described of providing electron beam heating of a high-density plasma to drive a fast liner to implode a structured microsphere. An annular relativistic electron beam is used to heat an annular plasma to kilovolt temperatures through streaming instabilities in the plasma. Energy deposited in the annular plasma then converges on a fast liner to explosively or ablatively drive the liner to convergence to implode the structured microsphere. (U.K.)

  2. A-coupled-expanding and distributional chaos

    International Nuclear Information System (INIS)

    Kim, Cholsan; Ju, Hyonhui; Chen, Minghao; Raith, Peter

    2015-01-01

    The concept of A-coupled-expanding maps is one of the more natural and useful ideas generalized from the horseshoe map which is commonly known as a criterion of chaos. It is well known that distributional chaos is one of the concepts which reflect strong chaotic behavior. In this paper, we focus on the relationship between A-coupled-expanding and distributional chaos. We prove two theorems which give sufficient conditions for a strictly A-coupled-expanding map to be distributionally chaotic in the senses of two kinds, where A is an m × m irreducible transition matrix

  3. Powerful strategy for polymerase chain reaction-based clonality assessment in T-cell malignancies Report of the BIOMED-2 Concerted Action BHM4 CT98-3936

    NARCIS (Netherlands)

    Brüggemann, M.; White, H.; Gaulard, P.; Garcia-Sanz, R.; Gameiro, P.; Oeschger, S.; Jasani, B.; Ott, M.; Delsol, G.; Orfao, A.; Tiemann, M.; Herbst, H.; Langerak, A. W.; Spaargaren, M.; Moreau, E.; Groenen, P. J. T. A.; Sambade, C.; Foroni, L.; Carter, G. I.; Hummel, M.; Bastard, C.; Davi, F.; Delfau-Larue, M.-H.; Kneba, M.; van Dongen, J. J. M.; Beldjord, K.; Molina, T. J.

    2007-01-01

    Polymerase chain reaction (PCR) assessment of clonal T-cell receptor (TCR) and immunoglobulin (Ig) gene rearrangements is an important diagnostic tool in mature T-cell neoplasms. However, lack of standardized primers and PCR protocols has hampered comparability of data in previous clonality studies.

  4. Plasma radiation in tokamak disruption simulation experiments

    International Nuclear Information System (INIS)

    Arkhipov, N.; Bakhtin, V.; Safronov, V.; Toporkov, D.; Vasenin, S.; Zhitlukhin, A.; Wuerz, H.

    1995-01-01

    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 micros 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 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

  5. RFP plasma experiment at INPE

    International Nuclear Information System (INIS)

    Ueda, M.; Aso, Y.

    1988-01-01

    Plasma experiments in CECI, a small Reversed Field Pinch (RFP) apparatus, are described. Preliminary measurements in this device shown the production of a plasma with peak current of 1.3kA and discharge duration of nearly 80μs, when a toroidal DC field of 100G was used. A loop voltage of 40V was measured and a maximum electron temperature of 3eV was estimated for these discharges. Experimental points in the F-θ diagram for CECI indicate that its plasma is approaching the RFP configuration when the discharge is optimize. The probe data also show that the plasma column expands outward. Numerical results indicate that leakage fields have to be reduced below 5G to form appropriate magnetic surfaces. (author) [pt

  6. Dusty plasmas

    International Nuclear Information System (INIS)

    Jones, M.E.; Winske, D.; Keinigs, R.; Lemons, D.

    1996-01-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The objective of this project has been to develop a fundamental understanding of dusty plasmas at the Laboratory. While dusty plasmas are found in space in galactic clouds, planetary rings, and cometary tails, and as contaminants in plasma enhanced fabrication of microelectronics, many of their properties are only partially understood. Our work has involved both theoretical analysis and self-consistent plasma simulations to understand basic properties of dusty plasmas related to equilibrium, stability, and transport. Such an understanding can improve the control and elimination of plasma dust in industrial applications and may be important in the study of planetary rings and comet dust tails. We have applied our techniques to the study of charging, dynamics, and coagulation of contaminants in plasma processing reactors for industrial etching and deposition processes and to instabilities in planetary rings and other space plasma environments. The work performed in this project has application to plasma kinetics, transport, and other classical elementary processes in plasmas as well as to plasma waves, oscillations, and instabilities

  7. Plasma chromatography

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    This book examines the fundamental theory and various applications of ion mobility spectroscopy. Plasma chromatography developed from research on the diffusion and mobility of ions. Topics considered include instrument design and description (e.g., performance, spectral interpretation, sample handling, mass spectrometry), the role of ion mobility in plasma chromatography (e.g., kinetic theory of ion transport), atmospheric pressure ionization (e.g., rate equations), the characterization of isomers by plasma chromatography (e.g., molecular ion characteristics, polynuclear aromatics), plasma chromatography as a gas chromatographic detection method (e.g., qualitative analysis, continuous mobility monitoring, quantitative analysis), the analysis of toxic vapors by plasma chromatography (e.g., plasma chromatograph calibration, instrument control and data processing), the analysis of semiconductor devices and microelectronic packages by plasma chromatography/mass spectroscopy (e.g., analysis of organic surface contaminants, analysis of water in sealed electronic packages), and instrument design and automation (hardware, software)

  8. Filamentary magnetohydrodynamic plasmas

    International Nuclear Information System (INIS)

    Kinney, R.; Tajima, T.; McWilliams, J.C.; Petviashvili, N.

    1994-01-01

    A filamentary construct of magnetohydrodynamical plasma dynamics based on the Elsaesser variables is developed. This approach is modeled after discrete vortex models of hydrodynamical turbulence, which cannot be expected in general to produce results identical to those based on a Fourier decomposition of the fields. In a highly intermittent plasma, the induction force is small compared to the convective motion, and when this force is neglected, the plasma vortex system is described by a Hamiltonian. A statistical treatment of a collection of discrete current-vorticity concentrations is given. Canonical and microcanonical statistical calculations show that both the vorticity and the current spectra are peaked at long wavelengths, and the expected states revert to known hydrodynamical states as the magnetic field vanishes. These results differ from previous Fourier-based statistical theories, but it is found that when the filament calculation is expanded to include the inductive force, the results approach the Fourier equilibria in the low-temperature limit, and the previous Hamiltonian plasma vortex results in the high-temperature limit. Numerical simulations of a large number of filaments are carried out and support the theory. A three-dimensional vortex model is presented as well, which is also Hamiltonian when the inductive force is neglected. A statistical calculation in the canonical ensemble and numerical simulations show that a nonzero large-scale magnetic field is statistically favored, and that the preferred shape of this field is a long, thin tube of flux. Possible applications to a variety of physical phenomena are suggested

  9. Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages

    Science.gov (United States)

    The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US are well known for emerging repeatedly as novel clonal lineages. These successions of dominant clones have historically been named US1-US24, in order of appearance, since their first characterization usi...

  10. Helium turbo-expander with an alternator

    International Nuclear Information System (INIS)

    Akiyama, Yoshitane

    1980-01-01

    Study was made on a helium turbo-expander, the heart of helium refrigerator systems, in order to develop a system which satisfies the required conditions. A helium turbo-expander with externally pressurized helium gas bearings at the temperature of liquid nitrogen and an alternator as a brake have been employed. The essential difference between a helium turbo-expander and a nitrogen turbo-expander was clarified. The gas bearing lubricated with nitrogen at room temperature and the gas bearing lubricated with helium at low temperature were tested. The flow rate of helium in a helium refrigerator for a large superconducting magnet is comparatively small, therefore a helium turbine must be small, but the standard for large turbine design can be applied to such small turbine. Using the alternator as a brake, the turbo-expander was easily controllable electrically. The prototype turbo-expander was made, and the liquefaction test with it and MHD power generation test were carried out. (Kako, I.)

  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 bla OXA-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 bla OXA-23-like including two that also harbored bla OXA-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

  12. Selection and Clonal Propagation of High Artemisinin Genotypes of Artemisia annua

    Science.gov (United States)

    Wetzstein, Hazel Y.; Porter, Justin A.; Janick, Jules; Ferreira, Jorge F. S.; Mutui, Theophilus M.

    2018-01-01

    Artemisinin, produced in the glandular trichomes of Artemisia annua L. is a vital antimalarial drug effective against Plasmodium falciparum resistant to quinine-derived medicines. Although work has progressed on the semi-synthetic production of artemisinin, field production of A. annua remains the principal commercial source of the compound. Crop production of artemisia must be increased to meet the growing worldwide demand for artemisinin combination therapies (ACTs) to treat malaria. Grower artemisinin yields rely on plants generated from seeds from open-pollinated parents. Although selection has considerably increased plant artemisinin concentration in the past 15 years, seed-generated plants have highly variable artemisinin content that lowers artemisinin yield per hectare. Breeding efforts to produce improved F1 hybrids have been hampered by the inability to produce inbred lines due to self-incompatibility. An approach combining conventional hybridization and selection with clonal propagation of superior genotypes is proposed as a means to enhance crop yield and artemisinin production. Typical seed-propagated artemisia plants produce less than 1% (dry weight) artemisinin with yields below 25 kg/ha. Genotypes were identified producing high artemisinin levels of over 2% and possessing improved agronomic characteristics such as high leaf area and shoot biomass production. Field studies of clonally-propagated high-artemisinin plants verified enhanced plant uniformity and an estimated gross primary productivity of up to 70 kg/ha artemisinin, with a crop density of one plant m-2. Tissue culture and cutting protocols for the mass clonal propagation of A. annua were developed for shoot regeneration, rooting, acclimatization, and field cultivation. Proof of concept studies showed that both tissue culture-regenerated plants and rooted cutting performed better than plants derived from seed in terms of uniformity, yield, and consistently high artemisinin content. Use of

  13. The Yaglom law in the expanding solar wind

    International Nuclear Information System (INIS)

    Gogoberidze, G.; Perri, S.; Carbone, V.

    2013-01-01

    We study the Yaglom law, which relates the mixed third-order structure function to the average dissipation rate of turbulence, in a uniformly expanding solar wind by using the two-scale expansion model of magnetohydrodynamic (MHD) turbulence. We show that due to the expansion of the solar wind, two new terms appear in the Yaglom law. The first term is related to the decay of the turbulent energy by nonlinear interactions, whereas the second term is related to the non-zero cross-correlation of the Elsässer fields. Using magnetic field and plasma data from WIND and Helios 2 spacecrafts, we show that at lower frequencies in the inertial range of MHD turbulence the new terms become comparable to Yaglom's third-order mixed moment, and therefore they cannot be neglected in the evaluation of the energy cascade rate in the solar wind.

  14. 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.

  15. Testing for disconnection and distance effects on physiological self-recognition within clonal fragments of Potentilla reptans

    NARCIS (Netherlands)

    Chen, Bin; Vermeulen, Peter; During, Heinjo; Anten, Niels

    2015-01-01

    Evidence suggests that belowground self-recognition in clonal plants can be disrupted between sister ramets by the loss of connections or long distances within a genet. However, these results may be confounded by severing connections between ramets in the setups. Using Potentilla reptans, we

  16. Clonal mobility and its implications for spatio-temporal patterns of plant communities: what do we need to know next?

    Czech Academy of Sciences Publication Activity Database

    Zobel, M.; Moora, M.; Herben, Tomáš

    2010-01-01

    Roč. 119, č. 5 (2010), s. 802-806 ISSN 0030-1299 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal mobility * spatio-temporal patterns * plant communities Subject RIV: EF - Botanics Impact factor: 3.393, year: 2010

  17. Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

    Science.gov (United States)

    Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study included US-8 (n=28), US-11 (n=27), US-23 (n=166), and US-24 (n=36), with isolates originating from 23 of the U...

  18. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

    Directory of Open Access Journals (Sweden)

    Jolene R Bowers

    Full Text Available 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.

  19. Marked heterogeneity in growth characteristics of myoblast clonal cultures and myoblast mixed cultures obtained from the same individual.

    Science.gov (United States)

    Maier, Andrea B; Cohen, Ron; Blom, Joke; van Heemst, Diana; Westendorp, Rudi G J

    2012-01-01

    Sarcopenia is defined as an age-related decrease in skeletal muscle mass and function while adjacent satellite cells are unable to compensate for this loss. However, myoblast cultures can be established even in the presence of sarcopenia. It is yet unknown whether satellite cells from failing muscle in older age are equally affected, as human satellite cells have been assessed using myoblast mixed cultures and not by using myoblast clonal cultures. We questioned to what extent myoblast mixed cultures reflect the in vivo characteristics of single satellite cells from adult skeletal muscle. We established a myoblast mixed culture and three myoblast clonal cultures out of the same muscle biopsy and cultured these cells for 100 days. Replicative capacity and oxidative stress resistance were compared. We found marked heterogeneity between the myoblast clonal cultures that all had a significantly lower replicative capacity when compared to the mixed culture. Replicative capacity of the clonal cultures was inversely related to the β-galactosidase activity after exposure to oxidative stress. Addition of L-carnosine enhanced the remaining replicative capacity in all cultures with a concomitant marginal decrease in β-galactosidase activity. It is concluded that myoblast mixed cultures in vitro do not reflect the marked heterogeneity between single isolated satellite cells. The consequences of the heterogeneity on muscle performance remain to be established. Copyright © 2011 S. Karger AG, Basel.

  20. Critical analysis of the stringent complete response in multiple myeloma: contribution of sFLC and bone marrow clonality.

    Science.gov (United States)

    Martínez-López, Joaquín; Paiva, Bruno; López-Anglada, Lucía; Mateos, María-Victoria; Cedena, Teresa; Vidríales, María-Belén; Sáez-Gómez, María Auxiliadora; Contreras, Teresa; Oriol, Albert; Rapado, Inmaculada; Teruel, Ana-Isabel; Cordón, Lourdes; Blanchard, María Jesús; Bengoechea, Enrique; Palomera, Luis; de Arriba, Felipe; Cueto-Felgueroso, Cecilia; Orfao, Alberto; Bladé, Joan; San Miguel, Jesús F; Lahuerta, Juan José

    2015-08-13

    Stringent complete response (sCR) criteria are used in multiple myeloma as a deeper response category compared with CR, but prospective validation is lacking, it is not always clear how evaluation of clonality is performed, and is it not known what the relative clinical influence is of the serum free light chain ratio (sFLCr) and bone marrow (BM) clonality to define more sCR. To clarify this controversy, we focused on 94 patients that reached CR, of which 69 (73%) also fulfilled the sCR criteria. Patients with sCR displayed slightly longer time to progression (median, 62 vs 53 months, respectively; P = .31). On analyzing this contribution to the prognosis of sFLCr or clonality, it was found that the sFLCr does not identify patients in CR at distinct risk; by contrast, low-sensitive multiparametric flow cytometry (MFC) immunophenotyping (2 colors), which is equivalent to immunohistochemistry, identifies a small number of patients (5 cases) with high residual tumor burden and dismal outcome; nevertheless, using traditional 4-color MFC, persistent clonal BM disease was detectable in 36% of patients, who, compared with minimal residual disease-negative cases, had a significantly inferior outcome. These results show that the current definition of sCR should be revised. © 2015 by The American Society of Hematology.

  1. CLO-PLA: a database of clonal and bud-bank traits of the Central European flora

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Danihelka, J.; Chrtek, Jindřich; de Bello, Francesco; Herben, Tomáš

    2017-01-01

    Roč. 98, č. 4 (2017), s. 1179 ISSN 0012-9658 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : Clonal traits * Central Europe * CLO-PLA database * bud-bank traits Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 4.809, year: 2016

  2. 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,

  3. Vegetative regeneration of invasive Ludwigia cytotypes from clonal bud banks across resource gradients: colonizing diploid outperforms polyploid

    Science.gov (United States)

    Understanding functional traits that underlie the colonization of invasive plants is key to developing sustainable management strategies to curtail invasions at the establishment phase. Although common, recruitment of clonal plant species from bud banks is often overlooked but may be a key transiti...

  4. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    Science.gov (United States)

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  5. Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains.

    NARCIS (Netherlands)

    Li, S.; Skov, R.L.; Han, X.; Larsen, A.R.; Larsen, J.; Sorum, M.; Wulf, M.; Voss, A.; Hiramatsu, K.; Ito, T.

    2011-01-01

    The structures of staphylococcal cassette chromosome mec (SCCmec) elements carried by 31 clonal complex 398 (CC398) methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from the participants at a conference were analyzed. The SCCmecs were classified into novel types, namely, IX, X,

  6. Variable effects of dexamethasone on protein synthesis in clonal rat osteosarcoma cells

    International Nuclear Information System (INIS)

    Hodge, B.O.; Kream, B.E.

    1988-01-01

    We examined the effects of dexamethasone on protein synthesis in clonal rat osteoblastic osteosarcoma (ROS) cell lines by measuring the incorporation of [ 3 H]proline into collagenase-digestible and noncollagen protein in the cell layer and medium of the cultures. In ROS 17/2 and subclone C12 of ROS 17/2.8, dexamethasone decreased collagen synthesis with no change in DNA content of the cultures. In ROS 17/2.8 and its subclone G2, dexamethasone stimulated collagen and noncollagen protein synthesis, with a concomitant decrease in the DNA content of the cells. These data indicate that ROS cell lines are phenotypically heterogeneous and suggest that in normal bone there may be distinct subpopulations of osteoblasts with varying phenotypic traits with respect to the regulation of protein synthesis

  7. Genetic structure of farmer-managed varieties in clonally-propagated crops.

    Science.gov (United States)

    Scarcelli, N; Tostain, S; Vigouroux, Y; Luong, V; Baco, M N; Agbangla, C; Daïnou, O; Pham, J L

    2011-08-01

    The relative role of sexual reproduction and mutation in shaping the diversity of clonally propagated crops is largely unknown. We analyzed the genetic diversity of yam-a vegetatively-propagated crop-to gain insight into how these two factors shape its diversity in relation with farmers' classifications. Using 15 microsatellite loci, we analyzed 485 samples of 10 different yam varieties. We identified 33 different genotypes organized in lineages supported by high bootstrap values. We computed the probability that these genotypes appeared by sexual reproduction or mutation within and between each lineage. This allowed us to interpret each lineage as a product of sexual reproduction that has evolved by mutation. Moreover, we clearly noted a similarity between the genetic structure and farmers' classifications. Each variety could thus be interpreted as being the product of sexual reproduction having evolved by mutation. This highly structured diversity of farmer-managed varieties has consequences for the preservation of yam diversity.

  8. Characterisation of free and glycosidically bound odourant compounds of Aragonez clonal musts by GC-O.

    Science.gov (United States)

    Botelho, Goreti; Mendes-Faia, Arlete; Clímaco, Maria Cristina

    2010-01-11

    To evaluate the potential aroma of Aragonez clonal red musts, several free and glycosidically bound odourant compounds were extracted. Then, the gas chromatography-olfactometry (GC-O) posterior intensity method was used to evaluate their odour intensity and the compounds were identified by gas chromatography-mass spectrometry (GC-MS). A group of eight sniffers evaluated free and bound fractions of Aragonez musts and perceived forty-three and twenty-two odourant peaks respectively. Furaneol (burnt sugar, candy-cotton) and vanillin (vanilla, sweet) were identified in both free and bound fractions of Aragonez musts, indicating their grape-derived origin. Principal component analysis (PCA) was applied to the posterior intensity method data and a relationship between the different odourant compound variables and the free fractions was established. Two principal components (PCs) were found which together explained 100% of the total variance. A large number of potentially important but yet unknown odourants was detected by the GC-O analysis.

  9. 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

    conditions and plant morphological characteristics. Conclusions: The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between......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....... Methods: Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity...

  10. Cell proliferation in the Drosophila adult brain revealed by clonal analysis and bromodeoxyuridine labelling

    Directory of Open Access Journals (Sweden)

    Brand Andrea H

    2009-03-01

    Full Text Available Abstract Background The production of new neurons during adulthood and their subsequent integration into a mature central nervous system have been shown to occur in all vertebrate species examined to date. However, the situation in insects is less clear and, in particular, it has been reported that there is no proliferation in the Drosophila adult brain. Results We report here, using clonal analysis and 5'-bromo-2'-deoxyuridine (BrdU labelling, that cell proliferation does occur in the Drosophila adult brain. The majority of clones cluster on the ventrolateral side of the antennal lobes, as do the BrdU-positive cells. Of the BrdU-labelled cells, 86% express the glial gene reversed polarity (repo, and 14% are repo negative. Conclusion We have observed cell proliferation in the Drosophila adult brain. The dividing cells may be adult stem cells, generating glial and/or non-glial cell types.

  11. 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...... clone 54B was found to dominate the parent 54A clone when grown as mixed subcutaneous xenografts in nude mice, whereas no dominance was exerted during in vitro growth. The in vivo dominance could not be explained by differences in growth kinetics between the two tumour cell lines, and the interaction...... was not dependent on 54B being in excess in mixed tumours. The dominance was dependent on close in vivo contact as no remote effect on the growth of 54A was found when the dominating 54B cells were growing in the opposite flank of tumour-bearing mice. Irradiation inactivated 54B cells were unable to exert...

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Clonal spread of Staphylococcus aureus with reduced susceptibility to oxacillin in a dermatological hospital unit

    DEFF Research Database (Denmark)

    Thomsen, Marianne Kragh; Rasmussen, Mads; Fuursted, Kurt

    2006-01-01

    transmission routes in order to intervene and prevent further spread. Clonality of the isolates was confirmed by pulsed field gel electrophoresis. Several breaches in infection control procedures were revealed suggesting both direct and indirect transmission between patients. Defective skin barriers, high...... carrier rates of S. aureus in dermatological patients and high consumption rates of dicloxacillin in the department might facilitate transmission. Following improvement of the general infection control measures, and after reassessment of the antibiotic policy in the department, the outbreak has......In November 2000, we became aware of isolates of Staphylococcus aureus with borderline resistance to oxacillin (BORSA) from patients in the Department of Dermatology, Aarhus University Hospital. The objective was to describe the isolates phenotypically and genotypically and to assess possible...

  17. The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally.

    Science.gov (United States)

    Díaz-Valderrama, J R; Aime, M C

    2016-06-01

    The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IA(s)) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IA(s) values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America.

  18. Clonal profile, virulence and resistance of Staphylococcus aureus isolated from sheep milk

    Directory of Open Access Journals (Sweden)

    Katheryne Benini Martins

    2015-06-01

    Full Text Available The objective of this study was to characterize the clonal profile, virulence factors and antimicrobial resistance, particularly oxacillin resistance, of Staphylococcus aureus isolated from sheep milk. Milk samples were collected from all teats for the California Mastitis Test (CMT, somatic cell count, identification of S. aureus, investigation in these strains of genes encoding toxins (sea, seb, sec, sed, tst, biofilm (icaA, icaC, icaD, bap, leukocidin (luk-PV oxacillin resistance by mecA gene detection and susceptibility testing (12 antibiotics. Messenger RNA expression was evaluated by RT-PCR in isolates carrying toxin and biofilm genes. Biofilm formation was also evaluated phenotypically by adherence to polystyrene plates. The clonal profile of S. aureus was investigated by pulsed-field gel electrophoresis. A total of 473 milk samples were collected from 242 animals on three farms and 20 S. aureus strains were isolated and none carried the mecA gene. The two sec gene-positive isolates and the isolates carrying the tst and luk-PV genes were positive by RT-PCR. Staphylococcus aureus isolated from the three flocks studied showed high susceptibility to the drugs tested and none was biofilm producer, indicating that biofilm formation was not a virulence factor causing infection by these strains. The typing of 17 S. aureus isolates revealed the presence of a common clone on the three farms studied, and the presence and expression of the sec and tst genes in one strain of this clone suggest the possible acquisition of virulence genes by this clone, a fact that is important for animal health and food hygiene.

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

    Science.gov (United States)

    Lomholt, Hans; Andersen, Klaus Ejner; Kilian, Mogens

    2005-11-01

    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, toxins, and were assigned to agr groups. S. aureus colonization patterns ranged from rare colonization over transient colonization to persistent colonization by a single clone or a dynamic exchange of up to five clones. Production of no single virulence factor including superantigens and toxins was significantly associated with exacerbation of eczema. In four children there was a shift between visits in agr group of colonizing clones. These shifts were associated with an increased SCORAD value of 19 (SE = 7, p = 0.009). Change of clones belonging to the same agr group was not associated with a higher 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 encoded octa peptides appeared to be active in vivo. Increased severity of eczema was related to a change in agr group and may have been because of inflammation triggered by the takeover of an antigenically different clone, as agr groups represent ancient phylogenetic lineages.

  20. Clonal profile, virulence and resistance of Staphylococcus aureus isolated from sheep milk.

    Science.gov (United States)

    Martins, Katheryne Benini; Faccioli-Martins, Patricia Yoshida; Riboli, Danilo Flávio Moraes; Pereira, Valéria Cataneli; Fernandes, Simone; Oliveira, Aline A; Dantas, Ariane; Zafalon, Luiz Francisco; da Cunha, Maria de Lourdes Ribeiro de Souza

    2015-06-01

    The objective of this study was to characterize the clonal profile, virulence factors and antimicrobial resistance, particularly oxacillin resistance, of Staphylococcus aureus isolated from sheep milk. Milk samples were collected from all teats for the California Mastitis Test (CMT), somatic cell count, identification of S. aureus, investigation in these strains of genes encoding toxins (sea, seb, sec, sed, tst), biofilm (icaA, icaC, icaD, bap), leukocidin (luk-PV) oxacillin resistance by mecA gene detection and susceptibility testing (12 antibiotics). Messenger RNA expression was evaluated by RT-PCR in isolates carrying toxin and biofilm genes. Biofilm formation was also evaluated phenotypically by adherence to polystyrene plates. The clonal profile of S. aureus was investigated by pulsed-field gel electrophoresis. A total of 473 milk samples were collected from 242 animals on three farms and 20 S. aureus strains were isolated and none carried the mecA gene. The two sec gene-positive isolates and the isolates carrying the tst and luk-PV genes were positive by RT-PCR. Staphylococcus aureus isolated from the three flocks studied showed high susceptibility to the drugs tested and none was biofilm producer, indicating that biofilm formation was not a virulence factor causing infection by these strains. The typing of 17 S. aureus isolates revealed the presence of a common clone on the three farms studied, and the presence and expression of the sec and tst genes in one strain of this clone suggest the possible acquisition of virulence genes by this clone, a fact that is important for animal health and food hygiene.

  1. Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate.

    Science.gov (United States)

    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

  2. Clonal profile, virulence and resistance of Staphylococcus aureus isolated from sheep milk

    Science.gov (United States)

    Martins, Katheryne Benini; Faccioli-Martins, Patricia Yoshida; Riboli, Danilo Flávio Moraes; Pereira, Valéria Cataneli; Fernandes, Simone; Oliveira, Aline A.; Dantas, Ariane; Zafalon, Luiz Francisco; da Cunha, Maria de Lourdes Ribeiro de Souza

    2015-01-01

    The objective of this study was to characterize the clonal profile, virulence factors and antimicrobial resistance, particularly oxacillin resistance, of Staphylococcus aureus isolated from sheep milk. Milk samples were collected from all teats for the California Mastitis Test (CMT), somatic cell count, identification of S. aureus, investigation in these strains of genes encoding toxins (sea, seb, sec, sed, tst), biofilm (icaA, icaC, icaD, bap), leukocidin (luk-PV) oxacillin resistance by mecA gene detection and susceptibility testing (12 antibiotics). Messenger RNA expression was evaluated by RT-PCR in isolates carrying toxin and biofilm genes. Biofilm formation was also evaluated phenotypically by adherence to polystyrene plates. The clonal profile of S. aureus was investigated by pulsed-field gel electrophoresis. A total of 473 milk samples were collected from 242 animals on three farms and 20 S. aureus strains were isolated and none carried the mecA gene. The two sec gene-positive isolates and the isolates carrying the tst and luk-PV genes were positive by RT-PCR. Staphylococcus aureus isolated from the three flocks studied showed high susceptibility to the drugs tested and none was biofilm producer, indicating that biofilm formation was not a virulence factor causing infection by these strains. The typing of 17 S. aureus isolates revealed the presence of a common clone on the three farms studied, and the presence and expression of the sec and tst genes in one strain of this clone suggest the possible acquisition of virulence genes by this clone, a fact that is important for animal health and food hygiene. PMID:26273271

  3. Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    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.

  4. 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.

  5. Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Gilbert Gwendolyn L

    2008-08-01

    Full Text Available Abstract Background Streptococcus agalactiae (Group B Streptococcus (GBS is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP based method for assigning GBS isolates to multilocus sequence typing (MLST-defined clonal complexes. Results It was found that a SNP set derived from the MLST database on the basis of maximisation of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. Conclusion A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.

  6. Anaphylactic Reactions After Discontinuation of Hymenoptera Venom Immunotherapy: A Clonal Mast Cell Disorder Should Be Suspected.

    Science.gov (United States)

    Bonadonna, Patrizia; Zanotti, Roberta; Pagani, Mauro; Bonifacio, Massimiliano; Scaffidi, Luigi; Olivieri, Elisa; Franchini, Maurizio; Reccardini, Federico; Costantino, Maria Teresa; Roncallo, Chiara; Mauro, Marina; Boni, Elisa; Rizzini, Fabio Lodi; Bilò, Maria Beatrice; Marcarelli, Anna Rosaria; Passalacqua, Giovanni

    2017-12-16

    Up to 75% of patients with severe anaphylactic reactions after Hymenoptera sting are at risk of further severe reactions if re-stung. Venom immunotherapy (VIT) is highly effective in protecting individuals with ascertained Hymenoptera venom allergy (HVA) and previous severe reactions. After a 3- to 5-year VIT course, most patients remain protected after VIT discontinuation. Otherwise, a lifelong treatment should be considered in high-risk patients (eg, in mastocytosis). Several case reports evidenced that patients with mastocytosis and HVA, although protected during VIT, can re-experience severe and sometimes fatal reactions after VIT discontinuation. To evaluate whether patients who lost protection after VIT discontinuation may suffer from clonal mast cell disorders. The survey describes the characteristics of patients who received a full course of VIT for previous severe reactions and who experienced another severe reaction at re-sting after VIT discontinuation. Those with a Red Española de Mastocitosis score of 2 or more or a serum basal tryptase level of more than 25 ng/mL underwent a hematological workup (bone marrow biopsy, KIT mutation, expression of aberrant CD25) and/or skin biopsy. Nineteen patients (mean age, 56.3 years; 89.5% males) were evaluated. All of them had received at least 4 years of VIT and were protected. After VIT discontinuation they were re-stung and developed, in all but 1 case, severe anaphylactic reactions (12 with loss of consciousness, in the absence of urticaria/angioedema). Eighteen patients (94.7%) had a clonal mast cell disorder, 8 of them with normal tryptase. Looking at this selected population, we suggest that mastocytosis should be considered in patients developing severe reactions at re-sting after VIT discontinuation and, as a speculation, patients with mastocytosis and HVA should be VIT-treated lifelong. Copyright © 2017. Published by Elsevier Inc.

  7. Antimicrobial Susceptibility and Clonality of Clinical Ureaplasma Isolates in the United States.

    Science.gov (United States)

    Fernández, Javier; Karau, Melissa J; Cunningham, Scott A; Greenwood-Quaintance, Kerryl E; Patel, Robin

    2016-08-01

    Ureaplasma urealyticum and Ureaplasma parvum are pathogens involved in urogenital tract and intrauterine infections and also in systemic diseases in newborns and immunosuppressed patients. There is limited information on the antimicrobial susceptibility and clonality of these species. In this study, we report the susceptibility of 250 contemporary isolates of Ureaplasma (202 U. parvum and 48 U. urealyticum isolates) recovered at Mayo Clinic, Rochester, MN. MICs of doxycycline, azithromycin, ciprofloxacin, tetracycline, erythromycin, and levofloxacin were determined by broth microdilution, with MICS of the last three interpreted according to CLSI guidelines. Levofloxacin resistance was found in 6.4% and 5.2% of U. parvum and U. urealyticum isolates, respectively, while 27.2% and 68.8% of isolates, respectively, showed ciprofloxacin MICs of ≥4 μg/ml. The resistance mechanism of levofloxacin-resistant isolates was due to mutations in parC, with the Ser83Leu substitution being most frequent, followed by Glu87Lys. No macrolide resistance was found among the 250 isolates studied; a single U. parvum isolate was tetracycline resistant. tet(M) was found in 10 U. parvum isolates, including the single tetracycline-resistant isolate, as well as in 9 isolates which had low tetracycline and doxycycline MICs. Multilocus sequence typing (MLST) performed on a selection of 46 isolates showed high diversity within the clinical Ureaplasma isolates studied, regardless of antimicrobial susceptibility. The present work extends previous knowledge regarding susceptibility to antimicrobial agents, resistance mechanisms, and clonality of Ureaplasma species in the United States. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

    Science.gov (United States)

    Herrera, C M; Pozo, M I; Bazaga, P

    2011-11-01

    Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

  9. Effects of aspect on clonal reproduction and biomass allocation of layering modules of Nitraria tangutorum in nebkha dunes.

    Directory of Open Access Journals (Sweden)

    Qinghe Li

    Full Text Available The formation of many nebkha dunes relies on the layering of clonal plants. The microenvironmental conditions of such phytogenic nebkha are heterogeneous depending on the aspect and slope. Exploring the effects of aspect on clonal reproduction and biomass allocation can be useful in understanding the ecological adaptation of species. We hypothesized that on the windward side layering propagation would be promoted, that biomass allocation to leaves and stems of ramets would increase, and that the effects of aspect would be greater in the layering with larger biomass. To test these hypotheses, we surveyed the depth of germination points of axillary buds, the rate of ramet sprouting, the density of adventitious root formation points, and the biomass of modules sprouting from layering located on the NE, SE, SW and NW, aspects of Nitraria tangutorum nebkhas. The windward side was located on the NW and SW aspects. The results indicated that conditions of the NW aspect were more conducive to clonal reproduction and had the highest rate of ramet sprouting and the highest density of adventitious formation points. For the modules sprouting from layering on the SW aspect, biomass allocation to leaves and stems was greatest with biomass allocation to adventitious roots being lowest. This result supported our hypothesis. Contrary to our hypothesis, the effects of aspect were greater in layering of smaller biomass. These results support the hypothesis that aspect does affect layering propagation capacity and biomass allocation in this species. Additionally, clonal reproduction and biomass allocation of modules sprouting from layering with smaller biomass was more affected by aspect. These results suggest that the clonal growth of N. tangutorum responses to the microenvironmental heterogeneity that results from aspect of the nebkha.

  10. Effects of aspect on clonal reproduction and biomass allocation of layering modules of Nitraria tangutorum in nebkha dunes.

    Science.gov (United States)

    Li, Qinghe; Xu, Jun; Li, Huiqing; Wang, Saixiao; Yan, Xiu; Xin, Zhiming; Jiang, Zeping; Wang, Linlong; Jia, Zhiqing

    2013-01-01

    The formation of many nebkha dunes relies on the layering of clonal plants. The microenvironmental conditions of such phytogenic nebkha are heterogeneous depending on the aspect and slope. Exploring the effects of aspect on clonal reproduction and biomass allocation can be useful in understanding the ecological adaptation of species. We hypothesized that on the windward side layering propagation would be promoted, that biomass allocation to leaves and stems of ramets would increase, and that the effects of aspect would be greater in the layering with larger biomass. To test these hypotheses, we surveyed the depth of germination points of axillary buds, the rate of ramet sprouting, the density of adventitious root formation points, and the biomass of modules sprouting from layering located on the NE, SE, SW and NW, aspects of Nitraria tangutorum nebkhas. The windward side was located on the NW and SW aspects. The results indicated that conditions of the NW aspect were more conducive to clonal reproduction and had the highest rate of ramet sprouting and the highest density of adventitious formation points. For the modules sprouting from layering on the SW aspect, biomass allocation to leaves and stems was greatest with biomass allocation to adventitious roots being lowest. This result supported our hypothesis. Contrary to our hypothesis, the effects of aspect were greater in layering of smaller biomass. These results support the hypothesis that aspect does affect layering propagation capacity and biomass allocation in this species. Additionally, clonal reproduction and biomass allocation of modules sprouting from layering with smaller biomass was more affected by aspect. These results suggest that the clonal growth of N. tangutorum responses to the microenvironmental heterogeneity that results from aspect of the nebkha.

  11. Plasma physics

    CERN Document Server

    Drummond, James E

    1961-01-01

    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

  12. Plasma generator

    International Nuclear Information System (INIS)

    Omichi, Takeo; Yamanaka, Toshiyuki.

    1976-01-01

    Object: To recycle a coolant in a sealed hollow portion formed interiorly of a plasma limiter itself to thereby to cause direct contact between the coolant and the plasma limiter and increase of contact area therebetween to cool the plasma limiter. Structure: The heat resulting from plasma generated during operation and applied to the body of the plasma limiter is transmitted to the coolant, which recycles through an inlet and outlet pipe, an inlet and outlet nozzle and a hollow portion to hold the plasma limiter at a level less than a predetermined temperature. On the other hand, the heater wire is, at the time of emergency operation, energized to heat the plasma limiter, but this heat is transmitted to the limiter body to increase the temperature thereof. However, the coolant recycling the hollow portion comes into direct contact with the limiter body, and since the plasma limiter surround the hollow portion, the heat amount transmitted from the limiter body to the coolant increases to sufficiently cool the plasma limiter. (Yoshihara, H.)

  13. Bridge between fusion plasma and plasma processing

    International Nuclear Information System (INIS)

    Ohno, Noriyasu; Takamura, Shuichi

    2008-01-01

    In the present review, relationship between fusion plasma and processing plasma is discussed. From boundary-plasma studies in fusion devices new applications such as high-density plasma sources, erosion of graphite in a hydrogen plasma, formation of helium bubbles in high-melting-point metals and the use of toroidal plasmas for plasma processing are emerging. The authors would like to discuss a possibility of knowledge transfer from fusion plasmas to processing plasmas. (T. Ikehata)

  14. The Expanded Large Scale Gap Test

    Science.gov (United States)

    1987-03-01

    NSWC TR 86-32 DTIC THE EXPANDED LARGE SCALE GAP TEST BY T. P. LIDDIARD D. PRICE RESEARCH AND TECHNOLOGY DEPARTMENT ’ ~MARCH 1987 Ap~proved for public...arises, to reduce the spread in the LSGT 50% gap value.) The worst charges, such as those with the highest or lowest densities, the largest re-pressed...Arlington, VA 22217 PE 62314N INS3A 1 RJ14E31 7R4TBK 11 TITLE (Include Security CIlmsilficatiorn The Expanded Large Scale Gap Test . 12. PEIRSONAL AUTHOR() T

  15. Semiclassical expanding discrete space-times

    International Nuclear Information System (INIS)

    Cobb, W.K.; Smalley, L.L.

    1981-01-01

    Given the close ties between general relativity and geometry one might reasonably expect that quantum effects associated with gravitation might also be tied to the geometry of space-time, namely, to some sort of discreteness in space-time itself. In particular it is supposed that space-time consists of a discrete lattice of points rather than the usual continuum. Since astronomical evidence seems to suggest that the universe is expanding, the lattice must also expand. Some of the implications of such a model are that the proton should presently be stable, and the universe should be closed although the mechanism for closure is quantum mechanical. (author)

  16. Theoretical models for recombination in expanding gas

    International Nuclear Information System (INIS)

    Avron, Y.; Kahane, S.

    1978-09-01

    In laser isotope separation of atomic uranium, one is confronted with the theoretical problem of estimating the concentration of thermally ionized uranium atoms. To investigate this problem theoretical models for recombination in an expanding gas and in the absence of local thermal equilibrium have been constructed. The expansion of the gas is described by soluble models of the hydrodynamic equation, and the recombination by rate equations. General results for the freezing effect for the suitable ranges of the gas parameters are obtained. The impossibility of thermal equilibrium in expanding two-component systems is proven

  17. Plasma waves

    National Research Council Canada - National Science Library

    Swanson, D. G

    1989-01-01

    ... Swanson, D.G. (Donald Gary), D a t e - Plasma waves. Bibliography: p. Includes index. 1. Plasma waves. QC718.5.W3S43 1989 ISBN 0-12-678955-X I. Title. 530.4'4 88-34388 Printed in the United Sta...

  18. Plasma properties

    International Nuclear Information System (INIS)

    Weitzner, H.

    1991-06-01

    The Magneto-Fluid Dynamics Division continues to study a broad range of problems originating in plasma physics. Its principal focus is fusion plasma physics, and most particularly topics of particular significance for the world magnetic fusion program. During the calendar year 1990 we explored a wide range of topics including RF-induced transport as a plasma control mechanism, edge plasma modelling, further statistical analysis of L and H mode tokamak plasmas, antenna design, simulation of the edge of a tokamak plasma and the L-H transition, interpretation of the CCT experimental results at UCLA, turbulent transport, studies in chaos, the validity of moment approximations to kinetic equations and improved neoclassical modelling. In more basic studies we examined the statistical mechanisms of Coulomb systems and applied plasma ballooning mode theory to conventional fluids in order to obtain novel fluid dynamics stability results. In space plasma physics we examined the problem of reconnection, the effect of Alfven waves in space environments, and correct formulation of boundary conditions of the Earth for waves in the ionosphere

  19. Plasma container

    International Nuclear Information System (INIS)

    Ebisawa, Katsuyuki.

    1985-01-01

    Purpose: To enable to easily detect that the thickness of material to be abraded is reduced to an allowable limit from the outerside of the plasma container even during usual operation in a plasma vessel for a thermonuclear device. Constitution: A labelled material is disposed to the inside or rear face of constituent members of a plasma container undergoing the irradiation of plasma particles. A limiter plate to be abraded in the plasma container is composed of an armour member and heat removing plate, in which the armour member is made of graphite and heat-removing plate is made of copper. If the armour member is continuously abraded under the effect of sputtering due to plasma particles, silicon nitride embedded so far in the graphite at last appears on the surface of the limiter plate to undergo the impact shocks of the plasma particles. Accordingly, abrasion of the limiter material can be detected by a detector comprising gas chromatography and it can easily be detected from the outside of the plasma content even during normal operation. (Horiuchi, T.)

  20. Cosmic plasma

    Energy Technology Data Exchange (ETDEWEB)

    Alfven, H [California Univ., San Diego, La Jolla (USA)

    1981-01-01

    The properties of space plasmas are analyzed, based on laboratory results and data obtained by in situ measurements in the magnetosphere (including the heliosphere). Attention is given to the question of how much knowledge can be gained by a systematic comparison of different regions of plasma, and plasmas are considered with linear dimensions varying from laboratory size up to the Hubble distance. The traditional magnetic field description of plasmas is supplemented by an electric current description and it is demonstrated that many problems are easier to understand with a dualistic approach. Using the general plasma properties obtained, the origin and evolution of the solar system is summarized and the evolution and present structure of the universe (cosmology) is discussed.

  1. Plasma device

    International Nuclear Information System (INIS)

    Thode, L.E.

    1981-01-01

    A relativistic electron beam generator or accelerator produces a high-voltage electron beam which is modulated to initiate electron bunching within the beam which is then applied to a high-density target plasma which typically comprises DT, DD, or similar thermonuclear gas at a density of 10 17 to 10 20 electrons per cubic centimeter. As a result, relativistic streaming instabilities are initiated within the high-density target plasma causing the relativistic electron beam to efficiently deposit its energy into a small localized region of the high-density plasma target. The high-temperature plasma can be used to heat a high Z material to generate radiation. Alternatively, a tunable radiation source is produced by using a moderate Z gas or a mixture of high Z and low Z gas as the target plasma. (author)

  2. Two Types of Expanding Lie Algebra and New Expanding Integrable Systems

    International Nuclear Information System (INIS)

    Dong Huanhe; Yang Jiming; Wang Hui

    2010-01-01

    From a new Lie algebra proposed by Zhang, two expanding Lie algebras and its corresponding loop algebras are obtained. Two expanding integrable systems are produced with the help of the generalized zero curvature equation. One of them has complex Hamiltion structure with the help of generalized Tu formula (GTM). (general)

  3. Superconducting plasmas

    International Nuclear Information System (INIS)

    Ohnuma, Toshiro; Ohno, J.

    1994-01-01

    Superconducting (SC) plasmas are proposed and investigated. The SC plasmas are not yet familiar and have not yet been studied. However, the existence and the importance of SC plasmas are stressed in this report. The existence of SC plasmas are found as follows. There is a fundamental property of Meissner effect in superconductors, which shows a repulsive effect of magnetic fields. Even in that case, in a microscopic view, there is a region of magnetic penetration. The penetration length λ is well-known as London's penetration depth, which is expressed as δ = (m s /μ 0 n s q s 2 ) 1/2 where m s , n s , q s and μ o show the mass, the density, the charge of SC electron and the permeability in free space, respectively. Because this expression is very simple, no one had tried it into more simple and meaningful form. Recently, one of the authors (T.O.) has found that the length can be expressed into more simple and understandable fundamental form as λ = c/ω ps where c = (ε 0 μ 0 ) -1/2 and ω ps = (n s q s 2 /m s ε 0 ) 1/2 are the light velocity and the superconducting plasma frequency. From this simple expression, the penetration depth of the magnetic field to SC is found as a SC plasma skin depth, that is, the fundamental property of SC can be expressed by the SC plasmas. This discovery indicates an importance of the studies of superconducting plasmas. From these points, several properties (propagating modes et al) of SC plasmas, which consist of SC electrons, normal electrons and lattice ions, are investigated in this report. Observations of SC plasma frequency is also reported with a use of Terahertz electromagnet-optical waves

  4. Stone extraction balloon-guided repeat self-expanding metal stent placement

    Institute of Scientific and Technical Information of China (English)

    Hyung; Hun; Kim; Jeong; Seop; Moon; Soo; Hyung; Ryu; Jung; Hwan; Lee; You; Sun; Kim

    2010-01-01

    Self-expanding metal stent (SEMS) placement offers safe and effective palliation in patients with upper gastrointestinal obstruction due to a malignancy. Well described complications of SEMS placement include tumor growth, obstruction, and stent migration. SEMS occlusions are treated by SEMS redeployment, argon plasma coagulation application, balloon dilation, and surgical bypass. At our center, we usually place the second SEMS into the first SEMS if there is complete occlusion by the tumor. We discovered a...

  5. Confinement of laser plasma expansion with strong external magnetic field

    Science.gov (United States)

    Tang, Hui-bo; Hu, Guang-yue; Liang, Yi-han; Tao, Tao; Wang, Yu-lin; Hu, Peng; Zhao, Bin; Zheng, Jian

    2018-05-01

    The evolutions of laser ablation plasma, expanding in strong (∼10 T) transverse external magnetic field, were investigated in experiments and simulations. The experimental results show that the magnetic field pressure causes the plasma decelerate and accumulate at the plasma-field interface, and then form a low-density plasma bubble. The saturation size of the plasma bubble has a scaling law on laser energy and magnetic field intensity. Magnetohydrodynamic simulation results support the observation and find that the scaling law (V max ∝ E p /B 2, where V max is the maximum volume of the plasma bubble, E p is the absorbed laser energy, and B is the magnetic field intensity) is effective in a broad laser energy range from several joules to kilo-joules, since the plasma is always in the state of magnetic field frozen while expanding. About 15% absorbed laser energy converts into magnetic field energy stored in compressed and curved magnetic field lines. The duration that the plasma bubble comes to maximum size has another scaling law t max ∝ E p 1/2/B 2. The plasma expanding dynamics in external magnetic field have a similar character with that in underdense gas, which indicates that the external magnetic field may be a feasible approach to replace the gas filled in hohlraum to suppress the wall plasma expansion and mitigate the stimulated scattering process in indirect drive ignition.

  6. 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 ...

  7. Expanding economic opportunities in protracted displacement

    OpenAIRE

    Miki Takahashi; Michael Moroz; Jonathan Peters; Jason Pronyk; Richard Barltrop

    2018-01-01

    Welcome progress has been made towards realising commitments made by international donors and host country governments to expand economic opportunities for Syrian refugees and host communities in neighbouring countries. However targets and commitments also bring new challenges, and evidence must underpin new policies.

  8. 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…

  9. Custom Ontologies for Expanded Network Analysis

    Science.gov (United States)

    2006-12-01

    for Expanded Network Analysis. In Visualising Network Information (pp. 6-1 – 6-10). Meeting Proceedings RTO-MP-IST-063, Paper 6. Neuilly-sur-Seine...Even to this day, current research groups are working to develop an approach that involves taking all available text, video, imagery and audio and

  10. 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.

  11. Expanding economic opportunities in protracted displacement

    Directory of Open Access Journals (Sweden)

    Miki Takahashi

    2018-02-01

    Full Text Available Welcome progress has been made towards realising commitments made by international donors and host country governments to expand economic opportunities for Syrian refugees and host communities in neighbouring countries. However targets and commitments also bring new challenges, and evidence must underpin new policies.

  12. 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

  13. Expanding the Audience for the Performing Arts.

    Science.gov (United States)

    Andreasen, Alan R.

    Becoming involved in the arts is a process that involves movement through several stages, from disinterest to active attendance at and enthusiasm for performing arts events. Since target consumers at any time will differ in their placement on this continuum, marketing programs to expand arts audiences must first identify where each target segment…

  14. Expanded austenite, crystallography and residual stress

    DEFF Research Database (Denmark)

    Christiansen, Thomas; Hummelshøj, Thomas Strabo; Somers, Marcel A. J.

    2010-01-01

    The identity of expanded austenite as developing during low temperature nitriding and/or carburising of austenitic stainless steel has been under debate since the very first observation of this phase. In the present article, recent results obtained with (a) homogeneous samples of various uniform ...

  15. Expanded austenite; crystallography and residual stress

    DEFF Research Database (Denmark)

    Christiansen, Thomas; Hummelshøj, Thomas Strabo; Somers, Marcel A. J.

    2009-01-01

    The identity of expanded austenite as developing during low temperature nitriding and/or carburizing of austenitic stainless steel has been under debate since the very first observation of this phase. In the present article recent results obtained with i) homogeneous samples of various uniform co...

  16. Expanding Greenland’s Glacial Record

    DEFF Research Database (Denmark)

    Bjørk, Anders Anker

    . On order to expand the glacial history of Greenland, this thesis explores physical and geological archives for evidence of the glaciers’ past response to climatic variations. Using aerial photographs, the dynamic history of the Greenland Ice Sheet is extended back to 1900 C.E. Glacier changes covering...

  17. An Expanding Universe in the Classroom.

    Science.gov (United States)

    Chandler, David

    1991-01-01

    Two computer-generated star charts that can be used as overlay transparencies to show an expanding universe are presented. Directions on how to use the star charts to determine the Hubble constant and the age of the universe are provided. (KR)

  18. 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 ...

  19. Expanding CEP290 mutational spectrum in ciliopathies

    NARCIS (Netherlands)

    Travaglini, Lorena; Brancati, Francesco; Attie-Bitach, Tania; Audollent, Sophie; Bertini, Enrico; Kaplan, Josseline; Perrault, Isabelle; Iannicelli, Miriam; Mancuso, Brunella; Rigoli, Luciana; Rozet, Jean-Michel; Swistun, Dominika; Tolentino, Jerlyn; Dallapiccola, Bruno; Gleeson, Joseph G.; Valente, Enza Maria; Zankl, A.; Leventer, R.; Grattan-Smith, P.; Janecke, A.; D'Hooghe, M.; Sznajer, Y.; van Coster, R.; Demerleir, L.; Dias, K.; Moco, C.; Moreira, A.; Kim, C. Ae; Maegawa, G.; Petkovic, D.; Abdel-Salam, G. M. H.; Abdel-Aleem, A.; Zaki, M. S.; Marti, I.; Quijano-Roy, S.; Sigaudy, S.; de Lonlay, P.; Romano, S.; Touraine, R.; Koenig, M.; Lagier-Tourenne, C.; Messer, J.; Collignon, P.; Wolf, N.; Philippi, H.; Kitsiou Tzeli, S.; Halldorsson, S.; Johannsdottir, J.; Ludvigsson, P.; Phadke, S. R.; Udani, V.; Stuart, B.; Magee, A.; Lev, D.; Michelson, M.; Ben-Zeev, B.; Fischetto, R.; Benedicenti, F.; Stanzial, F.; Borgatti, R.; Accorsi, P.; Battaglia, S.; Fazzi, E.; Giordano, L.; Pinelli, L.; Boccone, L.; Bigoni, S.; Ferlini, A.; Donati, M. A.; Caridi, G.; Divizia, M. T.; Faravelli, F.; Ghiggeri, G.; Pessagno, A.; Briguglio, M.; Briuglia, S.; Salpietro, C. D.; Tortorella, G.; Adami, A.; Castorina, P.; Lalatta, F.; Marra, G.; Riva, D.; Scelsa, B.; Spaccini, L.; Uziel, G.; del Giudice, E.; Laverda, A. M.; Ludwig, K.; Permunian, A.; Suppiej, A.; Signorini, S.; Uggetti, C.; Battini, R.; Di Giacomo, M.; Cilio, M. R.; Di Sabato, M. L.; Leuzzi, V.; Parisi, P.; Pollazzon, M.; Silengo, M.; de Vescovi, R.; Greco, D.; Romano, C.; Cazzagon, M.; Simonati, A.; Al-Tawari, A. A.; Bastaki, L.; Mégarbané, A.; Sabolic Avramovska, V.; de Jong, M. M.; Stromme, P.; Koul, R.; Rajab, A.; Azam, M.; Barbot, C.; Martorell Sampol, L.; Rodriguez, B.; Pascual-Castroviejo, I.; Teber, S.; Anlar, B.; Comu, S.; Karaca, E.; Kayserili, H.; Yüksel, A.; Akcakus, M.; Al Gazali, L.; Sztriha, L.; Nicholl, D.; Woods, C. G.; Bennett, C.; Hurst, J.; Sheridan, E.; Barnicoat, A.; Hennekam, R.; Lees, M.; Blair, E.; Bernes, S.; Sanchez, H.; Clark, A. E.; DeMarco, E.; Donahue, C.; Sherr, E.; Hahn, J.; Sanger, T. D.; Gallager, T. E.; Dobyns, W. B.; Daugherty, C.; Krishnamoorthy, K. S.; Sarco, D.; Walsh, C. A.; McKanna, T.; Milisa, J.; Chung, W. K.; de Vivo, D. C.; Raynes, H.; Schubert, R.; Seward, A.; Brooks, D. G.; Goldstein, A.; Caldwell, J.; Finsecke, E.; Maria, B. L.; Holden, K.; Cruse, R. P.; Swoboda, K. J.; Viskochil, D.

    2009-01-01

    Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert

  20. 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…

  1. Bank Directors’ Perceptions of Expanded Auditor's Reports

    DEFF Research Database (Denmark)

    Boolaky, Pran Krishansing; Quick, Reiner

    2016-01-01

    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 o...

  2. Plasma universe

    International Nuclear Information System (INIS)

    Alfven, H.

    1986-04-01

    Traditionally the views in our cosmic environment have been based on observations in the visual octave of the electromagnetic spectrum, during the last half-century supplemented by infrared and radio observations. Space research has opened the full spectrum. Of special importance are the X-ray-gamma-ray regions, in which a number of unexpected phenomena have been discovered. Radiations in these regions are likely to originate mainly from magnetised cosmic plasma. Such a medium may also emit synchrotron radiation which is observable in the radio region. If we try to base a model of the universe on the plasma phenomena mentioned we find that the plasma universe is drastically different from the traditional visual universe. Information about the plasma universe can also be obtained by extrapolation of laboratory experiments and magnetospheric in situ measurements of plasma. This approach is possible because it is likely that the basic properties of plasma are the same everywhere. In order to test the usefulness of the plasma universe model we apply it to cosmogony. Such an approach seems to be rather successful. For example, the complicated structure of the Saturnian C ring can be accounted for. It is possible to reconstruct certain phenomena 4-5 bilions years ago with an accuracy of better than 1 percent

  3. 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.

  4. Charged dust structures in plasmas

    International Nuclear Information System (INIS)

    Cramer, N.F.; Vladimirov, S.V.

    1999-01-01

    We report here on theoretical investigations of the mechanical-electrostatic modes of vibration of a dust-plasma crystal, extending earlier work on the transverse modes of a horizontal line of grains (where the ions flow vertically downward to a plane horizontal cathode), the modes of two such lines of grains, and the modes of a vertical string of grains. The last two arrangements have the unique feature that the effect of the background plasma on the mutual grain interaction is asymmetric because of the wake downstream of the grains studied in. The characteristic frequencies of the vibrations are dependent on the parameters of the plasma and the dust grains, such as the Debye length and the grain charge, and so measurement of the frequencies could provide diagnostics of these quantities. Although the current boom in dusty plasma research is driven mainly by such industrial applications as plasma etching, sputtering and deposition, the physical outcomes of investigations in this rapidly expanding field cover many important topics in space physics and astrophysics as well. Examples are the interaction of dust with spacecraft, the structure of planetary rings, star formation, supernova explosions and shock waves. In addition, the study of the influence of dust in environmental research, such as in the Earth's ionosphere and atmosphere, is important. The unique binding of dust particles in a plasma opens possibilities for so-called super-chemistry, where the interacting bound elements are not atoms but dust grains

  5. Plasma physics

    International Nuclear Information System (INIS)

    1979-01-01

    This report contains the papers delivered at the AEB - Natal University summer school on plasma physics held in Durban during January 1979. The following topics were discussed: Tokamak devices; MHD stability; trapped particles in tori; Tokamak results and experiments; operating regime of the AEB Tokamak; Tokamak equilibrium; high beta Tokamak equilibria; ideal Tokamak stability; resistive MHD instabilities; Tokamak diagnostics; Tokamak control and data acquisition; feedback control of Tokamaks; heating and refuelling; neutral beam injection; radio frequency heating; nonlinear drift wave induced plasma transport; toroidal plasma boundary layers; microinstabilities and injected beams and quasilinear theory of the ion acoustic instability

  6. Plasma centrifuge

    International Nuclear Information System (INIS)

    Ikehata, Takashi; Mase, Hiroshi

    1998-01-01

    The plasma centrifuge is one of statistical isotope separation processes which uses the centrifugal force of a J x B driven rotating plasma in a magnetic field to give rise to the mass-dependent radial transport of isotopic ions. The system has been developed as an alternative to the gas centrifuge because a much higher rotational velocity and separation factor have been achieved. In this review, the physical aspects of the plasma centrifuge followed by the recent experimental achievements are described, especially in comparison with the gas centrifuge. (author)

  7. Inflating metastable quark-gluon plasma universe

    International Nuclear Information System (INIS)

    Jenkovszky, L.L.; Kaempfer, B.; Sysoev, V.M.

    1990-01-01

    We show within the Friedmann model with the equation of state p(T)=aT 4 -AT that our universe has expanded exponentially when it was in a metastable quark-gluon plasma state. The scale factor during that epoch increased by many orders of magnitude. 13 refs.; 5 figs

  8. Spectral Methods in Numerical Plasma Simulation

    DEFF Research Database (Denmark)

    Coutsias, E.A.; Hansen, F.R.; Huld, T.

    1989-01-01

    An introduction is given to the use of spectral methods in numerical plasma simulation. As examples of the use of spectral methods, solutions to the two-dimensional Euler equations in both a simple, doubly periodic region, and on an annulus will be shown. In the first case, the solution is expanded...

  9. Strongyloidiasis and infective dermatitis alter human T lymphotropic virus-1 clonality in vivo.

    Directory of Open Access Journals (Sweden)

    Nicolas A Gillet

    Full Text Available Human T-lymphotropic Virus-1 (HTLV-1 is a retrovirus that persists lifelong by driving clonal proliferation of infected T-cells. HTLV-1 causes a neuroinflammatory disease and adult T-cell leukemia/lymphoma. Strongyloidiasis, a gastrointestinal infection by the helminth Strongyloides stercoralis, and Infective Dermatitis associated with HTLV-1 (IDH, appear to be risk factors for the development of HTLV-1 related diseases. We used high-throughput sequencing to map and quantify the insertion sites of the provirus in order to monitor the clonality of the HTLV-1-infected T-cell population (i.e. the number of distinct clones and abundance of each clone. A newly developed biodiversity estimator called "DivE" was used to estimate the total number of clones in the blood. We found that the major determinant of proviral load in all subjects without leukemia/lymphoma was the total number of HTLV-1-infected clones. Nevertheless, the significantly higher proviral load in patients with strongyloidiasis or IDH was due to an increase in the mean clone abundance, not to an increase in the number of infected clones. These patients appear to be less capable of restricting clone abundance than those with HTLV-1 alone. In patients co-infected with Strongyloides there was an increased degree of oligoclonal expansion and a higher rate of turnover (i.e. appearance and disappearance of HTLV-1-infected clones. In Strongyloides co-infected patients and those with IDH, proliferation of the most abundant HTLV-1⁺ T-cell clones is independent of the genomic environment of the provirus, in sharp contrast to patients with HTLV-1 infection alone. This implies that new selection forces are driving oligoclonal proliferation in Strongyloides co-infection and IDH. We conclude that strongyloidiasis and IDH increase the risk of development of HTLV-1-associated diseases by increasing the rate of infection of new clones and the abundance of existing HTLV-1⁺ clones.

  10. Simple method for clonal selection of hepatitis A virus based on recovery of virus from radioimmunofocus overlays

    Energy Technology Data Exchange (ETDEWEB)

    Lemon, S M; Jansen, R W

    1985-06-01

    Hepatitis A virus (HAV), has been quantitated in cell culture by autoradiographic detection of foci of viral replication developing beneath an agarose overlay following fixation and 'staining' of the cell sheet with radiolabelled antibody (radioimmunofocus assay). Using a modification of this basic technique, a clonal variant of HM-175 strain HAV was isolated from agarose overlying individual radioimmunofoci. Virus recovered from the agarose was amplified in small volume cultures of BS-C-1 cells and identified in supernatant culture fluids by cDNA-RNA hybridizaton. No virus was recovered from agarose which did not overlie a focus of viral replication. This method offers a simple, yet relatively rapid and certain means of selecting clonal variants of non-plaquing viruses such as hepatitis A virus.

  11. A simple method for clonal selection of hepatitis A virus based on recovery of virus from radioimmunofocus overlays

    International Nuclear Information System (INIS)

    Lemon, S.M.; Jansen, R.W.

    1985-01-01

    Hepatitis A virus (HAV), has been quantitated in cell culture by autoradiographic detection of foci of viral replication developing beneath an agarose overlay following fixation and 'staining' of the cell sheet with radiolabelled antibody (radioimmunofocus assay). Using a modification of this basic technique, a clonal variant of HM-175 strain HAV was isolated from agarose overlying individual radioimmunofoci. Virus recovered from the agarose was amplified in small volume cultures of BS-C-1 cells and identified in supernatant culture fluids by cDNA-RNA hybridizaton. No virus was recovered from agarose which did not overlie a focus of viral replication. This method offers a simple, yet relatively rapid and certain means of selecting clonal variants of non-plaquing viruses such as hepatitis A virus. (Auth.)

  12. Clonal Clusters and Virulence Factors of Group C and G Streptococcus Causing Severe Infections, Manitoba, Canada, 2012-2014.

    Science.gov (United States)

    Lother, Sylvain A; Demczuk, Walter; Martin, Irene; Mulvey, Michael; Dufault, Brenden; Lagacé-Wiens, Philippe; Keynan, Yoav

    2017-07-01

    The incidence of group C and G Streptococcus (GCGS) bacteremia, which is associated with severe disease and death, is increasing. We characterized clinical features, outcomes, and genetic determinants of GCGS bacteremia for 89 patients in Winnipeg, Manitoba, Canada, who had GCGS bacteremia during 2012-2014. Of the 89 patients, 51% had bacteremia from skin and soft tissue, 70% had severe disease features, and 20% died. Whole-genome sequencing analysis was performed on isolates derived from 89 blood samples and 33 respiratory sample controls: 5 closely related genetic lineages were identified as being more likely to cause invasive disease than non-clade isolates (83% vs. 57%, p = 0.002). Virulence factors cbp, fbp, speG, sicG, gfbA, and bca clustered clonally into these clades. A clonal distribution of virulence factors may account for severe and fatal cases of bacteremia caused by invasive GCGS.

  13. 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.

  14. Laser Plasmas

    Indian Academy of Sciences (India)

    -focusing in a plasma ... Center for Energy Studies, Indian Institute of Technology, New Delhi 110 016, India; Tata Consultancy Services, Gurgaon, India; Ideal Institute of Technology, Ghaziabad, India; Center for Research in Cognitive, ...

  15. Plasma will…

    Czech Academy of Sciences Publication Activity Database

    Lunov, Oleg

    2016-01-01

    Roč. 174, č. 3 (2016), s. 486-487 ISSN 0007-0963 Institutional support: RVO:68378271 Keywords : plasma * ionized gas Subject RIV: BO - Biophysics OBOR OECD: Biophysics Impact factor: 4.706, year: 2016

  16. Plasma technology

    International Nuclear Information System (INIS)

    Drouet, M.G.

    1984-03-01

    IREQ was contracted by the Canadian Electrical Association to review plasma technology and assess the potential for application of this technology in Canada. A team of experts in the various aspects of this technology was assembled and each team member was asked to contribute to this report on the applications of plasma pertinent to his or her particular field of expertise. The following areas were examined in detail: iron, steel and strategic-metals production; surface treatment by spraying; welding and cutting; chemical processing; drying; and low-temperature treatment. A large market for the penetration of electricity has been identified. To build up confidence in the technology, support should be provided for selected R and D projects, plasma torch demonstrations at full power, and large-scale plasma process testing

  17. Plasma metallization

    International Nuclear Information System (INIS)

    Crowther, J.M.

    1997-09-01

    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 surface contamination of the films due to plasma treatment was observed but was easily removed by argon ion cleaning. Hydrogen plasma reduction of glass supported silver(l) nitrate and palladium(ll) acetate films reveals that this metallization technique is applicable to a wide variety of metal salts and supports, and has also shown the ability of plasma reduction to retain the complex 'fern-like' structures seen for spin coated silver(l) nitrate layers. Some metal salts are susceptible to decomposition by X-rays. The reduction of Nylon 66 supported gold(lll) chloride films by soft X-rays to produce nanoscopic gold particles has been studied. The spontaneous reduction of these X-ray irradiated support gold(lll) chloride films on exposure to the atmosphere to produce gold rich metallic films has also been reported. (author)

  18. 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.

  19. Plasma Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Zaveryaev, V [Kurchatov Institute, Moscow (Russian Federation); others, and

    2012-09-15

    The success in achieving peaceful fusion power depends on the ability to control a high temperature plasma, which is an object with unique properties, possibly the most complicated object created by humans. Over years of fusion research a new branch of science has been created, namely plasma diagnostics, which involves knowledge of almost all fields of physics, from electromagnetism to nuclear physics, and up-to-date progress in engineering and technology (materials, electronics, mathematical methods of data treatment). Historically, work on controlled fusion started with pulsed systems and accordingly the methods of plasma parameter measurement were first developed for short lived and dense plasmas. Magnetically confined hot plasmas require the creation of special experimental techniques for diagnostics. The diagnostic set is the most scientifically intensive part of a plasma device. During many years of research operation some scientific tasks have been solved while new ones arose. New tasks often require significant changes in the diagnostic system, which is thus a very flexible part of plasma machines. Diagnostic systems are designed to solve several tasks. As an example here are the diagnostic tasks for the International Thermonuclear Experimental Reactor - ITER: (1) Measurements for machine protection and basic control; (2) Measurements for advanced control; (3) Additional measurements for performance evaluation and physics. Every new plasma machine is a further step along the path to the main goal - controlled fusion - and nobody knows in advance what new phenomena will be met on the way. So in the planning of diagnostic construction we should keep in mind further system upgrading to meet possible new scientific and technical challenges. (author)

  20. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    Science.gov (United States)

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. Copyright © 2016, American Society for Microbiology. All Rights