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Sample records for generation recombination instability

  1. Efficient Generation of Recombinant Influenza A Viruses Employing a New Approach to Overcome the Genetic Instability of HA Segments

    PubMed Central

    Mostafa, Ahmed; Kanrai, Pumaree; Petersen, Henning; Ibrahim, Sherif; Rautenschlein, Silke; Pleschka, Stephan

    2015-01-01

    Influenza A viruses (IAVs) are the most relevant and continual source of severe infectious respiratory complications in humans and different animal species, especially poultry. Therefore, an efficient vaccination that elicits protective and neutralizing antibodies against the viral hemagglutinin (HA) and neuraminidase (NA) is an important strategy to counter annual epidemics or occasional pandemics. With the help of plasmid-based reverse genetics technology, it is possible that IAV vaccine strains (IVVS) are rapidly generated. However, the genetic instability of some cloned HA-cDNAs after transformation into competent bacteria represents a major obstacle. Herein, we report efficient cloning strategies of different genetically volatile HA segments (H5- and H9-subtypes) employing either a newly constructed vector for reverse genetics (pMKPccdB) or by the use of the Escherichia coli strain HB101. Both approaches represent improved and generalizable strategies to establish functional reverse genetics systems preventing genetic changes to the cloned (HA) segments of IAV facilitating more efficient rescue of recombinant IAV for basic research and vaccine development. PMID:25615576

  2. Tidal instability and magnetic field generation

    NASA Astrophysics Data System (ADS)

    Le Gal, Patrice; Cébron, David; Herreman, Wietze; Le Bars, Michael; Le Dizès, Stéphane

    2010-11-01

    We are interested in the interaction of the elliptical instability and magnetic fields in liquid metal flows both on laboratory and planetary scales. We first discuss an experimental set-up that realizes an elliptical flow of Galinstan under an imposed field. The presence of a magnetic field is here of double interest. Elliptically excited flows are monitored through the magnetic fields they induce and the instability may be controlled by Joule damping. This study provides some new insight in the nonlinear stages of the elliptical instability. In a planetary context, it is likely that elliptical instability under imposed field occurs in the tidally deformed moon Io of Jupiter. We show how tidally excited flows may significantly deform the imposed field of Jupiter through an induction process. Finally, we also study whether tidally driven flows can be capable of generating and sustaining magnetic fields through the dynamo effect. We present a first numerical study on the possibility of tidally driven dynamo action in triaxial spheroids.

  3. Recombination-generation currents in degenerate semiconductors

    NASA Technical Reports Server (NTRS)

    Von Roos, O.

    1978-01-01

    The classical Shockley-Read-Hall theory of free carrier recombination and generation via traps is extended to degenerate semiconductors. A concise and simple expression is found which avoids completely the concept of a Fermi level, a concept which is alien to nonequilibrium situations. Assumptions made in deriving the recombination generation current are carefully delineated and are found to be basically identical to those made in the original theory applicable to nondegenerate semiconductors.

  4. Dynamo generated by the centrifugal instability

    NASA Astrophysics Data System (ADS)

    Marcotte, Florence; Gissinger, Christophe

    2016-10-01

    We present a scenario for magnetic field amplification where an electrically conducting fluid is confined in a differentially rotating, spherical shell with thin aspect ratio. When the angular momentum sufficiently decreases outwards, a hydrodynamic instability develops in the equatorial region, characterized by pairs of counter-rotating toroidal vortices similar to those observed in cylindrical Couette flow. These spherical Taylor-Couette vortices generate a subcritical dynamo magnetic field dominated by nonaxisymmetric components. We show that the critical magnetic Reynolds number seems to reach a constant value at large Reynolds number and that the global rotation can strongly decrease the dynamo onset. Our numerical results are understood within the framework of a simple dynamical system, and we propose a low-dimensional model for subcritical dynamo bifurcations. Implications for both laboratory dynamos and astrophysical magnetic fields are finally discussed.

  5. Pattern Generation by Dissipative Parametric Instability

    NASA Astrophysics Data System (ADS)

    Perego, A. M.; Tarasov, N.; Churkin, D. V.; Turitsyn, S. K.; Staliunas, K.

    2016-01-01

    Nonlinear instabilities are responsible for spontaneous pattern formation in a vast number of natural and engineered systems, ranging from biology to galaxy buildup. We propose a new instability mechanism leading to pattern formation in spatially extended nonlinear systems, which is based on a periodic antiphase modulation of spectrally dependent losses arranged in a zigzag way: an effective filtering is imposed at symmetrically located wave numbers k and -k in alternating order. The properties of the dissipative parametric instability differ from the features of both key classical concepts of modulation instabilities, i.e., the Benjamin-Feir instability and the Faraday instabiltyity. We demonstrate how the dissipative parametric instability can lead to the formation of stable patterns in one- and two-dimensional systems. The proposed instability mechanism is generic and can naturally occur or can be implemented in various physical systems.

  6. Overexpressed of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

    SciTech Connect

    Schild, David; Wiese, Claudia

    2009-10-15

    RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the 'recombination mediators'. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or comediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic restabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51.

  7. Overexpression of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

    PubMed Central

    Schild, David; Wiese, Claudia

    2010-01-01

    RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA-binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the ‘recombination mediators’. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as ‘recombination co-mediators’. Defects in either recombination mediators or co-mediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic re-stabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51 expression. PMID:19942681

  8. Shear flow instability generated by non-homogeneous external forcing

    NASA Technical Reports Server (NTRS)

    Durbin, P. A.

    1987-01-01

    An experiment has been designed and conducted in order to ascertain whether instability waves can be generated by nonhomogeneous forcing, using a biconvex vane located outside the mixing layer whose oscillation was induced by an electromagnetic shaker through a linkage. The vane was oscillated at 20 Hz, and the resulting spectra were computed by a spectrum analyzer. The data are judged to provide an example of instability waves generated solely through nonhomogeneous forcing.

  9. Pump instability phenomena generated by fluid forces

    NASA Technical Reports Server (NTRS)

    Gopalakrishnan, S.

    1985-01-01

    Rotor dynamic behavior of high energy centrifugal pumps is significantly affected by two types of fluid forces; one due to the hydraulic interaction of the impeller with the surrounding volute or diffuser and the other due to the effect of the wear rings. The available data on these forces is first reviewed. A simple one degree-of-freedom system containing these forces is analytically solved to exhibit the rotor dynamic effects. To illustrate the relative magnitude of these phenomena, an example of a multistage boiler feed pump is worked out. It is shown that the wear ring effects tend to suppress critical speed and postpone instability onset. But the volute-impeller forces tend to lower the critical speed and the instability onset speed. However, for typical boiler feed pumps under normal running clearances, the wear ring effects are much more significant than the destabilizing hydraulic interaction effects.

  10. Recombination regulator PRDM9 influences the instability of its own coding sequence in humans.

    PubMed

    Jeffreys, Alec J; Cotton, Victoria E; Neumann, Rita; Lam, Kwan-Wood Gabriel

    2013-01-08

    PRDM9 plays a key role in specifying meiotic recombination hotspot locations in humans and mice via recognition of hotspot sequence motifs by a variable tandem-repeat zinc finger domain in the protein. We now explore germ-line instability of this domain in humans. We show that repeat turnover is driven by mitotic and meiotic mutation pathways, the latter frequently resulting in substantial remodeling of zinc fingers. Turnover dynamics predict frequent allele switches in populations with correspondingly fast changes of the recombination landscape, fully consistent with the known rapid evolution of hotspot locations. We found variation in meiotic instability between men that correlated with PRDM9 status. One particular "destabilizer" variant caused hyperinstability not only of itself but also of otherwise-stable alleles in heterozygotes. PRDM9 protein thus appears to regulate the instability of its own coding sequence. However, destabilizer variants are strongly self-limiting in populations and probably have little impact on the evolution of the recombination landscape.

  11. Generation of instability waves at a leading edge

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1982-01-01

    Two cases are considered. The first is concerned with mean flows of the Blasius type wherein the instabilities are represented by Tollmien-Schlichting waves. It is shown that the latter are generated fairly far downstream of the edge and are the result of a wave length reduction process that tunes the free stream disturbances to the Tollmien-Schlichting wave length. The other case is concerned with inflectional, uni-directional, transversely sheared mean flows. Such idealized flows provide a fairly good local representation to the nearly parallel flows in jets. They can support inviscid instabilities of the Kelvin-Helmholtz type. The various mathematically permissible mechanisms that can couple these instabilities to the upstream disturbances are discussed.

  12. Multiple exciton generation and recombination in carbon nanotubes and nanocrystals.

    PubMed

    Kanemitsu, Yoshihiko

    2013-06-18

    Semiconducting nanomaterials such as single-walled carbon nanotubes (SWCNTs) and nanocrystals (NCs) exhibit unique size-dependent quantum properties. They have therefore attracted considerable attention from the viewpoints of fundamental physics and functional device applications. SWCNTs and NCs also provide an excellent new stage for experimental studies of many-body effects of electrons and excitons on optical processes in nanomaterials. In this Account, we discuss multiple exciton generation and recombination in SWCNTs and NCs for next-generation photovoltaics. Strongly correlated ensembles of conduction-band electrons and valence-band holes in semiconductors are complex quantum systems that exhibit unique optical phenomena. In bulk crystals, the carrier recombination dynamics can be described by a simple model, which includes the nonradiative single-carrier trapping rate, the radiative two-carrier recombination rate, and the nonradiative three-carrier Auger recombination rate. The nonradiative Auger recombination rate determines the carrier recombination dynamics at high carrier density and depends on the spatial localization of carriers in two-dimensional quantum wells. The Auger recombination and multiple exciton generation rates can be advantageously manipulated by nanomaterials with designated energy structures. In addition, SWCNTs and NCs show quantized recombination dynamics of multiple excitons and carriers. In one-dimensional SWCNTs, excitons have large binding energies and are very stable at room temperature. The extremely rapid Auger recombination between excitons determines the photoluminescence (PL) intensity, the PL linewidth, and the PL lifetime. SWCNTs can undergo multiple exciton generation, while strong exciton-exciton interactions and complicated exciton structures affect the quantized Auger rate and the multiple exciton generation efficiency. Interestingly, in zero-dimensional NC quantum dots, quantized Auger recombination causes unique

  13. CURVATURE-DRIFT INSTABILITY FAILS TO GENERATE PULSAR RADIO EMISSION

    SciTech Connect

    Kaganovich, Alexander; Lyubarsky, Yuri

    2010-10-01

    The curvature-drift instability has long been considered as a viable mechanism for pulsar radio emission. We reconsidered this mechanism by finding an explicit solution describing the propagation of short electromagnetic waves in a plasma flow along curved magnetic field lines. We show that even though the waves could be amplified, the amplification factor remains very close to unity; therefore, this mechanism is unable to generate high brightness temperature emission from initial weak fluctuations.

  14. A Rapid and Improved Method to Generate Recombinant Dengue Virus Vaccine Candidates.

    PubMed

    Govindarajan, Dhanasekaran; Guan, Liming; Meschino, Steven; Fridman, Arthur; Bagchi, Ansu; Pak, Irene; ter Meulen, Jan; Casimiro, Danilo R; Bett, Andrew J

    2016-01-01

    Dengue is one of the most important mosquito-borne infections accounting for severe morbidity and mortality worldwide. Recently, the tetravalent chimeric live attenuated Dengue vaccine Dengvaxia® was approved for use in several dengue endemic countries. In general, live attenuated vaccines (LAV) are very efficacious and offer long-lasting immunity against virus-induced disease. Rationally designed LAVs can be generated through reverse genetics technology, a method of generating infectious recombinant viruses from full length cDNA contained in bacterial plasmids. In vitro transcribed (IVT) viral RNA from these infectious clones is transfected into susceptible cells to generate recombinant virus. However, the generation of full-length dengue virus cDNA clones can be difficult due to the genetic instability of viral sequences in bacterial plasmids. To circumvent the need for a single plasmid containing a full length cDNA, in vitro ligation of two or three cDNA fragments contained in separate plasmids can be used to generate a full-length dengue viral cDNA template. However, in vitro ligation of multiple fragments often yields low quality template for IVT reactions, resulting in inconsistent low yield RNA. These technical difficulties make recombinant virus recovery less efficient. In this study, we describe a simple, rapid and efficient method of using LONG-PCR to recover recombinant chimeric Yellow fever dengue (CYD) viruses as potential dengue vaccine candidates. Using this method, we were able to efficiently generate several viable recombinant viruses without introducing any artificial mutations into the viral genomes. We believe that the techniques reported here will enable rapid and efficient recovery of recombinant flaviviruses for evaluation as vaccine candidates and, be applicable to the recovery of other RNA viruses.

  15. A Rapid and Improved Method to Generate Recombinant Dengue Virus Vaccine Candidates

    PubMed Central

    Govindarajan, Dhanasekaran; Guan, Liming; Meschino, Steven; Fridman, Arthur; Bagchi, Ansu; Pak, Irene; ter Meulen, Jan; Casimiro, Danilo R.; Bett, Andrew J.

    2016-01-01

    Dengue is one of the most important mosquito-borne infections accounting for severe morbidity and mortality worldwide. Recently, the tetravalent chimeric live attenuated Dengue vaccine Dengvaxia® was approved for use in several dengue endemic countries. In general, live attenuated vaccines (LAV) are very efficacious and offer long-lasting immunity against virus-induced disease. Rationally designed LAVs can be generated through reverse genetics technology, a method of generating infectious recombinant viruses from full length cDNA contained in bacterial plasmids. In vitro transcribed (IVT) viral RNA from these infectious clones is transfected into susceptible cells to generate recombinant virus. However, the generation of full-length dengue virus cDNA clones can be difficult due to the genetic instability of viral sequences in bacterial plasmids. To circumvent the need for a single plasmid containing a full length cDNA, in vitro ligation of two or three cDNA fragments contained in separate plasmids can be used to generate a full-length dengue viral cDNA template. However, in vitro ligation of multiple fragments often yields low quality template for IVT reactions, resulting in inconsistent low yield RNA. These technical difficulties make recombinant virus recovery less efficient. In this study, we describe a simple, rapid and efficient method of using LONG-PCR to recover recombinant chimeric Yellow fever dengue (CYD) viruses as potential dengue vaccine candidates. Using this method, we were able to efficiently generate several viable recombinant viruses without introducing any artificial mutations into the viral genomes. We believe that the techniques reported here will enable rapid and efficient recovery of recombinant flaviviruses for evaluation as vaccine candidates and, be applicable to the recovery of other RNA viruses. PMID:27008550

  16. Magnetic Field Generation by the Stationary Accretion Shock Instability

    SciTech Connect

    Endeve, Eirik; Cardall, Christian Y; Budiardja, R. D.; Mezzacappa, Anthony

    2008-01-01

    By adding a weak magnetic field to a spherically symmetric fluid configuration that caricatures a stalled shock in the post-bounce supernova environment, we explore the capacity of the stationary accretion shock instability (SASI) to generate magnetic fields. The SASI develops upon perturbation of the initial condition, and the ensuing flow generates - in the absence of rotation - dynamically significant magnetic fields (~ 10^{15} G) on a time scale that is relevant for the explosion mechanism of core collapse supernovae. We describe our model, present some recent results, and discuss their potential relevance for supernova models.

  17. Extreme waves generated by modulational instability on adverse currents

    NASA Astrophysics Data System (ADS)

    Ma, Yuxiang; Ma, Xiaozhou; Perlin, Marc; Dong, Guohai

    2013-11-01

    Physical experiments focusing on the propagation of gravity waves of finite depth on adverse currents were implemented to examine their effect on the development of the modulational instability and to study the geometric characteristics of extreme waves. A series of wave trains with varying initial steepness, perturbation frequency, and initial perturbed strength were mechanically generated in a wave-current flume. The present results show that opposing currents can speed the growth of the modulational instability, verifying the previous theory qualitatively. A current-modified nonlinear Schrödinger equation can predict the measured sideband growth rates well for wave trains with lower perturbation frequencies, but overestimated those with higher perturbation frequencies. On the other hand, the limiting steepness of extreme waves measured in the presence of opposing currents was smaller than that measured in quiescent water. Additionally, current strength was found to have limited influence on the geometric properties of extreme waves as well as on their limiting steepness.

  18. Paracentric inversions do not normally generate monocentric recombinant chromosomes

    SciTech Connect

    Sutherland, G.R.; Callen, D.F.; Gardner, R.J.M.

    1995-11-20

    Dr. Pettenati et al. recently reported a review of paracentric inversions in humans in which they concluded that carriers of these have a 3.8% risk of viable offspring with recombinant chromosomes. We are of the view that there are serious problems with this estimate which should be much closer to zero. The only recombinant chromosomes which can be generated by a paracentric inversion undergoing a normal meiotic division are dicentrics and acentric fragments. Only two such cases were found by Pettenati et al. Several of the alleged monocentric recombinants were originally reported as arising from parental insertions (3-break rearrangements) and it is not legitimate to include them in any analysis of paracentric inversions. Any monocentric recombinant chromosome can only arise from a paracentric inversion by some abnormal process which must involve chromatid breakage and reunion. 4 refs.

  19. Polarization instability of Raman solitons ejected during supercontinuum generation.

    PubMed

    Chao, Qing; Wagner, Kelvin H

    2015-12-28

    We numerically investigate polarization instability of soliton fission and the polarization dynamics of Raman solitons ejected during supercontinuum generation in a photonics crystal fiber using the coupled vector generalized nonlinear Schrödinger equations for both linear and circular birefringent fibers. The evolution of the state of polarizations of the ejected Raman soliton as representated on the Poincaré sphere is affected by both nonlinear and linear polarization rotations on the Poincaré sphere. The polarization dynamics reveal the presence of a polarization separatrix and the emergence of stable slow and unstable fast eigen-polarizations for the Raman solitons ejected in the supercontinuum generation process. Circularly birefringent fiber is investigated and found to simplify the nonlinear polarization dynamics.

  20. PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans.

    PubMed

    Berg, Ingrid L; Neumann, Rita; Lam, Kwan-Wood G; Sarbajna, Shriparna; Odenthal-Hesse, Linda; May, Celia A; Jeffreys, Alec J

    2010-10-01

    PRDM9 has recently been identified as a likely trans regulator of meiotic recombination hot spots in humans and mice. PRDM9 contains a zinc finger array that, in humans, can recognize a short sequence motif associated with hot spots, with binding to this motif possibly triggering hot-spot activity via chromatin remodeling. We now report that human genetic variation at the PRDM9 locus has a strong effect on sperm hot-spot activity, even at hot spots lacking the sequence motif. Subtle changes within the zinc finger array can create hot-spot nonactivating or enhancing variants and can even trigger the appearance of a new hot spot, suggesting that PRDM9 is a major global regulator of hot spots in humans. Variation at the PRDM9 locus also influences aspects of genome instability-specifically, a megabase-scale rearrangement underlying two genomic disorders as well as minisatellite instability-implicating PRDM9 as a risk factor for some pathological genome rearrangements.

  1. Boundary Layer Instabilities Generated by Freestream Laser Perturbations

    NASA Technical Reports Server (NTRS)

    Chou, Amanda; Schneider, Steven P.

    2015-01-01

    A controlled, laser-generated, freestream perturbation was created in the freestream of the Boeing/AFOSR Mach-6 Quiet Tunnel (BAM6QT). The freestream perturbation convected downstream in the Mach-6 wind tunnel to interact with a flared cone model. The geometry of the flared cone is a body of revolution bounded by a circular arc with a 3-meter radius. Fourteen PCB 132A31 pressure transducers were used to measure a wave packet generated in the cone boundary layer by the freestream perturbation. This wave packet grew large and became nonlinear before experiencing natural transition in quiet flow. Breakdown of this wave packet occurred when the amplitude of the pressure fluctuations was approximately 10% of the surface pressure for a nominally sharp nosetip. The initial amplitude of the second mode instability on the blunt flared cone is estimated to be on the order of 10 -6 times the freestream static pressure. The freestream laser-generated perturbation was positioned upstream of the model in three different configurations: on the centerline, offset from the centerline by 1.5 mm, and offset from the centerline by 3.0 mm. When the perturbation was offset from the centerline of a blunt flared cone, a larger wave packet was generated on the side toward which the perturbation was offset. The offset perturbation did not show as much of an effect on the wave packet on a sharp flared cone as it did on a blunt flared cone.

  2. Generation of hybrid human immunodeficiency virus by homologous recombination.

    PubMed Central

    Srinivasan, A; York, D; Jannoun-Nasr, R; Kalyanaraman, S; Swan, D; Benson, J; Bohan, C; Luciw, P A; Schnoll, S; Robinson, R A

    1989-01-01

    Human immunodeficiency virus (HIV) type 1, isolated from diverse sources, exhibits genomic diversity. The mechanisms by which the genomic diversity takes place in individuals exposed to multiple virus isolates is yet to be elucidated. Genetic variation, in general, might result from mutagenic events such as point mutations, rearrangements (insertions and deletions), and recombination. In an attempt to evaluate the process of genetic diversity, we designed experiments to analyze recombination between HIV DNAs by using DNA transfection in cell cultures. Here we report the successful recombination between truncated HIV proviral DNAs with an overlap homology of 53 base pairs that leads to the formation of viable hybrid virus. Recombination was also seen between exogenous DNA introduced into cells and homologous HIV sequences resident in the cells. These results indicate that recombination among various HIV isolates may play a significant role in the generation of genetic diversity of HIV. Further, the method used here enables the construction of hybrid HIV genomes to identify the viral determinants responsible for tropism, replication, and cytopathic effects. Images PMID:2474834

  3. UNIT 14A.4 Generation of Recombinant Vaccinia Viruses

    PubMed Central

    Earl, Patricia L.; Moss, Bernard; Wyatt, Linda S.

    2016-01-01

    This unit describes how to infect cells with vaccinia virus and then transfect them with a plasmid-transfer vector or PCR fragment to generate a recombinant virus. Selection and screening methods used to isolate recombinant viruses and a method for the amplification of recombinant viruses are described. Finally, a method for live immunostaining that has been used primarily for detection of recombinant modified vaccinia virus Ankara (MVA) is presented. This unit first describes how to infect cells with vaccinia virus and then transfect them with a plasmid-transfer vector or PCR fragment to generate a recombinant virus (see Basic Protocol 1). Also presented are selection and screening methods used to isolate recombinant viruses (see Basic Protocol 2) and a method for the amplification of recombinant viruses (see Basic Protocol 3). Finally, a method for live immunostaining that has been used primarily for detection of recombinant modified vaccinia virus Ankara (MVA) is presented (see Basic Protocol 4). HeLa S3 cells are recommended for large-scale growth of vaccinia virus. BS-C-1 cells may be used for xanthine-guanine phosphoribosyltransferase (XGPRT) and plaque size selection, fluorescent protein screening, transfection and determination of virus titer (UNIT 14A.3). For thymidine kinase (TK) selection, HuTK− 143B cells are used. With MVA, all steps are carried out in CEF or BHK-21 cells (UNIT 14A.3). CAUTION Proceed carefully and follow biosafety level 2 (BL-2) practices when working with standard vaccinia virus (see UNIT 14A.3 for safety precautions). [*Copy Editor: The original CPMB unit referenced CPMB Unit 16.15 for safety. The chapter editor asked that the authors include some of the safety information in the revised units – CPMB 16.16 and 16.17 – which are now CPMC Unit 14A.3 and 14A.4. As a result, the authors changed the safety citation here to “Unit 14A.3”, which doesn’t have nearly as much information as the original CPMB Unit 16.15. Perhaps the

  4. Stochastic Particle Acceleration in Turbulence Generated by Magnetorotational Instability

    NASA Astrophysics Data System (ADS)

    Kimura, Shigeo S.; Toma, Kenji; Suzuki, Takeru K.; Inutsuka, Shu-ichiro

    2016-05-01

    We investigate stochastic particle acceleration in accretion flows. It is believed that magnetorotational instability (MRI) generates turbulence inside accretion flows and that cosmic rays (CRs) are accelerated by the turbulence. We calculate equations of motion for CRs in the turbulent fields generated by MRI with the shearing box approximation and without back reaction to the field. Our results show that the CRs randomly gain or lose their energy through interaction with the turbulent fields. The CRs diffuse in the configuration space anisotropically: the diffusion coefficient in the direction of the unperturbed flow is about 20 times higher than the Bohm coefficient, while those in the other directions are only a few times higher than the Bohm. The momentum distribution is isotropic and its evolution can be described by the diffusion equation in momentum space where the diffusion coefficient is a power-law function of the CR momentum. We show that the shear acceleration works efficiently for energetic particles. We also cautiously note that in the shearing box approximation, particles that cross the simulation box many times along the radial direction undergo unphysical runaway acceleration by the Lorentz transformation, which needs to be taken into account with special care.

  5. Generation of Magnetic Fields by the Stationary Accretion Shock Instability

    SciTech Connect

    Endeve, Eirik; Cardall, Christian Y; Budiardja, R. D.; Mezzacappa, Anthony

    2010-01-01

    We begin an exploration of the capacity of the stationary accretion shock instability (SASI) to generate magnetic fields by adding a weak, stationary, and radial (but bipolar) magnetic field, and in some cases rotation, to an initially spherically symmetric fluid configuration that models a stalled shock in the post-bounce supernova environment. In axisymmetric simulations we find that cycles of latitudinal flows into and radial flows out of the polar regions amplify the field parallel to the symmetry axis, typically increasing the total magnetic energy by about two orders of magnitude. Nonaxisymmetric calculations result in fundamentally different flows and a larger magnetic energy increase: shearing associated with the SASI spiral mode contributes to a widespread and turbulent field amplification mechanism, boosting the magnetic energy by almost four orders of magnitude (a result which remains very sensitive to the spatial resolution of the numerical simulations). While the SASI may contribute to neutron star magnetization, these simulations do not show qualitatively new features in the global evolution of the shock as a result of SASI-induced magnetic field amplification.

  6. Azimuthal instability of vortex rings generated by an oscillating disk

    NASA Astrophysics Data System (ADS)

    Deng, Jian; Caulfield, C. P.

    2015-11-01

    We report the instabilities of vortex rings generated by an oscillating disk. Assuming sinusoidal variation in the azimuthal direction with mode number, m, a Floquet linear stability analysis is performed. We study the dynamics for a range of the two control parameters, the Keulegan-Carpenter number KC = 2 πA / c and the Stokes number β = fc2 / ν , where A is the amplitude of oscillation, f is the frequency of oscillation, c is the diameter of the disk, and ν is the kinematic viscosity of the fluid. We observe two distinctive flow regions in the (KC , β) parameter space. First, in the low β region, the flow breaks its symmetry with a single wavenumber mode getting a positive growth rate. Second, in the high β region, high-order unstable modes emerge, with the highest mode number m = 9 recorded. Furthermore, we carry out Direct Numerical Simulations (DNS) on the fully three-dimensional Navier-stokes equations. The results reproduce the main features of the high-order unstable modes predicted by the Floquet analysis, exhibiting the highest mode number m = 6 . We conjecture that the inconsistence in the highest mode number between the Floquet linear stability analysis and the DNS implies the non-linear characteristic of the current problem. Supported by the National Natural Science Foundation of China (Grant No: 11272283) and Zhejiang Provincial Natural Science Foundation of China (Grant No: LY12A02006).

  7. Applicability of Next Generation Sequencing Technology in Microsatellite Instability Testing

    PubMed Central

    Gan, Chun; Love, Clare; Beshay, Victoria; Macrae, Finlay; Fox, Stephen; Waring, Paul; Taylor, Graham

    2015-01-01

    Microsatellite instability (MSI) is a useful marker for risk assessment, prediction of chemotherapy responsiveness and prognosis in patients with colorectal cancer. Here, we describe a next generation sequencing approach for MSI testing using the MiSeq platform. Different from other MSI capturing strategies that are based on targeted gene capture, we utilize “deep resequencing”, where we focus the sequencing on only the microsatellite regions of interest. We sequenced a series of 44 colorectal tumours with normal controls for five MSI loci (BAT25, BAT26, BAT34c4, D18S55, D5S346) and a second series of six colorectal tumours (no control) with two mononucleotide loci (BAT25, BAT26). In the first series, we were able to determine 17 MSI-High, 1 MSI-Low and 26 microsatellite stable (MSS) tumours. In the second series, there were three MSI-High and three MSS tumours. Although there was some variation within individual markers, this NGS method produced the same overall MSI status for each tumour, as obtained with the traditional multiplex PCR-based method. PMID:25685876

  8. Sound generation and upstream influence due to instability waves interacting with non-uniform mean flows

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1984-01-01

    Attention is given to the sound produced by artificially excited, spatially growing instability waves on subsonic shear layers. Real flows that always diverge in the downstream direction allow sound to be produced by the interaction of the instability waves with the resulting streamwise variations of the flow. The upstream influence, or feedback, can interact with the splitter plate lip to produce a downstream-propagating instability wave that may under certain conditions be the same instability wave that originally generated the upstream influence. The present treatment is restricted to very low Mach number flows, so that compressibility effects can only become important over large distances.

  9. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  10. Genetic instability is prevented by Mrc1-dependent spatio-temporal separation of replicative and repair activities of homologous recombination

    PubMed Central

    Prado, Félix

    2014-01-01

    Homologous recombination (HR) is required to protect and restart stressed replication forks. Paradoxically, the Mrc1 branch of the S phase checkpoints, which is activated by replicative stress, prevents HR repair at breaks and arrested forks. Indeed, the mechanisms underlying HR can threaten genome integrity if not properly regulated. Thus, understanding how cells avoid genetic instability associated with replicative stress, a hallmark of cancer, is still a challenge. Here I discuss recent results that support a model by which HR responds to replication stress through replicative and repair activities that operate at different stages of the cell cycle (S and G2, respectively) and in distinct subnuclear structures. Remarkably, the replication checkpoint appears to control this scenario by inhibiting the assembly of HR repair centers at stressed forks during S phase, thereby avoiding genetic instability. PMID:24615940

  11. Instabilities of interacting vortex rings generated by an oscillating disk

    NASA Astrophysics Data System (ADS)

    Deng, Jian; Teng, Lubao; Caulfield, C. P.; Mao, Xuerui

    2016-09-01

    We propose a natural model to probe in a controlled fashion the instability of interacting vortex rings shed from the edge of an oblate spheroid disk of major diameter c , undergoing oscillations of frequency f0 and amplitude A . We perform a Floquet stability analysis to determine the characteristics of the instability modes, which depend strongly on the azimuthal (integer) wave number m . We vary two key control parameters, the Keulegan-Carpenter number KC=2 π A /c and the Stokes number β =f0c2/ν , where ν is the kinematic viscosity of the fluid. We observe two distinct flow regimes. First, for sufficiently small β , and hence low frequency of oscillation corresponding to relatively weak interaction between sequentially shedding vortex rings, symmetry breaking occurs directly to a single unstable mode with m =1 . Second, for sufficiently large yet fixed values of β , corresponding to a higher oscillation frequency and hence stronger ring-ring interaction, the onset of asymmetry is predicted to occur due to two branches of high m instabilities as the amplitude is increased, with m =1 structures being dominant only for sufficiently large values of KC. These two branches can be distinguished by the phase properties of the vortical structures above and below the disk. The region in (KC,β ) parameter space where these two high m instability branches arise can be described accurately in terms of naturally defined Reynolds numbers, using appropriately chosen characteristic length scales. We subsequently carry out direct numerical simulations of the fully three-dimensional flow to verify the principal characteristics of the Floquet analysis, in particular demonstrating that high wave-number symmetry-breaking generically occurs when vortex rings sequentially interact sufficiently strongly.

  12. Generation of continental rifts, basins, and swells by lithosphere instabilities

    NASA Astrophysics Data System (ADS)

    Fourel, LoïC.; Milelli, Laura; Jaupart, Claude; Limare, Angela

    2013-06-01

    Continents may be affected simultaneously by rifting, uplift, volcanic activity, and basin formation in several different locations, suggesting a common driving mechanism that is intrinsic to continents. We describe a new type of convective instability at the base of the lithosphere that leads to a remarkable spatial pattern at the scale of an entire continent. We carried out fluid mechanics laboratory experiments on buoyant blocks of finite size that became unstable due to cooling from above. Dynamical behavior depends on three dimensionless numbers, a Rayleigh number for the unstable block, a buoyancy number that scales the intrinsic density contrast to the thermal one, and the aspect ratio of the block. Within the block, instability develops in two different ways in an outer annulus and in an interior region. In the outer annulus, upwellings and downwellings take the form of periodically spaced radial spokes. The interior region hosts the more familiar convective pattern of polygonal cells. In geological conditions, such instabilities should manifest themselves as linear rifts striking at a right angle to the continent-ocean boundary and an array of domal uplifts, volcanic swells, and basins in the continental interior. Simple scaling laws for the dimensions and spacings of the convective structures are derived. For the subcontinental lithospheric mantle, these dimensions take values in the 500-1000 km range, close to geological examples. The large intrinsic buoyancy of Archean lithospheric roots prevents this type of instability, which explains why the widespread volcanic activity that currently affects Western Africa is confined to post-Archean domains.

  13. An experimental platform for generating Richtmyer-Meshkov instabilities on Z.

    SciTech Connect

    Harding, Eric; Martin, Matthew

    2013-04-01

    The Richtmyer-Meshkov (RM) instability results when a shock wave crosses a rippled interface between two different materials. The shock deposited vorticity causes the ripples to grow into long spikes. Ultimately this process encourages mixing in many warm dense matter and plasma flows of interest. However, generating pure RM instabilities from initially solid targets is difficult because longlived, steady shocks are required. As a result only a few relevant experiments exist, and current theoretical understanding is limited. Here we propose using a flyer-plate driven target to generate RM instabilities with the Z machine. The target consists of a Be impact layer with sinusoidal perturbations and is followed by a low-density carbon foam. Simulation results show that the RM instability grows for 60 ns before release waves reach the perturbation. This long drive time makes Z uniquely suited for generating the high-quality data that is needed by the community.

  14. Low and high frequency instabilities in an explosion-generated-plasma and possibility of wave triplet

    NASA Astrophysics Data System (ADS)

    Malik, O. P.; Singh, Sukhmander; Malik, Hitendra K.; Kumar, A.

    2015-01-01

    An explosion-generated-plasma is explored for low and high frequency instabilities by taking into account the drift of all the plasma species together with the dust particles which are charged. The possibility of wave triplet is also discussed based on the solution of dispersion equation and synchronism conditions. High frequency instability (HFI) and low frequency instability (LFI) are found to occur in this system. LFI grows faster with the higher concentration of dust particles, whereas its growth rate goes down if the mass of the dust is higher. The ion and electron temperatures affect its growth in opposite manner and the electron temperature causes this instability to grow. In addition to the instabilities, a simple wave is also observed to propagate, whose velocity is larger for larger wave number, smaller mass of the dust and higher ion temperature.

  15. DOUBLE-DIFFUSIVE INSTABILITIES OF A SHEAR-GENERATED MAGNETIC LAYER

    SciTech Connect

    Silvers, Lara J.; Proctor, Michael R. E.; Vasil, Geoffrey M.; Brummell, Nicholas H.

    2009-09-01

    Previous theoretical work has speculated about the existence of double-diffusive magnetic buoyancy instabilities of a dynamically evolving horizontal magnetic layer generated by the interaction of forced vertically sheared velocity and a background vertical magnetic field. Here, we confirm numerically that if the ratio of the magnetic to thermal diffusivities is sufficiently low then such instabilities can indeed exist, even for high Richardson number shear flows. Magnetic buoyancy may therefore occur via this mechanism for parameters that are likely to be relevant to the solar tachocline, where regular magnetic buoyancy instabilities are unlikely.

  16. Generation of Continental Rifts, Basins and Swells by Lithosphere Instabilities

    NASA Astrophysics Data System (ADS)

    Milelli, L.; Fourel, L.; Jaupart, C. P.

    2012-12-01

    Domal uplifts, volcanism, basin formation and rifting have often struck the same continent in different areas at the same time. Their characteristics and orientations are difficult to reconcile with mantle convection or tectonic forces and suggest a driving mechanism that is intrinsic to the continent. The rifts seem to develop preferentially at high angles to the edge of the continent whereas swells and basins seem confined to the interior. Another intriguing geometrical feature is that the rifts often branch out in complicated patterns at their landward end. In Western Africa, for example, magmatic activity currently occurs in a number of uplifted areas including the peculiar Cameroon Volcanic Line that stretches away from the continental margin over about 1000 km. Magmatic and volcanic activity has been sustained along this line for 70 My with no age progression. The mantle upwelling that feeds the volcanoes is not affected by absolute plate motions and hence is attached to the continent. The Cameroon Volcanic Line extends to the Biu swell to the North and the Jos plateau to the West defining a striking Y-shaped pattern. This structure segues into several volcanic domes including the Air, the Hoggar, the Darfur, the Tibesti and the Haruj domes towards the Mediterranean coast. Another example is provided by North America, where the late Proterozoic-early Ordovician saw the formation of four major basins, the Michigan, Illinois, Williston and Hudson Bay, as well as of major rifts in southern Oklahoma and the Mississipi Valley within a short time interval. At the same time, a series of uplifts developed, such as the Ozark and Nashville domes. Motivated by these observations, we have sought an explanation in the continental lithosphere itself. We describe a new type of convective instability at the base of the lithosphere that leads to a remarkable spatial pattern at the scale of an entire continent. We carried out fluid mechanics laboratory experiments on buoyant

  17. Generating Recombinant Antibodies against Putative Biomarkers of Retinal Injury

    PubMed Central

    Kierny, Michael R.; Cunningham, Thomas D.; Bouhenni, Rachida A.; Edward, Deepak P.; Kay, Brian K.

    2015-01-01

    Candidate biomarkers, indicative of disease or injury, are beginning to overwhelm the process of validation through immunological means. Recombinant antibodies developed through phage-display offer an alternative means of generating monoclonal antibodies faster than traditional immunization of animals. Peptide segments of putative biomarkers of laser induced injury in the rabbit, discovered through mass spectrometry, were used as targets for a selection against a library of phage-displayed human single-chain variable fragment (scFv) antibodies. Highly specific antibodies were isolated to four of these unique peptide sequences. One antibody against the retinal protein, Guanine Nucleotide-Binding Protein Beta 5 (GBB5), had a dissociation constant ~300 nM and recognized the full-length endogenous protein in retinal homogenates of three different animal species by western blot. Alanine scanning of the peptide target identified three charged and one hydrophobic amino acid as the critical binding residues for two different scFvs. To enhance the utility of the reagent, one scFv was dimerized through a Fragment-crystallizable hinge region (i.e., Fc) and expressed in HEK-293 cells. This dimeric reagent yielded a 25-fold lower detection limit in western blots. PMID:25902199

  18. Generating Recombinant Antibodies against Putative Biomarkers of Retinal Injury.

    PubMed

    Kierny, Michael R; Cunningham, Thomas D; Bouhenni, Rachida A; Edward, Deepak P; Kay, Brian K

    2015-01-01

    Candidate biomarkers, indicative of disease or injury, are beginning to overwhelm the process of validation through immunological means. Recombinant antibodies developed through phage-display offer an alternative means of generating monoclonal antibodies faster than traditional immunization of animals. Peptide segments of putative biomarkers of laser induced injury in the rabbit, discovered through mass spectrometry, were used as targets for a selection against a library of phage-displayed human single-chain variable fragment (scFv) antibodies. Highly specific antibodies were isolated to four of these unique peptide sequences. One antibody against the retinal protein, Guanine Nucleotide-Binding Protein Beta 5 (GBB5), had a dissociation constant ~300 nM and recognized the full-length endogenous protein in retinal homogenates of three different animal species by western blot. Alanine scanning of the peptide target identified three charged and one hydrophobic amino acid as the critical binding residues for two different scFvs. To enhance the utility of the reagent, one scFv was dimerized through a Fragment-crystallizable hinge region (i.e., Fc) and expressed in HEK-293 cells. This dimeric reagent yielded a 25-fold lower detection limit in western blots.

  19. Integrable turbulence generated from modulational instability of cnoidal waves

    NASA Astrophysics Data System (ADS)

    Agafontsev, D. S.; Zakharov, V. E.

    2016-11-01

    We study numerically the nonlinear stage of the modulational instability (MI) of cnoidal waves in the framework of the focusing one-dimensional nonlinear Schrödinger (NLS) equation. Cnoidal waves are exact periodic solutions of the NLS equation which can be represented as the lattices of overlapping solitons. The MI of these lattices leads to the development of ‘integrable turbulence’ (Zakharov 2009 Stud. Appl. Math. 122 219-34). We study the major characteristics of turbulence for the dn-branch of cnoidal waves and demonstrate how these characteristics depend on the degree of ‘overlapping’ between the solitons within the cnoidal wave. Integrable turbulence, which develops from the MI of the dn-branch of cnoidal waves, asymptotically approaches its stationary state in an oscillatory way. During this process, kinetic and potential energies oscillate around their asymptotic values. The amplitudes of these oscillations decay with time as {{t}-α} , 1<α <1.5 , the phases contain nonlinear phase shift decaying as t -1/2, and the frequency of the oscillations is equal to the double maximal growth rate of the MI, s=2{γ\\max} . In the asymptotic stationary state, the ratio of potential to kinetic energy is equal to  -2. The asymptotic PDF of the wave intensity is close to the exponential distribution for cnoidal waves with strong overlapping, and is significantly non-exponential for cnoidal waves with weak overlapping of the solitons. In the latter case, the dynamics of the system reduces to two-soliton collisions, which occur at an exponentially small rate and provide an up to two-fold increase in amplitude compared with the original cnoidal wave. For all cnoidal waves of the dn-branch, the rogue waves at the time of their maximal elevation have a quasi-rational profile similar to that of the Peregrine solution.

  20. In vitro characterization of felid herpesvirus 1 (FHV-1) mutants generated by recombineering in a recombinant BAC vector

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Felid herpesvirus 1 (FHV-1) mutants were constructed using two-step Red-mediated recombination techniques based on a virulent full-length FHV-1 BAC clone. The individual mutant viruses generated were deficient in glycoprotein C (gC), glycoprotein E (gE),US3 serine/threonine protein kinase (PK), or b...

  1. Generation and evaluation of a recombinant modified vaccinia virus Ankara vaccine for rabies.

    PubMed

    Weyer, Jacqueline; Rupprecht, Charles E; Mans, Janet; Viljoen, Gerrit J; Nel, Louis H

    2007-05-22

    Modified vaccinia virus Ankara (MVA) has become a vaccine vector of choice for recombinant vaccine development. A MVA-based rabies vaccine would be advantageous for use as a vaccine for dogs (and wildlife), particularly if it proves innocuous and efficacious by the oral route. Here, the generation and immunological testing of a recombinant MVA expressing a rabies virus glycoprotein gene is described. In a murine model, higher dosages of recombinant MVA were needed to induce equivocal immune responses as with Vaccinia Copenhagen or Vaccinia Western Reserve recombinants, when administered by a parenteral route. The MVA recombinant was not immunogenic or efficacious when administered per os in naïve mice. The ability of the recombinant MVA to induce anamnestic responses in dogs and raccoons was also investigated. Recombinant MVA boosted humoral immune responses in these animals when administered peripherally, but not when administered orally.

  2. Modulation instability and dissipative rogue waves in ion-beam plasma: Roles of ionization, recombination, and electron attachment

    SciTech Connect

    Guo, Shimin Mei, Liquan

    2014-11-15

    The amplitude modulation of ion-acoustic waves is investigated in an unmagnetized plasma containing positive ions, negative ions, and electrons obeying a kappa-type distribution that is penetrated by a positive ion beam. By considering dissipative mechanisms, including ionization, negative-positive ion recombination, and electron attachment, we introduce a comprehensive model for the plasma with the effects of sources and sinks. Via reductive perturbation theory, the modified nonlinear Schrödinger equation with a dissipative term is derived to govern the dynamics of the modulated waves. The effect of the plasma parameters on the modulation instability criterion for the modified nonlinear Schrödinger equation is numerically investigated in detail. Within the unstable region, first- and second-order dissipative ion-acoustic rogue waves are present. The effect of the plasma parameters on the characteristics of the dissipative rogue waves is also discussed.

  3. Topographic generation of submesoscale centrifugal instability and energy dissipation

    PubMed Central

    Gula, Jonathan; Molemaker, M. Jeroen; McWilliams, James C.

    2016-01-01

    Most of the ocean kinetic energy is contained in the large scale currents and the vigorous geostrophic eddy field, at horizontal scales of order 100 km. To achieve equilibrium the geostrophic currents must viscously dissipate their kinetic energy at much smaller scale. However, geostrophic turbulence is characterized by an inverse cascade of energy towards larger scale, and the pathways of energy toward dissipation are still in question. Here, we present a mechanism, in the context of the Gulf Stream, where energy is transferred from the geostrophic flow to submesoscale wakes through anticyclonic vertical vorticity generation in the bottom boundary layer. The submesoscale turbulence leads to elevated local dissipation and mixing outside the oceanic boundary layers. This process is generic for boundary slope currents that flow in the direction of Kelvin wave propagation. Topographic generation of submesoscale flows potentially provides a new and significant route to energy dissipation for geostrophic flows. PMID:27681822

  4. Topographic generation of submesoscale centrifugal instability and energy dissipation

    NASA Astrophysics Data System (ADS)

    Gula, Jonathan; Molemaker, M. Jeroen; McWilliams, James C.

    2016-09-01

    Most of the ocean kinetic energy is contained in the large scale currents and the vigorous geostrophic eddy field, at horizontal scales of order 100 km. To achieve equilibrium the geostrophic currents must viscously dissipate their kinetic energy at much smaller scale. However, geostrophic turbulence is characterized by an inverse cascade of energy towards larger scale, and the pathways of energy toward dissipation are still in question. Here, we present a mechanism, in the context of the Gulf Stream, where energy is transferred from the geostrophic flow to submesoscale wakes through anticyclonic vertical vorticity generation in the bottom boundary layer. The submesoscale turbulence leads to elevated local dissipation and mixing outside the oceanic boundary layers. This process is generic for boundary slope currents that flow in the direction of Kelvin wave propagation. Topographic generation of submesoscale flows potentially provides a new and significant route to energy dissipation for geostrophic flows.

  5. Topographic generation of submesoscale centrifugal instability and energy dissipation.

    PubMed

    Gula, Jonathan; Molemaker, M Jeroen; McWilliams, James C

    2016-09-29

    Most of the ocean kinetic energy is contained in the large scale currents and the vigorous geostrophic eddy field, at horizontal scales of order 100 km. To achieve equilibrium the geostrophic currents must viscously dissipate their kinetic energy at much smaller scale. However, geostrophic turbulence is characterized by an inverse cascade of energy towards larger scale, and the pathways of energy toward dissipation are still in question. Here, we present a mechanism, in the context of the Gulf Stream, where energy is transferred from the geostrophic flow to submesoscale wakes through anticyclonic vertical vorticity generation in the bottom boundary layer. The submesoscale turbulence leads to elevated local dissipation and mixing outside the oceanic boundary layers. This process is generic for boundary slope currents that flow in the direction of Kelvin wave propagation. Topographic generation of submesoscale flows potentially provides a new and significant route to energy dissipation for geostrophic flows.

  6. Magnetic Field Generation in Core-sheath Jets via the Kinetic Kelvin-Helmholtz Instability

    NASA Astrophysics Data System (ADS)

    Nishikawa, K.-I.; Hardee, P. E.; Duţan, I.; Niemiec, J.; Medvedev, M.; Mizuno, Y.; Meli, A.; Sol, H.; Zhang, B.; Pohl, M.; Hartmann, D. H.

    2014-09-01

    We have investigated magnetic field generation in velocity shears via the kinetic Kelvin-Helmholtz instability (kKHI) using a relativistic plasma jet core and stationary plasma sheath. Our three-dimensional particle-in-cell simulations consider plasma jet cores with Lorentz factors of 1.5, 5, and 15 for both electron-proton and electron-positron plasmas. For electron-proton plasmas, we find generation of strong large-scale DC currents and magnetic fields that extend over the entire shear surface and reach thicknesses of a few tens of electron skin depths. For electron-positron plasmas, we find generation of alternating currents and magnetic fields. Jet and sheath plasmas are accelerated across the shear surface in the strong magnetic fields generated by the kKHI. The mixing of jet and sheath plasmas generates a transverse structure similar to that produced by the Weibel instability.

  7. Supercontinuum and rogue soliton generation by induced modulational instability in photonic crystal fibre

    NASA Astrophysics Data System (ADS)

    Yang, Hua; Chen, Nengsong; Wang, Boyan; Tang, Pinghua; Zeng, Qilin

    2016-08-01

    We present an approach that enables active control of supercontinuum (SC) and rogue soliton (RS) generation through the modulation of a 500 fs input pulse by numerical simulations. The induced modulational instability contributes to the initial comb-like SC generation, which is fundamentally different from SC initiated by high-order soliton fission. The output spectrum shows great dependence on modulation frequencies and depths. It is interesting that we can manipulate the RS generation by adjusting the modulation parameters. And we also demonstrate the conditions which can be beneficial to RS generation: (i) very weak or large values of modulation depth; (ii) seeding in the vicinity of the peak of the modulational instability gain spectrum. Although RS degrades the smoothness of the SC, it is of great significance in the generation of tailored SC.

  8. Analyses of Injection-Coupled Combustion Instability from J-2X Gas Generator Development

    NASA Technical Reports Server (NTRS)

    Hulka, James R.; Kenny, R. Jeremy; Protz, Chris; Casiano, Matthew

    2011-01-01

    During development of the gas generator for the liquid oxygen/liquid hydrogen propellant J-2X rocket engine, combustion instabilities were observed near the frequency of the first longitudinal acoustic mode of the hot gas combustion chamber duct. These instabilities were similar to intermediate-frequency or buzz-type instabilities as described in historical programs, except for several aspects: 1) the frequencies were low, in the realm of chug; 2) at times the instability oscillation amplitudes were quite large, with peak-to-peak amplitudes exceeding 50% of the mean chamber pressure along with the appearance of harmonics; 3) the chamber excitation was related to but not exactly at the first longitudinal combustion chamber acoustic mode; and 4) the injector provided mass flow rate oscillations induced by capacitance and inertance effects in the injector rather than by organ pipe resonances of the coaxial oxidizer posts. This type of combustion instability is referred to as "injection coupling" because one critical driving source of the instability is mass flow rate oscillations from the injector. However, the type of injection coupling observed here is different than observed in previous instances of buzz instability with coaxial injectors, because of the lower frequencies and lack of influence from the oxidizer post organ pipe resonances. Test data and preliminary analyses of the initial combustion instabilities were presented in several papers at the 5th Liquid Propulsion Subcommittee meeting. Since that time, additional hot-fire tests with several new hardware configurations have been conducted, and additional analyses have been completed. The analytical models described in previous papers have been updated to include the influences of new geometrical configurations, including a different oxidizer injector manifold configuration and a branch pipe in the hot gas duct that supplies gaseous helium during the start transient to pre-spin the turbine. In addition, the

  9. Generation of recombinant antibodies and means for increasing their affinity.

    PubMed

    Altshuler, E P; Serebryanaya, D V; Katrukha, A G

    2010-12-01

    Highly specific interaction with foreign molecules is a unique feature of antibodies. Since 1975, when Keller and Milstein proposed the method of hybridoma technology and prepared mouse monoclonal antibodies, many antibodies specific to various antigens have been obtained. Recent development of methods for preparation of recombinant DNA libraries and in silico bioinformatics approaches for protein structure analysis makes possible antibody preparation using gene engineering approaches. The development of gene engineering methods allowed creating recombinant antibodies and improving characteristics of existing antibodies; this significantly extends the applicability of antibodies. By modifying biochemical and immunochemical properties of antibodies by changing their amino acid sequences it is possible to create antibodies with properties optimal for certain tasks. For example, application of recombinant technologies resulted in antibody preparation of high affinity significantly exceeding the initial affinity of natural antibodies. In this review we summarize information about the structure, modes of preparation, and application of recombinant antibodies and their fragments and also consider the main approaches used to increase antibody affinity.

  10. Generation of waves in the Venus mantle by the ion acoustic beam instability

    NASA Technical Reports Server (NTRS)

    Huba, J. D.

    1993-01-01

    The ion acoustic beam instability is suggested as a mechanism to produce wave turbulence observed in the Venus mantle at frequencies 100 Hz and 730 Hz. The plasma is assumed to consist of a stationary cold O(+) ion plasma and a flowing, shocked solar wind plasma. The O(+) ions appear as a beam relative to the flowing ionosheath plasma which provides the free energy to drive the instability. The plasma is driven unstable by inverse electron Landau damping of an ion acoustic wave associated with the cold ionospheric O(+) ions. The instability can directly generate the observed 100 Hz waves in the Venus mantle as well as the observed 730 Hz waves through the Doppler shift of the frequency caused by the satellite motion.

  11. Repeat instability: mechanisms of dynamic mutations.

    PubMed

    Pearson, Christopher E; Nichol Edamura, Kerrie; Cleary, John D

    2005-10-01

    Disease-causing repeat instability is an important and unique form of mutation that is linked to more than 40 neurological, neurodegenerative and neuromuscular disorders. DNA repeat expansion mutations are dynamic and ongoing within tissues and across generations. The patterns of inherited and tissue-specific instability are determined by both gene-specific cis-elements and trans-acting DNA metabolic proteins. Repeat instability probably involves the formation of unusual DNA structures during DNA replication, repair and recombination. Experimental advances towards explaining the mechanisms of repeat instability have broadened our understanding of this mutational process. They have revealed surprising ways in which metabolic pathways can drive or protect from repeat instability.

  12. Generation of pure spin currents via Auger recombination in quantum wells with Rashba splitting

    SciTech Connect

    Afanasiev, A. N. Greshnov, A. A. Greshnov, A. A.

    2015-10-15

    We propose a nonoptical mechanism for generating spin current via Auger recombination in semiconductor quantum wells (QWs) with spin–orbit splitting associated with structural QW asymmetry. It is shown that Auger recombination in narrow-bandgap semiconductors makes it possible to produce spin currents that exceed those that are obtained in the case of intraband as well as interband optical excitation. Analysis shows that the interference term in the expression for the Auger-recombination rate is responsible for the generation of spin currents.

  13. Observation of magnetic field generation via the Weibel instability in interpenetrating plasma flows

    NASA Astrophysics Data System (ADS)

    Huntington, C. M.; Fiuza, F.; Ross, J. S.; Zylstra, A. B.; Drake, R. P.; Froula, D. H.; Gregori, G.; Kugland, N. L.; Kuranz, C. C.; Levy, M. C.; Li, C. K.; Meinecke, J.; Morita, T.; Petrasso, R.; Plechaty, C.; Remington, B. A.; Ryutov, D. D.; Sakawa, Y.; Spitkovsky, A.; Takabe, H.; Park, H.-S.

    2015-02-01

    Collisionless shocks can be produced as a result of strong magnetic fields in a plasma flow, and therefore are common in many astrophysical systems. The Weibel instability is one candidate mechanism for the generation of sufficiently strong fields to create a collisionless shock. Despite their crucial role in astrophysical systems, observation of the magnetic fields produced by Weibel instabilities in experiments has been challenging. Using a proton probe to directly image electromagnetic fields, we present evidence of Weibel-generated magnetic fields that grow in opposing, initially unmagnetized plasma flows from laser-driven laboratory experiments. Three-dimensional particle-in-cell simulations reveal that the instability efficiently extracts energy from the plasma flows, and that the self-generated magnetic energy reaches a few percent of the total energy in the system. This result demonstrates an experimental platform suitable for the investigation of a wide range of astrophysical phenomena, including collisionless shock formation in supernova remnants, large-scale magnetic field amplification, and the radiation signature from gamma-ray bursts.

  14. The generation of magnetic fields by the Biermann battery and the interplay with the Weibel instability

    NASA Astrophysics Data System (ADS)

    Schoeffler, K. M.; Loureiro, N. F.; Fonseca, R. A.; Silva, L. O.

    2016-05-01

    An investigation of magnetic fields generated in an expanding bubble of plasma with misaligned temperature and density gradients (driving the Biermann battery mechanism) is performed. With gradient scales L, large-scale magnetic fields are generated by the Biermann battery mechanism with plasma β ˜ 1, as long as L is comparable to the ion inertial length di. For larger system sizes, L/de > 100 (where de is the electron inertial length), the Weibel instability generates magnetic fields of similar magnitude but with wavenumber kde ≈ 0.2. In both cases, the growth and saturation of these fields have a weak dependence on mass ratio mi/me, indicating electron mediated physics. A scan in system size is performed at mi/me = 2000, showing agreement with previous results with mi/me = 25. In addition, the instability found at large system sizes is quantitatively demonstrated to be the Weibel instability. Furthermore, magnetic and electric energy spectra at scales below the electron Larmor radius are found to exhibit power law behavior with spectral indices -16/3 and -4/3, respectively.

  15. Observation of magnetic field generation via the Weibel instability in interpenetrating plasma flows

    SciTech Connect

    Huntington, C. M.; Fiuza, F.; Ross, J. S.; Zylstra, A. B.; Drake, R. P.; Froula, D. H.; Gregori, G.; Kugland, N. L.; Kuranz, C. C.; Levy, M. C.; Li, C. K.; Meinecke, J.; Morita, T.; Petrasso, R.; Plechaty, C.; Remington, B. A.; Ryutov, D. D.; Sakawa, Y.; Spitkovsky, A.; Takabe, H.; Park, H.-S.

    2015-01-19

    Collisionless shocks can be produced as a result of strong magnetic fields in a plasma flow, and therefore are common in many astrophysical systems. The Weibel instability is one candidate mechanism for the generation of su fficiently strong fields to create a collisionless shock. Despite their crucial role in astrophysical systems, observation of the magnetic fields produced by Weibel instabilities in experiments has been challenging. Using a proton probe to directly image electromagnetic fields, we present evidence of Weibel-generated magnetic fields that grow in opposing, initially unmagnetized plasma flows from laser-driven laboratory experiments. Three-dimensional particle-in-cell simulations reveal that the instability effi ciently extracts energy from the plasma flows, and that the self-generated magnetic energy reaches a few percent of the total energy in the system. Furthermore, this result demonstrates an experimental platform suitable for the investigation of a wide range of astrophysical phenomena, including collisionless shock formation in supernova remnants, large-scale magnetic field amplification, and the radiation signature from gamma-ray bursts.

  16. Recombinational joints in a simian virus 40 variant generated in a persistent infection.

    PubMed

    Norkin, L C; Piatak, M

    1982-12-01

    SP1, a viable simian virus 40 (SV40) variant isolated from a persistent infection of rhesus monkey kidney cells, contains sequence rearrangements in the untranslated region of the SV40 genome which are transcribed into late mRNA leader sequences and in the region which encodes the large T antigen. Nucleotide sequences about the recombinational junctions in SP1 were determined. The sequence data show that in most instances there was not extensive homology between recombining sequences. The recombinant sequences are discussed with respect to the mechanisms by which they might have been generated.

  17. Analyses of Longitudinal Mode Combustion Instability in J-2X Gas Generator Development

    NASA Technical Reports Server (NTRS)

    Hulka, J. R.; Protz, C. S.; Casiano, M. J.; Kenny, R. J.

    2011-01-01

    The National Aeronautics and Space Administration (NASA) and Pratt & Whitney Rocketdyne are developing a liquid oxygen/liquid hydrogen rocket engine for future upper stage and trans-lunar applications. This engine, designated the J-2X, is a higher pressure, higher thrust variant of the Apollo-era J-2 engine. The contract for development was let to Pratt & Whitney Rocketdyne in 2006. Over the past several years, development of the gas generator for the J-2X engine has progressed through a variety of workhorse injector, chamber, and feed system configurations on the component test stand at the NASA Marshall Space Flight Center (MSFC). Several of the initial configurations resulted in combustion instability of the workhorse gas generator assembly at a frequency near the first longitudinal mode of the combustion chamber. In this paper, several aspects of these combustion instabilities are discussed, including injector, combustion chamber, feed system, and nozzle influences. To ensure elimination of the instabilities at the engine level, and to understand the stability margin, the gas generator system has been modeled at the NASA MSFC with two techniques, the Rocket Combustor Interaction Design and Analysis (ROCCID) code and a lumped-parameter MATLAB(TradeMark) model created as an alternative calculation to the ROCCID methodology. To correctly predict the instability characteristics of all the chamber and injector geometries and test conditions as a whole, several inputs to the submodels in ROCCID and the MATLAB(TradeMark) model were modified. Extensive sensitivity calculations were conducted to determine how to model and anchor a lumped-parameter injector response, and finite-element and acoustic analyses were conducted on several complicated combustion chamber geometries to determine how to model and anchor the chamber response. These modifications and their ramification for future stability analyses of this type are discussed.

  18. Design and generation of recombinant rabies virus vectors

    PubMed Central

    Osakada, Fumitaka; Callaway, Edward M.

    2014-01-01

    Rabies viruses, negative-strand RNA viruses, infect neurons through axon terminals and spread transsynaptically in a retrograde direction between neurons. Rabies viruses whose glycoprotein (G) gene is deleted from the genome cannot spread across synapses. Complementation of G in trans, however, enables transsynaptic spreading of G-deleted rabies viruses to directly-connected, presynaptic neurons. Recombinant rabies viruses can encode genes of interest for labeling cells, controlling gene expression, and monitoring or manipulating neural activity. Cre-dependent or bridge-protein-mediated transduction and single-cell electroporation via EnvA/TVA or EnvB/TVB system allow cell-type-specific or single-cell-specific targeting. These rabies virus-based approaches permit the linking of connectivity to cell morphology and circuit function for particular cell types or single cells. Here we describe methods for construction of rabies viral vectors, recovery of G-deleted rabies viruses from cDNA, amplification of the viruses, pseudotyping them with EnvA or EnvB, and concentration and titration of the viruses. The entire protocol takes 6–8 weeks. PMID:23887178

  19. Chaotic dynamics of a swirling flame front instability generated by a change in gravitational orientation

    NASA Astrophysics Data System (ADS)

    Gotoda, Hiroshi; Kobayashi, Hiroaki; Hayashi, Kenta

    2017-02-01

    We have intensively examined the dynamic behavior of flame front instability in a lean swirling premixed flame generated by a change in gravitational orientation [H. Gotoda, T. Miyano, and I. G. Shepherd, Phys. Rev. E 81, 026211 (2010), 10.1103/PhysRevE.81.026211] from the viewpoints of complex networks, symbolic dynamics, and statistical complexity. Here, we considered the permutation entropy in combination with the surrogate data method, the permutation spectrum test, and the multiscale complexity-entropy causality plane incorporating a scale-dependent approach, none of which have been considered in the study of flame front instabilities. Our results clearly show the possible presence of chaos in flame front dynamics induced by the coupling of swirl-buoyancy interaction in inverted gravity. The flame front dynamics also possesses a scale-free structure, which is reasonably shown by the probability distribution of the degree in ɛ -recurrence networks.

  20. Chaotic dynamics of a swirling flame front instability generated by a change in gravitational orientation.

    PubMed

    Gotoda, Hiroshi; Kobayashi, Hiroaki; Hayashi, Kenta

    2017-02-01

    We have intensively examined the dynamic behavior of flame front instability in a lean swirling premixed flame generated by a change in gravitational orientation [H. Gotoda, T. Miyano, and I. G. Shepherd, Phys. Rev. E 81, 026211 (2010)PLEEE81539-375510.1103/PhysRevE.81.026211] from the viewpoints of complex networks, symbolic dynamics, and statistical complexity. Here, we considered the permutation entropy in combination with the surrogate data method, the permutation spectrum test, and the multiscale complexity-entropy causality plane incorporating a scale-dependent approach, none of which have been considered in the study of flame front instabilities. Our results clearly show the possible presence of chaos in flame front dynamics induced by the coupling of swirl-buoyancy interaction in inverted gravity. The flame front dynamics also possesses a scale-free structure, which is reasonably shown by the probability distribution of the degree in ε-recurrence networks.

  1. Vortex lattices generated by the Kelvin-Helmholtz instability in the Gross-Pitaevskii equation

    SciTech Connect

    Ohta, A.; Kashiwa, R.; Sakaguchi, H.

    2010-11-15

    Vortex streets are formed from sheared initial conditions in classical fluids even without viscosity, which is called the Kelvin-Helmholtz instability. We demonstrate that similar vortex streets are generated from sheared initial conditions by the direct numerical simulation of the Gross-Pitaevskii (GP) equation which describes the dynamics of the Bose-Einstein condensates. Furthermore, we show the vortex-lattice formation from sheared initial conditions analogous to the rigid-body rotation in the GP equation under a rotating harmonic potential. The vortex-lattice formation by the dynamical instability in the system without energy dissipation differs from the vortex-lattice formation process by the imaginary time evolution of the GP equation where the lowest energy state is obtained.

  2. Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing

    PubMed Central

    Iles, James C.; Njouom, Richard; Foupouapouognigni, Yacouba; Bonsall, David; Bowden, Rory; Trebes, Amy; Piazza, Paolo; Barnes, Ellie; Pépin, Jacques; Klenerman, Paul

    2015-01-01

    The importance of recombination in the evolution and genetic diversity of the hepatitis C virus (HCV) is currently uncertain. Only a small number of intergenotypic recombinants have been identified so far, and each has core and envelope genes classified as belonging to genotype 2. Here, we investigated two putative genotype 4/1 recombinants from southern Cameroon using a number of approaches, including standard Sanger sequencing, genotype-specific PCR amplification, and non-HCV-specific Illumina RNA sequencing (RNA-seq). Recombination between genotypes 1 and 4 was confirmed in both samples, and the parental lineages of each recombinant belong to HCV subtypes that are cocirculating at a high prevalence in Cameroon. Using the RNA-seq approach, we obtained a complete genome for one sample, which contained a recombination breakpoint at the E2/P7 gene junction. We developed and applied a new method, called Deep SimPlot, which can be used to visualize and identify viral recombination directly from the short sequence reads created by next-generation sequencing in conjunction with a consensus sequence. PMID:26202126

  3. Analyses on the Ionization Instability of Non-Equilibrium Seeded Plasma in an MHD Generator

    NASA Astrophysics Data System (ADS)

    Le, Chi Kien

    2016-06-01

    Recently, closed cycle magnetohydrodynamic power generation system research has been focused on improving the isentropic efficiency and the enthalpy extraction ratio. By reducing the cross-section area ratio of the disk magnetohydrodynamic generator, it is believed that a high isentropic efficiency can be achieved with the same enthalpy extraction. In this study, the result relating to a plasma state which takes into account the ionization instability of non-equilibrium seeded plasma is added to the theoretical prediction of the relationship between enthalpy extraction and isentropic efficiency. As a result, the electron temperature which reaches the seed complete ionization state without the growth of ionization instability can be realized at a relatively high seed fraction condition. However, the upper limit of the power generation performance is suggested to remain lower than the value expected in the low seed fraction condition. It is also suggested that a higher power generation performance may be obtained by implementing the electron temperature range which reaches the seed complete ionization state at a low seed fraction.

  4. Embryonic stem cell gene targeting using bacteriophage lambda vectors generated by phage-plasmid recombination.

    PubMed Central

    Tsuzuki, T; Rancourt, D E

    1998-01-01

    Targeted mutagenesis is an extremely useful experimental approach in molecular medicine, allowing the generation of specialized animals that are mutant for any gene of interest. Currently the rate determining step in any gene targeting experiment is construction of the targeting vector (TV). In order to streamline gene targeting methods and avoid problems encountered with plasmid TVs, we describe the direct application of lambda phage in targeted mutagenesis. The recombination-proficient phage vector lambda2TK permits generation of TVs by conventional restriction-ligation or recombination-mediated methods. The resulting lambdaTV DNA can then be cleaved with restriction endonucleases to release the bacteriophage arms and can subsequently be electroporated directly into ES cells to yield gene targets. We demonstrate that in vivo phage-plasmid recombination can be used to introduce neo and lacZ - neo mutations into precise positions within a lambda2TK subclone via double crossover recombination. We describe two methods for eliminating single crossover recombinants, spi selection and size restriction, both of which result in phage TVs bearing double crossover insertions. Thus TVs can be easily and quickly generated in bacteriophage without plasmid subcloning and with little genomic sequence or restriction site information. PMID:9461458

  5. Generation of Recombinant Capripoxvirus Vectors for Vaccines and Gene Knockout Function Studies.

    PubMed

    Boshra, Hani; Cao, Jingxin; Babiuk, Shawn

    2016-01-01

    The ability to manipulate capripoxvirus through gene knockouts and gene insertions has become an increasingly valuable research tool in elucidating the function of individual genes of capripoxvirus, as well as in the development of capripoxvirus-based recombinant vaccines. The homologous recombination technique is used to generate capripoxvirus knockout viruses (KO), and is based on the targeting a particular viral gene of interest. This technique can also be used to insert a gene of interest. A protocol for the generation of a viral gene knockout is described. This technique involves the use of a plasmid which encodes the flanking sequences of the regions where the homologous recombination will occur, and will result in the insertion of an EGFP reporter gene for visualization of recombinant virus, as well as the E. coli gpt gene as a positive selection marker. If an additional gene is to be incorporated, this can be achieved by inserting a gene of interest for expression under a poxvirus promoter into the plasmid between the flanking regions for insertion. This chapter describes a protocol for generating such recombinant capripoxviruses.

  6. Instability of propagating axial symmetric waves generated by a vertically oscillating sphere

    NASA Astrophysics Data System (ADS)

    Shen, Meng; Liu, Yuming

    2015-11-01

    We study the instability of propagating axial symmetric waves in a basin that are generated by a vertically oscillating sphere. Laboratory experiments indicate that when the oscillation amplitude exceeds a threshold value, the axial symmetric propagating waves abruptly transfigure into non-axial symmetric waves. Fully-nonlinear time-domain numerical simulation of wave-body interaction is applied to describe the nonlinear temporal and spatial evolution dynamics of the propagating waves. Transition matrix method is employed to analyze the stability of the nonlinear time periodic wave-body interaction system. We identify the fundamental mechanism leading to the instability of the wave-body system and investigate the critical condition for the occurrence of the instability. We quantify the growth rate and dominant modes of unstable disturbances and study their dependence on physical parameters including body motion frequency and amplitude, body geometry, surface tension and basin size. Moreover, the long-time evolution dynamics of the unstable wave-bod y system including wave patterns and responsive body forces are also investigated.

  7. Three Dimensional modeling of instability development in MagLIF loads on the Z Generator

    NASA Astrophysics Data System (ADS)

    Jennings, C. A.; Harding, E. C.; Gomez, M. R.; Hansen, S. B.; Awe, T. J.; McBride, R. D.; Martin, M. R.; Peterson, K. J.; Chittenden, J. P.

    2015-11-01

    Liners imploded by a fast rising (<100ns) current to compress a magnetized, preheated fuel offer the potential to efficiently reach fusion conditions. Experiments with these Magnetized Liner Inertial Fusion (MagLIF) loads have demonstrated success. Performance may be limited by poor laser coupling in preheating the fuel to be imploded. However time integrated imaging also shows structure in the final fuel assembly indicating potential disruption from instabilities which may also limit neutron yield. We simulate the implosion and stagnation of MagLIF targets using the 3D MHD code GORGON. Generating synthetic diagnostics for comparison with data we discuss how implosion instabilities comparable to those diagnosed with radiography affect fuel compression and confinement. By further comparison of calculation results with PCD traces, time integrated spectra and crystal imaging we discuss how fuel conditions vary in response to feedthrough of implosion instabilities, and how structures formed may affect diagnostic interpretation. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under contract DE-AC04-94AL85000.

  8. No recombination of mtDNA after heteroplasmy for 50 generations in the mouse maternal germline

    PubMed Central

    Hagström, Erik; Freyer, Christoph; Battersby, Brendan J.; Stewart, James B.; Larsson, Nils-Göran

    2014-01-01

    Variants of mitochondrial DNA (mtDNA) are commonly used as markers to track human evolution because of the high sequence divergence and exclusive maternal inheritance. It is assumed that the inheritance is clonal, i.e. that mtDNA is transmitted between generations without germline recombination. In contrast to this assumption, a number of studies have reported the presence of recombinant mtDNA molecules in cell lines and animal tissues, including humans. If germline recombination of mtDNA is frequent, it would strongly impact phylogenetic and population studies by altering estimates of coalescent time and branch lengths in phylogenetic trees. Unfortunately, this whole area is controversial and the experimental approaches have been widely criticized as they often depend on polymerase chain reaction (PCR) amplification of mtDNA and/or involve studies of transformed cell lines. In this study, we used an in vivo mouse model that has had germline heteroplasmy for a defined set of mtDNA mutations for more than 50 generations. To assess recombination, we adapted and validated a method based on cloning of single mtDNA molecules in the λ phage, without prior PCR amplification, followed by subsequent mutation analysis. We screened 2922 mtDNA molecules and found no germline recombination after transmission of mtDNA under genetically and evolutionary relevant conditions in mammals. PMID:24163253

  9. Growth, morphology, and developmental instability of rainbow trout, Yellowstone cutthroat trout, and four hybrid generations

    USGS Publications Warehouse

    Ostberg, C.O.; Duda, J.J.; Graham, J.H.; Zhang, S.; Haywood, K. P.; Miller, B.; Lerud, T.L.

    2011-01-01

    Hybridization of cutthroat trout Oncorhynchus clarkii with nonindigenous rainbow trout O. mykiss contributes to the decline of cutthroat trout subspecies throughout their native range. Introgression by rainbow trout can swamp the gene pools of cutthroat trout populations, especially if there is little selection against hybrids. We used rainbow trout, Yellowstone cutthroat trout O. clarkii bouvieri, and rainbow trout × Yellowstone cutthroat trout F1 hybrids as parents to construct seven different line crosses: F1 hybrids (both reciprocal crosses), F2 hybrids, first-generation backcrosses (both rainbow trout and Yellowstone cutthroat trout), and both parental taxa. We compared growth, morphology, and developmental instability among these seven crosses reared at two different temperatures. Growth was related to the proportion of rainbow trout genome present within the crosses. Meristic traits were influenced by maternal, additive, dominant, overdominant, and (probably) epistatic genetic effects. Developmental stability, however, was not disturbed in F1 hybrids, F2 hybrids, or backcrosses. Backcrosses were morphologically similar to their recurrent parent. The lack of developmental instability in hybrids suggests that there are few genetic incompatibilities preventing introgression. Our findings suggest that hybrids are not equal: that is, growth, development, character traits, and morphology differ depending on the genomic contribution from each parental species as well as the hybrid generation.

  10. Pulmonary drug delivery using droplets generated by Rayleigh instability-driven breakup of filaments

    NASA Astrophysics Data System (ADS)

    Kong, Yen-Peng; Xu, Yuan; Tay, Francis E. H.

    2002-11-01

    For effective pulmonary drug delivery of insulin for example, drug particles must be in the range of 1 to 5 microns. A piezoelectrically actuated MEMS atomizer based on Rayleigh instability-driven breakup of filaments has been designed to produce drug particles in this range. Although the formation of droplets from jets have been used extensively in ink-jet printing, the currently presented mode of droplet formation has not yet been demonstrated by any MEMS device. Testing of the vaporiser reveals that the droplets generated lie primarily in the range of 1.0 through 3.0 microns, a range that covers the designed droplet size of 2.5 microns. We thus show that it is possible to implement this mode of droplet generation that will achieve better device efficiency.

  11. Homologous recombination is a primary pathway to repair DNA double-strand breaks generated during DNA rereplication.

    PubMed

    Truong, Lan N; Li, Yongjiang; Sun, Emily; Ang, Katrina; Hwang, Patty Yi-Hwa; Wu, Xiaohua

    2014-10-17

    Re-initiation of DNA replication at origins within a given cell cycle would result in DNA rereplication, which can lead to genome instability and tumorigenesis. DNA rereplication can be induced by loss of licensing control at cellular replication origins, or by viral protein-driven multiple rounds of replication initiation at viral origins. DNA double-strand breaks (DSBs) are generated during rereplication, but the mechanisms of how these DSBs are repaired to maintain genome stability and cell viability are poorly understood in mammalian cells. We generated novel EGFP-based DSB repair substrates, which specifically monitor the repair of rereplication-associated DSBs. We demonstrated that homologous recombination (HR) is an important mechanism to repair rereplication-associated DSBs, and sister chromatids are used as templates for such HR-mediated DSB repair. Micro-homology-mediated non-homologous end joining (MMEJ) can also be used but to a lesser extent compared to HR, whereas Ku-dependent classical non-homologous end joining (C-NHEJ) has a minimal role to repair rereplication-associated DSBs. In addition, loss of HR activity leads to severe cell death when rereplication is induced. Therefore, our studies identify HR, the most conservative repair pathway, as the primary mechanism to repair DSBs upon rereplication.

  12. Particle dynamics in discs with turbulence generated by the vertical shear instability

    NASA Astrophysics Data System (ADS)

    Stoll, Moritz H. R.; Kley, Wilhelm

    2016-10-01

    Context. Among the candidates for generating turbulence in accretion discs in situations with low intrinsic ionization, the vertical shear instability (VSI) has become an interesting candidate, since it relies purely on a vertical gradient in the angular velocity. Existing numerical simulations have shown that α-values a few times 10-4 can be generated. Aims: The particle growth in the early planet formation phase is determined by the dynamics of embedded dust particles. Here, we address, in particular, the efficiency of VSI-turbulence in concentrating particles to generate overdensities and low collision velocities. Methods: We perform three-dimensional (3D) numerical hydrodynamical simulations of accretion discs around young stars that include radiative transport and irradiation from the central star. The motion of embedded particles within a size range of a fraction of mm up to several m is followed using standard drag formula. Results: We confirm that, under realistic conditions, the VSI is able to generate turbulence in full 3D protoplanetary discs. The irradiated disc shows turbulence within 10 to 60 au. The mean radial motion of the gas is such that it is directed inward near the midplane and outward in the surface layers. We find that large particles drift inward with the expected speed, while small particles can experience phases of outward drift. Additionally, the particles show bunching behaviour with overdensities reaching five times the average value, which is strongest for dimensionless stopping times around unity. Conclusions: Particles in a VSI-turbulent discs are concentrated in large-scale turbulent eddies and show low relative speeds that allow for growing collisions. The reached overdensities will also enable the onset of streaming instabilities, further enhancing particle growth. The outward drift for small particles at higher disk elevations enable the transport of processed high temperature material in the solar system to greater distances.

  13. A Novel and Simple Method for Rapid Generation of Recombinant Porcine Adenoviral Vectors for Transgene Expression

    PubMed Central

    Ma, Jing; Wang, Wenbin; Zhang, Lu; Tikoo, Suresh K.; Yang, Zengqi

    2015-01-01

    Many human (different serotypes) and nonhuman adenovirus vectors are being used for gene delivery. However, the current system for isolating recombinant adenoviral vectors is either time-consuming or expensive, especially for the generation of recombinant non-human adenoviral vectors. We herein report a new and simple cloning approach for the rapid generation of a porcine adenovirus (PAdV-3) vector which shows promise for gene transfer to human cells and evasion of human adenovirus type 5 (HAdV-5) immunity. Based on the final cloning plasmid, pFPAV3-CcdB-Cm, and our modified SLiCE strategy (SLiCE cloning and lethal CcdB screening), the process for generating recombinant PAdV-3 plasmids required only one step in 3 days, with a cloning efficiency as high as 620±49.56 clones/ng and zero background (100% accuracy). The recombinant PAdV-3 plasmids could be successfully rescued in porcine retinal pigment epithelium cells (VR1BL), which constitutively express the HAdV-5 E1 and PAdV-3 E1B 55k genes, and the foreign genes were highly expressed at 24 h after transduction into swine testicle (ST) cells. In conclusion, this strategy for generating recombinant PAdV-3 vectors based on our modified SLiCE cloning system was rapid and cost-efficient, which could be used as universal cloning method for modification the other regions of PAdV-3 genome as well as other adenoviral genomes. PMID:26011074

  14. Tandem recombineering by SLIC cloning and Cre-LoxP fusion to generate multigene expression constructs for protein complex research.

    PubMed

    Haffke, Matthias; Viola, Cristina; Nie, Yan; Berger, Imre

    2013-01-01

    A robust protocol to generate recombinant DNA containing multigene expression cassettes by using sequence and ligation independent cloning (SLIC) followed by multiplasmid Cre-LoxP recombination in tandem for multiprotein complex research is described. The protocol includes polymerase chain reaction (PCR) amplification of the desired genes, seamless insertion into the target vector via SLIC, and Cre-LoxP recombination of specific donor and acceptor plasmid molecules, optionally in a robotic setup. This procedure, called tandem recombineering, has been implemented for multiprotein expression in E. coli and mammalian cells, and also for insect cells using a recombinant baculovirus.

  15. Thermoelectric instability induced by single pulses and alternating currents in second-generation superconducting tapes

    NASA Astrophysics Data System (ADS)

    Degtyarenko, P. N.; Dul'kin, I. N.; Fisher, L. M.; Kalinov, A. V.; Voloshin, I. F.; Yampol'skii, V. A.

    2011-02-01

    We have studied current flow instabilities in a second-generation superconducting tapes and the transition of the tapes into the resistive state. Contrary to the usual quasisteady instability regimes, here we consider the adiabatic case in which the sample is heated rapidly. Two kinds of measurements of the current-voltage characteristics (CVC) have been made, specifically, with excitation of the tape by a single sinusoidal current pulse I (t)=I0sin(ωt) at different amplitudes I0 and by a continuous ac current. The main results were obtained for current amplitudes I0 exceeding the critical current Ic. We find that the dynamic CVC are essentially reversible for low amplitudes, whereas they become irreversible and acquire an N-shape for higher current amplitudes. The dynamic CVC change radically if the dissipated energy attains a threshold value Wth roughly equal to 5mJ/cm for our tapes. When this energy is reached, the tape undergoes a transition to the resistive state owing to formation of normal domains. The development of the instability with steady ac currents was studied at relatively small amplitudes such that the energy dissipated per half cycle is much lower than Wth. Even in this case, a tape undergoes a transition to the resistive state because of energy accumulation (heat pumping). With this pumping, the transition takes place after a definite number of ac cycles, when the total accumulated energy reaches the same threshold value Wth. The specific features of the dynamic CVC are interpreted qualitatively, with the appearance of resistive domains taken into account. Estimates based on the CVC agree well with our experimental data. These results can be useful in the design of superconducting fault current limiters.

  16. On the generation of double layers from ion- and electron-acoustic instabilities

    NASA Astrophysics Data System (ADS)

    Fu, Xiangrong; Cowee, Misa M.; Gary, S. Peter; Winske, Dan

    2016-03-01

    A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric field structures traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs—electron acoustic DLs—generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e., the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. Linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric field structures that propagate at the electron thermal speed, suggesting another potential explanation for the observations.

  17. Controlled generation of high-intensity optical rogue waves by induced modulation instability

    PubMed Central

    Zhao, Saili; Yang, Hua; Chen, Nengsong; Zhao, Chujun

    2017-01-01

    Optical rogue waves are featured as the generation of high amplitude events at low probability in optical systems. Moreover, the formation of optical rogue waves is unpredictable and transient in photonic crystal fibers. In this paper, we put forward a method to generate high-intensity optical rogue waves in a more controlled way based on induced modulation instability, which can suppress the noise effect and hence play a leading role in the process of pulse evolution. Our numerical simulations indicate that the generation of rogue wave can be controlled when seeding at the optimal modulation frequency and the intensity of rogue wave can be enhanced with appropriate modulation depth. Further, high-intensity rogue wave can also be ejected in the fiber with a shorter propagation length by regulating the modulation depth. These results all provide a better understanding of optical rogue wave, which can contribute to the generation of tunable long-wavelength spectral components and selective excitation of mid-infrared supercontinuum. PMID:28051149

  18. Controlled generation of high-intensity optical rogue waves by induced modulation instability.

    PubMed

    Zhao, Saili; Yang, Hua; Chen, Nengsong; Zhao, Chujun

    2017-01-04

    Optical rogue waves are featured as the generation of high amplitude events at low probability in optical systems. Moreover, the formation of optical rogue waves is unpredictable and transient in photonic crystal fibers. In this paper, we put forward a method to generate high-intensity optical rogue waves in a more controlled way based on induced modulation instability, which can suppress the noise effect and hence play a leading role in the process of pulse evolution. Our numerical simulations indicate that the generation of rogue wave can be controlled when seeding at the optimal modulation frequency and the intensity of rogue wave can be enhanced with appropriate modulation depth. Further, high-intensity rogue wave can also be ejected in the fiber with a shorter propagation length by regulating the modulation depth. These results all provide a better understanding of optical rogue wave, which can contribute to the generation of tunable long-wavelength spectral components and selective excitation of mid-infrared supercontinuum.

  19. Controlled generation of high-intensity optical rogue waves by induced modulation instability

    NASA Astrophysics Data System (ADS)

    Zhao, Saili; Yang, Hua; Chen, Nengsong; Zhao, Chujun

    2017-01-01

    Optical rogue waves are featured as the generation of high amplitude events at low probability in optical systems. Moreover, the formation of optical rogue waves is unpredictable and transient in photonic crystal fibers. In this paper, we put forward a method to generate high-intensity optical rogue waves in a more controlled way based on induced modulation instability, which can suppress the noise effect and hence play a leading role in the process of pulse evolution. Our numerical simulations indicate that the generation of rogue wave can be controlled when seeding at the optimal modulation frequency and the intensity of rogue wave can be enhanced with appropriate modulation depth. Further, high-intensity rogue wave can also be ejected in the fiber with a shorter propagation length by regulating the modulation depth. These results all provide a better understanding of optical rogue wave, which can contribute to the generation of tunable long-wavelength spectral components and selective excitation of mid-infrared supercontinuum.

  20. Cell polarity-driven instability generates self-organized, fractal patterning of cell layers.

    PubMed

    Rudge, Timothy J; Federici, Fernán; Steiner, Paul J; Kan, Anton; Haseloff, Jim

    2013-12-20

    As a model system to study physical interactions in multicellular systems, we used layers of Escherichia coli cells, which exhibit little or no intrinsic coordination of growth. This system effectively isolates the effects of cell shape, growth, and division on spatial self-organization. Tracking the development of fluorescence-labeled cellular domains, we observed the emergence of striking fractal patterns with jagged, self-similar shapes. We then used a large-scale, cellular biophysical model to show that local instabilities due to polar cell-shape, repeatedly propagated by uniaxial growth and division, are responsible for generating this fractal geometry. Confirming this result, a mutant of E. coli with spherical shape forms smooth, nonfractal cellular domains. These results demonstrate that even populations of relatively simple bacterial cells can possess emergent properties due to purely physical interactions. Therefore, accurate physico-genetic models of cell growth will be essential for the design and understanding of genetically programmed multicellular systems.

  1. Limits on dynamically generated spin-orbit coupling: Absence of l =1 Pomeranchuk instabilities in metals

    NASA Astrophysics Data System (ADS)

    Kiselev, Egor I.; Scheurer, Mathias S.; Wölfle, Peter; Schmalian, Jörg

    2017-03-01

    An ordered state in the spin sector that breaks parity without breaking time-reversal symmetry, i.e., that can be considered dynamically generated spin-orbit coupling, was proposed to explain puzzling observations in a range of different systems. Here, we derive severe restrictions for such a state that follow from a Ward identity related to spin conservation. It is shown that l =1 spin-Pomeranchuk instabilities are not possible in nonrelativistic systems since the response of spin-current fluctuations is entirely incoherent and nonsingular. This rules out relativistic spin-orbit coupling as an emergent low-energy phenomenon. We illustrate the exotic physical properties of the remaining higher-angular-momentum analogs of spin-orbit coupling and derive a geometric constraint for spin-orbit vectors in lattice systems.

  2. Generation of recombinant arenavirus for vaccine development in FDA-approved Vero cells.

    PubMed

    Cheng, Benson Y H; Ortiz-Riaño, Emilio; de la Torre, Juan Carlos; Martínez-Sobrido, Luis

    2013-08-01

    The development and implementation of arenavirus reverse genetics represents a significant breakthrough in the arenavirus field. The use of cell-based arenavirus minigenome systems together with the ability to generate recombinant infectious arenaviruses with predetermined mutations in their genomes has facilitated the investigation of the contribution of viral determinants to the different steps of the arenavirus life cycle, as well as virus-host interactions and mechanisms of arenavirus pathogenesis. In addition, the development of trisegmented arenaviruses has permitted the use of the arenavirus genome to express additional foreign genes of interest, thus opening the possibility of arenavirus-based vaccine vector applications. Likewise, the development of single-cycle infectious arenaviruses capable of expressing reporter genes provides a new experimental tool to improve the safety of research involving highly pathogenic human arenaviruses. The generation of recombinant arenaviruses using plasmid-based reverse genetics techniques has so far relied on the use of rodent cell lines, which poses some barriers for the development of Food and Drug Administration (FDA)-licensed vaccine or vaccine vectors. To overcome this obstacle, we describe here the efficient generation of recombinant arenaviruses in FDA-approved Vero cells.

  3. Correlation of a generation-recombination center with a deep level trap in GaN

    SciTech Connect

    Nguyen, X. S. E-mail: elecsj@nus.edu.sg; Lin, K.; Zhang, Z.; Arehart, A. R.; Ringel, S. A.; McSkimming, B.; Speck, J. S.; Fitzgerald, E. A.; Chua, S. J. E-mail: elecsj@nus.edu.sg

    2015-03-09

    We report on the identification of a deep level trap centre which contributes to generation-recombination noise. A n-GaN epilayer, grown by MOCVD on sapphire, was measured by deep level transient spectroscopy (DLTS) and noise spectroscopy. DLTS found 3 well documented deep levels at E{sub c} − 0.26 eV, E{sub c} − 0.59 eV, and E{sub c} − 0.71 eV. The noise spectroscopy identified a generation recombination centre at E{sub c} − 0.65 ± 0.1 eV with a recombination lifetime of 65 μs at 300 K. This level is considered to be the same as the one at E{sub c} − 0.59 eV measured from DLTS, as they have similar trap densities and capture cross section. This result shows that some deep levels contribute to noise generation in GaN materials.

  4. Instability of, and generation of hydrogen peroxide by, phenolic compounds in cell culture media.

    PubMed

    Long, Lee Hua; Hoi, Aina; Halliwell, Barry

    2010-09-01

    Many papers in the literature have described complex effects of flavonoids and other polyphenols on cells in culture. In this paper we show that hydroxytyrosol, delphinidin chloride and rosmarinic acid are unstable in three commonly-used cell culture media (Dulbecco's modified Eagle's medium (DMEM), RPMI 1640 (RPMI) and Minimal Essential Medium Eagle (MEM)) and undergo rapid oxidation to generate H2O2. This may have confounded some previous studies on the cellular effects of these compounds. By contrast, apigenin, curcumin, hesperetin, naringenin, resveratrol and tyrosol did not generate significant H2O2 levels in these media. Nevertheless, curcumin and, to a lesser extent, resveratrol (but not tyrosol) were also unstable in DMEM, so the absence of detectable H2O2 production by a compound in cell culture media should not be equated to stability of that compound. Compound instability and generation of H2O2 must be taken into account in interpreting effects of phenolic compounds on cells in culture.

  5. Sound generated by instability waves of supersonic flows. I Two-dimensional mixing layers. II - Axisymmetric jets

    NASA Technical Reports Server (NTRS)

    Tam, C. K. W.; Burton, D. E.

    1984-01-01

    An investigation is conducted of the phenomenon of sound generation by spatially growing instability waves in high-speed flows. It is pointed out that this process of noise generation is most effective when the flow is supersonic relative to the ambient speed of sound. The inner and outer asymptotic expansions corresponding to an excited instability wave in a two-dimensional mixing layer and its associated acoustic fields are constructed in terms of the inner and outer spatial variables. In matching the solutions, the intermediate matching principle of Van Dyke and Cole is followed. The validity of the theory is tested by applying it to an axisymmetric supersonic jet and comparing the calculated results with experimental measurements. Very favorable agreements are found both in the calculated instability-wave amplitude distribution (the inner solution) and the near pressure field level contours (the outer solution) in each case.

  6. Double-electron recombination in high-order-harmonic generation driven by spatially inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Chacón, Alexis; Ciappina, Marcelo F.; Lewenstein, Maciej

    2016-10-01

    We present theoretical studies of high-order harmonic generation (HHG) driven by plasmonic fields in two-electron atomic systems. Comparing the single- and two-electron active approximation models of the hydrogen negative ion, we provide strong evidence that a nonsequential double-electron recombination mechanism appears to be mainly responsible for the HHG cutoff extension. Our analysis is carried out by means of a reduced one-dimensional numerical integration of the two-electron time-dependent Schrödinger equation, and on investigations of the classical electron trajectories, resulting from the Newton's equation of motion. Additional comparisons between the hydrogen negative ion and the helium atom suggest that the double recombination process depends distinctly on the atomic target. Our research paves the way to the understanding of strong field processes in multielectronic systems driven by spatially inhomogeneous fields.

  7. Influence of the backreaction of streaming cosmic rays on magnetic field generation and thermal instability

    SciTech Connect

    Nekrasov, Anatoly K.; Shadmehri, Mohsen E-mail: nekrasov.anatoly@gmail.com

    2014-06-10

    Using a multifluid approach, we investigate streaming and thermal instabilities of the electron-ion plasma with homogeneous cold cosmic rays propagating perpendicular to the background magnetic field. Perturbations are also considered to be across the magnetic field. The backreaction of cosmic rays resulting in strong streaming instabilities is taken into account. It is shown that, for sufficiently short wavelength perturbations, the growth rates can exceed the growth rate of cosmic-ray streaming instability along the magnetic field, found by Nekrasov and Shadmehri, which is in turn considerably larger than the growth rate of the Bell instability. The thermal instability is shown not to be subject to the action of cosmic rays in the model under consideration. The dispersion relation for the thermal instability has been derived, which includes sound velocities of plasma and cosmic rays and Alfvén and cosmic-ray streaming velocities. The relation between these parameters determines the kind of thermal instability ranging from the Parker to the Field instabilities. The results obtained can be useful for a more detailed investigation of electron-ion astrophysical objects, such as supernova remnant shocks, galaxy clusters, and others, including the dynamics of streaming cosmic rays.

  8. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins.

    PubMed

    Zhong, Nan; Loppnau, Peter; Seitova, Alma; Ravichandran, Mani; Fenner, Maria; Jain, Harshika; Bhattacharya, Anandi; Hutchinson, Ashley; Paduch, Marcin; Lu, Vincent; Olszewski, Michal; Kossiakoff, Anthony A; Dowdell, Evan; Koide, Akiko; Koide, Shohei; Huang, Haiming; Nadeem, Vincent; Sidhu, Sachdev S; Greenblatt, Jack F; Marcon, Edyta; Arrowsmith, Cheryl H; Edwards, Aled M; Gräslund, Susanne

    2015-01-01

    We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.

  9. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins

    PubMed Central

    Zhong, Nan; Loppnau, Peter; Seitova, Alma; Ravichandran, Mani; Fenner, Maria; Jain, Harshika; Bhattacharya, Anandi; Hutchinson, Ashley; Paduch, Marcin; Lu, Vincent; Olszewski, Michal; Kossiakoff, Anthony A.; Dowdell, Evan; Koide, Akiko; Koide, Shohei; Huang, Haiming; Nadeem, Vincent; Sidhu, Sachdev S.; Greenblatt, Jack F.; Marcon, Edyta; Arrowsmith, Cheryl H.; Edwards, Aled M.; Gräslund, Susanne

    2015-01-01

    We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols. PMID:26437229

  10. Generating Functional Recombinant NRPS Enzymes in the Laboratory Setting via Peptidyl Carrier Protein Engineering.

    PubMed

    Owen, Jeremy G; Calcott, Mark J; Robins, Katherine J; Ackerley, David F

    2016-11-17

    Non-ribosomal peptide synthetases (NRPSs) are modular enzymatic assembly lines where substrates and intermediates undergo rounds of transformation catalyzed by adenylation (A), condensation (C), and thioesterase (TE) domains. Central to the NRPS biosynthesis are peptidyl carrier protein (PCP) domains, small, catalytically inactive domains that shuttle substrates and intermediates between the catalytic modules and govern product release from TE domains. There is strong interest in recombination of NRPS systems to generate new chemical entities. However, the intrinsic complexity of these systems has been a major challenge. Here, we employ domain substitution and random mutagenesis to recapitulate NRPS evolution, focusing on PCP domains. Using NRPS model systems that produce two different pigmented molecules, pyoverdine and indigoidine, we found that only evolutionarily specialized recombinant PCP domains could interact effectively with the native TE domain for product release. Overall, we highlight that substituted PCP domains require very minor changes to result in functional NRPSs, and infer that positive selection pressure may improve recombinant NRPS outcomes.

  11. Role of microRNAs and DNA Methyltransferases in Transmitting Induced Genomic Instability between Cell Generations

    PubMed Central

    Huumonen, Katriina; Korkalainen, Merja; Viluksela, Matti; Lahtinen, Tapani; Naarala, Jonne; Juutilainen, Jukka

    2014-01-01

    There is limited understanding of how radiation or chemicals induce genomic instability, and how the instability is epigenetically transmitted to the progeny of exposed cells or organisms. Here, we measured the expression of microRNAs (miRNAs) and DNA methyltransferases (DNMTs) in murine embryonal fibroblasts exposed to ionizing radiation or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which were previously shown to induce genomic instability in this cell line. Cadmium was used as a reference agent that does not induce genomic instability in our experimental model. Measurements at 8 and 15 days after exposure did not identify any such persistent changes that could be considered as signals transmitting genomic instability to the progeny of exposed cells. However, measurements at 2 days after exposure revealed findings that may reflect initial stages of genomic instability. Changes that were common to TCDD and two doses of radiation (but not to cadmium) included five candidate signature miRNAs and general up-regulation of miRNA expression. Expression of DNMT3a, DNMT3b, and DNMT2 was suppressed by cadmium but not by TCDD or radiation, consistently with the hypothesis that sufficient expression of DNMTs is necessary in the initial phase of induced genomic instability. PMID:25309892

  12. Concurrent V(D)J recombination and DNA end instability increase interchromosomal trans-rearrangements in ATM-deficient thymocytes.

    PubMed

    Bowen, Steven; Wangsa, Darawalee; Ried, Thomas; Livak, Ferenc; Hodes, Richard J

    2013-04-01

    During the CD4(-)CD8(-) (DN) stage of T-cell development, RAG-dependent DNA breaks and V(D)J recombination occur at three T-cell receptor (TCR) loci: TCRβ, TCRγ and TCRδ. During this stage, abnormal trans-rearrangements also take place between TCR loci, occurring at increased frequency in absence of the DNA damage response mediator ataxia telangiectasia mutated (ATM). Here, we use this model of physiologic trans-rearrangement to study factors that predispose to rearrangement and the role of ATM in preventing chromosomal translocations. The frequency of DN thymocytes with DNA damage foci at multiple TCR loci simultaneously is increased 2- to 3-fold in the absence of ATM. However, trans-rearrangement is increased 10 000- to 100 000-fold, indicating that ATM function extends beyond timely resolution of DNA breaks. RAG-mediated synaptic complex formation occurs between recombination signal sequences with unequal 12 and 23 base spacer sequences (12/23 rule). TCR trans-rearrangements violate this rule, as we observed similar frequencies of 12/23 and aberrant 12/12 or 23/23 recombination products. This suggests that trans-rearrangements are not the result of trans-synaptic complex formation, but they are instead because of unstable cis synaptic complexes that form simultaneously at distinct TCR loci. Thus, ATM suppresses trans-rearrangement primarily through stabilization of DNA breaks at TCR loci.

  13. A new method for rapidly generating gene-targeting vectors by engineering BACs through homologous recombination in bacteria.

    PubMed

    Cotta-de-Almeida, Vinicius; Schonhoff, Susan; Shibata, Tomoyuki; Leiter, Andrew; Snapper, Scott B

    2003-09-01

    Generating knockout mice is still an expensive and highly time-consuming process. Target construct generation, the first labor-intensive step in this process, requires the manipulation of large fragments of DNA and numerous, and often cumbersome, cloning steps. Here we show the development of a rapid approach for generating targeting constructs that capitalizes on efficient homologous recombination between linear DNA fragments and circular plasmids in Escherichia coli ("recombineering"), the availability of bacterial artificial chromosomes (BACs), and the accessibility of the sequence of the mouse genome. Employing recombineering, we demonstrate with only 1-2 template plasmids, short homologies (40-50bp) between donor and target DNA, and one subcloning step that we can efficiently manipulate BACs in situ to generate a complicated targeting vector. This procedure avoids the need to construct or screen genomic libraries and permits the generation of most standard, conditional, or knock-in targeting vectors, often within two weeks.

  14. Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination

    PubMed Central

    Lee, Mi Ok; Bornelöv, Susanne; Andersson, Leif; Lamont, Susan J.; Chen, Junfeng; Womack, James E.

    2016-01-01

    Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6. The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins. PMID:27849592

  15. De novo generation of infectious prions with bacterially expressed recombinant prion protein.

    PubMed

    Zhang, Zhihong; Zhang, Yi; Wang, Fei; Wang, Xinhe; Xu, Yuanyuan; Yang, Huaiyi; Yu, Guohua; Yuan, Chonggang; Ma, Jiyan

    2013-12-01

    The prion hypothesis is strongly supported by the fact that prion infectivity and the pathogenic conformer of prion protein (PrP) are simultaneously propagated in vitro by the serial protein misfolding cyclic amplification (sPMCA). However, due to sPMCA's enormous amplification power, whether an infectious prion can be formed de novo with bacterially expressed recombinant PrP (rPrP) remains to be satisfactorily resolved. To address this question, we performed unseeded sPMCA with rPrP in a laboratory that has never been exposed to any native prions. Two types of proteinase K (PK)-resistant and self-perpetuating recombinant PrP conformers (rPrP-res) with PK-resistant cores of 17 or 14 kDa were generated. A bioassay revealed that rPrP-res(17kDa) was highly infectious, causing prion disease in wild-type mice with an average survival time of about 172 d. In contrast, rPrP-res(14kDa) completely failed to induce any disease. Our findings reveal that sPMCA is sufficient to initiate various self-perpetuating PK-resistant rPrP conformers, but not all of them possess in vivo infectivity. Moreover, generating an infectious prion in a prion-free environment establishes that an infectious prion can be formed de novo with bacterially expressed rPrP.

  16. Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination.

    PubMed

    Lee, Mi Ok; Bornelöv, Susanne; Andersson, Leif; Lamont, Susan J; Chen, Junfeng; Womack, James E

    2016-11-29

    Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.

  17. High-fidelity numerical simulations of compressible turbulence and mixing generated by hydrodynamic instabilities

    NASA Astrophysics Data System (ADS)

    Movahed, Pooya

    High-speed flows are prone to hydrodynamic interfacial instabilities that evolve to turbulence, thereby intensely mixing different fluids and dissipating energy. The lack of knowledge of these phenomena has impeded progress in a variety of disciplines. In science, a full understanding of mixing between heavy and light elements after the collapse of a supernova and between adjacent layers of different density in geophysical (atmospheric and oceanic) flows remains lacking. In engineering, the inability to achieve ignition in inertial fusion and efficient combustion constitute further examples of this lack of basic understanding of turbulent mixing. In this work, my goal is to develop accurate and efficient numerical schemes and employ them to study compressible turbulence and mixing generated by interactions between shocked (Richtmyer-Meshkov) and accelerated (Rayleigh-Taylor) interfaces, which play important roles in high-energy-density physics environments. To accomplish my goal, a hybrid high-order central/discontinuity-capturing finite difference scheme is first presented. The underlying principle is that, to accurately and efficiently represent both broadband motions and discontinuities, non-dissipative methods are used where the solution is smooth, while the more expensive and dissipative capturing schemes are applied near discontinuous regions. Thus, an accurate numerical sensor is developed to discriminate between smooth regions, shocks and material discontinuities, which all require a different treatment. The interface capturing approach is extended to central differences, such that smooth distributions of varying specific heats ratio can be simulated without generating spurious pressure oscillations. I verified and validated this approach against a stringent suite of problems including shocks, interfaces, turbulence and two-dimensional single-mode Richtmyer-Meshkov instability simulations. The three-dimensional code is shown to scale well up to 4000 cores

  18. Magnetic Field Generation by the Nonlinear Rayleigh--Taylor Instability in Laser-Driven Planar Plastic Targets

    NASA Astrophysics Data System (ADS)

    Gao, L.; Igumenshchev, I. V.; Hu, S. X.; Stoeckl, C.; Froula, D. H.; Nilson, P. M.; Davies, J. R.; Betti, R.; Meyerhofer, D. D.; Haines, M. G.

    2012-10-01

    Magnetic field generation during the nonlinear phase of the Rayleigh--Taylor (RT) instability in an ablatively driven plasma using ultrafast laser-driven proton radiography has been measured. Thin plastic foils were irradiated with ˜4-kJ, 2.5-ns laser pulses focused to an intensity of ˜10^14 W/cm^2 on the OMEGA EP Laser System. Target modulations were seeded by laser nonuniformities and amplified during target acceleration by the RT instability. The experimental data show the hydrodynamic evolution of the target and MG-level magnetic fields generated in the broken foil. The experimental data are in good agreement with predictions from 2-D magnetohydrodynamic simulations. This work was supported by the U.S. Department of Energy Office of Inertial Confinement Fusion under Cooperative Agreement No. DE-FC52-08NA28302.

  19. A New Model for the Brittle-to-Ductile Transition Based on a Collective Dislocation Generation Instability: Theory and Experiment

    DTIC Science & Technology

    2007-11-02

    Khantha 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Univ of Pennsylvania 133 South 36th St ., Suite 300 Philadelphia, PA 19104-3246 9...Khantha, D. P. Pope and V. Vitek, Acta mater. 45, 4687 (1997). 6. C. St . John , Philos. Mag. 32,1193 (1975). 7. H. A. Lipsitt, D. Shechtman and E...Collective Dislocation Generation Instability: Theory and Experiment 1998 5. FUNDING NUMBERS F49620-95-1-0143 6. AUTHOR( S ) V. Vitek, D. P. Pope, M

  20. Generation and evaluation of avian leukosis virus subgroup J envelope glycoprotein recombinant pseudovirions.

    PubMed

    Zhang, Zhenjie; Cui, Lina; Wang, Liang; Yang, Zhikun; Cui, Zhizhong; Chang, Weishan

    2014-06-01

    Retroviral and lentiviral vector pseudotypes (based on human immunodeficiency virus type 1, HIV-1) have been used for stable and safe gene transfer because of their broad host ranges and high mechanical strength. In the present study, a recombinant avian leukosis virus subgroup J (ALV-J) polypeptide pseudotyped with lentivirus membrane glycoproteins gp85 and gp37, HIV/env-ALV, was generated, characterized in vitro and evaluated for its ability to infect natural host cells. We optimized the newly developed micro-neutralization (MN) assay using recombinant pseudovirion HIV/env-ALV expressing enhanced green fluorescent protein and well-characterized sera from chickens with confirmed ALV-J disease or virus-free controls. HIV/env-ALV could infect CEF and DF-1 but not pk15, 293FT, MDCK or VERO E6 cells, therefore demonstrating a cellular tropism similar to the wild-type ALV-J. The MN assay indicated that the IC50 values of positive sera offered a considerable advantage in both speed and accuracy. These results suggest that this pseudotyped lentivirus is a good model for studying the functions of ALV-J env and that the MN assay is a reliable serological method for assessing antibody levels in investigating the actual status of the current ALV-J epidemic. These recombinant pseudovirions may prove to be useful for studying ALV-J biology in lower biosafety level laboratory environments, and also for the detection and quantification of neutralizing antibodies to ALV-J in a manner akin to ELISA assays, but that would also be applicable to other viruses.

  1. Magnetic field enhancement of generation-recombination and shot noise in organic light emitting diodes

    SciTech Connect

    Djidjou, T. K.; Basel, Tek; Rogachev, A.; Chen, Ying; Shinar, J.

    2015-03-21

    We have studied the effect of magnetic field on noise in series of 2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene-based organic light emitting diodes with dominant hole injection, dominant electron injection, and balanced electron and hole injection. The noise spectra of the balanced devices revealed the generation-recombination (g-r) noise term, which we associated with bimolecular electron-hole recombination. The presence of the g-r noise term is correlated with the strong organic magnetoresistance (up to 25%) observed in the balanced devices. The noise spectra also have the shot noise contribution with the Fano factor 0.25–0.4. We found that time constant of the g-r term decreases and the magnitude of shot noise increases when magnetic field is applied. This behavior can be consistently explained within the polaron-polaron model of organic magnetoresistance. We have not found any evidence that the magnetoresistance in studied devices is affected by traps.

  2. Simulation Study of Magnetic Fields Generated by the Electromagnetic Filamentation Instability

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Ramirez-Ruiz, E.; Hardee, P.; Hededal, C. B.; Mizuno, Y.; Fishman, G. J.

    2007-01-01

    We have investigated the effects of plasma instabilities driven by rapid e(sup plus or minus) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of the original spectrum. The injection of e(sup plus or minus) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup plus or minus) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup plus or minus) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

  3. Turbulence in binary Bose-Einstein condensates generated by highly nonlinear Rayleigh-Taylor and Kelvin-Helmholtz instabilities

    NASA Astrophysics Data System (ADS)

    Kobyakov, D.; Bezett, A.; Lundh, E.; Marklund, M.; Bychkov, V.

    2014-01-01

    Quantum turbulence (QT) generated by the Rayleigh-Taylor instability in binary immiscible ultracold 87Rb atoms at zero temperature is studied theoretically. We show that the quantum vortex tangle is qualitatively different from previously considered superfluids, which reveals deep relations between QT and classical turbulence. The present QT may be generated at arbitrarily small Mach numbers, which is a unique property not found in previously studied superfluids. By numerical solution of the coupled Gross-Pitaevskii equations we find that the Kolmogorov scaling law holds for the incompressible kinetic energy. We demonstrate that the phenomenon may be observed in the laboratory.

  4. Recombination-based generation of the agroinfectious clones of Peanut stunt virus.

    PubMed

    Wrzesińska, Barbara; Wieczorek, Przemysław; Obrępalska-Stęplowska, Aleksandra

    2016-11-01

    Full-length cDNA clones of Peanut stunt virus strain P (PSV-P) were constructed and introduced into Nicotiana benthamiana plants via Agrobacterium tumefaciens. The cDNA fragments corresponding to three PSV genomic RNAs and satellite RNA were cloned into pGreen binary vector between Cauliflower mosaic virus (CaMV) 35S promoter and nopaline synthase (NOS) terminator employing seamless recombinational cloning system. The plasmids were delivered into A. tumefaciens, followed by infiltration of hosts plants. The typical symptoms on systemic leaves of infected plants similar to those of wild-type PSV-P were observed. The presence of the virus was confirmed by means of RT-PCR and Western blotting. Re-inoculation to N. benthamiana, Phaseolus vulgaris, and Pisum sativum resulted in analogous results. Generation of infectious clones of PSV-P enables studies on virus-host interaction as well as revealing viral genes functions.

  5. Unraveling Charge Carriers Generation, Diffusion, and Recombination in Formamidinium Lead Triiodide Perovskite Polycrystalline Thin Film.

    PubMed

    Piatkowski, Piotr; Cohen, Boiko; Ponseca, Carlito S; Salado, Manuel; Kazim, Samrana; Ahmad, Shahzada; Sundström, Villy; Douhal, Abderrazzak

    2016-01-07

    We report on studies of the formamidinium lead triiodide (FAPbI3) perovskite film using time-resolved terahertz (THz) spectroscopy (TRTS) and flash photolysis to explore charge carriers generation, migration, and recombination. The TRTS results show that upon femtosecond excitation above the absorption edge, the initial high photoconductivity (∼75 cm(2) V(-1) s(-1)) remains constant at least up to 8 ns, which corresponds to a diffusion length of 25 μm. Pumping below the absorption edge results in a mobility of 40 cm(2) V(-1) s(-1) suggesting lower mobility of charge carriers located at the bottom of the conduction band or shallow sub-bandgap states. Furthermore, analysis of the THz kinetics reveals rising components of <1 and 20 ps, reflecting dissociation of excitons having different binding energies. Flash photolysis experiments indicate that trapped charge carriers persist for milliseconds.

  6. Generation of Recombinant Human IgG Monoclonal Antibodies from Immortalized Sorted B Cells.

    PubMed

    Nogales-Gadea, Gisela; Saxena, Abhishek; Hoffmann, Carolin; Hounjet, Judith; Coenen, Daniëlle; Molenaar, Peter; Losen, Mario; Martinez-Martinez, Pilar

    2015-06-05

    Finding new methods for generating human monoclonal antibodies is an active research field that is important for both basic and applied sciences, including the development of immunotherapeutics. However, the techniques to identify and produce such antibodies tend to be arduous and sometimes the heavy and light chain pair of the antibodies are dissociated. Here, we describe a relatively simple, straightforward protocol to produce human recombinant monoclonal antibodies from human peripheral blood mononuclear cells using immortalization with Epstein-Barr Virus (EBV) and Toll-like receptor 9 activation. With an adequate staining, B cells producing antibodies can be isolated for subsequent immortalization and clonal expansion. The antibody transcripts produced by the immortalized B cell clones can be amplified by PCR, sequenced as corresponding heavy and light chain pairs and cloned into immunoglobulin expression vectors. The antibodies obtained with this technique can be powerful tools to study relevant human immune responses, including autoimmunity, and create the basis for new therapeutics.

  7. High-harmonic generation in α -quartz by electron-hole recombination

    NASA Astrophysics Data System (ADS)

    Otobe, T.

    2016-12-01

    A calculation of the high-harmonic generation (HHG) in α -quartz using the time-dependent density functional theory is reported. The interband process is attributed to the dominant in HHG above the band gap. The photon energy is set to 1.55 eV, and the cutoff energy of the plateau region is found to be limited at the 19th harmonic (30 eV). The dependence of the HHG efficiency at the cutoff energy region on laser intensity is consistent with that of the hole density in the lowest-lying valence band. Numerical results indicate that electron-hole recombination plays a crucial role in HHG in α -quartz. It is found that a 200 attosecond pulse train is produced using HHG around the plateau cutoff energy.

  8. Carrier surface generation and recombination effects in photoconduction of HgI2 single crystals

    NASA Technical Reports Server (NTRS)

    Burshtein, Z.; Akujieze, Justin K.; Silberman, E.

    1986-01-01

    Dc photoconductivity characteristics of HgI2 single crystals have been measured in the range of 1.75-2.75 eV, using CuI as a transparent electrical contact. Hole and electron photocurrents could be separately measured by applying different voltage polarities to the illuminated electrode. It is shown that charge carrier generation near the surface is highly extrinsic, as displayed by differences in the hole and electron photogeneration spectra. Analysis of the photoconductivity versus voltage characteristics indicates that the hole and electron bulk trapping times satisfy greater than 70 and 3 microsec, respectively. The hole and electron surface recombination velocities were 1.0 x 10 to the 4th cm/s and 8 x 10 to the 5th cm/s, respectively.

  9. Generation and characterization of NV gene-knockout recombinant viral hemorrhagic septicemia virus (VHSV) genotype IVa.

    PubMed

    Kim, Min Sun; Kim, Dong Soo; Kim, Ki Hong

    2011-11-03

    A recombinant viral hemorrhagic septicemia virus (rVHSV-deltaNV-EGFP) containing the enhanced green fluorescent protein (EGFP) gene instead of the NV gene was produced using the reverse-genetics method. For use as a positive control, another recombinant virus (rVHSV-wild) was also generated, which had an identical nucleotide sequence to the wild-type VHSV genome except for a few artificially replaced nucleotides. The rVHSVs were rescued using a system controlled by T7 RNA polymerase supplied by a retroviral vector. Generation of rVHSV-deltaNV-EGFP and rVHSV-wild was confirmed by sequencing of RT-PCR products, and rescue of infectious rVHSVs was confirmed by observation of plaque formation. Replication efficiency of rVHSV-wild was distinctly lower than that of wild-type VHSV, suggesting that the artificially replaced nucleotides, especially when immediately preceding the G or NV gene start codons, might affect the replication of the virus. Replication of rVHSV-deltaNV-EGFP was slightly lower than that of rVHSV-wild when epithelioma papulosum cyprini cells were infected with multiplicity of infection (MOI) 1.0, but much lower when cells were infected with MOI 0.00001. These results suggest that the NV gene plays an important role in VHSV replication through interactions with host-cell responses, and the lower replication ability of rVHSV-wild compared to wild-type VHSV might be caused by replaced nucleotides just before the NV gene open reading frame (ORF) rather than the G gene ORF. In olive flounder Paralichthys olivaceus, rVHSV-wild produced slower-progressing mortalities than wild-type VHSV, whereas rVHSV-deltaNV-EGFP pathogenesis was highly attenuated. These results suggest that the NV protein of VHSV may play an important role not only in viral replication but also in viral pathogenesis.

  10. Closed cycle MHD generator with nonuniform gas-plasma flow driving recombinated plasma clots formed by high-energy electron beams

    SciTech Connect

    Danilov, V.V.; Laptev, S.S.; Slavin, V.S.

    1996-12-31

    A new concept of a closed cycle MHD generator without alkali seed has been suggested. The essence of it is the use of the high-energy electron beams technology for a nonuniform gas-plasma flow in MHD channel creation. At the inlet of MHD channel in supersonic flow of noble gas (He) the plasma clots with a density about 10{sup 15} cm{sup {minus}3} are formed by pulsed intense electron beams with energy about 100 keV. Gas flow drives these clots in a cross magnetic field along the MHD channel which has electrodes connected with a load by Faraday`s scheme. Because the nonuniform gas-plasma flow has not the conductivity in the Hall`s EMF direction a Faraday`s current can flow only through the narrow plasma layers. The energy dissipation and Joule`s heating in MHD channel support the nonequilibrium conductivity in these plasma layers. a gas flow pushes current layers and produces electric power at the expense of enthalpy extraction. The key element is a question of plasma layers stability in MHD channel. The most dangerous instability is the overheating instability. it is shown that taking into account the phenomenon of frozen conductivity for recombinated plasma which appears for noble gas at T{sub e} > 4,000 K the regime with {partial_derivative}{sigma}/{partial_derivative}T{sub e} < 0 can be realized. Due to the fulfillment of this condition the overheating instability is effectively suppressed. The numerical simulation has shown that a supersonic gas flow, containing about 4 current layers in MHD channel simultaneously, is braked without shock waves creation. Current layers provide no less than 30% enthalpy extraction and about 80% isentropic efficiency.

  11. Simulation Study of Magnetic Fields generated by the Electromagnetic Filamentation Instability driven by Pair Loading

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Ramirez-Ruiz, E.; Hededal, C.; Hardee, P.; Mizuno, Y.; Fishman, G. J.

    2007-01-01

    Using a 3-D relativistic particle-in-cell (RPIC) code, we have investigated particle acceleration associated with a relativistic electron-positron (cold) jet propagating into ambient electron-positron and electron-ion plasmas without initial magnetic fields in order to investigate the nonlinear stage of the Weibel instability. We have also performed simulations with broad Lorentz factor distribution of jet electrons and positrons, which are assumed to be created by the photon annihilation. The growth time and nonlinear saturation levels depend on the initial jet parallel velocity distributions and ambient plasma. Simulations show that the Weibel instability created in the collisionless shocks accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The nonlinear fluctuation amplitude of densities, currents, electric, and magnetic fields in the electron-ion ambient plasma are larger than those in the electron-positron ambient plasma. We have shown that plasma instabilities driven by these streaming electron-positron pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. These fields maintain a strong saturated level on timescales much longer than the electron skin depth at least for the duration of the simulations. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between electron-positron pairs and ions, and may help explain the origin of large upstream fields in GRB shock.

  12. Regulation of recombination and genomic maintenance.

    PubMed

    Heyer, Wolf-Dietrich

    2015-08-03

    Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.

  13. The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

    PubMed Central

    Delprat, Alejandra; Ruiz, Alfredo

    2009-01-01

    Background Transposable elements (TEs) are responsible for the generation of chromosomal inversions in several groups of organisms. However, in Drosophila and other Dipterans, where inversions are abundant both as intraspecific polymorphisms and interspecific fixed differences, the evidence for a role of TEs is scarce. Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii. Methodology/Principal Findings To assess the impact of TEs in Drosophila chromosomal evolution and shed light on the mechanism involved, we isolated and sequenced the two breakpoints of another widespread polymorphic inversion from D. buzzatii, 2z3. In the non inverted chromosome, the 2z3 distal breakpoint was located between genes CG2046 and CG10326 whereas the proximal breakpoint lies between two novel genes that we have named Dlh and Mdp. In the inverted chromosome, the analysis of the breakpoint sequences revealed relatively large insertions (2,870-bp and 4,786-bp long) including two copies of the transposon Galileo (subfamily Newton), one at each breakpoint, plus several other TEs. The two Galileo copies: (i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric. Conclusions/Significance Our observations provide the best evidence gathered so far for the role of TEs in the generation of Drosophila inversions. In addition, they show unequivocally that ectopic recombination is the causative mechanism. The fact that the three polymorphic D. buzzatii inversions investigated so far were generated by the same transposon family is remarkable and is conceivably due to Galileo's unusual structure and current (or recent) transpositional activity. PMID:19936241

  14. Generation of β-lactoglobulin-modified transgenic goats by homologous recombination.

    PubMed

    Zhu, Hongmei; Hu, Linyong; Liu, Jun; Chen, Huatao; Cui, Chenchen; Song, Yujie; Jin, Yaping; Zhang, Yong

    2016-12-01

    β-Lactoglobulin (BLG) is a dominant allergen present in the milk of goats and other ungulates, although it is not found in human breast milk. Thus, the presence of BLG restricts the consumption of goat's milk by humans. In the present study, we examined whether the disruption of the BLG gene in goats by homologous recombination (HR) reduced BLG content in goat's milk and decreased the allergic response to milk. In one approach, exon 2 of the BLG gene was efficiently targeted using HR with a BLG knockout vector. In a second approach to disrupt BLG gene expression and drive exogenous human α-lactalbumin (hLA) gene expression, two hLA knock-in constructs were used to target exons 1-4 of the BLG gene via HR, and expression of hLA was then confirmed in goat mammary epithelial cells in vitro. The recombinant clones from both approaches were then used for somatic cell nuclear transfer, generating two transgenic goats possessing a BLG knockout allele or site-specific hLA integration allele. Milk assays demonstrated a reduction in BLG levels in both the BLG knockout and hLA knock-in goats; furthermore, hLA was present in the hLA knock-in goat's milk. Allergenic analysis in mice indicated that the transgenic goat's milk was less allergenic than wild-type goat's milk. These results support the development of gene-targeted animals as an effective tool for reducing allergic reactions to milk and improving nutrition.

  15. Closed cycle MHD generator with nonuniform gas-plasma flow driving recombinated plasma clots

    SciTech Connect

    Slavin, V.S.; Danilov, V.V.; Sokolov, V.S.

    1996-12-31

    A new concept of a closed cycle MHD generator without alkali seed has been suggested. The essence of it is the phenomenon of frozen conductivity for recombined plasma which appears for noble gas at T{sub e} > 4,000 K. At the inlet of the MHD channel in supersonic flow of noble gas (He or Ar) the plasma clots with electron density about 10{sup 15} cm{sup {minus}3} are formed by pulsed intense electron beam with energy about 300 keV. Gas flow drives these clots in a cross magnetic field along the MHD channel which has electrodes connected with the load by Faraday scheme. The gas flow pushes plasma layers and produces electric power at the expense of enthalpy extraction. The numerical simulation has shown that a supersonic gas flow, containing about 4 plasma layers in the MHD channel simultaneously, is braked without shock waves creation. This type of the MHD generator can provide more than 30% enthalpy extraction ratio and about 80% isentropic efficiency. The advantages of the new concept are the following: (a) possibility of working at higher pressure and lower temperature, (b) operation with alkali seed.

  16. Secondary magnetic islands generated by the Kelvin-Helmholtz instability in a reconnecting current sheet.

    PubMed

    Fermo, R L; Drake, J F; Swisdak, M

    2012-06-22

    Magnetic islands or flux ropes produced by magnetic reconnection have been observed on the magnetopause, in the magnetotail, and in coronal current sheets. Particle-in-cell simulations of magnetic reconnection with a guide field produce elongated electron current layers that spontaneously produce secondary islands. Here, we explore the seed mechanism that gives birth to these islands. The most commonly suggested theory for island formation is the tearing instability. We demonstrate that in our simulations these structures typically start out, not as magnetic islands, but as electron flow vortices within the electron current sheet. When some of these vortices first form, they do not coincide with closed magnetic field lines, as would be the case if they were islands. Only after they have grown larger than the electron skin depth do they couple to the magnetic field and seed the growth of finite-sized islands. The streaming of electrons along the magnetic separatrix produces the flow shear necessary to drive an electron Kelvin-Helmholtz instability and produce the initial vortices. The conditions under which this instability is the dominant mechanism for seeding magnetic islands are explored.

  17. Generation of ELF and VLF waves by HF-modulated polar electrojet via a thermal instability process

    SciTech Connect

    Kuo, S.P. ); Lee, M.C. )

    1993-02-05

    Generation of ELF and VLF waves via a thermal instability process in a HF-modulated polar electrojet has been investigated. It is shown that a positive feedback through the electron-neutral collisional heating process can cause the transient response of the plasma to the modulated HF heater to grow exponentially. The threshold fields of the instability under normal electrojet conditions are found to be about 2.25 V/m and 1.13 V/m for the operation of the o-mode and x-mode heaters with a 50% duty cycle, respectively. For a heater wave field of, e.g., 1.5 V/m, the instability can be excited by the x-mode heater within a few tens of millisecond. The predicted dependence of the ELF/VLF radiation amplitude on the percentage of the duty cycle of the HF modulation is identical to that of the recent observational results of Barr and Stubbe. 28 refs., 2 figs.

  18. Genomic Instability Associated with p53 Knockdown in the Generation of Huntington’s Disease Human Induced Pluripotent Stem Cells

    PubMed Central

    Tidball, Andrew M.; Neely, M. Diana; Chamberlin, Reed; Aboud, Asad A.; Kumar, Kevin K.; Han, Bingying; Bryan, Miles R.; Aschner, Michael; Ess, Kevin C.; Bowman, Aaron B.

    2016-01-01

    Alterations in DNA damage response and repair have been observed in Huntington’s disease (HD). We generated induced pluripotent stem cells (iPSC) from primary dermal fibroblasts of 5 patients with HD and 5 control subjects. A significant fraction of the HD iPSC lines had genomic abnormalities as assessed by karyotype analysis, while none of our control lines had detectable genomic abnormalities. We demonstrate a statistically significant increase in genomic instability in HD cells during reprogramming. We also report a significant association with repeat length and severity of this instability. Our karyotypically normal HD iPSCs also have elevated ATM-p53 signaling as shown by elevated levels of phosphorylated p53 and H2AX, indicating either elevated DNA damage or hypersensitive DNA damage signaling in HD iPSCs. Thus, increased DNA damage responses in the HD genotype is coincidental with the observed chromosomal aberrations. We conclude that the disease causing mutation in HD increases the propensity of chromosomal instability relative to control fibroblasts specifically during reprogramming to a pluripotent state by a commonly used episomal-based method that includes p53 knockdown. PMID:26982737

  19. REVIEWS OF TOPICAL PROBLEMS: Instabilities of a multicomponent plasma with accelerated particles and magnetic field generation in astrophysical objects

    NASA Astrophysics Data System (ADS)

    Bykov, Andrei M.; Toptygin, Igor'N.

    2007-02-01

    A system of MHD equations for the description of a magnetized nonequilibrium astrophysical plasma with neutral atoms and suprathermal (in particular, relativistic) particles is formulated. The instabilities of such a plasma, which arise from the presence of neutral and relativistic components, are considered. It is shown that the presence of nonthermal particles interacting with the thermal plasma component via regular and fluctuating electromagnetic fields is responsible for the emergence of specific mechanisms of MHD wave generation. The main generation mechanisms of static and turbulent magnetic fields near shock wave fronts in the Galaxy and interplanetary space are analyzed. We discuss the application of the generation effects of long-wave magnetic fluctuations to the problems of magnetic field origin and relativistic particle acceleration in astrophysical objects of various natures.

  20. Development of a Recombination System for the Generation of Occlusion Positive Genetically Modified Anticarsia Gemmatalis Multiple Nucleopolyhedrovirus

    PubMed Central

    Haase, Santiago; McCarthy, Christina B.; Ferrelli, M. Leticia; Pidre, Matias L.; Sciocco-Cap, Alicia; Romanowski, Victor

    2015-01-01

    Anticarsia gemmatalis is an important pest in legume crops in South America and it has been successfully controlled using Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV) in subtropical climate zones. Nevertheless, in temperate climates its speed of kill is too slow. Taking this into account, genetic modification of AgMNPV could lead to improvements of its biopesticidal properties. Here we report the generation of a two-component system that allows the production of recombinant AgMNPV. This system is based on a parental AgMNPV in which the polyhedrin gene (polh) was replaced by a bacterial β-galactosidase (lacZ) gene flanked by two target sites for the homing endonuclease I-PpoI. Co-transfection of insect cells with linearized (I-PpoI-digested) parental genome and a transfer vector allowed the restitution of polh and the expression of a heterologous gene upon homologous recombination, with a low background of non-recombinant AgMNPV. The system was validated by constructing a recombinant occlusion-positive (polh+) AgMNPV expressing the green fluorescent protein gene (gfp). This recombinant virus infected larvae normally per os and led to the expression of GFP in cell culture as well as in A. gemmatalis larvae. These results demonstrate that the system is an efficient method for the generation of recombinant AgMNPV expressing heterologous genes, which can be used for manifold purposes, including biotechnological and pharmaceutical applications and the production of orally infectious recombinants with improved biopesticidal properties. PMID:25835531

  1. Streak instability and generation of hairpin-vortices by a slotted jet in channel crossflow: Experiments and linear stability analysis

    NASA Astrophysics Data System (ADS)

    Philip, Jimmy; Karp, Michael; Cohen, Jacob

    2016-01-01

    Streaks and hairpin-vortices are experimentally generated in a laminar plane Poiseuille crossflow by injecting a continuous jet through a streamwise slot normal to the crossflow, with air as the working media. Small disturbances form stable streaks, however, higher disturbances cause the formation of streaks which undergo instability leading to the generation of hairpin vortices. Particular emphasis is placed on the flow conditions close to the generation of hairpin-vortices. Measurements are carried out in the cases of natural and phase-locked disturbance employing smoke visualisation, particle image velocimetry, and hot-wire anemometry, which include, the dominant frequency, wavelength, and the disturbance shape (or eigenfunctions) associated with the coherent part of the velocity field. A linear stability analysis for both one- and two-dimensional base-flows is carried out to understand the mechanism of instability and good agreement of wavelength and eigenfunctions are obtained when compared to the experimental data, and a slight under-prediction of the growth-rates by the linear stability analysis consistent with the final nonlinear stages in transitional flows. Furthermore, an energy analysis for both the temporal and spatial stability analysis revels the dominance of the symmetric varicose mode, again, in agreement with the experiments, which is found to be governed by the balance of the wallnormal shear and dissipative effects rather than the spanwise shear. In all cases the anti-symmetric sinuous modes governed by the spanwise shear are found to be damped both in analysis and in our experiments.

  2. Highly Efficient CRISPR/Cas9-Mediated Homologous Recombination Promotes the Rapid Generation of Bacterial Artificial Chromosomes of Pseudorabies Virus

    PubMed Central

    Guo, Jin-Chao; Tang, Yan-Dong; Zhao, Kuan; Wang, Tong-Yun; Liu, Ji-Ting; Gao, Jia-Cong; Chang, Xiao-Bo; Cui, Hong-Yu; Tian, Zhi-Jun; Cai, Xue-Hui; An, Tong-Qing

    2016-01-01

    Bacterial artificial chromosomes (BACs) are powerful tools for the manipulation of the large genomes of DNA viruses, such as herpesviruses. However, the methods currently used to construct the recombinant viruses, an important intermediate link in the generation of BACs, involve the laborious process of multiple plaque purifications. Moreover, some fastidious viruses may be lost or damaged during these processes, making it impossible to generate BACs from these large-genome DNA viruses. Here, we introduce the CRISPR/Cas9 as a site-specific gene knock-in instrument that promotes the homologs recombination of a linearized transfer vector and the Pseudorabies virus genome through double incisions. The efficiency of recombination is as high as 86%. To our knowledge, this is the highest efficiency ever reported for Pseudorabies virus recombination. We also demonstrate that the positions and distances of the CRISPR/Cas9 single guide RNAs from the homology arms correlate with the efficiency of homologous recombination. Our work show a simple and fast cloning method of BACs with large genome inserted by greatly enhancing the HR efficiencies through CRISPR/Cas9-mediated homology-directed repair mechanism, and this method could be of helpful for manipulating large DNA viruses, and will provide a successful model for insertion of large DNA fragments into other viruses. PMID:28066407

  3. Transport noise arising from diffusion and bulk or surface generation recombination in semiconductors

    NASA Astrophysics Data System (ADS)

    Mehta, H.

    The type of noise spectra in solids or solid state devices, which can arise from noise due to a combination of causes, such as diffusion of carriers, generation and recombination (g-r) processes of carriers in the bulk and at the surface was studied using techniques to be described apply equally well to the problem of heat diffusion, with heat transfer or reflection at the boundaries of the system, we have, however, mainly the carrier noise problem in mind. The physical noise sources, the diffusion source, g-r source and surface source, Clarke and Voss' P source are discussed as well as transport noise in symmetrical embedded bodies, in nonsymmetrical embedded bodies, in symmetrical nonembedded bodies and in nonsymmetrical nonembedded bodies. Results indicate that volume g-r and diffusion processes give rather smooth spectra, but, without a l/f range. The high frequency asymptote is always w-3/2 (embedded case) or omega to the minus 2 power (nonembedded case).

  4. A generation/recombination model assisted with two trap centers in wide band-gap semiconductors

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Ken; Kuwabara, Takuhito; Uda, Tsuyoshi

    2013-03-01

    A generation/recombination (GR) model assisted with two trap centers has been proposed for studying reverse current on pn junctions in wide band-gap semiconductors. A level (Et1) has been assumed to be located near the bottom of the conduction band and the other (Et2) to be near the top of the valence band. The GR model has been developed by assuming (1) a high-electric field; F, (2) a short distance; d, between trap centers, (3) reduction in an energy-difference; Δeff = |Et1 - Et2| - eFd, and (4) hopping or tunneling conductions between trap centers with the same energy-level (Δeff ≈ 0). The GR rate has been modeled by trap levels, capture cross-sections, trap densities, and transition rate between trap centers. The GR rate, about 1010 greater than that estimated from the single-level model, has been predicted on pn junctions in a material with band-gap of 3.1 eV. Device simulations using the proposed GR model have been demonstrated for SiC diodes with and without a guard ring. A reasonable range for reverse current at room temperature has been simulated and stable convergence has been obtained in a numerical scheme for analyzing diodes with an electrically floating region.

  5. Junction optimization in HgCdTe: Shockley-Read-Hall generation-recombination suppression

    NASA Astrophysics Data System (ADS)

    Schuster, J.; DeWames, R. E.; DeCuir, E. A.; Bellotti, E.; Wijewarnasuriya, P. S.

    2015-07-01

    Heterojunction device design concepts are leveraged to reduce depletion layer generation-recombination (G-R) dark current in planar P+-on-n SWIR HgCdTe infrared detectors. Shockley-Read-Hall (SRH) depletion dark current (when present) is expected to be the dominant dark current component at low temperatures, and in fact, it is beneficial for the transition from diffusion to G-R to be at such relatively low temperatures. However, it is empirically observed that even for relatively long values of the SRH lifetime ( 20 μ s ), the transition occurs at relatively high temperatures (>200 K) for material with a cut-off wavelength of 2.5 μ m . A key device design parameter of P+-on-n photodiodes is the position of the electrical junction relative to the hetero-metallurgical interface. Junction formation via p-type arsenic implantation into the narrow-gap absorber layer is typically chosen for efficient collection of diffusion current, however, other configurations are possible as well. In this letter, we numerically explore the conditions that reduce depletion dark current without reducing the quantum efficiency (QE). The findings support the assertion that device design conditions exist in SWIR HgCdTe that essentially eliminate the depletion dark current without significantly reducing the QE.

  6. Flux Rope Formation and Self-Generated Turbulent Reconnection Driven by the Plasmoid Instability in the Heliosphere

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, A.; Huang, Y. M.

    2015-12-01

    It has been established that the Sweet-Parker current layer in high Lundquist number reconnection is unstable to the super-Alfvénic plasmoid instability. Past two-dimensional magnetohydrodynamic simulations have demonstrated that the plasmoid instability leads to a new regime where the Sweet-Parker current layer changes into a chain of plasmoids connected by secondary current sheets, and the averaged reconnection rate becomes nearly independent of the Lundquist number. In this work, three-dimensional simulations with a guide field shows that the additional degree of freedom allows plasmoid instabilities to grow at oblique angles. We present a scenario in which large-scale oblique tearing modes overlap with each other, break flux surfaces, and stir up a spectrum of smaller-scale tearing modes, leading eventually to self-generated turbulent reconnection. The averaged reconnection rate in the self-generated turbulent state is of the order of a hundredth of the characteristic Alfvén speed, which is similar to the two-dimensional result but is an order of magnitude lower than the fastest reconnection rate reported in recent studies of externally driven three-dimensional turbulent reconnection. Kinematic and magnetic energy fluctuations both form elongated eddies along the direction of local magnetic field, which is a signature of anisotropic magnetohydrodynamic turbulence. Both energy fluctuations satisfy power-law spectra in the inertial range. The anisotropy of turbulence eddies is found to be nearly scale-independent, in contrast with the prediction of the Goldreich-Sridhar (GS) theory for anisotropic turbulence in a homogeneous plasma permeated by a uniform magnetic field. The effect of varying the magnitude of the toroidal field on the critical balance condition underlying the GS theory is discussed.

  7. Thermal ionization instability development in air plasma generated by repetitive ns dielectric barrier discharge

    NASA Astrophysics Data System (ADS)

    Starikovskiy, Andrey; Shneider, Mikhael; Marinov, Daniil; Starikovskaia, Svetlana; PU Team; LPP Team

    2013-09-01

    The aim of this paper is to study a transformation of a nanosecond discharge under conditions of high repetitive frequency in a barrier configuration of the electrodes. Nanosecond DBDs at atmospheric pressure are widely used for research in plasma medicine. At atmospheric pressure conditions the discharge develops as a set of microchannels bridging a gap between the electrodes covered with dielectric, the current in each microchannel is restricted by charging of a dielectric surface. With pressure decrease, a discharge becomes more uniform, still it is known that a slight change of a gas mixture composition, f.e. add of a fuel, may lead to significant problems with the uniformity. Estimations were made to analyze the possibility of discharge contruction due to thermal ionization instability development. We used the assumption that there is no convective cooling of the gas in the discharge cell. It was shown that NS discharge in DBD geometry is non-uniform. Initial electrical fields distribution and thermal ionization instability development form the non-uniform energy distribution in the discharge. This non-uniformity can play a key role in kinetic experiments in this type of the discharge.

  8. Generation of waves by jet-stream instabilities in winter polar stratosphere/mesosphere

    NASA Astrophysics Data System (ADS)

    Shpynev, B. G.; Churilov, S. M.; Chernigovskaya, M. A.

    2015-12-01

    In the paper we investigate the manifestation of large-scale and middle-scale atmospheric irregularities observed on stratosphere/mesosphere heights. We consider typical patterns of circulation in stratosphere and lower mesosphere which are formed due to a difference of air potential energy between equatorial and polar latitudes, especially in polar night conditions. On the base of ECMWF Era Interim reanalysis data we consider the dynamics of midlatitude winter jet-streams which transfer heat from low latitudes to polar region and which develop due to equator/pole baroclinic instabilities. We consider typical patterns of general circulation in stratosphere/lower mesosphere and reasons for creation of flaky structure of polar stratosphere. Also we analyze conditions that are favorable for splitting of winter circumpolar vortex during sudden stratosphere warming events and role of phase difference tides in this process. The analysis of vertical structure of the stratosphere wind shows the presence of regions with significant shear of horizontal velocity which favors for inducing of shear-layer instability that appears as gravity wave on boundary surface. During powerful sudden stratosphere warming events the main jet-stream can amplify these gravity waves to very high amplitudes that causes wave overturning and releasing of wave energy into the heat due to the cascade breakdown and turbulence. For the dynamics observed in reanalysis data we consider physical mechanisms responsible for observed phenomena.

  9. Generation of directional, coherent matter beams through dynamical instabilities in Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Dennis, Graham R.; Johnsson, Mattias T.

    2010-09-01

    We present a theoretical analysis of a coupled, two-state Bose-Einstein condensate with nonequal scattering lengths and show that dynamical instabilities can be excited. We demonstrate that these instabilities are exponentially amplified, resulting in highly directional, oppositely propagating, coherent matter beams at specific momenta. To accomplish this we prove that the mean field of our system is periodic and extend the standard Bogoliubov approach to consider a time-dependent, but cyclic, background. This allows us to use Floquet’s theorem to gain analytic insight into such systems, rather than employing the usual Bogoliubov-de Gennes approach, which is usually limited to numerical solutions. We apply our theory to the metastable helium atom laser experiment by Dall [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.79.011601 79, 011601(R) (2009)] and show that it explains the anomalous beam profiles they observed. Finally, we demonstrate that the paired particle beams will be Einstein-Podolsky-Rosen entangled on formation.

  10. Generation of hypoxanthine phosphoribosyltransferase gene knockout rabbits by homologous recombination and gene trapping through somatic cell nuclear transfer.

    PubMed

    Yin, Mingru; Jiang, Weihua; Fang, Zhenfu; Kong, Pengcheng; Xing, Fengying; Li, Yao; Chen, Xuejin; Li, Shangang

    2015-11-02

    The rabbit is a common animal model that has been employed in studies on various human disorders, and the generation of genetically modified rabbit lines is highly desirable. Female rabbits have been successfully cloned from cumulus cells, and the somatic cell nuclear transfer (SCNT) technology is well established. The present study generated hypoxanthine phosphoribosyltransferase (HPRT) gene knockout rabbits using recombinant adeno-associated virus-mediated homologous recombination and SCNT. Gene trap strategies were employed to enhance the gene targeting rates. The male and female gene knockout fibroblast cell lines were derived by different strategies. When male HPRT knockout cells were used for SCNT, no live rabbits were obtained. However, when female HPRT(+/-) cells were used for SCNT, live, healthy rabbits were generated. The cloned HPRT(+/-) rabbits were fertile at maturity. We demonstrate a new technique to produce gene-targeted rabbits. This approach may also be used in the genetic manipulation of different genes or in other species.

  11. Suprathermal Electrons Generated by the Two-Plasmon-Decay Instability in Gas-Filled Hohlraums

    SciTech Connect

    Regan, S P; Seka, W; Stoeckl, C; Glebov, V Y; Sangster, T C; Meyerhofer, D D; McCrory, R L; Meezan, N B; Suter, L J; Glenzer, S H; Strozzi, D J; Meeker, D; Williams, E A; Jones, O S; Callahan, D A; Rosen, M D; Landen, O L; Sorce, C; MacGowan, B J; Kruer, W L

    2008-06-03

    For the first time a burst of suprathermal electrons is observed from the exploding laser-entrance-hole window of gas-filled hohlraums driven with 13.5 kJ of 351-nm laser light. The two-plasmon-decay instability appears to produce up to 20 J of hot electrons with T{sub hot} {approx} 75 keV at early times and has a sharp laser-intensity threshold between 0.3 and 0.5 x 10{sup 15} W/cm{sup 2}. The observed threshold can be exploited to mitigate preheat by window hot electrons in ignition hohlraums for the National Ignition Facility and achieve high-density, high-pressure conditions in indirect drive implosions.

  12. Artificial plasma cusp generated by upper hybrid instabilities in HF heating experiments at HAARP

    NASA Astrophysics Data System (ADS)

    Kuo, Spencer; Snyder, Arnold

    2013-05-01

    High Frequency Active Auroral Research Program digisonde was operated in a fast mode to record ionospheric modifications by the HF heating wave. With the O mode heater of 3.2 MHz turned on for 2 min, significant virtual height spread was observed in the heater off ionograms, acquired beginning the moment the heater turned off. Moreover, there is a noticeable bump in the virtual height spread of the ionogram trace that appears next to the plasma frequency (~ 2.88 MHz) of the upper hybrid resonance layer of the HF heating wave. The enhanced spread and the bump disappear in the subsequent heater off ionograms recorded 1 min later. The height distribution of the ionosphere in the spread situation indicates that both electron density and temperature increases exceed 10% over a large altitude region (> 30 km) from below to above the upper hybrid resonance layer. This "mini cusp" (bump) is similar to the cusp occurring in daytime ionograms at the F1-F2 layer transition, indicating that there is a small ledge in the density profile reminiscent of F1-F2 layer transitions. Two parametric processes exciting upper hybrid waves as the sidebands by the HF heating waves are studied. Field-aligned purely growing mode and lower hybrid wave are the respective decay modes. The excited upper hybrid and lower hybrid waves introduce the anomalous electron heating which results in the ionization enhancement and localized density ledge. The large-scale density irregularities formed in the heat flow, together with the density irregularities formed through the parametric instability, give rise to the enhanced virtual height spread. The results of upper hybrid instability analysis are also applied to explain the descending feature in the development of the artificial ionization layers observed in electron cyclotron harmonic resonance heating experiments.

  13. X chromosomal recombination--a family study analyzing 26 X-STR Loci in Chinese Han three-generation pedigrees.

    PubMed

    Liu, Qiu-Ling; Li, Ze-Dong; Li, Cheng-Tao; Zhao, Hu; Wu, Ye-Da; Li, Quan; Lu, De-Jian

    2013-11-01

    The aim of this study is to investigate genetic linkage and recombination fractions of 26 X chromosomal (X-STR) loci with two multiplex PCR systems (MX15-STR and MX12-STR). MX15-STR (including DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079) and MX12-STR (including DXS6854, DXS9902, DXS6800, GATA172D05, DXS7423, HPRTB, DXS6807, DXS6803, DXS6804, DXS6799, DXS8378, and DXS8377) were successful analyzed on 206 two-generation families with two or more children and 33 three-generation families with 72 grandsons. Segregation analysis and calculation of recombination fractions between pairs of markers were performed. Linkage analysis of pairs of markers showed that there existed significant linkage (maximum LOD scores >2.0) within the physical distance of 48.5 Mb. Recombination events could be observed within the clusters of closed linked makers spanning <1.0 Mb. These results indicate that close cluster X-STRs used and recombination fractions of the selected loci will be very useful for biostatistical calculations in complex kinship analysis.

  14. The generation of O(1S) from the dissociative recombination of O2(+)

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.; Giusti-Suzor, Annick

    1991-01-01

    The multichannel quantum defect theory (MQDT) method and large scale wave functions are applied to the calculation of the cross sections and rates for dissociative recombination of O2(+) along the 1Sigma-u(+) dissociative potential. Indirect dissociative recombination is accounted for by simultaneously including both the vibronic and electronic coupling to the intermediate Rydberg resonances. An enhanced MQDT approach involving a second-order K matrix is described. Cross sections and rates for the lowest three vibrational levels of the ion are reported. The shapes of the cross sections are discussed in terms of Fano's profile index. It is found that, for each of the three ion vibrational levels, the intermediate Rydberg resonances reduce the dissociative recombination rate below the direct recombination rate. Just above threshold, resonances with centers below threshold play an important role.

  15. The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination

    SciTech Connect

    March, R.E.; Putt, W.; Hollyoake, M.; Ives, J.H.; Lovegrove, J.U.; Hopkinson, D.A.; Edwards, Y.H.; Whitehouse D.B. )

    1993-11-15

    The molecular basis of the classical human phosphoglucomutase 1 (PGM1) isozyme polymorphism has been established. In 1964, when this genetic polymorphism was first described, two common allelozymes PGM1 1 and PGM1 2 were identified by starch gel electrophoresis. The PGM1 2 isozyme showed a greater anodal electrophoresis mobility than PGM1 1. Subsequently, it was found that each of these allelozymes could be split, by isoelectric focusing, into two subtypes; the acidic isozymes were given the suffix + and the basic isozymes 1 +, 1-, 2+, and 2- were identified. The authors have now analyzed the whole of the coding region of the human PGM1 gene by DNA sequencing in individuals of known PGM1 protein phenotype. Only two mutations have been found, both C to T transitions, at nt 723 and 1320. The mutation at position 723, which changes the amino acid sequence from Arg to Cys at residue 220, showed complete association with the PGM1 2/1 protein polymorphism: DNA from individuals showing the PGM1 1 isozyme carried the Arg codon CGT, whereas individuals showing the PGM1 2 isozyme carried the Cys codon TGT. Similarly, the mutation at position 1320, which leads to a Tyr to His substitution at residue 419, showed complete association with the PGM1+/- protein polymorphism: individuals with the + isozyme carried the Tyr codon TAT, whereas individuals with the - isozyme carried the His codon CAT. The charge changes predicted by these amino acid substitutions are entirely consistent with the charge intervals calculated from the isoelectric profiles of these four PGM1 isozymes. The authors therefore conclude that the mutations are solely responsible for the classical PGM1 protein polymorphism. Thus, the findings strongly support the view that only two point mutations are involved in the generation of the four common alleles and that one allele must have arisen by homologous intragenic recombination between these mutation sites.

  16. Transgenic rice seeds accumulating recombinant hypoallergenic birch pollen allergen Bet v 1 generate giant protein bodies.

    PubMed

    Wang, Shuyi; Takahashi, Hideyuki; Kajiura, Hiroyuki; Kawakatsu, Taiji; Fujiyama, Kazuhito; Takaiwa, Fumio

    2013-06-01

    A versatile hypoallergenic allergen derivative against multiple allergens is an ideal tolerogen for allergen-specific immunotherapy. Such a tolerogen should exhibit high efficacy, without side effects, when administered at high doses and should be applicable to several allergens. Tree pollen chimera 7 (TPC7), a hypoallergenic Bet v 1 tolerogen against birch pollen allergy, was previously selected by DNA shuffling of 14 types of Fagales tree pollen allergens. In this study, transgenic rice seed accumulating TPC7 was generated as an oral vaccine against birch pollen allergy by expressing this protein as a secretory protein using the N-terminal signal peptide and the C-terminal KDEL tag under the control of an endosperm-specific glutelin promoter. The highest level of TPC7 accumulation was approximately 207 µg grain(-1). Recombinant TPC7 is a glycoprotein with high mannose-type N-glycan, but without β1,2-xylose or α1,3-fucose, suggesting that TPC7 is retained in the endoplasmic reticulum (ER). TPC7 is deposited as a novel, giant spherical ER-derived protein body, >20 µm in diameter, which is referred to as the TPC7 body. Removal of the KDEL retention signal or mutation of a cysteine residue resulted in an alteration of TPC7 body morphology, and deletion of the signal peptide prevented the accumulation of TPC7 in rice seeds. Therefore, the novel TPC7 bodies may have formed aggregates within the ER lumen, primarily due to the intrinsic physicochemical properties of the protein.

  17. Application of an artificial neural network for a direct estimation of atmospheric instability from a next-generation imager

    NASA Astrophysics Data System (ADS)

    Lee, Su Jeong; Ahn, Myoung-Hwan; Lee, Yeonjin

    2016-02-01

    Atmospheric instability information derived from satellites plays an important role in short-term weather forecasting, especially the forecasting of severe convective storms. For the next generation of weather satellites for Korea's multi-purpose geostationary satellite program, a new imaging instrument has been developed. Although this imaging instrument is not designed to perform full sounding missions and its capability is limited, its multi-spectral infrared channels provide information on vertical sounding. To take full advantage of the observation data from the much improved spatiotemporal resolution of the imager, the feasibility of an artificial neural network approach for the derivation of the atmospheric instability is investigated. The multi-layer perceptron model with a feed-forward and back-propagation training algorithm shows quite a sensitive response to the selection of the training dataset and model architecture. Through an extensive performance test with a carefully selected training dataset of 7197 independent profiles, the model architectures are selected to be 12, 5000, and 0.3 for the number of hidden nodes, number of epochs, and learning rate, respectively. The selected model gives a mean absolute error, RMSE, and correlation coefficient of 330 J kg-1, 420 J kg-1, and 0.9, respectively. The feasibility is further demonstrated via application of the model to real observation data from a similar instrument that has comparable observation channels with the planned imager.

  18. The generation of Biermann battery fields in laser-plasma interactions and the interplay with the Weibel instability

    NASA Astrophysics Data System (ADS)

    Schoeffler, Kevin

    2015-11-01

    Recent experiments with intense lasers are probing the dynamics of self-generated large scale magnetic fields with unprecedented detail. In these scenarios the Biermann battery effect is critical to understand the field dynamics but a multi-dimensional detailed study of this mechanism was not present yet in the literature. Moreover, the interplay between the Biermann battery effect and plasma micro instabilities and the evolution of plasma turbulence is still unknown. In this work, particle-in-cell simulations are used to investigate the formation of magnetic fields, B, in plasmas with perpendicular electron density and temperature gradients. For system sizes, L, comparable to the ion skin depth, di, it is shown that β ~di / L , consistent with the Biermann battery effect. However, for large L /di , it is found that the Weibel instability (due to electron temperature anisotropy) supersedes the Biermann battery as the main producer of B. The Weibel-produced fields saturate at a finite amplitude (plasma β ~ 1), independent of L. The magnetic energy spectra below the electron Larmor radius scale are well fitted by power law with slope - 16 / 3 , as predicted in.The relevance of these results for several ongoing experiments is also discussed.

  19. Genomic Characterization of Two Novel HIV-1 Second-Generation Recombinant Forms Among Men Who Have Sex with Men in Beijing, China

    PubMed Central

    Li, Zheng; Wei, Huamian; Feng, Yi; Li, Jia; Kalish, Marcia L.; Lu, Hongyan; Yin, Lu; Liao, Lingjie; Qian, Han-Zhu; Frost, Simon D.W.; Ruan, Yuhua; Vermund, Sten H.; Shao, Yiming

    2015-01-01

    Abstract We report two different unique HIV-1 recombinant viruses from two HIV-positive men who have sex with men (MSM) in Beijing, China. Phylogenetic analysis of near full-length genomes (NFLG) showed that the unique recombinant forms (URFs) were comprised of gene regions from two circulating recombinant forms, CRF01_AE and CRF07_BC, both common in China. The parental CRF01_AE region of the recombinants clustered together with a previously described cluster 4 lineage of CRF01_AE. The CRF07_BC regions of both the recombinants clustered within the CRF07_BC radiation, but were distinct from other CRF07_BC reference sequences. The two recombinant forms had two breakpoints in common. The emergence of the two URFs indicates the ongoing generation of recombinant viruses involving CRF01_AE and CRF07_BC, and may provide insight into our understanding of the dynamics and complexity of the HIV-1 epidemic in China. PMID:25495675

  20. Acoustic streaming and thermal instability of flow generated by ultrasound in a cylindrical container

    NASA Astrophysics Data System (ADS)

    Green, Adam; Marshall, Jeffrey S.; Ma, Dong; Wu, Junru

    2016-10-01

    A vertically orientated ultrasonic transducer contained within a closed cylindrical Pyrex tube was used to study the acoustic streaming flow within a cylindrical container. A particle-image velocimetry (PIV) system incorporating fluorescent 1.5 μm seeding particles suspended in a mixture of diethyl-phthalate and ethanol, whose optical index was matched to that of Pyrex, was used to allow for undistorted PIV imaging within the Pyrex tube. Temperature on the end-wall surface and acoustic pressure within the cylinder were measured for different end-wall materials. Variables considered included acoustic absorption and reflection coefficients, ultrasound intensity, container height, and thermal properties of the end-wall material. It was observed that a quasi-steady flow field driven by acoustic streaming is rapidly established within the container, which is typically dominated by a stationary vortex ring with downward flow along the ring axis. After sufficient time this quasi-stationary flow exhibits a thermal instability causing it to transform into a secondary flow state. Different types of secondary flow states were observed, including cases where the flow along the cylinder axis is oriented upward toward the ultrasound transducer and cases where the axial flow changes directions along the cylinder axis.

  1. Generation of auroral Omega bands by shear instability of the neutral winds

    NASA Technical Reports Server (NTRS)

    Lyons, L. R.; Walterscheid, R. L.

    1985-01-01

    Thermospheric neutral wind acceleration via ion drag in the conducting E-region of the ionosphere is greatly increased by electron precipitation associated with auroras. This increased acceleration can lead to the development of significant horizontal wind shears, which were found to be unstable to the Kelvin-Helmholtz shear instability. Numerical simulation of the neutral response to an intense, postmidnight, diffuse aurora shows tne formation of an E-region 'jet stream' within the aurora, with peak winds speeds greather than 700 m/s after one hour. It is proposed that this jet stream produces unstable Kelvin-Helmholtz waves, which can drive waves of discrete aurora along the poleward boundary of the preexisting diffuse aurora. It is suggested that such auroral waves, driven by the neutral winds, form eastward propagating waves (omega bands) occasionally observed along the poleward boundary of postmidnight diffuse auroras. It was found that neutral wind shears that develop in response to discrete auroral arcs are unstable; however, the resulting wind waves are not expected to drive significant auroral waves along discrete arcs.

  2. Coupling mechanism of interface-induced generation-recombination current with the floating source in nMOSFET

    NASA Astrophysics Data System (ADS)

    Chen, Haifeng; Xie, Duan; Guo, Lixin

    2016-11-01

    This paper presents a detailed investigation of the interface trap-induced generation-recombination current IGR in an n-type MOSFET. Under the positive drain bias VD-step-mode measurement, IGR demonstrates some abnormal changes and even transforms from the generation current to the recombination current. These phenomena ascribe to the coupling mechanism of IGR with the floating source. The core of this mechanism is that the floating source leads to the variable ΔEFN, which is the difference of the electron's quasi-Fermi levels between the source and the drain. The plus-minus sign of ΔEFN determines the function of the interface trap serving as the generation or recombination center, and the magnitude of ΔEFN determines the shape of IGR curve. Additionally, the area Ω of IGR curve is introduced to verify and quantitatively describe this coupling mechanism. It is found that Ω has the linear relationship with ΔEFN and the slope is 19 p/eV. This coupling mechanism provides a potential way to control the pA current based on the interface trap.

  3. Comparison of three transposons for the generation of highly productive recombinant CHO cell pools and cell lines.

    PubMed

    Balasubramanian, Sowmya; Rajendra, Yashas; Baldi, Lucia; Hacker, David L; Wurm, Florian M

    2016-06-01

    Several naturally occurring vertebrate transposable elements have been genetically modified to enable the transposition of recombinant genes in mammalian cells. We compared three transposons-piggyBac, Tol2, and Sleeping Beauty-for their ability to generate cell pools (polyclonal cultures of recombinant cells) and clonal cell lines for the large-scale production of recombinant proteins using Chinese hamster ovary cells (CHO-DG44) as the host. Transfection with each of the dual-vector transposon systems resulted in cell pools with volumetric yields of tumor necrosis factor receptor-Fc fusion protein (TNFR:Fc) that were about ninefold higher than those from cell pools generated by conventional plasmid transfection. On average, the cell pools had 10-12 integrated copies of the transgene per cell. In the absence of selection, the volumetric productivity of the cell pools decreased by 50% over a 2-month cultivation period and then remained constant. The average volumetric TNFR:Fc productivity of clonal cell lines recovered from cell pools was about 25 times higher than that of cell lines generated by conventional transfection. In 14-day fed-batch cultures, TNFR:Fc levels up to 900 mg/L were obtained from polyclonal cell pools and up to 1.5 g/L from clonal cell lines using any of the three transposons. Biotechnol. Bioeng. 2016;113: 1234-1243. © 2015 Wiley Periodicals, Inc.

  4. Generation of plane shocks using intense heavy ion beams: Application to Richtmyer-Meshkov instability growth studies

    SciTech Connect

    Tahir, N. A.; Stoehlker, Th.; Shutov, A.; Zharkov, A. P.; Piriz, A. R.

    2011-03-15

    A design of a novel experiment that allows the generation of a well defined, steady, and strong plane shock wave employing an intense uranium ion beam that is incident on a wedge shaped compound target is presented. This technique will open up the possibility of carrying out unique high energy density physics experiments using these shock waves. One such experiment is to study the growth of Richtmyer-Meshkov instability in fluids as well as in solids, both in the linear and nonlinear regimes, as shown by detailed numerical simulations presented in this paper. The ion beam parameters used in this study correspond to those that will be available at the Facility for Antiprotons and Ion Research (FAIR) at Darmstadt.

  5. Broadband sidebands generated by parametric instability in lower hybrid current drive experiments on EAST

    SciTech Connect

    Amicucci, L. Castaldo, C.; Cesario, R.; Giovannozzi, E.; Tuccillo, A. A.; Ding, B. J.; Li, M. H.

    2015-12-10

    Modern research on nuclear fusion energy, based on the tokamak concept, has strong need of tools for actively driving non-inductive current especially at the periphery of plasma column, where tools available so far have poor efficiency. This is essential for solving one of the most critical problems for thermonuclear reactor, consisting in how to achieve the figure of fusion gain in the context of sufficient stability. The lower hybrid current drive (LHCD) effect has the potential capability of driving current at large radii of reactor plasma with high efficiency [1]. Experiments recently carried out on EAST showed that a strong activity of LH sideband waves (from the RF probe spectra), accompanied by weak core penetration of the coupled LH power, is present when operating at relatively high plasma densities. Previous theoretical results, confirmed by experiments on FTU, showed that the LH sideband phenomenon is produced by parametric instability (PI), which are mitigated by higher plasma edge temperatures. This condition is thus useful for enabling the LH power propagation when operating with profiles having high plasma densities even at the edge. In the present work, we show new PI modeling of EAST plasmas data, obtained in condition of higher plasma edge temperature due to chamber lithisation. The obtained trend of the PI frequencies and growth rates is consistent with data of RF probe spectra, available in different regimes of lithisated and not lithisated vessel. Moreover, these spectra are interpreted as PI effect occurring at the periphery of plasma column, however in the low field side where the LH power is coupled.

  6. The neuromuscular fatigue induced by repeated scrums generates instability that can be limited by appropriate recovery.

    PubMed

    Morel, B; Hautier, C A

    2017-02-01

    The aim of this study was to evaluate the influence of the fatigue on the machine scrum pushing sagittal forces during repeated scrums and to determine the origin of the knee extensor fatigue. Twelve elite U23 rugby union front row players performed six 6-s scrums every 30 s against a dynamic scrum machine with passive or active recovery. The peak, average, and the standard deviation of the force were measured. A neuromuscular testing procedure of the knee extensors was carried out before and immediately after the repeated scrum protocol including maximal voluntary force, evoked force, and voluntary activation. The average and peak forces did not decrease after six scrums with passive recovery. The standard deviation of the force increased by 70.2 ± 42.7% (P < 0.001). Maximal voluntary/evoked force and voluntary activation decreased (respectively 25.1 ± 7.0%, 14.6 ± 5.5%, and 24 ± 9.9%; P < 0.001). The standard deviation of the force did not increase with active recovery and was associated with lower decrease of maximal voluntary/evoked force and voluntary activation (respectively 12.8 ± 7.9%, 4.9 ± 6.5%, and 7.6 ± 4.1%; all P < 0.01). As a conclusion repeated scrummaging induced an increased machine scrum pushing instability associated with central and peripheral fatigue of the knee extensors. Active recovery seems to limit all these manifestations of fatigue.

  7. Broadband sidebands generated by parametric instability in lower hybrid current drive experiments on EAST

    NASA Astrophysics Data System (ADS)

    Amicucci, L.; Ding, B. J.; Castaldo, C.; Cesario, R.; Giovannozzi, E.; Li, M. H.; Tuccillo, A. A.

    2015-12-01

    Modern research on nuclear fusion energy, based on the tokamak concept, has strong need of tools for actively driving non-inductive current especially at the periphery of plasma column, where tools available so far have poor efficiency. This is essential for solving one of the most critical problems for thermonuclear reactor, consisting in how to achieve the figure of fusion gain in the context of sufficient stability. The lower hybrid current drive (LHCD) effect has the potential capability of driving current at large radii of reactor plasma with high efficiency [1]. Experiments recently carried out on EAST showed that a strong activity of LH sideband waves (from the RF probe spectra), accompanied by weak core penetration of the coupled LH power, is present when operating at relatively high plasma densities. Previous theoretical results, confirmed by experiments on FTU, showed that the LH sideband phenomenon is produced by parametric instability (PI), which are mitigated by higher plasma edge temperatures. This condition is thus useful for enabling the LH power propagation when operating with profiles having high plasma densities even at the edge. In the present work, we show new PI modeling of EAST plasmas data, obtained in condition of higher plasma edge temperature due to chamber lithisation. The obtained trend of the PI frequencies and growth rates is consistent with data of RF probe spectra, available in different regimes of lithisated and not lithisated vessel. Moreover, these spectra are interpreted as PI effect occurring at the periphery of plasma column, however in the low field side where the LH power is coupled.

  8. Edge instability in a chiral stripe domain under an electric current and skyrmion generation

    SciTech Connect

    Lin, Shi -Zeng

    2016-07-05

    Motivated by the recent experimental observations on the skyrmion creation by cutting chiral stripe domains under a current drive [Jiang et al., Science 349, 283 (2015)], we study the mechanism of skyrmion generation by simulating the dynamics of stripe domains. Our theory for skyrmion generation is based on the fact that there are two half skyrmions attached to the ends of a stripe domain. These half skyrmions move due to the coupling between the skyrmion topological charge and current. As a consequence, the stripe domain is bent or stretched depending on the direction of motion of the half skyrmions. For a large current, skyrmions are created by chopping the stripe domains via strong bending or stretching. Our theory provides an explanation to the experiments and is supported by the new experiments. Moreover, we predict that skyrmions can also be generated using a Bloch stripe domain under a spin transfer torque which can be realized in B20 compounds.

  9. Generating recombinant C-terminal prion protein fragments of exact native sequence.

    PubMed

    Johanssen, V A; Barnham, K J; Masters, C L; Hill, A F; Collins, S J

    2012-02-01

    Transmissibility and distinctive neuropathology are hallmark features of prion diseases differentiating them from other neurodegenerative disorders, with pathogenesis and transmission appearing closely linked to misfolded conformers (PrP(Sc)) of the ubiquitously expressed cellular form of the prion protein (PrP(C)). Given the apparent pathogenic primacy of misfolded PrP, the utilisation of peptides based on the prion protein has formed an integral approach for providing insights into misfolding pathways and pathogenic mechanisms. In parallel with studies employing prion peptides, similar approaches in other neurodegenerative disorders such as Alzheimer Disease, have demonstrated that differential processing of parent proteins and quite minor variations in the primary sequence of cognate peptides generated from the same constitutive processing (such as Aβ1-40 versus Aβ1-42 produced from γ-secretase activity) can be associated with very different pathogenic consequences. PrP(C) also undergoes constitutive α- or β-cleavage yielding C1 (residues 112-231 human sequence) or C2 (residues 90-231), respectively, with the full cell biological significance of such processing unresolved; however, it is noteworthy that in prion diseases, such as Creutzfeldt-Jakob disease (CJD) and murine models, the moderately extended C2 fragment predominates in the brain suggesting that the two cleavage events and the consequent C-terminal fragments may differ in their pathogenic significance. Accordingly, studies characterising biologically relevant peptides like C1 and C2, would be most valid if undertaken using peptides completely free of any inherent non-native sequence that arises as a by-product of commonly employed recombinant production techniques. To achieve this aim and thereby facilitate more representative biophysical and neurotoxicity studies, we adapted the combination of high fidelity Taq TA cloning with a SUMO-Hexa-His tag-type approach, incorporating the SUMO protease

  10. Generation of Recombinant Oropouche Viruses Lacking the Nonstructural Protein NSm or NSs

    PubMed Central

    Randall, Richard E.; Elliott, Richard M.

    2015-01-01

    ABSTRACT Oropouche virus (OROV) is a midge-borne human pathogen with a geographic distribution in South America. OROV was first isolated in 1955, and since then, it has been known to cause recurring outbreaks of a dengue-like illness in the Amazonian regions of Brazil. OROV, however, remains one of the most poorly understood emerging viral zoonoses. Here we describe the successful recovery of infectious OROV entirely from cDNA copies of its genome and generation of OROV mutant viruses lacking either the NSm or the NSs coding region. Characterization of the recombinant viruses carried out in vitro demonstrated that the NSs protein of OROV is an interferon (IFN) antagonist as in other NSs-encoding bunyaviruses. Additionally, we demonstrate the importance of the nine C-terminal amino acids of OROV NSs in IFN antagonistic activity. OROV was also found to be sensitive to IFN-α when cells were pretreated; however, the virus was still capable of replicating at doses as high as 10,000 U/ml of IFN-α, in contrast to the family prototype BUNV. We found that OROV lacking the NSm protein displayed characteristics similar to those of the wild-type virus, suggesting that the NSm protein is dispensable for virus replication in the mammalian and mosquito cell lines that were tested. IMPORTANCE Oropouche virus (OROV) is a public health threat in Central and South America, where it causes periodic outbreaks of dengue-like illness. In Brazil, OROV is the second most frequent cause of arboviral febrile illness after dengue virus, and with the current rates of urban expansion, more cases of this emerging viral zoonosis could occur. To better understand the molecular biology of OROV, we have successfully rescued the virus along with mutants. We have established that the C terminus of the NSs protein is important in interferon antagonism and that the NSm protein is dispensable for virus replication in cell culture. The tools described in this paper are important in terms of

  11. Hot-electron generation by ``cavitating'' Langmuir turbulence in the nonlinear stage of the two-plasmon-decay instability

    NASA Astrophysics Data System (ADS)

    Vu, H. X.; DuBois, D. F.; Russell, D. A.; Myatt, J. F.

    2012-10-01

    The kinetic reduced-description particle-in-cell simulation technique has been applied to study the nonlinear stage of two-plasmon-decay (TPD) instability in an inhomogeneous plasma driven by crossed laser beams. The TPD instability is found to be a prolific generator of "cavitating" Langmuir turbulence. Langmuir "cavitons"—localized longitudinal electric fields, oscillating near the local electron plasma frequency, trapped in ponderomotive density depressions—collapse to dimensions of a few electron Debye lengths, where the electric field energy is collisionlessly transferred to electron kinetic energy. The resulting hot electrons can attain instantaneous temperatures up to 100 keV with net suprathermal heat flux out of the system of up to a few percent of the input laser energy. Scaling laws for this hot-electron generation by TPD, in regimes motivated by recent experiments on the Omega laser, were presented recently by Vu et al. (H. X. Vu, D. F. DuBois, D. A. Russell, and J. F. Myatt, Phys. Plasmas 19, 102703 (2012)). This paper concentrates on the microscopic mechanisms for hot-electron generation. The spatial distribution of the maxima of the electric field envelope modulus is found to be very spiky, with the distribution of electric field envelope maxima obeying Gaussian statistics. The cavitons are produced in density-depletion trenches produced by the combined ponderomotive interference of the crossed laser beams and the ponderomotive beats of the primary backward-going TPD Langmuir waves (LWs) resulting from the crossed beams. The Langmuir turbulence is strongest in the electron-density region near 0.241× the laser's critical density, where the forward LWs from the crossed-beam TPD are degenerate. Nucleation of cavitons is assisted by the modulation of the electron density in the trenches, which in turn is caused by the beating of the common forward-going LW and the pair of backward-going LWs. The autocorrelation function of the LW envelope field

  12. Hot-electron generation by 'cavitating' Langmuir turbulence in the nonlinear stage of the two-plasmon-decay instability

    SciTech Connect

    Vu, H. X.; DuBois, D. F.; Russell, D. A.; Myatt, J. F.

    2012-10-15

    The kinetic reduced-description particle-in-cell simulation technique has been applied to study the nonlinear stage of two-plasmon-decay (TPD) instability in an inhomogeneous plasma driven by crossed laser beams. The TPD instability is found to be a prolific generator of 'cavitating' Langmuir turbulence. Langmuir 'cavitons'-localized longitudinal electric fields, oscillating near the local electron plasma frequency, trapped in ponderomotive density depressions-collapse to dimensions of a few electron Debye lengths, where the electric field energy is collisionlessly transferred to electron kinetic energy. The resulting hot electrons can attain instantaneous temperatures up to 100 keV with net suprathermal heat flux out of the system of up to a few percent of the input laser energy. Scaling laws for this hot-electron generation by TPD, in regimes motivated by recent experiments on the Omega laser, were presented recently by Vu et al. (H. X. Vu, D. F. DuBois, D. A. Russell, and J. F. Myatt, Phys. Plasmas 19, 102703 (2012)). This paper concentrates on the microscopic mechanisms for hot-electron generation. The spatial distribution of the maxima of the electric field envelope modulus is found to be very spiky, with the distribution of electric field envelope maxima obeying Gaussian statistics. The cavitons are produced in density-depletion trenches produced by the combined ponderomotive interference of the crossed laser beams and the ponderomotive beats of the primary backward-going TPD Langmuir waves (LWs) resulting from the crossed beams. The Langmuir turbulence is strongest in the electron-density region near 0.241 Multiplication-Sign the laser's critical density, where the forward LWs from the crossed-beam TPD are degenerate. Nucleation of cavitons is assisted by the modulation of the electron density in the trenches, which in turn is caused by the beating of the common forward-going LW and the pair of backward-going LWs. The autocorrelation function of the LW

  13. Generation of Recombinant Modified Vaccinia Virus Ankara Encoding VP2, NS1, and VP7 Proteins of Bluetongue Virus.

    PubMed

    Marín-López, Alejandro; Ortego, Javier

    2016-01-01

    Modified Vaccinia Virus Ankara (MVA) is employed widely as an experimental vaccine vector for its lack of replication in mammalian cells and high expression level of foreign/heterologous genes. Recombinant MVAs (rMVAs) are used as platforms for protein production as well as vectors to generate vaccines against a high number of infectious diseases and other pathologies. The portrait of the virus combines desirable elements such as high-level biological safety, the ability to activate appropriate innate immune mediators upon vaccination, and the capacity to deliver substantial amounts of heterologous antigens. Recombinant MVAs encoding proteins of bluetongue virus (BTV), an Orbivirus that infects domestic and wild ruminants transmitted by biting midges of the Culicoides species, are excellent vaccine candidates against this virus. In this chapter we describe the methods for the generation of rMVAs encoding VP2, NS1, and VP7 proteins of bluetongue virus as a model example for orbiviruses. The protocols included cover the cloning of VP2, NS1, and VP7 BTV-4 genes in a transfer plasmid, the construction of recombinant MVAs, the titration of virus working stocks and the protein expression analysis by immunofluorescence and radiolabeling of rMVA infected cells as well as virus purification.

  14. Generation of polyclonal antibodies against recombinant human glucocerebrosidase produced in Escherichia coli.

    PubMed

    Novo, Juliana Branco; Oliveira, Maria Leonor Sarno; Magalhães, Geraldo Santana; Morganti, Ligia; Raw, Isaías; Ho, Paulo Lee

    2010-11-01

    Deficiency of the lysosomal glucocerebrosidase (GCR) enzyme results in Gaucher's disease, the most common inherited storage disorder. Treatment consists of enzyme replacement therapy by the administration of recombinant GCR produced in Chinese hamster ovary cells. The production of anti-GCR antibodies has already been described with placenta-derived human GCR that requires successive chromatographic procedures. Here, we report a practical and efficient method to obtain anti-GCR polyclonal antibodies against recombinant GCR produced in Escherichia coli and further purified by a single step through nickel affinity chromatography. The purified GCR was used to immunize BALB/c mice and the induction of anti-GCR antibodies was evaluated by enzyme-linked immunosorbent assay. The specificity of the antiserum was also evaluated by western blot analysis against recombinant GCR produced by COS-7 cells or against endogenous GCR of human cell lines. GCR was strongly recognized by the produced antibodies, either as cell-associated or as secreted forms. The detected molecular masses of 59-66 kDa are in accordance to the expected size for glycosylated GCR. The GCR produced in E. coli would facilitate the production of polyclonal (shown here) and monoclonal antibodies and their use in the characterization of new biosimilar recombinant GCRs coming in the near future.

  15. Edge instability in a chiral stripe domain under an electric current and skyrmion generation

    DOE PAGES

    Lin, Shi -Zeng

    2016-07-05

    Motivated by the recent experimental observations on the skyrmion creation by cutting chiral stripe domains under a current drive [Jiang et al., Science 349, 283 (2015)], we study the mechanism of skyrmion generation by simulating the dynamics of stripe domains. Our theory for skyrmion generation is based on the fact that there are two half skyrmions attached to the ends of a stripe domain. These half skyrmions move due to the coupling between the skyrmion topological charge and current. As a consequence, the stripe domain is bent or stretched depending on the direction of motion of the half skyrmions. Formore » a large current, skyrmions are created by chopping the stripe domains via strong bending or stretching. Our theory provides an explanation to the experiments and is supported by the new experiments. Moreover, we predict that skyrmions can also be generated using a Bloch stripe domain under a spin transfer torque which can be realized in B20 compounds.« less

  16. Edge instability in a chiral stripe domain under an electric current and skyrmion generation

    NASA Astrophysics Data System (ADS)

    Lin, Shi-Zeng

    2016-07-01

    Motivated by the recent experimental observations on the skyrmion creation by cutting chiral stripe domains under a current drive [Jiang et al., Science 349, 283 (2015), 10.1126/science.aaa1442], we study the mechanism of skyrmion generation by simulating the dynamics of stripe domains. Our theory for skyrmion generation is based on the fact that there are two half skyrmions attached to the ends of a stripe domain. These half skyrmions move due to the coupling between the skyrmion topological charge and current. As a consequence, the stripe domain is bent or stretched depending on the direction of motion of the half skyrmions. For a large current, skyrmions are created by chopping the stripe domains via strong bending or stretching. Our theory provides an explanation to the experiments and is supported by the new experiments. Furthermore, we predict that skyrmions can also be generated using a Bloch stripe domain under a spin transfer torque which can be realized in B20 compounds.

  17. Generation and Evolution of Channels due to the Melt Chennel Instability

    NASA Astrophysics Data System (ADS)

    Mueller, K.; Schmeling, H.

    2005-12-01

    We investigate melt transport in partially molten rocks under different stress fieldsunder hydrous and anhydrous conditions. We model such aggregates with the 2D-FD code FDCON [1] by means of a porous deformable matrix with melt to clarify the following key questions: Could channeling occur in a matrix containing a random melt distribution under a given stress field? How do channels evolve during finite simple shear? Is it possible to achieve a focussing of melt towards an MOR (dykes)? How does a Plume influence the orientation of dykes? In a deforming partially molten aggregate, weakening of the solid matrix due to the presence of melt creates an instability in which melt is localized by the following mechanism: regions of initially high meltfraction are areas of low viscosity and pressure, so that melt is drawn into these regions from higher pressure surroundings.This further enhances the melt weakening, producing a self-excited localization mechanism [2]. For both, simple as well as pure shear, the growth rate α for an inclined 1D sine pertubation is highest for an orientation parallel to the direction of the maximum compressive stress (MCS). α is proportional to the applied stress, the reverse of the Melt Retention Number [1] and the wavenumber k of the 1D sine. This also confirms the theoretical growth rate α found by Stevenson [2]. Small-scale simulations (~1 km×1 km box dimensions) with inclined 1D sine, 1D single channel-like pertubations, 2D ellipses, random fields and large-scale Plume-MOR simulations are investigated. In our isothermal models we found that the influence of water reduces the growth rate, in contrast to non-isothermal models of Hall [3]. Under simple as well as pure shear (small-scale simulations), melt channels evolve from an irregular melt distribution (mean porosity 3±0.5%) at angles parallel to the MCS (45° and 0°, resp.). Upon further straining in the simple shear case they slightly rotate out of the orientation of maximum

  18. Walk-Off-Induced Modulation Instability, Temporal Pattern Formation, and Frequency Comb Generation in Cavity-Enhanced Second-Harmonic Generation.

    PubMed

    Leo, F; Hansson, T; Ricciardi, I; De Rosa, M; Coen, S; Wabnitz, S; Erkintalo, M

    2016-01-22

    We derive a time-domain mean-field equation to model the full temporal and spectral dynamics of light in singly resonant cavity-enhanced second-harmonic generation systems. We show that the temporal walk-off between the fundamental and the second-harmonic fields plays a decisive role under realistic conditions, giving rise to rich, previously unidentified nonlinear behavior. Through linear stability analysis and numerical simulations, we discover a new kind of quadratic modulation instability which leads to the formation of optical frequency combs and associated time-domain dissipative structures. Our numerical simulations show excellent agreement with recent experimental observations of frequency combs in quadratic nonlinear media [Phys. Rev. A 91, 063839 (2015)]. Thus, in addition to unveiling a new, experimentally accessible regime of nonlinear dynamics, our work enables predictive modeling of frequency comb generation in cavity-enhanced second-harmonic generation systems. We expect our findings to have wide impact on the study of temporal and spectral dynamics in a diverse range of dispersive, quadratically nonlinear resonators.

  19. Development of a reverse genetics system to generate recombinant Marburg virus derived from a bat isolate.

    PubMed

    Albariño, César G; Uebelhoer, Luke S; Vincent, Joel P; Khristova, Marina L; Chakrabarti, Ayan K; McElroy, Anita; Nichol, Stuart T; Towner, Jonathan S

    2013-11-01

    Recent investigations have shown the Egyptian fruit bat (Rousettus aegyptiacus) to be a natural reservoir for marburgviruses. To better understand the life cycle of these viruses in the natural host, a new reverse genetics system was developed for the reliable rescue of a Marburg virus (MARV) originally isolated directly from a R. aegyptiacus bat (371Bat). To develop this system, the exact terminal sequences were first determined by 5' and 3' RACE, followed by the cloning of viral proteins NP, VP35, VP30 and L into expression plasmids. Novel conditions were then developed to efficiently replicate virus mini-genomes followed by the construction of full-length genomic clones from which recombinant wild type and GFP-containing MARVs were rescued. Surprisingly, when these recombinant MARVs were propagated in primary human macrophages, a dramatic difference was found in their ability to grow and to elicit anti-viral cytokine responses.

  20. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes

    PubMed Central

    Norman, Paul J.; Abi-Rached, Laurent; Gendzekhadze, Ketevan; Hammond, John A.; Moesta, Achim K.; Sharma, Deepti; Graef, Thorsten; McQueen, Karina L.; Guethlein, Lisbeth A.; Carrington, Christine V.F.; Chandanayingyong, Dasdayanee; Chang, Yih-Hsin; Crespí, Catalina; Saruhan-Direskeneli, Güher; Hameed, Kamran; Kamkamidze, Giorgi; Koram, Kwadwo A.; Layrisse, Zulay; Matamoros, Nuria; Milà, Joan; Park, Myoung Hee; Pitchappan, Ramasamy M.; Ramdath, D. Dan; Shiau, Ming-Yuh; Stephens, Henry A.F.; Struik, Siske; Tyan, Dolly; Verity, David H.; Vaughan, Robert W.; Davis, Ronald W.; Fraser, Patricia A.; Riley, Eleanor M.; Ronaghi, Mostafa; Parham, Peter

    2009-01-01

    Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric “half” was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family. PMID:19411600

  1. Generation of Recombinant Human AChE Op-Scavengers With Extended Circulatory Longevity

    DTIC Science & Technology

    2005-04-01

    AChE PEGylation results in a major reduction of the immunogenicity of the enzyme. In structure -function studies of AChE, we compared the reactivities...BChE). Extensive structural and biochemical analyses of over twenty forms of recombinant AChEs allowed us to determine an hierarchical pattern by...glycan structures that do not conform with the classical complex-type of oligosaccharides typical of animal cell proteins or which were entirely devoid of

  2. A general method to modify BACs to generate large recombinant DNA fragments.

    PubMed

    Shen, Wei; Huang, Yue; Tang, Yi; Liu, De-Pei; Liang, Chih-Chuan

    2005-11-01

    Bacterial artificial chromosome (BAC) has the capacity to clone DNA fragments in excess of 300 kb. It also has the considerable advantages of stable propagation and ease of purification. These features make BAC suitable in genetic research, such as library construction, transgenic mice production, and gene targeting constructs. Homologous recombination in Escherichia coli, a process named recombineering, has made the modification of BACs easy and reliable. We report here a modified recombineering method that can efficiently mediate the fusion of large DNA fragments from two or more different BACs. With the introduction of kanamycin-resistant gene and proposed rare-cutting restriction endonuclease (RCRE) sites into two BACs, a 82.6-kb DNA fragment containing the inverted human alpha-globin genes (theta, alpha1, alpha2, and zeta) from BAC191K2 and the locus control region (LCR) of human beta-globin gene locus (from the BAC186D7) was reconstructed. This approach for combining different BAC DNA fragments should facilitate many kinds of genomic experiments.

  3. Generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted RNA secondary structure.

    PubMed Central

    Rowe, C L; Fleming, J O; Nathan, M J; Sgro, J Y; Palmenberg, A C; Baker, S C

    1997-01-01

    Coronavirus RNA evolves in the central nervous systems (CNS) of mice during persistent infection. This evolution can be monitored by detection of a viral quasispecies of spike deletion variants (SDVs) (C. L. Rowe, S. C. Baker, M. J. Nathan, and J. O. Fleming, J. Virol. 71:2959-2969, 1997). We and others have found that the deletions cluster in the region from 1,200 to 1,800 nucleotides from the 5' end of the spike gene sequence, termed the "hypervariable" region. To address how SDVs might arise, we generated the predicted folding structures of the positive- and negative-strand senses of the entire 4,139-nt spike RNA sequence. We found that a prominent, isolated stem-loop structure is coincident with the hypervariable region in each structure. To determine if this predicted stem-loop is a "hot spot" for RNA recombination, we assessed whether this region of the spike is more frequently deleted than three other selected regions of the spike sequence in a population of viral sequences isolated from the CNS of acutely and persistently infected mice. Using differential colony hybridization of cloned spike reverse transcription-PCR products, we detected SDVs in which the hot spot was deleted but did not detect SDVs in which other regions of the spike sequence were exclusively deleted. Furthermore, sequence analysis and mapping of the crossover sites of 25 distinct patterns of SDVs showed that the majority of crossover sites clustered to two regions at the base of the isolated stem-loop, which we designated as high-frequency recombination sites 1 and 2. Interestingly, the majority of the left and right crossover sites of the SDVs were directly across from or proximal to one another, suggesting that these SDVs are likely generated by intramolecular recombination. Overall, our results are consistent with there being an important role for the spike RNA secondary structure as a contributing factor in the generation of SDVs during persistent infection. PMID:9223514

  4. Generation of Recombinant Polioviruses Harboring RNA Affinity Tags in the 5' and 3' Noncoding Regions of Genomic RNAs.

    PubMed

    Flather, Dylan; Cathcart, Andrea L; Cruz, Casey; Baggs, Eric; Ngo, Tuan; Gershon, Paul D; Semler, Bert L

    2016-02-04

    Despite being intensely studied for more than 50 years, a complete understanding of the enterovirus replication cycle remains elusive. Specifically, only a handful of cellular proteins have been shown to be involved in the RNA replication cycle of these viruses. In an effort to isolate and identify additional cellular proteins that function in enteroviral RNA replication, we have generated multiple recombinant polioviruses containing RNA affinity tags within the 3' or 5' noncoding region of the genome. These recombinant viruses retained RNA affinity sequences within the genome while remaining viable and infectious over multiple passages in cell culture. Further characterization of these viruses demonstrated that viral protein production and growth kinetics were unchanged or only slightly altered relative to wild type poliovirus. However, attempts to isolate these genetically-tagged viral genomes from infected cells have been hindered by high levels of co-purification of nonspecific proteins and the limited matrix-binding efficiency of RNA affinity sequences. Regardless, these recombinant viruses represent a step toward more thorough characterization of enterovirus ribonucleoprotein complexes involved in RNA replication.

  5. Development of a reverse genetics system to generate a recombinant Ebola virus Makona expressing a green fluorescent protein

    SciTech Connect

    Albariño, César G. Wiggleton Guerrero, Lisa; Lo, Michael K.; Nichol, Stuart T.; Towner, Jonathan S.

    2015-10-15

    Previous studies have demonstrated the potential application of reverse genetics technology in studying a broad range of aspects of viral biology, including gene regulation, protein function, cell entry, and pathogenesis. Here, we describe a highly efficient reverse genetics system used to generate recombinant Ebola virus (EBOV) based on a recent isolate from a human patient infected during the 2014–2015 outbreak in Western Africa. We also rescued a recombinant EBOV expressing a fluorescent reporter protein from a cleaved VP40 protein fusion. Using this virus and an inexpensive method to quantitate the expression of the foreign gene, we demonstrate its potential usefulness as a tool for screening antiviral compounds and measuring neutralizing antibodies. - Highlights: • Recombinant Ebola virus (EBOV) derived from Makona variant was rescued. • New protocol for viral rescue allows 100% efficiency. • Modified EBOV expresses a green fluorescent protein from a VP40-fused protein. • Modified EBOV was tested as tool to screen antiviral compounds and measure neutralizing antibodies.

  6. Construction of an expression system for bioactive IL-18 and generation of recombinant canine distemper virus expressing IL-18.

    PubMed

    Liu, Yuxiu; Sato, Hiroki; Hamana, Masahiro; Moonan, Navita Anisia; Yoneda, Misako; Xia, Xianzhu; Kai, Chieko

    2014-09-01

    Interleukin 18 (IL-18) plays an important role in the T-helper-cell type 1 immune response against intracellular parasites, bacteria and viral infections. It has been widely used as an adjuvant for vaccines and as an anticancer agent. However, IL-18 protein lacks a typical signal sequence and requires cleavage into its mature active form by caspase 1. In this study, we constructed mammalian expression vectors carrying cDNA encoding mature canine IL-18 (cIL-18) or mouse IL-18 (mIL-18) fused to the human IL-2 (hIL-2) signal sequence. The expressed proIL-18 proteins were processed to their mature forms in the cells. The supernatants of cells transfected with these plasmids induced high interferon-γ production in canine peripheral blood mononuclear cells or mouse splenocytes, respectively, indicating the secretion of bioactive IL-18. Using reverse genetics, we also generated a recombinant canine distemper virus that expresses cIL-18 or mIL-18 fused to the hIL-2 signal sequence. As expected, both recombinant viruses produced mature IL-18 in the infected cells, which secreted bioactive IL-18. These results indicate that the signal sequence from hIL-2 is suitable for the secretion of mature IL-18. These recombinant viruses can also potentially be used as immunoadjuvants and agents for anticancer therapies in vivo.

  7. Generation of hypoxanthine phosphoribosyltransferase gene knockout rabbits by homologous recombination and gene trapping through somatic cell nuclear transfer

    PubMed Central

    Yin, Mingru; Jiang, Weihua; Fang, Zhenfu; Kong, Pengcheng; Xing, Fengying; Li, Yao; Chen, Xuejin; Li, Shangang

    2015-01-01

    The rabbit is a common animal model that has been employed in studies on various human disorders, and the generation of genetically modified rabbit lines is highly desirable. Female rabbits have been successfully cloned from cumulus cells, and the somatic cell nuclear transfer (SCNT) technology is well established. The present study generated hypoxanthine phosphoribosyltransferase (HPRT) gene knockout rabbits using recombinant adeno-associated virus-mediated homologous recombination and SCNT. Gene trap strategies were employed to enhance the gene targeting rates. The male and female gene knockout fibroblast cell lines were derived by different strategies. When male HPRT knockout cells were used for SCNT, no live rabbits were obtained. However, when female HPRT+/− cells were used for SCNT, live, healthy rabbits were generated. The cloned HPRT+/− rabbits were fertile at maturity. We demonstrate a new technique to produce gene-targeted rabbits. This approach may also be used in the genetic manipulation of different genes or in other species. PMID:26522387

  8. Generation of deformation waves in the processes of photoexcitation and recombination of nonequilibrium carriers in silicon

    NASA Astrophysics Data System (ADS)

    Avanesyan, S. M.; Gusev, V. E.; Zheludev, N. I.

    1986-07-01

    The shape of acoustic pulses excited in crystalline silicon during absorption of Nd3+ YAG laser radiation was studied as a function of incident light intensity. It was revealed that the amplitude of the dilatation wave is saturated while the duration of the compression pulse is shortened. A theoretical model is suggested which explains the above experimental facts by a decrease in the time of Auger recombination for nonequilibrium carriers with an increase in their concentration for higher intensity of the optical excitation. The value of the Auger constant obtained from the experiment is ˜5×10-31 cm6s-1.

  9. Extreme ultraviolet source using a forced recombination process in lithium plasma generated by a pulsed laser

    SciTech Connect

    Nagano, Akihisa; Inoue, Takahiro; Nica, Petru-Edward; Amano, Sho; Miyamoto, Shuji; Mochizuki, Takayasu

    2007-04-09

    An extreme ultraviolet source having a tamper has been studied. This target scheme recombines forcedly lithium ions by low temperature electrons from the tamper, converting Li{sup 3+} rapidly to excited Li{sup 2+} which emit intense 1s-2p Lyman {alpha} emissions at 13.5 nm. A strong 13.5 nm emission appeared at 20-30 ns after the time of laser peak within a small space volume near the tamper. The authors obtained an enhancement of extreme ultraviolet conversion efficiency by a factor of about 2 with the tamper against that of a target without the tamper at the same laser irradiation condition00.

  10. Identification of a Putative Crf Splice Variant and Generation of Recombinant Antibodies for the Specific Detection of Aspergillus fumigatus

    PubMed Central

    Schütte, Mark; Thullier, Philippe; Pelat, Thibaut; Wezler, Xenia; Rosenstock, Philip; Hinz, Dominik; Kirsch, Martina Inga; Hasenberg, Mike; Frank, Ronald; Schirrmann, Thomas; Gunzer, Matthias

    2009-01-01

    Background Aspergillus fumigatus is a common airborne fungal pathogen for humans. It frequently causes an invasive aspergillosis (IA) in immunocompromised patients with poor prognosis. Potent antifungal drugs are very expensive and cause serious adverse effects. Their correct application requires an early and specific diagnosis of IA, which is still not properly achievable. This work aims to a specific detection of A. fumigatus by immunofluorescence and the generation of recombinant antibodies for the detection of A. fumigatus by ELISA. Results The A. fumigatus antigen Crf2 was isolated from a human patient with proven IA. It is a novel variant of a group of surface proteins (Crf1, Asp f9, Asp f16) which belong to the glycosylhydrolase family. Single chain fragment variables (scFvs) were obtained by phage display from a human naive antibody gene library and an immune antibody gene library generated from a macaque immunized with recombinant Crf2. Two different selection strategies were performed and shown to influence the selection of scFvs recognizing the Crf2 antigen in its native conformation. Using these antibodies, Crf2 was localized in growing hyphae of A. fumigatus but not in spores. In addition, the antibodies allowed differentiation between A. fumigatus and related Aspergillus species or Candida albicans by immunofluorescence microscopy. The scFv antibody clones were further characterized for their affinity, the nature of their epitope, their serum stability and their detection limit of Crf2 in human serum. Conclusion Crf2 and the corresponding recombinant antibodies offer a novel approach for the early diagnostics of IA caused by A. fumigatus. PMID:19675673

  11. Probing Photocurrent Generation, Charge Transport, and Recombination Mechanisms in Mesostructured Hybrid Perovskite through Photoconductivity Measurements.

    PubMed

    Sveinbjörnsson, Kári; Aitola, Kerttu; Zhang, Xiaoliang; Pazoki, Meysam; Hagfeldt, Anders; Boschloo, Gerrit; Johansson, Erik M J

    2015-11-05

    Conductivity of methylammonium lead triiodide (MAPbI3) perovskite was measured on different mesoporous metal oxide scaffolds: TiO2, Al2O3, and ZrO2, as a function of incident light irradiation and temperature. It was found that MAPbI3 exhibits intrinsic charge separation, and its conductivity stems from a majority of free charge carriers. The crystal morphology of the MAPbI3 was found to significantly affect the photoconductivity, whereas in the dark the conductivity is governed by the perovskite in the pores of the mesoporous scaffold. The temperature-dependent conductivity measurements also indicate the presence of states within the band gap of the perovskite. Despite a relatively large amount of crystal defects in the measured material, the main recombination mechanism of the photogenerated charges is bimolecular (band-to-band), which suggests that the defect states are rather inactive in the recombination. This may explain the remarkable efficiencies obtained for perovskite solar cells prepared with wet-chemical methods.

  12. A novel approach to generate a recombinant toxoid vaccine against Clostridium difficile.

    PubMed

    Donald, Robert G K; Flint, Mike; Kalyan, Narender; Johnson, Erik; Witko, Susan E; Kotash, Cheryl; Zhao, Ping; Megati, Shakuntala; Yurgelonis, Irina; Lee, Phillip Kwok; Matsuka, Yury V; Severina, Elena; Deatly, Anne; Sidhu, Mini; Jansen, Kathrin U; Minton, Nigel P; Anderson, Annaliesa S

    2013-07-01

    The Clostridium difficile toxins A and B are primarily responsible for symptoms of C. difficile associated disease and are prime targets for vaccine development. We describe a plasmid-based system for the production of genetically modified toxins in a non-sporulating strain of C. difficile that lacks the toxin genes tcdA and tcdB. TcdA and TcdB mutations targeting established glucosyltransferase cytotoxicity determinants were introduced into recombinant plasmids and episomally expressed toxin mutants purified from C. difficile transformants. TcdA and TcdB mutants lacking glucosyltransferase and autoproteolytic processing activities were ~10 000-fold less toxic to cultured human IMR-90 cells than corresponding recombinant or native toxins. However, both mutants retained residual cytotoxicity that could be prevented by preincubating the antigens with specific antibodies or by formalin treatment. Such non-toxic formalin-treated mutant antigens were immunogenic and protective in a hamster model of infection. The remaining toxicity of untreated TcdA and TcdB mutant antigens was associated with cellular swelling, a phenotype consistent with pore-induced membrane leakage. TcdB substitution mutations previously shown to block vesicular pore formation and toxin translocation substantially reduced residual toxicity. We discuss the implications of these results for the development of a C. difficile toxoid vaccine.

  13. Genetic instability is prevented by Mrc1-dependent spatio-temporal separation of replicative and repair activities of homologous recombination: homologous recombination tolerates replicative stress by Mrc1-regulated replication and repair activities operating at S and G2 in distinct subnuclear compartments.

    PubMed

    Prado, Félix

    2014-05-01

    Homologous recombination (HR) is required to protect and restart stressed replication forks. Paradoxically, the Mrc1 branch of the S phase checkpoints, which is activated by replicative stress, prevents HR repair at breaks and arrested forks. Indeed, the mechanisms underlying HR can threaten genome integrity if not properly regulated. Thus, understanding how cells avoid genetic instability associated with replicative stress, a hallmark of cancer, is still a challenge. Here I discuss recent results that support a model by which HR responds to replication stress through replicative and repair activities that operate at different stages of the cell cycle (S and G2, respectively) and in distinct subnuclear structures. Remarkably, the replication checkpoint appears to control this scenario by inhibiting the assembly of HR repair centers at stressed forks during S phase, thereby avoiding genetic instability.

  14. Instability Thresholds And Generation of the Electron-Cloud in the GLC/NLC And Tesla Damping Rings

    SciTech Connect

    Pivi, M.

    2005-04-11

    In the beam pipe of the Damping Ring (DR) of a linear collider, an electron cloud may be produced by ionization of residual gas or photoelectrons and develop by the secondary emission process [1]. Coupling between the electrons and the circulating beam can cause coupled-bunch instabilities, coherent single-bunch instabilities or incoherent tune spreads that may lead to increased emittance, beam blow-up and ultimately to beam losses. We present recent computer simulation results for the electron cloud instability thresholds in the GLC/NLC (X-Band) main DR and for the TESLA DR.

  15. Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form Originated from CRF01_AE and CRF08_BC in Dali Prefecture of Yunnan Province, China.

    PubMed

    Li, Jianjian; Li, Lin; Li, Huiqin; Li, Jingyun; Yang, Shaomin; Zhang, Mi; Ouyang, Hongmei

    2016-06-01

    Yunnan seems to be a "hot spot" region of HIV-1 recombination. CRF01_AE and subtype CRF08_BC are two main HIV-1 clades circulating in Yunnan. We report here a novel HIV-1 second-generation recombinant form originated from CRF01_AE and CRF08_BC. The strain (12YN10551) was isolated from a HIV-positive male infected through heterosexual contact in Dali prefecture of Yunnan province, China. This is the first report of HIV-1 near full-length genomic sequence in Dali. Recombinant analysis shows that 12YN10551 was composed of two well-established circulating recombinant forms (CRF01_AE and CRF08_BC). Two CRF01_AE recombinant fragments were inserted into the CRF08_BC backbone genome in the pol/vif/vpr/tat/rev and nef gene regions, respectively. The discovery and characterization of this new recombinant indicate that intersubtype recombination is continuously generating new forms of HIV-1. More work is needed to better monitor the genetic diversity of HIV-1 in this region.

  16. Instability in Rotating Machinery

    NASA Technical Reports Server (NTRS)

    1985-01-01

    The proceedings contain 45 papers on a wide range of subjects including flow generated instabilities in fluid flow machines, cracked shaft detection, case histories of instability phenomena in compressors, turbines, and pumps, vibration control in turbomachinery (including antiswirl techniques), and the simulation and estimation of destabilizing forces in rotating machines. The symposium was held to serve as an update on the understanding and control of rotating machinery instability problems.

  17. Human Recombinant Cytochrome P450 Enzymes Display Distinct Hydrogen Peroxide Generating Activities During Substrate Independent NADPH Oxidase Reactions

    PubMed Central

    Mishin, Vladimir; Heck, Diane E.; Laskin, Debra L.; Laskin, Jeffrey D.

    2014-01-01

    Microsomal enzymes generate H2O2 in the presence of NADPH. In this reaction, referred to as “oxidase” activity, H2O2 is generated directly or indirectly via the formation of superoxide anion. In the presence of redox active transition metals, H2O2 can form highly toxic hydroxyl radicals and, depending on the “oxidase” activity of individual cytochrome P450 isoenzymes, this can compromise cellular functioning and contribute to tissue injury. In the present studies, we compared the initial rates of H2O2 generating activity of microsomal preparations containing various human recombinant cytochromes P450s. In the absence of cytochrome P450s the human recombinant NADPH cytochrome P450 reductase (CPR) generated low, but detectable amounts of H2O2 (∼0.04 nmol H2O2/min/100 units of reductase). Significantly greater activity was detected in preparations containing individual cytochrome P450s coexpressed with CPR (from 6.0 nmol H2O2/min/nmol P450 to 0.2 nmol/min/nmol P450); CYP1A1 was the most active, followed by CYP2D6, CYP3A4, CYP2E1, CYP4A11, CYP1A2, and CYP2C subfamily enzymes. H2O2 generating activity of the cytochrome P450s was independent of the ratio of CYP/CPR. Thus, similar H2O2 generating activity was noted with the same cytochrome P450s (CYP3A4, CYP2E1, and CYP2C9) expressed at or near the ratio of CYP/CPR in human liver microsomes (5–7), and when CPR was present in excess (CYP/CPR = 0.2–0.3). Because CYP3A4/5/7 represent up to 40% of total cytochrome P450 in the liver, these data indicate that these enzymes are the major source of H2O2 in human liver microsomes. PMID:25061110

  18. Identification of Novel Recombinant Forms of Hepatitis B Virus Generated from Genotypes Ae and G in HIV-1-Positive Japanese Men Who Have Sex with Men

    PubMed Central

    Kawahata, Takuya; Mori, Haruyo; Furubayashi, Keiichi; Taniguchi, Yasushi; Itoda, Ichiro; Komano, Jun

    2015-01-01

    Abstract The rare hepatitis B virus (HBV) genotype G (HBV/G) coinfects HIV-1-positive individuals along with HBV/A and generates recombinants. However, the circulation of HBV A/G recombinants remains poorly understood. This molecular epidemiologic study examined HBV A/G recombinants in Japanese HIV-1-positive men who have sex with men (MSM). Initially, blood specimens submitted for confirmatory tests of HIV infection in Osaka and Tokyo, Japan, from 2006 to 2013 were examined for HIV-1, and HIV-1-positive specimens were screened for HBV. Among 817 specimens from HIV-1-positive individuals, HBsAg was detected in 59 specimens; of these, HBV/Ae (alternatively A2), a subgenotype of HBV/A prevalent in Europe and North America, was identified in 70.2%, HBV/C in 17.5%, and HBV/G in 10.5%, and HBV/E in 1.8% according to the core gene sequence. The full-length genome analysis of HBV was performed on HBV/G-positive specimens because some HBV A/G recombinants were historically overlooked by genotyping based on a partial genome analysis. It revealed that five of the specimens contained novel Ae/G recombinants, the core gene of which had a high sequence similarity to HBV/G. Detailed analyses showed that novel recombinants were coinfected with HBV/Ae in a recombinant-dominant fashion. No major drug-resistant mutations were found in the newly identified HBV Ae/G recombinants. Some of the individuals asymptomatically coinfected with HIV/HBV suffered mild liver injury. This study demonstrated that novel Ae/G HBV recombinants were identified in Japanese HIV-1-positive MSM. The pathogenicity of novel HBV Ae/G recombinants should be examined in a future longitudinal study. Surveillance of such viruses in HIV-1-positive individuals should be emphasized. PMID:25825936

  19. Identification of Novel Recombinant Forms of Hepatitis B Virus Generated from Genotypes Ae and G in HIV-1-Positive Japanese Men Who Have Sex with Men.

    PubMed

    Kojima, Yoko; Kawahata, Takuya; Mori, Haruyo; Furubayashi, Keiichi; Taniguchi, Yasushi; Itoda, Ichiro; Komano, Jun

    2015-07-01

    The rare hepatitis B virus (HBV) genotype G (HBV/G) coinfects HIV-1-positive individuals along with HBV/A and generates recombinants. However, the circulation of HBV A/G recombinants remains poorly understood. This molecular epidemiologic study examined HBV A/G recombinants in Japanese HIV-1-positive men who have sex with men (MSM). Initially, blood specimens submitted for confirmatory tests of HIV infection in Osaka and Tokyo, Japan, from 2006 to 2013 were examined for HIV-1, and HIV-1-positive specimens were screened for HBV. Among 817 specimens from HIV-1-positive individuals, HBsAg was detected in 59 specimens; of these, HBV/Ae (alternatively A2), a subgenotype of HBV/A prevalent in Europe and North America, was identified in 70.2%, HBV/C in 17.5%, and HBV/G in 10.5%, and HBV/E in 1.8% according to the core gene sequence. The full-length genome analysis of HBV was performed on HBV/G-positive specimens because some HBV A/G recombinants were historically overlooked by genotyping based on a partial genome analysis. It revealed that five of the specimens contained novel Ae/G recombinants, the core gene of which had a high sequence similarity to HBV/G. Detailed analyses showed that novel recombinants were coinfected with HBV/Ae in a recombinant-dominant fashion. No major drug-resistant mutations were found in the newly identified HBV Ae/G recombinants. Some of the individuals asymptomatically coinfected with HIV/HBV suffered mild liver injury. This study demonstrated that novel Ae/G HBV recombinants were identified in Japanese HIV-1-positive MSM. The pathogenicity of novel HBV Ae/G recombinants should be examined in a future longitudinal study. Surveillance of such viruses in HIV-1-positive individuals should be emphasized.

  20. Generation of infectious recombinant Adeno-associated virus in Saccharomyces cerevisiae

    PubMed Central

    Aponte-Ubillus, Juan Jose; Akeefe, Hassibullah; Cinek, Tomas; Peltier, Joseph; Gold, Daniel

    2017-01-01

    The yeast Saccharomyces cerevisiae has been successfully employed to establish model systems for a number of viruses. Such model systems are powerful tools to study the virus biology and in particular for the identification and characterization of host factors playing a role in the viral infection cycle. Adeno-associated viruses (AAV) are heavily studied due to their use as gene delivery vectors. AAV relies on other helper viruses for successful replication and on host factors for several aspects of the viral life cycle. However the role of host and helper viral factors is only partially known. Production of recombinant AAV (rAAV) vectors for gene delivery applications depends on knowledge of AAV biology and the limited understanding of host and helper viral factors may be precluding efficient production, particularly in heterologous systems. Model systems in simpler eukaryotes like the yeast S. cerevisiae would be useful tools to identify and study the role of host factors in AAV biology. Here we show that expression of AAV2 viral proteins VP1, VP2, VP3, AAP, Rep78, Rep52 and an ITR-flanked DNA in yeast leads to capsid formation, DNA replication and encapsidation, resulting in formation of infectious particles. Many of the AAV characteristics observed in yeast resemble those in other systems, making it a suitable model system. Future findings in the yeast system could be translatable to other AAV host systems and aid in more efficient production of rAAV vectors. PMID:28355224

  1. On the generation of charge-carrier recombination centers in the sapphire substrates of silicon-on-sapphire structures

    SciTech Connect

    Aleksandrov, P. A. Belova, N. E.; Demakov, K. D.; Shemardov, S. G.

    2015-08-15

    A method for the production of high-quality radiation-resistant silicon-on-sapphire structures through the fabrication of a layer of nanopores in sapphire by helium ion implantation, i.e., by creating charge-carrier recombination centers, is proposed. In this case, the quality of the silicon layer is simultaneously improved. The problem of the thermal stability of the pores is discussed with the aim of analyzing the possibility of producing a microcircuit on the resultant modified silicon-on-sapphire sample. The layer of pores possesses a large total surface area and, hence, decreases the lifetime of charge carriers generated during irradiation of the operating microcircuit. This effect reduces the charge at the silicon-sapphire interface and improves radiation resistance.

  2. A rapid and robust selection procedure for generating drug-selectable marker-free recombinant malaria parasites

    PubMed Central

    Manzoni, Giulia; Briquet, Sylvie; Risco-Castillo, Veronica; Gaultier, Charlotte; Topçu, Selma; Ivănescu, Maria Larisa; Franetich, Jean-François; Hoareau-Coudert, Bénédicte; Mazier, Dominique; Silvie, Olivier

    2014-01-01

    Experimental genetics have been widely used to explore the biology of the malaria parasites. The rodent parasites Plasmodium berghei and less frequently P. yoelii are commonly utilised, as their complete life cycle can be reproduced in the laboratory and because they are genetically tractable via homologous recombination. However, due to the limited number of drug-selectable markers, multiple modifications of the parasite genome are difficult to achieve and require large numbers of mice. Here we describe a novel strategy that combines positive-negative drug selection and flow cytometry-assisted sorting of fluorescent parasites for the rapid generation of drug-selectable marker-free P. berghei and P. yoelii mutant parasites expressing a GFP or a GFP-luciferase cassette, using minimal numbers of mice. We further illustrate how this new strategy facilitates phenotypic analysis of genetically modified parasites by fluorescence and bioluminescence imaging of P. berghei mutants arrested during liver stage development. PMID:24755823

  3. A rapid and robust selection procedure for generating drug-selectable marker-free recombinant malaria parasites.

    PubMed

    Manzoni, Giulia; Briquet, Sylvie; Risco-Castillo, Veronica; Gaultier, Charlotte; Topçu, Selma; Ivănescu, Maria Larisa; Franetich, Jean-François; Hoareau-Coudert, Bénédicte; Mazier, Dominique; Silvie, Olivier

    2014-04-23

    Experimental genetics have been widely used to explore the biology of the malaria parasites. The rodent parasites Plasmodium berghei and less frequently P. yoelii are commonly utilised, as their complete life cycle can be reproduced in the laboratory and because they are genetically tractable via homologous recombination. However, due to the limited number of drug-selectable markers, multiple modifications of the parasite genome are difficult to achieve and require large numbers of mice. Here we describe a novel strategy that combines positive-negative drug selection and flow cytometry-assisted sorting of fluorescent parasites for the rapid generation of drug-selectable marker-free P. berghei and P. yoelii mutant parasites expressing a GFP or a GFP-luciferase cassette, using minimal numbers of mice. We further illustrate how this new strategy facilitates phenotypic analysis of genetically modified parasites by fluorescence and bioluminescence imaging of P. berghei mutants arrested during liver stage development.

  4. A three-fluid approach in bipolar semiconductors with generation-recombination: constitutive laws and Onsager symmetry

    NASA Astrophysics Data System (ADS)

    Rossani, A.

    2016-11-01

    If electrons (e) and holes (h) in metals or semiconductors are heated to the temperatures Te and Th greater than the lattice temperature Tp, the electron-phonon interaction causes energy relaxation. In the nonuniform case, a momentum relaxation occurs as well. In view of such an application, a new model based on an asymptotic procedure for solving the kinetic equations of carriers and phonons is proposed, with generation-recombination of electrons and holes, which gives naturally the displaced Maxwellian at the leading order. After that, balance equations for the electron number, hole number, energy densities, and momentum densities are constructed, which constitute now a system of eight equations for the chemical potentials (carriers), the temperatures (carriers and phonons), and the drift velocities (carriers and phonons). In the drift-diffusion approximation the constitutive laws are derived and the Onsager relations recovered.

  5. Teaching Generative Reading Via Recombination of Minimal Textual Units: A Legacy of Verbal Behavior to Children in Brazil

    PubMed Central

    de Souza, Deisy G.; de Rose, Julio C.; Faleiros, Thais C.; Bortoloti, Renato; Hanna, Elenice Seixas; McIlvane, William J.

    2009-01-01

    This paper reports results of two studies that sought to teach generative reading skills to a large group of Brazilian children who were exhibiting protracted failure in school. Inspired by Skinner’s analysis of verbal relations and minimal verbal units, the methodology took advantage of certain characteristics of Portuguese. Many words in this language are comprised of two-letter syllabic units (e.g., BO+LA= ball, CA+BO= handle, LA+TA= can) that can be recombined to form new words (e.g., BOCA= mouth, BOTA= boot), thus establishing a route to generative reading via recombinative generalization. Such syllabic units were incorporated within curricular framework that used matching-to-sample and learning by exclusion methods to teach matching relations involving pictures, printed and spoken words, and printed and spoken syllables. Study 1 was conducted within a university-based learning center that maintained certain aspects of laboratory conditions. It showed that teaching textual relations between dictated and printed syllables could control procedurally the inter- and intra-participant variability observed in past studies that lacked this feature -resulting in virtually universally positive teaching outcomes. Study 2 was conducted in a public school programs that applied the same basic training methodology. Positive training outcomes in an experimental group were approximately 3–5 times greater than that in a placebo control group. Together, these studies illustrate that the functional analysis in Verbal Behavior is having a direct impact in educational science in Brazil. It has led to procedures that can be effectively translated from the laboratory to the community via delivery systems that can be implemented in the developing world. PMID:19960112

  6. Generation, characterization, and docking studies of DNA-hydrolyzing recombinant F(ab) antibodies.

    PubMed

    Zein, Haggag S; El-Sehemy, Ahmed A; Fares, Mohamed O; ElHefnawi, Mahmoud; da Silva, Jaime A Teixeira; Miyatake, Kazutaka

    2011-01-01

    Previously we established a series of catalytic antibodies (catAbs) capable of hydrolyzing DNA prepared by hybridoma technology. A group of these catAbs exhibited high reactivity and substrate specificity. To determine the molecular basis for these catAbs, we cloned, sequenced, and expressed the variable regions of this group of antibodies as functional F(ab) fragments. The nucleotide and deduced amino acid sequences of the expressed light chain (Vκ) germline gene assignments confidently belonged to germline family Vκ1A, gene bb1.1 and GenBank accession number EF672207 while heavy chain variable region V(H) genes belonged to V(H) 1/V(H) J558, gene V130.3 and GenBank accession number EF672221. A well-established expression system based on the pARA7 vector was examined for its ability to produce catalytically active antibodies. Recombinant F(ab) (rF(ab) ) fragments were purified and their hydrolyzing activity was analyzed against supercoiled pUC19 plasmid DNA (scDNA). The study of rF(ab) provides important information about the potential catalytic activities of antibodies whose structure allows us to understand their basis of catalysis. Molecular surface analysis and docking studies were performed on the molecular interactions between the antibodies and poly(dA9), poly(dG9), poly(dT9), and poly(dC9) oligomers. Surface analysis identified the important sequence motifs at the binding sites, and different effects exerted by arginine and tyrosine residues at different positions in the light and heavy chains. This study demonstrates the potential usefulness of the protein DNA surrogate in the investigation of the origin of anti-DNA antibodies. These studies may define important features of DNA catAbs.

  7. Generation of brain tumours in mice by Cre-mediated recombination of neural progenitors in situ with the tamoxifen metabolite endoxifen.

    PubMed

    Benedykcinska, Anna; Ferreira, Andreia; Lau, Joanne; Broni, Jessica; Richard-Loendt, Angela; Henriquez, Nico V; Brandner, Sebastian

    2016-02-01

    Targeted cell- or region-specific gene recombination is widely used in the functional analysis of genes implicated in development and disease. In the brain, targeted gene recombination has become a mainstream approach to study neurodegeneration or tumorigenesis. The use of the Cre-loxP system to study tumorigenesis in the adult central nervous system (CNS) can be limited, when the promoter (such as GFAP) is also transiently expressed during development, which can result in the recombination of progenies of different lineages. Engineering of transgenic mice expressing Cre recombinase fused to a mutant of the human oestrogen receptor (ER) allows the circumvention of transient developmental Cre expression by inducing recombination in the adult organism. The recombination of loxP sequences occurs only in the presence of tamoxifen. Systemic administration of tamoxifen can, however, exhibit toxicity and might also recombine unwanted cell populations if the promoter driving Cre expression is active at the time of tamoxifen administration. Here, we report that a single site-specific injection of an active derivative of tamoxifen successfully activates Cre recombinase and selectively recombines tumour suppressor genes in neural progenitor cells of the subventricular zone in mice, and we demonstrate its application in a model for the generation of intrinsic brain tumours.

  8. Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis

    PubMed Central

    Dago, Angel E.; Leitz, Laura J.; Wang, Yipeng; Lee, Jerry; Werner, Shannon L.; Gendreau, Steven; Patel, Premal; Jia, Shidong; Zhang, Liangxuan; Tucker, Eric K.; Malchiodi, Michael; Graf, Ryon P.; Dittamore, Ryan; Marrinucci, Dena; Landers, Mark

    2016-01-01

    Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression. To that end, we developed a single cell Copy Number Variation (CNV) Assay to evaluate genomic instability and CNVs in patient CTCs. For proof of concept, prostate cancer cell lines, LNCaP, PC3 and VCaP, were spiked into healthy donor blood to create mock patient-like samples for downstream single cell genomic analysis. In addition, samples from seven metastatic castration resistant prostate cancer (mCRPC) patients were included to evaluate clinical feasibility. CTCs were enumerated and characterized using the Epic Sciences CTC Platform. Identified single CTCs were recovered, whole genome amplified, and sequenced using an Illumina NextSeq 500. CTCs were then analyzed for genome-wide copy number variations, followed by genomic instability analyses. Large-scale state transitions (LSTs) were measured as surrogates of genomic instability. Genomic instability scores were determined reproducibly for LNCaP, PC3, and VCaP, and were higher than white blood cell (WBC) controls from healthy donors. A wide range of LST scores were observed within and among the seven mCRPC patient samples. On the gene level, loss of the PTEN tumor suppressor was observed in PC3 and 5/7 (71%) patients. Amplification of the androgen receptor (AR) gene was observed in VCaP cells and 5/7 (71%) mCRPC patients. Using an in silico down-sampling approach, we determined that DNA copy

  9. Kinetic Modeling Sheds Light on the Mode of Action of Recombinant Factor VIIa on Thrombin Generation

    DTIC Science & Technology

    2011-01-01

    numerical model to generate activated factor VII (FVIIa) titration curves in the cases of normal blood composition, hemophilia A and B blood, blood...as a hemostatic agent for patients with hemophilia , congenital FVII deficiency, and Glanzmann’s thrombocytopenia [3]. Following its initial approval...normal blood composition, hemophilia A and B blood, blood lacking factor VII, blood lacking tissue factor pathway inhibitor, and diluted blood. We

  10. Radiation Induced Genomic Instability

    SciTech Connect

    Morgan, William F.

    2011-03-01

    Radiation induced genomic instability can be observed in the progeny of irradiated cells multiple generations after irradiation of parental cells. The phenotype is well established both in vivo (Morgan 2003) and in vitro (Morgan 2003), and may be critical in radiation carcinogenesis (Little 2000, Huang et al. 2003). Instability can be induced by both the deposition of energy in irradiated cells as well as by signals transmitted by irradiated (targeted) cells to non-irradiated (non-targeted) cells (Kadhim et al. 1992, Lorimore et al. 1998). Thus both targeted and non-targeted cells can pass on the legacy of radiation to their progeny. However the radiation induced events and cellular processes that respond to both targeted and non-targeted radiation effects that lead to the unstable phenotype remain elusive. The cell system we have used to study radiation induced genomic instability utilizes human hamster GM10115 cells. These cells have a single copy of human chromosome 4 in a background of hamster chromosomes. Instability is evaluated in the clonal progeny of irradiated cells and a clone is considered unstable if it contains three or more metaphase sub-populations involving unique rearrangements of the human chromosome (Marder and Morgan 1993). Many of these unstable clones have been maintained in culture for many years and have been extensively characterized. As initially described by Clutton et al., (Clutton et al. 1996) many of our unstable clones exhibit persistently elevated levels of reactive oxygen species (Limoli et al. 2003), which appear to be due dysfunctional mitochondria (Kim et al. 2006, Kim et al. 2006). Interestingly, but perhaps not surprisingly, our unstable clones do not demonstrate a “mutator phenotype” (Limoli et al. 1997), but they do continue to rearrange their genomes for many years. The limiting factor with this system is the target – the human chromosome. While some clones demonstrate amplification of this chromosome and thus lend

  11. Comparing CDRH3 diversity captured from secondary lymphoid organs for the generation of recombinant human antibodies.

    PubMed

    Venet, Sophie; Kosco-Vilbois, Marie; Fischer, Nicolas

    2013-01-01

    The plasticity of natural immunoglobulin repertoires can be exploited for the generation of phage display libraries. Secondary lymphoid organs, such as the spleen and the lymph nodes, constitute interesting sources of diversity because they are rich in B cells, part of which can be affinity matured. These organs, however, differ in their anatomical structure, reflecting the different fluids they drain, which affects the B cell repertoires. The CDRH3 repertoires from these organs, extracted from naïve or immunized mice, were compared in the context of phage display libraries using human antibody framework families. Deep sequencing analysis revealed that all libraries displayed different CDRH3 repertoires, but the one derived from lymph nodes of naïve mice was the most diverse. Library performance was assessed by in vitro selection. For both organs, immunization increased substantially the frequency of molecules able to bind to the immunogen. The library derived from lymph nodes from naïve mice, however, was the most effective in generating diverse and high affinity candidates. These results illustrate that the use of a biased CDRH3 repertoire increases the performance of libraries, but reduces the clonal diversity, which may be detrimental for certain strategies.

  12. Combination of FACS and homologous recombination for the generation of stable and high-expression engineered cell lines.

    PubMed

    Shi, Lei; Chen, Xuesi; Tang, Wenying; Li, Zhenyi; Liu, Jin; Gao, Feng; Sang, Jianli

    2014-01-01

    Traditionally, cell line generation requires several months and involves screening of over several hundred cell clones for high productivity before dozens are selected as candidate cell lines. Here, we have designed a new strategy for the generation of stable and high-expression cell lines by combining homologous recombination (HR) and fluorescence-activated cell sorting (FACS). High expression was indicated by the expression of secreted green fluorescent protein (SEGFP). Parental cell lines with the highest expression of SEGFP were then selected by FACS and identified by stability analysis. Consequently, HR vectors were constructed using the cassette for SEGFP as the HR region. After transfecting the HR vector, the cells with negative SEGFP expression were enriched by FACS. The complete exchange between SEGFP and target gene (TNFR-Fc) cassettes was demonstrated by DNA analysis. Compared with the traditional method, by integrating the cassette containing the gene of interest into the pre-selected site, the highest producing cells secreted a more than 8-fold higher titer of target protein. Hence, this new strategy can be applied to isolated stable cell lines with desirable expression of any gene of interest. The stable cell lines can rapidly produce proteins for researching protein structure and function and are even applicable in drug discovery.

  13. Engineering of Conditional Class I Hdac Knockout Mice and Generation of a Time-Spatial Knockout by a Dual Recombination System.

    PubMed

    Bayer, Sieglinde; Wirth, Matthias

    2017-01-01

    The protein sequences of class I HDACs in mice and humans are 96-99 % identical. These highly conserved proteins have crucial roles in biological processes, such as proliferation and development, which is reflected in the lethality that occurs in conventional whole body knockout mice. Therefore, conditional knockouts are inevitable to investigate the functions of class I HDACs in mice. Here, we describe the generation of conditional class I Hdac knockout mice, using Hdac1 as an example. We explain a relatively quick procedure to generate the necessary target vectors by recombination-mediated genetic engineering and gateway techniques. Furthermore, we show how to culture, target, and screen for positively recombined ES cells. Additionally, we present a dual recombination system, which allows the deletion of class I Hdacs at any time by a tamoxifen inducible Cre.

  14. Enhanced late gas generation potential of petroleum source rocks via recombination reactions: Evidence from the Norwegian North Sea

    NASA Astrophysics Data System (ADS)

    Erdmann, Michael; Horsfield, Brian

    2006-08-01

    Gas generation in the deep reaches of sedimentary basins is usually considered to take place via the primary cracking of short alkyl groups from overmature kerogen or the secondary cracking of petroleum. Here, we show that recombination reactions ultimately play the dominant role in controlling the timing of late gas generation in source rocks which contain mixtures of terrigeneous and marine organic matter. These reactions, taking place at low levels of maturation, result in the formation of a thermally stable bitumen, which is the major source of methane at very high maturities. The inferences come from pyrolysis experiments performed on samples of the Draupne Formation (liptinitic Type II kerogen) and Heather Formation (mixed marine-terrigeneous Type III kerogen), both Upper Jurassic source rocks stemming from the Norwegian northern North Sea Viking Graben system. Non-isothermal closed system micro scale sealed vessel (MSSV) pyrolysis, non-isothermal open system pyrolysis and Rock Eval type pyrolysis were performed on the solvent extracted, concentrated kerogens of the two immature samples. The decrease of C 6+ products in the closed system MSSV pyrolysis provided the basis for the calculation of secondary gas (C 1-5) formation. Subtraction of the calculated secondary gas from the total observed gas yields a "remaining" gas. In the case of the Draupne Formation this is equivalent to primary gas cracked directly from the kerogen, as detected by a comparison with multistep open pyrolysis data. For the Heather Formation the calculated remaining gas formation profile is initially attributable to primary gas but there is a second major gas pulse at very high temperature (>550 °C at 5.0 K min -1) that is not primary. This has been explained by a recondensation process where first formed high molecular weight compounds in the closed system yield a macromolecular material that undergoes secondary cracking at elevated temperatures. The experiments provided the input for

  15. A Robust High Throughput Platform to Generate Functional Recombinant Monoclonal Antibodies Using Rabbit B Cells from Peripheral Blood

    PubMed Central

    Seeber, Stefan; Ros, Francesca; Thorey, Irmgard; Tiefenthaler, Georg; Kaluza, Klaus; Lifke, Valeria; Fischer, Jens André Alexander; Klostermann, Stefan; Endl, Josef; Kopetzki, Erhard; Pashine, Achal; Siewe, Basile; Kaluza, Brigitte; Platzer, Josef; Offner, Sonja

    2014-01-01

    We have developed a robust platform to generate and functionally characterize rabbit-derived antibodies using B cells from peripheral blood. The rapid high throughput procedure generates a diverse set of antibodies, yet requires only few animals to be immunized without the need to sacrifice them. The workflow includes (i) the identification and isolation of single B cells from rabbit blood expressing IgG antibodies, (ii) an elaborate short term B-cell cultivation to produce sufficient monoclonal antigen specific IgG for comprehensive phenotype screens, (iii) the isolation of VH and VL coding regions via PCR from B-cell clones producing antigen specific and functional antibodies followed by the sequence determination, and (iv) the recombinant expression and purification of IgG antibodies. The fully integrated and to a large degree automated platform (demonstrated in this paper using IL1RL1 immunized rabbits) yielded clonal and very diverse IL1RL1-specific and functional IL1RL1-inhibiting rabbit antibodies. These functional IgGs from individual animals were obtained at a short time range after immunization and could be identified already during primary screening, thus substantially lowering the workload for the subsequent B-cell PCR workflow. Early availability of sequence information permits one to select early-on function- and sequence-diverse antibodies for further characterization. In summary, this powerful technology platform has proven to be an efficient and robust method for the rapid generation of antigen specific and functional monoclonal rabbit antibodies without sacrificing the immunized animal. PMID:24503933

  16. Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length 'imprecise' intermediates.

    PubMed

    Lowry, Kym; Woodman, Andrew; Cook, Jonathan; Evans, David J

    2014-06-01

    Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of 'evolution by duplication' in the positive-strand RNA viruses.

  17. Overcoming temporal polarization instabilities from the latent birefringence in all-normal dispersion, wave-breaking-extended nonlinear fiber supercontinuum generation

    PubMed Central

    Domingue, Scott R.; Bartels, Randy A.

    2013-01-01

    The intrinsic weak birefringence in all-normal dispersion highly nonlinear fiber, particularly ultra-high-numerical-aperture fiber, generates supercontinuum with long term polarization instabilities, even for seed pulses launched along the perceived slow axis of the fiber. Highly co/anti-correlated fluctuations in energy between regions of power spectral density mask the extent of the spectral noise in total integrated power measurements. The instability exhibits a seed pulse power threshold above which the output polarization state of the supercontinuum seeds from noise. Eliminating this instability through the utilization of nonlinear fiber with a large designed birefringence, encourages the exploration of compression schemes and seed sources. Here, we include an analysis of the difficulties for seeding supercontinuum with the highly attractive ANDi-type lasers. Lastly, we introduce an intuitive approach for understanding supercontinuum development and evolution. By modifying the traditional characteristic dispersion and nonlinear lengths to track pulse properties within the nonlinear fiber, we find simple, descriptive handles for supercontinuum evolution. PMID:23736583

  18. Photoexcited electron and hole dynamics in semiconductor quantum dots: phonon-induced relaxation, dephasing, multiple exciton generation and recombination

    NASA Astrophysics Data System (ADS)

    Hyeon-Deuk, Kim; Prezhdo, Oleg V.

    2012-09-01

    Photoexcited dynamics of electrons and holes in semiconductor quantum dots (QD), including phonon-induced relaxation, multiple exciton generation, fission and recombination (MEG, MEF and MER), were simulated by combining ab initio time-dependent density functional theory and non-adiabatic molecular dynamics. These nonequilibrium phenomena govern the optical properties and photoexcited dynamics of QDs, determining the branching between electronic processes and thermal energy losses. Our approach accounts for QD size and shape as well as defects, core-shell distribution, surface ligands and charge trapping, which significantly influence the properties of photoexcited QDs. The method creates an explicit time-domain representation of photoinduced processes and describes various kinetic regimes owing to the non-perturbative treatment of quantum dynamics. QDs of different sizes and materials, with and without ligands, are considered. The simulations provide direct evidence that the high-frequency ligand modes on the QD surface play a pivotal role in the electron-phonon relaxation, MEG, MEF and MER. The insights reported here suggest novel routes for controlling the photoinduced processes in semiconductor QDs and lead to new design principles for increasing the efficiencies of photovoltaic devices.

  19. A novel bromodeoxyuridine-resistant wild boar lung cell line facilitates generation of African swine fever virus recombinants.

    PubMed

    Keil, Günther M; Giesow, Katrin; Portugal, Raquel

    2014-09-01

    Manipulation of African swine fever virus (ASFV) genomes, in particular those from field strains, is still a challenge. We have shown recently that generation of a green-fluorescent-protein-expressing, thymidine-kinase-negative (TK-) mutant of the low-pathogenic African swine fever virus field strain NHV was supported by a TK- Vero cell line. Since NHV, like other ASFV field strains, does not replicate well in Vero cells, a bromodeoxyuridine (BrdU)- resistant cell line derived from wild boar lung (WSL) cells, named WSL-Bu, was selected. WSL cells were used because they are suitable for productive replication of NHV and other ASFV field strains. Here, we show that WSL-Bu cells enable positive selection of both TK- and TK+ ASFV recombinants, which allows for novel strategies for construction of ASFV mutants. We further demonstrate for a low-pathogenic ASFV strain that TK expression is required for infectious replication in macrophages infected at low multiplicity and that vaccinia TK fully complements ASFV TK in this respect.

  20. Heterojunction depth in P+-on-n eSWIR HgCdTe infrared detectors: generation-recombination suppression

    NASA Astrophysics Data System (ADS)

    Schuster, J.; DeWames, R. E.; DeCuir, E. A.; Bellotti, E.; Dhar, N.; Wijewarnasuriya, P. S.

    2015-08-01

    A key design feature of P+-on-n HgCdTe detectors is the depth of the p-type region. Normally, homojunction architectures are utilized where the p-type region extends into the narrow-gap absorber layer. This facilitates the collection of photo-carriers from the absorber layer to the contact; however, this may result in excess generation-recombination (G-R) current if defects are present. Alternatively, properly adopting a heterojunction architecture confines the p-type region (and the majority of the electric field) solely to the wide-gap layer. Junction placement is critical since the detector performance is now dependent on the following sensitivity parameters: p-type region depth, doping, valence band offset, lifetime and detector bias. Understanding the parameter dependence near the hetero-metallurgical interface where the compositional grading occurs and the doping is varied as either a Gaussian or error function is vital to device design. Numerical modeling is now essential to properly engineer the electric field in the device to suppress G-R current while accounting for the aforementioned sensitivity parameters. The simulations reveal that through proper device design the p-type region can be confined to the wide-gap layer, reducing G-R related dark current, without significantly reducing the quantum efficiency at the operating bias V = -0.100V.

  1. Generation and characterization of murine monoclonal antibodies to genus-specific 31-kilodalton recombinant cell surface protein of Brucella abortus.

    PubMed

    Kumar, Sanjay; Tuteja, Urmil; Batra, Harsh Vardhan

    2007-08-01

    In the present study hybridomas were produced from fusion with splenocytes of BALB/c mice immunized with the recombinant 31-kDa cell surface protein (r31CSP) specific for Brucella species. A set of eight stabilized hybridoma cell lines was generated against r31CSP. Monoclonal antibodies (MAbs) produced by all these clones exhibited reactivity for r31CSP as well as with the protein of 31-kDa, derived from whole-cell lysate of 31-kDa Brucella abortus 544. Four of eight MAbs were IgG1, two IgG2b, and two IgM in nature. These MAbs did not show any cross-reaction with whole-cell lysate of Yersinia enterocolitica O: 9, Vibrio cholerae, Salmonella typhimurium and Escherichia coli 0157 by Western blotting. Reactivity of these MAbs was further assessed with other organisms of Brucella species namely, B. abortus S99, B. canis, B. melitensis 16M, B. suis, and a clinical isolate of B. melitensis. Collectively, these data suggest that these MAbs may have the potential for use in the detection of Brucella species with high specificity.

  2. Purification of recombinant adeno-associated virus type 8 vectors by ion exchange chromatography generates clinical grade vector stock.

    PubMed

    Davidoff, Andrew M; Ng, Catherine Y C; Sleep, Susan; Gray, John; Azam, Selina; Zhao, Yuan; McIntosh, Jenny H; Karimipoor, Morteza; Nathwani, Amit C

    2004-11-01

    Recombinant vectors based on the recently isolated AAV serotype 8 (rAAV-8) shows great promise for gene therapy, particularly for disorders affecting the liver. Transition of this vector system to the clinic, however, is limited by the lack of an efficient scaleable purification method. In this report, we describe a simple method for purification of rAAV-8 vector particles based on ion exchange chromatography that generates vector stocks with greater than 90% purity. The average yield of purified rAAV-8 from five different vector preparation was 41%. Electron microscopy of these purified stocks revealed typical icosohedral virions with less than 10% empty particles. Liver targeted delivery of ion-exchange purified rAAV-8 vector encoding the human factor IX (hFIX) gene, resulted in plasma hFIX levels approaching 30% of normal in immunocompetent mice, which is 20-fold higher than observed with an equivalent number of rAAV-5 ion exchange purified vector particles. The method takes less then 5 h to process and purify rAAV-8 vector from producer cells and represents a significant advance on the CsCl density centrifugation technique in current use for purification of rAAV-8 vector systems and will likely facilitate the transition of the rAAV-8 vector system to the clinic.

  3. Organometal halide perovskite solar cell materials rationalized: ultrafast charge generation, high and microsecond-long balanced mobilities, and slow recombination.

    PubMed

    Ponseca, Carlito S; Savenije, Tom J; Abdellah, Mohamed; Zheng, Kaibo; Yartsev, Arkady; Pascher, Tobjörn; Harlang, Tobias; Chabera, Pavel; Pullerits, Tonu; Stepanov, Andrey; Wolf, Jean-Pierre; Sundström, Villy

    2014-04-09

    Organometal halide perovskite-based solar cells have recently been reported to be highly efficient, giving an overall power conversion efficiency of up to 15%. However, much of the fundamental photophysical properties underlying this performance has remained unknown. Here, we apply photoluminescence, transient absorption, time-resolved terahertz and microwave conductivity measurements to determine the time scales of generation and recombination of charge carriers as well as their transport properties in solution-processed CH3NH3PbI3 perovskite materials. We found that electron-hole pairs are generated almost instantaneously after photoexcitation and dissociate in 2 ps forming highly mobile charges (25 cm(2) V(-1) s(-1)) in the neat perovskite and in perovskite/alumina blends; almost balanced electron and hole mobilities remain very high up to the microsecond time scale. When the perovskite is introduced into a TiO2 mesoporous structure, electron injection from perovskite to the metal oxide is efficient in less than a picosecond, but the lower intrinsic electron mobility of TiO2 leads to unbalanced charge transport. Microwave conductivity measurements showed that the decay of mobile charges is very slow in CH3NH3PbI3, lasting up to tens of microseconds. These results unravel the remarkable intrinsic properties of CH3NH3PbI3 perovskite material if used as light absorber and charge transport layer. Moreover, finding a metal oxide with higher electron mobility may further increase the performance of this class of solar cells.

  4. Adjuvant poly(N-isopropylacrylamide) generates more efficient monoclonal antibodies against truncated recombinant histidine-rich protein2 of Plasmodium falciparum for malaria diagnosis.

    PubMed

    Verma, Reena; Ravichandran, Ramakrishnan; Jayaprakash, Naatamai S; Kumar, Ashok; Vijayalakshmi, Mookambeswaran A; Venkataraman, Krishnan

    2015-05-01

    Adjuvants play an important role in eliciting immune responses and subsequent generation of antibodies with high specificity. Recently, poly(N-isopropylacrylamide) (PNiPAAm), also known as a "smart" polymer, has been proposed as a potential adjuvant for making antibodies and vaccines. This material exhibits efficient delivery, protection against degradation, and preservation of antigen epitopes. In this work, we used both CFA and smart polymer to develop a highly specific murine monoclonal antibody (mAb) against recombinant truncated histidine rich protein2 (HRP2) of Plasmodium falciparum. Our results indicate that the mAbs developed using these adjuvants were able to recognize recombinant HRP2 and native PfHRP2 protein from spent medium. The mAbs generated against recombinant truncated HRP2 showed better sensitivity to the antigen and importantly mAbs generated using PNiPAAm adjuvant were in the range of 10(8)-10(9) M(-1). The mAbs generated using PNiPAAm are very efficient and sensitive in detecting HRP2. To the best of our knowledge, this is the first report of such comparison having been made between these two adjuvants and we propose that the smart polymer has huge potential as an alternative to CFA. Additionally, we discuss the utility of the mAbs generated through PNiPAAm for specific diagnosis of malaria caused by P. falciparum.

  5. Immune responses to recombinants of the South African vaccine strain of lumpy skin disease virus generated by using thymidine kinase gene insertion.

    PubMed

    Wallace, David B; Viljoen, Gerrit J

    2005-04-27

    The South African vaccine strain of lumpy skin disease virus (type SA-Neethling) is currently being developed as a vector for recombinant vaccines of economically important livestock diseases throughout Africa. In this study, the feasibility of using the viral thymidine kinase gene as the site of insertion was investigated and recombinant viruses were evaluated in animal trials. Two separate recombinants were generated and selected for homogeneity expressing either the structural glycoprotein gene of bovine ephemeral fever virus (BEFV) or the two structural glycoprotein genes of Rift Valley fever virus (RVFV). Both recombinants incorporate the enhanced green fluorescent protein (EGFP) as a visual marker and the Escherichia coli guanine phosphoribosyl transferase (gpt) gene for dominant positive selection. The LSDV-RVFV recombinant construct (rLSDV-RVFV) protected mice against virulent RVFV challenge. In a small-scale BEFV-challenge cattle trial the rLSDV-BEFV construct failed to fully protect the cattle against virulent challenge, although both a humoral and cellular BEFV-specific immune response was elicited.

  6. Recombinative plasma in electron runaway discharge

    SciTech Connect

    Kuznetsov, Yu.K.; Galvao, R.M.O.; Usuriaga, O.C.; Krasheninnikov, S.I.; Soboleva, T.K.; Tsypin, V.S.; Fonseca, A.M.M.; Ruchko, L.F.; Sanada, E.K.

    2005-07-15

    Cold recombinative plasma is the basic feature of the new regime of runaway discharges recently discovered in the Tokamak Chauffage Alfven Bresilien tokamak [R. M. O. Galvao et al., Plasma Phys. Controlled Fusion 43, 1181 (2001)]. With low plasma temperature, the resistive plasma current and primary Dreicer process of runaway generation are strongly suppressed at the stationary phase of the discharge. In this case, the runaway avalanche, which has been recently recognized as a novel important mechanism for runaway electron generation in large tokamaks, such as International Thermonuclear Experimental Reactor, during disruptions, and for electric breakdown in matter, is the only mechanism responsible for toroidal current generation and can be easily observed. The measurement of plasma temperature by the usual methods is a difficult task in fully runaway discharges. In the present work, various indirect evidences for low-temperature recombinative plasma are presented. The direct observation of recombinative plasma is obtained as plasma detachment from the limiter. The model of cold recombinative plasma is also supported by measurements of plasma density and H{sub {alpha}} emission radial profiles, analysis of time variations of these parameters due to the relaxation instability, estimations of plasma resistivity from voltage spikes, and energy and particle balance calculations.

  7. Generation and Characterization of Human Monoclonal Antibodies Targeting Anthrax Protective Antigen following Vaccination with a Recombinant Protective Antigen Vaccine.

    PubMed

    Chi, Xiangyang; Li, Jianmin; Liu, Weicen; Wang, Xiaolin; Yin, Kexin; Liu, Ju; Zai, Xiaodong; Li, Liangliang; Song, Xiaohong; Zhang, Jun; Zhang, Xiaopeng; Yin, Ying; Fu, Ling; Xu, Junjie; Yu, Changming; Chen, Wei

    2015-05-01

    The anthrax protective antigen (PA) is the central component of the three-part anthrax toxin, and it is the primary immunogenic component in the approved AVA anthrax vaccine and the "next-generation" recombinant PA (rPA) anthrax vaccines. Animal models have indicated that PA-specific antibodies (AB) are sufficient to protect against infection with Bacillus anthracis. In this study, we investigated the PA domain specificity, affinity, mechanisms of neutralization, and synergistic effects of PA-specific antibodies from a single donor following vaccination with the rPA vaccine. Antibody-secreting cells were isolated 7 days after the donor received a boost vaccination, and 34 fully human monoclonal antibodies (hMAb) were identified. Clones 8H6, 4A3, and 22F1 were able to neutralize lethal toxin (LeTx) both in vitro and in vivo. Clone 8H6 neutralized LeTx by preventing furin cleavage of PA in a dose-dependent manner. Clone 4A3 enhanced degradation of nicked PA, thereby interfering with PA oligomerization. The mechanism of 22F1 is still unclear. A fourth clone, 2A6, that was protective only in vitro was found to be neutralizing in vivo in combination with a toxin-enhancing antibody, 8A7, which binds to domain 3 of PA and PA oligomers. These results provide novel insights into the antibody response elicited by the rPA vaccine and may be useful for PA-based vaccine and immunotherapeutic cocktail design.

  8. Bystander effects in radiation-induced genomic instability

    NASA Technical Reports Server (NTRS)

    Morgan, William F.; Hartmann, Andreas; Limoli, Charles L.; Nagar, Shruti; Ponnaiya, Brian

    2002-01-01

    Exposure of GM10115 hamster-human hybrid cells to X-rays can result in the induction of chromosomal instability in the progeny of surviving cells. This instability manifests as the dynamic production of novel sub-populations of cells with unique cytogenetic rearrangements involving the "marker" human chromosome. We have used the comet assay to investigate whether there was an elevated level of endogenous DNA breaks in chromosomally unstable clones that could provide a source for the chromosomal rearrangements and thus account for the persistent instability observed. Our results indicate no significant difference in comet tail measurement between non-irradiated and radiation-induced chromosomally unstable clones. Using two-color fluorescence in situ hybridization we also investigated whether recombinational events involving the interstitial telomere repeat-like sequences in GM10115 cells were involved at frequencies higher than random processes would otherwise predict. Nine of 11 clones demonstrated a significantly higher than expected involvement of these interstitial telomere repeat-like sequences at the recombination junction between the human and hamster chromosomes. Since elevated levels of endogenous breaks were not detected in unstable clones we propose that epigenetic or bystander effects (BSEs) lead to the activation of recombinational pathways that perpetuate the unstable phenotype. Specifically, we expand upon the hypothesis that radiation induces conditions and/or factors that stimulate the production of reactive oxygen species (ROS). These reactive intermediates then contribute to a chronic pro-oxidant environment that cycles over multiple generations, promoting chromosomal recombination and other phenotypes associated with genomic instability.

  9. Spontaneous generation of pure ice streams via flow instability: Role of longitudinal shear stresses and subglacial till

    NASA Astrophysics Data System (ADS)

    Sayag, Roiy; Tziperman, Eli

    2008-05-01

    A significant portion of the ice discharge in ice sheets is drained through ice streams, with subglacial sediment (till) acting as a lubricant. The known importance of horizontal friction in shear margins to ice stream dynamics suggests a critical role of longitudinal stresses. The effects of subglacial till and longitudinal stresses on the stability of an ice sheet flow are studied by linear stability analysis of an idealized ice-till model in two horizontal dimensions. A power law-viscous constitutive relation is used, explicitly including longitudinal shear stresses. The till, which has compressible viscous rheology, affects the ice flow through bottom friction. We examine the possibility that pure ice streams develop via a spontaneous instability of ice flow. We demonstrate that this model can be made intrinsically unstable for a seemingly relevant range of parameters and that the wavelengths and growth rates that correspond to the most unstable modes are in rough agreement with observed pure ice streams. Instabilities occur owing to basal friction and meltwater production at the ice-till interface. The most unstable wavelength arise because of selective dissipation of both short and long perturbation scales. Longitudinal stress gradients stabilize short transverse wavelengths, while Nye diffusion stabilizes long transverse wavelengths. The selection of an intermediate unstable wavelength occurs, however, only for certain parameter and perturbation structure choices. These results do not change qualitatively for a Newtonian ice flow law, indicating no significant role to shear thinning, although this may very well be due to the restrictive assumptions of the model and analysis.

  10. Hybrid simulation of the Z-pinch instabilities for profiles generated during wire array implosion in the Saturn pulsed power generator

    SciTech Connect

    Sotnikov, V.I.; Leboeuf, J.N.; Deeney, C.; Coverdale, C.A.; Hellinger, P.; Travnicek, P.; Fiala, V.

    2005-09-15

    Experimental evidence suggests that the energy balance between processes in play during wire array implosions is not well understood. In fact the radiative yields can exceed by several times the implosion kinetic energy. A possible explanation is that the coupling from magnetic energy to kinetic energy as magnetohydrodynamic plasma instabilities develop provides additional energy. It is thus important to model the instabilities produced in the after implosion stage of the wire array in order to determine how the stored magnetic energy can be connected with the radiative yields. To this aim three-dimensional hybrid simulations have been performed. They are initialized with plasma radial density profiles, deduced in recent experiments [C. Deeney et al., Phys. Plasmas 6, 3576 (1999)] that exhibited large x-ray yields, together with the corresponding magnetic field profiles. Unlike previous work, these profiles do not satisfy pressure balance and differ substantially from those of a Bennett equilibrium. They result in faster growth with an associated transfer of magnetic energy to plasma motion and hence kinetic energy.

  11. Hybrid simulation of the Z-pinch instabilities for profiles generated in the process of wire array implosion in the Saturn pulsed power generator.

    SciTech Connect

    Coverdale, Christine Anne; Travnicek, P.; Hellinger, P.; Fiala, V.; Leboeuf, J. N.; Deeney, Christopher; Sotnikov, Vladimir Isaakovich

    2005-02-01

    Experimental evidence suggests that the energy balance between processes in play during wire array implosions is not well understood. In fact the radiative yields can exceed by several times the implosion kinetic energy. A possible explanation is that the coupling from magnetic energy to kinetic energy as magnetohydrodynamic plasma instabilities develop provides additional energy. It is thus important to model the instabilities produced in the after implosion stage of the wire array in order to determine how the stored magnetic energy can be connected with the radiative yields. To this aim three-dimensional hybrid simulations have been performed. They are initialized with plasma radial density profiles, deduced in recent experiments [C. Deeney et al., Phys. Plasmas 6, 3576 (1999)] that exhibited large x-ray yields, together with the corresponding magnetic field profiles. Unlike previous work, these profiles do not satisfy pressure balance and differ substantially from those of a Bennett equilibrium. They result in faster growth with an associated transfer of magnetic energy to plasma motion and hence kinetic energy.

  12. Collective instabilities

    SciTech Connect

    K.Y. Ng

    2003-08-25

    The lecture covers mainly Sections 2.VIII and 3.VII of the book ''Accelerator Physics'' by S.Y. Lee, plus mode-coupling instabilities and chromaticity-driven head-tail instability. Besides giving more detailed derivation of many equations, simple interpretations of many collective instabilities are included with the intention that the phenomena can be understood more easily without going into too much mathematics. The notations of Lee's book as well as the e{sup jwt} convention are followed.

  13. Quantification of the internal quantum efficiency in GaN via analysis of the heat generated by non-radiative recombination processes

    SciTech Connect

    Kawakami, Yoichi Inoue, Kohei; Kaneta, Akio; Funato, Mitsuru; Okamoto, Koichi

    2015-03-14

    The internal quantum efficiency (IQE) in a GaN epilayer is quantified using transient lens (TL) spectroscopy and numerical simulations. TL spectroscopy can optically detect temperature and carrier changes induced in a photo-pumped GaN layer, and the observed temperature change is closely associated with non-radiative recombination processes that create heat. Then numerically solving diffusion equations, which represent the diffusion processes of the photo-generated heat and carriers, provide the spatiotemporal distributions. These distributions are subsequently converted into the refractive index distributions, which act as transient convex or concave lenses. Finally, ray-tracing simulations predict the TL signals. Comparing the experimentally obtained and simulated TL signals quantifies the generated heat and the IQE without the often-adopted assumption that non-radiative recombination processes are negligible at low temperatures.

  14. Simulation of ultraviolet- and soft X-ray-pulse generation as a result of cooperative recombination of excitons in diamond nanocrystals embedded in a polymer film

    SciTech Connect

    Kukushkin, V. A.

    2013-11-15

    Using numerical simulation, it is shown that the recombination of free excitons photoexcited in diamond nanocrystals embedded in a polymer film can occur in the cooperative mode. It is found that this mode can be implemented despite the fact that diamond is an 'indirect' semiconductor. It is shown that the power of the generated radiation at the pulse peak during the cooperative recombination of free excitons can exceed that of the incoherent spontaneous emission of the same initial number of free excitons by more than an order of magnitude. Finally, it is shown that the process under consideration can be used to generate picosecond pulses of ultraviolet and soft X-ray electromagnetic field at a wavelength of 235 nm.

  15. The extent and position of homoeologous recombination in a distant hybrid of Alstroemeria: a molecular cytogenetic assessment of first generation backcross progenies.

    PubMed

    Kamstra, S A; Kuipers, A G; De Jeu, M J; Ramanna, M S; Jacobsen, E

    1999-04-01

    To estimate the extent and position of homoeologous recombination during meiosis in an interspecific hybrid between two distantly related Alstroemeria species, the chromosome constitution of six first generation backcross (BC1) plants was analysed using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) analysis. Four different probes were used for the FISH analysis: two species-specific and two rDNA probes. The six BC1 plants were obtained from crosses between the hybrid A. aurea x A. inodora with its parent A. inodora. GISH clearly identified all chromosomes of both parental genomes as well as recombinant chromosomes. The sequential GISH and FISH analysis enabled the accurate identification of all individual chromosomes in the BC1 plants, resulting in the construction of detailed karyotypes of the plants. The identification of the recombinant chromosomes provided evidence which chromosomes of the two species are homoeologous. Two of the BC1 plants were aneuploid (2n=2x+1=17) and four triploid (2n=3x=24), indicating that both n and 2n gametes were functional in the F1 hybrid. Using GISH, it was possible to estimate homeologous recombination in two different types of gametes in the F1 hyrid. The positions of the crossover points ranged from highly proximal to distal and the maximum number of crossover points per chromosome arm was three. Compared with the aneuploid plants, the triploid plants (which received 2n gametes) clearly possessed fewer crossovers per chromosome, indicating reduced chromosome pairing/recombination prior to the formation of the 2n gametes. Besides homeologous recombination, evidence was found for the presence of structural rearrangements (inversion and translocation) between the chromosomes of the parental species. The presence of the ancient translocation was confirmed through FISH analysis of mitotic and meiotic chromosomes.

  16. Production of Ca(2+)-Independent and Acidstable Recombinant α-Amylase of Bacillus acidicola Extracellularly and its Applicability in Generating Maltooligosaccharides.

    PubMed

    Parashar, Deepak; Satyanarayana, T

    2016-11-01

    The recombinant acidstable α-amylase (Ba-amy) of acidophilic bacterium Bacillus acidicola TSAS1 has been produced extracellularly using a combination of cloning (E. coli and P. pastoris) and physico-chemical treatment strategies. A total of 150,000 U/L of Ba-amy were attained under constitutive promoter in P. pastoris, which is 15-fold higher than that of the wild strain B. acidicola (10,000 U/L). The recombinant P. pastoris integrated two copies of Ba-amy under GAP promoter. The pure Ba-amy expressed in P. pastoris is a glycoprotein of 66 kDa, which is optimally active at pH 4.0 and 60 °C with a T 1/2 of 25 min at 70 °C. The K m, V max and K cat values of the recombinant Ba-amy are 1.66 mg/mL, 53.6 µmol/mg/min and 106.8/s, respectively. The enzyme generates maltose (30 %), maltotriose (20 %) and other higher maltooligosaccharides from starch, thus, useful in baking as an antistale. This is the first report on the optimization of extracellular production of recombinant acidic α-amylase of an acidophilic bacterium.

  17. Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof

    PubMed Central

    Nolden, T.; Pfaff, F.; Nemitz, S.; Freuling, C. M.; Höper, D.; Müller, T.; Finke, Stefan

    2016-01-01

    Reverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache’s reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level. PMID:27046474

  18. Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof.

    PubMed

    Nolden, T; Pfaff, F; Nemitz, S; Freuling, C M; Höper, D; Müller, T; Finke, Stefan

    2016-04-05

    Reverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache's reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level.

  19. Human immunodeficiency virus type 1 drug susceptibility determination by using recombinant viruses generated from patient sera tested in a cell-killing assay.

    PubMed Central

    Boucher, C A; Keulen, W; van Bommel, T; Nijhuis, M; de Jong, D; de Jong, M D; Schipper, P; Back, N K

    1996-01-01

    A simple approach for the determination of drug susceptibilities by using human immunodeficiency virus type 1 (HIV-1) RNA from the sera of patients is described. HIV-1 RNA was extracted from patient sera, and the 5' part of the reverse transcriptase (RT) gene was transcribed into DNA and amplified in a nested PCR. The amplified fragment covers the 3' part of the protease gene and amino acids 1 to 304 of the RT gene. This fragment can be introduced through homologous recombination, as described previously, into a novel HIV-1 reference strain (pHXB2 delta 2-261RT) from which amino acids 2 to 261 of RT have been deleted. The resulting recombinant virus expresses all properties of the HXB2 reference strain except for those encoded by the introduced part of the patient RT gene. Recombinant viruses were subsequently tested for drug susceptibility in a microtiter format killing assay [3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay] as well as in the standard HeLa CD4+ plaque reduction assay. Similar susceptibility profiles were obtained by each assay with recombinant viruses derived from patients receiving alternating nevirapine and zidovudine treatment or lamivudine-zidovudine combination therapy. In conclusion, this approach enables high-through-put determination of the drug susceptibilities of serum RNA-derived RT genes, independent of the patient's viral background, and generates the possibility of relating changes in susceptibility to changes in viral genotypes. PMID:8891152

  20. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

    SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

  1. Carrier generation, recombination, trapping, and transport in semiconductors with position-dependent composition. [in junction solar cells

    NASA Technical Reports Server (NTRS)

    Sah, C.-T.; Lindholm, F. A.

    1977-01-01

    The spatial variation of the chemical composition of a semiconductor modifies the ideal one-electron energy band model as well as the Shockley equations for carrier recombination and transport in two important ways. The random component of the spatial variation introduces localized states in the energy gap by perturbing the band states. The nonrandom component gives rise to the position dependences of the conduction and valence band edges or the electron affinity and the energy gap. This paper gives the modifications of the Shockley equations from these two effects as well as an example of the steady-state recombination rate from distributed gap states in junction solar cells

  2. Generation and evaluation of a LaSota strain-based recombinant Newcastle disease virus (NDV) expressing the glycoprotein (G) of avian metapneumovirus subgroup C (aMPV-C) as a bivalent vaccine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To develop a bivalent vaccine, a recombinant Newcastle disease virus was generated by using the NDV LaSota strain with insertion of the G gene of aMPV-C. The biological assessments of the recombinant virus, rLS/aMPV-CG, by conducting the mean death time, intracerebral pathogenicity index, and growth...

  3. Understanding the origins of UV-induced recombination through manipulation of sister chromatid cohesion.

    PubMed

    Covo, Shay; Ma, Wenjian; Westmoreland, James W; Gordenin, Dmitry A; Resnick, Michael A

    2012-11-01

    Ultraviolet light (UV) can provoke genome instability, partly through its ability to induce homologous recombination (HR). However, the mechanism(s) of UV-induced recombination is poorly understood. Although double-strand breaks (DSBs) have been invoked, there is little evidence for their generation by UV. Alternatively, single-strand DNA lesions that stall replication forks could provoke recombination. Recent findings suggest efficient initiation of UV-induced recombination in G1 through processing of closely spaced single-strand lesions to DSBs. However, other scenarios are possible, since the recombination initiated in G1 can be completed in the following stages of the cell cycle. We developed a system that could address UV-induced recombination events that start and finish in G2 by manipulating the activity of the sister chromatid cohesion complex. Here we show that sister-chromatid cohesion suppresses UV-induced recombination events that are initiated and resolved in G2. By comparing recombination frequencies and survival between UV and ionizing radiation, we conclude that a substantial portion of UV-induced recombination occurs through DSBs. This notion is supported by a direct physical observation of UV-induced DSBs that are dependent on nucleotide excision repair. However, a significant role of nonDSB intermediates in UV-induced recombination cannot be excluded.

  4. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

    PubMed Central

    Kawakami, Takeshi; Smeds, Linnéa; Backström, Niclas; Husby, Arild; Qvarnström, Anna; Mugal, Carina F; Olason, Pall; Ellegren, Hans

    2014-01-01

    Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes. PMID:24863701

  5. Generation and characterization of a Leishmania tarentolae strain for site-directed in vivo biotinylation of recombinant proteins.

    PubMed

    Klatt, Stephan; Hartl, Daniela; Fauler, Beatrix; Gagoski, Dejan; Castro-Obregón, Susana; Konthur, Zoltán

    2013-12-06

    Leishmania tarentolae is a non-human-pathogenic Leishmania species of growing interest in biotechnology, as it is well-suited for the expression of human recombinant proteins. For many applications it is desirable to express recombinant proteins with a tag allowing easy purification and detection. Hence, we adopted a scheme to express recombinant proteins with a His6-tag and, additionally, to site-specifically in vivo biotinylate them for detection. Biotinylation is a relatively rare modification of endogenous proteins that allows easy detection with negligible cross-reactivity. Here, we established a genetically engineered L. tarentolae strain constitutively expressing the codon-optimized biotin-protein ligase from Escherichia coli (BirA). We thoroughly analyzed the strain for functionality using 2-D polyacrylamide-gel electrophoresis (PAGE), mass spectrometry, and transmission electron microscopy (TEM). We could demonstrate that neither metabolic changes (growth rate) nor structural abnormalities (TEM) occurred. To our knowledge, we show the first 2-D PAGE analyses of L. tarentolae. Our results demonstrate the great benefit of the established L. tarentolae in vivo biotinylation strain for production of dual-tagged recombinant proteins. Additionally, 2-D PAGE and TEM results give insights into the biology of L. tarentolae, helping to better understand Leishmania species. Finally, we envisage that the system is transferable to human-pathogenic species.

  6. The generation of tens kT magnetic fields by transport instability of laser generated electrons in a near critical preformed plasma

    NASA Astrophysics Data System (ADS)

    Toncian, Toma; Hegelich, Bjorn Manuel; Willi, Oswald; Lehmann, Goetz

    2014-10-01

    First direct measurements of the electron transport along extended wire targets by Quinn et al. [PRL 102 (2009)] revealed a charging current and associated magnetic field moving close to the speed of light away from focal volume of the employed heating laser. The motion of the electrons is bound electrostatic to the proximity of the solid. A return current compensating the escaping charge is formed at the surface of the solid, the overall current loop sustaining kT magnetic fields, with traversal decay lengths of μm. In our study we show by means of numerical 2 dimensional particle in cell simulations that the motion of the hot electrons and dynamic of the charge compensating return current can be dramatically affected by a preformed μm scale length plasma gradient on the solid surface. In particularly the two velocities distribution and two antiparallel currents developing in the near critical plasma are unstable in respect of two stream and Kevin Helmholtz instability. The particle motion becomes locally magnetized resulting in current eddies trapping particles and localized magnetic and electric fields with values of tens of kT and TV/m sustained on μm scales and with characteristic decay times of ps.

  7. V(D)J recombination generates a high frequency of nonstandard TCR D[delta]-associated rearrangements in thymocytes

    SciTech Connect

    Carroll, A.M.; Slack, J.K.; Mu, Xiaochun )

    1993-03-15

    The standard products of V(D)J recombination are coding junctions, which encode Ag receptor polypeptide, and their commonly excised reciprocal products, signal junctions. Additional nonstandard products also have been detected, mostly in artificial recombination substrate studies. The occurrence of nonstandard products, including pseudonormal, hybrid, and open/shut junctions, indicates significant indeterminacy of the V(D)J recombinase. However, the incidence of nonstandard products of endogenous Ag receptor genes in vivo has not been specifically addressed. The data presented here show that for the TCR-[delta] locus, D element-associated recombination in mouse thymocytes results in a high incidence of nonstandard recombination products. D[delta]1-D[delta]2 rearrangements, both chromosome retained and excised episomal products, were studied by polymerase chain reaction amplification, cloning, and sequence analysis. The proximity of D[delta]1 and D[delta]2 elements, and the fact that both are flanked by 5[prime] and 3[prime] recombination signal sequences with 12-bp and 23-bp spacers, respectively, results in frequent pseudonormal joining. The resulting products are signal junctions retained on the chromosome. Excised episomal products include coding junctions, hybrid junctions formed in apparent violation of the 12/23 spacer rule, and standard signal junctions; some signal junctions show evidence of imprecise cleavage. Evidence for open/shut and/or oligonucleotide capture events was also seen. Similar rearrangements were detectable in thymocytes of mutant scid mice. These findings indicate a high degree of indeterminancy of V(D)J recombinase-mediated D[delta]1-D[delta]2 rearrangement in both wild-type and scid thymocytes. This indeterminacy affects the productive potential of TCR-[delta] loci. 45 refs., 4 figs.

  8. Slight instability of a FMR-1 allele over three generations in a family from the general population

    SciTech Connect

    Abramowicz, M.J.; Parma, J.; Cochaux, P.

    1996-08-09

    We report on a family segregating a FMR-1 allele within the {open_quotes}grey zone{close_quotes} of triplet repeat length (n = 51). The allele showed a 1-unit increment when transmitted through a female meiosis and a 1-unit increment when transmitted through a male of the next generation. At the following generation, a pregnant woman had amniocentesis performed. The latter showed she transmitted the allele unchanged (n = 53) to her male fetus. This family was not ascertained through an affected subject, and there was no family history of mental retardation. Thus our observation reflects the natural history of an unstable allele in the general population. Systematic analysis of such alleles may help refine our understanding of the grey zone of triplet repeat length. 5 refs., 1 fig.

  9. Characterization of recombinant pectate lyase refolded from inclusion bodies generated in E. coli BL21(DE3).

    PubMed

    Kumar, Sandeep; Jain, Kavish Kumar; Singh, Anupam; Panda, Amulya K; Kuhad, Ramesh Chander

    2015-06-01

    Pectate lyase (EC 4.2.2.2) gene from Bacillus subtilis RCK was cloned and expressed in Escherichia coli to maximize its production. In addition to soluble fraction, bioactive pectate lyase was also obtained from inclusion body aggregates by urea solubilization and refolding under in vitro conditions. Enzyme with specific activity ∼3194IU/mg and ∼1493IU/mg were obtained from soluble and inclusion bodies (IBs) fraction with recovery of 56% and 74% in terms of activity, respectively. The recombinant enzyme was moderately thermostable (t1/2 60min at 50°C) and optimally active in wider alkaline pH range (7.0-10.5). Interaction of protein with its cofactor CaCl2 was found to stimulate the change in tertiary structure as revealed by near UV CD spectra. Intrinsic tryptophan fluorescence spectra indicated that tryptophan is involved in substrate binding and there might be independent binding of Ca(2+) and polygalacturonic acid to the active site. The recombinant enzyme was found to be capable of degrading pectin and polygalacturonic acid. The work reports novel conditions for refolding to obtain active recombinant pectate lyase from inclusion bodies and elucidates the effect of ligand and substrate binding on protein conformation by circular dichroism (CD) and fluorescence spectrofluorometry.

  10. Study of cavitating inducer instabilities

    NASA Technical Reports Server (NTRS)

    Young, W. E.; Murphy, R.; Reddecliff, J. M.

    1972-01-01

    An analytic and experimental investigation into the causes and mechanisms of cavitating inducer instabilities was conducted. Hydrofoil cascade tests were performed, during which cavity sizes were measured. The measured data were used, along with inducer data and potential flow predictions, to refine an analysis for the prediction of inducer blade suction surface cavitation cavity volume. Cavity volume predictions were incorporated into a linearized system model, and instability predictions for an inducer water test loop were generated. Inducer tests were conducted and instability predictions correlated favorably with measured instability data.

  11. The rapid generation of recombinant functional monoclonal antibodies from individual, antigen-specific bone marrow-derived plasma cells isolated using a novel fluorescence-based method

    PubMed Central

    Clargo, Alison M; Hudson, Ashley R; Ndlovu, Welcome; Wootton, Rebecca J; Cremin, Louise A; O'Dowd, Victoria L; Nowosad, Carla R; Starkie, Dale O; Shaw, Sophie P; Compson, Joanne E; White, Dominic P; MacKenzie, Brendon; Snowden, James R; Newnham, Laura E; Wright, Michael; Stephens, Paul E; Griffiths, Meryn R; Lawson, Alastair DG; Lightwood, Daniel J

    2014-01-01

    Single B cell technologies, which avoid traditional hybridoma fusion and combinatorial display, provide a means to interrogate the naturally-selected antibody repertoire of immunized animals. Many methods enable the sampling of memory B cell subsets, but few allow for the direct interrogation of the plasma cell repertoire, i.e., the subset of B cells responsible for producing immunoglobulin in serum. Here, we describe the use of a robust and simple fluorescence-based technique, called the fluorescent foci method, for the identification and isolation of antigen-specific IgG-secreting cells, such as plasma cells, from heterogeneous bone marrow preparations. Following micromanipulation of single cells, cognate pairs of heavy and light chain variable region genes were recovered by reverse transcription (RT)-polymerase chain reaction (PCR). During the PCR, variable regions were combined with a promoter fragment and a relevant constant region fragment to produce two separate transcriptionally-active PCR (TAP) fragments that were directly co-transfected into a HEK-293F cell line for recombinant antibody expression. The technique was successfully applied to the generation of a diverse panel of high-affinity, functional recombinant antibodies to human tumor necrosis factor (TNF) receptor 2 and TNF derived from the bone marrow of immunized rabbits and rats, respectively. Progression from a bone marrow sample to a panel of functional recombinant antibodies was possible within a 2-week timeframe. PMID:24423622

  12. Dislocation motion and instability

    NASA Astrophysics Data System (ADS)

    Zhu, Yichao; Chapman, Stephen Jonathan; Acharya, Amit

    2013-08-01

    The Peach-Koehler expression for the stress generated by a single (non-planar) curvilinear dislocation is evaluated to calculate the dislocation self stress. This is combined with a law of motion to give the self-induced motion of a general dislocation curve. A stability analysis of a rectilinear, uniformly translating dislocation is then performed. The dislocation is found to be susceptible to a helical instability, with the maximum growth rate occurring when the dislocation is almost, but not exactly, pure screw. The non-linear evolution of the instability is determined numerically, and implications for slip band formation and non-Schmid behavior in yielding are discussed.

  13. Effect of monovalent cations and G-quadruplex structures on the outcome of intramolecular homologous recombination.

    PubMed

    Barros, Paula; Boán, Francisco; Blanco, Miguel G; Gómez-Márquez, Jaime

    2009-06-01

    Homologous recombination is a very important cellular process, as it provides a major pathway for the repair of DNA double-strand breaks. This complex process is affected by many factors within cells. Here, we have studied the effect of monovalent cations (K+, Na+, and NH4+) on the outcome of recombination events, as their presence affects the biochemical activities of the proteins involved in recombination as well as the structure of DNA. For this purpose, we used an in vitro recombination system that includes a protein nuclear extract, as a source of recombination machinery, and two plasmids as substrates for intramolecular homologous recombination, each with two copies of different alleles of the human minisatellite MsH43. We found that the presence of monovalent cations induced a decrease in the recombination frequency, accompanied by an increase in the fidelity of the recombination. Moreover, there is an emerging consensus that secondary structures of DNA have the potential to induce genomic instability. Therefore, we analyzed the effect of the sequences capable of forming G-quadruplex on the production of recombinant molecules, taking advantage of the capacity of some MsH43 alleles to generate these kinds of structure in the presence of K+. We observed that the MsH43 recombinants containing duplications, generated in the presence of K+, did not include the repeats located towards the 5'-side of the G-quadruplex motif, suggesting that this structure may be involved in the recombination events leading to duplications. Our results provide new insights into the molecular mechanisms underlying the recombination of repetitive sequences.

  14. Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities

    NASA Astrophysics Data System (ADS)

    Drouot, T.; Gravier, E.; Reveille, T.; Collard, M.

    2015-10-01

    This paper presents a study of zonal flows generated by trapped-electron mode and trapped-ion mode micro turbulence as a function of two plasma parameters—banana width and electron temperature. For this purpose, a gyrokinetic code considering only trapped particles is used. First, an analytical equation giving the predicted level of zonal flows is derived from the quasi-neutrality equation of our model, as a function of the density fluctuation levels and the banana widths. Then, the influence of the banana width on the number of zonal flows occurring in the system is studied using the gyrokinetic code. Finally, the impact of the temperature ratio Te/Ti on the reduction of zonal flows is shown and a close link is highlighted between reduction and different gyro-and-bounce-average ion and electron density fluctuation levels. This reduction is found to be due to the amplitudes of gyro-and-bounce-average density perturbations ne and ni gradually becoming closer, which is in agreement with the analytical results given by the quasi-neutrality equation.

  15. Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities

    SciTech Connect

    Drouot, T.; Gravier, E.; Reveille, T.; Collard, M.

    2015-10-15

    This paper presents a study of zonal flows generated by trapped-electron mode and trapped-ion mode micro turbulence as a function of two plasma parameters—banana width and electron temperature. For this purpose, a gyrokinetic code considering only trapped particles is used. First, an analytical equation giving the predicted level of zonal flows is derived from the quasi-neutrality equation of our model, as a function of the density fluctuation levels and the banana widths. Then, the influence of the banana width on the number of zonal flows occurring in the system is studied using the gyrokinetic code. Finally, the impact of the temperature ratio T{sub e}/T{sub i} on the reduction of zonal flows is shown and a close link is highlighted between reduction and different gyro-and-bounce-average ion and electron density fluctuation levels. This reduction is found to be due to the amplitudes of gyro-and-bounce-average density perturbations n{sub e} and n{sub i} gradually becoming closer, which is in agreement with the analytical results given by the quasi-neutrality equation.

  16. Immunogenicity of next-generation HPV vaccines in non-human primates: Measles-vectored HPV vaccine versus Pichia pastoris recombinant protein vaccine.

    PubMed

    Gupta, Gaurav; Giannino, Viviana; Rishi, Narayan; Glueck, Reinhard

    2016-09-07

    Human papillomavirus (HPV) infection is the most common sexually transmitted disease worldwide. HPVs are oncogenic small double-stranded DNA viruses that are the primary causal agent of cervical cancer and other types of cancers, including in the anus, oropharynx, vagina, vulva, and penis. Prophylactic vaccination against HPV is an attractive strategy for preventing cervical cancer and some other types of cancers. However, there are few safe and effective vaccines against HPV infections. Current first-generation commercial HPV vaccines are expensive to produce and deliver. The goal of this study was to develop an alternate potent HPV recombinant L1-based vaccines by producing HPV virus-like particles into a vaccine that is currently used worldwide. Live attenuated measles virus (MV) vaccines have a well-established safety and efficacy record, and recombinant MV (rMV) produced by reverse genetics may be useful for generating candidate HPV vaccines to meet the needs of the developing world. We studied in non-human primate rMV-vectored HPV vaccine in parallel with a classical alum adjuvant recombinant HPV16L1 and 18L1 protein vaccine produced in Pichia pastoris. A combined prime-boost approach using both vaccines was evaluated, as well as immune interference due to pre-existing immunity against the MV. The humoral immune response induced by the MV, Pichia-expressed vaccine, and their combination as priming and boosting approaches was found to elicit HPV16L1 and 18L1 specific total IgG and neutralizing antibody titres. Pre-existing antibodies against measles did not prevent the immune response against HPV16L1 and 18L1.

  17. Generation of Recombinant Viral Hemorrhagic Septicemia Virus (rVHSV) Expressing Two Foreign Proteins and Effect of Lengthened Viral Genome on Viral Growth and In Vivo Virulence.

    PubMed

    Kim, Min Sun; Lee, Su Jin; Kim, Dong Soo; Kim, Ki Hong

    2016-04-01

    In this study, a new recombinant VHSV (rVHSV-Arfp-Bgfp) was generated by insertion of a red fluorescent protein (RFP) gene between N and P genes, a green fluorescent protein (GFP) gene between P and M genes of VHSV genome, the expression of each heterologous gene in infected cells, and effects of the lengthened recombinant VHSV's genome on the replication ability and in vivo virulence to olive flounder (Paralichthys olivaceus) fingerlings were compared with previously generated rVHSVs (rVHSV-wild, rVHSV-Arfp, and rVHSV-Brfp). The expression of RFP and GFP in cells infected with rVHSV-Arfp-Bgfp was verified through fluorescent microscopy and FACS analysis. In the viral growth analysis, rVHSV-Arfp and rVHSV-Brfp showed significantly lower viral titers than rVHSV-wild, and the replication of rVHSV-Arfp-Bgfp was significantly decreased compared to that of even rVHSV-Arfp or rVHSV-Brfp. These results suggest that the genome length is a critical factor for the determination of rVHSVs replication efficiency. In the in vivo virulence experiment, the cumulative mortalities of olive flounder fingerlings infected with each rVHSV were inversely proportional to the length of the viral genome, suggesting that decreased viral growth rate due to the lengthened viral genome is accompanied with the decrease of in vivo virulence of rVHSVs. Recombinant viruses expressing multiple foreign antigens can be used for the development of combined vaccines. However, as the present rVHSV-Arfp-Bgfp still possesses an ability to kill hosts (although very weakened), researches on the producing more attenuated viruses or propagation-deficient replicon particles are needed to solve safety-related problems.

  18. Recombinant Pvs48/45 Antigen Expressed in E. coli Generates Antibodies that Block Malaria Transmission in Anopheles albimanus Mosquitoes

    PubMed Central

    Arévalo-Herrera, Myriam; Vallejo, Andrés F.; Rubiano, Kelly; Solarte, Yezid; Marin, Catherin; Castellanos, Angélica; Céspedes, Nora; Herrera, Sócrates

    2015-01-01

    Transmission of malaria parasites from humans to Anopheles mosquitoes can be inhibited by specific antibodies elicited during malaria infection, which target surface Plasmodium gametocyte/gamete proteins. Some of these proteins may have potential for vaccine development. Pvs48/45 is a P. vivax gametocyte surface antigen orthologous to Pfs48/45, which may play a role during parasite fertilization and thus has potential for transmission blocking (TB) activity. Here we describe the expression of a recombinant Pvs48/45 protein expressed in Escherichia coli as a ∼60kDa construct which we tested for antigenicity using human sera and for its immunogenicity and transmission blocking activity of specific anti-mouse and anti-monkey Pvs48/45 antibodies. The protein reacted with sera of individuals from malaria-endemic areas and in addition induced specific IgG antibody responses in BALB/c mice and Aotus l. griseimembra monkeys. Sera from both immunized animal species recognized native P. vivax protein in Western blot (WB) and immunofluorescence assays. Moreover, sera from immunized mice and monkeys produced significant inhibition of parasite transmission to An. Albimanus mosquitoes as shown by membrane feeding assays. Results indicate the presence of reactive epitopes in the Pvs48/45 recombinant product that induce antibodies with TB activity. Further testing of this protein is ongoing to determine its vaccine potential. PMID:25775466

  19. A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy.

    PubMed

    Dong, Biao; Moore, Andrea R; Dai, Jihong; Roberts, Sean; Chu, Kirk; Kapranov, Philipp; Moss, Bernard; Xiao, Weidong

    2013-07-01

    Scalable and efficient production of high-quality recombinant adeno-associated virus (rAAV) for gene therapy remains a challenge despite recent clinical successes. We developed a new strategy for scalable and efficient rAAV production by sequestering the AAV helper genes and the rAAV vector DNA in two different subcellular compartments, made possible by using cytoplasmic vaccinia virus as a carrier for the AAV helper genes. For the first time, the contamination of replication-competent AAV particles (rcAAV) can be completely eliminated in theory by avoiding ubiquitous nonhomologous recombination. Vector DNA can be integrated into the host genomes or delivered by a nuclear targeting vector such as adenovirus. In suspension HeLa cells, the achieved vector yield per cell is similar to that from traditional triple-plasmid transfection method. The rcAAV contamination was undetectable at the limit of our assay. Furthermore, this new concept can be used not only for production of rAAV, but also for other DNA vectors.

  20. Recombinant Pvs48/45 antigen expressed in E. coli generates antibodies that block malaria transmission in Anopheles albimanus mosquitoes.

    PubMed

    Arévalo-Herrera, Myriam; Vallejo, Andrés F; Rubiano, Kelly; Solarte, Yezid; Marin, Catherin; Castellanos, Angélica; Céspedes, Nora; Herrera, Sócrates

    2015-01-01

    Transmission of malaria parasites from humans to Anopheles mosquitoes can be inhibited by specific antibodies elicited during malaria infection, which target surface Plasmodium gametocyte/gamete proteins. Some of these proteins may have potential for vaccine development. Pvs48/45 is a P. vivax gametocyte surface antigen orthologous to Pfs48/45, which may play a role during parasite fertilization and thus has potential for transmission blocking (TB) activity. Here we describe the expression of a recombinant Pvs48/45 protein expressed in Escherichia coli as a ∼60kDa construct which we tested for antigenicity using human sera and for its immunogenicity and transmission blocking activity of specific anti-mouse and anti-monkey Pvs48/45 antibodies. The protein reacted with sera of individuals from malaria-endemic areas and in addition induced specific IgG antibody responses in BALB/c mice and Aotus l. griseimembra monkeys. Sera from both immunized animal species recognized native P. vivax protein in Western blot (WB) and immunofluorescence assays. Moreover, sera from immunized mice and monkeys produced significant inhibition of parasite transmission to An. Albimanus mosquitoes as shown by membrane feeding assays. Results indicate the presence of reactive epitopes in the Pvs48/45 recombinant product that induce antibodies with TB activity. Further testing of this protein is ongoing to determine its vaccine potential.

  1. Generation and Characterization of Six Recombinant Botulinum Neurotoxins as Reference Material to Serve in an International Proficiency Test.

    PubMed

    Weisemann, Jasmin; Krez, Nadja; Fiebig, Uwe; Worbs, Sylvia; Skiba, Martin; Endermann, Tanja; Dorner, Martin B; Bergström, Tomas; Muñoz, Amalia; Zegers, Ingrid; Müller, Christian; Jenkinson, Stephen P; Avondet, Marc-Andre; Delbrassinne, Laurence; Denayer, Sarah; Zeleny, Reinhard; Schimmel, Heinz; Åstot, Crister; Dorner, Brigitte G; Rummel, Andreas

    2015-11-26

    The detection and identification of botulinum neurotoxins (BoNT) is complex due to the existence of seven serotypes, derived mosaic toxins and more than 40 subtypes. Expert laboratories currently use different technical approaches to detect, identify and quantify BoNT, but due to the lack of (certified) reference materials, analytical results can hardly be compared. In this study, the six BoNT/A1-F1 prototypes were successfully produced by recombinant techniques, facilitating handling, as well as improving purity, yield, reproducibility and biosafety. All six BoNTs were quantitatively nicked into active di-chain toxins linked by a disulfide bridge. The materials were thoroughly characterized with respect to purity, identity, protein concentration, catalytic and biological activities. For BoNT/A₁, B₁ and E₁, serotypes pathogenic to humans, the catalytic activity and the precise protein concentration were determined by Endopep-mass spectrometry and validated amino acid analysis, respectively. In addition, BoNT/A₁, B₁, E₁ and F₁ were successfully detected by immunological assays, unambiguously identified by mass spectrometric-based methods, and their specific activities were assigned by the mouse LD50 bioassay. The potencies of all six BoNT/A1-F1 were quantified by the ex vivo mouse phrenic nerve hemidiaphragm assay, allowing a direct comparison. In conclusion, highly pure recombinant BoNT reference materials were produced, thoroughly characterized and employed as spiking material in a worldwide BoNT proficiency test organized by the EQuATox consortium.

  2. Generation of high-titre virus stocks using BrK.219, a B-cell line infected stably with recombinant Kaposi's sarcoma-associated herpesvirus.

    PubMed

    Kati, Semra; Hage, Elias; Mynarek, Martin; Ganzenmueller, Tina; Indenbirken, Daniela; Grundhoff, Adam; Schulz, Thomas F

    2015-06-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2-lymphotropic human oncogenic herpesvirus associated with Kaposi's sarcoma (KS) and two B-cell lymphoproliferative diseases, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). KSHV establishes latency soon after infection in vivo and in vitro. Consequently, it is technically difficult to generate high-titre virus stocks required for infection experiments in tissue culture. Currently used methods of KSHV stock production involve induction of the lytic/productive cycle in PEL cell lines or in adherent cell lines harbouring recombinant KSHV genomes. In this study, the BJAB-derived B-cell line BrK.219, which is infected latently with a recombinant KSHV (rKSHV.219), is used to produce high-titre virus stocks. BrK.219 cells enter the lytic KSHV replication cycle upon cross-linking of B-cell receptors (BCRs) with anti-IgM antibodies without the need for additional, potentially toxic chemical inducers. High cell concentrations can be cultured and induced easily in spinner flasks, saving time and resources. The established protocol allows the generation of KSHV virus stocks with titres of up to 10(6) IU/ml in unconcentrated culture supernatants, representing a 10(3)-10(4)-fold improvement compared to conventional methods.

  3. Study of shock waves generation, hot electron production and role of parametric instabilities in an intensity regime relevant for the shock ignition

    NASA Astrophysics Data System (ADS)

    Antonelli, L.; Köster, P.; Folpini, G.; Maheut, Y.; Baffigi, F.; Cristoforetti, G.; Labate, L.; Levato, T.; Gizzi, L. A.; Consoli, F.; De Angelis, R.; Kalinowska, Z.; Chodukowski, T.; Rosinski, M.; Parys, P.; Pisarczyk, T.; Raczka, P.; Ryc, L.; Badziak, J.; Wolowski, J.; Smid, M.; Renner, O.; Krousky, E.; Pfeifer, M.; Skala, J.; Ullschmied, J.; Nicolaï, P.; Ribeyre, X.; Shurtz, G.; Atzeni, S.; Marocchino, A.; Schiavi, A.; Spindloe, C.; Dell, T. O.; Rhee, Y. J.; Richetta, M.; Batani, D.

    2016-03-01

    We present experimental results at intensities relevant to Shock Ignition obtained at the sub-ns Prague Asterix Laser System in 2012. We studied shock waves produced by laser-matter interaction in presence of a pre-plasma. We used a first beam at 1ω (1315 nm) at 7 x 1013 W/cm2 to create a pre-plasma on the front side of the target and a second at 3ω (438 nm) at ∼ 1016 W/cm2 to create the shock wave. Multilayer targets composed of 25 (or 40 µm) of plastic (doped with Cl), 5 µm of Cu (for Kα diagnostics) and 20 µm of Al for shock measurement were used. We used X-ray spectroscopy of Cl to evaluate the plasma temperature, Kα imaging and spectroscopy to evaluate spatial and spectral properties of the fast electrons and a streak camera for shock breakout measurements. Parametric instabilities (Stimulated Raman Scattering, Stimulated Brillouin Scattering and Two Plasmon Decay) were studied by collecting the back scattered light and analysing its spectrum. Back scattered energy was measured with calorimeters. To evaluate the maximum pressure reached in our experiment we performed hydro simulations with CHIC and DUED codes. The maximum shock pressure generated in our experiment at the front side of the target during laser-interaction is 90 Mbar. The conversion efficiency into hot electrons was estimated to be of the order of ∼ 0.1% and their mean energy in the order ∼50 keV.

  4. Characterization of ectromelia virus deficient in EVM036, the homolog of vaccinia virus F13L, and its application for rapid generation of recombinant viruses.

    PubMed

    Roscoe, Felicia; Xu, Ren-Huan; Sigal, Luis J

    2012-12-01

    The orthopoxvirus (OPV) vaccinia virus (VACV) requires an intact F13L gene to produce enveloped virions (EV) and to form plaques in cell monolayers. Simultaneous introduction of an exogenous gene and F13L into F13L-deficient VACV results in expression of the foreign gene and restoration of plaque size. This is used as a method to rapidly generate VACV recombinants without the need for drug selection. However, whether other OPVs require the orthologs of F13L to generate EV and form plaques, whether F13L orthologs and EV are important for OPV pathogenesis in natural hosts, and whether a system based on F13L ortholog deficiency can be used to generate recombinant OPVs other than VACV have not been reported. The F13L ortholog in ectromelia virus (ECTV), the agent of mousepox, is EVM036. We show that ECTV lacking EVM036 formed small plaques and was highly attenuated in vivo but still induced strong antibody responses. Reintroduction of EVM036 in tandem with the DsRed gene resulted in a virus that expressed DsRed in infected cells but was indistinguishable from wild-type ECTV in terms of plaque size and in vivo virulence. Thus, our data show that, like F13L in VACV, EVM036 is required for ECTV plaque formation and that EVM036 and EV are important for ECTV virulence. Our experiments also suggest that OPVs deficient in F13L orthologs could serve as safer anti-OPV vaccines. Further, our results demonstrate that ECTV deficient in EVM036 can be exploited for the rapid generation of fully virulent ECTV expressing foreign genes of interest.

  5. Inhibition of telomere recombination by inactivation of KEOPS subunit Cgi121 promotes cell longevity.

    PubMed

    Peng, Jing; He, Ming-Hong; Duan, Yi-Ming; Liu, Yu-Ting; Zhou, Jin-Qiu

    2015-03-01

    DNA double strand break (DSB) is one of the major damages that cause genome instability and cellular aging. The homologous recombination (HR)-mediated repair of DSBs plays an essential role in assurance of genome stability and cell longevity. Telomeres resemble DSBs and are competent for HR. Here we show that in budding yeast Saccharomyces cerevisiae telomere recombination elicits genome instability and accelerates cellular aging. Inactivation of KEOPS subunit Cgi121 specifically inhibits telomere recombination, and significantly extends cell longevity in both telomerase-positive and pre-senescing telomerase-negative cells. Deletion of CGI121 in the short-lived yku80(tel) mutant restores lifespan to cgi121Δ level, supporting the function of Cgi121 in telomeric single-stranded DNA generation and thus in promotion of telomere recombination. Strikingly, inhibition of telomere recombination is able to further slow down the aging process in long-lived fob1Δ cells, in which rDNA recombination is restrained. Our study indicates that HR activity at telomeres interferes with telomerase to pose a negative impact on cellular longevity.

  6. Generation and Characterization of Six Recombinant Botulinum Neurotoxins as Reference Material to Serve in an International Proficiency Test

    PubMed Central

    Weisemann, Jasmin; Krez, Nadja; Fiebig, Uwe; Worbs, Sylvia; Skiba, Martin; Endermann, Tanja; Dorner, Martin B.; Bergström, Tomas; Muñoz, Amalia; Zegers, Ingrid; Müller, Christian; Jenkinson, Stephen P.; Avondet, Marc-Andre; Delbrassinne, Laurence; Denayer, Sarah; Zeleny, Reinhard; Schimmel, Heinz; Åstot, Crister; Dorner, Brigitte G.; Rummel, Andreas

    2015-01-01

    The detection and identification of botulinum neurotoxins (BoNT) is complex due to the existence of seven serotypes, derived mosaic toxins and more than 40 subtypes. Expert laboratories currently use different technical approaches to detect, identify and quantify BoNT, but due to the lack of (certified) reference materials, analytical results can hardly be compared. In this study, the six BoNT/A1–F1 prototypes were successfully produced by recombinant techniques, facilitating handling, as well as improving purity, yield, reproducibility and biosafety. All six BoNTs were quantitatively nicked into active di-chain toxins linked by a disulfide bridge. The materials were thoroughly characterized with respect to purity, identity, protein concentration, catalytic and biological activities. For BoNT/A1, B1 and E1, serotypes pathogenic to humans, the catalytic activity and the precise protein concentration were determined by Endopep-mass spectrometry and validated amino acid analysis, respectively. In addition, BoNT/A1, B1, E1 and F1 were successfully detected by immunological assays, unambiguously identified by mass spectrometric-based methods, and their specific activities were assigned by the mouse LD50 bioassay. The potencies of all six BoNT/A1–F1 were quantified by the ex vivo mouse phrenic nerve hemidiaphragm assay, allowing a direct comparison. In conclusion, highly pure recombinant BoNT reference materials were produced, thoroughly characterized and employed as spiking material in a worldwide BoNT proficiency test organized by the EQuATox consortium. PMID:26703728

  7. Ultrafast transient optical studies of charge pair generation and recombination in poly-3-hexylthiophene(P3ht):[6,6]phenyl C61 butyric methyl acid ester (PCBM) blend films.

    PubMed

    Kirkpatrick, James; Keivanidis, Panagiotis E; Bruno, Annalisa; Ma, Fei; Haque, Saif A; Yarstev, Arkady; Sundstrom, Villy; Nelson, Jenny

    2011-12-29

    Charge generation and recombination are studied in blend films of poly-3-hexylthiophene (P3HT) and [6,6']phenyl C61 butyric acid methyl ester (PCBM) using ultrafast transient absorption spectroscopy. We find that the charge generation yield depends upon both blend film composition and thermal annealing. The data suggest that recombination occurs over a wide range of time scales and that, in the least favorable cases, the fastest charge recombination occurs on a time scale similar to exciton diffusion. The results are explained using a simple model that incorporates the effect of P3HT domain size on exciton diffusion and uses empirical models of recombination kinetics. We propose our method as a route to interpretation of spectroscopic data where different processes occur on similar time scales.

  8. Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings.

    PubMed

    Wang, Jianzhong; Cong, Yanlong; Yin, Renfu; Feng, Na; Yang, Songtao; Xia, Xianzhu; Xiao, Yueqiang; Wang, Wenxiu; Liu, Xiufan; Hu, Shunlin; Ding, Chan; Yu, Shengqing; Wang, Chunfeng; Ding, Zhuang

    2015-05-04

    Newcastle disease virus (NDV) and Goose parvovirus (GPV) are considered to be two of the most important and widespread viruses infecting geese. In this study, we generated a recombinant rmNA-VP3, expressing GPV VP3 using a modified goose-origin NDV NA-1 by changing the multi-basic cleavage site motif RRQKR↓F of the F protein to the dibasic motif GRQGR↓L as that of the avirulent strain LaSota as a vaccine vector. Expression of the VP3 protein in rmNA-VP3 infected cells was detected by immunofluorescence and Western blot assay. The genetic stability was examined by serially passaging 10 times in 10-day-old embryonated SPF chicken eggs. Goslings were inoculated with rmNA-VP3 showed no apparent signs of disease and developed a strong GPV and NDV neutralizing antibodies response. This is the first study demonstrating that recombinant NDV has the potential to serve as bivalent live vaccine against Goose parvovirus and Newcastle disease virus infection in birds.

  9. Generation of Newcastle Disease Virus (NDV) Recombinants Expressing the Infectious Laryngotracheitis Virus (ILTV) Glycoprotein gB or gD as Dual Vaccines.

    PubMed

    Zhao, Wei; Spatz, Stephen; Zsak, Laszlo; Yu, Qingzhong

    2016-01-01

    Infectious laryngotracheitis (ILT) is a highly contagious acute respiratory disease of chickens caused by infection with infectious laryngotracheitis virus (ILTV), a member of the family Herpesviridae. The current commercial ILT vaccines are either unsafe or ineffective. Therefore, there is a pressing need to develop safer and more efficacious vaccines. Newcastle disease (ND), caused by infection with Newcastle disease virus (NDV), a member of the family Paramyxoviridae, is one of the most serious infectious diseases of poultry. The NDV LaSota strain, a naturally occurring low-virulence NDV strain, has been routinely used as a live vaccine throughout the world. This chapter describes the generation of Newcastle disease virus (NDV) LaSota vaccine strain-based recombinant viruses expressing glycoprotein B (gB) or glycoprotein D (gD) of ILTV as dual vaccines against ND and ILT using reverse genetics technology.

  10. A novel recombinant Leishmania donovani p45, a partial coding region of methionine aminopeptidase, generates protective immunity by inducing a Th1 stimulatory response against experimental visceral leishmaniasis.

    PubMed

    Gupta, Reema; Kushawaha, Pramod K; Tripathi, Chandra Dev Pati; Sundar, Shyam; Dube, Anuradha

    2012-05-01

    The development of a vaccine against visceral leishmaniasis (VL) conferring long-lasting immunity remains a challenge. Identification and proteomic characterization of parasite proteins led to the detection of p45, a member of the methionine aminopeptidase family. To our knowledge the present study is the first known report that describes the molecular and immunological characterization of p45. Recombinant Leishmania donovani p45 (rLdp45) induced cellular responses in cured hamsters and generated Th1-type cytokines from peripheral blood mononuclear cells of cured/endemic VL patients. Immunization with rLdp45 exerted considerable prophylactic efficacy (∼85%) supported by an increase in mRNA expression of iNOS, IFN-γ, TNF-α and IL-12 and decrease in TGF-β and IL-4, indicating its potential as a vaccine candidate against VL.

  11. A Method for the Generation of Ectromelia Virus (ECTV) Recombinants: In Vivo Analysis of ECTV vCD30 Deletion Mutants

    PubMed Central

    Alejo, Ali; Saraiva, Margarida; Ruiz-Argüello, Maria Begoña; Viejo-Borbolla, Abel; de Marco, Mar Fernández; Salguero, Francisco Javier; Alcami, Antonio

    2009-01-01

    Background Ectromelia virus (ECTV) is the causative agent of mousepox, a lethal disease of mice with similarities to human smallpox. Mousepox progression involves replication at the initial site of infection, usually the skin, followed by a rapid spread to the secondary replicative organs, spleen and liver, and finally a dissemination to the skin, where the typical rash associated with this and other orthopoxviral induced diseases appears. Case fatality rate is genetically determined and reaches up to 100% in susceptible mice strains. Like other poxviruses, ECTV encodes a number of proteins with immunomodulatory potential, whose role in mousepox progression remains largely undescribed. Amongst these is a secreted homologue of the cellular tumour necrosis factor receptor superfamily member CD30 which has been proposed to modulate a Th1 immune response in vivo. Methodology/Principal Findings To evaluate the contribution of viral CD30 (vCD30) to virus pathogenesis in the infected host, we have adapted a novel transient dominant method for the selection of recombinant ECTVs. Using this method, we have generated an ECTV vCD30 deletion mutant, its corresponding revertant control virus as well as a virus encoding the extracellular domain of murine CD30. These viruses contain no exogenous marker DNA sequences in their genomes, as opposed to other ECTVs reported up to date. Conclusions/Significance We show that the vCD30 is expressed as a secreted disulfide linked trimer and that the absence of vCD30 does not impair mousepox induced fatality in vivo. Replacement of vCD30 by a secreted version of mouse CD30 caused limited attenuation of ECTV. The recombinant viruses generated may be of use in the study of the role of the cellular CD30-CD30L interaction in the development of the immune response. The method developed might be useful for the construction of ECTV mutants for the study of additional genes. PMID:19365546

  12. Cloning of adeno-associated virus type 4 (AAV4) and generation of recombinant AAV4 particles.

    PubMed Central

    Chiorini, J A; Yang, L; Liu, Y; Safer, B; Kotin, R M

    1997-01-01

    We have cloned and characterized the full-length genome of adeno-associated virus type 4 (AAV4). The genome of AAV4 is 4,767 nucleotides in length and contains an expanded p5 promoter region compared to AAV2 and AAV3. Within the inverted terminal repeat (ITR), several base changes were identified with respect to AAV2. However, these changes did not affect the ability of this region to fold into a hairpin structure. Within the ITR, the terminal resolution site and Rep binding sites were conserved; however, the Rep binding site was expanded from three GAGC repeats to four. The Rep gene product of AAV4 shows greater than 90% homology to the Rep products of serotypes 2 and 3, with none of the changes occurring in regions which had previously been shown to affect the known functions of Rep68 or Rep78. Most of the differences in the capsid proteins lie in regions which are thought to be on the exterior surface of the viral capsid. It is these unique regions which are most likely to be responsible for the lack of cross-reacting antibodies and the altered tissue tropism compared to AAV2. The results of our studies, performed with a recombinant version of AAV4 carrying a lacZ reporter gene, suggest that AAV4 can transduce human, monkey, and rat cells. Furthermore, comparison of transduction efficiencies in a number of cell lines, competition cotransduction experiments, and the effect of trypsin on transduction efficiency all suggest that the cellular receptor for AAV4 is distinct from that of AAV2. PMID:9261407

  13. Hydrodynamic Instability of Ionization Fronts in HII Regions

    SciTech Connect

    Mizuta, A; Kane, J; Ryutov, D; Remington, B; Takabe, H; Pound, M

    2003-08-21

    The authors investigate hydrodynamic instability of accelerating ionization fronts with two dimensional hydrodynamic simulations. When recombination in the ionized region is turned off, Rayleigh-Taylor instability is effective. Perturbation grows up with classical Rayleigh-Taylor growth rate. In the case with recombination, the local difference of absorption profile works to smooth the surface. The perturbation does not grow and the amplitude follows a damped oscillations with time.

  14. Remarkable stability of an instability-prone lentiviral vector plasmid in Escherichia coli Stbl3.

    PubMed

    Al-Allaf, Faisal A; Tolmachov, Oleg E; Zambetti, Lia Paola; Tchetchelnitski, Viktoria; Mehmet, Huseyin

    2013-02-01

    Large-scale production of plasmid DNA to prepare therapeutic gene vectors or DNA-based vaccines requires a suitable bacterial host, which can stably maintain the plasmid DNA during industrial cultivation. Plasmid loss during bacterial cell divisions and structural changes in the plasmid DNA can dramatically reduce the yield of the desired recombinant plasmid DNA. While generating an HIV-based gene vector containing a bicistronic expression cassette 5'-Olig2cDNA-IRES-dsRed2-3', we encountered plasmid DNA instability, which occurred in homologous recombination deficient recA1 Escherichia coli strain Stbl2 specifically during large-scale bacterial cultivation. Unexpectedly, the new recombinant plasmid was structurally changed or completely lost in 0.5 L liquid cultures but not in the preceding 5 mL cultures. Neither the employment of an array of alternative recA1 E. coli plasmid hosts, nor the lowering of the culture incubation temperature prevented the instability. However, after the introduction of this instability-prone plasmid into the recA13E. coli strain Stbl3, the transformed bacteria grew without being overrun by plasmid-free cells, reduction in the plasmid DNA yield or structural changes in plasmid DNA. Thus, E. coli strain Stbl3 conferred structural and maintenance stability to the otherwise instability-prone lentivirus-based recombinant plasmid, suggesting that this strain can be used for the faithful maintenance of similar stability-compromised plasmids in large-scale bacterial cultivations. In contrast to Stbl2, which is derived wholly from the wild type isolate E. coli K12, E. coli Stbl3 is a hybrid strain of mixed E. coli K12 and E. coli B parentage. Therefore, we speculate that genetic determinants for the benevolent properties of E. coli Stbl3 for safe plasmid propagation originate from its E. coli B ancestor.

  15. Magnetohydrodynamic instability

    NASA Technical Reports Server (NTRS)

    Priest, E. R.; Cargill, P.; Forbes, T. G.; Hood, A. W.; Steinolfson, R. S.

    1986-01-01

    There have been major advances in the theory of magnetic reconnection and of magnetic instability, with important implications for the observations, as follows: (1) Fast and slow magnetic shock waves are produced by the magnetohydrodynamics of reconnection and are potential particle accelerators. (2) The impulsive bursty regime of reconnection gives a rapid release of magnetic energy in a series of bursts. (3) The radiative tearing mode creates cool filamentary structures in the reconnection process. (4) The stability analyses imply that an arcade can become unstable when either its height or twist of plasma pressure become too great.

  16. Gravitational Instabilities in Circumstellar Disks

    NASA Astrophysics Data System (ADS)

    Kratter, Kaitlin; Lodato, Giuseppe

    2016-09-01

    Star and planet formation are the complex outcomes of gravitational collapse and angular momentum transport mediated by protostellar and protoplanetary disks. In this review, we focus on the role of gravitational instability in this process. We begin with a brief overview of the observational evidence for massive disks that might be subject to gravitational instability and then highlight the diverse ways in which the instability manifests itself in protostellar and protoplanetary disks: the generation of spiral arms, small-scale turbulence-like density fluctuations, and fragmentation of the disk itself. We present the analytic theory that describes the linear growth phase of the instability supplemented with a survey of numerical simulations that aim to capture the nonlinear evolution. We emphasize the role of thermodynamics and large-scale infall in controlling the outcome of the instability. Despite apparent controversies in the literature, we show a remarkable level of agreement between analytic predictions and numerical results. In the next part of our review, we focus on the astrophysical consequences of the instability. We show that the disks most likely to be gravitationally unstable are young and relatively massive compared with their host star, Md/M*≥0.1. They will develop quasi-stable spiral arms that process infall from the background cloud. Although instability is less likely at later times, once infall becomes less important, the manifestations of the instability are more varied. In this regime, the disk thermodynamics, often regulated by stellar irradiation, dictates the development and evolution of the instability. In some cases the instability may lead to fragmentation into bound companions. These companions are more likely to be brown dwarfs or stars than planetary mass objects. Finally, we highlight open questions related to the development of a turbulent cascade in thin disks and the role of mode-mode coupling in setting the maximum angular

  17. Generation and Efficacy Evaluation of a Recombinant Pseudorabies Virus Variant Expressing the E2 Protein of Classical Swine Fever Virus in Pigs.

    PubMed

    Wang, Yimin; Yuan, Jin; Cong, Xin; Qin, Hua-Yang; Wang, Chun-Hua; Li, Yongfeng; Li, Su; Luo, Yuzi; Sun, Yuan; Qiu, Hua-Ji

    2015-10-01

    Classical swine fever (CSF) is an economically important infectious disease of pigs caused by classical swine fever virus (CSFV). Pseudorabies (PR), which is caused by pseudorabies virus (PRV), is another important infectious disease of pigs and other animals. Coinfections of pigs with PRV and CSFV occur occasionally in the field. The modified live vaccine Bartha-K61 strain has played an important role in the control of PR in many countries, including China. Since late 2011, however, increasing PR outbreaks caused by an emerging PRV variant have been reported in Bartha-K61-vaccinated swine populations on many farms in China. Previously, we generated a gE/gI-deleted PRV (rPRVTJ-delgE) based on this PRV variant, which was shown to be safe and can provide rapid and complete protection against lethal challenge with the PRV variant in pigs. Here, we generated a new recombinant PRV variant expressing the E2 gene of CSFV (rPRVTJ-delgE/gI-E2) and evaluated its immunogenicity and efficacy in pigs. The results showed that rPRVTJ-delgE/gI-E2 was safe for pigs, induced detectable anti-PRV and anti-CSFV neutralizing antibodies, and provided complete protection against the lethal challenge with either the PRV TJ strain or the CSFV Shimen strain. The data indicate that rPRVTJ-delgE/gI-E2 is a promising candidate bivalent vaccine against PRV and CSFV coinfections.

  18. Spatial fluctuation enhancement and nonradiative-recombination-center generation due to high Si-doping into GaAs/AlAs short-period-superlattices

    NASA Astrophysics Data System (ADS)

    Kobori, H.; Shigetani, A.; Umezu, I.; Sugimura, A.

    2006-04-01

    Through the time-resolved photoluminescence (TR-PL) measurement for excitons, we have studied the enhancement of spatial fluctuation (SF) and the generation of nonradiative-recombination-centers (NRC) due to high Si-doping into GaAs/AlAs short-period-superlattices (SPS's). We have carried out the exciton transport analysis according to Krivorotov et al. [I.N. Krivorotov, T. Chang, G.D. Gilliland, L.P. Fu, K.K. Bajaj, Phys. Rev. B 58 (1998) 10687]. From this analysis, we have obtained the temperature dependence of the exciton diffusivity, the concentration of the NRC and the average distant between adjacent localized states of excitons. The temperature dependence of the exciton diffusivity is found to be given by the sum of the temperature-independent contribution and the activation-type contribution. For the exciton diffusivity in undoped GaAs/AlAs SPS's, only the activation-type contribution has been observed. Therefore, we point out the possibility that the temperature-independent contribution comes from the tunneling through the impurities. In this experiment, the activation energy and the concentration of the NRC are found to be larger than those of undoped GaAs/AlAs SPS's. We infer that high Si-doping into GaAs/AlAs SPS causes the enhancement of the SF and the generation of NRC.

  19. Strategies for selecting recombinant CHO cell lines for cGMP manufacturing: improving the efficiency of cell line generation.

    PubMed

    Porter, Alison J; Racher, Andrew J; Preziosi, Richard; Dickson, Alan J

    2010-01-01

    Transfectants with a wide range of cellular phenotypes are obtained during the process of cell line generation. For the successful manufacture of a therapeutic protein, a means is required to identify a cell line with desirable growth and productivity characteristics from this phenotypically wide-ranging transfectant population. This identification process is on the critical path for first-in-human studies. We have stringently examined a typical selection strategy used to isolate cell lines suitable for cGMP manufacturing. One-hundred and seventy-five transfectants were evaluated as they progressed through the different assessment stages of the selection strategy. High producing cell lines, suitable for cGMP manufacturing, were identified. However, our analyses showed that the frequency of isolation of the highest producing cell lines was low and that ranking positions were not consistent between each assessment stage, suggesting that there is potential to improve upon the strategy. Attempts to increase the frequency of isolation of the 10 highest producing cell lines, by in silico analysis of alternative selection strategies, were unsuccessful. We identified alternative strategies with similar predictive capabilities to the typical selection strategy. One alternate strategy required fewer cell lines to be progressed at the assessment stages but the stochastic nature of the models means that cell line numbers are likely to change between programs. In summary, our studies illuminate the potential for improvement to this and future selection strategies, based around use of assessments that are more informative or that reduce variance, paving the way to improved efficiency of generation of manufacturing cell lines.

  20. Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'-deoxycytidine.

    PubMed

    Ohshima, Motohiro; Tadakuma, Tomomi; Hayashi, Hideki; Inoue, Kazuyuki; Itoh, Kunihiko

    2010-01-01

    We generated a single-chain variable fragment (scFv) against 5-methyl-2'-deoxycytidine (m(5)dCyd) using phage display technology. The heavy and light chain variable region genes were amplified by the polymerase chain reaction (PCR) from hybridoma cell line FMC9 and assembled as an scFv fragment with a flexible linker (Gly(4)-Ser)(3). The scFv DNA fragment was then cloned into pCANTAB-5E, and a phage displaying the scFv was produced. Antigen-positive phage clones were successfully selected by enzyme-linked immunosorbent assay (ELISA). The scFv was modified with FLAG and His tags for detection and purification. The scFv reacted strongly with m(5)dCyd and weakly with 5-methylcytidine (m(5)Cyd) but not with cytidine (Cyd) and 1-methyladenosine in a manner similar to the monoclonal antibody (MoAb). Although the specificities of scFv and MoAb were almost identical, the sensitivity of the scFv (IC(50) 0.054 microg/ml) was approximately 80 times higher than that of the parent MoAb (IC(50) 4.27 microg/ml), determined by inhibition ELISA. As a biochemical application of this scFv, we quantified the m(5)dCyd content of genomic DNA by enzymatic hydrolysis using inhibition ELISA. The cancer cell lines HeLa, HeLa S3 and MDA-MB-453 contained approximately 1% of the methylated DNA in total genomic DNA, as did peripheral blood cell genomic DNA from healthy volunteers, but HT29 and T-47D showed hypomethylation compared with the HeLa, HeLa S3 and MDA-MB-453 cell lines. The scFv generated here may be applicable to the assessment of cellular DNA methylation levels and is more sensitive than the MoAb.

  1. Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae.

    PubMed

    Lindstrom, Derek L; Leverich, Christina K; Henderson, Kiersten A; Gottschling, Daniel E

    2011-03-01

    Somatic mutations contribute to the development of age-associated disease. In earlier work, we found that, at high frequency, aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA, leading to loss of respiration competence and increased loss of heterozygosity (LOH) in the nuclear genome. Here we used the recently developed Mother Enrichment Program to ask whether aging cells that maintain the ability to produce respiration-competent daughters also experience increased genomic instability. We discovered that this population exhibits a distinct genomic instability phenotype that primarily affects the repeated ribosomal RNA gene array (rDNA array). As diploid cells passed their median replicative life span, recombination rates between rDNA arrays on homologous chromosomes progressively increased, resulting in mutational events that generated LOH at >300 contiguous open reading frames on the right arm of chromosome XII. We show that, while these recombination events were dependent on the replication fork block protein Fob1, the aging process that underlies this phenotype is Fob1-independent. Furthermore, we provide evidence that this aging process is not driven by mechanisms that modulate rDNA recombination in young cells, including loss of cohesion within the rDNA array or loss of Sir2 function. Instead, we suggest that the age-associated increase in rDNA recombination is a response to increasing DNA replication stress generated in aging cells.

  2. Generation and evaluation of recombinant Newcastle disease viruses (NDV) expressing the F and G proteins of avian metapneumovirus subtype C (aMPV-C) as bivalent vaccine against NDV and aMPV challenges in turkeys

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously we generated a Newcastle disease virus (NDV) LaSota strain-based recombinant virus expressing the glycoprotein (G) of avian metapneumovirus subgroup C (aMPV-C) as a bivalent vaccine, which provided a partial protection against aMPV-C challenge in turkeys. To improve the vaccine efficacy,...

  3. Evaporative instabilities in climbing films

    NASA Astrophysics Data System (ADS)

    Hosoi, A. E.; Bush, John W. M.

    2001-09-01

    We consider flow in a thin film generated by partially submerging an inclined rigid plate in a reservoir of ethanol or methanol water solution and wetting its surface. Evaporation leads to concentration and surface tension gradients that drive flow up the plate. An experimental study indicates that the climbing film is subject to two distinct instabilities. The first is a convective instability characterized by flattened convection rolls aligned in the direction of flow and accompanied by free-surface deformations; in the meniscus region, this instability gives rise to pronounced ridge structures aligned with the mean flow. The second instability, evident when the plate is nearly vertical, takes the form of transverse surface waves propagating up the plate.

  4. Genetic Recombination

    ERIC Educational Resources Information Center

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

  5. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

    PubMed Central

    Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S.

    2016-01-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  6. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

    PubMed

    Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

    2016-05-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  7. Orientation Dependence in Homologous Recombination

    PubMed Central

    Yamamoto, K.; Takahashi, N.; Fujitani, Y.; Yoshikura, H.; Kobayashi, I.

    1996-01-01

    Homologous recombination was investigated in Escherichia coli with two plasmids, each carrying the homologous region (two defective neo genes, one with an amino-end deletion and the other with a carboxyl-end deletion) in either direct or inverted orientation. Recombination efficiency was measured in recBC sbcBC and recBC sbcA strains in three ways. First, we measured the frequency of cells carrying neo(+) recombinant plasmids in stationary phase. Recombination between direct repeats was much more frequent than between inverted repeats in the recBC sbcBC strain but was equally frequent in the two substrates in the recBC sbcA strain. Second, the fluctuation test was used to exclude bias by a rate difference between the recombinant and parental plasmids and led to the same conclusion. Third, direct selection for recombinants just after transformation with or without substrate double-strand breaks yielded essentially the same results. Double-strand breaks elevated recombination in both the strains and in both substrates. These results are consistant with our previous findings that the major route of recombination in recBC sbcBC strains generates only one recombinant DNA from two DNAs and in recBC sbcA strains generates two recombinant DNAs from two DNAs. PMID:8722759

  8. Influence of the equatorial irregularities and precipitations in the South Atlantic magnetic anomaly on the generation of auroral-type plasma instabilities

    SciTech Connect

    Prange, R.; Bruston, P.

    1980-08-01

    Observational evidence of upward field-aligned beams in the keV range has been obtained in the sub-equatorial ionosphere above South America. These events can be related to coupled magnetic and ionospheric activity (magnetic storm, ionospheric irregularities). This result is in opposition with the current theory of the low-latitude ionosphere. Its interpretation must assume that conditions exist for the growth of plasma instabilities. This implies a low plasma density, a close coupling between the ionosphere and the magnetosphere, and field-aligned currents. Such suitable conditions have independently been observed in ionospheric irregularities (density, currents) or during magnetic storms (energetic particle precipitation) or they are deduced from the structure of the Anomaly (field-aligned currents). This allows us to suggest that the South Atlantic Anomaly sometimes compares to the auroral oval and may develop some current-driven plasma instabilities.

  9. Rapid and Efficient Generation of Recombinant Human Pluripotent Stem Cells by Recombinase-mediated Cassette Exchange in the AAVS1 Locus

    PubMed Central

    Pistoni, Mariaelena; Chen, Yemiao; Sambathkumar, Rangarajan; Helsen, Nicky; Vanhove, Jolien; Berckmans, Pieter; Cai, Qing; Vanuytsel, Kim; Raitano, Susanna; Verfaillie, Catherine M.

    2016-01-01

    Even with the revolution of gene-targeting technologies led by CRISPR-Cas9, genetic modification of human pluripotent stem cells (hPSCs) is still time consuming. Comparative studies that use recombinant lines with transgenes integrated into safe harbor loci could benefit from approaches that use site-specific targeted recombinases, like Cre or FLPe, which are more rapid and less prone to off-target effects. Such methods have been described, although they do not significantly outperform gene targeting in most aspects. Using Zinc-finger nucleases, we previously created a master cell line in the AAVS1 locus of hPSCs that contains a GFP-Hygromycin-tk expressing cassette, flanked by heterotypic FRT sequences. Here, we describe the procedures to perform FLPe recombinase-mediated cassette exchange (RMCE) using this line. The master cell line is transfected with a RMCE donor vector, which contains a promoterless Puromycin resistance, and with FLPe recombinase. Application of both a positive (Puromycin) and negative (FIAU) selection program leads to the selection of RMCE without random integrations. RMCE generates fully characterized pluripotent polyclonal transgenic lines in 15 d with 100% efficiency. Despite the recently described limitations of the AAVS1 locus, the ease of the system paves the way for hPSC transgenesis in isogenic settings, is necessary for comparative studies, and enables semi-high-throughput genetic screens for gain/loss of function analysis that would otherwise be highly time consuming. PMID:27911376

  10. Ion heating, burnout of the high-frequency field, and ion sound generation under the development of a modulation instability of an intense Langmuir wave in a plasma

    SciTech Connect

    Kirichok, A. V. Kuklin, V. M.; Pryimak, A. V.; Zagorodny, A. G.

    2015-09-15

    The development of one-dimensional parametric instabilities of intense long plasma waves is considered in terms of the so-called hybrid models, with electrons being treated as a fluid and ions being regarded as particles. The analysis is performed for both cases when the average plasma field energy is lower (Zakharov's hybrid model—ZHM) or greater (Silin's hybrid model—SHM) than the plasma thermal energy. The efficiency of energy transfer to ions and to ion perturbations under the development of the instability is considered for various values of electron-to-ion mass ratios. The energy of low-frequency oscillations (ion-sound waves) is found to be much lower than the final ion kinetic energy. We also discuss the influence of the changes in the damping rate of the high-frequency (HF) field on the instability development. The decrease of the absorption of the HF field inhibits the HF field burnout within plasma density cavities and gives rise to the broadening of the HF spectrum. At the same time, the ion velocity distribution tends to the normal distribution in both ZHM and SHM.

  11. Ion heating, burnout of the high-frequency field, and ion sound generation under the development of a modulation instability of an intense Langmuir wave in a plasma

    NASA Astrophysics Data System (ADS)

    Kirichok, A. V.; Kuklin, V. M.; Pryimak, A. V.; Zagorodny, A. G.

    2015-09-01

    The development of one-dimensional parametric instabilities of intense long plasma waves is considered in terms of the so-called hybrid models, with electrons being treated as a fluid and ions being regarded as particles. The analysis is performed for both cases when the average plasma field energy is lower (Zakharov's hybrid model—ZHM) or greater (Silin's hybrid model—SHM) than the plasma thermal energy. The efficiency of energy transfer to ions and to ion perturbations under the development of the instability is considered for various values of electron-to-ion mass ratios. The energy of low-frequency oscillations (ion-sound waves) is found to be much lower than the final ion kinetic energy. We also discuss the influence of the changes in the damping rate of the high-frequency (HF) field on the instability development. The decrease of the absorption of the HF field inhibits the HF field burnout within plasma density cavities and gives rise to the broadening of the HF spectrum. At the same time, the ion velocity distribution tends to the normal distribution in both ZHM and SHM.

  12. Generation of recombinant newcastle disease viruses, expressing the glycoprotein (G) of avian metapneumovirus, subtype A, or B, for use as bivalent vaccines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using reverse genetics technology, Newcastle disease virus (NDV) LaSota strain-based recombinant viruses were engineered to express the glycoprotein (G) of avian metapneumovirus (aMPV), subtype A, or B, as bivalent vaccines. These recombinant viruses, rLS/aMPV-A G and rLS/aMPV-B G, were slightly att...

  13. Generation and characterization of a recombinant Newcastle disease virus expressing the red fluorescent protein for use in co-infection studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Newcastle disease virus (NDV) is known for its rapid evolutionary dynamics. Mutations introduced by the viral RNA polymerase during replication seem to play a major role in the evolution of the virus, while recombination has only been rarely reported for NDV. The low frequency of recombination in ...

  14. Generation of recombinant pandemic H1N1 influenza virus with the HA cleavable by bromelain and identification of the residues influencing HA bromelain cleavage.

    PubMed

    Wang, Weijia; Suguitan, Amorsolo L; Zengel, James; Chen, Zhongying; Jin, Hong

    2012-01-20

    The proteolytic enzyme bromelain has been traditionally used to cleave the hemagglutinin (HA) protein at the C-terminus of the HA2 region to release the HA proteins from influenza virions. The bromelain cleaved HA (BHA) has been routinely used as an antigen to generate antiserum that is essential for influenza vaccine product release. The HA of the 2009 pandemic H1N1 influenza A/California/7/2009 (CA09) virus could not be cleaved efficiently by bromelain. To ensure timely delivery of BHA for antiserum production, we generated a chimeric virus that contained the HA1 region from CA09 and the HA2 region from the seasonal H1N1 A/South Dakota/6/2007 (SD07) virus that is cleavable by bromelain. The BHA from this chimeric virus was antigenically identical to CA09 and induced high levels of HA-specific antibodies and protected ferrets from wild-type H1N1 CA09 virus challenge. To determine the molecular basis of inefficient cleavage of CA09 HA by bromelain, the amino acids that differed between the HA2 of CA09 and SD07 were introduced into recombinant CA09 virus to assess their effect on bromelain cleavage. The D373N or E374G substitution in the HA2 stalk region of CA09 HA enabled efficient cleavage of CA09 HA by bromelain. Sequence analysis of the pandemic H1N1-like viruses isolated from 2010 revealed emergence of the E374K change. We found that K374 enabled the HA to be cleaved by bromelain and confirmed that the 374 residue is critical for HA bromelain cleavage.

  15. Epidemiological, biological and histological characterization of patients with indeterminate third-generation recombinant immunoblot assay antibody results for hepatitis C virus.

    PubMed

    Ríos, M; Diago, M; Rivera, P; Tuset, C; Cors, R; García, V; Carbonel, P; Gonzalez, C

    2006-03-01

    We studied the epidemiological, laboratory and histological characteristics of a group of patients with positive antibodies against hepatitis C virus (HCV) as determined by third-generation enzyme-linked immunosorbent assay (ELISA), and with indeterminate HCV antibody positivity as established by third-generation recombinant immunoblot assay (RIBA-3). The results obtained were compared with those recorded in a group of RIBA-3-positive patients. Both groups correspond to blood donors in whom the prevalence of hepatitis C is low. There were no statistically significant intergroup differences in mean age, or in the presence of infection risk factors. RNA positivity was much more frequent in the RIBA-positive group (71%vs 10%; P < 0.05), as was transaminase elevation during the 3 years of follow-up (54%vs 13%; P < 0.05). In 46% of the RIBA-indeterminate patients the liver biopsy proved normal, or only liver steatosis or minimal changes were detected, while 33% had persistent chronic hepatitis, and 21% showed active chronic hepatitis. A mean Knodell index score of 2.28 was recorded; 50% of the subjects showed no fibrosis, 46% grade 1 fibrosis (fibrous portal expansion), 4% grade 2 fibrosis (bridging fibrosis), and none grade 3 fibrosis (liver cirrhosis). In the RIBA-positive group, a greater percentage of patients had active chronic hepatitis, a greater Knodell index, and increased-grade fibrosis. It can be concluded that the RIBA-3-indeterminate group is epidemiologically similar to the RIBA-3-positive series, although with a lesser prevalence of laboratory test alterations, a lower viral replication index, and more likely to have benign disease - particularly in subjects without viral replication.

  16. Generation and characterization of a recombinant Moloney murine leukemia virus containing the v-myc oncogene of avian MC29 virus: in vitro transformation and in vivo pathogenesis.

    PubMed Central

    Brightman, B K; Pattengale, P K; Fan, H

    1986-01-01

    A new retrovirus consisting of the v-myc oncogene sequences of avian MC29 virus inserted into the genome of Moloney murine leukemia virus (M-MuLV) was generated. This was accomplished by constructing a recombinant DNA clone containing the desired organization, introducing the recombinant DNA into mouse NIH 3T3 cells, and superinfecting the cells with replication-competent M-MuLV. The construction was designed so that an M-MuLV gag-myc fusion protein would be produced. The resulting virus, M-MuLV(myc), morphologically transformed uninfected NIH 3T3 cells. Stocks of M-MuLV(myc)-M-MuLV were infected into secondary mouse embryo cultures. M-MuLV(myc) induced striking growth and proliferation of hematopoietic cells. These cells were of the myeloid lineage by morphology, phagocytic properties, and surface staining with Mac-1 and Mac-2 monoclonal antibodies. They resembled mature macrophages, although they displayed minor properties of immaturity. The myeloid cells were transformed in comparison with uninfected myeloid cells since they were less adherent and had unlimited proliferative capacity and reduced growth factor requirements. The transformed myeloid cells with proliferative potential were actually myeloid progenitors which apparently underwent terminal differentiation to macrophages. It was possible to derive a permanent line of factor-independent macrophages from M-MuLV(myc)-transformed myeloid cells. M-MuLV(myc) also immortalized and morphologically transformed mouse embryo fibroblasts. These in vitro properties closely resembled the biological activity of MC29 virus in avian cells and suggested that the nature of the v-myc oncogene was an important determinant in transformation specificity. Neonatal NIH Swiss mice inoculated intraperitoneally with M-MuLV(myc)-M-MuLV only developed lymphoblastic lymphoma characteristic of the M-MuLV helper alone, and no acute fibrosarcomas or myeloid tumors resulted. In light of the strong myeloid transformation observed in vitro

  17. Optimising expression of the recombinant fusion protein biopesticide ω-hexatoxin-Hv1a/GNA in Pichia pastoris: sequence modifications and a simple method for the generation of multi-copy strains.

    PubMed

    Pyati, Prashant; Fitches, Elaine; Gatehouse, John A

    2014-08-01

    Production of recombinant protein bio-insecticides on a commercial scale can only be cost effective if host strains with very high expression levels are available. A recombinant fusion protein containing an arthropod toxin, ω-hexatoxin-Hv1a, (from funnel web spider Hadronyche versuta) linked to snowdrop lectin (Galanthus nivalis agglutinin; GNA) is an effective oral insecticide and candidate biopesticide. However, the fusion protein was vulnerable to proteolysis during production in the yeast Pichia pastoris. To prevent proteolysis, the Hv1a/GNA fusion expression construct was modified by site-directed mutagenesis to remove a potential Kex2 cleavage site at the C-terminus of the Hv1a peptide. To obtain a high expressing clone of P. pastoris to produce recombinant Hv1a/GNA, a straightforward method was used to produce multi-copy expression plasmids, which does not require multiple integrations to give clones of P. pastoris containing high copy numbers of the introduced gene. Removal of the Kex2 site resulted in increased levels of intact fusion protein expressed in wild-type P. pastoris strains, improving levels of intact recombinant protein recoverable. Incorporation of a C-terminal (His)6 tag enabled single step purification of the fusion protein. These modifications did not affect the insecticidal activity of the recombinant toxin towards lepidopteran larvae. Introduction of multiple expression cassettes increased the amount of secreted recombinant fusion protein in a laboratory scale fermentation by almost tenfold on a per litre of culture basis. Simple modifications in the expression construct can be advantageous for the generation of high expressing P. pastoris strains for production of a recombinant protein, without altering its functional properties.

  18. Single cell cloning and recombinant monoclonal antibodies generation from RA synovial B cells reveal frequent targeting of citrullinated histones of NETs

    PubMed Central

    Corsiero, Elisa; Bombardieri, Michele; Carlotti, Emanuela; Pratesi, Federico; Robinson, William; Migliorini, Paola; Pitzalis, Costantino

    2016-01-01

    Objectives Rheumatoid arthritis (RA) is characterised by breach of self-tolerance towards citrullinated antigens with generation of anti-citrullinated peptide/proteins antibodies (ACPA). Currently, the nature and source of citrullinated antigens driving the humoral autoimmune response within synovial ectopic lymphoid structures (ELS) is a crucial unknown aspect of RA pathogenesis. Here we characterised the autoreactive B-cell response of lesional B cells isolated from ELS+RA synovium. Methods Single synovial tissue CD19+cells were Fluorescence Activated Cell Sorting (FACS)-sorted and VH/VL Ig genes cloned to generate recombinant monoclonal antibodies (rmAbs) from patients with ELS+/ACPA+RA. Results RA-rmAbs immunoreactivity analysis provided the following key findings: (1) in a chIP-based array containing 300 autoantigens and in a ‘citrullinome’ multiplex assay, a strong reactivity against citrullinated histones H2A/H2B (citH2A/H2B) was observed in ∼40% of RA-rmAbs, followed by cit-fibrinogen and cit-vimentin; (2) anti-citH2A/H2B-reactive RA-rmAbs (but not anti-citH2A/H2B negative) selectively recognised neutrophil extracellular traps (NETs) from peripheral blood and/or RA joint neutrophils; (3) anti-citH2A/citH2B and anti-NET immunobinding was dependent on affinity maturation and was completely abrogated following reversion of hypermutated IgVH/VL genes to germline sequences; (4) ELS+ (not ELS−) RA synovial tissues engrafted into Severe Combined ImmunoDeficiency (SCID) mice released human anti-citH2A/citH2B and anti-NET antibodies in association with the intra-graft expression of CXCL13 and lymphotoxin (LT)-β, two master regulators of ELS. Conclusion We provided novel evidence that B cells differentiated within synovial ELS in the RA joints frequent target deiminated proteins which could be generated during NETosis of RA synovial neutrophils including histones. Thus, NETs could represent a source of citrullinated antigens fuelling the ACPA autoimmune

  19. Near full-length genome sequence of a novel HIV type 1 second-generation recombinant form (CRF01_AE/CRF07_BC) identified among men who have sex with men in Jilin, China.

    PubMed

    Li, Xingguang; Ning, Chuanyi; He, Xiang; Yang, Yao; Xing, Hui; Hong, Kunxue; Shao, Yiming; Yang, Rongge

    2013-12-01

    We report here a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) composed of CRF01_AE and CRF07_BC, identified among men who have sex with men (MSM) in Jilin, with four breakpoints observed in the pol, vif, and vpr genes. The CRF01_AE regions of the recombinant were clustered with the CRF01_AE lineage, which is mainly circulating among MSM in northern China, with the support of 100% bootstrap value, indicating that the parental origin of the CRF01_AE regions was from MSM, in which recombination events may be more likely to occur. To the best of our knowledge, this is the first detection of a novel HIV-1 second-generation recombinant form (CRF01AE/CRF07_BC) in Jilin, which indicates active transmission networks of HIV-1 infection among MSM in the region. Therefore, it is necessary to continue monitoring the molecular epidemiology of HIV-1 among MSM in Jilin to obtain a better understanding of the transmission and potential public health impact of HIV-1 among MSM in the region.

  20. Mode-locking via dissipative Faraday instability

    NASA Astrophysics Data System (ADS)

    Tarasov, Nikita; Perego, Auro M.; Churkin, Dmitry V.; Staliunas, Kestutis; Turitsyn, Sergei K.

    2016-08-01

    Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system--spectrally dependent losses--achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin-Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering.

  1. Mode-locking via dissipative Faraday instability

    PubMed Central

    Tarasov, Nikita; Perego, Auro M.; Churkin, Dmitry V.; Staliunas, Kestutis; Turitsyn, Sergei K.

    2016-01-01

    Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin–Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system—spectrally dependent losses—achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin–Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering. PMID:27503708

  2. Mode-locking via dissipative Faraday instability.

    PubMed

    Tarasov, Nikita; Perego, Auro M; Churkin, Dmitry V; Staliunas, Kestutis; Turitsyn, Sergei K

    2016-08-09

    Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system-spectrally dependent losses-achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin-Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering.

  3. Recombinant pro-apoptotic Mycobacterium tuberculosis generates CD8+ T cell responses against human immunodeficiency virus type 1 Env and M. tuberculosis in neonatal mice.

    PubMed

    Ranganathan, Uma Devi K; Larsen, Michelle H; Kim, John; Porcelli, Steven A; Jacobs, William R; Fennelly, Glenn J

    2009-12-10

    Mycobacterium bovis BCG is an attractive vaccine vector against breast milk HIV transmission because it elicits Th1-type responses in newborns. However, BCG causes disease in HIV-infected infants. Genetically attenuated Mycobacterium tuberculosis (Mtb) mutants represent a safer alternative for immunocompromised populations. In the current study, we compared the immunogenicity in mice of three different recombinant attenuated Mtb strains expressing an HIV envelope (Env) antigen construct. Two of these strains (DeltalysA DeltapanCD Mtb and DeltaRD1 DeltapanCD Mtb) failed to induce significant levels of HIV Env-specific CD8(+) T cell responses. In striking contrast, an HIV-1 Env-expressing attenuated DeltalysA Mtb containing a deletion in secA2, which encodes a virulence-related secretion system involved in evading adaptive immunity, generated consistently measurable Env-specific CD8(+) T cell responses that were significantly greater than those observed after immunization with BCG expressing HIV Env. Similarly, another strain of DeltalysA DeltasecA2 Mtb expressing SIV Gag induced Gag- and Mtb-specific CD8(+) T cells producing perforin or IFNgamma, and Gag-specific CD4(+) T cells producing IFNgamma within 3 weeks after immunization in adult mice; in addition, IFNgamma-producing Gag-specific CD8(+) T cells and Mtb-specific CD4(+) T cells were observed in neonatal mice within 1 week of immunization. We conclude that DeltalysA DeltasecA2 Mtb is a promising vaccine platform to construct a safe combination HIV-TB vaccine for use in neonates.

  4. Bulk and interface trap generation under negative bias temperature instability stress of p-channel metal-oxide-semiconductor field-effect transistors with nitrogen and silicon incorporated HfO2 gate dielectrics

    NASA Astrophysics Data System (ADS)

    Choi, Changhwan; Lee, Jack C.

    2011-02-01

    Negative bias temperature instabilities (NBTIs) of p-channel metal-oxide-semiconductor field-effect-transistor with HfO2, HfOxNy, and HfSiON were investigated. Higher bulk trap generation (ΔNot) is mainly attributed to threshold voltage shift rather than interface trap generation (ΔNit). ΔNit, ΔNot, activation energy (Ea), and lifetime were exacerbated with incorporated nitrogen while improved with adding Si into gate dielectrics. Compared to HfO2, HfOxNy showed worse NBTI due to nitrogen pile-up at Si interface. However, adding Si into HfOxNy placed nitrogen peak profile away from Si/oxide interface and NBTI was reduced. This improvement is ascribed to reduced ΔNot and ΔNit, resulting from less nitrogen at Si interface.

  5. Interfacial Instability during Granular Erosion.

    PubMed

    Lefebvre, Gautier; Merceron, Aymeric; Jop, Pierre

    2016-02-12

    The complex interplay between the topography and the erosion and deposition phenomena is a key feature to model granular flows such as landslides. Here, we investigated the instability that develops during the erosion of a wet granular pile by a dry dense granular flow. The morphology and the propagation of the generated steps are analyzed in relation to the specific erosion mechanism. The selected flowing angle of the confined flow on a dry heap appears to play an important role both in the final state of the experiment, and for the shape of the structures. We show that the development of the instability is governed by the inertia of the flow through the Froude number. We model this instability and predict growth rates that are in agreement with the experiment results.

  6. Recombinant allergens

    PubMed Central

    Jutel, Marek; Solarewicz-Madejek, Katarzyna; Smolinska, Sylwia

    2012-01-01

    Allergen specific immunotherapy (SIT) is the only known causative treatment of allergic diseases. Recombinant allergen-based vaccination strategies arose from a strong need to both to improve safety and enhance efficacy of SIT. In addition, new vaccines can be effective in allergies including food allergy or atopic dermatitis, which poorly respond to the current treatment with allergen extracts. A number of successful clinical studies with both wild-type and hypoallergenic derivatives of recombinant allergens vaccines have been reported for the last decade. They showed high efficacy and safety profile as well as very strong modulation of T and B cell responses to specific allergens. PMID:23095874

  7. Interfacial Instabilities on a Droplet

    NASA Astrophysics Data System (ADS)

    Jalaal, Maziyar; Mehravaran, Kian

    2013-11-01

    The fragmentation of droplets is an essential stage of several natural and industrial applications such as fuel atomization and rain phenomena. In spite of its relatively long history, the mechanism of fragmentation is not clear yet. This is mainly due to small length and time scales as well as the non-linearity of the process. In the present study, two and three-dimensional numerical simulations have been performed to understand the early stages of the fragmentation of an initially spherical droplet. Simulations are performed for high Reynolds and a range of relatively high Weber numbers (shear breakup). To resolve the small-scale instabilities generated over the droplet, a second-order adaptive finite volume/volume of fluids (FV/VOF) method is employed, where the grid resolution is increased with the curvature of the gas-liquid interface as well as the vorticity magnitude. The study is focused on the onset and growth of interfacial instabilities. The role of Kelvin-Helmholtz instability (in surface wave formation) and Rayleigh-Taylor instability (in azimuthal transverse modulation) are shown and the obtained results are compared with the linear instability theories for zero and non-zero vorticity layers. Moreover, the analogy between the fragmentation of a single drop and a co-axial liquid jet is discussed. The current results can be used for the further development of the current secondary atomization models.

  8. Two-Fluid Interface Instability Being Studied

    NASA Technical Reports Server (NTRS)

    Niederhaus, Charles E.

    2003-01-01

    The interface between two fluids of different density can experience instability when gravity acts normal to the surface. The relatively well known Rayleigh-Taylor (RT) instability results when the gravity is constant with a heavy fluid over a light fluid. An impulsive acceleration applied to the fluids results in the Richtmyer-Meshkov (RM) instability. The RM instability occurs regardless of the relative orientation of the heavy and light fluids. In many systems, the passing of a shock wave through the interface provides the impulsive acceleration. Both the RT and RM instabilities result in mixing at the interface. These instabilities arise in a diverse array of circumstances, including supernovas, oceans, supersonic combustion, and inertial confinement fusion (ICF). The area with the greatest current interest in RT and RM instabilities is ICF, which is an attempt to produce fusion energy for nuclear reactors from BB-sized pellets of deuterium and tritium. In the ICF experiments conducted so far, RM and RT instabilities have prevented the generation of net-positive energy. The $4 billion National Ignition Facility at Lawrence Livermore National Laboratory is being constructed to study these instabilities and to attempt to achieve net-positive yield in an ICF experiment.

  9. Electron heat flux instability

    NASA Astrophysics Data System (ADS)

    Saeed, Sundas; Sarfraz, M.; Yoon, P. H.; Lazar, M.; Qureshi, M. N. S.

    2017-02-01

    The heat flux instability is an electromagnetic mode excited by a relative drift between the protons and two-component core-halo electrons. The most prominent application may be in association with the solar wind where drifting electron velocity distributions are observed. The heat flux instability is somewhat analogous to the electrostatic Buneman or ion-acoustic instability driven by the net drift between the protons and bulk electrons, except that the heat flux instability operates in magnetized plasmas and possesses transverse electromagnetic polarization. The heat flux instability is also distinct from the electrostatic counterpart in that it requires two electron species with relative drifts with each other. In the literature, the heat flux instability is often called the 'whistler' heat flux instability, but it is actually polarized in the opposite sense to the whistler wave. This paper elucidates all of these fundamental plasma physical properties associated with the heat flux instability starting from a simple model, and gradually building up more complexity towards a solar wind-like distribution functions. It is found that the essential properties of the instability are already present in the cold counter-streaming electron model, and that the instability is absent if the protons are ignored. These instability characteristics are highly reminiscent of the electron firehose instability driven by excessive parallel temperature anisotropy, propagating in parallel direction with respect to the ambient magnetic field, except that the free energy source for the heat flux instability resides in the effective parallel pressure provided by the counter-streaming electrons.

  10. Recombinant renewable polyclonal antibodies.

    PubMed

    Ferrara, Fortunato; D'Angelo, Sara; Gaiotto, Tiziano; Naranjo, Leslie; Tian, Hongzhao; Gräslund, Susanne; Dobrovetsky, Elena; Hraber, Peter; Lund-Johansen, Fridtjof; Saragozza, Silvia; Sblattero, Daniele; Kiss, Csaba; Bradbury, Andrew R M

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.

  11. Recombinant gonadotropins.

    PubMed

    Lathi, R B; Milki, A A

    2001-10-01

    Recombinant DNA technology makes it possible to produce large amounts of human gene products for pharmacologic applications, supplanting the need for human tissues. The genes for the alpha and beta subunits of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and human chorionic gonadotropin (hCG) have been characterized and cloned. Recombinant FSH (rFSH) has been shown to be safe and effective in the treatment of fertility disorders. In comparison with the urinary gonadotropin products, human menopausal gonadotropins (HMG), and urinary follitropins (uFSH), rFSH is more potent and better tolerated by patients. Recombinant HCG appears to be as efficacious as urinary HCG with the benefit of improved local tolerance. Recombinant LH (rLH) is likely to be recommended as a supplement to rFSH for ovulation induction in hypogonadotropic women. It may also benefit in vitro fertilization patients undergoing controlled ovarian hyperstimulation with rFSH combined with pituitary suppression, with a gonadotropin-releasing hormone agonist or antagonist.

  12. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

    Describes several methods of executing lecture demonstrations involving the recombination of the spectrum. Groups the techniques into two general classes: bringing selected portions of the spectrum together using lenses or mirrors and blurring the colors by rapid movement or foreshortening. (JM)

  13. Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells.

    PubMed

    Karpf, Adam R; Matsui, Sei-ichi

    2005-10-01

    DNA methyltransferase 1 (DNMT1)-deficient mice are tumor-prone, and this has been proposed to result from the induction of genomic instability. To address whether loss of DNMT1, or the related protein DNMT3b, results in genomic instability in human cancer cells, we used a near-diploid human colorectal cancer cell line, HCT116, in which one or both DNMT genes were disrupted by homologous recombination. Array-based comparative genomic hybridization analyses indicated that double, but not single, DNMT knock-out cells display two specific alterations in regional DNA copy number, suggesting that DNMT deficiency and genomic DNA hypomethylation are not associated with widespread genomic amplifications or deletions in human cancer cells. However, spectral karyotype analyses revealed that DNMT-deficient HCT116 cells are highly unstable with respect to large-scale chromosomal alterations; furthermore, this effect is characterized by a high degree of individual cell heterogeneity. The induction of chromosomal alterations in DNMT-deficient cells was evidenced both by aneuploidy and by large increases in the number of novel chromosomal translocations. Studies of double knock-out cells indicated that the generation of chromosomal alterations is spontaneous and persistent in vitro, meeting the formal definition of genomic instability. In summary, we show that DNMT deficiency in human cancer cells results in constitutive genomic instability manifested by chromosomal translocations.

  14. Turbine instabilities: Case histories

    NASA Technical Reports Server (NTRS)

    Laws, C. W.

    1985-01-01

    Several possible causes of turbine rotor instability are discussed and the related design features of a wide range of turbomachinery types and sizes are considered. The instrumentation options available for detecting rotor instability and assessing its severity are also discussed.

  15. Kinesics of Affective Instability.

    ERIC Educational Resources Information Center

    Dil, Nasim

    1979-01-01

    Discusses the rationale of studying kinesics of affective instability, describes the phenonmenon of affective instability, examines the role of kinesics in the overall process of communication, and presents three case studies. (Author/AM)

  16. Submarine slope earthquake-induced instability and associated tsunami generation potential along the Hyblean-Malta Escarpment (offshore eastern Sicily, Italy)

    NASA Astrophysics Data System (ADS)

    Ausilia Paparo, Maria; Pagnoni, Gianluca; Zaniboni, Filippo; Tinti, Stefano

    2016-04-01

    The stability analysis of offshore margins is an important step for the assessment of natural hazard: the main challenge is to evaluate the potential slope failures and the consequent occurrence of submarine tsunamigenic landslides to mitigate the potential coastal damage to inhabitants and infrastructures. But the limited geotechnical knowledge of the underwater soil and the controversial scientific interpretation of the tectonic units make it often difficult to carry out this type of analysis reliably. We select the Hyblean-Malta Escarpment (HME), the main active geological structure offshore eastern Sicily, because the amount of data from historical chronicles, the records about strong earthquakes and tsunami, and the numerous geological offshore surveys carried out in recent years make the region an excellent scenario to evaluate slope failures, mass movements triggered by earthquakes and the consequent tsunamis. We choose several profiles along the HME and analyse their equilibrium conditions using the Minimun Lithostatic Deviation (MLD) method (Tinti and Manucci, 2006, 2008; Paparo et al. 2013), that is based on the limit-equilibrium theory. Considering the morphological and geotechnical features of the offshore slopes, we prove that large-earthquake shaking may lead some zones of the HME to instability, we evaluate the expected volumes involved in sliding and compute the associated landslide-tsunami through numerical tsunami simulations. This work was carried out in the frame of the EU Project called ASTARTE - Assessment, STrategy And Risk Reduction for Tsunamis in Europe (Grant 603839, 7th FP, ENV.2013.6.4-3).

  17. First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates.

    PubMed Central

    Samollow, Paul B; Kammerer, Candace M; Mahaney, Susan M; Schneider, Jennifer L; Westenberger, Scott J; VandeBerg, John L; Robinson, Edward S

    2004-01-01

    The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation. PMID:15020427

  18. Regulation of Meiotic Recombination

    SciTech Connect

    Gregory p. Copenhaver

    2011-11-09

    for assaying recombination using tetrad analysis in a higher eukaryotic system (6). This system enabled the measurement of the frequency and distribution of recombination events at a genome wide level in wild type Arabidopsis (7), construction of genetic linkage maps which include positions for each centromere (8), and modeling of the strength and pattern of interference (9). This proposal extends the use of tetrad analysis in Arabidopsis by using it as the basis for assessing the phenotypes of mutants in genes important for recombination and the regulation of crossover interference and performing a novel genetic screen. In addition to broadening our knowledge of a classic genetic problem - the regulation of recombination by crossover interference - this proposal also provides broader impact by: generating pedagogical tools for use in hands-on classroom experience with genetics, building interdisciplinary collegial partnerships, and creating a platform for participation by junior scientists from underrepresented groups. There are three specific aims: (1) Isolate mutants in Arabidopsis MUS81 homologs using T-DNA and TILLING (2) Characterize recombination levels and interference in mus81 mutants (3) Execute a novel genetic screen, based on tetrad analysis, for genes that regulate meiotic recombination

  19. Generation of recombinant bacillus Calmette-Guérin and Mycobacterium smegmatis expressing BfpA and intimin as vaccine vectors against enteropathogenic Escherichia coli.

    PubMed

    Vasconcellos, Halyka Luzorio Franzotti; Scaramuzzi, Karina; Nascimento, Ivan Pereira; Da Costa Ferreira, Jorge M; Abe, Cecilia M; Piazza, Roxane M F; Kipnis, Andre; Dias da Silva, Wilmar

    2012-09-07

    Enteropathogenic Escherichia coli (EPEC) is an important cause of diarrhea in children. EPEC adheres to the intestinal epithelium and causes attaching and effacing (A/E) lesions. Recombinant Mycobacterium smegmatis (Smeg) and Mycobacterium bovis BCG strains were constructed to express either BfpA or intimin. The entire bfpA gene and a portion of the intimin gene were amplified by PCR from EPEC genomic DNA and inserted into the pMIP12 vector at the BamHI/KpnI sites. The pMIP_bfpA and pMIP_intimin vectors were introduced separately into Smeg and BCG. Recombinant clones were selected based on kanamycin resistance and designated rSmeg_pMIP_(bfpA or intimin) and rBCG_pMIP_(bfpA or intimin). The expression of bfpA and intimin was detected by Immunoblotting using polyclonal anti-BfpA and anti-intimin antibodies. The immunogenicity of these proteins was assessed in C57BL/6 mice by assaying the feces and serum for the presence of anti-BfpA and anti-intimin IgA and IgG antibodies. TNF-α and INF-γ were produced in vitro by spleen cells from mice immunized with recombinant BfpA, whereas TNF-γ was produced in mice immunized with recombinant intimin. The adhesion of EPEC (E2348/69) to HEp-2 target cells was blocked by IgA or IgG antibodies from mice immunized with recombinant BfpA or intimin but not by antibodies from non-immunized mice. Immunogenic non-infectious vectors containing relevant EPEC virulence genes may be promising vaccine candidates.

  20. Analysis of nuclear reactor instability phenomena

    SciTech Connect

    Lahey, R.T. Jr.

    1993-01-01

    The phenomena known as density-wave instability often occurs in phase change systems, such as boiling water nuclear reactors (BWRS). Our current understanding of density-wave oscillations is in fairly good shape for linear phenomena (eg, the onset of instabilities) but is not very advanced for non-linear phenomena [Lahey and Podowski, 1989]. In particular, limit cycle and chaotic instability modes are not well understood in boiling systems such as current and advanced generation BWRs (eg, SBWR). In particular, the SBWR relies on natural circulation and is thus inherently prone to problems with density-wave instabilities. The purpose of this research is to develop a quantitative understanding of nonlinear nuclear-coupled density-wave instability phenomena in BWRS. This research builds on the work of Achard et al [1985] and Clausse et al [1991] who showed, respectively, that Hopf bifurcations and chaotic oscillations may occur in boiling systems.

  1. Instability of rectangular jets

    NASA Technical Reports Server (NTRS)

    Tam, Christopher K. W.; Thies, Andrew T.

    1992-01-01

    The instability of rectangular jets is investigated using a vortex sheet model. It is shown that such jets support four linearly independent families of instability waves. Within each family there are infinitely many modes. A way to classify these modes according to the characteristics of their mode shapes or eigenfunctions is proposed. A parametric study of the instability wave characteristics has been carried out. A sample of the numerical results is reported here. It is found that the first and third modes of each instability wave family are corner modes. The pressure fluctuations associated with these instability waves are localized near the corners of the jet. The second mode, however, is a center mode with maximum fluctuations concentrated in the central portion of the jet flow. The center mode has the largest spatial growth rate. It is anticipated that as the instability waves propagate downstream the center mode would emerge as the dominant instability of the jet.

  2. Recombineering linear BACs.

    PubMed

    Chen, Qingwen; Narayanan, Kumaran

    2015-01-01

    Recombineering is a powerful genetic engineering technique based on homologous recombination that can be used to accurately modify DNA independent of its sequence or size. One novel application of recombineering is the assembly of linear BACs in E. coli that can replicate autonomously as linear plasmids. A circular BAC is inserted with a short telomeric sequence from phage N15, which is subsequently cut and rejoined by the phage protelomerase enzyme to generate a linear BAC with terminal hairpin telomeres. Telomere-capped linear BACs are protected against exonuclease attack both in vitro and in vivo in E. coli cells and can replicate stably. Here we describe step-by-step protocols to linearize any BAC clone by recombineering, including inserting and screening for presence of the N15 telomeric sequence, linearizing BACs in vivo in E. coli, extracting linear BACs, and verifying the presence of hairpin telomere structures. Linear BACs may be useful for functional expression of genomic loci in cells, maintenance of linear viral genomes in their natural conformation, and for constructing innovative artificial chromosome structures for applications in mammalian and plant cells.

  3. Baroclinic instability in stellar radiation zones

    SciTech Connect

    Kitchatinov, L. L.

    2014-03-20

    Surfaces of constant pressure and constant density do not coincide in differentially rotating stars. Stellar radiation zones with baroclinic stratification can be unstable. Instabilities in radiation zones are of crucial importance for angular momentum transport, mixing of chemical species, and, possibly, for magnetic field generation. This paper performs linear analysis of baroclinic instability in differentially rotating stars. Linear stability equations are formulated for differential rotation of arbitrary shape and then solved numerically for rotation nonuniform in radius. As the differential rotation increases, r- and g-modes of initially stable global oscillations transform smoothly into growing modes of baroclinic instability. The instability can therefore be interpreted as stability loss to r- and g-modes excitation. Regions of stellar parameters where r- or g-modes are preferentially excited are defined. Baroclinic instability onsets at a very small differential rotation of below 1%. The characteristic time of instability growth is about 1000 rotation periods. Growing disturbances possess kinetic helicity. Magnetic field generation by the turbulence resulting from baroclinic instability in differentially rotating radiation zones is therefore possible.

  4. Long inverted repeats are an at-risk motif for recombination in mammalian cells.

    PubMed

    Waldman, A S; Tran, H; Goldsmith, E C; Resnick, M A

    1999-12-01

    Certain DNA sequence motifs and structures can promote genomic instability. We have explored instability induced in mouse cells by long inverted repeats (LIRs). A cassette was constructed containing a herpes simplex virus thymidine kinase (tk) gene into which was inserted an LIR composed of two inverted copies of a 1.1-kb yeast URA3 gene sequence separated by a 200-bp spacer sequence. The tk gene was introduced into the genome of mouse Ltk(-) fibroblasts either by itself or in conjunction with a closely linked tk gene that was disrupted by an 8-bp XhoI linker insertion; rates of intrachromosomal homologous recombination between the markers were determined. Recombination between the two tk alleles was stimulated 5-fold by the LIR, as compared to a long direct repeat (LDR) insert, resulting in nearly 10(-5) events per cell per generation. Of the tk(+) segregants recovered from LIR-containing cell lines, 14% arose from gene conversions that eliminated the LIR, as compared to 3% of the tk(+) segregants from LDR cell lines, corresponding to a >20-fold increase in deletions at the LIR hotspot. Thus, an LIR, which is a common motif in mammalian genomes, is at risk for the stimulation of homologous recombination and possibly other genetic rearrangements.

  5. In vitro-generated interspecific recombinants between bovine herpesviruses 1 and 5 show attenuated replication characteristics and establish latency in the natural host

    PubMed Central

    2011-01-01

    Background Interspecific recombinant viruses R1ΔgC and R2ΔgI were isolated after in vitro co-infection with BoHV-1 and BoHV-5, two closely related alphaherpesviruses that infect cattle. The genetic characterization of R1ΔgC and R2ΔgI showed that they are composed of different sections of the parental genomes. The aim of this study was the characterization of the in vivo behavior of these recombinants in the natural host. Results Four groups of four 3-month-old calves of both genders were intranasally inoculated with either the recombinant or parental viruses. A control group of two animals was also included. Viral excretion and clinical signs were monitored after infection. Histopathological examination of the central nervous system (CNS) was performed and the establishment of latency in trigeminal ganglia was analyzed by PCR. The humoral response was also evaluated using ELISA tests. Three out of four animals from the BoHV-5 infected group excreted virus for 4-10 days. Two calves shed R1ΔgC virus for one day. In R2ΔgI and BoHV-1.2ΔgCΔgI groups, infectious virus was isolated only after two or three blind passages. None of the infected animals developed neurological signs, although those infected with BoHV-5 showed histopathological evidence of viral infection. Latent viral DNA was detected in at least one calf from each infected group. Serum and/or mucosal antibodies were detected in all groups. Conclusion Both BoHV-1/-5 recombinants and the BoHV-1 parental strain are attenuated in calves, although they are able to replicate in animals at low rates and to establish latent infections. PMID:21592326

  6. Lending sociodynamics and economic instability

    NASA Astrophysics Data System (ADS)

    Hawkins, Raymond J.

    2011-11-01

    We show how the dynamics of economic instability and financial crises articulated by Keynes in the General Theory and developed by Minsky as the Financial Instability Hypothesis can be formalized using Weidlich’s sociodynamics of opinion formation. The model addresses both the lending sentiment of a lender in isolation as well as the impact on that lending sentiment of the behavior of other lenders. The risk associated with lending is incorporated through a stochastic treatment of loan dynamics that treats prepayment and default as competing risks. With this model we are able to generate endogenously the rapid changes in lending opinion that attend slow changes in lending profitability and find these dynamics to be consistent with the rise and collapse of the non-Agency mortgage-backed securities market in 2007/2008. As the parameters of this model correspond to well-known phenomena in cognitive and social psychology, we can both explain why economic instability has proved robust to advances in risk measurement and suggest how policy for reducing economic instability might be formulated in an experimentally sound manner.

  7. Generations.

    PubMed

    Chambers, David W

    2005-01-01

    Groups naturally promote their strengths and prefer values and rules that give them an identity and an advantage. This shows up as generational tensions across cohorts who share common experiences, including common elders. Dramatic cultural events in America since 1925 can help create an understanding of the differing value structures of the Silents, the Boomers, Gen Xers, and the Millennials. Differences in how these generations see motivation and values, fundamental reality, relations with others, and work are presented, as are some applications of these differences to the dental profession.

  8. Weibel instability in relativistic quantum plasmas

    NASA Astrophysics Data System (ADS)

    Mendonça, J. T.; Brodin, G.

    2015-08-01

    Generation of quasi-static magnetic fields, due to the Weibel instability is studied in a relativistic quantum plasma. This instability is induced by a temperature anisotropy. The dispersion relation and growth rates for low frequency electromagnetic perturbations are derived using a wave-kinetic equation which describes the evolution of the electron Wigner quasi-distribution. The influence of parallel kinetic effects is discussed in detail.

  9. Radiative heat transport instability in a laser produced inhomogeneous plasma

    SciTech Connect

    Bychenkov, V. Yu.; Rozmus, W.

    2015-08-15

    A laser produced high-Z plasma in which an energy balance is achieved due to radiation emission and radiative heat transfer supports ion acoustic instability. A linear dispersion relation is derived, and instability is compared to the radiation cooling instability [R. G. Evans, Plasma Phys. Controlled Fusion 27, 751 (1985)]. Under conditions of indirect drive fusion experiments, the driving term for the instability is the radiative heat flux and, in particular, the density dependence of the radiative heat conductivity. A specific example of thermal Bremsstrahlung radiation source has been considered. This instability may lead to plasma jet formation and anisotropic x-ray generation, thus affecting inertial confinement fusion related experiments.

  10. Generalities on combustion instabilities

    NASA Astrophysics Data System (ADS)

    Kuentzmann, Paul

    The main manifestations of combustion instabilities are reviewed, and the specific characteristics of instabilities in solid-propellant rocket engines are analyzed, with the Minuteman III third-stage engine and the SRB engine of Titan 34 D considered as examples. The main approaches for predicting combustion instabilities are discussed, including the linear approach based on the acoustic balance, the nonlinear mode-coupling approach, and the nonlinear approach using numerical calculation. Projected directions for future research are also examined.

  11. Ordinary electromagnetic mode instability

    NASA Technical Reports Server (NTRS)

    Cheng, C. Z.

    1974-01-01

    The instability of the ordinary electromagnetic mode propagating perpendicular to an external magnetic field is studied for a single-species plasma with ring velocity distribution. The marginal instability boundaries for both the purely growing mode and the propagating growing modes are calculated from the instability criteria. The dispersion characteristics for various sets of plasma parameters are also given. The typical growth rates are of the order of the cyclotron frequency.

  12. Circulation in blast driven instabilities

    NASA Astrophysics Data System (ADS)

    Henry de Frahan, Marc; Johnsen, Eric

    2016-11-01

    Mixing in many natural phenomena (e.g. supernova collapse) and engineering applications (e.g. inertial confinement fusion) is often initiated through hydrodynamic instabilities. Explosions in these systems give rise to blast waves which can interact with perturbations at interfaces between different fluids. Blast waves are formed by a shock followed by a rarefaction. This wave profile leads to complex time histories of interface acceleration. In addition to the instabilities induced by the acceleration field, the rarefaction from the blast wave decompresses the material at the interface, further increasing the perturbation growth. After the passage of the wave, circulation circulation generated by the blast wave through baroclinic vorticity continues to act upon the interface. In this talk, we provide scaling laws for the circulation and amplitude growth induced by the blast wave. Numerical simulations of the multifluid Euler equations solved using a high-order accurate Discontinuous Galerkin method are used to validate the theoretical results.

  13. Diversity of the G3 genes of human rotaviruses in isolates from Spain from 2004 to 2006: cross-species transmission and inter-genotype recombination generates alleles.

    PubMed

    Martínez-Laso, Jorge; Román, Angela; Rodriguez, Miriam; Cervera, Isabel; Head, Jacqueline; Rodríguez-Avial, Iciar; Picazo, Juan J

    2009-04-01

    Rotavirus evolves by using multiple genetic mechanisms which are an accumulation of spontaneous point mutations and reassortment events. Other mechanisms, such as cross-species transmission and inter-genotype recombination, may be also involved. One of the most interesting genotypes in the accumulation of these events is the G3 genotype. In this work, six new Spanish G3 sequences belonging to 0-2-year-old patients from Madrid were analysed and compared with 160 others of the same genotype obtained from humans and other host species to establish the evolutionary pathways of the G3 genotype. The following results were obtained: (i) there are four different lineages of the G3 genotype which have evolved in different species; (ii) Spanish G3 rotavirus sequences are most similar to the described sequences that belong to lineage I; (iii) several G3 genotype alleles were reassigned as other G genotypes; and (iv) inter-genotype recombination events in G3 viruses involving G1 and G2 were described. These findings strongly suggest multiple inter-species transmission events between different non-human mammalian species and humans.

  14. Effect of sex, age, and breed on genetic recombination features in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Usin...

  15. Predictors for Surgery in Shoulder Instability

    PubMed Central

    Lebus, George F.; Raynor, Martin B.; Nwosu, Samuel K.; Wagstrom, Emily; Jani, Sunil S.; Carey, James L.; Hettrich, Carolyn M.; Cox, Charles L.; Kuhn, John E.

    2015-01-01

    Background: Shoulder instability is a common cause of pain and dysfunction in young, active patients. While studies have analyzed risk factors for recurrent instability and failure after instability surgery, few have examined which variables are associated with initial surgery in this patient population. Purpose: To identify variables that may be associated with surgical intervention in patients with shoulder instability in the context of the FEDS (frequency, etiology, direction, severity) classification, a system that may be useful in the surgical treatment of shoulder instability patients. Study Design: Cohort study (prognosis); Level of evidence, 2. Methods: A database of patients treated for shoulder instability from 3 separate institutions from 2005 to 2010 was generated using International Classification of Diseases–9th Revision data. Data were collected via retrospective review. Injury data were categorized according to the FEDS system. Data were analyzed for significance, with the primary outcome of surgical intervention. Summary statistics were used to assess which variables were associated with eventual surgery. To test the unadjusted bivariate associations between shoulder surgery and each data point, Pearson chi-square tests were used for categorical variables and Wilcoxon tests were used for continuous variables. Results: Over the study time period, 377 patients were treated for shoulder instability. Patients who had surgery were more likely younger, had recurrent instability, and had their initial injury while playing a sport. Most patients had anterior instability; however, there was a greater proportion of posterior instability patients in the operative group. Severity of dislocation, measured by whether the patient required help to relocate the shoulder, was not significantly associated with eventual surgery. While imaging was not available for all patients, surgical patients were more likely to have magnetic resonance imaging findings of

  16. Controlling contractile instabilities in the actomyosin cortex

    PubMed Central

    Nishikawa, Masatoshi; Naganathan, Sundar Ram; Jülicher, Frank; Grill, Stephan W

    2017-01-01

    The actomyosin cell cortex is an active contractile material for driving cell- and tissue morphogenesis. The cortex has a tendency to form a pattern of myosin foci, which is a signature of potentially unstable behavior. How a system that is prone to such instabilities can rveliably drive morphogenesis remains an outstanding question. Here, we report that in the Caenorhabditis elegans zygote, feedback between active RhoA and myosin induces a contractile instability in the cortex. We discover that an independent RhoA pacemaking oscillator controls this instability, generating a pulsatory pattern of myosin foci and preventing the collapse of cortical material into a few dynamic contracting regions. Our work reveals how contractile instabilities that are natural to occur in mechanically active media can be biochemically controlled to robustly drive morphogenetic events. DOI: http://dx.doi.org/10.7554/eLife.19595.001 PMID:28117665

  17. Selection of Recombinant Human Antibodies.

    PubMed

    Tomszak, Florian; Weber, Susanne; Zantow, Jonas; Schirrmann, Thomas; Hust, Michael; Frenzel, André

    2016-01-01

    Since the development of therapeutic antibodies the demand of recombinant human antibodies is steadily increasing. Traditionally, therapeutic antibodies were generated by immunization of rat or mice, the generation of hybridoma clones, cloning of the antibody genes and subsequent humanization and engineering of the lead candidates. In the last few years, techniques were developed that use transgenic animals with a human antibody gene repertoire. Here, modern recombinant DNA technologies can be combined with well established immunization and hybridoma technologies to generate already affinity maturated human antibodies. An alternative are in vitro technologies which enabled the generation of fully human antibodies from antibody gene libraries that even exceed the human antibody repertoire. Specific antibodies can be isolated from these libraries in a very short time and therefore reduce the development time of an antibody drug at a very early stage.In this review, we describe different technologies that are currently used for the in vitro and in vivo generation of human antibodies.

  18. Inhibition of homologous recombination repair with Pentoxifylline targets G2 cells generated by radiotherapy and induces major enhancements of the toxicity of cisplatin and melphalan given after irradiation

    PubMed Central

    Bohm, Lothar

    2006-01-01

    The presentation reviews the modus operandi of the dose modifying drug Pentoxifylline and the dose enhancement factors which can be achieved in different cell types. Preclinical and clinical data show that Pentoxifylline improves the oxygenation of hypoxic tumours and enhances tumour control by irradiation. In vitro experiments demonstrate that Pentoxifylline also operates when oxygen is not limiting and produces dose modifying factors in the region of 1.2 – 2.0. This oxygen independent effect is poorly understood. In p53 mutant cells irradiation induces a G2 block which is abrogated by Pentoxifylline. The enhancement of cell kill observed when Pentoxifylline and irradiation are given together could arise from rapid entry of damaged tumour cells into mitosis and propagation of DNA lesions as the result of curtailment of repair time. Recovery ratios and repair experiments using CFGE after high dose irradiation demonstrate that Pentoxifylline inhibits repair directly and that curtailment of repair time is not the explanation. Use of the repair defective xrs1 and the parental repair competent CHO-K1 cell line shows that Pentoxifylline inhibits homologous recombination repair which operates predominantly in the G2 phase of the cell cycle. When irradiated cells residing in G2 phase are exposed to very low doses of cisplatin at a toxic dose of 5 %. (TC: 0.05) massive toxicity enhancements up to a factor of 80 are observed in melanoma, squamous carcinoma and prostate tumour cell lines. Enhancements of radiotoxicity seen when Pentoxifylline and radiation are applied together are small and do not exceed a factor of 2.0. The capacity of Pentoxifyline to inhibit homologous recombination repair has not as yet been clinically utilized. A suitable application could be in the treatment of cervical carcinoma where irradiation and cisplatin are standard modality. In vitro data also strongly suggest that regimes where irradiation is used in combination with alkylating drugs may

  19. Inhibition of homologous recombination repair with Pentoxifylline targets G2 cells generated by radiotherapy and induces major enhancements of the toxicity of cisplatin and melphalan given after irradiation.

    PubMed

    Bohm, Lothar

    2006-05-03

    The presentation reviews the modus operandi of the dose modifying drug Pentoxifylline and the dose enhancement factors which can be achieved in different cell types. Preclinical and clinical data show that Pentoxifylline improves the oxygenation of hypoxic tumours and enhances tumour control by irradiation. In vitro experiments demonstrate that Pentoxifylline also operates when oxygen is not limiting and produces dose modifying factors in the region of 1.2-2.0. This oxygen independent effect is poorly understood. In p53 mutant cells irradiation induces a G2 block which is abrogated by Pentoxifylline. The enhancement of cell kill observed when Pentoxifylline and irradiation are given together could arise from rapid entry of damaged tumour cells into mitosis and propagation of DNA lesions as the result of curtailment of repair time. Recovery ratios and repair experiments using CFGE after high dose irradiation demonstrate that Pentoxifylline inhibits repair directly and that curtailment of repair time is not the explanation. Use of the repair defective xrs1 and the parental repair competent CHO-K1 cell line shows that Pentoxifylline inhibits homologous recombination repair which operates predominantly in the G2 phase of the cell cycle. When irradiated cells residing in G2 phase are exposed to very low doses of cisplatin at a toxic dose of 5%. (TC: 0.05) massive toxicity enhancements up to a factor of 80 are observed in melanoma, squamous carcinoma and prostate tumour cell lines. Enhancements of radiotoxicity seen when Pentoxifylline and radiation are applied together are small and do not exceed a factor of 2.0. The capacity of Pentoxifyline to inhibit homologous recombination repair has not as yet been clinically utilized. A suitable application could be in the treatment of cervical carcinoma where irradiation and cisplatin are standard modality. In vitro data also strongly suggest that regimes where irradiation is used in combination with alkylating drugs may also

  20. Recombinant immunoglobulin variable domains generated from synthetic genes provide a system for in vitro characterization of light-chain amyloid proteins.

    PubMed Central

    Stevens, P. W.; Raffen, R.; Hanson, D. K.; Deng, Y. L.; Berrios-Hammond, M.; Westholm, F. A.; Murphy, C.; Eulitz, M.; Wetzel, R.; Solomon, A.

    1995-01-01

    The primary structural features that render human monoclonal light chains amyloidogenic are presently unknown. To gain further insight into the physical and biochemical factors that result in the pathologic deposition of these proteins as amyloid fibrils, we have selected for detailed study three closely homologous protein products of the light-chain variable-region single-gene family VkIV. Two of these proteins, REC and SMA, formed amyloid fibrils in vivo. The third protein, LEN, was excreted by the patient at levels of 50 g/day with no indication of amyloid deposits. Sequences of amyloidogenic proteins REC and SMA differed from the sequence of the nonpathogenic protein LEN at 14 and 8 amino acid positions, respectively, and these amino acid differences have been analyzed in terms of the three-dimensional structure of the LEN dimer. To provide a replenishable source of these human proteins, we constructed synthetic genes coding for the REC, SMA, and LEN variable domains and expressed these genes in Escherichia coli. Immunochemical and biophysical comparisons demonstrated that the recombinant VkIV products have tertiary structural features comparable to those of the patient-derived proteins. This well-defined set of three clinically characterized human kIV light chains, together with the capability to produce these kIV proteins recombinantly, provide a system for biophysical and structural comparisons of two different amyloidogenic light-chain proteins and a nonamyloidogenic protein of the same subgroup. This work lays the foundation for future investigations of the structural basis of light-chain amyloidogenicity. PMID:7795526

  1. Dielectronic recombination lines of C{sup +}

    SciTech Connect

    Sochi, Taha Storey, Peter J.

    2013-11-15

    The present paper presents atomic data generated to investigate the recombination lines of C II in the spectra of planetary nebulae. These data include energies of bound and autoionizing states, oscillator strengths and radiative transition probabilities, autoionization probabilities, and recombination coefficients. The R-matrix method of electron scattering theory was used to describe the C{sup 2+} plus electron system.

  2. Buckling instability in arteries.

    PubMed

    Vandiver, Rebecca M

    2015-04-21

    Arteries can become tortuous in response to abnormal growth stimuli, genetic defects and aging. It is suggested that a buckling instability is a mechanism that might lead to artery tortuosity. Here, the buckling instability in arteries is studied by examining asymmetric modes of bifurcation of two-layer cylindrical structures that are residually stressed. These structures are loaded by an axial force, internal pressure and have nonlinear, anisotropic, hyperelastic responses to stresses. Strain-softening and reduced opening angle are shown to lower the critical internal pressure leading to buckling. In addition, the ratio of the media thickness to the adventitia thickness is shown to have a dramatic impact on arterial instability.

  3. Generation of recombinant monoclonal antibodies to study structure-function of envelope protein VP28 of white spot syndrome virus from shrimp

    SciTech Connect

    Wang Yuzhen; Zhang Xiaohua; Yuan Li; Xu Tao; Rao Yu; Li Jia; Dai Heping

    2008-08-08

    White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP28 is one of the most important envelope proteins of WSSV. In this study, a recombinant antibody library, as single-chain fragment variable (scFv) format, displayed on phage was constructed using mRNA from spleen cells of mice immunized with full-length VP28 expressed in Escherichia coli. After several rounds of panning, six scFv antibodies specifically binding to the epitopes in the N-terminal, middle, and C-terminal regions of VP28, respectively, were isolated from the library. Using these scFv antibodies as tools, the epitopes in VP28 were located on the envelope of the virion by immuno-electron microscopy. Neutralization assay with these antibodies in vitro suggested that these epitopes may not be the attachment site of WSSV to host cell receptor. This study provides a new way to investigate the structure and function of the envelope proteins of WSSV.

  4. Second-Generation Recombination-Based In Vivo Expression Technology for Large-Scale Screening for Vibrio cholerae Genes Induced during Infection of the Mouse Small Intestine

    PubMed Central

    Osorio, C. G.; Crawford, J. A.; Michalski, J.; Martinez-Wilson, H.; Kaper, J. B.; Camilli, A.

    2005-01-01

    We have constructed an improved recombination-based in vivo expression technology (RIVET) and used it as a screening method to identify Vibrio cholerae genes that are transcriptionally induced during infection of infant mice. The improvements include the introduction of modified substrate cassettes for resolvase that can be positively and negatively selected for, allowing selection of resolved strains from intestinal homogenates, and three different tnpR alleles that cover a range of translation initiation efficiencies, allowing identification of infection-induced genes that have low-to-moderate basal levels of transcription during growth in vitro. A transcriptional fusion library of 8,734 isolates of a V. cholerae El Tor strain that remain unresolved when the vibrios are grown in vitro was passed through infant mice, and 40 infection-induced genes were identified. Nine of these genes were inactivated by in-frame deletions, and their roles in growth in vitro and fitness during infection were measured by competition assays. Four mutant strains were attenuated >10-fold in vivo compared with the parental strain, demonstrating that infection-induced genes are enriched in genes essential for virulence. PMID:15664940

  5. Generation and characterization of a scFv against recombinant coat protein of the geminivirus tomato leaf curl New Delhi virus.

    PubMed

    Zakri, Adel M; Ziegler, Angelika; Torrance, Lesley; Fischer, Rainer; Commandeur, Ulrich

    2010-03-01

    We report the establishment of a hybridoma cell line secreting the monoclonal antibody (mAb) HAV, which recognizes the coat (AV1) protein of tomato leaf curl New Delhi virus (ToLCNDV), a begomovirus. The cell line was obtained following immunization of mice with purified recombinant AV1 fused to glutathione S-transferase (GST). A single-chain variable fragment (scFv-SAV) was assembled from hybridoma cDNA, but sequence analysis revealed a single nucleotide deletion causing a frame shift that resulted in a 21-residue N-terminal truncation. The missing nucleotide was restored by in vitro site-directed mutagenesis to create scFv-RWAV. The binding properties of mAb HAV and the corresponding scFvs were characterized by western blot, ELISA and surface plasmon resonance spectroscopy. MAb HAV bound to AV1 with nanomolar affinity but reacted neither with the N-terminal region of the protein nor with the GST fusion partner. This suggested that the antibody recognized a linear epitope in a region of the coat protein that is conserved among begomoviruses. Both scFvs retained the antigen specificity of mAb HAV, although the dissociation rate constant of scFv-RWAV was tenfold greater than that of scFv-SAV, showing the importance of restoring the 21 N-terminal amino acids.

  6. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses

    PubMed Central

    Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G.; Oropallo, Michael; Gaylord, Michelle; Ungaro, Ryan; Cunningham-Rundles, Charlotte; Alexandropoulos, Konstantina; Mucida, Daniel; Merad, Miriam; Cerutti, Andrea

    2016-01-01

    Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103+ and CD24+CD11b+ DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell–dependent or –independent pathways. Compared with lung DCs (LDC), lung CD64+ macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-β (TGF-β) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid–dependent up-regulation of α4β7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT–specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs. PMID:26712806

  7. Site-specific DNA double-strand break generated by I-SceI endonuclease enhances ectopic homologous recombination in Pyricularia oryzae.

    PubMed

    Arazoe, Takayuki; Younomaru, Tetsuya; Ohsato, Shuichi; Kimura, Makoto; Arie, Tsutomu; Kuwata, Shigeru

    2014-03-01

    To evaluate the contribution of DNA double-strand breaks (DSBs) to somatic homologous recombination (HR) in Pyricularia oryzae, we established a novel detection/selection system of DSBs-mediated ectopic HR. This system consists of donor and recipient nonfunctional yellow fluorescent protein (YFP)/blasticidin S deaminase (BSD) fusion genes and the yeast endonuclease I-SceI gene as a recipient-specific DSB inducer. The system enables to detect and select ectopic HR events by the restoration of YFP fluorescence and blasticidin S resistance. The transformed lines with donor and recipient showed low frequencies of endogenous ectopic HR (> 2.1%). Compared with spontaneous HR, c. 20-fold increases in HR and absolute frequency of HR as high as 40% were obtained by integration of I-SceI gene, indicating that I-SceI-mediated DSB was efficiently repaired via ectopic HR. Furthermore, to validate the impact of DSB on targeted gene replacement (TGR), the transformed lines with a recipient gene were transfected with an exogenous donor plasmid in combination with the DSB inducer. TGR events were not observed without the DSB inducer, whereas hundreds of colonies resulting from TGR events were obtained with the DSB inducer. These results clearly demonstrated that the introduction of site-specific DSB promotes ectopic HR repair in P. oryzae.

  8. Mirror Instability in the Turbulent Solar Wind

    NASA Astrophysics Data System (ADS)

    Hellinger, Petr; Landi, Simone; Matteini, Lorenzo; Verdini, Andrea; Franci, Luca

    2017-04-01

    The relationship between a decaying strong turbulence and the mirror instability in a slowly expanding plasma is investigated using two-dimensional hybrid expanding box simulations. We impose an initial ambient magnetic field perpendicular to the simulation box, and we start with a spectrum of large-scale, linearly polarized, random-phase Alfvénic fluctuations that have energy equipartition between kinetic and magnetic fluctuations and a vanishing correlation between the two fields. A turbulent cascade rapidly develops, magnetic field fluctuations exhibit a Kolmogorov-like power-law spectrum at large scales and a steeper spectrum at sub-ion scales. The imposed expansion (taking a strictly transverse ambient magnetic field) leads to the generation of an important perpendicular proton temperature anisotropy that eventually drives the mirror instability. This instability generates large-amplitude, nonpropagating, compressible, pressure-balanced magnetic structures in a form of magnetic enhancements/humps that reduce the perpendicular temperature anisotropy.

  9. Current Trends of HIV Recombination Worldwide

    PubMed Central

    Lau, Katherine A.; Wong, Justin J.L.

    2013-01-01

    One of the major characteristics of HIV-1 is its high genetic variability and extensive heterogeneity. This characteristic is due to its molecular traits, which in turn allows it to vary, recombine, and diversify at a high frequency. As such, it generates complex molecular forms, termed recombinants, which evade the human immune system and so survive. There is no sequence constraint to the recombination pattern as it appears to occur at inter-group (between groups M and O), as well as interand intra-subtype within group M. Rapid emergence and active global transmission of HIV-1 recombinants, known as circulating recombinant forms (CRFs) and unique recombinant forms (URFs), requires urgent attention. To date, 55 CRFs have been reported around the world. The first CRF01_AE originated from Central Africa but spread widely in Asia. The most recent CRF; CRF55_01B is a recombinant form of CRF01_AE and subtype B, although its origin is yet to be publicly disclosed. HIV-1 recombination is an ongoing event and plays an indispensable role in HIV epidemics in different regions. Africa, Asia and South America are identified as recombination hot-spots. They are affected by continual emergence and cocirculation of newly emerging CRFs and URFs, which are now responsible for almost 20% of HIV-1 infections worldwide. Better understanding of recombinants is necessary to determine their biological and molecular attributes. PMID:24470968

  10. Distal Radioulnar Joint Instability

    PubMed Central

    Mirghasemi, Ali R.; Lee, Daniel J.; Rahimi, Narges; Rashidinia, Shervin

    2015-01-01

    Distal radioulnar joint (DRUJ) instability is a common clinical condition but a frequently missed diagnosis. Both surgical and nonsurgical treatments are possible for chronic cases of DRUJ instability. Nonsurgical treatment can be considered as the primary therapy in less active patients, while surgery should be considered to recover bone and ligament injuries if nonsurgical treatment fails to restore forearm stability and function. The appropriate choice of treatment depends on the individual patient and specific derangement of the DRUJ PMID:26328241

  11. Prediction of Algebraic Instabilities

    NASA Astrophysics Data System (ADS)

    Zaretzky, Paula; King, Kristina; Hill, Nicole; Keithley, Kimberlee; Barlow, Nathaniel; Weinstein, Steven; Cromer, Michael

    2016-11-01

    A widely unexplored type of hydrodynamic instability is examined - large-time algebraic growth. Such growth occurs on the threshold of (exponentially) neutral stability. A new methodology is provided for predicting the algebraic growth rate of an initial disturbance, when applied to the governing differential equation (or dispersion relation) describing wave propagation in dispersive media. Several types of algebraic instabilities are explored in the context of both linear and nonlinear waves.

  12. Improving baculovirus recombination

    PubMed Central

    Zhao, Yuguang; Chapman, David A. G.; Jones, Ian M.

    2003-01-01

    Recombinant baculoviruses have established themselves as a favoured technology for the high-level expression of recombinant proteins. The construction of recombinant viruses, however, is a time consuming step that restricts consideration of the technology for high throughput developments. Here we use a targeted gene knockout technology to inactivate an essential viral gene that lies adjacent to the locus used for recombination. Viral DNA prepared from the knockout fails to initiate an infection unless rescued by recombination with a baculovirus transfer vector. Modified viral DNA allows 100% recombinant virus formation, obviates the need for further virus purification and offers an efficient means of mass parallel recombinant formation. PMID:12527795

  13. Topographic-driven instabilities in terrestrial bodies

    NASA Astrophysics Data System (ADS)

    Vantieghem, S.; Cebron, D.; Herreman, W.; Lacaze, L.

    2013-12-01

    Models of internal planetary fluid layers (core flows, subsurface oceans) commonly assume that these fluid envelopes have a spherical shape. This approximation however entails a serious restriction from the fluid dynamics point of view. Indeed, in the presence of mechanical forcings (precession, libration, nutation or tides) due to gravitational interaction with orbiting partners, boundary topography (e.g. of the core-mantle boundary) may excite flow instabilities and space-filling turbulence. These phenomena may affect heat transport and dissipation at the main order. Here, we focus on instabilities driven by longitudinal libration. Using a suite of theoretical tools and numerical simulations, we are able to discern a parameter range for which instability may be excited. We thereby consider deformations of different azimuthal order. This study gives the first numerical evidence of the tripolar instability. Furthermore, we explore the non-linear regime and investigate the amplitude as well as the dissipation of the saturated instability. Indeed, these two quantities control the torques on the solid layers and the thermal transport. Furthermore, based on this results, we address the issue of magnetic field generation associated with these flows (by induction or by dynamo process). This instability mechanism applies to both synchronized as non-synchronized bodies. As such, our results show that a tripolar instability might be present in various terrestrial bodies (Early Moon, Gallilean moons, asteroids, etc.), where it could participate in dynamo action. Simulation of a libration-driven tripolar instability in a deformed spherical fluid layer: snapshot of the velocity magnitude, where a complex 3D flow pattern is established.

  14. Equilibrium Electroconvective Instability

    NASA Astrophysics Data System (ADS)

    Rubinstein, I.; Zaltzman, B.

    2015-03-01

    Since its prediction 15 years ago, hydrodynamic instability in concentration polarization at a charge-selective interface has been attributed to nonequilibrium electro-osmosis related to the extended space charge which develops at the limiting current. This attribution had a double basis. On the one hand, it has been recognized that neither equilibrium electro-osmosis nor bulk electroconvection can yield instability for a perfectly charge-selective solid. On the other hand, it has been shown that nonequilibrium electro-osmosis can. The first theoretical studies in which electro-osmotic instability was predicted and analyzed employed the assumption of perfect charge selectivity for the sake of simplicity and so did the subsequent studies of various time-dependent and nonlinear features of electro-osmotic instability. In this Letter, we show that relaxing the assumption of perfect charge selectivity (tantamount to fixing the electrochemical potential of counterions in the solid) allows for the equilibrium electroconvective instability. In addition, we suggest a simple experimental test for determining the true, either equilibrium or nonequilibrium, origin of instability in concentration polarization.

  15. Toxicity evaluation of e-juice and its soluble aerosols generated by electronic cigarettes using recombinant bioluminescent bacteria responsive to specific cellular damages.

    PubMed

    Bharadwaj, Shiv; Mitchell, Robert J; Qureshi, Anjum; Niazi, Javed H

    2017-04-15

    Electronic-cigarettes (e-cigarette) are widely used as an alternative to traditional cigarettes but their safety is not well established. Herein, we demonstrate and validate an analytical method to discriminate the deleterious effects of e-cigarette refills (e-juice) and soluble e-juice aerosol (SEA) by employing stress-specific bioluminescent recombinant bacterial cells (RBCs) as whole-cell biosensors. These RBCs carry luxCDABE-operon tightly controlled by promoters that specifically induced to DNA damage (recA), superoxide radicals (sodA), heavy metals (copA) and membrane damage (oprF). The responses of the RBCs following exposure to various concentrations of e-juice/SEA was recorded in real-time that showed dose-dependent stress specific-responses against both the e-juice and vaporized e-juice aerosols produced by the e-cigarette. We also established that high doses of e-juice (4-folds diluted) lead to cell death by repressing the cellular machinery responsible for repairing DNA-damage, superoxide toxicity, ion homeostasis and membrane damage. SEA also caused the cellular damages but the cells showed enhanced bioluminescence expression without significant growth inhibition, indicating that the cells activated their global defense system to repair these damages. DNA fragmentation assay also revealed the disintegration of total cellular DNA at sub-toxic doses of e-juice. Despite their state of matter, the e-juice and its aerosols induce cytotoxicity and alter normal cellular functions, respectively that raises concerns on use of e-cigarettes as alternative to traditional cigarette. The ability of RBCs in detecting both harmful effects and toxicity mechanisms provided a fundamental understanding of biological response to e-juice and aerosols.

  16. Generating controlled reducing environments in aerobic recombinant Escherichia coli fermentations: effects on cell growth, oxygen uptake, heat shock protein expression, and in vivo CAT activity.

    PubMed

    Gill, R T; Cha, H J; Jain, A; Rao, G; Bentley, W E

    1998-07-20

    The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/microgram total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/microgram CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (sigma32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/microgram CAT min. ) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations.

  17. An alternative splicing event which occurs in mouse pachytene spermatocytes generates a form of DNA ligase III with distinct biochemical properties that may function in meiotic recombination.

    PubMed Central

    Mackey, Z B; Ramos, W; Levin, D S; Walter, C A; McCarrey, J R; Tomkinson, A E

    1997-01-01

    Three mammalian genes encoding DNA ligases have been identified. However, the role of each of these enzymes in mammalian DNA metabolism has not been established. In this study, we show that two forms of mammalian DNA ligase III, alpha and beta, are produced by a conserved tissue-specific alternative splicing mechanism involving exons encoding the C termini of the polypeptides. DNA ligase III-alpha cDNA, which encodes a 103-kDa polypeptide, is expressed in all tissues and cells, whereas DNA ligase III-beta cDNA, which encodes a 96-kDa polypeptide, is expressed only in the testis. During male germ cell differentiation, elevated expression of DNA ligase III-beta mRNA is restricted, beginning only in the latter stages of meiotic prophase and ending in the round spermatid stage. In 96-kDa DNA ligase III-beta, the C-terminal 77 amino acids of DNA ligase III-alpha are replaced by a different 17- to 18-amino acid sequence. As reported previously, the 103-kDa DNA ligase III-alpha interacts with the DNA strand break repair protein encoded by the human XRCC1 gene. In contrast, the 96-kDa DNA ligase III-beta does not interact with XRCC1, indicating that DNA ligase III-beta may play a role in cellular functions distinct from the DNA repair pathways involving the DNA ligase III-alpha x XRCC1 complex. The distinct biochemical properties of DNA ligase III-beta, in combination with the tissue- and cell-type-specific expression of DNA ligase III-beta mRNA, suggest that this form of DNA ligase III is specifically involved in the completion of homologous recombination events that occur during meiotic prophase. PMID:9001252

  18. DNA recombination. Recombination initiation maps of individual human genomes.

    PubMed

    Pratto, Florencia; Brick, Kevin; Khil, Pavel; Smagulova, Fatima; Petukhova, Galina V; Camerini-Otero, R Daniel

    2014-11-14

    DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here, we present high-resolution maps of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors may dictate the efficiency of DSB formation. We find evidence for both GC-biased gene conversion and mutagenesis around meiotic DSB hotspots, while frequent colocalization of DSB hotspots with chromosome rearrangement breakpoints implicates the aberrant repair of meiotic DSBs in genomic disorders. Furthermore, our data indicate that DSB frequency is a major determinant of crossover rate. These maps provide new insights into the regulation of meiotic recombination and the impact of meiotic recombination on genome function.

  19. The Use of Recombinant Pseudotype Virus-Like Particles Harbouring Inserted Target Antigen to Generate Antibodies against Cellular Marker p16INK4A

    PubMed Central

    Lasickienė, Rita; Gedvilaite, Alma; Norkiene, Milda; Simanaviciene, Vaida; Sezaite, Indre; Dekaminaviciute, Dovile; Shikova, Evelina; Zvirbliene, Aurelija

    2012-01-01

    Protein engineering provides an opportunity to generate new immunogens with desired features. Previously, we have demonstrated that hamster polyomavirus major capsid protein VP1-derived virus-like particles (VLPs) are highly immunogenic and can be employed for the insertion of foreign epitopes at certain surface-exposed positions. In the current study, we have designed pseudotype VLPs consisting of an intact VP1 protein and VP2 protein fused with the target antigen—cellular marker p16INK4A—at its N terminus. Both proteins coexpressed in yeast were self-assembled to pseudotype VLPs harbouring the inserted antigen on the surface. The pseudotype VLPs were used for generation of antibodies against p16INK4A that represents a potential biomarker for cells transformed by high-risk human papillomavirus (HPV). The pseudotype VLPs induced in immunized mice a strong immune response against the target antigen. The antisera raised against pseudotype VLPs showed specific immunostaining of p16INK4A protein in malignant cervical tissue. Spleen cells of the immunized mice were used to generate monoclonal antibodies against p16INK4A protein. The specificity of antibodies was proven by the immunostaining of HPV-transformed cells. In conclusion, the current study demonstrates the potential of pseudotype VLPs with inserted target antigen as a new type of immunogens to generate antibodies of high diagnostic value. PMID:22629125

  20. Regional Educational Inequality and Political Instability.

    ERIC Educational Resources Information Center

    Monchar, Philip Harris

    1981-01-01

    From a study of 46 nations over the period 1957 to 1973, it is argued that regional educational inequality indicates the presence of other regional social, political, and economic inequalities, and it is all of these factors together that generate feelings of relative deprivation and the pursuant political instability. (Author/SJL)

  1. Propagating Instabilities in Solids

    NASA Astrophysics Data System (ADS)

    Kyriakides, Stelios

    1998-03-01

    Instability is one of the factors which limit the extent to which solids can be loaded or deformed and plays a pivotal role in the design of many structures. Such instabilities often result in localized deformation which precipitates catastrophic failure. Some materials have the capacity to recover their stiffness following a certain amount of localized deformation. This local recovery in stiffness arrests further local deformation and spreading of the instability to neighboring material becomes preferred. Under displacement controlled loading the propagation of the transition fronts can be achieved in a steady-state manner at a constant stress level known as the propagation stress. The stresses in the transition fronts joining the highly deformed zone to the intact material overcome the instability nucleation stresses and, as a result, the propagation stress is usually much lower than the stress required to nucleate the instability. The classical example of this class of material instabilities is L/"uders bands which tend to affect mild steels and other metals. Recent work has demonstrated that propagating instabilities occur in several other materials. Experimental and analytical results from four examples will be used to illustrate this point: First the evolution of L=FCders bands in mild steel strips will be revisited. The second example involves the evolution of stress induced phase transformations (austenite to martensite phases and the reverse) in a shape memory alloy under displacement controlled stretching. The third example is the crushing behavior of cellular materials such as honeycombs and foams made from metals and polymers. The fourth example involves the axial broadening/propagation of kink bands in aligned fiber/matrix composites under compression. The microstructure and, as a result, the micromechanisms governing the onset, localization, local arrest and propagation of instabilities in each of the four materials are vastly different. Despite this

  2. Role of intrinsic flame instability in the excitation of combustion chamber instability

    NASA Astrophysics Data System (ADS)

    Akkerman, V'yacheslav; Law, Chung K.

    2011-11-01

    While considerable progress was made on understanding the various modes of flame instability at the fundamental level, and substantial empirical information and phenomenological descriptions was also accumulated on combustion instability within combustion chambers such as those of rocket engines, few attempts were made to explore the possible macro-scale excitation of the latter through the micro-scale manifestation of the former. Here we present an initial attempt towards identifying such a possibility and the associated coupling mechanisms. We shall incorporate the flame parameters into the classical theories of liquid-propellant rocket engines, and then implement the rocket dynamics into the analyses of premixed and diffusion flame segments. The analyses are conducted for the various instability modes, including the diffusional-thermal, Darrieus-Landau, and Rayleigh-Taylor (body-force) instabilities for premixed flames, and the Kelvin-Helmholtz and body-force instabilities for diffusion flames. The role of chamber-generated sound on stabilizing the inherent flame instabilities and triggering the parametric instability is also considered.

  3. Design and Fabrication of a Hele-Shaw Apparatus for Observing Instabilities of Diffusion Flames

    NASA Technical Reports Server (NTRS)

    Wichman, I. S.; Oravecz-Simpkins, L.; Olson, S.

    2001-01-01

    Examinations of flame fronts spreading over solid fuels in an opposed flow of oxidizer have shown that the flame front fragments into smaller (cellular) flames. These 'flamelets' will oscillate, recombine, or extinguish, indicating that they are in the near extinction limit regime (i.e., to one side of the quenching branch of the flammability map). Onset of unstable cellular flamelet formation for flame spread over thin fuels occurs when a heat-sink substrate is placed a small distance from the underside of the fuel. This heat-sink substrate (or backing) displaces the quenching branch of the flammability map in a direction that causes the instabilities to occur at higher air velocities. Similar near-limit behavior has been observed in other works using different fuels, thus suggesting that these dynamic mechanisms are fuel-independent and therefore fundamental attributes of flames in this near-limit flame spread regime. The objective of this project is to determine the contributions of the hydrodynamic and thermodiffusive mechanisms to the observed formation of flame instabilities. From this, a model of diffusion flame instabilities shall be generated. Previously, experiments were conducted in NASA drop towers, thereby limiting observation time to O(1-5 sec). The NASA tests exhibited flamelet survival for the entire drop time, suggesting that flamelets (i.e., small cellular flames) might exist, if permitted, for longer time periods. By necessity, experiments were limited to thermally thin cellulose fuels (approximately 0.001 in thick): instabilities could form by virtue of faster spread rates over thin fuels. Unstable behavior was unlikely in the short drop time for thicker fuels. In the International Space Station (ISS), microgravity time is unlimited, so both thin and thick fuels can be tested.

  4. A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing

    PubMed Central

    Davidsson, Marcus; Diaz-Fernandez, Paula; Schwich, Oliver D.; Torroba, Marcos; Wang, Gang; Björklund, Tomas

    2016-01-01

    Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode. PMID:27874090

  5. Genomic Instability in Cancer

    PubMed Central

    Abbas, Tarek; Keaton, Mignon A.; Dutta, Anindya

    2013-01-01

    One of the fundamental challenges facing the cell is to accurately copy its genetic material to daughter cells. When this process goes awry, genomic instability ensues in which genetic alterations ranging from nucleotide changes to chromosomal translocations and aneuploidy occur. Organisms have developed multiple mechanisms that can be classified into two major classes to ensure the fidelity of DNA replication. The first class includes mechanisms that prevent premature initiation of DNA replication and ensure that the genome is fully replicated once and only once during each division cycle. These include cyclin-dependent kinase (CDK)-dependent mechanisms and CDK-independent mechanisms. Although CDK-dependent mechanisms are largely conserved in eukaryotes, higher eukaryotes have evolved additional mechanisms that seem to play a larger role in preventing aberrant DNA replication and genome instability. The second class ensures that cells are able to respond to various cues that continuously threaten the integrity of the genome by initiating DNA-damage-dependent “checkpoints” and coordinating DNA damage repair mechanisms. Defects in the ability to safeguard against aberrant DNA replication and to respond to DNA damage contribute to genomic instability and the development of human malignancy. In this article, we summarize our current knowledge of how genomic instability arises, with a particular emphasis on how the DNA replication process can give rise to such instability. PMID:23335075

  6. Expression of recombinant antibodies.

    PubMed

    Frenzel, André; Hust, Michael; Schirrmann, Thomas

    2013-01-01

    Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with "human-like" post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.

  7. Expression of Recombinant Antibodies

    PubMed Central

    Frenzel, André; Hust, Michael; Schirrmann, Thomas

    2013-01-01

    Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with “human-like” post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications. PMID:23908655

  8. Control of low-frequency plasma instabilities by a nonuniform radial electric field

    SciTech Connect

    Komori, A.; Watanabe, K.; Kawai, Y.

    1988-01-01

    Flute instability of a magnetoplasma is generated and controlled experimentally by a nonuniform weak radial electric field. Six concentric electrodes, biased separately, are used to change the radial electric field. The instability, which is different from the velocity shear flute instability, is observed in a plasma with well-type potential and hill-type density profiles.

  9. Oscillatory interfacial instability between miscible fluids

    NASA Astrophysics Data System (ADS)

    Shevtsova, Valentina; Gaponenko, Yuri; Mialdun, Aliaksandr; Torregrosa, Marita; Yasnou, Viktar

    Interfacial instabilities occurring between two fluids are of fundamental interest in fluid dynamics, biological systems and engineering applications such as liquid storage, solvent extraction, oil recovery and mixing. Horizontal vibrations applied to stratified layers of immiscible liquids may generate spatially periodic waving of the interface, stationary in the reference frame of the vibrated cell, referred to as a "frozen wave". We present experimental evidence that frozen wave instability exists between two ordinary miscible liquids of similar densities and viscosities. At the experiments and at the numerical model, two superimposed layers of ordinary liquids, water-alcohol of different concentrations, are placed in a closed cavity in a gravitationally stable configuration. The density and viscosity of these fluids are somewhat similar. Similar to the immiscible fluids this instability has a threshold. When the value of forcing is increased the amplitudes of perturbations grow continuously displaying a saw-tooth structure. The decrease of gravity drastically changes the structure of frozen waves.

  10. Metal pad instabilities in liquid metal batteries

    NASA Astrophysics Data System (ADS)

    Zikanov, Oleg

    2016-11-01

    Strong variations between the electrical conductivities of electrolyte and metal layers in a liquid metal battery indicate the possibility of 'metal pad' instabilities. Deformations of the electrolyte-metal interfaces cause strong perturbations of electric currents, which, hypothetically, can generate Lorentz forces enhancing the deformations. We investigate this possibility using two models: a mechanical analogy and a two-dimensional linearized approximation. It is found that the battery is prone to instabilities of two types. One is similar to the sloshing-wave instability observed in the Hall-Héroult aluminum reduction cells. Another is new and related to the interactions of current perturbations with the azimuthal magnetic field induced by the base current. Financial support was provided by the U.S. National Science Foundation (Grant CBET 1435269).

  11. Bunched beam longitudinal instability: Coherent dipole motion

    SciTech Connect

    Zhang, S.Y.; Weng, W.T.

    1993-04-23

    In this paper, the authors present a new formulation for the longitudinal coherent dipole motion, where a quadrature response of the environmental impedance is shown to be the effective longitudinal impedance for the beam instability. The Robinson-Pedersen formulation for the longitudinal dipole motion is also presented, the difference of the two approaches is discussed in the comparison. The results by using the Sacherer integral equation for the coherent dipole motion can generate the same results as by using the other two approaches, except for a scaling difference. The formulation is further generalized to the rigid bunch motion using signal analysis method, where a form factor shows up naturally. Finally, the formulation is applied to solve the coupled bunch instabilities. Examples of the AGS Booster and the AGS coupled bunch instabilities are used to illustrate the applications of the formulation.

  12. Recombinant protein production technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  13. Therapeutic Recombinant Monoclonal Antibodies

    ERIC Educational Resources Information Center

    Bakhtiar, Ray

    2012-01-01

    During the last two decades, the rapid growth of biotechnology-derived techniques has led to a myriad of therapeutic recombinant monoclonal antibodies with significant clinical benefits. Recombinant monoclonal antibodies can be obtained from a number of natural sources such as animal cell cultures using recombinant DNA engineering. In contrast to…

  14. Genome instability, cancer and aging

    PubMed Central

    Maslov, Alexander Y.; Vijg, Jan

    2015-01-01

    DNA damage-driven genome instability underlies the diversity of life forms generated by the evolutionary process but is detrimental to the somatic cells of individual organisms. The cellular response to DNA damage can be roughly divided in two parts. First, when damage is severe, programmed cell death may occur or, alternatively, temporary or permanent cell cycle arrest. This protects against cancer but can have negative effects on the long term, e.g., by depleting stem cell reservoirs. Second, damage can be repaired through one or more of the many sophisticated genome maintenance pathways. However, erroneous DNA repair and incomplete restoration of chromatin after damage is resolved, produce mutations and epimutations, respectively, both of which have been shown to accumulate with age. An increased burden of mutations and/or epimutations in aged tissues increases cancer risk and adversely affects gene transcriptional regulation, leading to progressive decline in organ function. Cellular degeneration and uncontrolled cell proliferation are both major hallmarks of aging. Despite the fact that one seems to exclude the other, they both may be driven by a common mechanism. Here, we review age related changes in the mammalian genome and their possible functional consequences, with special emphasis on genome instability in stem/progenitor cells. PMID:19344750

  15. Electromagnetic ion beam instabilities

    NASA Technical Reports Server (NTRS)

    Gary, S. P.; Foosland, D. W.; Smith, C. W.; Lee, M. A.; Goldstein, M. L.

    1984-01-01

    The linear theory of electromagnetic instabilities driven by an energetic ion beam streaming parallel to a magnetic field in a homogeneous Vlasov plasma is considered. Numerical solutions of the full dispersion equation are presented. At propagation parallel to the magnetic field, there are four distinct instabilities. A sufficiently energetic beam gives rise to two unstable modes with right-hand polarization, one resonant with the beam, the other nonresonant. A beam with sufficiently large T (perpendicular to B)/T (parallel to B) gives rise to the left-hand ion cyclotron anisotropy instability at relatively small beam velocities, and a sufficiently hot beam drives unstable a left-hand beam resonant mode. The parametric dependences of the growth rates for the three high beam velocity instabilities are presented here. In addition, some properties at oblique propagation are examined. It is demonstrated that, as the beam drift velocity is increased, relative maxima in growth rates can arise at harmonics of the ion cyclotron resonance for both right and left elliptically polarized modes.

  16. Partial Torus Instability

    NASA Astrophysics Data System (ADS)

    Olmedo, Oscar; Zhang, J.

    2010-05-01

    Flux ropes are now generally accepted to be the magnetic configuration of Coronal Mass Ejections (CMEs), which may be formed prior or during solar eruptions. In this study, we model the flux rope as a current-carrying partial torus loop with its two footpoints anchored in the photosphere, and investigate its instability in the context of the torus instability (TI). Previous studies on TI have focused on the configuration of a circular torus and revealed the existence of a critical decay index. Our study reveals that the critical index is a function of the fractional number of the partial torus, defined by the ratio between the arc length of the partial torus above the photosphere and the circumference of a circular torus of equal radius. We refer to this finding the partial torus instability (PTI). It is found that a partial torus with a smaller fractional number has a smaller critical index, thus requiring a more gradually decreasing magnetic field to stabilize the flux rope. On the other hand, the partial torus with a larger fractional number has a larger critical index. In the limit of a circular torus when the fractional number approaches one, the critical index goes to a maximum value that depends on the distribution of the external magnetic field. We demonstrate that the partial torus instability helps us to understand the confinement, growth, and eventual eruption of a flux rope CME.

  17. [Psychodynamics of childhood instability].

    PubMed

    Flavigny, C

    1988-01-01

    This work focuses on the Anglo-Saxon idea concerning "hyperactivity" and "hyperkinesis" and the French-language idea of "child psycho-motor instability". The author's own personal study (having two separate parts, on the one hand studying the psychic functioning of parent and their interaction with their child, and on the other, studying material gathered on the individual psychotherapy of unstable children), goes along with the French school of thought, highlighting the extent of incestuous sexual advances toward children (especially boys) in the family unit and the sexual nature (in the sense of child sexuality) of this excitement as the source of their instability, justifying a comparison between the unstable child and a Don Juan-type of instability. What comes out is epistemological thinking on Anglo-Saxon and French-language ideas, in particular criticism of the pre-suppositions in the Anglo-Saxon way of seeing things, which seems only to envisage the characterization of a syndromic range, rather than an organic etiology, this being more often implicit; distanced by the idea of psychodynamics, which predominate in the French-language studies, integrating the symptom of "psycho-motor instability" in the general "wholeness" of the child and evaluating ways of parent-child interaction.

  18. Roles of RECQ helicases in recombination based DNA repair, genomic stability and aging

    PubMed Central

    Singh, Dharmendra Kumar; Ahn, Byungchan

    2009-01-01

    The maintenance of the stability of genetic material is an essential feature of every living organism. Organisms across all kingdoms have evolved diverse and highly efficient repair mechanisms to protect the genome from deleterious consequences of various genotoxic factors that might tend to destabilize the integrity of the genome in each generation. One such group of proteins that is actively involved in genome surveillance is the RecQ helicase family. These proteins are highly conserved DNA helicases, which have diverse roles in multiple DNA metabolic processes such as DNA replication, recombination and DNA repair. In humans, five RecQ helicases have been identified and three of them namely, WRN, BLM and RecQL4 have been linked to genetic diseases characterized by genome instability, premature aging and cancer predisposition. This helicase family plays important roles in various DNA repair pathways including protecting the genome from illegitimate recombination during chromosome segregation in mitosis and assuring genome stability. This review mainly focuses on various roles of human RecQ helicases in the process of recombination-based DNA repair to maintain genome stability and physiological consequences of their defects in the development of cancer and premature aging. PMID:19083132

  19. Telomerase Deficiency Affects the Formation of Chromosomal Translocations by Homologous Recombination in Saccharomyces cerevisiae

    PubMed Central

    Meyer, Damon H.; Bailis, Adam M.

    2008-01-01

    Telomerase is a ribonucleoprotein complex required for the replication and protection of telomeric DNA in eukaryotes. Cells lacking telomerase undergo a progressive loss of telomeric DNA that results in loss of viability and a concomitant increase in genome instability. We have used budding yeast to investigate the relationship between telomerase deficiency and the generation of chromosomal translocations, a common characteristic of cancer cells. Telomerase deficiency increased the rate of formation of spontaneous translocations by homologous recombination involving telomere proximal sequences during crisis. However, telomerase deficiency also decreased the frequency of translocation formation following multiple HO-endonuclease catalyzed DNA double-strand breaks at telomere proximal or distal sequences before, during and after crisis. This decrease correlated with a sequestration of the central homologous recombination factor, Rad52, to telomeres determined by chromatin immuno-precipitation. This suggests that telomerase deficiency results in the sequestration of Rad52 to telomeres, limiting the capacity of the cell to repair double-strand breaks throughout the genome. Increased spontaneous translocation formation in telomerase-deficient yeast cells undergoing crisis is consistent with the increased incidence of cancer in elderly humans, as the majority of our cells lack telomerase. Decreased translocation formation by recombinational repair of double-strand breaks in telomerase-deficient yeast suggests that the reemergence of telomerase expression observed in many human tumors may further stimulate genome rearrangement. Thus, telomerase may exert a substantial effect on global genome stability, which may bear significantly on the appearance and progression of cancer in humans. PMID:18830407

  20. Roles of RECQ helicases in recombination based DNA repair, genomic stability and aging.

    PubMed

    Singh, Dharmendra Kumar; Ahn, Byungchan; Bohr, Vilhelm A

    2009-06-01

    The maintenance of the stability of genetic material is an essential feature of every living organism. Organisms across all kingdoms have evolved diverse and highly efficient repair mechanisms to protect the genome from deleterious consequences of various genotoxic factors that might tend to destabilize the integrity of the genome in each generation. One such group of proteins that is actively involved in genome surveillance is the RecQ helicase family. These proteins are highly conserved DNA helicases, which have diverse roles in multiple DNA metabolic processes such as DNA replication, recombination and DNA repair. In humans, five RecQ helicases have been identified and three of them namely, WRN, BLM and RecQL4 have been linked to genetic diseases characterized by genome instability, premature aging and cancer predisposition. This helicase family plays important roles in various DNA repair pathways including protecting the genome from illegitimate recombination during chromosome segregation in mitosis and assuring genome stability. This review mainly focuses on various roles of human RecQ helicases in the process of recombination-based DNA repair to maintain genome stability and physiological consequences of their defects in the development of cancer and premature aging.

  1. Modelling Fluidelastic Instability Forces in Tube Arrays

    NASA Astrophysics Data System (ADS)

    Anderson, J. Burns

    Historically, heat exchangers have been among the most failure prone components in nuclear power plants. Most of these failures are due to tube failures as a result of corrosion, fatigue and fretting wear. Fatigue and fretting wear are a result of flow induced vibration through turbulent buffeting and fluidelastic instability mechanisms. Fluidelastic instability is by far the most important and complex mechanism. This research deals with modelling fluidelastic instability and the resulting tube response. The proposed time domain model uses the concept of a flow cell (Hassan & Hayder [16]) to represent the complex flow field inside a shell and tube heat exchanger and accounts for temporal variations in the flow separation points as a result of tube motion. The fluidelastic forces are determined by predicting the attachment lengths. The predicted forces are used to simulate the response of a single flexible tube inside a shell and tube heat exchanger. It was found that accounting for temporal variations in the separation points predicted lower critical flow velocities, than that of fixed attachment and separation points. Once unstable a phase lag is predicted between the fluidelastic forces and tube response. It was determined that the predicted critical flow velocities agreed well with available experimental data. The developed model represents an important step towards a realistic fluidelastic instability model which can be used to design the new generation nuclear steam generators.

  2. High recombination potential of subtype A HIV-1.

    PubMed

    Nikolaitchik, Olga; Keele, Brandon; Gorelick, Robert; Alvord, W Gregory; Mazurov, Dmitriy; Pathak, Vinay K; Hu, Wei-Shau

    2015-10-01

    Recombination can assort polymorphic alleles to increase diversity in the HIV-1 population. To better understand the recombination potential of subtype A HIV-1, we generated viruses containing sequences from two variants circulating in Russia and analyzed the polymerase gene (pol) of the recombinants after one round of HIV-1 replication using single-genome sequencing. We observed that recombination occurred throughout pol and could easily assort alleles containing mutations that conferred resistance to currently approved antivirals. We measured the recombination rate in various regions of pol including a G-rich region that has been previously proposed to be a recombination hot spot. Our study does not support a recombination hot spot in this G-rich region. Importantly, of the 58 proviral sequences containing crossover event(s) in pol, we found that each sequence was a unique genotype indicating that recombination is a powerful genetic mechanism in assorting the genomes of subtype A HIV-1 variants.

  3. Photoionization and Recombination

    NASA Technical Reports Server (NTRS)

    Nahar, Sultana N.

    2000-01-01

    Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

  4. Gravitational Instability in Suspension Flows

    NASA Technical Reports Server (NTRS)

    Carpen, Ileana C.; Brady, John F.

    2002-01-01

    The gravity-driven flow of non-neutrally buoyant suspensions is shown to be unstable to spanwise perturbations when the shearing motion generates a density profile that increases with height. The instability is simply due to having heavier material over light. The wavelength of the perturbation is found to be on the order of the thickness of the suspension layer. The parameters important to the problem are the angle of inclination of the layer relative to gravity, the relative density difference between the particles and fluid, the ratio of the particle size to the suspension layer, and the bulk volume fraction of particles. An example showing the growth rate as a function of wave number is shown.

  5. Mapping Instabilities in Polymer Friction

    NASA Astrophysics Data System (ADS)

    Rand, Charles; Crosby, Alfred

    2005-03-01

    Schallamach waves are instabilities that occur as interfaces between a soft elastomer and rigid surface slide past each other.(1) The presence of Schallamach waves can lead to drastic changes in frictional properties. Although the occurrence of Schallamach waves has been studied for the past several decades, a general map relating fundamental material properties, geometry, and operating conditions (i.e. speed and temperature) has not been established. Using a combinatorial approach, we illustrate the role of modulus, testing velocity and surface energetics of crosslinked poly(dimethyl siloxane) on the generation Schallamach waves. This knowledge will be used with polymer patterning processes to fabricate responsive coatings for applications such as anti-fouling coatings. (1)Schallamach, A.;Wear 1971,17, 301-312.

  6. Implications of recombination for HIV diversity.

    PubMed

    Ramirez, Bertha Cecilia; Simon-Loriere, Etienne; Galetto, Roman; Negroni, Matteo

    2008-06-01

    The human immunodeficiency virus (HIV) population is characterised by extensive genetic variability that results from high error and recombination rates of the reverse transcription process, and from the fast turnover of virions in HIV-infected individuals. Among the viral variants encountered at the global scale, recombinant forms are extremely abundant. Some of these recombinants (known as circulating recombinant forms) become fixed and undergo rapid expansion in the population. The reasons underlying their epidemiological success remain at present poorly understood and constitute a fascinating area for future research to improve our understanding of immune escape, pathogenicity and transmission. Recombinant viruses are generated during reverse transcription as a consequence of template switching between the two genetically different genomic RNAs present in a heterozygous virus. Recombination can thereby generate shortcuts in evolution by producing mosaic reverse transcription products of parental genomes. Therefore, in a single infectious cycle multiple mutations that are positively selected can be combined or, conversely, negatively selected mutations can be removed. Recombination is therefore involved in different aspects of HIV evolution, adaptation to its host, and escape from antiviral treatments.

  7. Thermal instability in the inner coma of a comet

    NASA Technical Reports Server (NTRS)

    Milikh, G. M.; Sharma, A. S.

    1995-01-01

    The spacecraft and ground based observations of comet Halley inner coma showed a localized ion density depletion region whose origin is not well understood. Although it has been linked to a thermal instability associated with negative ions, the photodetachment lifetime of negative ions (approximately 1 sec) is too short compared to the electron attachment time scale (approximately 100 sec) for this process to have a significant effect. A mechanism for the ion density depletion based on the thermal instability of the cometary plasma due to the excitation of rotational and vibrational levels of water molecules is proposed. The electron energy losses due to these processes peak near 4000 K (0.36 eV) and at temperatures higher than this value a localized cooling leads to further cooling (thermal instability) due to the increased radiation loss. The resulting increase in recombination leads to an ion density depletion and the estimates for this depletion at comet Halley agree with the observations.

  8. Identifying Recombination Hot Spots in the HIV-1 Genome

    PubMed Central

    Smyth, Redmond P.; Schlub, Timothy E.; Grimm, Andrew J.; Waugh, Caryll; Ellenberg, Paula; Chopra, Abha; Mallal, Simon; Cromer, Deborah

    2014-01-01

    ABSTRACT HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified full-length HIV-1 genome and high-throughput sequence analysis to study recombination in gag and pol in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies. IMPORTANCE The ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in gag and pol and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of

  9. Analysis of nuclear reactor instability phenomena. Progress report

    SciTech Connect

    Lahey, R.T. Jr.

    1993-03-01

    The phenomena known as density-wave instability often occurs in phase change systems, such as boiling water nuclear reactors (BWRS). Our current understanding of density-wave oscillations is in fairly good shape for linear phenomena (eg, the onset of instabilities) but is not very advanced for non-linear phenomena [Lahey and Podowski, 1989]. In particular, limit cycle and chaotic instability modes are not well understood in boiling systems such as current and advanced generation BWRs (eg, SBWR). In particular, the SBWR relies on natural circulation and is thus inherently prone to problems with density-wave instabilities. The purpose of this research is to develop a quantitative understanding of nonlinear nuclear-coupled density-wave instability phenomena in BWRS. This research builds on the work of Achard et al [1985] and Clausse et al [1991] who showed, respectively, that Hopf bifurcations and chaotic oscillations may occur in boiling systems.

  10. INSTABILITY OF MAGNETIZED IONIZATION FRONTS SURROUNDING H II REGIONS

    SciTech Connect

    Kim, Jeong-Gyu; Kim, Woong-Tae E-mail: wkim@astro.snu.ac.kr

    2014-12-20

    An ionization front (IF) surrounding an H II region is a sharp interface where a cold neutral gas makes the transition to a warm ionized phase by absorbing UV photons from central stars. We investigate the instability of a plane-parallel D-type IF threaded by parallel magnetic fields, by neglecting the effects of recombination within the ionized gas. We find that weak D-type IFs always have the post-IF magnetosonic Mach number M{sub M2}≤1. For such fronts, magnetic fields increase the maximum propagation speed of the IFs, while reducing the expansion factor α by a factor of 1 + 1/(2β{sub 1}) compared to the unmagnetized case, with β{sub 1} denoting the plasma beta in the pre-IF region. IFs become unstable to distortional perturbations owing to gas expansion across the fronts, exactly analogous to the Darrieus-Landau instability of ablation fronts in terrestrial flames. The growth rate of the IF instability is proportional linearly to the perturbation wavenumber, as well as the upstream flow speed, and approximately to α{sup 1/2}. The IF instability is stabilized by gas compressibility and becomes completely quenched when the front is D-critical. The instability is also stabilized by magnetic pressure when the perturbations propagate in the direction perpendicular to the fields. When the perturbations propagate in the direction parallel to the fields, on the other hand, it is magnetic tension that reduces the growth rate, completely suppressing the instability when M{sub M2}{sup 2}<2/(2β{sub 1}−1). When the front experiences an acceleration, the IF instability cooperates with the Rayleigh-Taylor instability to make the front more unstable.

  11. Instability in poroelastic media

    NASA Astrophysics Data System (ADS)

    Pramanik, Satyajit; Wettlaufer, John

    2016-11-01

    Fluid flow in deformable porous materials, which play significant role in different biological and geological systems of wide range of scales, is a highly nonlinear problem. Feedback from the elastic deformation of the solid skeleton on the fluid flow and vice-versa gives rise to pattern formation in the porosity structure of the skeleton. We view some of these patterns as instabilities of the coupled fluid-solid system. Due to highly nonlinear nature of the problem, very little has been understood about this instability. Here, we use a minimal poroelastic theory to understand the pattern formation in a fluid-saturated poroelastic material and discuss the similarities/differences with viscous fingering in non-deformable porous media.

  12. [Orthostatic tremor inducing instability].

    PubMed

    Manrique-Huarte, Raquel; Arcocha, Juan; Pérez-Fernández, Nicolás

    2012-01-01

    Orthostatic tremor (OT) is a neurological disease of unknown aetiology. It is defined by the presence of a 10-20 Hz tremor in the legs while standing still. Symptoms described are dizziness and instability that diminish if the patient sits down or leans on something; drinking small amounts of alcohol significantly reduces OT. Due to the dizziness and/or unsteadiness, these patients are usually referred to the neuro-otology department. We report 4 cases diagnosed with OT. The diagnosis of OT should be considered for patients with instability. The clinical history is a key factor to suspect this entity, and the diagnosis is given by the register of 10-20 Hz contractions on limb electromyography. Treatment for this disease consists of medical treatment; the first option is clonazepam.

  13. Wrist Instability After Injury

    PubMed Central

    Muminagic, Sahib; Kapidzic, Tarik

    2012-01-01

    Fractures of the bones that make the wrist joint together with injury to the ligaments and joint capsules are frequent traumas. It can cause besides limited movement also the pathological mobility. These mild injuries often do not provide the degree of recognizable symptoms and signs. They are diagnosed by X-ray imaging, stress images. Before arthrography was an important method, but nowadays arthroscopy has the advantage. Fresh bone and ligament injuries can be and should be repaired in the early posttraumatic period. Unrecognized and undiagnosed injuries are leading to instability of the wrist, to motion abnormalities or impingement overload syndrome. In the treatment of instability important place have reconstruction of the ligaments and arthrodesis of the wrist. PMID:23678318

  14. Modulation instability: The beginning

    NASA Astrophysics Data System (ADS)

    Noskov, Roman; Belov, Pavel; Kivshar, Yuri

    2012-11-01

    The study of metal nanoparticles plays a central role in the emerging novel technologies employing optics beyond the diffraction limit. Combining strong surface plasmon resonances, high intrinsic nonlinearities and deeply subwavelength scales, arrays of metal nanoparticles offer a unique playground to develop novel concepts for light manipulation at the nanoscale. Here we suggest a novel principle to control localized optical energy in chains of nonlinear subwavelength metal nanoparticles based on the fundamental nonlinear phenomenon of modulation instability. In particular, we demonstrate that modulation instability can lead to the formation of long-lived standing and moving nonlinear localized modes of several distinct types such as bright and dark solitons, oscillons, and domain walls. We analyze the properties of these nonlinear localized modes and reveal different scenarios of their dynamics including transformation of one type of mode to another. We believe this work paves a way towards the development of nonlinear nanophotonics circuitry.

  15. Instabilities in sensory processes

    NASA Astrophysics Data System (ADS)

    Balakrishnan, J.

    2014-07-01

    In any organism there are different kinds of sensory receptors for detecting the various, distinct stimuli through which its external environment may impinge upon it. These receptors convey these stimuli in different ways to an organism's information processing region enabling it to distinctly perceive the varied sensations and to respond to them. The behavior of cells and their response to stimuli may be captured through simple mathematical models employing regulatory feedback mechanisms. We argue that the sensory processes such as olfaction function optimally by operating in the close proximity of dynamical instabilities. In the case of coupled neurons, we point out that random disturbances and fluctuations can move their operating point close to certain dynamical instabilities triggering synchronous activity.

  16. Open field lines instabilities

    SciTech Connect

    Pozzoli, R. |

    1995-09-01

    The results of some recent theoretical papers dealing with flute-like instabilities in the scrape-off layer of a tokamak with limiter configuration, where the magnetic field intersects conducting walls, are briefly recalled. Attention is then paid to the instability driven by the electron temperature gradient across the field in conjunction with the formation of the Debye sheath at the boundary, and to the effects due to the inclination of the end walls with respect to the magnetic field. When a divertor configuration is considered, important modifications are found owing to the strong deformations of the flux tubes passing near the {ital x}-point, which contrast the onset of flute-like perturbations, and to the stochasticity of field lines that can be excited by magnetic field perturbations. {copyright} {ital 1995 American Institute of Physics.}

  17. Modulation instability: The beginning

    NASA Astrophysics Data System (ADS)

    Zakharov, V. E.; Ostrovsky, L. A.

    2009-03-01

    We discuss the early history of an important field of “sturm and drang” in modern theory of nonlinear waves. It is demonstrated how scientific demand resulted in independent and almost simultaneous publications by many different authors on modulation instability, a phenomenon resulting in a variety of nonlinear processes such as envelope solitons, envelope shocks, freak waves, etc. Examples from water wave hydrodynamics, electrodynamics, nonlinear optics, and convection theory are given.

  18. Chronic ankle instability: Current perspectives

    PubMed Central

    Al-Mohrej, Omar A.; Al-Kenani, Nader S.

    2016-01-01

    Ankle sprain is reported to be among the most common recurrent injuries. About 20% of acute ankle sprain patients develop chronic ankle instability. The failure of functional rehabilitation after acute ankle sprain leads to the development of chronic ankle instability. Differentiation between functional and anatomical ankle instability is very essential to guide the proper treatment. Stability testing by varus stress test and anterior drawer test should be carried out. Subtalar instability is an important pathology that is commonly by passed during the assessment of chronic ankle instability. Unlike acute ankle sprain, chronic ankle instability might require surgical intervention. The surgical and conservative management options can be very much developed by in-depth knowledge of the ankle anatomy, biomechanics, and pathology. Anatomical repair, augmentation by tendon, or both are the basic methods of surgical intervention. Arthroscopy is becoming more popular in the management of chronic ankle instability. PMID:27843798

  19. Combustion instability analysis

    NASA Technical Reports Server (NTRS)

    Chung, T. J.

    1990-01-01

    A theory and computer program for combustion instability analysis are presented. The basic theoretical foundation resides in the concept of entropy-controlled energy growth or decay. Third order perturbation expansion is performed on the entropy-controlled acoustic energy equation to obtain the first order integrodifferential equation for the energy growth factor in terms of the linear, second, and third order energy growth parameters. These parameters are calculated from Navier-Stokes solutions with time averages performed on as many Navier-Stokes time steps as required to cover at least one peak wave period. Applications are made for a 1-D Navier-Stokes solution for the Space Shuttle Main Engine (SSME) thrust chamber with cross section area variations taken into account. It is shown that instability occurs when the mean pressure is set at 2000 psi with 30 percent disturbances. Instability also arises when the mean pressure is set at 2935 psi with 20 percent disturbances. The system with mean pressures and disturbances more adverse that these cases were shown to be unstable.

  20. Identifying the Important HIV-1 Recombination Breakpoints

    PubMed Central

    Fan, Jun; Simon-Loriere, Etienne; Arts, Eric J.; Negroni, Matteo; Robertson, David L.

    2008-01-01

    Recombinant HIV-1 genomes contribute significantly to the diversity of variants within the HIV/AIDS pandemic. It is assumed that some of these mosaic genomes may have novel properties that have led to their prevalence, particularly in the case of the circulating recombinant forms (CRFs). In regions of the HIV-1 genome where recombination has a tendency to convey a selective advantage to the virus, we predict that the distribution of breakpoints—the identifiable boundaries that delimit the mosaic structure—will deviate from the underlying null distribution. To test this hypothesis, we generate a probabilistic model of HIV-1 copy-choice recombination and compare the predicted breakpoint distribution to the distribution from the HIV/AIDS pandemic. Across much of the HIV-1 genome, we find that the observed frequencies of inter-subtype recombination are predicted accurately by our model. This observation strongly indicates that in these regions a probabilistic model, dependent on local sequence identity, is sufficient to explain breakpoint locations. In regions where there is a significant over- (either side of the env gene) or under- (short regions within gag, pol, and most of env) representation of breakpoints, we infer natural selection to be influencing the recombination pattern. The paucity of recombination breakpoints within most of the envelope gene indicates that recombinants generated in this region are less likely to be successful. The breakpoints at a higher frequency than predicted by our model are approximately at either side of env, indicating increased selection for these recombinants as a consequence of this region, or at least part of it, having a tendency to be recombined as an entire unit. Our findings thus provide the first clear indication of the existence of a specific portion of the genome that deviates from a probabilistic null model for recombination. This suggests that, despite the wide diversity of recombinant forms seen in the viral

  1. Weibel Instability Driven by Spatially Anisotropic Density Structures

    NASA Astrophysics Data System (ADS)

    Tomita, Sara; Ohira, Yutaka

    2016-07-01

    Observations of afterglows of gamma-ray bursts (GRBs) suggest that post-shock magnetic fields are strongly amplified to about 100 times the shock-compressed value. The Weibel instability appears to play an important role in generating the magnetic field. However, recent simulations of collisionless shocks in homogeneous plasmas show that the magnetic field generated by the Weibel instability rapidly decays. There must be some density fluctuations in interstellar and circumstellar media. The density fluctuations are anisotropically compressed in the downstream region of relativistic shocks. In this paper, we study the Weibel instability in electron-positron plasmas with spatially anisotropic density distributions by means of two-dimensional particle-in-cell simulations. We find that large magnetic fields are maintained for a longer time by the Weibel instability driven by spatially anisotropic density structure. Particles anisotropically escape from the high density region, so that a temperature anisotropy is generated and the Weibel instability becomes unstable. Our simulation results suggest that the Weibel instability driven by an anisotropic density structure can generate sufficiently large magnetic fields and they can cover sufficiently large regions to explain the afterglow emission of GRBs.

  2. Mechanism of Secondary Instability of Flow around a Circular Cylinder

    NASA Astrophysics Data System (ADS)

    Dou, Hua-Shu; Ben, An-Qing; Fluid Mechanics Research Team Team

    2016-11-01

    Flow around a circular cylinder in infinite domain is simulated with large eddy simulation at Re =200, and the mechanism of the origin of secondary vortex street is analyzed. The simulation results show that the vortex street generated in the cylinder near wake disappears as the flow moving downstream. Secondary instability occurs in far wake of the cylinder after the primary vortex street dying away. The processes of first instability and secondary instability in the cylinder wake are recorded in the simulation. The instability of the entire flow field is studied with the energy gradient theory. It is found that it is the high value of the energy gradient function generated by the zero velocity gradients that leads to the instability. As the vortex developing at rear of the cylinder, the value of the energy gradient function becomes low downstream, which leads to the vortex dying away. At further downstream, the value of the energy gradient function is enlarged again because of the role of perturbation, which leads to the secondary instability. It can be concluded that the interaction of the variation of the value of the energy gradient function and the perturbation leads to the occurrence of secondary instability.

  3. Recombination of cluster ions

    NASA Technical Reports Server (NTRS)

    Johnsen, Rainer

    1993-01-01

    Some of our recent work on molecular band emissions from recombination of molecular dimer ions (N4(+) and CO(+) CO) is discussed. Much of the experimental work was done by Y. S. Cao; the results on N4(+) recombination have been published. A brief progress report is given on our ongoing measurements of neutral products of recombination using the flowing-afterglow Langmuir-probe technique in conjunction with laser-induced fluorescence.

  4. The collisionless magnetoviscous-thermal instability

    SciTech Connect

    Islam, Tanim

    2014-05-20

    It is likely that nearly all central galactic massive and supermassive black holes are nonradiative: their accretion luminosities are orders of magnitude below what can be explained by efficient black hole accretion within their ambient environments. These objects, of which Sagittarius A* is the best-known example, are also dilute (mildly collisional to highly collisionless) and optically thin. In order for accretion to occur, magnetohydrodynamic (MHD) instabilities must develop that not only transport angular momentum, but also gravitational energy generated through matter infall, outward. A class of new magnetohydrodynamical fluid instabilities—the magnetoviscous-thermal instability (MVTI)—was found to transport angular momentum and energy along magnetic field lines through large (fluid) viscosities and thermal conductivities. This paper describes the analog to the MVTI, the collisionless MVTI (CMVTI), that similarly transports energy and angular momentum outward, expected to be important in describing the flow properties of hot, dilute, and radiatively inefficient accretion flows around black holes. We construct a local equilibrium for MHD stability analysis in this differentially rotating disk. We then find and characterize specific instabilities expected to be important in describing their flow properties, and show their qualitative similarities to instabilities derived using the fluid formalism. We conclude with further work needed in modeling this class of accretion flow.

  5. Instabilities of soft films on compliant substrates

    NASA Astrophysics Data System (ADS)

    Holland, M. A.; Li, B.; Feng, X. Q.; Kuhl, E.

    2017-01-01

    Instabilities in bilayered systems can generate a wide variety of patterns ranging from simple folds, wrinkles, and creases to complex checkerboards, hexagons, and herringbones. Physics-based theories traditionally model these systems as a thin film on a thick substrate under confined compression and assume that the film is orders of magnitude stiffer than the substrate. However, instability phenomena in soft films on soft substrates remain insufficiently understood. Here we show that soft bilayered systems are highly sensitive to the stiffness ratio, boundary conditions, and mode of compression. In a systematic analysis over a wide range of stiffness ratios, from 0.1 < β < 1000 , for eight different compression modes including whole-domain compression, substrate prestretch, and film growth, we observe significantly different instability characteristics in the low-stiffness-contrast regime, for β < 10 . While systems with inverse stiffness ratios under whole-domain compression are unstable for a wide range of wrinkling modes, under film-only compression, the same systems display distinct wrinkling modes.Strikingly, these discrepancies disappear when using measures of effective strain, effective stiffness, and effective wavelength. Our study suggests that future instability studies should use these effective measures to standardize their findings. Our results have important applications in soft matter and living matter physics, where stiffness contrasts are low and small environmental changes can have large effects on morphogenesis, pattern tabselection, and the evolution of shape.

  6. Remote feedback stabilization of tokamak instabilities

    SciTech Connect

    Sen, A.K. )

    1994-05-01

    A novel remote suppressor consisting of an injected ion beam has been used for the stabilization of plasma instabilities. A collisionless curvature-driven trapped-particle instability, an [bold E][times][bold B] flute mode and an ion temperature gradient (ITG) instability have been successfully suppressed down to noise levels using this scheme. Furthermore, the first experimental demonstration of a multimode feedback stabilization with a single sensor--suppressor pair has been achieved. Two modes (an [bold E][times][bold B] flute and an ITG mode) were simultaneously stabilized with a simple state-feedback-type method where more state'' information was generated from a single-sensor Langmuir probe by appropriate signal processing. The above experiments may be considered as paradigms for controlling several important tokamak instabilities. First, feedback suppression of edge fluctuations in a tokamak with a suitable form of insulated segmented poloidal limiter sections used as Langmuir-probe-like suppressors is proposed. Other feedback control schemes are proposed for the suppression of electrostatic core fluctuations via appropriately phased ion density input from a modulated neutral beam. Most importantly, a scheme to control major disruptions in tokamaks via feedback suppression of kink (and possibly) tearing modes is discussed. This may be accomplished by using a modulated neutral beam suppressor in a feedback loop, which will supply a momentum input of appropriate phase and amplitude. Simple theoretical models predict modest levels of beam energy, current, and power.

  7. Collisionless shock waves mediated by Weibel Instability

    NASA Astrophysics Data System (ADS)

    Naseri, Neda; Ruan, Panpan; Zhang, Xi; Khudik, Vladimir; Shvets, Gennady

    2015-11-01

    Relativistic collisionless shocks are common events in astrophysical environments. They are thought to be responsible for generating ultra-high energy particles via the Fermi acceleration mechanism. It has been conjectured that the formation of collisionless shocks is mediated by the Weibel instability that takes place when two initially cold, unmagnetized plasma shells counter-propagate into each other with relativistic drift velocities. Using a PIC code, VLPL, which is modified to suppress numerical Cherenkov instabilities, we study the shock formation and evolution for asymmetric colliding shells with different densities in their own proper reference frame. Plasma instabilities in the region between the shock and the precursor are also investigated using a moving-window simulation that advances the computational domain at the shock's speed. This method helps both to save computation time and avoid severe numerical Cherenkov instabilities, and it allows us to study the shock evolution in a longer time period. Project is supported by US DOE grants DE-FG02-04ER41321 and DE-FG02-07ER54945.

  8. Electronegative Plasma Instabilities in Industrial Pulsed Plasmas

    NASA Astrophysics Data System (ADS)

    Pribyl, Patrick; Hansen, Anders; Gekelman, Walter

    2016-10-01

    Electronegative gases that are important for industrial etch processes have a series of instabilities that occur at process relevant conditions. These have been studied since the 1990s, but are becoming a much more important today as plasma reactors are being pushed to produce ever finer features, and tight control of the etch process is becoming crucial. The experiments are being done in a plasma etch tool that closely simulates a working industrial device. ICP coils in different configurations are driven by a pulsed RF generators operating at 2-5 MHz. A computer controlled automated probe drive can access a volume above the substrate. The probe can be a Langmuir probe, a ``Bdot'' probe, or an emissive probe the latter used for more accurate determination of plasma potential. A microwave interferometer is available to measure line-averaged electron density. The negative ion instability is triggered depending upon the gas mix (Ar,SF6) , pressure and RF power. The instability can be ``burned through'' by rapidly pulsing the RF power. In this study we present measurements of plasma current and density distribution over the wafer before, after and during the rapid onset of the instability. Work suported by NSF-GOALI Award and done at the BAPSF.

  9. Recombinant protein polymers in biomaterials.

    PubMed

    Kim, Wookhyun

    2013-01-01

    Naturally occurring protein-based materials have been found that function as critical components in biomechanical response, fibers and adhesives. A relatively small but growing number of recombinant protein-based materials that mimic the desired features of their natural sources, such as collagens, elastins and silks, are considered as an alternative to conventional synthetic polymers. Advances in genetic engineering have facilitated the synthesis of repetitive protein polymers with precise control of molecular weights which are designed by using synthetic genes encoding tandem repeats of oligopeptide originating from a modular domain of natural proteins. Many repeat sequences as protein polymer building blocks adopt a well-defined secondary structure and undergo self-assembly to result in physically cross-linked networks or with chemical cross-linking so that further form three-dimensional architectures similar to natural counterparts. In this review, recombinant protein polymers currently developed will be presented that have emerged as promising class of next generation biomaterials.

  10. Interfacial instabilities in vibrated fluids

    NASA Astrophysics Data System (ADS)

    Porter, Jeff; Laverón-Simavilla, Ana; Tinao Perez-Miravete, Ignacio; Fernandez Fraile, Jose Javier

    2016-07-01

    Vibrations induce a range of different interfacial phenomena in fluid systems depending on the frequency and orientation of the forcing. With gravity, (large) interfaces are approximately flat and there is a qualitative difference between vertical and horizontal forcing. Sufficient vertical forcing produces subharmonic standing waves (Faraday waves) that extend over the whole interface. Horizontal forcing can excite both localized and extended interfacial phenomena. The vibrating solid boundaries act as wavemakers to excite traveling waves (or sloshing modes at low frequencies) but they also drive evanescent bulk modes whose oscillatory pressure gradient can parametrically excite subharmonic surface waves like cross-waves. Depending on the magnitude of the damping and the aspect ratio of the container, these locally generated surfaces waves may interact in the interior resulting in temporal modulation and other complex dynamics. In the case where the interface separates two fluids of different density in, for example, a rectangular container, the mass transfer due to vertical motion near the endwalls requires a counterflow in the interior region that can lead to a Kelvin-Helmholtz type instability and a ``frozen wave" pattern. In microgravity, the dominance of surface forces favors non-flat equilibrium configurations and the distinction between vertical and horizontal applied forcing can be lost. Hysteresis and multiplicity of solutions are more common, especially in non-wetting systems where disconnected (partial) volumes of fluid can be established. Furthermore, the vibrational field contributes a dynamic pressure term that competes with surface tension to select the (time averaged) shape of the surface. These new (quasi-static) surface configurations, known as vibroequilibria, can differ substantially from the hydrostatic state. There is a tendency for the interface to orient perpendicular to the vibrational axis and, in some cases, a bulge or cavity is induced

  11. Bayesian inference of shared recombination hotspots between humans and chimpanzees.

    PubMed

    Wang, Ying; Rannala, Bruce

    2014-12-01

    Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies.

  12. Suppressing shape instabilities to discover the Bjerknes force instability (L).

    PubMed

    Alibakhshi, Mohammad A; Holt, R Glynn

    2011-11-01

    For sufficiently strong acoustic forcing in a standing wave field, subresonant size bubbles are predicted to be repelled from the pressure antinode. Single bubble sonoluminescence (SBSL) conditions in water do not allow the observation of this instability. This study investigates the possibility that increasing the viscosity of the host liquid can preferentially suppress shape instabilities of a bubble and allow SBSL experiments to be limited by the Bjerknes force instability.

  13. Instability issues for the ESS linac and rings

    SciTech Connect

    Rees, G. H.

    1999-12-03

    Comments are made on beam instability issues in the ESS linac and rings. The topics of interest in the linac are halo generation in the absence and presence of machine imperfections, and also the stability of the momentum ramping of the output beam. In the case of the rings, the main concern is for fast coherent transverse instabilities due to the combined effect of coupled electron-proton oscillations and interaction with the wall impedances.

  14. Recombinant baculoviruses for insect control.

    PubMed

    Inceoglu, A B; Kamita, S G; Hinton, A C; Huang, Q; Severson, T F; Kang, K; Hammock, B D

    2001-10-01

    Baculoviruses are double-stranded DNA viruses which are highly selective for several insect groups. They are valuable natural control agents, but their utility in many agricultural applications has been limited by their slow speed of kill and narrow host specificity. Baculoviruses have been genetically modified to express foreign genes under powerful promoters in order to accelerate their speed of kill. In our and other laboratories, the expression of genes coding for insect juvenile hormone esterases and various peptide neurotoxins has resulted in recombinant baculoviruses with promise as biological insecticides. These viruses are efficacious in the laboratory, greenhouse and field and dramatically reduce damage caused by insect feeding. The recombinant viruses synergize and are synergized by classical pesticides such as pyrethroids. Since they are highly selective for pest insects, they can be used without disrupting biological control. Because the recombinant virus produces fewer progeny in infected larvae than the wild-type virus, they are rapidly out-competed in the ecosystem. The viruses can be used effectively with crops expressing endotoxins of Bacillus thuringiensis. They can be produced industrially but also by village industries, indicating that they have the potential to deliver sustainable pest control in developing countries. It remains to be seen, however, whether the current generation of recombinant baculoviruses will be competitive with the new generation of synthetic chemical pesticides. Current research clearly indicates, though, that the use of biological vectors of genes for insect control will find a place in agriculture. Baculoviruses will also prove valuable in testing the potential utility of proteins and peptides for insect control.

  15. Radiative-convective instability

    NASA Astrophysics Data System (ADS)

    Emanuel, Kerry; Wing, Allison A.; Vincent, Emmanuel M.

    2014-03-01

    equilibrium (RCE) is a simple paradigm for the statistical equilibrium the earth's climate would exhibit in the absence of lateral energy transport. It has generally been assumed that for a given solar forcing and long-lived greenhouse gas concentration, such a state would be unique, but recent work suggests that more than one stable equilibrium may be possible. Here we show that above a critical specified sea surface temperature, the ordinary RCE state becomes linearly unstable to large-scale overturning circulations. The instability migrates the RCE state toward one of the two stable equilibria first found by Raymond and Zeng (2000). It occurs when the clear-sky infrared opacity of the lower troposphere becomes so large, owing to high water vapor concentration, that variations of the radiative cooling of the lower troposphere are governed principally by variations in upper tropospheric water vapor. We show that the instability represents a subcritical bifurcation of the ordinary RCE state, leading to either a dry state with large-scale descent, or to a moist state with mean ascent; these states may be accessed by finite amplitude perturbations to ordinary RCE in the subcritical state, or spontaneously in the supercritical state. As first suggested by Raymond (2000) and Sobel et al. (2007), the latter corresponds to the phenomenon of self-aggregation of moist convection, taking the form of cloud clusters or tropical cyclones. We argue that the nonrobustness of self-aggregation in cloud system resolving models may be an artifact of running such models close to the critical temperature for instability.

  16. Heterologous Plasmid DNA Prime-Recombinant Human Adenovirus 5 Boost Vaccination Generates a Stable Pool of Protective Long-Lived CD8+ T Effector Memory Cells Specific for a Human Parasite, Trypanosoma cruzi▿†

    PubMed Central

    Rigato, Paula Ordonhez; de Alencar, Bruna C.; de Vasconcelos, José Ronnie C.; Dominguez, Mariana R.; Araújo, Adriano F.; Machado, Alexandre V.; Gazzinelli, Ricardo T.; Bruna-Romero, Oscar; Rodrigues, Mauricio M.

    2011-01-01

    Recently, we described a heterologous prime-boost strategy using plasmid DNA followed by replication-defective human recombinant adenovirus type 5 as a powerful strategy to elicit long-lived CD8+ T-cell-mediated protective immunity against experimental systemic infection of mice with a human intracellular protozoan parasite, Trypanosoma cruzi. In the present study, we further characterized the protective long-lived CD8+ T cells. We compared several functional and phenotypic aspects of specific CD8+ T cells present 14 or 98 days after the last immunizing dose and found the following: (i) the numbers of specific cells were similar, as determined by multimer staining or by determining the number of gamma interferon (IFN-γ)-secreting cells by enzyme-linked immunospot (ELISPOT) assay; (ii) these cells were equally cytotoxic in vivo; (iii) following in vitro stimulation, a slight decline in the frequency of multifunctional cells (CD107a+ IFN-γ+ or CD107a+ IFN-γ+ tumor necrosis factor alpha positive [TNF-α+]) was paralleled by a significant increase of CD107a singly positive cells after 98 days; (iv) the expression of several surface markers was identical, except for the reexpression of CD127 after 98 days; (v) the use of genetically deficient mice revealed a role for interleukin-12 (IL-12)/IL-23, but not IFN-γ, in the maintenance of these memory cells; and (vi) subsequent immunizations with an unrelated virus or a plasmid vaccine or the depletion of CD4+ T cells did not significantly erode the number or function of these CD8+ T cells during the 15-week period. From these results, we concluded that heterologous plasmid DNA prime-adenovirus boost vaccination generated a stable pool of functional protective long-lived CD8+ T cells with an effector memory phenotype. PMID:21357719

  17. Recombinant generation of two fragments of the rat complement inhibitory factor H [FH(SCR1-7) and FH(SCR1-4)] and their structural and functional characterization in comparison to FH isolated from rat serum.

    PubMed

    Demberg, T; Heine, I; Götze, O; Altermann, W W; Seliger, B; Schlaf, G

    2006-01-01

    Factor H (FH) is the predominant soluble inhibitor of the complement system. With a concentration of 200-800 microg/ml in human and rat plasma it acts as a cofactor for the soluble factor I (FI)-mediated cleavage of the component C3b to iC3b. Furthermore it competes with factor B for binding to C3b and C3(H2O) and promotes the dissociation of the C3bBb complex. FH is a monomer of about 155 kDa which comprises 20 short consensus repeats (SCR), each of which is composed of approximately 60 amino acid (aa) residues. Two functional fragments of FH comprising the SCR1-4 or SCR1-7 were generated using either the Baculovirus system or stably transfected human embryonal kidney cells, respectively. These fragments, as well as FH purified from rat serum, were first analyzed for their relative molecular weights (Mr) using non-reducing or reducing SDS-PAGE. The Mr of the FH variants differed by about 20% depending on the experimental conditions employed. Only the Mr of proteins separated under reducing conditions were in accordance with the MW calculated from the aa sequence. Analyses of the glycosylation patterns using PAS-staining showed a lack of staining of the recombinant variants (SCR1-4 and SCR1-7) in contrast to FH(SCR1-20) from serum. Using a complement hemolysis assay (CH50-assay) all three variants exhibited a molar complement inhibitory activity of FH(1-20)/FH(1-7)/FH(1-4) of about 3/1/1. These data support the postulated model of FH bearing three binding sites for its ligand C3b, from which one is located in the SCR1-4, whereas the other two are located in the SCR8-20.

  18. THE MAGNETOVISCOUS-THERMAL INSTABILITY

    SciTech Connect

    Islam, Tanim

    2012-02-10

    Accretion flows onto underluminous black holes, such as Sagittarius A* at the center of our galaxy, are dilute (mildly collisional to highly collisionless), optically thin, and radiatively inefficient. Therefore, the accretion properties of such dilute flows are expected to be modified by their large viscosities and thermal conductivities. Second, turbulence within these systems needs to transport angular momentum as well as thermal energy generated through gravitational infall outward in order to allow accretion to occur. This is in contrast to classical accretion flows, in which the energy generated through accretion down a gravitational well is locally radiated. In this paper, using an incompressible fluid treatment of an ionized gas, we expand on previous research by considering the stability properties of a magnetized rotating plasma wherein the thermal conductivity and viscosity are not negligible and may be dynamically important. We find a class of MHD instabilities that can transport angular momentum and thermal energy outward. They are plausible candidates to describe accretion in radiatively inefficient accretion flows. We finish by discussing the implications for analytic models and numerical MHD simulations of mildly dilute or collisionless astrophysical plasmas, and immediate directions for further research.

  19. Chromosome instability syndromes

    SciTech Connect

    1993-12-31

    Chapter 11, discusses chromosome instability syndromes. The focus is on the most extensively studied genotypic chromosomal aberrations which include Bloom syndrome, Fanconi anemia, ataxia telangiectasia, and xeroderma pigmentosum. The great interest in these syndromes is out of proportion to their rare occurrence; however, studies of genotypic chromosome breakage have been inspired by the hope of throwing light on chromosome structure and behavior. A table is given which relates chromosomal aberrations in Bloom syndrome which may cause or promote cancer. 34 refs., 3 figs., 1 tab.

  20. Interplay between modifications of chromatin and meiotic recombination hotspots.

    PubMed

    Brachet, Elsa; Sommermeyer, Vérane; Borde, Valérie

    2012-02-01

    Meiotic recombination lies at the heart of sexual reproduction. It is essential for producing viable gametes with a normal haploid genomic content and its dysfunctions can be at the source of aneuploidies, such as the Down syndrome, or many genetic disorders. Meiotic recombination also generates genetic diversity that is transmitted to progeny by shuffling maternal and paternal alleles along chromosomes. Recombination takes place at non-random chromosomal sites called 'hotspots'. Recent evidence has shown that their location is influenced by properties of chromatin. In addition, many studies in somatic cells have highlighted the need for changes in chromatin dynamics to allow the process of recombination. In this review, we discuss how changes in the chromatin landscape may influence the recombination map, and reciprocally, how recombination events may lead to epigenetic modifications at sites of recombination, which could be transmitted to progeny.

  1. An Experimental Investigation of Incompressible Richtmyer-Meshkov Instability

    NASA Technical Reports Server (NTRS)

    Jacobs, J. W.; Niederhaus, C. E.

    2002-01-01

    Richtmyer-Meshkov (RM) instability occurs when two different density fluids are impulsively accelerated in the direction normal to their nearly planar interface. The instability causes small perturbations on the interface to grow and eventually become a turbulent flow. It is closely related to Rayleigh-Taylor instability, which is the instability of a planar interface undergoing constant acceleration, such as caused by the suspension of a heavy fluid over a lighter one in the earth's gravitational field. Like the well-known Kelvin-Helmholtz instability, RM instability is a fundamental hydrodynamic instability which exhibits many of the nonlinear complexities that transform simple initial conditions into a complex turbulent flow. Furthermore, the simplicity of RM instability (in that it requires very few defining parameters), and the fact that it can be generated in a closed container, makes it an excellent test bed to study nonlinear stability theory as well as turbulent transport in a heterogeneous system. However, the fact that RM instability involves fluids of unequal densities which experience negligible gravitational force, except during the impulsive acceleration, requires RM instability experiments to be carried out under conditions of microgravity. This experimental study investigates the instability of an interface between incompressible, miscible liquids with an initial sinusoidal perturbation. The impulsive acceleration is generated by bouncing a rectangular tank containing two different density liquids off a retractable vertical spring. The initial perturbation is produced prior to release by oscillating the tank in the horizontal direction to produce a standing wave. The instability evolves in microgravity as the tank travels up and then down the vertical rails of a drop tower until hitting a shock absorber at the bottom. Planar Laser Induced Fluorescence (PLIF) is employed to visualize the flow. PLIF images are captured by a video camera that travels

  2. Non-conventional Fishbone Instabilities

    SciTech Connect

    Ya.I. Kolesnichenko; V.V. Lutsenko; V.S. Marchenko; R.B. White

    2004-11-10

    New instabilities of fishbone type are predicted. First, a trapped-particle-induced m = n = 1 instability with the mode structure having nothing to do with the conventional rigid kink displacement. This instability takes place when the magnetic field is weak, so that the precession frequency of the energetic ions is not small as compared to the frequency of the corresponding Alfven continuum at r = 0 and the magnetic shear is small inside the q = 1 radius [the case relevant to spherical tori]. Second, an Energetic Particle Mode fishbone instability driven by circulating particles. Third, a double-kink-mode instability driven by the circulating energetic ions. In particular, the latter can have two frequencies simultaneously: we refer to it as ''doublet'' fishbones. This instability can occur when the radial profile of the energetic ions has an off-axis maximum inside the region of the mode localization.

  3. Epigenetic control of meiotic recombination in plants.

    PubMed

    Yelina, Natasha; Diaz, Patrick; Lambing, Christophe; Henderson, Ian R

    2015-03-01

    Meiotic recombination is a deeply conserved process within eukaryotes that has a profound effect on patterns of natural genetic variation. During meiosis homologous chromosomes pair and undergo DNA double strand breaks generated by the Spo11 endonuclease. These breaks can be repaired as crossovers that result in reciprocal exchange between chromosomes. The frequency of recombination along chromosomes is highly variable, for example, crossovers are rarely observed in heterochromatin and the centromeric regions. Recent work in plants has shown that crossover hotspots occur in gene promoters and are associated with specific chromatin modifications, including H2A.Z. Meiotic chromosomes are also organized in loop-base arrays connected to an underlying chromosome axis, which likely interacts with chromatin to organize patterns of recombination. Therefore, epigenetic information exerts a major influence on patterns of meiotic recombination along chromosomes, genetic variation within populations and evolution of plant genomes.

  4. Observation of Beam ION Instability in Spear3

    SciTech Connect

    Teytelman, D.; Cai, Y.; Corbett, W.J.; Raubenheimer, T.O.; Safranek, J.A.; Schmerge, J.F.; Sebek, J.J.; Wang, L.; /SLAC

    2011-12-14

    Weak vertical coupled bunch instability with oscillation amplitude at {mu}m level has been observed in SPEAR3. The instability becomes stronger when there is a vacuum pressure rise by partially turning off vacuum pumps and it becomes weaker when the vertical beam emittance is increased by turning off the skew quadrupole magnets. These confirmed that the instability was driven by ions in the vacuum. The threshold of the beam ion instability when running with a single bunch train is just under 200 mA. This paper presents the comprehensive observations of the beam ion instability in SPEAR3. The effects of vacuum pressure, beam current, beam filling pattern, chromaticity, beam emittance and bunch-by-bunch feedback are investigated in great detail. In an electron accelerator, ions generated from the residual gas molecules can be trapped by the beam. Then these trapped ions interact resonantly with the beam and cause beam instability and emittance blow-up. Most existing light sources use a long single bunch train filling pattern, followed by a long gap to avoid multi-turn ion trapping. However, such a gap does not preclude ions from accumulating during one passage of the single bunch train beam, and those ions can still cause a Fast Ion Instability (FII) as predicted by Raubenheimer and Zimmermann. FII has been observed in ALS, and PLS by artificially increasing the vacuum pressure by injecting helium gas into the vacuum chamber or by turning off the ion pumps in order to observe the beam ion instability. In some existing rings, for instance B factory, the beam ion instability was observed at the beginning of the machine operation after a long period of shutdown and then it automatically disappeared when the vacuum was better. However, when the beam emittance becomes smaller, the FII can occur at nominal conditions as observed in PLS, SOLEIL and SSRF. This paper reports the observations of beam ion instabilities in SPEAR3 under different condition during a period of one

  5. Recombinant Baculovirus Isolation.

    PubMed

    King, Linda A; Hitchman, Richard; Possee, Robert D

    2016-01-01

    Although there are several different methods available of making recombinant baculovirus expression vectors (reviewed in Chapter 3 ), all require a stage in which insect cells are transfected with either the virus genome alone (Bac-to-Bac(®) or BaculoDirect™, Invitrogen) or virus genome and transfer vector. In the latter case, this allows the natural process of homologous recombination to transfer the foreign gene, under control of the polyhedrin or other baculovirus gene promoter, from the transfer vector to the virus genome to create the recombinant virus. Previously, many methods required a plaque-assay to separate parental and recombinant virus prior to amplification and use of the recombinant virus. Fortunately, this step is no longer required for most systems currently available. This chapter provides an overview of the historical development of increasingly more efficient systems for the isolation of recombinant baculoviruses (Chapter 3 provides a full account of the different systems and transfer vectors available). The practical details cover: transfection of insect cells with either virus DNA or virus DNA and plasmid transfer vector; a reliable plaque-assay method that can be used to separate recombinant virus from parental (nonrecombinant) virus where this is necessary; methods for the small-scale amplification of recombinant virus; and subsequent titration by plaque-assay or real-time polymerase chain reaction (PCR). Methods unique to the Bac-to-Bac(®) system are also covered and include the transformation of bacterial cells and isolation of bacmid DNA ready for transfection of insect cells.

  6. Novel Cauchy-horizon instability

    SciTech Connect

    Maeda, Hideki; Torii, Takashi; Harada, Tomohiro

    2005-03-15

    The evolution of weak discontinuity is investigated on horizons in the n-dimensional static solutions in the Einstein-Maxwell-scalar-{lambda} system, including the Reissner-Nordstroem-(anti) de Sitter black hole. The analysis is essentially local and nonlinear. We find that the Cauchy horizon is unstable, whereas both the black hole event horizon and the cosmological event horizon are stable. This new instability, the so-called kink instability, of the Cauchy horizon is completely different from the well-known 'infinite-blueshift' instability. The kink instability makes the analytic continuation beyond the Cauchy horizon unstable.

  7. PARTIAL TORUS INSTABILITY

    SciTech Connect

    Olmedo, Oscar; Zhang Jie

    2010-07-20

    Flux ropes are now generally accepted to be the magnetic configuration of coronal mass ejections (CMEs), which may be formed prior to or during solar eruptions. In this study, we model the flux rope as a current-carrying partial torus loop with its two footpoints anchored in the photosphere, and investigate its stability in the context of the torus instability (TI). Previous studies on TI have focused on the configuration of a circular torus and revealed the existence of a critical decay index of the overlying constraining magnetic field. Our study reveals that the critical index is a function of the fractional number of the partial torus, defined by the ratio between the arc length of the partial torus above the photosphere and the circumference of a circular torus of equal radius. We refer to this finding as the partial torus instability (PTI). It is found that a partial torus with a smaller fractional number has a smaller critical index, thus requiring a more gradually decreasing magnetic field to stabilize the flux rope. On the other hand, a partial torus with a larger fractional number has a larger critical index. In the limit of a circular torus when the fractional number approaches 1, the critical index goes to a maximum value. We demonstrate that the PTI helps us to understand the confinement, growth, and eventual eruption of a flux-rope CME.

  8. Partial Torus Instability

    NASA Astrophysics Data System (ADS)

    Olmedo, Oscar; Zhang, Jie

    2010-07-01

    Flux ropes are now generally accepted to be the magnetic configuration of coronal mass ejections (CMEs), which may be formed prior to or during solar eruptions. In this study, we model the flux rope as a current-carrying partial torus loop with its two footpoints anchored in the photosphere, and investigate its stability in the context of the torus instability (TI). Previous studies on TI have focused on the configuration of a circular torus and revealed the existence of a critical decay index of the overlying constraining magnetic field. Our study reveals that the critical index is a function of the fractional number of the partial torus, defined by the ratio between the arc length of the partial torus above the photosphere and the circumference of a circular torus of equal radius. We refer to this finding as the partial torus instability (PTI). It is found that a partial torus with a smaller fractional number has a smaller critical index, thus requiring a more gradually decreasing magnetic field to stabilize the flux rope. On the other hand, a partial torus with a larger fractional number has a larger critical index. In the limit of a circular torus when the fractional number approaches 1, the critical index goes to a maximum value. We demonstrate that the PTI helps us to understand the confinement, growth, and eventual eruption of a flux-rope CME.

  9. [Genomic instability in atherosclerosis].

    PubMed

    Dzhokhadze, T A; Buadze, T Zh; Gaiozishvili, M N; Kakauridze, N G; Lezhava, T A

    2014-11-01

    A comparative study of the level of genomic instability, parameters of quantitative and structural mutations of chromosomes (aberration, aneuploidy, polyploidy) in lymphocyte cultures from patients with atherosclerosis of age 80 years and older (control group - 30-35 years old) was conducted. The possibility of correction of disturbed genomic indicators by peptide bioregulators - Livagen (Lys-Glu-Asp-Ala) and cobalt ions with separate application or in combination was also studied. Control was lymphocyte culture of two healthy respective age groups. It was also shown that patients with atherosclerosis exhibit high level of genomic instability in all studied parameters, regardless of age, which may suggest that there is marked increase in chromatin condensation in atherosclerosis. It was also shown that Livagen (characterized by modifying influence on chromatin) separately and in combination with cobalt ions, promotes normalization of altered genomic indicators of atherosclerosis in both age groups. The results show that Livagen separately and in combination with cobalt ions has impact on chromatin of patients with atherosclerosis. The identified protective action of Livagen proves its efficacy in prevention of atherosclerosis.

  10. Microtearing instability in ITER*

    NASA Astrophysics Data System (ADS)

    Wong, King-Lap; Mikkelsen, David; Budny, Robert; Breslau, Joshua

    2010-11-01

    Microtearing modes are found to be unstable in some regions of a simulated ITER H-mode plasma [1] with the GS2 code [2]. Modes with kρs>1 are in the interior (r/a˜0.65-0.85) while longer wavelength modes are in the pedestal region. This instability may keep the pedestal within the peeling-ballooning stability boundary [3]. Microtearing modes can produce stochastic magnetic field similar to RMP coils; they may have similar effects on ELMs by increasing the pedestal width. The possibility of using this technique for ELM mitigation in ITER is explored. We propose to use a deuterium gas jet to control the microtearing instability and the Chirikov parameter at the edge. Preliminary evaluation of its effectiveness will be presented and the limitations of the GS2 code will be discussed based on our understanding from NSTX [4]. *This work is supported by USDoE contract DE-AC02-09CH11466. [4pt] [1] R. V. Budny, Nucl. Fusion (2009)[0pt] [2] W. Dorland et al., Phys. Rev. Lett. (2000).[0pt] [3] P. B. Snyder et al.,Nucl. Fusion (2009).[0pt] [4] K. L. Wong et al., Phys. Rev. Lett. (2007).

  11. Elliptical instability in terrestrial planets and moons

    NASA Astrophysics Data System (ADS)

    Cebron, D.; Le Bars, M.; Moutou, C.; Le Gal, P.

    2012-03-01

    Context. The presence of celestial companions means that any planet may be subject to three kinds of harmonic mechanical forcing: tides, precession/nutation, and libration. These forcings can generate flows in internal fluid layers, such as fluid cores and subsurface oceans, whose dynamics then significantly differ from solid body rotation. In particular, tides in non-synchronized bodies and libration in synchronized ones are known to be capable of exciting the so-called elliptical instability, i.e. a generic instability corresponding to the destabilization of two-dimensional flows with elliptical streamlines, leading to three-dimensional turbulence. Aims: We aim here at confirming the relevance of such an elliptical instability in terrestrial bodies by determining its growth rate, as well as its consequences on energy dissipation, on magnetic field induction, and on heat flux fluctuations on planetary scales. Methods: Previous studies and theoretical results for the elliptical instability are re-evaluated and extended to cope with an astrophysical context. In particular, generic analytical expressions of the elliptical instability growth rate are obtained using a local WKB approach, simultaneously considering for the first time (i) a local temperature gradient due to an imposed temperature contrast across the considered layer or to the presence of a volumic heat source and (ii) an imposed magnetic field along the rotation axis, coming from an external source. Results: The theoretical results are applied to the telluric planets and moons of the solar system as well as to three Super-Earths: 55 CnC e, CoRoT-7b, and GJ 1214b. For the tide-driven elliptical instability in non-synchronized bodies, only the early Earth core is shown to be clearly unstable. For the libration-driven elliptical instability in synchronized bodies, the core of Io is shown to be stable, contrary to previously thoughts, whereas Europa, 55 CnC e, CoRoT-7b, and GJ 1214b cores can be unstable

  12. Instability vaccination: A structural design to reduce Rayleigh Taylor instability

    NASA Astrophysics Data System (ADS)

    Esmaeili, Amin

    2013-10-01

    Instability vaccination can be defined as designing a structure to stimulate the system in order to develop immunity against its instability. In this work we have tried to do this stabilization by a new technique. Previously some suppression of R-M instability was done by insertion of magnetic field, but in this work we have tried to do this suppression by proposing a configuration similar to the shape of instability, we call it instability vaccination. This design will reduce the rotations (mostly rotations of Rayleigh Taylor instability) in the fluids that cause more mixing and instabilities. In this paper, we consider the evolution of the interface between two ideal semi-infinite fluid surfaces, using two-dimensional Riemann solver, to solve the Euler equations. First, we performed evolution of a rectangular disorder between the 2 surfaces using two-dimensional Riemann problem for the equations of Euler. Next, the interface was replaced with a perturbation that was part rectangular and part semi-circular (like a mushroom). The simulation was continued till some time steps using the HLL method. We have seen that the rotations of Rayleigh Taylor (R-T) instability were decreased in the second case. Email: amin@cavelab.cs.tsukuba.ac.jp

  13. Interchromosomal recombination in Zea mays.

    PubMed Central

    Hu, W; Timmermans, M C; Messing, J

    1998-01-01

    A new allele of the 27-kD zein locus in maize has been generated by interchromosomal recombination between chromosomes of two different inbred lines. A continuous patch of at least 11,817 bp of inbred W64A, containing the previously characterized Ra allele of the 27-kD zein gene, has been inserted into the genome of A188 by a single crossover. While both junction sequences are conserved, sequences of the two homologs between these junctions differ considerably. W64A contains the 7313-bp-long retrotransposon, Zeon-1. A188 contains a second copy of the 27-kD zein gene and a 2-kb repetitive element. Therefore, recombination results in a 7.3-kb insertion and a 14-kb deletion compared to the original S+A188 allele. If nonpairing sequences are looped out, 206 single base changes, frequently clustered, are present. The structure of this allele may explain how a recently discovered example of somatic recombination occurred in an A188/W64A hybrid. This would indicate that despite these sequence differences, pairing between these alleles could occur early during plant development. Therefore, such a somatically derived chimeric chromosome can also be heritable and give rise to new alleles. PMID:9799274

  14. Thermal instability of forced convection boundary layers

    NASA Astrophysics Data System (ADS)

    Chen, K.; Chen, M. M.

    1981-11-01

    The thermal instability of forced convection boundary layers with non-zero streamwise pressure gradient is examined. An analysis is carried out for the family of Falkner-Skan flows, and only the streamwise buoyancy generated instability for fluid layers with shear at low Reynolds number are considered. When the wedge angle is equal to one, the perturbation equations based on the boundary layer equations are identical to the exact perturbation equations for the stagnation flow. Calculated critical Rayleigh numbers and wave numbers are found to be independent of wedge angle in the limiting case of infinite Prandtl number, and results are compared with previous experimental results by Gilpin et al. (1978), showing good agreement.

  15. Deployment Instabilities of Lobed-Pumpkin Balloon

    NASA Astrophysics Data System (ADS)

    Nakashino, Kyoichi

    A lobed-pumpkin balloon, currently being developed in ISAS/JAXA as well as in NASA, is a promising vehicle for long duration scientific observations in the stratosphere. Recent ground and flight experiments, however, have revealed that the balloon has deployment instabilities under certain conditions. In order to overcome the instability problems, a next generation SPB called 'tawara' type balloon has been proposed, in which an additional cylindrical part is appended to the standard lobed-pumpkin balloon. The present study investigates the deployment stability of tawara type SPB in comparison to that of standard lobed-pumpkin SPB through eigenvalue analysis on the basis of finite element methods. Our numerical results show that tawara type SPB enjoys excellent deployment performance over the standard lobed-pumpkin SPBs.

  16. Numerical Simulations of Instabilities in Single-Hole Office Elements

    NASA Technical Reports Server (NTRS)

    Ahuja, Vineet; Hosangadi, Ashvin; Hitt, Matthew A.; Lineberry, David M.

    2013-01-01

    An orifice element is commonly used in liquid rocket engine test facilities either as a flow metering device, a damper for acoustic resonance or to provide a large reduction in pressure over a very small distance in the piping system. While the orifice as a device is largely effective in stepping down pressure, it is also susceptible to a wake-vortex type instability that generates pressure fluctuations that propagate downstream and interact with other elements of the test facility resulting in structural vibrations. Furthermore in piping systems an unstable feedback loop can exist between the vortex shedding and acoustic perturbations from upstream components resulting in an amplification of the modes convecting downstream. Such was the case in several tests conducted at NASA as well as in the Ariane 5 strap-on P230 engine in a static firing test where pressure oscillations of 0.5% resulted in 5% thrust oscillations. Exacerbating the situation in cryogenic test facilities, is the possibility of the formation of vapor clouds when the pressure in the wake falls below the vapor pressure leading to a cavitation instability that has a lower frequency than the primary wake-vortex instability. The cavitation instability has the potential for high amplitude fluctuations that can cause catastrophic damage in the facility. In this paper high-fidelity multi-phase numerical simulations of an orifice element are used to characterize the different instabilities, understand the dominant instability mechanisms and identify the tonal content of the instabilities.

  17. Elastic instabilities in planar elongational flow of monodisperse polymer solutions

    PubMed Central

    Haward, Simon J.; McKinley, Gareth H.; Shen, Amy Q.

    2016-01-01

    We investigate purely elastic flow instabilities in the almost ideal planar stagnation point elongational flow field generated by a microfluidic optimized-shape cross-slot extensional rheometer (OSCER). We use time-resolved flow velocimetry and full-field birefringence microscopy to study the behavior of a series of well-characterized viscoelastic polymer solutions under conditions of low fluid inertia and over a wide range of imposed deformation rates. At low deformation rates the flow is steady and symmetric and appears Newtonian-like, while at high deformation rates we observe the onset of a flow asymmetry resembling the purely elastic instabilities reported in standard-shaped cross-slot devices. However, for intermediate rates, we observe a new type of elastic instability characterized by a lateral displacement and time-dependent motion of the stagnation point. At the onset of this new instability, we evaluate a well-known dimensionless criterion M that predicts the onset of elastic instabilities based on geometric and rheological scaling parameters. The criterion yields maximum values of M which compare well with critical values of M for the onset of elastic instabilities in viscometric torsional flows. We conclude that the same mechanism of tension acting along curved streamlines governs the onset of elastic instabilities in both extensional (irrotational) and torsional (rotational) viscoelastic flows. PMID:27616181

  18. Elastic instabilities in planar elongational flow of monodisperse polymer solutions.

    PubMed

    Haward, Simon J; McKinley, Gareth H; Shen, Amy Q

    2016-09-12

    We investigate purely elastic flow instabilities in the almost ideal planar stagnation point elongational flow field generated by a microfluidic optimized-shape cross-slot extensional rheometer (OSCER). We use time-resolved flow velocimetry and full-field birefringence microscopy to study the behavior of a series of well-characterized viscoelastic polymer solutions under conditions of low fluid inertia and over a wide range of imposed deformation rates. At low deformation rates the flow is steady and symmetric and appears Newtonian-like, while at high deformation rates we observe the onset of a flow asymmetry resembling the purely elastic instabilities reported in standard-shaped cross-slot devices. However, for intermediate rates, we observe a new type of elastic instability characterized by a lateral displacement and time-dependent motion of the stagnation point. At the onset of this new instability, we evaluate a well-known dimensionless criterion M that predicts the onset of elastic instabilities based on geometric and rheological scaling parameters. The criterion yields maximum values of M which compare well with critical values of M for the onset of elastic instabilities in viscometric torsional flows. We conclude that the same mechanism of tension acting along curved streamlines governs the onset of elastic instabilities in both extensional (irrotational) and torsional (rotational) viscoelastic flows.

  19. Elastic instabilities in planar elongational flow of monodisperse polymer solutions

    NASA Astrophysics Data System (ADS)

    Haward, Simon J.; McKinley, Gareth H.; Shen, Amy Q.

    2016-09-01

    We investigate purely elastic flow instabilities in the almost ideal planar stagnation point elongational flow field generated by a microfluidic optimized-shape cross-slot extensional rheometer (OSCER). We use time-resolved flow velocimetry and full-field birefringence microscopy to study the behavior of a series of well-characterized viscoelastic polymer solutions under conditions of low fluid inertia and over a wide range of imposed deformation rates. At low deformation rates the flow is steady and symmetric and appears Newtonian-like, while at high deformation rates we observe the onset of a flow asymmetry resembling the purely elastic instabilities reported in standard-shaped cross-slot devices. However, for intermediate rates, we observe a new type of elastic instability characterized by a lateral displacement and time-dependent motion of the stagnation point. At the onset of this new instability, we evaluate a well-known dimensionless criterion M that predicts the onset of elastic instabilities based on geometric and rheological scaling parameters. The criterion yields maximum values of M which compare well with critical values of M for the onset of elastic instabilities in viscometric torsional flows. We conclude that the same mechanism of tension acting along curved streamlines governs the onset of elastic instabilities in both extensional (irrotational) and torsional (rotational) viscoelastic flows.

  20. Atmospheric-pressure plasma jet induces DNA double-strand breaks that require a Rad51-mediated homologous recombination for repair in Saccharomyces cerevisiae.

    PubMed

    Lee, Yoonna; Kim, Kangil; Kang, Kyu-Tae; Lee, Jong-Soo; Yang, Sang Sik; Chung, Woo-Hyun

    2014-10-15

    Non-thermal plasma generated under atmospheric pressure produces a mixture of chemically reactive molecules and has been developed for a number of biomedical applications. Recently, plasma jet has been proposed as novel cancer therapies based on the observation that free radicals generated by plasma jet induce mitochondria-mediated apoptotic cell death. We show here that air plasma jet induces DNA double-strand breaks (DSBs) in yeast chromosomes leading to genomic instability and loss of viability, which are alleviated by Rad51, the yeast homolog of Escherichiacoli RecA recombinase, through DNA damage repair by a homologous recombination (HR) process. Hypersensitivity of rad51 mutant to air plasma was not restored by antioxidant treatment unlike sod1 mutant that was highly sensitive to reactive oxygen species (ROS) challenge, suggesting that plasma jet induces DSB-mediated cell death independent of ROS generation. These results may provide a new insight into the mechanism of air plasma jet-induced cell death.

  1. Radiation-induced genomic instability and its implications for radiation carcinogenesis

    NASA Technical Reports Server (NTRS)

    Huang, Lei; Snyder, Andrew R.; Morgan, William F.

    2003-01-01

    Radiation-induced genomic instability is characterized by an increased rate of genetic alterations including cytogenetic rearrangements, mutations, gene amplifications, transformation and cell death in the progeny of irradiated cells multiple generations after the initial insult. Chromosomal rearrangements are the best-characterized end point of radiation-induced genomic instability, and many of the rearrangements described are similar to those found in human cancers. Chromosome breakage syndromes are defined by chromosome instability, and individuals with these diseases are cancer prone. Consequently, chromosomal instability as a phenotype may underlie some fraction of those changes leading to cancer. Here we attempt to relate current knowledge regarding radiation-induced chromosome instability with the emerging molecular information on the chromosome breakage syndromes. The goal is to understand how genetic and epigenetic factors might influence the onset of chromosome instability and the role of chromosomal instability in carcinogenesis.

  2. Liquid propellant rocket combustion instability

    NASA Technical Reports Server (NTRS)

    Harrje, D. T.

    1972-01-01

    The solution of problems of combustion instability for more effective communication between the various workers in this field is considered. The extent of combustion instability problems in liquid propellant rocket engines and recommendations for their solution are discussed. The most significant developments, both theoretical and experimental, are presented, with emphasis on fundamental principles and relationships between alternative approaches.

  3. Research on aviation fuel instability

    NASA Technical Reports Server (NTRS)

    Baker, C. E.; Bittker, D. A.; Cohen, S. M.; Seng, G. T.

    1983-01-01

    The underlying causes of fuel thermal degradation are discussed. Topics covered include: nature of fuel instability and its temperature dependence, methods of measuring the instability, chemical mechanisms involved in deposit formation, and instrumental methods for characterizing fuel deposits. Finally, some preliminary thoughts on design approaches for minimizing the effects of lowered thermal stability are briefly discussed.

  4. Bony instability of the shoulder.

    PubMed

    Bushnell, Brandon D; Creighton, R Alexander; Herring, Marion M

    2008-09-01

    Instability of the shoulder is a common problem treated by many orthopaedists. Instability can result from baseline intrinsic ligamentous laxity or a traumatic event-often a dislocation that injures the stabilizing structures of the glenohumeral joint. Many cases involve soft-tissue injury only and can be treated successfully with repair of the labrum and ligamentous tissues. Both open and arthroscopic approaches have been well described, with recent studies of arthroscopic soft-tissue techniques reporting results equal to those of the more traditional open techniques. Over the last decade, attention has focused on the concept of instability of the shoulder mediated by bony pathology such as a large bony Bankart lesion or an engaging Hill-Sachs lesion. Recent literature has identified unrecognized large bony lesions as a primary cause of failure of arthroscopic reconstruction for instability, a major cause of recurrent instability, and a difficult diagnosis to make. Thus, although such bony lesions may be relatively rare compared with soft-tissue pathology, they constitute a critically important entity in the management of shoulder instability. Smaller bony lesions may be amenable to arthroscopic treatment, but larger lesions often require open surgery to prevent recurrent instability. This article reviews recent developments in the diagnosis and treatment of bony instability.

  5. Instabilities in uranium plasma.

    NASA Technical Reports Server (NTRS)

    Tidman, D. A.

    1971-01-01

    The nonlinear evolution of unstable sound waves in a uranium plasma has been calculated using a multiple time-scale asymptotic expansion scheme. The fluid equations used include the fission power density, radiation diffusion, and the effects of the changing degree of ionization of the uranium atoms. The nonlinear growth of unstable waves is shown to be limited by mode coupling to shorter wavelength waves which are damped by radiation diffusion. This mechanism limits the wave pressure fluctuations to values of order delta P/P equal to about .00001 in the plasma of a typical gas-core nuclear rocket engine. The instability is thus not expected to present a control problem for this engine.

  6. Marital instability after midlife.

    PubMed

    Wu, Z; Penning, M J

    1997-09-01

    "Divorce in later life has been shown to produce dramatic declines in the economic, psychological, and physical well-being of marital partners. This study examines the prevalence and determinants of marital disruption after midlife using Becker's theory of marital instability. Using recent Canadian national data, the marital outcomes of women and men who were married as of age 40 are tracked across the remaining years of the marriage. Cox proportional hazard regression models indicate stabilizing effects of the duration of the marriage, the age at first marriage, the presence of young children, as well as of remarriage for middle-aged and older persons. Other significant risk factors include education, heterogamous marital status, premarital cohabitation, number of siblings, and region."

  7. Neurocardiovascular Instability and Cognition

    PubMed Central

    O’Callaghan, Susan; Kenny, Rose Anne

    2016-01-01

    Neurocardiovascular instability (NCVI) refers to abnormal neural control of the cardiovascular system affecting blood pressure and heart rate behavior. Autonomic dysfunction and impaired cerebral autoregulation in aging contribute to this phenomenon characterized by hypotension and bradyarrhythmia. Ultimately, this increases the risk of falls and syncope in older people. NCVI is common in patients with neurodegenerative disorders including dementia. This review discusses the various syndromes that characterize NCVI icluding hypotension, carotid sinus hypersensitivity, postprandial hypotension and vasovagal syncope and how they may contribute to the aetiology of cognitive decline. Conversely, they may also be a consequence of a common neurodegenerative process. Regardless, recognition of their association is paramount in optimizing management of these patients. PMID:27505017

  8. Dissociative recombination in aeronomy

    NASA Technical Reports Server (NTRS)

    Fox, J. L.

    1989-01-01

    The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

  9. Combustion Instabilities Modeled

    NASA Technical Reports Server (NTRS)

    Paxson, Daniel E.

    1999-01-01

    NASA Lewis Research Center's Advanced Controls and Dynamics Technology Branch is investigating active control strategies to mitigate or eliminate the combustion instabilities prevalent in lean-burning, low-emission combustors. These instabilities result from coupling between the heat-release mechanisms of the burning process and the acoustic flow field of the combustor. Control design and implementation require a simulation capability that is both fast and accurate. It must capture the essential physics of the system, yet be as simple as possible. A quasi-one-dimensional, computational fluid dynamics (CFD) based simulation has been developed which may meet these requirements. The Euler equations of mass, momentum, and energy have been used, along with a single reactive species transport equation to simulate coupled thermoacoustic oscillations. A very simple numerical integration scheme was chosen to reduce computing time. Robust boundary condition procedures were incorporated to simulate various flow conditions (e.g., valves, open ends, and choked inflow) as well as to accommodate flow reversals that may arise during large flow-field oscillations. The accompanying figure shows a sample simulation result. A combustor with an open inlet, a choked outlet, and a large constriction approximately two thirds of the way down the length is shown. The middle plot shows normalized, time-averaged distributions of the relevant flow quantities, and the bottom plot illustrates the acoustic mode shape of the resulting thermoacoustic oscillation. For this simulation, the limit cycle peak-to-peak pressure fluctuations were 13 percent of the mean. The simulation used 100 numerical cells. The total normalized simulation time was 50 units (approximately 15 oscillations), which took 26 sec on a Sun Ultra2.

  10. Internal rotor friction instability

    NASA Technical Reports Server (NTRS)

    Walton, J.; Artiles, A.; Lund, J.; Dill, J.; Zorzi, E.

    1990-01-01

    The analytical developments and experimental investigations performed in assessing the effect of internal friction on rotor systems dynamic performance are documented. Analytical component models for axial splines, Curvic splines, and interference fit joints commonly found in modern high speed turbomachinery were developed. Rotor systems operating above a bending critical speed were shown to exhibit unstable subsynchronous vibrations at the first natural frequency. The effect of speed, bearing stiffness, joint stiffness, external damping, torque, and coefficient of friction, was evaluated. Testing included material coefficient of friction evaluations, component joint quantity and form of damping determinations, and rotordynamic stability assessments. Under conditions similar to those in the SSME turbopumps, material interfaces experienced a coefficient of friction of approx. 0.2 for lubricated and 0.8 for unlubricated conditions. The damping observed in the component joints displayed nearly linear behavior with increasing amplitude. Thus, the measured damping, as a function of amplitude, is not represented by either linear or Coulomb friction damper models. Rotordynamic testing of an axial spline joint under 5000 in.-lb of static torque, demonstrated the presence of an extremely severe instability when the rotor was operated above its first flexible natural frequency. The presence of this instability was predicted by nonlinear rotordynamic time-transient analysis using the nonlinear component model developed under this program. Corresponding rotordynamic testing of a shaft with an interference fit joint demonstrated the presence of subsynchronous vibrations at the first natural frequency. While subsynchronous vibrations were observed, they were bounded and significantly lower in amplitude than the synchronous vibrations.

  11. The presence of extra chromosomes leads to genomic instability.

    PubMed

    Passerini, Verena; Ozeri-Galai, Efrat; de Pagter, Mirjam S; Donnelly, Neysan; Schmalbrock, Sarah; Kloosterman, Wigard P; Kerem, Batsheva; Storchová, Zuzana

    2016-02-15

    Aneuploidy is a hallmark of cancer and underlies genetic disorders characterized by severe developmental defects, yet the molecular mechanisms explaining its effects on cellular physiology remain elusive. Here we show, using a series of human cells with defined aneuploid karyotypes, that gain of a single chromosome increases genomic instability. Next-generation sequencing and SNP-array analysis reveal accumulation of chromosomal rearrangements in aneuploids, with break point junction patterns suggestive of replication defects. Trisomic and tetrasomic cells also show increased DNA damage and sensitivity to replication stress. Strikingly, we find that aneuploidy-induced genomic instability can be explained by the reduced expression of the replicative helicase MCM2-7. Accordingly, restoring near-wild-type levels of chromatin-bound MCM helicase partly rescues the genomic instability phenotypes. Thus, gain of chromosomes triggers replication stress, thereby promoting genomic instability and possibly contributing to tumorigenesis.

  12. The presence of extra chromosomes leads to genomic instability

    PubMed Central

    Passerini, Verena; Ozeri-Galai, Efrat; de Pagter, Mirjam S.; Donnelly, Neysan; Schmalbrock, Sarah; Kloosterman, Wigard P.; Kerem, Batsheva; Storchová, Zuzana

    2016-01-01

    Aneuploidy is a hallmark of cancer and underlies genetic disorders characterized by severe developmental defects, yet the molecular mechanisms explaining its effects on cellular physiology remain elusive. Here we show, using a series of human cells with defined aneuploid karyotypes, that gain of a single chromosome increases genomic instability. Next-generation sequencing and SNP-array analysis reveal accumulation of chromosomal rearrangements in aneuploids, with break point junction patterns suggestive of replication defects. Trisomic and tetrasomic cells also show increased DNA damage and sensitivity to replication stress. Strikingly, we find that aneuploidy-induced genomic instability can be explained by the reduced expression of the replicative helicase MCM2-7. Accordingly, restoring near-wild-type levels of chromatin-bound MCM helicase partly rescues the genomic instability phenotypes. Thus, gain of chromosomes triggers replication stress, thereby promoting genomic instability and possibly contributing to tumorigenesis. PMID:26876972

  13. Genome-Wide Association Study of Meiotic Recombination Phenotypes

    PubMed Central

    Begum, Ferdouse; Chowdhury, Reshmi; Cheung, Vivian G.; Sherman, Stephanie L.; Feingold, Eleanor

    2016-01-01

    Meiotic recombination is an essential step in gametogenesis, and is one that also generates genetic diversity. Genome-wide association studies (GWAS) and molecular studies have identified genes that influence of human meiotic recombination. RNF212 is associated with total or average number of recombination events, and PRDM9 is associated with the locations of hotspots, or sequences where crossing over appears to cluster. In addition, a common inversion on chromosome 17 is strongly associated with recombination. Other genes have been identified by GWAS, but those results have not been replicated. In this study, using new datasets, we characterized additional recombination phenotypes to uncover novel candidates and further dissect the role of already known loci. We used three datasets totaling 1562 two-generation families, including 3108 parents with 4304 children. We estimated five different recombination phenotypes including two novel phenotypes (average recombination counts within recombination hotspots and outside of hotspots) using dense SNP array genotype data. We then performed gender-specific and combined-sex genome-wide association studies (GWAS) meta-analyses. We replicated associations for several previously reported recombination genes, including RNF212 and PRDM9. By looking specifically at recombination events outside of hotspots, we showed for the first time that PRDM9 has different effects in males and females. We identified several new candidate loci, particularly for recombination events outside of hotspots. These include regions near the genes SPINK6, EVC2, ARHGAP25, and DLGAP2. This study expands our understanding of human meiotic recombination by characterizing additional features that vary across individuals, and identifying regulatory variants influencing the numbers and locations of recombination events. PMID:27733454

  14. Genome-Wide Association Study of Meiotic Recombination Phenotypes.

    PubMed

    Begum, Ferdouse; Chowdhury, Reshmi; Cheung, Vivian G; Sherman, Stephanie L; Feingold, Eleanor

    2016-12-07

    Meiotic recombination is an essential step in gametogenesis, and is one that also generates genetic diversity. Genome-wide association studies (GWAS) and molecular studies have identified genes that influence of human meiotic recombination. RNF212 is associated with total or average number of recombination events, and PRDM9 is associated with the locations of hotspots, or sequences where crossing over appears to cluster. In addition, a common inversion on chromosome 17 is strongly associated with recombination. Other genes have been identified by GWAS, but those results have not been replicated. In this study, using new datasets, we characterized additional recombination phenotypes to uncover novel candidates and further dissect the role of already known loci. We used three datasets totaling 1562 two-generation families, including 3108 parents with 4304 children. We estimated five different recombination phenotypes including two novel phenotypes (average recombination counts within recombination hotspots and outside of hotspots) using dense SNP array genotype data. We then performed gender-specific and combined-sex genome-wide association studies (GWAS) meta-analyses. We replicated associations for several previously reported recombination genes, including RNF212 and PRDM9 By looking specifically at recombination events outside of hotspots, we showed for the first time that PRDM9 has different effects in males and females. We identified several new candidate loci, particularly for recombination events outside of hotspots. These include regions near the genes SPINK6, EVC2, ARHGAP25, and DLGAP2 This study expands our understanding of human meiotic recombination by characterizing additional features that vary across individuals, and identifying regulatory variants influencing the numbers and locations of recombination events.

  15. Fullerene concentration dependent bimolecular recombination in organic photovoltaic films

    NASA Astrophysics Data System (ADS)

    Kaake, Loren G.; Sun, Yanming; Bazan, Guillermo C.; Heeger, Alan J.

    2013-04-01

    Organic photovoltaic devices made of a solution processed small molecule and a fullerene show a decrease in short circuit current with decreasing fullerene amounts. Transient absorption experiments show that the rate of bimolecular recombination increases as the system is deprived of fullerene. A simple expression for the bimolecular recombination coefficient derived by accounting for intrinsic carrier generation reproduces the observed behavior.

  16. Dissociation of recombinant prion autocatalysis from infectivity.

    PubMed

    Noble, Geoffrey P; Supattapone, Surachai

    2015-01-01

    Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication--that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and non-infectious pair of autocatalytic recombinant PrP conformers derived from the same initial prion strain. (1) We identified restricted, C-terminal structural differences between these 2 conformers and provided evidence that these relatively subtle differences prevent the non-infectious conformer from templating the conversion of native PrP(C) substrates containing a glycosylphosphatidylinositol (GPI) anchor. (1) In this article we discuss a model, consistent with these findings, in which recombinant PrP, lacking post-translational modifications and associated folding constraints, is capable of adopting a wide variety of autocatalytic conformations. Only a subset of these recombinant conformers can be adopted by post-translationally modified native PrP(C), and this subset represents the recombinant conformers with high specific infectivity. We examine this model's implications for the generation of highly infectious recombinant prions and the protein-only hypothesis of prion replication.

  17. Enhanced homologous recombination is induced by alpha-particle radiation in somatic cells of Arabidopsis thaliana

    NASA Astrophysics Data System (ADS)

    Bian, Po; Liu, Ping; Wu, Yuejin

    Almost 9 percent of cosmic rays which strike the earth's atmosphere are alpha particles. As one of the ionizing radiations (IR), its biological effects have been widely studied. However, the plant genomic instability induced by alpha-particle radiation was not largely known. In this research, the Arabidopsis thaliana transgenic for GUS recombination substrate was used to evaluate the genomic instability induced by alpha-particle radiation (3.3MeV). The pronounced effects of systemic exposure to alpha-particle radiation on the somatic homologous recombination frequency (HRF) were found at different doses. The 10Gy dose of radiation induced the maximal HRF which was 1.9-fold higher than the control. The local radiation of alpha-particle (10Gy) on root also resulted in a 2.5-fold increase of somatic HRF in non-radiated aerial plant, indicating that the signal(s) of genomic instability was transferred to non-radiated parts and initiated their genomic instability. Concurrent treatment of seedlings of Arabidopsis thaliana with alpha-particle and DMSO(ROS scavenger) both in systemic and local radiation signifi- cantly suppressed the somatic HR, indicating that the free radicals produced by alpha-particle radiation took part in the production of signal of genomic instability rather than the signal transfer. Key words: alpha-particle radiation, somatic homologous recombination, genomic instability

  18. Gas recombination assembly for electrochemical cells

    DOEpatents

    Levy, Isaac; Charkey, Allen

    1989-01-01

    An assembly for recombining gases generated in electrochemical cells wherein a catalyst strip is enveloped within a hydrophobic, gas-porous film which, in turn, is encased between gas-porous, metallic layers. The sandwich construction of metallic layers and film is formed into a spiral with a tab for connection to the cell.

  19. Measuring Diffusion and Recombination in Polycrystalline Silicon

    NASA Technical Reports Server (NTRS)

    Zook, J. D.

    1983-01-01

    Light-beam-induced currents yield information about solar cell material. Apparatus measures short-circuit current generated when spot of concentrated light is scanned across grains and grain boundaries in material under test. Technique used to evaluate SOC samples for diffusion and recombination effects of cell processing and chemical and structural defects.

  20. Activated recombinant adenovirus proteinases

    DOEpatents

    Anderson, C.W.; Mangel, W.F.

    1999-08-10

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described. 29 figs.

  1. Activated recombinant adenovirus proteinases

    DOEpatents

    Anderson, Carl W.; Mangel, Walter F.

    1999-08-10

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying said peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described.

  2. Multiphoton Assisted Recombination

    NASA Astrophysics Data System (ADS)

    Shuman, E. S.; Jones, R. R.; Gallagher, T. F.

    2008-12-01

    We have observed multiphoton assisted recombination in the presence of a 38.8 GHz microwave field. Stimulated emission of up to ten microwave photons results in energy transfer from continuum electrons, enabling recombination. The maximum electron energy loss is far greater than the 2Up predicted by the standard “simpleman’s” model. The data are well reproduced by both an approximate analytic expression and numerical simulations in which the combined Coulomb and radiation fields are taken into account.

  3. Overexpression of c-fos increases recombination frequency in human osteosarcoma cells.

    PubMed

    van den Berg, S; Rahmsdorf, H J; Herrlich, P; Kaina, B

    1993-05-01

    We have shown previously that overexpression of c-Ha-ras, v-mos or c-fos increases the spontaneous level of chromosomal aberrations and gene mutations in NIH 3T3 cells, and that reduction of the Fos protein level inhibits aberration induction by c-Ha-ras and v-mos and also by irradiation with ultraviolet light (van den Berg et al., Mol. Carcinogenesis, 4, 460-466). In order to examine whether fos is also involved in DNA recombination, thymidine kinase (tk) deficient human osteosarcoma cells containing two versions of the herpes simplex virus tk gene inactivated by base insertion were either transiently or stably transfected with various fos expression plasmids. The frequency of tk+ revertants was significantly enhanced both upon transient transfection with RSV-promoter-fos gene constructs and by stimulation of Fos synthesis in stably transfected cells harbouring an inducible metallothionein promoter-fos construct. No such increases were observed in cells transfected with plasmids containing a truncated version of c-fos. The data indicate that c-fos is involved in generating various types of genetic changes including homologous recombination; a role of c-fos in genetic instability may contribute to its action in tumor promotion and progression.

  4. Dynamic instability of collective myosin II motors

    NASA Astrophysics Data System (ADS)

    Li, Jin-Fang; Wang, Zi-Qing; Li, Qi-Kun; Xing, Jian-Jun; Wang, Guo-Dong

    2016-11-01

    Some kinds of muscles can oscillate spontaneously, which is related to the dynamic instability of the collective motors. Based on the two-state ratchet model and with consideration of the motor stiffness, the dynamics of collective myosin II motors are studied. It is shown that when the motor stiffness is small, the velocity of the collective motors decreases monotonically with load increasing. When the motor stiffness becomes large, dynamic instability appears in the force-velocity relationship of the collective-motor transport. For a large enough motor stiffness, the zero-velocity point lies in the unstable range of the force-velocity curve, and the motor system becomes unstable before the motion is stopped, so spontaneous oscillations can be generated if the system is elastically coupled to its environment via a spring. The oscillation frequency is related to the motor stiffness, motor binding rate, spring stiffness, and the width of the ATP excitation interval. For a medium motor stiffness, the zero-velocity point lies outside the unstable range of the force-velocity curve, and the motion will be stopped before the instability occurs. Project supported by the National Natural Science Foundation of China (Grant No. 11205123).

  5. Precessionaly driven instability in the Lunar core.

    NASA Astrophysics Data System (ADS)

    Noir, J.; Lin, Y.

    2015-12-01

    Since Yoder 1981, the large dissipation at the period of precession associated with the misalignment of the lunar rotation axis with respect to the Cassini plan has been attributed to turbulent mixing in a liquid outer core. However, no precession driven instability mechanism supported this scenario without invoking unrealistic Core-Mantle boundary ellipticity. Meanwhile, recent numerical simulations (Lin et al., PoF 2014) and experiments (Goto et al., JFM 2014) have shown that internal shear layers spawned by the viscous boundary in a precessing spherical liquid shell can generate parametric-like instabilities. Based on the consistent scaling laws proposed in these two studies, we show that the present Lunar core is highly super critical, hence supporting the idea of turbulent dissipation. In my presentation I will briefly review the observations suggesting the presence of a large dissipation at the period of precession in the lunar core and present the shear driven instability mechanism, showing that precession driven turbulence is indeed plausible.

  6. Observation of an antenna-plasma instability

    SciTech Connect

    Kellogg, P.J.; Monson, S.J. ); Whalen, B.A. )

    1990-06-01

    During a rocket flight to high altitude (585 km) a narrow band signal on an electric antenna was sometimes observed, whose frequency varied as the rocket turned. Such a signal cannot be natural, but apparently must be generated by the interaction of the rocket-antenna system with the ambient plasma. Conditions for development of the instability are investigated. Maximum oscillation amplitude occurs when the antenna is aligned with the Earth's magnetic field. Similar observations have been reported by Gurnett and Mosier (1969). Several attempts are made to understand the nature of this interaction, but without success. The instability treated by Fiala, due to the interaction of an inductive antenna impedance with stray capacitance to a phase shifted point in the preamplifier, can be ruled out. It appears that a negative antenna resistance due to interaction with waves Doppler-shifted through zero is an unlikely explanation. The rocket velocity seems too small to give such an anomalous Doppler shift, and even if the observations of plasma density and temperature are stretched, the positive sheath resistance is larger than calculated negative resistances. Ion transit time instability in the sheath would only work at 10 times higher frequency. Interaction of the flowing plasma with sheath waves around the antenna is suggested and appears promising but the theory is not sufficiently developed for meaningful comparison.

  7. The plasmoid instability and Hall effect during chromospheric magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Murphy, Nicholas Arnold; Lukin, Vyacheslav

    2016-01-01

    Magnetic reconnection is a ubiquitous process in the partially ionized solar chromosphere. Recent two-dimensional simulations have shown that the plasmoid instability onsets during partially ionized reconnection [1-4]. We use the plasma-neutral module of the HiFi framework to simulate the nonlinear evolution of the plasmoid instability during symmetric and asymmetric reconnection. These simulations model the plasma and neutrals as separate fluids and include ionization, recombination, charge exchange, thermal conduction, and the Hall effect. The Hall effect leads to the development of significant out-of-plane magnetic fields in the current sheet region in the laminar phase, but we do not observe shortening of the current sheet or significant acceleration of the reconnection rate as a result. After the onset of the plasmoid instability, structure develops on scales comparable to the ion inertial length. We compare simulations of the plasmoid instability with and without the Hall effect to determine its impact on the reconnection process. Finally, we discuss ongoing efforts to connect these simulations with solar observations and laboratory experiments.[1] Leake et al. 2012, ApJ, 760, 109 [2] Leake et al. 2013, PhPl, 20, 062102 [3] Ni et al. 2015, ApJ, 799, 79 [4] Murphy & Lukin 2015, ApJ, 805, 134

  8. Direct Measurements of the Baroclinic Instability in the Ocean

    NASA Astrophysics Data System (ADS)

    Sadek, Mahmoud; Aluie, Hussein; Hecht, Matthew; Vallis, Geoffrey

    2016-11-01

    The ocean is mechanically driven by wind and buoyancy at the surface which produce sloping isopycnals with a reservoir of available potential energy (APE). Large scale APE can be converted to kinetic energy via the baroclinic instability, which produces mesoscale eddies. Mesoscale eddies are ubiquitous in mid- and high-latitudes, and play a primary role in determining the strength and trajectories of currents and in generating intrinsic climate variability. The widespread belief that mesoscale eddies are generated through baroclinic instability is based on general accord between observations and linear stability analysis and the predicted behavior of nonlinear models. However, these models are unable to give us quantitative evidence of the extent to which the instability is responsible for eddy generation at various locations in the ocean. To this end, we implement a new coarse-graining framework, recently developed to study flow on a sphere, to directly analyze the baroclinic instability as a function of scale and geographic location, and implement it using strongly eddying high-resolution simulations in the North Atlantic and in the Southern Ocean. The results give us new information about location and intensity of the instability in both physical and spectral space. Partial support was provided by National Science Foundation (NSF) Grant OCE-1259794, US Department of Energy (US DOE) Grant DE-SC0014318, and the LANL LDRD program through Project Number 20150568ER.

  9. Transposable Elements and Genetic Instabilities in Crop Plants

    DOE R&D Accomplishments Database

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  10. Transposable elements and genetic instabilities in crop plants

    SciTech Connect

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  11. Phase Instability in Semiconductor Lasers

    NASA Astrophysics Data System (ADS)

    Gil, L.; Lippi, G. L.

    2014-11-01

    For many years, the apparent absence of a phase instability has characterized lasers as peculiar nonlinear oscillators. We show that this unusual feature is solely due to the approximations used in writing the standard models. A new, careful derivation of the fundamental equations, based on codimension 2 bifurcation theory, shows the possible existence of dynamical regimes displaying either a pure phase instability, or mixed phase-amplitude turbulence. A comparison to existing experimental results convincingly shows that the Benjamin-Feir instability, common to all nonlinear wave problems, is a fundamental, satisfactory interpretation for their deterministic multimode dynamics.

  12. Analysis of structures causing instabilities.

    PubMed

    Wilhelm, Thomas

    2007-07-01

    We present a simple new method to systematically identify all topological structures (e.g., positive feedback loops) potentially leading to locally unstable steady states: ICSA-The instability causing structure analysis. Systems without any instability causing structure (i.e., not fulfilling the necessary topological condition for instabilities) cannot have unstable steady states. It follows that common bistability or multistability and Hopf bifurcations are excluded and sustained oscillations and deterministic chaos are most unlikely. The ICSA leads to new insights into the topological organization of chemical and biochemical systems, such as metabolic, gene regulatory, and signal transduction networks.

  13. Polarization modulation instability in photonic crystal fibers.

    PubMed

    Kruhlak, R J; Wong, G K; Chen, J S; Murdoch, S G; Leonhardt, R; Harvey, J D; Joly, N Y; Knight, J C

    2006-05-15

    Polarization modulation instability (PMI) in birefringent photonic crystal fibers has been observed in the normal dispersion regime with a frequency shift of 64 THz between the generated frequencies and the pump frequency. The generated sidebands are orthogonally polarized to the pump. From the observed PMI frequency shift and the measured dispersion, we determined the phase birefringence to be 5.3 x 10(-5) at a pump wavelength of 647.1 nm. This birefringence was used to estimate the PMI gain as a function of pump wavelength. Four-wave mixing experiments in both the normal and the anomalous dispersion regimes generated PMI frequency shifts that show good agreement with the predicted values over a 70 THz range. These results could lead to amplifiers and oscillators based on PMI.

  14. Resistive instabilities in tokamaks

    SciTech Connect

    Rutherford, P.H.

    1985-10-01

    Low-m tearing modes constitute the dominant instability problem in present-day tokamaks. In this lecture, the stability criteria for representative current profiles with q(0)-values slightly less than unit are reviewed; ''sawtooth'' reconnection to q(0)-values just at, or slightly exceeding, unity is generally destabilizing to the m = 2, n = 1 and m = 3, n = 2 modes, and severely limits the range of stable profile shapes. Feedback stabilization of m greater than or equal to 2 modes by rf heating or current drive, applied locally at the magnetic islands, appears feasible; feedback by island current drive is much more efficient, in terms of the radio-frequency power required, then feedback by island heating. Feedback stabilization of the m = 1 mode - although yielding particularly beneficial effects for resistive-tearing and high-beta stability by allowing q(0)-values substantially below unity - is more problematical, unless the m = 1 ideal-MHD mode can be made positively stable by strong triangular shaping of the central flux surfaces. Feedback techniques require a detectable, rotating MHD-like signal; the slowing of mode rotation - or the excitation of non-rotating modes - by an imperfectly conducting wall is also discussed.

  15. Chronic ankle instability.

    PubMed

    Gerstner Garces, Juan Bernardo

    2012-09-01

    Chronic instability of the ankle and anterolateral impingement syndrome are abnormalities that present as a result of inversion and forced plantar-flexion traumas of the foot, despite strict conservative management in the ER and in rehabilitation. A conservative approach is always the first choice of treatment, including anti-inflammatory medications, rehabilitation and proprioception, infiltration with steroids in impingement cases, and use of orthotics, whose true effectiveness is the subject of multiple studies and much debate. Good to excellent results can be obtained surgically with a minimally invasive approach, such as the arthroscopic technique presented herein. Such an approach is useful in managing a combination of conditions such as anterolateral impingement, synovitis, and osteochondral lesions of the talus. The method is easily reproducible, its learning curve is rapid, and it has the advantage of not preventing the use other arthroscopic methods, or open anatomic or nonanatomic methods (tendon transfers), in the case of failure. No nerve lesion was recorded, probably owing to the use of the security zone, and neither was there any arthrofibrosis, possibly related to the use of nonsteroidal anti-inflammatory medications in the immediate postsurgical period coupled with aggressive rehabilitation from the fourth week. The success of the technique is due to multidisciplinary team work leading to the ultimate achievement of patient satisfaction. This technique is not indicated for patients with a high sports demand or for sport professionals, until further biomechanical studies on its use and success are completed.

  16. Instabilities in the aether

    SciTech Connect

    Carroll, Sean M.; Dulaney, Timothy R.; Gresham, Moira I.; Tam, Heywood

    2009-03-15

    We investigate the stability of theories in which Lorentz invariance is spontaneously broken by fixed-norm vector 'aether' fields. Models with generic kinetic terms are plagued either by ghosts or by tachyons, and are therefore physically unacceptable. There are precisely three kinetic terms that are not manifestly unstable: a sigma model ({partial_derivative}{sub {mu}}A{sub {nu}}){sup 2}, the Maxwell Lagrangian F{sub {mu}}{sub {nu}}F{sup {mu}}{sup {nu}}, and a scalar Lagrangian ({partial_derivative}{sub {mu}}A{sup {mu}}){sup 2}. The timelike sigma-model case is well defined and stable when the vector norm is fixed by a constraint; however, when it is determined by minimizing a potential there is necessarily a tachyonic ghost, and therefore an instability. In the Maxwell and scalar cases, the Hamiltonian is unbounded below, but at the level of perturbation theory there are fewer degrees of freedom and the models are stable. However, in these two theories there are obstacles to smooth evolution for certain choices of initial data.

  17. Mobilization of LINE-1 in irradiated mammary gland tissue may potentially contribute to low dose radiation-induced genomic instability.

    PubMed

    Luzhna, Lidia; Ilnytskyy, Yaroslav; Kovalchuk, Olga

    2015-01-01

    It is known that cellular stresses such as ionizing radiation activate LINE-1 (long interspersed nuclear element type 1, L1), but the molecular mechanisms of LINE-1 activation have not been fully elucidated. There is a possibility that DNA methylation changes induced by genotoxic stresses might contribute to LINE-1 activation in mammalian cells. L1 insertions usually cause major genomic rearrangements, such as deletions, transductions, the intrachromosomal homologous recombination between L1s, and the generation of pseudogenes, which could lead to genomic instability. The purpose of this study was to evaluate the effects of low and high doses of ionizing radiation on the DNA methylation status of LINE-1 transposable elements in rat mammary glands. Here we describe radiation-induced hypomethylation and activation of LINE-1 ORF1 in rat mammary gland tissues. We show that radiation exposure has also led to the translation of the LINE-1 element, whereby the 148 kDa LINE-1 protein level was increased 96 hours after treatment with a low dose and low energy level radiation and remained elevated for 24 weeks after treatment. The mobilization of LINE-1 in irradiated tissue may potentially contribute to genomic instability. The observed activation of mobile elements in response to radiation exposure is consistently discussed as a plausible mechanism of cancer etiology and development.

  18. Rarefaction solitons initiated by sheath instability

    SciTech Connect

    Levko, Dmitry

    2015-09-15

    The instability of the cathode sheath initiated by the cold energetic electron beam is studied by the one-dimensional fluid model. Numerical simulations show the generation of travelling rarefaction solitons at the cathode. It is obtained that the parameters of these solitons strongly depend on the parameters of electron beam. The “stretched” variables are derived using the small-amplitude analysis. These variables are used in order to obtain the Korteweg-de Vries equation describing the propagation of the rarefaction solitons through the plasma with cold energetic electron beam.

  19. The Many Landscapes of Recombination in Drosophila melanogaster

    PubMed Central

    Comeron, Josep M.; Ratnappan, Ramesh; Bailin, Samuel

    2012-01-01

    Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricted to qualitative trends due to the lack of detailed characterization of recombination rate variation across genomes and within species. The use of imprecise recombination rates can also skew population genetic analyses designed to assess the presence and mode of selection across genomes. Here we report the first integrated high-resolution description of genomic and population variation in recombination, which also distinguishes between the two outcomes of meiotic recombination: crossing over (CO) and gene conversion (GC). We characterized the products of 5,860 female meioses in Drosophila melanogaster by genotyping a total of 139 million informative SNPs and mapped 106,964 recombination events at a resolution down to 2 kilobases. This approach allowed us to generate whole-genome CO and GC maps as well as a detailed description of variation in recombination among individuals of this species. We describe many levels of variation in recombination rates. At a large-scale (100 kb), CO rates exhibit extreme and highly punctuated variation along chromosomes, with hot and coldspots. We also show extensive intra-specific variation in CO landscapes that is associated with hotspots at low frequency in our sample. GC rates are more uniformly distributed across the genome than CO rates and detectable in regions with reduced or absent CO. At a local scale, recombination events are associated with numerous sequence motifs and tend to occur within transcript regions, thus suggesting that chromatin accessibility favors double-strand breaks. All these non-independent layers of variation in recombination across genomes and among individuals need to be taken into account in order to obtain relevant estimates of recombination rates, and should

  20. Radiation induction of delayed recombination in Schizosaccharomyces pombe.

    PubMed

    Takeda, Jun; Uematsu, Norio; Shiraishi, Satomi; Toyoshima, Megumi; Matsumoto, Tomohiro; Niwa, Ohtsura

    2008-08-02

    Ionizing radiation is known to induce delayed chromosome and gene mutations in the descendants of the irradiated tissue culture cells. Molecular mechanisms of such delayed mutations are yet to be elucidated, since high genomic complexity of mammalian cells makes it difficult to analyze. We now tested radiation induction of delayed recombination in the fission yeast Schizosaccharomyces pombe by monitoring the frequency of homologous recombination after X-irradiation. A reporter with 200 bp tandem repeats went through spontaneous recombination at a frequency of 1.0 x 10(-4), and the frequency increased dose-dependently to around 10 x 10(-4) at 500 Gy of X-irradiation. Although the repair of initial DNA damage was thought to be completed before the restart of cell division cycle, the elevation of the recombination frequency persisted for 8-10 cell generations after irradiation (delayed recombination). The delayed recombination suggests that descendants of the irradiated cells keep a memory of the initial DNA damage which upregulates recombination machinery for 8-10 generations even in the absence of DNA double-strand breaks (DSBs). Since radical scavengers were ineffective in inhibiting the delayed recombination, a memory by continuous production of DNA damaging agents such as reactive oxygen species (ROS) was excluded. Recombination was induced in trans in a reporter on chromosome III by a DNA DSB at a site on chromosome I, suggesting the untargeted nature of delayed recombination. Interestingly, Rad22 foci persisted in the X-irradiated population in parallel with the elevation of the recombination frequency. These results suggest that the epigenetic damage memory induced by DNA DSB upregulates untargeted and delayed recombination in S. pombe.

  1. Electromechanical instability in soft materials: Theory, experiments and applications

    NASA Astrophysics Data System (ADS)

    Suo, Zhigang

    2013-03-01

    Subject to a voltage, a membrane of a dielectric elastomer reduces thickness and expands area, possibly straining over 100%. The phenomenon is being developed as transducers for broad applications, including soft robots, adaptive optics, Braille displays, and electric generators. The behavior of dielectric elastomers is closely tied to electromechanical instability. This instability may limit the performance of devices, and may also be used to achieve giant actuation strains. This talk reviews the theory of dielectric elastomers, coupling large deformation and electric potential. The theory is developed within the framework of continuum mechanics and thermodynamics. The theory attempts to answer commonly asked questions. How do mechanics and electrostatics work together to generate large deformation? How efficiently can a material convert energy from one form to another? How do molecular processes affect macroscopic behavior? The theory is used to describe electromechanical instability, and is related to recent experiments.

  2. Instability Analysis of Formation of Multiple Arc Anode Attachments

    NASA Astrophysics Data System (ADS)

    Yang, Guang; Heberlein, Joachim

    2007-10-01

    To understand the origin of the multiple arc-anode attachments and the origin of the restrike behavior in the anode region of high intensity arcs, linear stability analyses of a non-uniform singly-ionized argon plasma and of the arc-anode interface are performed. The short characteristic times of such anode phenomena allow significant simplification and linearization of the governing equations, from which dispersion relations of the plasma are obtained. According to the calculations, we propose that the electron overheating instability and the anode evaporation-ionization instability are responsible for the formation of these anode phenomena. The electron overheating instability, which generates an electron temperature run-away situation, is excited by small-amplitude fluctuations in the plasma with specific combination of current flow, electric field, electron temperature and electron density. The vaporation-ionization instability, which leads to current run-away in a small area, is encouraged by large electric fields accelerating electrons towards the anode. The regions of these instabilities are identified with our experimental measurements. The results show that the multiple arc-anode attachments form in the fringes of the arc, and that the restrike behavior starts from flow instabilities, which bring high electron temperature cloud to the anode surface. Observations to the anode surface confirm the analysis results.

  3. Chromosomal Instability in the progeny of human irradiated cells

    NASA Astrophysics Data System (ADS)

    Testard, I.; Boissière, A.; Martins, L. M.; Sabatier, L.

    Manned space missions recently increased in number and duration, thus it became important to estimate the biological risks encountered by astronauts. They are exposed to cosmic and galactic rays, a complex mixture of different radiations. In addition to the measurements realized by physical dosimeters, it becomes essential to estimate real biologically effective doses and compare them to physical doses. Biological dosimetry of radiation exposures has been widely performed using cytogenetic analysis of chromosomes. This approach has been used for many years in order to estimate absorbed doses in accidental or chronic overexposures of humans. Recent studies show that some alterations can appear many cell generations after the initial radiation exposure as a delayed genomic instability. This delayed instability is characterized by the accumulation of cell alterations leading to cell transformation, delayed cell death and mutations. Chromosome instability was shown in vitro in different model systems (Sabatier et al., 1992; Marder and Morgan, 1993; Kadhim et al., 1994 and Holmberg et al., 1993, 1995). All types of radiation used induce chromosome instability; however, heavy ions cause the most damage. The period of chromosome instability followed by the formation of clones with unbalanced karyotypes seems to be shared by cancer cells. The shortening of telomere sequences leading to the formation of telomere fusions is an important factor in the appearance of this chromosome instability.

  4. Particle Acceleration in Relativistic Jets Due to Weibel Instability

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

    2004-01-01

    Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a three-dimensional relativistic electromagnetic particle code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. While some Fermi acceleration may occur at the jet front, the majority of electron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron s transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

  5. Particle Acceleration in Relativistic Jets due to Weibel Instability

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.; Hardee, P. E.; Richardson, G. A.; Preece, R. D.; Sol, H.; Fishman, G. J.

    2003-01-01

    Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron s transverse deflection behind the jet head. The jitter radiation (Medvedev 2000) from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

  6. Live-Cell Imaging of Vaccinia Virus Recombination.

    PubMed

    Paszkowski, Patrick; Noyce, Ryan S; Evans, David H

    2016-08-01

    Recombination between co-infecting poxviruses provides an important mechanism for generating the genetic diversity that underpins evolution. However, poxviruses replicate in membrane-bound cytoplasmic structures known as factories or virosomes. These are enclosed structures that could impede DNA mixing between co-infecting viruses, and mixing would seem to be essential for this process. We hypothesize that virosome fusion events would be a prerequisite for recombination between co-infecting poxviruses, and this requirement could delay or limit viral recombination. We have engineered vaccinia virus (VACV) to express overlapping portions of mCherry fluorescent protein fused to a cro DNA-binding element. In cells also expressing an EGFP-cro fusion protein, this permits live tracking of virus DNA and genetic recombination using confocal microscopy. Our studies show that different types of recombination events exhibit different timing patterns, depending upon the relative locations of the recombining elements. Recombination between partly duplicated sequences is detected soon after post-replicative genes are expressed, as long as the reporter gene sequences are located in cis within an infecting genome. The same kinetics are also observed when the recombining elements are divided between VACV and transfected DNA. In contrast, recombination is delayed when the recombining sequences are located on different co-infecting viruses, and mature recombinants aren't detected until well after late gene expression is well established. The delay supports the hypothesis that factories impede inter-viral recombination, but even after factories merge there remain further constraints limiting virus DNA mixing and recombinant gene assembly. This delay could be related to the continued presence of ER-derived membranes within the fused virosomes, membranes that may once have wrapped individual factories.

  7. Live-Cell Imaging of Vaccinia Virus Recombination

    PubMed Central

    Paszkowski, Patrick; Noyce, Ryan S.; Evans, David H.

    2016-01-01

    Recombination between co-infecting poxviruses provides an important mechanism for generating the genetic diversity that underpins evolution. However, poxviruses replicate in membrane-bound cytoplasmic structures known as factories or virosomes. These are enclosed structures that could impede DNA mixing between co-infecting viruses, and mixing would seem to be essential for this process. We hypothesize that virosome fusion events would be a prerequisite for recombination between co-infecting poxviruses, and this requirement could delay or limit viral recombination. We have engineered vaccinia virus (VACV) to express overlapping portions of mCherry fluorescent protein fused to a cro DNA-binding element. In cells also expressing an EGFP-cro fusion protein, this permits live tracking of virus DNA and genetic recombination using confocal microscopy. Our studies show that different types of recombination events exhibit different timing patterns, depending upon the relative locations of the recombining elements. Recombination between partly duplicated sequences is detected soon after post-replicative genes are expressed, as long as the reporter gene sequences are located in cis within an infecting genome. The same kinetics are also observed when the recombining elements are divided between VACV and transfected DNA. In contrast, recombination is delayed when the recombining sequences are located on different co-infecting viruses, and mature recombinants aren’t detected until well after late gene expression is well established. The delay supports the hypothesis that factories impede inter-viral recombination, but even after factories merge there remain further constraints limiting virus DNA mixing and recombinant gene assembly. This delay could be related to the continued presence of ER-derived membranes within the fused virosomes, membranes that may once have wrapped individual factories. PMID:27525721

  8. Atom Recombination on Surface

    NASA Astrophysics Data System (ADS)

    Kim, Young Chai

    Upon high speed re-entry of the Space Shuttle Orbiter (SSO) through the earth's atmosphere, oxygen and nitrogen atoms produced in the shock wave in front of the SSO recombine on the surface of the SSO, releasing heat. To minimize the rise of surface temperature due to the reaction, surface material of the SSO should have a low recombination probability, gamma, of atoms impinging on it. To design such material, it is necessary to understand the mechanism of atom recombination. With this in mind, gamma values were measured for recombination of O, N, and H atoms in a diffusion tube reactor between 700 and 1250 K (HT), 300 and 700 K (MT), and at 194 K (LT) on silica. The rate of recombination was first order with respect to the atom concentration from LT to HT. The Arrhenius plots, gamma vs. 1/T, were very complex. All observations are explained by assuming a surface with a small fraction of active sites that irreversibly bind chemisorbed atoms. Everything happens as if the active sites were surrounded by collection zones within which all atoms striking the surface are adsorbed reversibly with an assumed sticking probability of unity. These atoms then diffuse on the surface. Some of them reach the active sites where they can recombine with the chemisorbed atoms. At LT, all atoms striking the surface reach the active sites. As a result of desorption at MT, the collection zones shrink with increasing temperature. At HT, only atoms striking active sites directly from the gas phase lead to recombination. An analytical solution of the diffusion-reaction problem obtained for a model where the active sites are distributed uniformly fits with the experimental data from LT to HT. The two novel features of this work are the identification of the active sites on silica for recombination of H on silica at HT as surface OH groups and the suggestion that another kind of active site is responsible for recombination of O and N atoms at HT as well as for H atoms at LT and MT. Although

  9. Clustering instability of focused swimmers

    NASA Astrophysics Data System (ADS)

    Lauga, Eric; Nadal, Francois

    2016-12-01

    One of the hallmarks of active matter is its rich nonlinear dynamics and instabilities. Recent numerical simulations of phototactic algae showed that a thin jet of swimmers, obtained from hydrodynamic focusing inside a Poiseuille flow, was unstable to longitudinal perturbations with swimmers dynamically clustering (Jibuti L. et al., Phys. Rev. E, 90, (2014) 063019). As a simple starting point to understand these instabilities, we consider in this paper an initially homogeneous one-dimensional line of aligned swimmers moving along the same direction, and characterise its instability using both a continuum framework and a discrete approach. In both cases, we show that hydrodynamic interactions between the swimmers lead to instabilities in density for which we compute the growth rate analytically. Lines of pusher-type swimmers are predicted to remain stable while lines of pullers (such as flagellated algae) are predicted to always be unstable.

  10. Fluid Instabilities inside Astrophysical Explosions

    NASA Astrophysics Data System (ADS)

    Chen, Ke-Jung; Woosley, Stan; Heger, Alexander; Almgren, Ann; Zheng, Weiqun

    2014-11-01

    We present our results from the simulations of fluid instabilities inside supernovae with a new radiation-hydrodynamic code, CASTRO. Massive stars are ten times more massive than Sun. Observational and theoretical studies suggest that these massive stars tend to end their lives with energetic explosions, so-called supernovae. Many fluid instabilities occur during the supernova explosions. The fluid instabilities can be driven by hydrodynamics, nuclear burning, or radiation. In this talk, we discuss about the possible physics of fluid instabilities found in our simulations and how the resulting mixing affects the observational signatures of supernovae. This work was supported by the DOE HEP Program under contract DE-SC0010676; the National Science Foundation (AST 0909129) and the NASA Theory Program (NNX14AH34G).

  11. Waves and instabilities in plasmas

    SciTech Connect

    Chen, L.

    1987-01-01

    The contents of this book are: Plasma as a Dielectric Medium; Nyquist Technique; Absolute and Convective Instabilities; Landau Damping and Phase Mixing; Particle Trapping and Breakdown of Linear Theory; Solution of Viasov Equation via Guilding-Center Transformation; Kinetic Theory of Magnetohydrodynamic Waves; Geometric Optics; Wave-Kinetic Equation; Cutoff and Resonance; Resonant Absorption; Mode Conversion; Gyrokinetic Equation; Drift Waves; Quasi-Linear Theory; Ponderomotive Force; Parametric Instabilities; Problem Sets for Homework, Midterm and Final Examinations.

  12. Instability following total knee arthroplasty.

    PubMed

    Rodriguez-Merchan, E Carlos

    2011-10-01

    Background Knee prosthesis instability (KPI) is a frequent cause of failure of total knee arthroplasty. Moreover, the degree of constraint required to achieve immediate and long-term stability in total knee arthroplasty (TKA) is frequently debated. Questions This review aims to define the problem, analyze risk factors, and review strategies for prevention and treatment of KPI. Methods A PubMed (MEDLINE) search of the years 2000 to 2010 was performed using two key words: TKA and instability. One hundred and sixty-five initial articles were identified. The most important (17) articles as judged by the author were selected for this review. The main criteria for selection were that the articles addressed and provided solutions to the diagnosis and treatment of KPI. Results Patient-related risk factors predisposing to post-operative instability include deformity requiring a large surgical correction and aggressive ligament release, general or regional neuromuscular pathology, and hip or foot deformities. KPI can be prevented in most cases with appropriate selection of implants and good surgical technique. When ligament instability is anticipated post-operatively, the need for implants with a greater degree of constraint should be anticipated. In patients without significant varus or valgus malalignment and without significant flexion contracture, the posterior cruciate ligament (PCL) can be retained. However, the PCL should be sacrificed when deformity exists particularly in patients with rheumatoid arthritis, previous patellectomy, previous high tibial osteotomy or distal femoral osteotomy, and posttraumatic osteoarthritis with disruption of the PCL. In most cases, KPI requires revision surgery. Successful outcomes can only be obtained if the cause of KPI is identified and addressed. Conclusions Instability following TKA is a common cause of the need for revision. Typically, knees with deformity, rheumatoid arthritis, previous patellectomy or high tibial osteotomy, and

  13. Magnetothermal instability in cooling flows

    NASA Technical Reports Server (NTRS)

    Loewenstein, Michael

    1990-01-01

    The effect of magnetic fields on thermal instability in cooling flows is investigated using linear, Eulerian perturbation analysis. As contrasted with the zero magnetic-field case, hydromagnetic stresses support perturbations against acceleration caused by buoyancy - comoving evolution results and global growth rates are straightforward to obtain for a given cooling flow entropy distribution. In addition, background and induced magnetic fields ensure that conductive damping of thermal instability is greatly reduced.

  14. Material Instabilities in Particulate Systems

    NASA Technical Reports Server (NTRS)

    Goddard, J. D.

    1999-01-01

    Following is a brief summary of a theoretical investigation of material (or constitutive) instability associated with shear induced particle migration in dense particulate suspensions or granular media. It is shown that one can obtain a fairly general linear-stability analysis, including the effects of shear-induced anisotropy in the base flow as well as Reynolds dilatancy. A criterion is presented here for simple shearing instability in the absence of inertia and dilatancy.

  15. Genetics of meiosis and recombination in mice.

    PubMed

    Bolcun-Filas, Ewelina; Schimenti, John C

    2012-01-01

    Meiosis is one of the most critical developmental processes in sexually reproducing organisms. One round of DNA replication followed by two rounds of cell divisions results in generation of haploid gametes (sperm and eggs in mammals). Meiotic failure typically leads to infertility in mammals. In the process of meiotic recombination, maternal and paternal genomes are shuffled, creating new allelic combinations and thus genetic variety. However, in order to achieve this, meiotic cells must self-inflict DNA damage in the form of programmed double-strand breaks (DSBs). Complex processes evolved to ensure proper DSB repair, and to do so in a way that favors interhomolog reciprocal recombination and crossovers. The hallmark of meiosis, a structurally conserved proteinaceous structure called the synaptonemal complex, is found only in meiotic cells. Conversely, meiotic homologous recombination is an adaptation of the mitotic DNA repair process but involving specialized proteins. In this chapter, we summarize current developments in mammalian meiosis enabled by genetically modified mice.

  16. Instability of enclosed horizons

    NASA Astrophysics Data System (ADS)

    Kay, Bernard S.

    2015-03-01

    We point out that there are solutions to the scalar wave equation on dimensional Minkowski space with finite energy tails which, if they reflect off a uniformly accelerated mirror due to (say) Dirichlet boundary conditions on it, develop an infinite stress-energy tensor on the mirror's Rindler horizon. We also show that, in the presence of an image mirror in the opposite Rindler wedge, suitable compactly supported arbitrarily small initial data on a suitable initial surface will develop an arbitrarily large stress-energy scalar near where the two horizons cross. Also, while there is a regular Hartle-Hawking-Israel-like state for the quantum theory between these two mirrors, there are coherent states built on it for which there are similar singularities in the expectation value of the renormalized stress-energy tensor. We conjecture that in other situations with analogous enclosed horizons such as a (maximally extended) Schwarzschild black hole in equilibrium in a (stationary spherical) box or the (maximally extended) Schwarzschild-AdS spacetime, there will be similar stress-energy singularities and almost-singularities—leading to instability of the horizons when gravity is switched on and matter and gravity perturbations are allowed for. All this suggests it is incorrect to picture a black hole in equilibrium in a box or a Schwarzschild-AdS black hole as extending beyond the past and future horizons of a single Schwarzschild (/Schwarzschild-AdS) wedge. It would thus provide new evidence for 't Hooft's brick wall model while seeming to invalidate the picture in Maldacena's ` Eternal black holes in AdS'. It would thereby also support the validity of the author's matter-gravity entanglement hypothesis and of the paper ` Brick walls and AdS/CFT' by the author and Ortíz.

  17. Elastic instabilities in rubber

    NASA Astrophysics Data System (ADS)

    Gent, Alan

    2009-03-01

    Materials that undergo large elastic deformations can exhibit novel instabilities. Several examples are described: development of an aneurysm on inflating a rubber tube; non-uniform stretching on inflating a spherical balloon; formation of internal cracks in rubber blocks at a critical level of triaxial tension or when supersaturated with a dissolved gas; surface wrinkling of a block at a critical amount of compression; debonding or fracture of constrained films on swelling, and formation of ``knots'' on twisting stretched cylindrical rods. These various deformations are analyzed in terms of a simple strain energy function, using Rivlin's theory of large elastic deformations, and the results are compared with experimental measurements of the onset of unstable states. Such comparisons provide new tests of Rivlin's theory and, at least in principle, critical tests of proposed strain energy functions for rubber. Moreover the onset of highly non-uniform deformations has serious implications for the fatigue life and fracture resistance of rubber components. [4pt] References: [0pt] R. S. Rivlin, Philos. Trans. Roy. Soc. Lond. Ser. A241 (1948) 379--397. [0pt] A. Mallock, Proc. Roy. Soc. Lond. 49 (1890--1891) 458--463. [0pt] M. A. Biot, ``Mechanics of Incremental Deformations'', Wiley, New York, 1965. [0pt] A. N. Gent and P. B. Lindley, Proc. Roy. Soc. Lond. A 249 (1958) 195--205. [0pt] A. N. Gent, W. J. Hung and M. F. Tse, Rubb. Chem. Technol. 74 (2001) 89--99. [0pt] A. N. Gent, Internatl. J. Non-Linear Mech. 40 (2005) 165--175.

  18. Vector-Resonance-Multimode Instability

    NASA Astrophysics Data System (ADS)

    Sergeyev, S. V.; Kbashi, H.; Tarasov, N.; Loiko, Yu.; Kolpakov, S. A.

    2017-01-01

    The modulation and multimode instabilities are the main mechanisms which drive spontaneous spatial and temporal pattern formation in a vast number of nonlinear systems ranging from biology to laser physics. Using an Er-doped fiber laser as a test bed, here for the first time we demonstrate both experimentally and theoretically a new type of a low-threshold vector-resonance-multimode instability which inherits features of multimode and modulation instabilities. The same as for the multimode instability, a large number of longitudinal modes can be excited without mode synchronization. To enable modulation instability, we modulate the state of polarization of the lasing signal with the period of the beat length by an adjustment of the in-cavity birefringence and the state of polarization of the pump wave. As a result, we show the regime's tunability from complex oscillatory to periodic with longitudinal mode synchronization in the case of resonance matching between the beat and cavity lengths. Apart from the interest in laser physics for unlocking the tunability and stability of dynamic regimes, the proposed mechanism of the vector-resonance-multimode instability can be of fundamental interest for the nonlinear dynamics of various distributed systems.

  19. Vertical Instability at IPNS RCS.

    SciTech Connect

    Wang, S.; Brumwell, F. R.; Dooling, J. C.; Harkay, K. C.; Kustom, R.; McMichael, G. E.; Middendorf, M. E.; Nassiri, A.; Accelerator Systems Division

    2008-01-01

    The rapid cycling synchrotron (RCS) of the intense pulsed neutron source (IPNS) at ANL accelerates > 3.0 times 10{sup 12} protons from 50 MeV to 450 MeV with 30-Hz repetition frequency. During the acceleration cycle, the rf frequency varies from 2.21 MHz to 5.14 MHz. Presently, the beam current is limited by a vertical instability. By analyzing turn-by-turn beam position monitor (BPM) data, large- amplitude mode 0 and mode 1 vertical beam centroid oscillations were observed in the later part of the acceleration cycle. The oscillations start in the tail of the bunch, build up, and remain localized in the tail half of the bunch. This vertical instability was compared with a head-tail instability that was intentionally induced in the RCS by adjusting the trim sextupoles. It appears that our vertical instability is not a classical head-tail instability [1]. More data analysis and experiments were performed to characterize the instability.

  20. Stable Expression of Lentiviral Antigens by Quality-Controlled Recombinant Mycobacterium bovis BCG Vectors

    PubMed Central

    Hart, Bryan E.; Asrican, Rose; Lim, So-Yon; Sixsmith, Jaimie D.; Lukose, Regy; Souther, Sommer J. R.; Rayasam, Swati D. G.; Saelens, Joseph W.; Chen, Ching-ju; Seay, Sarah A.; Berney-Meyer, Linda; Magtanong, Leslie; Vermeul, Kim; Pajanirassa, Priyadharshini; Jimenez, Amanda E.; Ng, Tony W.; Tobin, David M.; Porcelli, Steven A.; Larsen, Michelle H.; Schmitz, Joern E.; Haynes, Barton F.; Jacobs, William R.; Lee, Sunhee

    2015-01-01

    The well-established safety profile of the tuberculosis vaccine strain, Mycobacterium bovis bacille Calmette-Guérin (BCG), makes it an attractive vehicle for heterologous expression of antigens from clinically relevant pathogens. However, successful generation of recombinant BCG strains possessing consistent insert expression has encountered challenges in stability. Here, we describe a method for the development of large recombinant BCG accession lots which stably express the lentiviral antigens, human immunodeficiency virus (HIV) gp120 and simian immunodeficiency virus (SIV) Gag, using selectable leucine auxotrophic complementation. Successful establishment of vaccine stability stems from stringent quality control criteria which not only screen for highly stable complemented BCG ΔleuCD transformants but also thoroughly characterize postproduction quality. These parameters include consistent production of correctly sized antigen, retention of sequence-pure plasmid DNA, freeze-thaw recovery, enumeration of CFU, and assessment of cellular aggregates. Importantly, these quality assurance procedures were indicative of overall vaccine stability, were predictive for successful antigen expression in subsequent passaging both in vitro and in vivo, and correlated with induction of immune responses in murine models. This study has yielded a quality-controlled BCG ΔleuCD vaccine expressing HIV gp120 that retained stable full-length expression after 1024-fold amplification in vitro and following 60 days of growth in mice. A second vaccine lot expressed full-length SIV Gag for >1068-fold amplification in vitro and induced potent antigen-specific T cell populations in vaccinated mice. Production of large, well-defined recombinant BCG ΔleuCD lots can allow confidence that vaccine materials for immunogenicity and protection studies are not negatively affected by instability or differences between freshly grown production batches. PMID:25924766

  1. Strategy to approach stable production of recombinant nattokinase in Bacillus subtilis.

    PubMed

    Chen, Po Ting; Chiang, Chung-Jen; Chao, Yun-Peng

    2007-01-01

    Bacillus subtilis (B. subtilis) is widely accepted as an excellent host cell for the secretory production of recombinant proteins. In this study, a shuttle vector was constructed by fusion of Staphylococcus aureus (S. aureus) plasmid pUB110 with Escherichia coli (E. coli) plasmid pUC18 and used for the expression of nattokinase in B. subtilis. The pUB110/pUC-based plasmid was found to exhibit high structural instability with the identification of a DNA deletion between two repeated regions. An initial attempt was made to eliminate the homologous site in the plasmid, whereas the stability of the resulting plasmid was not improved. In an alternative way, the pUC18-derived region in this hybrid vector was replaced by the suicidal R6K plasmid origin of E. coli. As a consequence, the pUB110/R6K-based plasmid displayed full structural stability, leading to a high-level production of recombinant nattokinase in the culture broth. This was mirrored by the detection of a very low level of high molecular weight DNAs generated by the plasmid. Moreover, 2-fold higher nattokinase production was obtained by B. subtilis strain carrying the pUB110/R6K-based plasmid as compared to the cell with the pAMbeta1-derived vector, a plasmid known to have high structural stability. Overall, it indicates the feasibility of the approach by fusing two compatible plasmid origins for stable and efficient production of recombinant nattokinase in B. subtilis.

  2. An exactly solvable model of random site-specific recombinations

    PubMed Central

    Wei, Yi; Koulakov, Alexei A.

    2017-01-01

    Cre-lox and other systems are used as genetic tools to control site-specific recombination (SSR) events in genomic DNA. If multiple recombination sites are organized in a compact cluster within the same genome, a series of random recombination events may generate substantial cell specific genomic diversity. This diversity is used, for example, to distinguish neurons in the brain of the same multicellular mosaic organism, within the brainbow approach to neuronal connectome. In this paper we study an exactly solvable statistical model for SSR operating on a cluster of recombination sites. We consider two types of recombination events: inversions and excisions. Both of these events are available in the Cre-lox system. We derive three properties of the sequences generated by multiple recombination events. First, we describe the set of sequences that can in principle be generated by multiple inversions operating on the given initial sequence. We call this description the ergodicity theorem. On the basis of this description we calculate the number of sequences that can be generated from an initial sequence. This number of sequences is experimentally testable. Second, we demonstrate that after a large number of random inversions every sequence that can be generated is generated with equal probability. Lastly, we derive the equations for the probability to find a sequence as a function of time in the limit when excisions are much less frequent than inversions, such as in shufflon sequences. PMID:23151958

  3. RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence.

    PubMed

    Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone; Acevedo, Ashley; Goldstein, Elizabeth Faul; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

    2016-04-13

    Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations.

  4. Space-Charge Waves and Instabilities in Intense Beams

    NASA Astrophysics Data System (ADS)

    Wang, J. G.

    1997-11-01

    Advancced accelerator applications, such as drivers for heavy ion inertial fusion, high-intensity synchrotrons for spallation neutron sources, high energy boosters, free electron lasers, high-power microwave generators, etc., require ever-increasing beam intensity. An important beam dynamics issue in such beams is the collective behavior of charged particles due to their space charge effects. This includes the phenomena of space-charge waves and instabilities excited on beams by external perturbations. It is very crucial to fully understand these phenomena in order to develop advanced accelerators for various applications. At the University of Maryland we have been conducting experimental programs to study space-charge waves and longitudinal instabilities by employing low-energy, high-current, space-charge dominated electron beams. Localized perturbations on the beams are generated from a gridded electron gun. In a conducting transport channel focused by short solenoids, these perturbations evolve into space-charge waves propagating on the beams. The wave speed is measured and many beam parameters are determined with this technique. The reflection of space-charge waves at the shoulder of an initially rectangular beam bunch is also observed. In a resistive-wall channel focused by a uniform long solenoid, the space-charge waves suffer longitudinal instability. The properties of the instabilities are studied in detail in the long wavelength range. In this talk we review our experimental results on the waves and instabilities and compare with theory.

  5. Recombination in Eukaryotic Single Stranded DNA Viruses

    PubMed Central

    Martin, Darren P.; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

    2011-01-01

    Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. PMID:21994803

  6. Polyploidization increases meiotic recombination frequency in Arabidopsis

    PubMed Central

    2011-01-01

    Background Polyploidization is the multiplication of the whole chromosome complement and has occurred frequently in vascular plants. Maintenance of stable polyploid state over generations requires special mechanisms to control pairing and distribution of more than two homologous chromosomes during meiosis. Since a minimal number of crossover events is essential for correct chromosome segregation, we investigated whether polyploidy has an influence on the frequency of meiotic recombination. Results Using two genetically linked transgenes providing seed-specific fluorescence, we compared a high number of progeny from diploid and tetraploid Arabidopsis plants. We show that rates of meiotic recombination in reciprocal crosses of genetically identical diploid and autotetraploid Arabidopsis plants were significantly higher in tetraploids compared to diploids. Although male and female gametogenesis differ substantially in meiotic recombination frequency, both rates were equally increased in tetraploids. To investigate whether multivalent formation in autotetraploids was responsible for the increased recombination rates, we also performed corresponding experiments with allotetraploid plants showing strict bivalent pairing. We found similarly increased rates in auto- and allotetraploids, suggesting that the ploidy effect is independent of chromosome pairing configurations. Conclusions The evolutionary success of polyploid plants in nature and under domestication has been attributed to buffering of mutations and sub- and neo-functionalization of duplicated genes. Should the data described here be representative for polyploid plants, enhanced meiotic recombination, and the resulting rapid creation of genetic diversity, could have also contributed to their prevalence. PMID:21510849

  7. Recombination in eukaryotic single stranded DNA viruses.

    PubMed

    Martin, Darren P; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

    2011-09-01

    Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

  8. The nucleus is the target for radiation-induced chromosomal instability

    NASA Technical Reports Server (NTRS)

    Kaplan, M. I.; Morgan, W. F.

    1998-01-01

    We have previously described chromosomal instability in cells of a human-hamster hybrid cell line after exposure to X rays. Chromosomal instability in these cells is characterized by the appearance of novel chromosomal rearrangements multiple generations after exposure to ionizing radiation. To identify the cellular target(s) for radiation-induced chromosomal instability, cells were treated with 125I-labeled compounds and frozen. Radioactive decays from 125I cause damage to the cell primarily at the site of their decay, and freezing the cells allows damage to accumulate in the absence of other cellular processes. We found that the decay of 125I-iododeoxyuridine, which is incorporated into the DNA, caused chromosomal instability. While cell killing and first-division chromosomal rearrangements increased with increasing numbers of 125I decays, the frequency of chromosomal instability was independent of dose. Chromosomal instability could also be induced from incorporation of 125I-iododeoxyuridine without freezing the cells for accumulation of decays. This indicates that DNA double-strand breaks in frozen cells resulting from 125I decays failed to lead to instability. Incorporation of an 125I-labeled protein (125I-succinyl-concanavalin A), which was internalized into the cell and/or bound to the plasma membrane, neither caused chromosomal instability nor potentiated chromosomal instability induced by 125I-iododeoxyuridine. These results show that the target for radiation-induced chromosomal instability in these cells is the nucleus.

  9. The Use of Directed Evolution to Create a Stable and Immunogenic Recombinant BCG Expressing a Modified HIV-1 Gag Antigen

    PubMed Central

    Shephard, Enid; Stutz, Helen; Douglass, Nicola; Mgwebi, Thandi; Meyers, Ann; Chin'ombe, Nyasha; Williamson, Anna-Lise

    2014-01-01

    Numerous features make Mycobacterium bovis BCG an attractive vaccine vector for HIV. It has a good safety profile, it elicits long-lasting cellular immune responses and in addition manufacturing costs are affordable. Despite these advantages it is often difficult to express viral antigens in BCG, which results in genetic instability and low immunogenicity. The aim of this study was to generate stable recombinant BCG (rBCG) that express high levels of HIV antigens, by modification of the HIV genes. A directed evolution process was applied to recombinant mycobacteria that expressed HIV-1 Gag fused to the green fluorescent protein (GFP). Higher growth rates and increased GFP expression were selected for. Through this process a modified Gag antigen was selected. Recombinant BCG that expressed the modified Gag (BCG[pWB106] and BCG[pWB206]) were more stable, produced higher levels of antigen and grew faster than those that expressed the unmodified Gag (BCG[pWB105]). The recombinant BCG that expressed the modified HIV-1 Gag induced 2 to 3 fold higher levels of Gag-specific CD4 T cells than those expressing the unmodified Gag (BCG[pWB105]). Mice primed with 107 CFU BCG[pWB206] and then boosted with MVA-Gag developed Gag-specific CD8 T cells with a frequency of 1343±17 SFU/106 splenocytes, 16 fold greater than the response induced with MVA-Gag alone. Levels of Gag-specific CD4 T cells were approximately 5 fold higher in mice primed with BCG[pWB206] and boosted with MVA-Gag than in those receiving the MVA-Gag boost alone. In addition mice vaccinated with BCG[pWB206] were protected from a surrogate vaccinia virus challenge. PMID:25061753

  10. Theoretical analysis of mode instability in high-power fiber amplifiers.

    PubMed

    Hansen, Kristian Rymann; Alkeskjold, Thomas Tanggaard; Broeng, Jes; Lægsgaard, Jesper

    2013-01-28

    We present a simple theoretical model of transverse mode instability in high-power rare-earth doped fiber amplifiers. The model shows that efficient power transfer between the fundamental and higher-order modes of the fiber can be induced by a nonlinear interaction mediated through the thermo-optic effect, leading to transverse mode instability. The temporal and spectral characteristics of the instability dynamics are investigated, and it is shown that the instability can be seeded by both quantum noise and signal intensity noise, while pure phase noise of the signal does not induce instability. It is also shown that the presence of a small harmonic amplitude modulation of the signal can lead to generation of higher harmonics in the output intensity when operating near the instability threshold.

  11. Role of chromosome instability in long term effect of manned-space missions

    NASA Astrophysics Data System (ADS)

    Ducray, C.; Sabatier, L.

    Astronauts are exposed to heavy ions during space missions and heavy ion induced-chromosome damages have been observed in their lymphocytes. This raises the problem of the consequence of longer space flights. Recent studies show that some alterations can appear many cell generations after the initial radiation exposure as a delayed genomic instability. This delayed instability is characterized by the accumulation of cell alterations leading to cell transformation, delayed cell death and mutations. Chromosome instability was shown in vitro in different model systems. All types of radiation used induce a chromosome instability, however, heavy ions cause the most damage. The period of chromosome instability followed by the formation of clones with unbalanced karyotypes seems to be shared by cancer cells. The shortening of telomere sequences leading to the formation of telomere fusions is an important factor in the appearance of this chromosome instability.

  12. Kelvin-Helmholtz instability in a strongly coupled dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar; Das, Amita; Patel, Bhavesh G.; Angom, Dilip; Kaw, Predhiman

    2012-07-15

    The Kelvin-Helmholtz (KH) instability in the context of strongly coupled dusty plasma medium has been investigated. In particular, the role of transverse shear and the compressional acoustic modes in both the linear and nonlinear regimes of the KH instability has been studied. It is observed that in addition to the conventional nonlocal KH instability, there exists a local instability in the strong coupling case. The interplay of the KH mode with this local instability shows up in the simulations as an interesting phenomenon of recurrence in the nonlinear regime. Thus, a cyclic KH instability process is observed to occur. These cyclic events are associated with bursts of activity in terms of transverse and compressional wave generation in the medium.

  13. How homologous recombination maintains telomere integrity.

    PubMed

    Tacconi, Eliana M C; Tarsounas, Madalena

    2015-06-01

    Telomeres protect the ends of linear chromosomes against loss of genetic information and inappropriate processing as damaged DNA and are therefore crucial to the maintenance of chromosome integrity. In addition to providing a pathway for genome-wide DNA repair, homologous recombination (HR) plays a key role in telomere replication and capping. Consistent with this, the genomic instability characteristic of HR-deficient cells and tumours is driven in part by telomere dysfunction. Here, we discuss the mechanisms by which HR modulates the response to intrinsic cellular challenges that arise during telomere replication, as well as its impact on the assembly of telomere protective structures. How normal and tumour cells differ in their ability to maintain telomeres is deeply relevant to the search for treatments that would selectively eliminate cells whose capacity for HR-mediated repair has been compromised.