Science.gov

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

    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. 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.

  3. 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.

  4. 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.

  5. Marital Instability: A Study of Its Transmission Between Generations

    ERIC Educational Resources Information Center

    Mueller, Charles W.; Pope, Hallowell

    1977-01-01

    A 1970 national sample of white ever-married females is used to explore the process of the intergenerational transmission of marital instability. The research examines the possibility that mate-selection outcomes operate as intervening variables between parent and child generation marital instability. Partial support is found for this. (Author)

  6. Genome-Wide Demethylation Promotes Triplet Repeat Instability Independently of Homologous Recombination

    PubMed Central

    Dion, Vincent; Lin, Yunfu; Price, Brandee A.; Fyffe, Sharyl L.; Seluanov, Andrei; Gorbunova, Vera; Wilson, John H.

    2008-01-01

    Trinucleotide repeat instability is intrinsic to a family of human neurodegenerative diseases. The mechanism leading to repeat length variation is unclear. We previously showed that treatment with the demethylating agent 5-aza-2′-deoxycytidine (5-aza-CdR) dramatically increases triplet repeat instability in mammalian cells. Based on previous reports that demethylation increases homologous recombination (HR), and our own observations that HR destabilizes triplet repeats, we hypothesized that demethylation alters repeat stability by stimulating HR. Here, we test that hypothesis at the Aprt (adenosine phosphoribosyl transferase) locus in CHO cells, where CpG demethylation and HR have both been shown to increase CAG repeat instability. We find that the rate of HR at the Aprt locus is not altered by demethylation. The spectrum of recombinants, however, was shifted from the usual 6:1 ratio of conversions to crossovers to more equal proportions in 5-aza-CdR-treated cells. The subtle influences of demethylation on HR at the Aprt locus are not sufficient to account for its dramatic effects on repeat instability. We conclude that 5-aza-CdR promotes triplet repeat instability independently of HR. PMID:18083071

  7. Recombination between defective tombusvirus RNAs generates functional hybrid genomes

    SciTech Connect

    White, K.A.; Morris, T.J.

    1994-04-26

    The tombusviruses represent a group of small icosahedral plant viruses that contain monopartite positive-sense RNA genomes. Tombusviruses are able to generate small replicating deletion mutants of their genomes (i.e., defective interfering RNAs) during infections via RNA recombination and/or rearrangement. To further study the process of RNA recombination and to determine whether tombusviruses were capable of trans-recombination, protoplasts were coinoculated with in vitro-generated transcripts of a nonreplicating 3{prime}-truncated genomic RNA of cucumber necrosis tombusvirus and either replicative or replication-defective DI RNAs of tomato bushy stunt tombusvirus. After 48-hr incubation, two dominant replicative chimeric recombinant viral RNA populations were detected that contained various large contiguous 5{prime} segments of the cucumber necrosis tombusvirus genomic RNA fused to 3{prime}-terminal regions of the tomato bushy stunt tombusvirus defective interfering RNA. Some of the larger chimeric recombinants formed in protoplasts were able to systemically infect plants and induce wild-type symptoms. In addition, a functional chimeric genome was generated in planta after direct coinoculation of whole plants with the defective RNA components. These results indicate that (i) RNA recombination can occur relatively efficiently in single-cell infections, (ii) trans-recombination can occur with nonreplicating viral RNA components, and (iii) functional chimeric genomes can be generated via recombination. Possible mechanisms for the formation of the recombinants are proposed, and evolutionary implications are discussed.

  8. 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.

  9. 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

  10. 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. PMID:27008550

  11. 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.

  12. Turbulence generated by flux tube instabilities in the solar wind

    NASA Astrophysics Data System (ADS)

    Vörös, Zoltan; Zaqarashvili, Teimuraz; Sasunov, Jury; Semenov, Vladimir; Bruno, Roberto

    2015-04-01

    Magnetic flux tubes represent basic structures on the Sun and in the solar wind. Flux tubes of solar origin can become magnetically twisted at photospheric, chromospheric or coronal levels and transported into interplanetary space. Twisted or untwisted flux tubes can also be generated by magnetic reconnection in the solar wind. We show here that flux tube instabilities, such as the Kelvin-Helmholtz and the kink instabilities, may significantly contribute to the local generation of turbulence, reconnection and dissipation in the solar wind. The associated "fresh" turbulence may change the field and plasma conditions supporting different local dissipation mechanisms at their characteristic wavenumbers. Recent analytical and numerical calculations show that twisted tubes embedded into twisted external magnetic fields are Kelvin-Helmholtz unstable even for sub-Alfvenic flows. Moving tubes with strong twists are unstable against the kink instability resulting in magnetic reconnection and dissipation. Vörös et al., ApJL, 797:L10, 2014. Zaqarashvili et al., A&A, 561, A62, 2014. Zaqarashvili et al., ApJL, 783:L19, 2014.

  13. 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.

  14. Generation of E3-deleted canine adenoviruses expressing canine parvovirus capsid by homologous recombination in bacteria.

    PubMed

    Morrison, Mark D; Reid, Dorothy; Onions, David; Spibey, Norman; Nicolson, Lesley

    2002-02-01

    E3-deleted canine adenovirus type 1 (CAV-1) was generated by homologous recombination in bacterial cells, using an antibiotic resistance marker to facilitate the recovery of recombinants. This marker was flanked by unique restriction endonuclease sites, which allowed its subsequent removal and the insertion of cassettes expressing the canine parvovirus capsid at the E3 locus. Infectious virus was recovered following transfection of canine cells and capsid expression was observed by RT-PCR from one of the virus constructs. A second construct, containing a different promoter, showed delayed growth and genome instability which, based on the size difference between these inserts, suggests a maximum packaging size of 106 to 109% wild-type genome size for CAV-1. PMID:11853396

  15. Recombination and population inversion in plasmas generated by tunneling ionization.

    PubMed

    Pert, G J

    2006-06-01

    Above-threshold ionization (ATI) ionization by linearly polarized light has been proposed by several authors as a means of driving recombination lasers in the soft x-ray spectral region. The pump radiation generates a cold electron plasma with ions in a single ionization stage, which is an ideal starting condition for strong recombination. Population inversions form during the recombination cascade to the ground state of the next ionization stage. In the absence of any relaxation the electron distribution is strongly peaked near zero energy. However, a number of different processes all heat the cold electrons towards Maxwellian, and may thereby reduce the recombination rate in the higher levels. Using numerical models we investigate these relaxation processes and their effect on recombination. We show that the recombination can be well described by the standard cascade model, provided an appropriate temperature is used. We examine two cases in detail, hydrogen-like lithium where the inversion is with respect to the ground state, and lithium-like nitrogen where it is with the first excited state. The two cases differ markedly in the degree of relaxation achieved, and in the duration of the population inversion.

  16. Generation and Selection of Orf Virus (ORFV) Recombinants.

    PubMed

    Rziha, Hanns-Joachim; Rohde, Jörg; Amann, Ralf

    2016-01-01

    Orf virus (ORFV) is an epitheliotropic poxvirus, which belongs to the genus Parapoxvirus. Among them the highly attenuated, apathogenic strain D1701-V is regarded as a promising candidate for novel virus vector vaccines. Our recent work demonstrated that those ORFV-based recombinants were able to induce protective, long-lasting immunity in various hosts that are non-permissive for ORFV. In this chapter we describe procedures for the generation, selection, propagation, and titration of ORFV recombinants as well as transgene detection by PCR or immunohistochemical staining.

  17. 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. PMID:26832032

  18. 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.

  19. 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.

  20. Characteristics of gravity waves generated in a baroclinic instability simulation

    NASA Astrophysics Data System (ADS)

    Kim, Y.-H.; Chun, H.-Y.; Park, S.-H.; Song, I.-S.; Choi, H.-J.

    2015-11-01

    An idealized baroclinic instability case is simulated using a ~ 10 km resolution global model to investigate the characteristics of gravity waves (GWs) generated in the baroclinic life cycle. Three groups of GWs (W1-W3) appear around the high-latitude surface trough at the mature stage of the baroclinic wave. They have horizontal and vertical wavelengths of 40-400 and 2.9-9.8 km, respectively, in the upper troposphere. The two-dimensional phase-velocity spectrum of the waves is arc-shaped with a peak at 17 m s-1 eastward, which is difficult for the waves to propagate upward through the tropospheric westerly jet. At the breaking stage of the baroclinic wave, a midlatitude surface low is isolated from the higher-latitude trough, and two groups of quasi-stationary GWs (W4 and W5) appear near the surface low. These waves have horizontal and vertical wavelengths of 60-400 and 4.9-14 km, respectively, and are able to propagate vertically for long distances. The generation mechanism of the simulated GWs is discussed.

  1. A general approach for the prediction of localized instability generation in boundary layer flows

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan; Ng, Lian; Streett, Craig L.

    1991-01-01

    The present approach to the prediction of instability generation that is due to the interaction of freestream disturbances with regions of subscale variations in surface boundary conditions can account for the finite Reynolds number effects, while furnishing a framework for the study of receptivity in compressible flow and in 3D boundary layers. The approach is illustrated for the case of Tollmien-Schlichting wave generation in a Blasius boundary layer, due to the interaction of a freestream acoustic wave with a localized wall inhomogeneity. Results are presented for the generation of viscous and inviscid instabilities in adverse pressure-gradient boundary layers, supersonic boundary layer instabilities, and cross-flow vortex instabilities.

  2. Generation of helper-dependent adenoviral vectors by homologous recombination.

    PubMed

    Toietta, Gabriele; Pastore, Lucio; Cerullo, Vincenzo; Finegold, Milton; Beaudet, Arthur L; Lee, Brendan

    2002-02-01

    Helper-dependent adenoviral vectors (HD-Ad) represent a potentially valuable tool for safe and prolonged gene expression in vivo. The current approach for generating these vectors is based on ligation of the expression cassette into large plasmids containing the viral inverted terminal repeats flanking "stuffer" DNA to maintain a final size above the lower limit for efficient packaging into the adenovirus capsid (approximately 28 kb). The ligation to produce the viral plasmid is generally very inefficient. Similar problems in producing first-generation adenoviral (FG-Ad) vectors were circumvented with the development of a system taking advantage of efficient homologous recombination between a shuttle plasmid containing the expression cassette and a FG-Ad vector backbone in the Escherichia coli strain BJ5183. Here we describe a method for fast and efficient generation of HD-Ad vector plasmids that can accommodate expression cassettes of any size up to 35 kb. To validate the system, we generated a HD-Ad vector expressing the fusion protein between beta-galactosidase and neomycin resistance genes under the control of the SR alpha promoter, and one expressing the enhanced green fluorescent protein under the control of the cytomegalovirus promoter. The viruses were rescued and tested in vitro and for in vivo expression in mice. The data collected indicate the possibility for achieving a high level of hepatocyte transduction using HD-Ad vectors derived from plasmids obtained by homologous recombination in E. coli, with no significant alteration of liver enzymes and a less severe, transient thrombocytopenia in comparison with previous reports with similar doses of a FG-Ad vector. PMID:11829528

  3. Precise numerical estimation of the magnetic field generated around recombination

    NASA Astrophysics Data System (ADS)

    Fidler, Christian; Pettinari, Guido; Pitrou, Cyril

    2016-05-01

    We investigate the generation of magnetic fields from nonlinear effects around recombination. As tight-coupling is gradually lost when approaching z ≃1100 , the velocity difference between photons and baryons starts to increase, leading to an increasing Compton drag of the photons on the electrons. The protons are then forced to follow the electrons due to the electric field created by the charge displacement; the same field, following Maxwell's laws, eventually induces a magnetic field on cosmological scales. Since scalar perturbations do not generate any magnetic field as they are curl-free, one has to resort to second-order perturbation theory to compute the magnetic field generated by this effect. We reinvestigate this problem numerically using the powerful second-order Boltzmann code SONG. We show that: (i) all previous studies do not have a high enough angular resolution to reach a precise and consistent estimation of the magnetic field spectrum; (ii) the magnetic field is generated up to z ≃10 ; (iii) it is in practice impossible to compute the magnetic field with a Boltzmann code for scales smaller than 1 Mpc. Finally we confirm that for scales of a few Mpc, this magnetic field is of order 2 ×10-29 G , many orders of magnitude smaller than what is currently observed on intergalactic scales.

  4. 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.

  5. 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.

  6. 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

  7. Structured spheres generated by an in-fibre fluid instability.

    PubMed

    Kaufman, Joshua J; Tao, Guangming; Shabahang, Soroush; Banaei, Esmaeil-Hooman; Deng, Daosheng S; Liang, Xiangdong; Johnson, Steven G; Fink, Yoel; Abouraddy, Ayman F

    2012-07-26

    From drug delivery to chemical and biological catalysis and cosmetics, the need for efficient fabrication pathways for particles over a wide range of sizes, from a variety of materials, and in many different structures has been well established. Here we harness the inherent scalability of fibre production and an in-fibre Plateau-Rayleigh capillary instability for the fabrication of uniformly sized, structured spherical particles spanning an exceptionally wide range of sizes: from 2 mm down to 20 nm. Thermal processing of a multimaterial fibre controllably induces the instability, resulting in a well-ordered, oriented emulsion in three dimensions. The fibre core and cladding correspond to the dispersed and continuous phases, respectively, and are both frozen in situ on cooling, after which the particles are released when needed. By arranging a variety of structures and materials in a macroscopic scaled-up model of the fibre, we produce composite, structured, spherical particles, such as core-shell particles, two-compartment 'Janus' particles, and multi-sectioned 'beach ball' particles. Moreover, producing fibres with a high density of cores allows for an unprecedented level of parallelization. In principle, 10(8) 50-nm cores may be embedded in metres-long, 1-mm-diameter fibre, which can be induced to break up simultaneously throughout its length, into uniformly sized, structured spheres. PMID:22810590

  8. 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.

  9. Ad 2.0: a novel recombineering platform for high-throughput generation of tailored adenoviruses

    PubMed Central

    Mück-Häusl, Martin; Solanki, Manish; Zhang, Wenli; Ruzsics, Zsolt; Ehrhardt, Anja

    2015-01-01

    Recombinant adenoviruses containing a double-stranded DNA genome of 26–45 kb were broadly explored in basic virology, for vaccination purposes, for treatment of tumors based on oncolytic virotherapy, or simply as a tool for efficient gene transfer. However, the majority of recombinant adenoviral vectors (AdVs) is based on a small fraction of adenovirus types and their genetic modification. Recombineering techniques provide powerful tools for arbitrary engineering of recombinant DNA. Here, we adopted a seamless recombineering technology for high-throughput and arbitrary genetic engineering of recombinant adenoviral DNA molecules. Our cloning platform which also includes a novel recombination pipeline is based on bacterial artificial chromosomes (BACs). It enables generation of novel recombinant adenoviruses from different sources and switching between commonly used early generation AdVs and the last generation high-capacity AdVs lacking all viral coding sequences making them attractive candidates for clinical use. In combination with a novel recombination pipeline allowing cloning of AdVs containing large and complex transgenes and the possibility to generate arbitrary chimeric capsid-modified adenoviruses, these techniques allow generation of tailored AdVs with distinct features. Our technologies will pave the way toward broader applications of AdVs in molecular medicine including gene therapy and vaccination studies. PMID:25609697

  10. 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

  11. Generation of monoclonal antibodies to recombinant vascular endothelial growth factor.

    PubMed

    Shein, S A; Gurina, O I; Leopol'd, A V; Baklaushev, V P; Korchagina, A A; Grinenko, N F; Ivanova, N V; Volgina, N E; Ryabukhin, I A; Chekhonin, V P

    2012-05-01

    Female BALB/c mice were subcutaneously immunized with recombinant VEGF-164. After 3 immunization cycles, splenic B cells from immunized mouse were fused with immortalized myeloma culture SP2/0-Ag14 cells. Screening of hybrid cells producing anti-VEGF antibodies was performed by ELISA and immunocytochemical analysis on cultured C6 glioma cells. Subsequent cloning yielded hybridoma stably expressing monoclonal anti-VEGF antibodies recognizing recombinant and native VEGF. PMID:22808513

  12. 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...

  13. 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.

  14. Particles Generation and Bose Instability in Primordial Rotating Black Holes

    NASA Astrophysics Data System (ADS)

    Gaina, Alex

    Black Hole's angular momentum (Instability) will be a Bose Instablity of Black Holes. It is mentioned that the Black Holes rotation does not change drastically the Levels real part of the Energy, but only the imaginary part of the Energy. The problem of motion of quantum particles in the gravitational field of a Black Hole presents a didactical interest, at least. It is showing at the same time the evolution of concepts in Science, since Kepler to Ours days.

  15. 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.

  16. Evolution of the magnetic field generated by the Kelvin-Helmholtz instability

    NASA Astrophysics Data System (ADS)

    Modestov, M.; Bychkov, V.; Brodin, G.; Marklund, M.; Brandenburg, A.

    2014-07-01

    The Kelvin-Helmholtz instability in an ionized plasma is studied with a focus on the magnetic field generation via the Biermann battery (baroclinic) mechanism. The problem is solved by using direct numerical simulations of two counter-directed flows in 2D geometry. The simulations demonstrate the formation of eddies and their further interaction and merging resulting in a large single vortex. In contrast to general belief, it is found that the instability generated magnetic field may exhibit significantly different structures from the vorticity field, despite the mathematically identical equations controlling the magnetic field and vorticity evolution. At later stages of the nonlinear instability development, the magnetic field may keep growing even after the hydrodynamic vortex strength has reached its maximum and started decaying due to dissipation.

  17. Evolution of the magnetic field generated by the Kelvin-Helmholtz instability

    SciTech Connect

    Modestov, M.; Bychkov, V.; Brodin, G.; Marklund, M.; Brandenburg, A.

    2014-07-15

    The Kelvin-Helmholtz instability in an ionized plasma is studied with a focus on the magnetic field generation via the Biermann battery (baroclinic) mechanism. The problem is solved by using direct numerical simulations of two counter-directed flows in 2D geometry. The simulations demonstrate the formation of eddies and their further interaction and merging resulting in a large single vortex. In contrast to general belief, it is found that the instability generated magnetic field may exhibit significantly different structures from the vorticity field, despite the mathematically identical equations controlling the magnetic field and vorticity evolution. At later stages of the nonlinear instability development, the magnetic field may keep growing even after the hydrodynamic vortex strength has reached its maximum and started decaying due to dissipation.

  18. 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

  19. 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.

  20. 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.

  1. Magnetic field generation in core-sheath jets via the kinetic Kelvin-Helmholtz instability

    SciTech Connect

    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.

    2014-09-20

    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.

  2. Extensive Recombination Due to Heteroduplexes Generates Large Amounts of Artificial Gene Fragments during PCR

    PubMed Central

    Liu, Jia; Song, Hongshuo; Liu, Donglai; Zuo, Tao; Lu, Fengmin; Zhuang, Hui; Gao, Feng

    2014-01-01

    Artificial recombinants can be generated during PCR when more than two genetically distinct templates coexist in a single PCR reaction. These recombinant amplicons can lead to the false interpretation of genetic diversity and incorrect identification of biological phenotypes that do not exist in vivo. We investigated how recombination between 2 or 35 genetically distinct HIV-1 genomes was affected by different PCR conditions using the parallel allele-specific sequencing (PASS) assay and the next generation sequencing method. In a standard PCR condition, about 40% of amplicons in a PCR reaction were recombinants. The high recombination frequency could be significantly reduced if the number of amplicons in a PCR reaction was below a threshold of 1013–1014 using low thermal cycles, fewer input templates, and longer extension time. Heteroduplexes (each DNA strand from a distinct template) were present at a large proportion in the PCR products when more thermal cycles, more templates, and shorter extension time were used. Importantly, the majority of recombinants were identified in heteroduplexes, indicating that the recombinants were mainly generated through heteroduplexes. Since prematurely terminated extension fragments can form heteroduplexes by annealing to different templates during PCR amplification, recombination has a better chance to occur with samples containing different genomes when the number of amplicons accumulate over the threshold. New technologies are warranted to accurately characterize complex quasispecies gene populations. PMID:25211143

  3. 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

  4. Magnetic-field generation by the ablative nonlinear Rayleigh–Taylor instability

    SciTech Connect

    Nilson, P. M.; Gao, L.; Igumenshchev, I. V.; Fiksel, G.; Yan, R.; Davies, J. R.; Martinez, D.; Smalyuk, V. A.; Haines, M. G.; Blackman, E. G.; Froula, D. H.; Betti, R.; Meyerhofer, D. D.

    2015-04-01

    Experiments reporting magnetic-field generation by the ablative nonlinear Rayleigh–Taylor (RT) instability are reviewed. The experiments show how large-scale magnetic fields can, under certain circumstances, emerge and persist in strongly driven laboratory and astrophysical flows at drive pressures exceeding one million times atmospheric pressure.

  5. Subpicosecond-pulse generation through cross-phase-modulation-induced modulational instability in optical fibers.

    PubMed

    Gouveia-Neto, A S; Faldon, M E; Sombra, A S; Wigley, P G; Taylor, J R

    1988-10-01

    We report subpicosecond-pulse generation at 1.319 microm in a single-mode optical fiber by modulational instability induced through cross-phase modulation by 1.06-microm pulses propagating in the normal dispersion regime. Pulse-repetition rates approaching 300 GHz were achieved.

  6. 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.

  7. Population inversion in plasmas generated during recombination cascades.

    PubMed

    Pert, G J

    2007-11-01

    The collisional-radiative model for hydrogenlike ions is used to investigate the scaling of recombination at low temperatures in order to identify the necessary conditions of electron density and temperature, which will allow population inversion between the first excited state and the ground state to be developed. Numerical calculations show that at low temperatures the population growth in the hydrogenic states can be represented by similarity relations. The physical origin of these forms is presented. A table of minimum densities at which inversion will occur is given as a function of temperature for ions of arbitrary atomic number.

  8. Cell-induced flow-focusing instability in gelatin methacrylate microdroplet generation.

    PubMed

    Jung, Jinmu; Oh, Jonghyun

    2014-05-01

    Photo-crosslinkable gelatin methacrylate (GelMa) microspheres are applicable to deliver cells or drugs in biological or biomedical applications. To fabricate GelMa microdroplets, a flow focusing technique with advantages of size control and rapid production was used in a T-junction microfluidic device. Instability played an important role in promoting microdroplet uniformity. 5 wt. % GelMa prepolymer solution mixed with cells affected cell-induced instability. At low flow rate ratio of GelMa to mineral oil below 0.200, stability was maintained regardless of GelMa concentration (5 and 8 wt. %) and cell presence, which led to uniform microdroplet generation. In contrast, instability at high flow rate ratio above 0.200 was worsened by cell presence and unstable jetting length, resulting in the generation of non-uniform cell-laden microdroplets. Therefore, the effect of cell-induced instability on microdroplet generation was minimized at a low flow rate ratio.

  9. Cell-induced flow-focusing instability in gelatin methacrylate microdroplet generation

    PubMed Central

    Jung, Jinmu; Oh, Jonghyun

    2014-01-01

    Photo-crosslinkable gelatin methacrylate (GelMa) microspheres are applicable to deliver cells or drugs in biological or biomedical applications. To fabricate GelMa microdroplets, a flow focusing technique with advantages of size control and rapid production was used in a T-junction microfluidic device. Instability played an important role in promoting microdroplet uniformity. 5 wt. % GelMa prepolymer solution mixed with cells affected cell-induced instability. At low flow rate ratio of GelMa to mineral oil below 0.200, stability was maintained regardless of GelMa concentration (5 and 8 wt. %) and cell presence, which led to uniform microdroplet generation. In contrast, instability at high flow rate ratio above 0.200 was worsened by cell presence and unstable jetting length, resulting in the generation of non-uniform cell-laden microdroplets. Therefore, the effect of cell-induced instability on microdroplet generation was minimized at a low flow rate ratio. PMID:24932318

  10. Exploring pulse-voltage-triggered optically induced electrohydrodynamic instability for femtolitre droplet generation

    NASA Astrophysics Data System (ADS)

    Wang, Feifei; Fei, Fei; Liu, Lianqing; Yu, Haibo; Yu, Peng; Wang, Yuechao; Lee, Gwo-Bin; Jung Li, Wen

    2014-06-01

    We present a multipoint "virtual dispenser" to draw femtolitre droplets from a dielectric fluidic thin film using pulse-voltage-triggered optically induced electrohydrodynamic instability (PVT-OEHI). The "virtual dispenser" generates instability nucleation sites by controlling the optically induced lateral electrical stress and thermocapillary flow inside an optoelectronics chip. A time scale analysis shows that the electrohydrodynamic (EHD) instability phenomenon is present; however, its external manifestation is suppressed by OEHI. We observed two droplet dispensing mechanisms which correspond to different EHD states: Taylor cone formation and optically induced EHD jet. The EHD states transition could be realized by adjusting the pulse voltage parameters to alter the morphology of dispensed micron-scale polymer droplets, which could then be formed into organized arrays of microlenses with controllable diameter and curvature based on surface tension effect.

  11. Generation of recombinant antibody fragments for membrane protein crystallization.

    PubMed

    Mir, Syed H; Escher, Claudia; Kao, Wei-Chun; Birth, Dominic; Wirth, Christophe; Hunte, Carola

    2015-01-01

    Membrane proteins are challenging targets for crystallization and structure determination by X-ray crystallography. Hurdles can be overcome by antibody-mediated crystallization. More than 25 unique structures of membrane protein:antibody complexes have already been determined. In the majority of cases, hybridoma-derived antibody fragments either in Fab or Fv fragment format were employed for these complexes. We will briefly introduce the background and current status of the strategy and describe in detail the current protocols of well-established methods for the immunization, the selection, and the characterization of antibodies, as well as the cloning, the production, and the purification of recombinant antibodies useful for structural analysis of membrane proteins.

  12. Generation of spatially periodic patterns by a mechanical instability: a mechanical alternative to the Turing model.

    PubMed

    Harris, A K; Stopak, D; Warner, P

    1984-04-01

    We have studied the generation of spatial patterns created by mechanical (rather than chemical) instabilities. When dissociated fibroblasts are suspended in a gel of reprecipitated collagen, and the contraction of the gel as a whole is physically restrained by attachment of its margin to a glass fibre meshwork, then the effect of the fibroblasts' traction is to break up the cell-matrix mixture into a series of clumps or aggregations of cells and compressed matrix. These aggregations are interconnected by linear tracts of collagen fibres aligned under the tensile stress exerted by fibroblast traction. The patterns generated by this mechanical instability vary depending upon cell population density and other factors. Over a certain range of cell concentrations, this mechanical instability yields geometric patterns which resemble but are usually much less regular than the patterns which develop normally in the dermis of developing bird skin. We propose that an equivalent mechanical instability, occurring during the embryonic development of this skin, could be the cause not only of the clumping of dermal fibroblasts to form the feather papillae, but also of the alignment of collagen fibres into the characteristic polygonal network of fibre bundles - which interconnect these papillae and which presage the subsequent pattern of the dermal muscles serving to control feather movements. More generally, we suggest that this type of mechanical instability can serve the morphogenetic functions for which Turing's chemical instability and other reaction-diffusion systems have been proposed. Mechanical instabilities can create physical structures directly, in one step, in contrast to the two or more steps which would be required if positional information first had to be specified by chemical gradients and then only secondarily implemented in physical form. In addition, physical forces can act more quickly and at much longer range than can diffusing chemicals and can generate a

  13. Topographic vorticity generation, submesoscale instability and vortex street formation in the Gulf Stream

    NASA Astrophysics Data System (ADS)

    Gula, J.; Molemaker, M. J.; McWilliams, J. C.

    2015-05-01

    Meanders and eddies are routinely observed in the Gulf Stream along the South Atlantic Bight. We analyze here the instability processes that lead to the formation of submesoscale eddies on the cyclonic side of the Gulf Stream at the exit of the Florida Straits using very high resolution realistic simulations. The positive relative vorticity and potential vorticity on the cyclonic side of the Gulf Stream are strongly intensified in the Straits due to topographic drag along the continental slope. The bottom drag amplifies the cyclonic shear by generating large positive vertical vorticity values within the sloped turbulent bottom boundary layer. Downstream from the Straits the current becomes unstable to horizontal shear instability, rolls up, and forms a street of submesoscale vortices. The vortices expand as they propagate northward along the shelf, where they can generate large vertical displacements and enhance cross-shelf exchanges.

  14. Design and generation of recombinant rabies virus vectors.

    PubMed

    Osakada, Fumitaka; Callaway, Edward M

    2013-08-01

    Rabies viruses, negative-strand RNA viruses, infect neurons through axon terminals and spread trans-synaptically 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 trans-synaptic 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 the EnvA-TVA or EnvB-TVB (envelope glycoprotein and its specific receptor for avian sarcoma leukosis virus subgroup A or B) 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.

  15. Magnetic field generation by Biermann battery and Weibel instability in laboratory shock waves

    NASA Astrophysics Data System (ADS)

    Gregori, G.; Miniati, F.; Reville, B.; Drake, R. P.

    2012-02-01

    Magnetic field generation in the Universe is still an open problem. Possible mechanisms involve the Weibel instability, due to anisotropic phase-space distributions, as well as the Biermann battery, due to misaligned density and temperature gradients. These mechanisms can be reproduced in scaled laboratory experiments. In this contribution we estimate the relative importance of these two processes and explore the laser-energy requirements for producing Weibel dominated shocks.

  16. A nanoflare distribution generated by repeated relaxations triggered by kink instability

    NASA Astrophysics Data System (ADS)

    Bareford, M. R.; Browning, P. K.; van der Linden, R. A. M.

    2010-10-01

    Context. It is thought likely that vast numbers of nanoflares are responsible for the corona having a temperature of millions of degrees. Current observational technologies lack the resolving power to confirm the nanoflare hypothesis. An alternative approach is to construct a magnetohydrodynamic coronal loop model that has the ability to predict nanoflare energy distributions. Aims: This paper presents the initial results generated by a coronal loop model that flares whenever it becomes unstable to an ideal MHD kink mode. A feature of the model is that it predicts heating events with a range of sizes, depending on where the instability threshold for linear kink modes is encountered. The aims are to calculate the distribution of event energies and to investigate whether kink instability can be predicted from a single parameter. Methods: The loop is represented as a straight line-tied cylinder. The twisting caused by random photospheric motions is captured by two parameters, representing the ratio of current density to field strength for specific regions of the loop. Instability onset is mapped as a closed boundary in the 2D parameter space. Dissipation of the loop's magnetic energy begins during the nonlinear stage of the instability, which develops as a consequence of current sheet reconnection. After flaring, the loop evolves to the state of lowest energy where, in accordance with relaxation theory, the ratio of current to field is constant throughout the loop and helicity is conserved. Results: There exists substantial variation in the radial magnetic twist profiles for the loop states along the instability threshold. These results suggest that instability cannot be predicted by any simple twist-derived property reaching a critical value. The model is applied such that the loop undergoes repeated episodes of instability followed by energy-releasing relaxation. Hence, an energy distribution of the nanoflares produced is collated. This paper also presents the

  17. 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.

  18. 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.

  19. 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

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

    PubMed

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

    2015-10-01

    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.

  1. 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.

  2. Chronic Social Instability Induces Anxiety and Defective Social Interactions Across Generations

    PubMed Central

    Saavedra-Rodríguez, Lorena; Feig, Larry A.

    2013-01-01

    Background Chronic social instability during adolescence and early adulthood is known to produce a variety of long-lasting effects that may contribute to future psychiatric disorders. However, its potential to affect future generations has not been tested. Methods Female and male mice were exposed to chronic social stress involving social instability and disruption of social hierarchy from postnatal day 27 to 76. After treatment, a group of animals was used to evaluate long-term behavioral effects of the stress exposure, and other mice were used to generate F1, F2, and F3 offspring, to test for behavioral effects across generations. Results Chronic social instability during adolescence and early adulthood induces persistent behavioral alterations, including enhanced anxiety and social deficits that are transmitted predominantly to females across at least three generations. Both mothers and fathers can transmit all of these altered behaviors to their F1 offspring. However, only F1 fathers transmit all of them to their F2 and F3 daughters. In the F1 generation, enhanced anxiety and social deficits are associated with elevated serum corticosterone levels; however, in the F2 and F3 generations, they are not. Conclusions These findings support the idea that individual risk for psychiatric disorders that involve enhanced anxiety and/or social dysfunction may be dependent not only on the specific alleles of genes that are inherited from one’s parents and on one’s own experiences, but also on the experiences of one’s parents when they were young. PMID:22906514

  3. 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.

  4. 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. PMID:26458835

  5. 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.

  6. 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.

  7. In vivo recombination as a tool to generate molecular diversity in phage antibody libraries.

    PubMed

    Sblattero, D; Lou, J; Marzari, R; Bradbury, A

    2001-06-01

    The creation of diversity in populations of polypeptides has become an important tool in the derivation of polypeptides with useful characteristics. This requires efficient methods to create diversity coupled with methods to select polypeptides with desired properties. In this review we describe the use of in vivo recombination as a powerful way to generate diversity. The novel principles for the recombination process and several applications of this process for the creation of phage antibody libraries are described. The advantage and disadvantages are discussed and possible future exploitation presented.

  8. Large-scale Magnetic Field Generation via the Kinetic Kelvin-Helmholtz Instability in Unmagnetized Scenarios

    NASA Astrophysics Data System (ADS)

    Alves, E. P.; Grismayer, T.; Martins, S. F.; Fiúza, F.; Fonseca, R. A.; Silva, L. O.

    2012-02-01

    Collisionless plasma instabilities are fundamental in magnetic field generation in astrophysical scenarios, but their role has been addressed in scenarios where velocity shear is absent. In this work we show that velocity shears must be considered when studying realistic astrophysical scenarios, since these trigger the collisionless Kelvin-Helmholtz instability (KHI). We present the first self-consistent three-dimensional particle-in-cell simulations of the KHI in conditions relevant for unmagnetized relativistic outflows with velocity shear, such as active galactic nuclei and gamma-ray bursts. We show the generation of a strong large-scale DC magnetic field, which extends over the entire shear-surface, reaching thicknesses of a few tens of electron skin depths, and persisting on timescales much longer than the electron timescale. This DC magnetic field is not captured by magnetohydrodynamic models since it arises from intrinsically kinetic effects. Our results indicate that the KHI can generate intense magnetic fields yielding equipartition values up to epsilon B /epsilon p ~= 10-3-10-2 in the electron timescale. The KHI-induced magnetic fields have a characteristic structure that will lead to a distinct radiation signature and can seed the turbulent dynamo amplification process. The dynamics of the KHI are relevant for non-thermal radiation modeling and can also have a strong impact on the formation of relativistic shocks in presence of velocity shears.

  9. Instability of relativistic electron-beam-dielectric system as a mechanism for microwave generation

    NASA Astrophysics Data System (ADS)

    Kong, Ling-Bao; Du, Chao-Hai; Liu, Pu-Kun; Xiao, Liu

    2007-11-01

    The dispersion relation of relativistic rectilinear electron beam propagating along a guide magnetic field in a dielectric is investigated by cold fluid model. In such a system, due to anomalous Doppler effect, the instability occurs when the electron velocity exceeds the wave phase velocity. The growth rate and spatial growth rate are studied analytically and the nonlinear saturated efficiency is given analytically for the first time. Numerical results show that the saturated efficiency approaches about 10%-30%. The distinctive interaction mechanism is promising for the design of a new kind of compact high-power microwave generation devices.

  10. Dynamics of density cavities generated by frictional heating: Formation, distortion, and instability

    NASA Astrophysics Data System (ADS)

    Zettergren, M. D.; Semeter, J. L.; Dahlgren, H.

    2015-12-01

    A simulation study of the generation and evolution of mesoscale density cavities in the polar ionosphere is conducted using a time-dependent, nonlinear, quasi-electrostatic model. The model demonstrates that density cavities, generated by frictional heating, can form in as little as 90 s due to strong electric fields of ˜120 mV/m, which are sometimes observed near auroral zone and polar cap arcs. Asymmetric density cavity features and strong plasma density gradients perpendicular to the geomagnetic field are naturally generated as a consequence of the strong convection and finite extent of the auroral feature. The walls of the auroral density cavities are shown to be susceptible to large-scale distortion and gradient-drift instability, hence indicating that arc-related regions of frictional heating may be a source of polar ionospheric density irregularities.

  11. 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

  12. A novel and simple method for rapid generation of recombinant porcine adenoviral vectors for transgene expression.

    PubMed

    Zhang, Peng; Du, Enqi; 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.

  13. On the possibility of coherently stimulated recombination and cosmological structure generation: cosmological consequences.

    PubMed Central

    Schramm, D N; Rosner, R; Luo, X; Klemperer, W

    1995-01-01

    Given a specific physical mechanism for instabilities during cosmological recombination discussed in an earlier paper, we examine the nonlinear growth of density structures to form fractal-like structural patterns out to the horizon scale at that epoch (approximately 200 Mpc today). A model for such fractal patterns is presented. Such effects could explain observed large-scale structure patterns and the formation of objects at high z, while keeping microwave background anisotropies at the observed minimal levels. We also discuss possible microwave background implications of such a transition and note a potentially observable spectral signature at lambda approximately 0.18 mm as well as a weak line near the peak in the microwave background. PMID:11607553

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

    PubMed

    Tai, S-H Sheldon; Holz, Carine; Engstrom, Michael D; Cheng, Hans H; Maes, Roger K

    2016-08-01

    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 both gE and thymidine kinase (TK). The gC- mutant virus produced plaques that were similar in size to those resulting from infection with the C-27 parent strain. In contrast, the gE(-), PK(-), and gE(-)PK(-) deletion mutants produced plaques that were significantly smaller. Multistep in vitro growth kinetics of the gE(-), PK(-), and gE(-)PK(-) viruses were slightly delayed compared to those of the C-27 parent strain. Peak progeny titers of these three mutants were approximately 10-fold lower than those generated with the C-27 strain. There was no delay in the growth kinetics of the gC- mutant, but the progeny virus titer obtained with this mutant was at least 3 logs lower compared to the parental strain titer. Based upon their in vitro characteristics, these mutants will be useful for the development of novel immunization strategies against this important feline pathogen. PMID:27157860

  15. 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.

  16. Efficient generation and rapid isolation via stoplight recombination of Herpes simplex viruses expressing model antigenic and immunological epitopes.

    PubMed

    Sanchez, Rebecca L; Ramsay, Alistair J; Foster, Timothy P

    2012-01-01

    Generation and isolation of recombinant herpesviruses by traditional homologous recombination methods can be a tedious, time-consuming process. Therefore, a novel stoplight recombination selection method was developed that facilitated rapid identification and purification of recombinant viruses expressing fusions of immunological epitopes with EGFP. This "traffic-light" approach provided a visual indication of the presence and purity of recombinant HSV-1 isolates by producing three identifying signals: (1) red fluorescence indicates non-recombinant viruses that should be avoided; (2) yellow fluorescence indicates cells co-infected with non-recombinant and recombinant viruses that are chosen with caution; (3) green fluorescence indicates pure recombinant isolates and to proceed with preparation of viral stocks. Adaptability of this system was demonstrated by creating three recombinant viruses that expressed model immunological epitopes. Diagnostic PCR established that the fluorescent stoplight indicators were effective at differentiating between the presence of background virus contamination and pure recombinant viruses specifying immunological epitopes. This enabled isolation of pure recombinant viral stocks that exhibited wildtype-like viral replication and cell-to-cell spread following three rounds of plaque purification. Expression of specific immunological epitopes was confirmed by western analysis, and the utility of these viruses for examining host immune responses to HSV-1 was determined by a functional T cell assay.

  17. 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.

  18. Shot noise suppression in p-n junctions due to carrier generation-recombination

    NASA Astrophysics Data System (ADS)

    Maione, I. A.; Pellegrini, B.; Fiori, G.; Macucci, M.; Guidi, L.; Basso, G.

    2011-04-01

    We present a theoretical and experimental investigation of shot noise suppression in gallium arsenide and silicon p-n junctions due the to effect of generation-recombination phenomena. In particular, the availability of the cross-correlation technique and of ultra-low-noise amplifiers has allowed us to significantly extend, down to 10 pA, the range of bias current values for which results were available in the literature. To provide a quantitative understanding of the observed V-shape noise behavior, we have extended the Shockley-Read-Hall model for the trap-assisted generation-recombination mechanism. Such a model has represented the theoretical background for the performed Monte Carlo noise simulations, which have provided good agreement with the experimental results.

  19. 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.

  20. 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.

  1. Ion-acoustic enhancements generated by beam-plasma instability in an auroral cavity

    NASA Astrophysics Data System (ADS)

    Ziebell, L. F.; Yoon, P. H.; Pavan, J.; Gaelzer, R.

    2011-03-01

    This article demonstrates the generation of enhanced ion-acoustic waves by beam-plasma instability in a density cavity. The self-consistent equations of weak turbulence theory that include quasi-linear, decay, and scattering processes as well as convective and dispersive effects are numerically solved for a one-dimensional density cavity. It is shown that significant enhancements of ion-acoustic waves occur in the presence of counterstreaming electron beams and that the enhanced ion-acoustic waves are initially localized near the center of the density cavity at large wavelengths. Later in the evolution, the enhancement in the spectrum of ion-acoustic waves spreads out toward the edges of the cavity, with a shift to smaller wavelengths, while the enhancement near the center of the cavity tends to decrease in magnitude. The significance of the present findings is discussed.

  2. A simplified system for generating recombinant E3-deleted canine adenovirus-2.

    PubMed

    Yu, Zuo; Jiang, Qian; Liu, Jiasen; Guo, Dongchun; Quan, Chuansong; Li, Botao; Qu, Liandong

    2015-01-01

    Canine adenovirus type 2 (CAV-2) has been used extensively as a vector for studying gene therapy and vaccine applications. We describe a simple strategy for generating a replication-competent recombinant CAV-2 using a backbone vector and a shuttle vector. The backbone plasmid containing the full-length CAV-2 genome was constructed by homologous recombination in Escherichia coli strain BJ5183. The shuttle plasmid, which has a deletion of 1478 bp in the nonessential E3 viral genome region, was generated by subcloning a fusion fragment containing the flanking sequences of the CAV-2 E3 region and expression cassette sequences from pcDNA3.1(+) into modified pUC18. To determine system effectiveness, a gene for enhanced green fluorescent protein (EGFP) was inserted into the shuttle plasmid and cloned into the backbone plasmid using two unique NruI and SalI sites. Transfection of Madin-Darby canine kidney (MDCK) cells with the recombinant adenovirus genome containing the EGFP expression cassette resulted in infectious viral particles. This strategy provides a solid foundation for developing candidate vaccines using CAV-2 as a delivery vector. PMID:25450764

  3. Generation of recombinant antibody fragments with toxin-neutralizing potential in loxoscelism.

    PubMed

    Karim-Silva, Sabrina; Moura, Juliana de; Noiray, Magali; Minozzo, Joao Carlos; Aubrey, Nicolas; Alvarenga, Larissa M; Billiald, Philippe

    2016-08-01

    Loxosceles spider bites often lead to serious envenomings and no definite therapy has yet been established. In such a context, it is of interest to consider an antibody-based targeted therapy. We have previously prepared a murine monoclonal IgG (LiMab7) that binds to 32-35kDa components of Loxosceles intermedia venom and neutralizes the dermonecrotic activity of the venom. Here, we re-engineered LiMab7 into a recombinant diabody. The protein was produced in bacteria and then it was functionally characterized. It proved to be efficient at neutralizing sphingomyelinase and hemolytic activities of the crude venom despite the slightly altered binding kinetic constants and the limited stability of the dimeric configuration. This is the first report of a specific recombinant antibody for a next-generation of Loxosceles antivenoms. PMID:27288291

  4. 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.

  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. 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. PMID:26437229

  7. 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

  8. Transient dominant selection for the modification and generation of recombinant infectious bronchitis coronaviruses.

    PubMed

    Keep, Sarah M; Bickerton, Erica; Britton, Paul

    2015-01-01

    We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here, we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA; this has been successfully used for the substitution of specific nucleotides, deletion of genomic regions, and the exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA, containing the modified IBV cDNA, into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependent RNA polymerase.

  9. PHz-wide Supercontinua of Nondispersing Subcycle Pulses Generated by Extreme Modulational Instability

    NASA Astrophysics Data System (ADS)

    Tani, F.; Travers, J. C.; Russell, P. St. J.

    2013-07-01

    Modulational instability (MI) of 500 fs, 5μJ pulses, propagating in gas-filled hollow-core kagome photonic crystal fiber, is studied numerically and experimentally. By tuning the pressure and launched energy, we control the duration of the pulses emerging as a consequence of MI and hence are able to study two regimes: the classical MI case leading to few-cycle solitons of the nonlinear Schrödinger equation; and an extreme case leading to the formation of nondispersing subcycle pulses (0.5 to 2 fs) with peak intensities of order 1014Wcm-2. Insight into the two regimes is obtained using a novel statistical analysis of the soliton parameters. Numerical simulations and experimental measurements show that, when a train of these pulses is generated, strong ionization of the gas occurs. This extreme MI is used to experimentally generate a high energy (>1μJ) and spectrally broad supercontinuum extending from the deep ultraviolet (320 nm) to the infrared (1300 nm).

  10. PHz-wide supercontinua of nondispersing subcycle pulses generated by extreme modulational instability.

    PubMed

    Tani, F; Travers, J C; Russell, P St J

    2013-07-19

    Modulational instability (MI) of 500 fs, 5 μJ pulses, propagating in gas-filled hollow-core kagome photonic crystal fiber, is studied numerically and experimentally. By tuning the pressure and launched energy, we control the duration of the pulses emerging as a consequence of MI and hence are able to study two regimes: the classical MI case leading to few-cycle solitons of the nonlinear Schrödinger equation; and an extreme case leading to the formation of nondispersing subcycle pulses (0.5 to 2 fs) with peak intensities of order 10(14) W cm(-2). Insight into the two regimes is obtained using a novel statistical analysis of the soliton parameters. Numerical simulations and experimental measurements show that, when a train of these pulses is generated, strong ionization of the gas occurs. This extreme MI is used to experimentally generate a high energy (>1 μJ) and spectrally broad supercontinuum extending from the deep ultraviolet (320 nm) to the infrared (1300 nm).

  11. Characteristics of gravity waves generated in the jet-front system in a baroclinic instability simulation

    NASA Astrophysics Data System (ADS)

    Kim, Young-Ha; Chun, Hye-Yeong; Park, Sang-Hun; Song, In-Sun; Choi, Hyun-Joo

    2016-04-01

    An idealized baroclinic instability case is simulated using a ˜ 10 km resolution global model to investigate the characteristics of gravity waves generated in the baroclinic life cycle. Three groups of gravity waves appear around the high-latitude surface trough at the mature stage of the baroclinic wave. They have horizontal and vertical wavelengths of 40-400 and 2.9-9.8 km, respectively, in the upper troposphere. The two-dimensional phase-velocity spectrum of the waves is arc shaped with a peak at 17 m s-1 eastward. These waves have difficulty in propagating upward through the tropospheric westerly jet. At the breaking stage of the baroclinic wave, a midlatitude surface low is isolated from the higher-latitude trough, and two groups of quasi-stationary gravity waves appear near the surface low. These waves have horizontal and vertical wavelengths of 60-400 and 4.9-14 km, respectively, and are able to propagate vertically for long distances. The simulated gravity waves seem to be generated by surface fronts, given that the structures and speeds of wave phases are coherent with those of the fronts.

  12. Novel strategy for generation and titration of recombinant adeno-associated virus vectors.

    PubMed

    Shiau, Ai-Li; Liu, Pu-Ste; Wu, Chao-Liang

    2005-01-01

    Recombinant adeno-associated virus (rAAV) vectors have many advantages for gene therapeutic applications compared with other vector systems. Several methods that use plasmids or helper viruses have been reported for the generation of rAAV vectors. Unfortunately, the preparation of large-scale rAAV stocks is labor-intensive. Moreover, the biological titration of rAAV is still difficult, which may limit its preclinical and clinical applications. For this study, we developed a novel strategy to generate and biologically titrate rAAV vectors. A recombinant pseudorabies virus (PrV) with defects in its gD, gE, and thymidine kinase genes was engineered to express the AAV rep and cap genes, yielding PS virus, which served as a packaging and helper virus for the generation of rAAV vectors. PS virus was useful not only for generating high-titer rAAV vectors by cotransfection with an rAAV vector plasmid, but also for amplifying rAAV stocks. Notably, the biological titration of rAAV vectors was also feasible when cells were coinfected with rAAV and PS virus. Based on this strategy, we produced an rAAV that expresses prothymosin alpha (ProT). Expression of the ProT protein in vitro and in vivo mediated by rAAV/ProT gene transfer was detected by immunohistochemistry and a bioassay. Taken together, our results demonstrate that the PrV vector-based system is useful for generating rAAV vectors carrying various transgenes.

  13. Self-Consistent Calculation of Half-Harmonics Emission Generated by the Two-Plasmon-Decay Instability

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Myatt, J. F.; Maximov, A. V.; Short, R. W.; Dubois, D. F.; Russell, D. A.; Vu, H. X.

    2014-10-01

    Half-harmonics emission can be used as an effective diagnostic tool for the two-plasmon-decay (TPD) instability. However, interpretation of the half-harmonics spectrum is difficult because of its complicated generation mechanism. We have developed a code that can calculate half-harmonics emission self-consistently with the TPD instability. The results would be useful to interpret experimental data and help design experiments. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  14. 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.

  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. Generation of polygonal gas interfaces by soap film for Richtmyer-Meshkov instability study

    NASA Astrophysics Data System (ADS)

    Wang, Minghu; Si, Ting; Luo, Xisheng

    2012-12-01

    A simple method of generating polygonal gas interfaces is proposed by using the soap film technique. Thin pins are used as angular vertexes to connect the adjacent sides of polygonal soap films in order to avoid the pressure singularities around the vertexes caused by the surface tension. As a demonstration, three polygonal interfaces (i.e., square, equilateral triangle and diamond) are created in the test section of a shock tube. Experiments are then carried out for a planar shock wave (Mach number about 1.2) interacting with air/SF6 polygonal interfaces. Numerical simulations are also performed to validate the proposed method of the interface formation. Wave systems and interface structures can be clearly identified in experimental schlieren images and agree well with the numerical results. It is also indicated that the presences of thin pins and fine chamfers only have limited effects on the interface evolution and can be ignored at the very early stage. Experimental and numerical results about the movement of the distorted interface, the width and height of the interface structures are further compared and good agreement is achieved. It is then concluded that the polygonal interface formed by the proposed method is applicable for the Richtmyer-Meshkov instability study.

  17. Generation of polygonal gas interfaces by soap film for Richtmyer-Meshkov instability study

    NASA Astrophysics Data System (ADS)

    Wang, Minghu; Si, Ting; Luo, Xisheng

    2013-01-01

    A simple method of generating polygonal gas interfaces is proposed by using the soap film technique. Thin pins are used as angular vertexes to connect the adjacent sides of polygonal soap films in order to avoid the pressure singularities around the vertexes caused by the surface tension. As a demonstration, three polygonal interfaces (i.e., square, equilateral triangle and diamond) are created in the test section of a shock tube. Experiments are then carried out for a planar shock wave (Mach number about 1.2) interacting with air/SF6 polygonal interfaces. Numerical simulations are also performed to validate the proposed method of the interface formation. Wave systems and interface structures can be clearly identified in experimental schlieren images and agree well with the numerical results. It is also indicated that the presences of thin pins and fine chamfers only have limited effects on the interface evolution and can be ignored at the very early stage. Experimental and numerical results about the movement of the distorted interface, the width and height of the interface structures are further compared and good agreement is achieved. It is then concluded that the polygonal interface formed by the proposed method is applicable for the Richtmyer-Meshkov instability study.

  18. Generation of recombinant destabilase-lysozyme from medicinal leeches in three different expression systems.

    PubMed

    Manuvera, Valentin A; Kurdyumov, Alexey S; Filonova, Kseniya A; Lazarev, Vassili N

    2015-12-01

    Destabilase-lysozyme (mlDL) is an enzyme secreted by the salivary gland cells of medicinal leeches. Destabilase-lysozyme possesses lysozyme and isopeptidase activities. We generated recombinant destabilase-lysozyme isoform 2 in three expression systems, i.e., in the bacteria Escherichia coli, in the yeast Pichia pastoris, and in the human cell line Expi293F. In E. coli, we generated both polypeptide in inclusion bodies that was later undergone to the refolding and soluble protein that had been fused with the chaperone SlyD. The chaperone was later cleaved by a specific TEV-protease. In cultures of the yeast P. pastoris and the human cell line Expi293F, the soluble form of destabilase-lysozyme was accumulated in the culture media. For the generated enzymes, we determined the lysozyme, isopeptidase and fibrinolytic activities and tested their general antimicrobial effects. The comparisons of the enzymes generated in the different expression systems revealed that all of the destabilase-lysozymes obtained in the soluble forms possessed equal levels of lysozyme, isopeptidase and fibrinolytic activities that exceeded several to ten times the levels of the same activities of the destabilase-lysozyme renaturated from the inclusion bodies. A similar pattern of the differences in the levels of the general antimicrobial effects was observed for the destabilase-lysozymes generated in the soluble form and as inclusion bodies.

  19. Hose Instability and Wake Generation By An Intense Electron Beam in a Self-Ionized Gas

    SciTech Connect

    Deng, S.; Barnes, C.D.; Clayton, C.E.; O'Connell, C.; Decker, F.J.; Fonseca, R.A.; Huang, C.; Hogan, M.J.; Iverson, R.; Johnson, D.K.; Joshi, C.; Katsouleas, T.; Krejcik, P.; Lu, W.; Mori, W.B.; Muggli, P.; Oz, E.; Tsung, F.; Walz, D.; Zhou, M.; /Southern California U. /UCLA /SLAC

    2006-04-12

    The propagation of an intense relativistic electron beam through a gas that is self-ionized by the beam's space charge and wakefields is examined analytically and with 3D particle-in-cell simulations. Instability arises from the coupling between a beam and the offset plasma channel it creates when it is perturbed. The traditional electron hose instability in a preformed plasma is replaced with this slower growth instability depending on the radius of the ionization channel compared to the electron blowout radius. A new regime for hose stable plasma wakefield acceleration is suggested.

  20. Hose instability and wake generation by an intense electron beam in a self-ionized gas.

    PubMed

    Deng, S; Barnes, C D; Clayton, C E; O'Connell, C; Decker, F J; Fonseca, R A; Huang, C; Hogan, M J; Iverson, R; Johnson, D K; Joshi, C; Katsouleas, T; Krejcik, P; Lu, W; Mori, W B; Muggli, P; Oz, E; Tsung, F; Walz, D; Zhou, M

    2006-02-01

    The propagation of an intense relativistic electron beam through a gas that is self-ionized by the beam's space charge and wakefields is examined analytically and with 3D particle-in-cell simulations. Instability arises from the coupling between a beam and the offset plasma channel it creates when it is perturbed. The traditional electron hose instability in a preformed plasma is replaced with this slower growth instability depending on the radius of the ionization channel compared to the electron blowout radius. A new regime for hose stable plasma wakefield acceleration is suggested.

  1. Instabilities during the growth of dust successive generations in silane-based plasmas

    SciTech Connect

    Cavarroc, Marjorie; Mikikian, Maxime; Tessier, Yves; Boufendi, Laiefa

    2008-10-15

    Dust growth in silane-based plasmas is known to be a cyclic phenomenon as long as silane is provided. This continuous dust growth leads to an unstable behavior of the complex plasma, characterized by well-defined instabilities. In this paper, a complete study of these instabilities is presented. The electrical analysis is corroborated by an optical one, and high speed video imaging is used to get an insight in the dust cloud behavior. A possible cause of this instability phenomenon is also discussed.

  2. 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.

  3. Overcoming Instability of Antibody-Nanomaterial Conjugates: Next Generation Targeted Nanomedicines Using Bispecific Antibodies.

    PubMed

    Howard, Christopher B; Fletcher, Nicholas; Houston, Zachary H; Fuchs, Adrian V; Boase, Nathan R B; Simpson, Joshua D; Raftery, Lyndon J; Ruder, Tim; Jones, Martina L; de Bakker, Christopher J; Mahler, Stephen M; Thurecht, Kristofer J

    2016-08-01

    Targeted nanomaterials promise improved therapeutic efficacy, however their application in nanomedicine is limited due to complexities associated with protein conjugations to synthetic nanocarriers. A facile method to generate actively targeted nanomaterials is developed and exemplified using polyethylene glycol (PEG)-functional nanostructures coupled to a bispecific antibody (BsAb) with dual specificity for methoxy PEG (mPEG) epitopes and cancer targets such as epidermal growth factor receptor (EGFR). The EGFR-mPEG BsAb binds with high affinity to recombinant EGFR (KD : 1 × 10(-9) m) and hyperbranched polymer (HBP) consisting of mPEG (KD : 10 × 10(-9) m) and demonstrates higher avidity for HBP compared to linear mPEG. The binding of BsAb-HBP bioconjugate to EGFR on MDA-MB-468 cancer cells is investigated in vitro using a fluorescently labeled polymer, and in in vivo xenograft models by small animal optical imaging. The antibody-targeted nanostructures show improved accumulation in tumor cells compared to non-targeted nanomaterials. This demonstrates a facile approach for tuning targeting ligand density on nanomaterials, by modulating surface functionality. Antibody fragments are tethered to the nanomaterial through simple mixing prior to administration to animals, overcoming the extensive procedures encountered for developing targeted nanomedicines.

  4. Overcoming Instability of Antibody-Nanomaterial Conjugates: Next Generation Targeted Nanomedicines Using Bispecific Antibodies.

    PubMed

    Howard, Christopher B; Fletcher, Nicholas; Houston, Zachary H; Fuchs, Adrian V; Boase, Nathan R B; Simpson, Joshua D; Raftery, Lyndon J; Ruder, Tim; Jones, Martina L; de Bakker, Christopher J; Mahler, Stephen M; Thurecht, Kristofer J

    2016-08-01

    Targeted nanomaterials promise improved therapeutic efficacy, however their application in nanomedicine is limited due to complexities associated with protein conjugations to synthetic nanocarriers. A facile method to generate actively targeted nanomaterials is developed and exemplified using polyethylene glycol (PEG)-functional nanostructures coupled to a bispecific antibody (BsAb) with dual specificity for methoxy PEG (mPEG) epitopes and cancer targets such as epidermal growth factor receptor (EGFR). The EGFR-mPEG BsAb binds with high affinity to recombinant EGFR (KD : 1 × 10(-9) m) and hyperbranched polymer (HBP) consisting of mPEG (KD : 10 × 10(-9) m) and demonstrates higher avidity for HBP compared to linear mPEG. The binding of BsAb-HBP bioconjugate to EGFR on MDA-MB-468 cancer cells is investigated in vitro using a fluorescently labeled polymer, and in in vivo xenograft models by small animal optical imaging. The antibody-targeted nanostructures show improved accumulation in tumor cells compared to non-targeted nanomaterials. This demonstrates a facile approach for tuning targeting ligand density on nanomaterials, by modulating surface functionality. Antibody fragments are tethered to the nanomaterial through simple mixing prior to administration to animals, overcoming the extensive procedures encountered for developing targeted nanomedicines. PMID:27283923

  5. 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.

  6. Directional and direct cloning strategy for high-throughput generation of recombinant baculoviruses.

    PubMed

    Ma, Qi; Zhou, Li; Ma, Lixin; Huo, Keke

    2006-10-01

    The baculovirus expression vector system (BEVS) has become one of the most widely used systems for routine protein expression. We have developed an improved strategy to clone foreign genes directionally and directly into the baculovirus genome vector via a one-step procedure to generate recombinant viruses in a week. In this work, we constructed a host strain Escherichia coli DH10BacHB1.1, which contains the modified baculovirus shuttle genome vector pHBMBacmid1.1 for the cloning vector. The treated PCR products of foreign genes were ligated with the Bsu36I-digested vector. Then Spodoptera frugiperda (Sf9) cells were transfected directly with the ligation mixture. Using this method, the DsRed fluorescence protein and mannanase genes have been cloned in the baculovirus genome and expressed in the Sf9 cells. This strategy not only provides a means for high-throughput construction of recombinant baculoviruses, but also offers an idea of constructing other large plasmids and DNA virus-based expression vectors.

  7. 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

  8. 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

    2016-01-01

    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. PMID:26703885

  9. Geminate recombination of hydroxyl radicals generated in 200 nm photodissociation of aqueous hydrogen peroxide.

    SciTech Connect

    Crowell, R. A.; Lian, R.; Oulianov, D. A.; Shkrob, I. A.; Chemistry

    2004-01-15

    The picosecond dynamics of hydroxyl radicals generated in 200 nm photoinduced dissociation of aqueous hydrogen peroxide have been observed through their transient absorbance at 266 nm. It is shown that these kinetics are nearly exponential, with a decay time of ca. 30 ps. The prompt quantum yield for the decomposition of H2O2 is 0.56, and the fraction of hydroxyl radicals escaping from the solvent cage to the water bulk is 64-68%. These recombination kinetics suggest strong caging of the geminate hydroxyl radicals by water. Phenomenologically, these kinetics may be rationalized in terms of the diffusion of hydroxide radicals out of a shallow potential well (a solvent cage) with an Onsager radius of 0.24 nm.

  10. A robust method for the rapid generation of recombinant Zika virus expressing the GFP reporter gene.

    PubMed

    Gadea, Gilles; Bos, Sandra; Krejbich-Trotot, Pascale; Clain, Elodie; Viranaicken, Wildriss; El-Kalamouni, Chaker; Mavingui, Patrick; Desprès, Philippe

    2016-10-01

    Zika virus (ZIKV) infection is a major public health problem with severe human congenital and neurological anomalies. The screening of anti-ZIKV compounds and neutralizing antibodies needs reliable and rapid virus-based assays. Here, we described a convenient method leading to the rapid production of molecular clones of ZIKV. To generate a molecular clone of ZIKV strain MR766(NIID), the viral genome was directly assembled into Vero cells after introduction of four overlapping synthetic fragments that cover the full-length genomic RNA sequence. Such strategy has allowed the production of a recombinant ZIKV expressing the GFP reporter gene that is stable over two culturing rounds on Vero cells. Our data demonstrate that the ZIKV reporter virus is a very reliable GFP-based tool for analyzing viral growth and measuring the neutralizing antibody as well as rapid screening of antiviral effect of different classes of inhibitors.

  11. Frequency-domain interpretation of the plateaus in laser-assisted recombination and high-order harmonic generation

    SciTech Connect

    Cheng, Taiwang; Li, Xiaofeng; Ao, Shuyan; Wu, Ling-An; Fu, Panming

    2003-09-01

    The plateaus in laser-assisted recombination and high-order harmonic generation are investigated in the frequency domain. It is found that the probability amplitude of finding an electron with a given energy is given by a generalized Bessel function, which can be represented as a coherent superposition of contributions from a few electronic quantum trajectories. This concept is illustrated by comparing the spectral density of the electron with the laser-assisted recombination spectrum. On the other hand, the plateau of high-order harmonic generation reflects the spectral density of the electron at the location of the nucleus after above-threshold ionization.

  12. 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.

  13. Physical instability, aggregation and conformational changes of recombinant human bone morphogenetic protein-2 (rhBMP-2).

    PubMed

    Luca, Ludmila; Capelle, Martinus A H; Machaidze, Gia; Arvinte, Tudor; Jordan, Olivier; Gurny, Robert

    2010-05-31

    The influence of two different pH values on the physical stability of recombinant human bone morphogenetic protein-2 (rhBMP-2) in aqueous solution was evaluated in the present work. RhBMP-2 in solution at pH 4.5 or 6.5 was characterized by intrinsic and extrinsic (Nile Red and 1,8-ANS) fluorescence spectroscopy, 90 degrees light-scattering and transmission electron microscopy (TEM). Compared to the pH 4.5 solution, rhBMP-2 at pH 6.5 had (i) a stronger intrinsic fluorescence intensity, (ii) a longer fluorescence lifetime, (iii) a stronger 90 degrees light-scattering intensity, (iv) a stronger Nile Red fluorescence intensity, (v) a higher Nile Red fluorescence anisotropy, (vi) a lower 1,8-ANS fluorescence intensity, (vii) a higher 1,8-ANS fluorescence anisotropy and (viii) a longer 1,8-ANS fluorescence lifetime. Electron microscopy showed that rhBMP-2 at pH 4.5 contained aggregates of about 100 nm in diameter. More and larger protein aggregates (0.1-2 microm) were observed in solution at pH 6.5. Taken together, these results indicate conformational changes and increased aggregation of rhBMP-2 at pH 6.5 compared to pH 4.5, demonstrating a strong influence of pH on rhBMP-2 physical stability. These observations must be considered when developing a delivery system for rhBMP-2.

  14. 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

  15. The Generation and Characterization of Recombinant Protein and Antibodies of Clostridium perfringens Beta2 Toxin

    PubMed Central

    Zeng, Jin; Song, Fuyang; Yang, Yi; Ma, Chenjie; Deng, Guangcun; Li, Yong; Wang, Yujiong

    2016-01-01

    Introduction. Clostridium perfringens (C. perfringens) beta2 toxin (CPB2) is an important virulent factor of necrotic enteritis in both animals and humans. However, studies of its pathogenic roles and functional mechanisms have been hampered due to the difficulty of purification and lack of specific antibodies against this toxin. Methods. A recombinant His-tagged C. perfringens beta2 (rCPB2) toxin and monoclonal antibodies (McAbs) against CPB2 were generated and characterized by assays of cytotoxicity, immunoblotting, ELISA, neutralization, and immunofluorescence. Results. A His-tagged rCPB2 with integrity and cytotoxicity of native CPB2 was purified from E. coli expressing system, which exhibited a moderate cytotoxicity on NCM460 human intestinal epithelial cells. The rCPB2 could induce apoptotic cell death rather than necrotic death in part through a pathway involved in caspase-3 signaling. Mechanistically, rCPB2 was able to first bind to cell membrane and dynamically translocate into cytoplasm for its cytotoxic activity. Three McAbs 1E23, 2G7 and 2H7 were characterized to be able to immunologically react with CPB2 and neutralize rCPB2 cytotoxicity on NCM460 cells. Conclusion. These results indicated the rCPB2 and antibodies generated in this study are useful tools for studies of biological functions and pathogenic mechanisms of CPB2 in future, which warrants for further investigations.

  16. The Generation and Characterization of Recombinant Protein and Antibodies of Clostridium perfringens Beta2 Toxin

    PubMed Central

    Zeng, Jin; Song, Fuyang; Yang, Yi; Ma, Chenjie; Deng, Guangcun; Li, Yong; Wang, Yujiong

    2016-01-01

    Introduction. Clostridium perfringens (C. perfringens) beta2 toxin (CPB2) is an important virulent factor of necrotic enteritis in both animals and humans. However, studies of its pathogenic roles and functional mechanisms have been hampered due to the difficulty of purification and lack of specific antibodies against this toxin. Methods. A recombinant His-tagged C. perfringens beta2 (rCPB2) toxin and monoclonal antibodies (McAbs) against CPB2 were generated and characterized by assays of cytotoxicity, immunoblotting, ELISA, neutralization, and immunofluorescence. Results. A His-tagged rCPB2 with integrity and cytotoxicity of native CPB2 was purified from E. coli expressing system, which exhibited a moderate cytotoxicity on NCM460 human intestinal epithelial cells. The rCPB2 could induce apoptotic cell death rather than necrotic death in part through a pathway involved in caspase-3 signaling. Mechanistically, rCPB2 was able to first bind to cell membrane and dynamically translocate into cytoplasm for its cytotoxic activity. Three McAbs 1E23, 2G7 and 2H7 were characterized to be able to immunologically react with CPB2 and neutralize rCPB2 cytotoxicity on NCM460 cells. Conclusion. These results indicated the rCPB2 and antibodies generated in this study are useful tools for studies of biological functions and pathogenic mechanisms of CPB2 in future, which warrants for further investigations. PMID:27672668

  17. 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.

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

    SciTech Connect

    Dennis, Graham R.; Johnsson, Mattias T.

    2010-09-15

    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 et al. [Phys. Rev. A 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.

  19. Antigenic composition and immunoreactivity differences between HEV recombinant capsid proteins generated from different genotypes.

    PubMed

    Behloul, Nouredine; Wen, Jiyue; Dai, Xing; Dong, Chen; Meng, Jihong

    2015-08-01

    Appreciable variability has been observed in hepatitis E virus (HEV) serological diagnostics. Four recombinant proteins (p166s) were generated from position 452 to 617 aa of ORF2 of different HEV genotypes and used in an indirect ELISA to detect anti-HEV IgMs and IgGs in serially diluted sera of patients infected with different HEV genotypes (genotype 1, n=15; genotype 3, n=12; genotype 4, n=17). To evaluate the differences at a conformational level, 3D-structure models of p166s were predicted, and different bioinformatics tools were used to analyze the antigenic composition. With both anti-HEV IgMs and IgGs antibodies, there was a considerable variability between the four antigens immunoreactivities. In silico results revealed the region 483-533 aa with the highest antigenic potential and contains six key aa at positions 488, 489, 512, 533, 483 and 530. This immunoreactivity variation could affect diagnosis results and seroprevalence estimations and the identification in silico of a region highly antigenic would guide the development of efficient serological assays and epitope-based vaccines. PMID:26122075

  20. Generation of periodic signatures at Saturn through Titan's interaction with the centrifugal interchange instability

    NASA Astrophysics Data System (ADS)

    Winglee, R. M.; Kidder, A.; Harnett, E.; Ifland, N.; Paty, C.; Snowden, D.

    2013-07-01

    The origin of the periodicities in the radio, plasma, and magnetic fields of Saturn has long been debated. Given the high degree of alignment of Saturn's dipole with its rotation axis, no strong rotational periodicities are expected. However, Cassini data demonstrated the existence of such periodicities not only in Saturn's kilometric radio emissions (SKR) but in the plasma and magnetic field signatures. It is shown that the development of the centrifugal interchange instability that originates from mass loading from the Enceladus torus contains information about the planetary rotation period. However, the planetary period is masked by high-frequency components of the instability. The presence of Titan is shown to damp the high-frequency components and enables the fundamental frequency near the planetary rotation frequency to grow at the expense of the high-frequency components. As a result, the interchange instability is seen to change from one where five to seven large interchange fingers dominate to one where there are about three which cause the modulation of magnetospheric parameters near the planetary period. This modulation includes the movement of the magnetopause, the injection of energetic particles into the inner magnetosphere and the plasma density at high latitudes, both of which control SKR. Controlling factors on the frequency include Titan's drag on the plasma sheet which produces asymmetries between the Northern and Southern Hemispheres, solar wind conditions, and the density of the Enceladus plasma torus. The resultant magnetic perturbations are shown to have similar size and frequency as that seen in Cassini data.

  1. Generation of Recombinant Porcine Parvovirus Virus-Like Particles in Saccharomyces cerevisiae and Development of Virus-Specific Monoclonal Antibodies

    PubMed Central

    Tamošiūnas, Paulius Lukas; Petraitytė-Burneikienė, Rasa; Lasickienė, Rita; Sereika, Vilimas; Lelešius, Raimundas; Žvirblienė, Aurelija; Sasnauskas, Kęstutis

    2014-01-01

    Porcine parvovirus (PPV) is a widespread infectious virus that causes serious reproductive diseases of swine and death of piglets. The gene coding for the major capsid protein VP2 of PPV was amplified using viral nucleic acid extract from swine serum and inserted into yeast Saccharomyces cerevisiae expression plasmid. Recombinant PPV VP2 protein was efficiently expressed in yeast and purified using density gradient centrifugation. Electron microscopy analysis of purified PPV VP2 protein revealed the self-assembly of virus-like particles (VLPs). Nine monoclonal antibodies (MAbs) against the recombinant PPV VP2 protein were generated. The specificity of the newly generated MAbs was proven by immunofluorescence analysis of PPV-infected cells. Indirect IgG ELISA based on the recombinant VLPs for detection of PPV-specific antibodies in swine sera was developed and evaluated. The sensitivity and specificity of the new assay were found to be 93.4% and 97.4%, respectively. In conclusion, yeast S. cerevisiae represents a promising expression system for generating recombinant PPV VP2 protein VLPs of diagnostic relevance. PMID:25045718

  2. Generation of recombinant porcine parvovirus virus-like particles in Saccharomyces cerevisiae and development of virus-specific monoclonal antibodies.

    PubMed

    Tamošiūnas, Paulius Lukas; Petraitytė-Burneikienė, Rasa; Lasickienė, Rita; Akatov, Artiomas; Kundrotas, Gabrielis; Sereika, Vilimas; Lelešius, Raimundas; Žvirblienė, Aurelija; Sasnauskas, Kęstutis

    2014-01-01

    Porcine parvovirus (PPV) is a widespread infectious virus that causes serious reproductive diseases of swine and death of piglets. The gene coding for the major capsid protein VP2 of PPV was amplified using viral nucleic acid extract from swine serum and inserted into yeast Saccharomyces cerevisiae expression plasmid. Recombinant PPV VP2 protein was efficiently expressed in yeast and purified using density gradient centrifugation. Electron microscopy analysis of purified PPV VP2 protein revealed the self-assembly of virus-like particles (VLPs). Nine monoclonal antibodies (MAbs) against the recombinant PPV VP2 protein were generated. The specificity of the newly generated MAbs was proven by immunofluorescence analysis of PPV-infected cells. Indirect IgG ELISA based on the recombinant VLPs for detection of PPV-specific antibodies in swine sera was developed and evaluated. The sensitivity and specificity of the new assay were found to be 93.4% and 97.4%, respectively. In conclusion, yeast S. cerevisiae represents a promising expression system for generating recombinant PPV VP2 protein VLPs of diagnostic relevance.

  3. 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

  4. 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.

  5. Modulation instability and short-pulse generation in media with relaxing Kerr nonlinearity and high self-steepening

    SciTech Connect

    Zolotovskii, I O; Korobko, D A; Lapin, V A

    2014-01-31

    The modulation instability in waveguides with high Kerr nonlinearity, characterised by a delayed nonlinear response, has been investigated with allowance for the self-steepening parameter and third-order dispersion. General expressions for the modulation gain are obtained. The influence of the waveguide parameters on the gain is analysed. It is shown that the joint effect of the delayed nonlinear response and negative nonlinearity dispersion leads to an increase in the modulation gain. The relations obtained are confirmed by numerical simulation. The results of this study can be used to design compact generators of high-frequency pulse trains. (nonlinear optical phenomena)

  6. 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.

  7. Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination.

    PubMed

    Camara, Pablo G; Rosenbloom, Daniel I S; Emmett, Kevin J; Levine, Arnold J; Rabadan, Raul

    2016-07-01

    Meiotic recombination is a fundamental evolutionary process driving diversity in eukaryotes. In mammals, recombination is known to occur preferentially at specific genomic regions. Using topological data analysis (TDA), a branch of applied topology that extracts global features from large data sets, we developed an efficient method for mapping recombination at fine scales. When compared to standard linkage-based methods, TDA can deal with a larger number of SNPs and genomes without incurring prohibitive computational costs. We applied TDA to 1,000 Genomes Project data and constructed high-resolution whole-genome recombination maps of seven human populations. Our analysis shows that recombination is generally under-represented within transcription start sites. However, the binding sites of specific transcription factors are enriched for sites of recombination. These include transcription factors that regulate the expression of meiosis- and gametogenesis-specific genes, cell cycle progression, and differentiation blockage. Additionally, our analysis identifies an enrichment for sites of recombination at repeat-derived loci matched by piwi-interacting RNAs. PMID:27345159

  8. Ultrashort light pulses generated from modulation instability: background removal and soliton content

    NASA Astrophysics Data System (ADS)

    Mahnke, Christoph; Mitschke, Fedor

    2014-07-01

    Modulation instability can be used to convert a continuous light wave into a train of pulses on a constant background. It is a longstanding discussion whether these pulses can be converted into solitons. We clarify the situation by using a more general mathematical context, invoking the Akhmediev breather, Peregrine soliton and Kuznetsov-Ma soliton solutions of the wave equation, and suggest the use of a Mach-Zehnder interferometer to remove the background. Expressions for the pulse widths and peak powers thus obtained are presented, and their soliton content is determined. It turns out that more than 95 % of each pulse's energy can be converted to a soliton.

  9. Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity.

    PubMed

    Weng, Ziming; Barthelson, Roger; Gowda, Siddarame; Hilf, Mark E; Dawson, William O; Galbraith, David W; Xiong, Zhongguo

    2007-01-01

    Recombination and reassortment of viral genomes are major processes contributing to the creation of new, emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may possess novel host-colonizing and pathogenicity traits. In some plants, successive vegetative propagation of infected tissues and introduction of new genotypes of a virus by vector transmission allows for viral populations to increase in complexity for hundreds of years allowing co-replication and subsequent recombination of the multiple viral genotypes. Using a resequencing microarray, we examined a persistent infection by a Citrus tristeza virus (CTV) complex in citrus, a vegetatively propagated, globally important fruit crop, and found that the complex comprised three major and a number of minor genotypes. Subsequent deep sequencing analysis of the viral population confirmed the presence of the three major CTV genotypes and, in addition, revealed that the minor genotypes consisted of an extraordinarily large number of genetic variants generated by promiscuous recombination between the major genotypes. Further analysis provided evidence that some of the recombinants underwent subsequent divergence, further increasing the genotypic complexity. These data demonstrate that persistent infection of multiple viral genotypes within a host organism is sufficient to drive the large-scale production of viral genetic variants that may evolve into new and emerging viruses. PMID:17878952

  10. 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.

  11. 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.

  12. Recombinant outer membrane protein C of Aeromonas hydrophila elicits mixed immune response and generates agglutinating antibodies.

    PubMed

    Yadav, Sunita Kumari; Meena, Jitendra Kumar; Sharma, Mahima; Dixit, Aparna

    2016-08-01

    Aeromonas hydrophila is a gram-negative fish pathogenic bacterium, also responsible for causing opportunistic pathological conditions in humans. It causes a number of diseases in fish due to which the fish industry incurs huge economic losses annually. Due to problems of antibiotic resistance, and the rapidity with which the infection spreads among fishes, vaccination remains the most effective strategy to combat this infection in fish populations. Among various virulence factors associated with bacterial virulence, outer membrane proteins have been widely evaluated for their vaccine potential owing to their surface exposure and related role in pathogenicity. In the present study, we have investigated the immunogenic potential of a non-specific porin, outer membrane protein C (OmpC) whose expression is regulated by the two-component regulatory system and plays a major role in the survival of A. hydrophila under different osmolaric conditions. The full-length gene (~1 kb) encoding OmpC of A. hydrophila was cloned, characterized and expressed in E. coli. High yield (~112 mg/L at shake flask level) of the recombinant OmpC (rOmpC) (~40 kDa) of A. hydrophila was obtained upon purification from inclusion bodies using Ni(2+)-NTA affinity chromatography. Immunization with purified rOmpC in murine model generated high endpoint (>1:40,000) titers. IgG isotyping, ELISA and ELISPOT assay indicated mixed immune response with a TH2 bias. Also, the anti-rOmpC antibodies were able to agglutinate A. hydrophila in vitro and exhibited specific cross-reactivity with different Aeromonas strains, which will facilitate easy detection of different Aeromonas isolates in infected samples. Taken together, these data clearly indicate that rOmpC could serve as an effective vaccine against different strains of Aeromonas, a highly heterogenous group of bacteria. PMID:27328672

  13. 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.

  14. 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.

  15. To Be or not to Be a Source of Shot Noise: an Open Problem of Generation Recombination Noise

    NASA Astrophysics Data System (ADS)

    Gomila, G.; Reggiani, L.

    2003-05-01

    We address the fundamental question wether generation recombination noise can transform into shot noise at increasing values of the applied bias (current or voltage). From the seminal work of Van Vliet and Fassett (1965) the analytical answer to this question is affirmative. By contrast, recent numerical results by Bonani and Ghione (1999) provided a negative answer. For a simple semiconductor two level model consisting of a conducting band and an impurity level which provides charge carriers we solve exactly the appropriate second order stochastic differential equation self-consistently coupled with the Poisson solver. The effect of the diffusion current, neglected in the first analytical approach, is found to inhibit the cross-over between generation-recombination and shot noise, thus confirming more recent numerical results. Open problems related to the microscopic interpretation of these new results are pointed out.

  16. 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.

  17. Recent Developments in Reconnection Theory: the Plasmoid Instability, Self-Generated Turbulence, and Implications for Laboratory and Space Plasmas

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Amitava

    2015-11-01

    In recent years, new developments in reconnection theory have challenged classical nonlinear reconnection models. One of these developments is the so-called plasmoid instability of thin current sheets that grows at super-Alfvenic growth rates. Within the resistive MHD model, this instability alters qualitatively the predictions of the Sweet-Parker model, leading to a new nonlinear regime of fast reconnection in which the reconnection rate itself becomes independent of S. This regime has also been seen in Hall MHD as well as fully kinetic simulations, and thus appears to be a universal feature of thin current sheet dynamics, including applications to reconnection forced by the solar wind in the heliosphere and spontaneously unstable sawtooth oscillations in tokamaks. Plasmoids, which can grow by coalescence to large sizes, provide a powerful mechanism for coupling between global and kinetic scales as well as an efficient accelerator of particles to high energies. In two dimensions, the plasmoids are characterized by power-law distribution functions followed by exponential tails. In three dimensions, the instability produces self-generated and strongly anisotropic turbulence in which the reconnection rate for the mean-fields remain approximately at the two-dimensional value, but the energy spectra deviate significantly from anisotropic strong MHD turbulence phenomenology. A new phase diagram of fast reconnection has been proposed, guiding the design of future experiments in magnetically confined and high-energy-density plasmas, and have important implications for explorations of the reconnection layer in the recently launched Magnetospheric Multiscale (MMS) mission. This research is supported by DOE, NASA, and NSF.

  18. 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

  19. 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.

  20. 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.

  1. The Acoustic Field Generated by Interaction of a Shear-Layer Instability Wave with the Downstream Lip of a Cavity

    NASA Astrophysics Data System (ADS)

    Kerschen, E. J.

    1997-11-01

    High amplitude acoustic resonances may develop in cavities that are exposed to high-speed flows. These resonances arise from a feedback loop which involves a downstream-propagating instability wave in the shear layer across the open face of the cavity, and an upstream-propagating acoustic field inside the cavity. These two wave fields are coupled by the interactions at the edges of the cavity. A theory is presented for the acoustic field generated by the interaction of a shear-layer instability wave with a thin overhanging downstream lip of a cavity. The theory addresses the case of a supersonic free stream and utilizes the vortex-sheet approximation for the shear layer. The linearized unsteady flow is described by a mixed boundary value problem which is solved utilizing the Wiener-Hopf technique. The upstream-propagating acoustic field within the cavity is expressed as a eigenfunction series in terms of the leaky-cavity modes. Results for the pressure distribution along the bottom surface of the cavity are presented for a representative case. For shallow cavities, the feedback to the upstream lip is dominated by the first few leaky-cavity modes.

  2. 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.

  3. Nucleotide-Resolution Profiling of RNA Recombination in the Encapsidated Genome of a Eukaryotic RNAVirus by Next-Generation Sequencing

    PubMed Central

    Routh, Andrew; Ordoukhanian, Phillip; Johnson, John E.

    2012-01-01

    Next-Generation Sequencing has been used in numerous investigations to characterize andquantifythe genetic diversity of a virus samplethrough the mapping of polymorphisms and measurement of mutation frequencies.Next-Generation Sequencing has also been employed to identifyrecombinationevents occurring within the genomes of higher organisms, for example, detecting alternative RNA splicing events and oncogenic chromosomal rearrangements. Here, we combine these two approaches toprofile RNA recombination within the encapsidated genome of a eukaryotic RNA virus, Flock House Virus. We detect hundreds of thousands of recombination events, with single-nucleotide resolution, which result indiversity in the encapsidated genome rivaling that due to mismatch mutation. We detect previously identified Defective-RNAs as well as many other abundant and novel Defective-RNAs. Our approach is exceptionally sensitive, unbiased, and requires no prior knowledge beyond the virus genome sequence. RNA recombination is a powerful driving force behind the evolution and adaptation of RNA viruses. The strategy implemented here is widely applicable and provides a highly detailed description of the complex mutational landscape of the transmissible viral genome. PMID:23069247

  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. Exact and approximate expressions of energy generation rates and their impact on the explosion properties of pair instability supernovae

    NASA Astrophysics Data System (ADS)

    Takahashi, Koh; Yoshida, Takashi; Umeda, Hideyuki; Sumiyoshi, Kohsuke; Yamada, Shoichi

    2016-02-01

    Energetics of nuclear reaction is fundamentally important to understand the mechanism of pair instability supernovae (PISNe). Based on the hydrodynamic equations and thermodynamic relations, we derive exact expressions for energy conservation suitable to be solved in simulation. We also show that some formulae commonly used in the literature are obtained as approximations of the exact expressions. We simulate the evolution of very massive stars of ˜100-320 M⊙ with zero- and 1/10 Z⊙, and calculate further explosions as PISNe, applying each of the exact and approximate formulae. The calculations demonstrate that the explosion properties of PISN, such as the mass range, the 56Ni yield, and the explosion energy, are significantly affected by applying the different energy generation rates. We discuss how these results affect the estimate of the PISN detection rate, which depends on the theoretical predictions of such explosion properties.

  6. 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.

  7. 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.

  8. 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.

  9. Construction of an Expression System for Bioactive IL-18 and Generation of Recombinant Canine Distemper Virus Expressing IL-18

    PubMed Central

    LIU, Yuxiu; SATO, Hiroki; HAMANA, Masahiro; MOONAN, Navita Anisia; YONEDA, Misako; XIA, Xianzhu; KAI, Chieko

    2014-01-01

    ABSTRACT 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. PMID:24898077

  10. 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. PMID:24898077

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

    PubMed Central

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

    2016-01-01

    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. PMID:26861382

  12. 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.

  13. Fullerene-Free Polymer Solar Cells with Highly Reduced Bimolecular Recombination and Field-Independent Charge Carrier Generation.

    PubMed

    Roland, Steffen; Schubert, Marcel; Collins, Brian A; Kurpiers, Jona; Chen, Zhihua; Facchetti, Antonio; Ade, Harald; Neher, Dieter

    2014-08-21

    Photogeneration, recombination, and transport of free charge carriers in all-polymer bulk heterojunction solar cells incorporating poly(3-hexylthiophene) (P3HT) as donor and poly([N,N'-bis(2-octyldodecyl)-naphthelene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)) (P(NDI2OD-T2)) as acceptor polymer have been investigated by the use of time delayed collection field (TDCF) and time-of-flight (TOF) measurements. Depending on the preparation procedure used to dry the active layers, these solar cells comprise high fill factors (FFs) of up to 67%. A strongly reduced bimolecular recombination (BMR), as well as a field-independent free charge carrier generation are observed, features that are common to high performance fullerene-based solar cells. Resonant soft X-ray measurements (R-SoXS) and photoluminescence quenching experiments (PQE) reveal that the BMR is related to domain purity. Our results elucidate the similarities of this polymeric acceptor with the superior recombination properties of fullerene acceptors. PMID:26278084

  14. 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

  15. 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.

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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.

  18. Local mapping of generation and recombination lifetime in BiFeO3 single crystals by scanning probe photoinduced transient spectroscopy.

    PubMed

    Alexe, Marin

    2012-05-01

    Carrier lifetime in photoelectric processes is the average time an excited carrier is free before recombining or trapping. Lifetime is directly related to defects and it is a key parameter in analyzing photovoltaic effects in semiconductors. We show here a scanning probe method combined with photoinduced current spectroscopy that allows mapping with nanoscale resolution of the generation and recombination lifetimes. Using this method we have analyzed the mechanism of the abnormal photovoltaic effect in multiferroic bismuth ferrite, BiFeO(3). We found that generation and recombination lifetimes in BiFeO(3) are large due to complex generation and recombination processes that involve shallow energy levels in the band gap. The domain walls do not play a major role in the photovoltaic mechanism.

  19. Electrostatic solitary waves and hole structures generated by bump-on-tail instability in electron-positron plasmas.

    PubMed

    Jao, C-S; Hau, L-N

    2014-05-01

    Electrostatic solitary waves (ESWs) and solitons are widely present in the solar system plasma environment. Many theoretical and numerical studies have been carried out to address the formation and structure of ESWs and solitons in electron-ion plasmas. Due to the inertia symmetry, the issue of whether solitons can exist in pair plasmas has been raised and has been discussed in a number of papers. Recently, we have shown that interlacing electron and positron holes in phase space associated with periodic positive and negative potentials may be generated by current-free electron and positron beams streaming in stationary electron-positron background plasmas [Jao and Hau, Phys. Rev. E 86, 056401 (2012)]. The question remains of whether pure electron or positron holes with positive or negative polarity may exist in neutral electron-positron plasmas. In this paper, we show the formation of electron (positron) holes associated with ESWs of positive (negative) potential based on the particle-in-cell simulations of bump-on-tail streaming instability in pair plasmas. The fluid theory shows that the coexistence of two unstable modes with different wavelengths is the essential condition for the generation of electrostatic solitons and hole structures in an electron-positron plasma. PMID:25353901

  20. Stable supercontinuum pulse generated by modulation instability in a dispersion-managed fiber

    NASA Astrophysics Data System (ADS)

    Duan, Liang; Yang, Zhan-Ying; Zhao, Li-Chen; Yang, Wen-Li

    2016-08-01

    We study on non-linear localized waves on continuous wave background in a dispersion and non-linearity management fibre. We find a stable supercontinuum pulse can be generated from a small modulation on continuous wave in a proper management way, for which the pulse spectrum width and its growth rate can be controlled well by the management parameters. Additionally, we demonstrate a Kuznetsov-Ma breather like non-linear localized wave can exist in a periodic dispersion management fibre, and its spectrum evolution is distinctive from the Kuznetsov-Ma breather's.

  1. Screening strategy to generate cell specific recombination: a case report with the RIP-Cre mice.

    PubMed

    Spinelli, Valeria; Martin, Céline; Dorchies, Emilie; Vallez, Emmanuelle; Dehondt, Hélène; Trabelsi, Mohamed-Sami; Tailleux, Anne; Caron, Sandrine; Staels, Bart

    2015-10-01

    Conditional gene knockout technology is a powerful tool to study the function of a gene in a specific tissue, organ or cell lineage. The most commonly used procedure applies the Cre-LoxP strategy, where the choice of the Cre driver promoter is critical to determine the efficiency and specificity of the system. However, a considered choice of an appropriate promoter does not always protect against the risk of unwanted recombination and the consequent deletion of the gene in other tissues than the desired one(s), due to phenomena of non-specific activation of the Cre transgene. Furthermore, the causes of these phenomena are not completely understood and this can potentially affect every strain of Cre-mice. In our study on the deletion of a same gene in two different tissues, we show that the incidence rate of non-specific recombination in unwanted tissues depends on the Cre driver strain, ranging from 100%, rendering it useless (aP2-Cre strain), to ~5%, which is still compatible with their use (RIP-Cre strain). The use of a simple PCR strategy conceived to detect this occurrence is indispensable when producing a tissue-specific knockout mouse. Therefore, when choosing the Cre-driver promoter, researchers not only have to be careful about its tissue-specificity and timing of activation, but should also include a systematical screening in order to exclude mice in which atypical recombination has occurred and to limit the unnecessary use of laboratory animals in uninterpretable experiments. PMID:26091792

  2. A Review of LOX/Kerosene Combustion Instability in American and Russian Combustion Devices in Application to Next-Generation Launch Technology

    NASA Technical Reports Server (NTRS)

    Rocker, Marvin; Nesman, Tomas E.; Hulka, James R.; Dougherty, N. Sam

    2003-01-01

    The Next-Generation Launch Technology (NGLT) project was introduced with its objectives. To meet the objectives, NASA has directed aerospace industry to perform advances and risk reduction of relevant technologies, including propulsion. Originally, the propulsion industry focused on producing both LOWLH2 and LOWkerosene flight engine technology demonstrators. These flight engine technology demonstrators were briefly reviewed. NASA recently redirected this focus to Lowkerosene only. Discussion of LOWkerosene combustion devices was and is prefaced by grave concerns about combustion instability. These concerns have prompted a review of LOWkerosene combustion instability in American and Russian combustion devices. In the review of the Russian propulsion industry's experience in eliminating LOWkerosene combustion instabilities, the history of principal Russian rocket scientists and their role in the development of LOXkerosene combustion devices is presented. The innovative methods implemented by the Russians of eliminations combustion instabilities in LOXkerosene combustion devices were reviewed. The successful elimination of these combustion instabilities has resulted in two generations of Russian-produced, high-performance LOWkerosene combustion devices.

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

    PubMed Central

    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.

    2013-01-01

    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. PMID:23629868

  4. 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.

  5. HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing.

    PubMed

    Gaspareto, Karine Vieira; Ribeiro, Roberto Marques; de Mello Malta, Fernanda; Gomes-Gouvêa, Michele Soares; Muto, Nair Hideko; Mendes-Correa, Maria Cassia; Rozanski, Andrei; Carrilho, Flair José; Sabino, Ester Cerdeira; Pinho, João Renato Rebello

    2016-08-01

    Next-generation sequencing (NGS) provides a practical approach to HCV complete-genome sequencing, detecting low-frequency variants and allowing analysis of viral genetic diversity (quasispecies) in the sample, and so far, it is very useful for identifying preexisting drug-resistant mutants and emerging escape mutations, as well as detecting viral recombinants containing genomic regions from different genotypes and subtypes. The aim of this study was to analyze the complete coding region of hepatitis C virus (HCV) genotype 1 (subtypes 1a and 1b) from patients with chronic infection who were direct-acting antiviral (DAA) naïve. Next-generation sequencing (Ion Torrent™ PGM) was used to determine the sequence of the complete coding region of 100 HCV-monoinfected DAA-naïve patients (51 and 49 subtypes 1a and 1b, respectively). We report the first description of nearly complete HCV genome sequences of subtype 1a and 1b isolates from a large population of Brazilian patients with chronic hepatitis C, and HCV-1a grouped in two different clades. Using this methodology, an inter-subtype 1a/1b recombinant was identified in this study. PMID:27194536

  6. Different roles of electron beam in two stream instability in an elliptical waveguide for generation and amplification of THz electromagnetic waves

    NASA Astrophysics Data System (ADS)

    Safari, S.; Jazi, B.; Jahanbakht, S.

    2016-08-01

    In this work, two stream instability in a metallic waveguide with elliptical cross-section and with a hollow annular dielectric layer is studied for generation and amplification of THz electromagnetic waves. Dispersion relation of waves and their dependents to geometric dimensions and characteristics of the electron beam are analyzed. In continuation, the diagrams of growth rate for some operating frequencies are presented, so that effective factors on the growth rates, such as geometrical dimensions, dielectric constant of dielectric layer, accelerating voltage, and applied current intensity are analyzed. It is shown that while an electron beam is responsible for instability, another electron beam plays a stabilizing role.

  7. Charge generation and recombination dynamics in poly(3-hexylthiophene)/fullerene blend films with different regioregularities and morphologies.

    PubMed

    Guo, Jiamo; Ohkita, Hideo; Benten, Hiroaki; Ito, Shinzaburo

    2010-05-01

    The charge generation and recombination dynamics in blend films of a poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) were comprehensively studied by transient absorption spectroscopy in the wavelength region from 450 to 1650 nm under various excitation intensities and different excitation wavelengths. In homogeneously mixed blend films of regiorandom P3HT (RRa-P3HT) and PCBM, virtually all the excitons can reach the interface of RRa-P3HT/PCBM and then form bound radical pairs. However, two-thirds of them geminately recombine to the ground state, and only one-third of them can be dissociated into free polarons that survive up to milliseconds. In phase-separated blend films of regioregular P3HT (RR-P3HT) and PCBM, almost all the excitons can reach the interface of RR-P3HT/PCBM, where most of them can be dissociated into free polarons efficiently and the rest of them form bound radical pairs. There are two pathways for the polaron generation: the prompt formation from hot excitons generated near the interface on a time scale of <100 fs and the delayed formation via the exciton migration to the interface on a time scale of approximately 10 ps. The thermal annealing improves the charge dissociation efficiency of bound radical pairs. On the basis of such spectroscopic data, a series of fundamental photovoltaic conversion processes are quantitatively analyzed. Consequently, it is concluded that there is not much difference in the charge generation yield between RRa-P3HT/PCBM(50 wt %) and RR-P3HT/PCBM(50 wt %) blend films. Rather, the charge dissociation and collection have a critical impact on the overall device performance of P3HT/PCBM solar cells, where the phase-separated blend structures have a high tendency to form free carriers and transport these free carriers to the electrode.

  8. Carrier generation/recombination processes and polaron effect in perovskite manganite thin films

    NASA Astrophysics Data System (ADS)

    Wu, Guang-Ri; Inoue, Masasi; Sasaki, Minoru; Negishi, Hiroshi; Xiong, Guang-Cheng

    2000-07-01

    Pulsed-laser-induced transient thermoelectric effect (TTE) for perovskite manganite films, La 0.6Ca 0.4MnO 3 (LCMO), Pr 0.67Sr 0.33MnO 3 (PSMO), La 0.7Sr 0.3MnO 3 (LSMO), has been measured under DC electric and magnetic fields. The photoinduced TTE voltage and its sign are strongly dependent on both temperature and magnetic field, which is due to the formation of a bipolar state of photogenerated electrons and holes. It is found that Jahn-Teller and polaron effects are appreciable near the Curie temperature for the carrier recombination, in particular, for LCMO with small ionic radius of Ca 2+ ions.

  9. Generation of capillary instabilities by external disturbances in a liquid jet. Ph.D. Thesis - State Univ. of N.Y.

    NASA Technical Reports Server (NTRS)

    Leib, S. J.

    1985-01-01

    The receptivity problem in a circular liquid jet is considered. A time harmonic axial pressure gradient is imposed on the steady, parallel flow of a jet of liquid emerging from a circular duct. Using a technique developed in plasma physics a casual solution to the forced problem is obtained over certain ranges of Weber number for a number of mean velocity profiles. This solution contains a term which grows exponentially in the downstream direction and can be identified with a capillary instability wave. Hence, it is found that the externally imposed disturbances can indeed trigger instability waves in a liquid jet. The amplitude of the instability wave generated relative to the amplitude of the forcing is computed numerically for a number of cases.

  10. Generation of self-induced-transparency gap solitons by modulational instability in uniformly doped fiber Bragg gratings

    SciTech Connect

    Kalithasan, B.; Porsezian, K.; Senthilnathan, K.; Tchofo Dinda, P.

    2010-05-15

    We consider the continuous-wave (cw) propagation through a fiber Bragg grating that is uniformly doped with two-level resonant atoms. Wave propagation is governed by a system of nonlinear coupled-mode Maxwell-Bloch (NLCM-MB) equations. We identify modulational instability (MI) conditions required for the generation of ultrashort pulses in both anomalous and normal dispersion regimes. From a detailed linear stability analysis, we find that the atomic detuning frequency has a strong influence on the MI. That is, the atomic detuning frequency induces nonconventional MI sidebands at the photonic band gap (PBG) edges and near the PBG edges. Especially in the normal dispersion regime, MI occurs without any threshold condition, which is in contrast with that of conventional fiber Bragg gratings. We also perform a numerical analysis to solve the NLCM-MB equations. The numerical results of the prediction of both the optimum modulation wave number and the optimum gain agree well with that of the linear stability analysis. Another main result of the present work is the prediction of the existence of both bright and dark self-induced transparency gap solitons at the PBG edges.

  11. Laser-driven parametric instability and generation of entangled photon-plasmon states in graphene and topological insulators

    NASA Astrophysics Data System (ADS)

    Belyanin, Alexey; Wang, Yongrui; Oladyshkin, Ivan; Tokman, Mikhail

    Massless Dirac electrons in graphene and on the surface of topological insulators such as Bi2Se3 demonstrate strong nonlinear optical response and support tightly confined surface plasmon modes. Although both systems constitute an isotropic medium for low-energy in-plane electron excitations, their second-order nonlinear susceptibility becomes non-zero when its spatial dispersion is taken into account. In this case the anisotropy is induced by in-plane wave vectors of obliquely incident or in-plane propagating electromagnetic waves. In this work we show that a strong (0.1-1 MW/cm2) near-infrared or mid-infrared laser beam obliquely incident on graphene can experience a parametric instability with respect to decay into lower-frequency (idler) photons and THz surface plasmons. The parametric gain leads to efficient generation of THz plasmons. Furthermore, the parametric decay process gives rise to quantum entanglement of idler photon and surface plasmon states. This enables diagnostics and control of surface plasmons by detecting idler photons. A similar parametric process can be implemented in topological insulator thin films. This work has been supported in part by the Air Force Office for Scientific Research through Grant FA9550-15-1-0153.

  12. Data for the inhibition effects of recombinant lamprey CRBGP on the tube formation of HUVECs and new blood vessel generation in CAM models.

    PubMed

    Jiang, Qi; Liu, Yu; Gou, Meng; Han, Jianmei; Wang, Jihong; Li, Qingwei; Xiao, Rong

    2016-03-01

    In the present data article, lamprey cysteine-rich buccal gland protein (CRBGP) which belongs to cysteine-rich secretory proteins (CRISPs) family was recombinant and expressed in Rosetta blue cells. After identification, the recombinant protein was purified through affinity chromatograph. The inhibition effects of recombinant lamprey CRBGP (rL-CRBGP) on tube formation of human umbilical vein endothelial cells (HUVECs) and new blood vessel generation in chick chorioallantoic membrane (CAM) models were analyzed. This paper contains data related to research concurrently published in "Anti-angiogenic activities of CRBGP from buccal glands of lampreys (Lampetra japonica)" [1]. PMID:26909383

  13. Data for the inhibition effects of recombinant lamprey CRBGP on the tube formation of HUVECs and new blood vessel generation in CAM models.

    PubMed

    Jiang, Qi; Liu, Yu; Gou, Meng; Han, Jianmei; Wang, Jihong; Li, Qingwei; Xiao, Rong

    2016-03-01

    In the present data article, lamprey cysteine-rich buccal gland protein (CRBGP) which belongs to cysteine-rich secretory proteins (CRISPs) family was recombinant and expressed in Rosetta blue cells. After identification, the recombinant protein was purified through affinity chromatograph. The inhibition effects of recombinant lamprey CRBGP (rL-CRBGP) on tube formation of human umbilical vein endothelial cells (HUVECs) and new blood vessel generation in chick chorioallantoic membrane (CAM) models were analyzed. This paper contains data related to research concurrently published in "Anti-angiogenic activities of CRBGP from buccal glands of lampreys (Lampetra japonica)" [1].

  14. Generation and phenotypic analysis of a transgenic line of rabbits secreting active recombinant human erythropoietin in the milk.

    PubMed

    Mikus, Tomás; Poplstein, Martin; Sedláková, Jirina; Landa, Vladimír; Jeníkova, Gabriela; Trefil, Pavel; Lidický, Jan; Malý, Petr

    2004-10-01

    Production of recombinant human erythropoietin (rhEPO) for therapeutic purposes relies on its expression in selected clones of transfected mammalian cells. Alternatively, this glycoprotein can be produced by targeted secretion into the body fluid of transgenic mammals. Here, we report on the generation of a transgenic rabbits producing rhEPO in the lactating mammary gland. Transgenic individuals are viable, fertile and transmit the rhEPO gene to the offspring. Northern blot data indicated that the expression of the transgene in the mammary gland is controlled by whey acidic protien (WAP) regulatory sequences during the period of lactation. While the hybridization with total RNA revealed the expression only in the lactating mammary gland, the highly sensitive combinatory approach using RT-PCR/hybridization technique detected a minor ectopic expression. The level of rhEPO secretion in the founder female, measured in the period of lactation, varied in the range of 60-178 and 60-162 mIU/ml in the milk and blood plasma, respectively. Biological activity of the milk rhEPO was confirmed by a standard [3H]-thymidine incorporation test. Thus, we describe the model of a rhEPO-transgenic rabbit, valuable for studies of rhEPO glycosylation and function, which can be useful for the development of transgenic approaches designed for the preparation of recombinant proteins by alternative biopharmaceutical production.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Experience with a third generation recombinant factor VIII concentrate (Advate) for immune tolerance induction in patients with haemophilia A.

    PubMed

    Valentino, L A; Recht, M; Dipaola, J; Shapiro, A D; Pipe, S W; Ewing, N; Urgo, J; Bullock, T; Simmons, M; Deguzman, C

    2009-05-01

    The development of an inhibitor represents one of the most challenging complications in patients with haemophilia A. Optimal management is immune tolerance induction (ITI), typically through the administration of high doses of factor VIII (FVIII) concentrate. Among 12 patients who underwent ITI using Advate, a third-generation recombinant FVIII product that is free of animal and human protein additives, tolerance was achieved in nine (75%), including seven of 10 patients (70%) with high-titre inhibitors. ITI is ongoing in two patients and not yet successful; immune tolerance failed in the third patient. The median time to success was 4.0 months for group as a whole and for patients with high-titre inhibitors. Treatment was well tolerated, and no adverse events were observed. Advate was found to be equivalent to other FVIII products with regard to both ITI success rates and the incidence of adverse effects when used in these immune tolerance regimens. PMID:19298383

  20. 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.

  1. Recombination activity associated with thermal donor generation in monocrystalline silicon and effect on the conversion efficiency of heterojunction solar cells

    NASA Astrophysics Data System (ADS)

    Tomassini, M.; Veirman, J.; Varache, R.; Letty, E.; Dubois, S.; Hu, Y.; Nielsen, Ø.

    2016-02-01

    The recombination properties of the carrier lifetime-limiting center formed during the generation of oxygen-related thermal donors (so called "old" thermal donors) in n-type Czochralski silicon were determined over a wide range of thermal donors' concentrations. The procedure involved (1) determining the various energy levels associated with dopants with the help of temperature Hall effect measurements, (2) clarifying which energy level limits the carrier lifetime by temperature lifetime spectroscopy, and (3) determining the recombination parameters of the involved defect from room-temperature carrier lifetime curves. Our results support the fact that a deep energy level in the range of 0.2-0.3 eV below the conduction band limits the carrier lifetime. The second family of thermal donors, featuring bistable properties, was tentatively identified as the corresponding defect. From the obtained experimental data, the influence of the defect on the amorphous/crystalline silicon heterojunction solar cell conversion efficiency was simulated. It is observed that for extended donor generation, the carrier lifetime is reduced by orders-of-magnitude, leading to unacceptable losses in photovoltaic conversion efficiency. A key result is that even for samples with thermal donor concentrations of 1015 cm-3—often met in seed portions of commercial ingots—simulations reveal efficiency losses greater than 1% absolute for state-of-the-art cells, in agreement with recent experimental studies from our group. This result indicates to crystal growers the importance to mitigate the formation of thermal donors or to develop cost-effective processes to suppress them at the ingot/wafer scale. This is even more critical as ingot cool-down is likely to be slower for future larger ingots, thus promoting the formation of thermal donors.

  2. Formation of cosmic structure by Doppler instability

    NASA Technical Reports Server (NTRS)

    Hogan, Craig J.

    1991-01-01

    A new mechanism is described which can create an instability in homogeneous gaseous matter at very low density. When an isotropic background radiation field has, near an electronic resonance, a spectral feature for which photon occupation number increases with frequency, moving atoms increase their speed by taking energy from the photon distribution. In a cosmological setting, a sufficiently intense spectral feature can interact with neutral atomic gas, after recombination, to generate protogalactic perturbations of the scale and magnitude needed to explain large-scale cosmic structure.

  3. 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

  4. Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond

    PubMed Central

    Ting, Jonathan T.; Feng, Guoping

    2014-01-01

    The development and application of diverse BAC transgenic rodent lines has enabled rapid progress for precise molecular targeting of genetically-defined cell types in the mammalian central nervous system. These transgenic tools have played a central role in the optogenetic revolution in neuroscience. Indeed, an overwhelming proportion of studies in this field have made use of BAC transgenic Cre driver lines to achieve targeted expression of optogenetic probes in the brain. In addition, several BAC transgenic mouse lines have been established for direct cell-type specific expression of Channelrhodopsin-2 (ChR2). While the benefits of these new tools largely outweigh any accompanying challenges, many available BAC transgenic lines may suffer from confounds due in part to increased gene dosage of one or more “extra” genes contained within the large BAC DNA sequences. Here we discuss this under-appreciated issue and propose strategies for developing the next generation of BAC transgenic lines that are devoid of extra genes. Furthermore, we provide evidence that these strategies are simple, reproducible, and do not disrupt the intended cell-type specific transgene expression patterns for several distinct BAC clones. These strategies may be widely implemented for improved BAC transgenesis across diverse disciplines. PMID:24772073

  5. 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

  6. A robust high throughput platform to generate functional recombinant monoclonal antibodies using rabbit B cells from peripheral blood.

    PubMed

    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.

  7. 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.

  8. Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination.

    PubMed

    Hurley, C K; Gregersen, P; Steiner, N; Bell, J; Hartzman, R; Nepom, G; Silver, J; Johnson, A H

    1988-02-01

    The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a serologically undefined DQ allelic product. DNA restriction fragment analysis with the use of several unrelated individuals and an informative family has allowed us to identify unique DQ alpha- and beta-fragments associated with the DR3, DQw- haplotype. Based on fragment size, the DQ alpha genes of the DR3, DQw- and DRw8, DQw- haplotypes are similar as are the DQ beta genes of DR3, DQw-; DRw8, DQw-; and DR4, DQw- haplotypes. In addition, a DX beta gene polymorphism has been identified which is associated with some DR3 haplotypes including the American black DR3, DQw- haplotype. cDNA sequence analysis has revealed a DQw2-like alpha gene and a DQ beta gene which is similar to that previously described for a DR4, DQw- haplotype. It is postulated that recombination between DQ alpha and DQ beta genes and between the DQ and DX subregions has generated the various DR3 haplotypes and has played an important role in creating diversity in the HLA-D region. PMID:2892884

  9. 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

    2014-04-01

    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.

  10. Generation of a recombinant rabies Flury LEP virus carrying an additional G gene creates an improved seed virus for inactivated vaccine production.

    PubMed

    Tao, Lihong; Ge, Jinying; Wang, Xijun; Wen, Zhiyuan; Zhai, Hongyue; Hua, Tao; Zhao, Bolin; Kong, Dongni; Yang, Chinglai; Bu, Zhigao

    2011-01-01

    The rabies Flury Low Egg Passage virus (LEP) has been widely used as a seed virus to generate inactive vaccine. Here, we established a reverse genetic system for LEP and generated a recombinant LEP virus (rLEP-G) that carries two identical G genes. This recombinant virus showed similar properties to those of LEP with respect to in vitro growth, neurotropism index, and virulence in mice. rLEP-G produced 4.3-fold more G protein than did LEP in BHK-21 cells. The inactivated vaccine generated from rLEP-G induced significantly higher virus neutralization titers in mice and dogs than those produced in response to LEP-derived vaccine. Our results suggest that rLEP-G is an improved seed virus candidate for inactivated rabies virus vaccine manufacture.

  11. 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. PMID:25641957

  12. A simulation study of the convective instability and subsequent generation of Acoustic-gravity waves in the troposphere to MLT region

    NASA Astrophysics Data System (ADS)

    Tiwari, B. R.; Kherani, E. A.; Sobral, J. H. A.

    2014-12-01

    The convective instability (CI) is excited in the troposphere in the presence of negative temperature gradient. The rising bubbles generated by the instability act like pressure disturbances at the top of the troposphere and subsequently excite the acoustic-gravity waves (AGWs) in the atmosphere. These AGWs propagate radially outward towards overlying MLT region while their amplitude increases exponentially with increasing altitude. In the MLT region, these waves encounter thermal and density ducts, leading to the dissipation of these waves and subsequent generation of secondary AGWs. In this work, we present the simulation study of coupled convective instability - AGWs dynamics in the atmosphere covering troposphere to MLT region. We derive the governing hydrodynamics equations for the CI and AGWs that include the non-adiabatic dynamics of CI in the troposphere and compressible and ducting dynamics of AGWs above troposphere. These equations are solved using Finite-Time-Centered-Space difference method complemented by the Crank-Nicolson implicit scheme for the integration and Gradient-Conjugate method to solve the matrix equation. The simulation domain consists of altitude-longitude-latitude covering the tropical Brazilian region. The novel features of the present study are as follows: (1) Owing to the non-adiabatic dynamics, the CI in the troposphere grows for the adiabatically stable temperature profile (2) The growth remains linear and excite the bubbles reaching up to the base of the tropopause (~10 km altitude), (3) Thereafter, AGWs are excited attaining large amplitude in the MLT region, (4) In the MLT region, these large amplitude waves become ducted and as a result, the AGWs with short period equals to the Brunt-Vaisala period of MLT region, are amplified, (5) These ducting dynamics excite the atmospheric disturbances consist of ripples and bands, respectively associated with the short and long period AGWs.

  13. 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.

  14. 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.

  15. 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.

  16. Hip instability.

    PubMed

    Smith, Matthew V; Sekiya, Jon K

    2010-06-01

    Hip instability is becoming a more commonly recognized source of pain and disability in patients. Traumatic causes of hip instability are often clear. Appropriate treatment includes immediate reduction, early surgery for acetabular rim fractures greater than 25% or incarcerated fragments in the joint, and close follow-up to monitor for avascular necrosis. Late surgical intervention may be necessary for residual symptomatic hip instability. Atraumatic causes of hip instability include repetitive external rotation with axial loading, generalized ligamentous laxity, and collagen disorders like Ehlers-Danlos. Symptoms caused by atraumatic hip instability often have an insidious onset. Patients may have a wide array of hip symptoms while demonstrating only subtle findings suggestive of capsular laxity. Traction views of the affected hip can be helpful in diagnosing hip instability. Open and arthroscopic techniques can be used to treat capsular laxity. We describe an arthroscopic anterior hip capsular plication using a suture technique. PMID:20473129

  17. Some aspects of two-phase flow, heat transfer and dynamic instabilities in medium and high pressure steam generators

    NASA Astrophysics Data System (ADS)

    Unal, H. C.

    1981-03-01

    Experimental data for void fraction, incipient point of boiling, initial point of net vapor generation, bubble dynamics, dryout, two-phase flow pressure drop and density-wave oscillations were obtained in long, sodium heated steam generator tubes of different geometries for a wide range of operating conditions and at medium and high pressures. These data and data from literature taken in sodium and electrically heated steam generator tubes were correlated. Aspects of two-phase flow, heat transfer and density-wave oscillations in these steam generators disclosed include the distribution factor in small- and medium-size diameter steam generator tubes, the characteristic of the transitions at the incipient point of boiling and initial point of net vapor generation, bubble growth during subcooled nucleate flow boiling, the importance of the equivalent length for dryout in non-uniformly heated steam generator tubes and the mechanisms of density-wave oscillations in once-through steam generator tubes.

  18. 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.

  19. 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

  20. Generation of Recombinant Monoclonal Antibodies from Immunised Mice and Rabbits via Flow Cytometry and Sorting of Antigen-Specific IgG+ Memory B Cells

    PubMed Central

    Starkie, Dale. O; Compson, Joanne E.; Rapecki, Stephen; Lightwood, Daniel J.

    2016-01-01

    Single B cell screening strategies, which avoid both hybridoma fusion and combinatorial display, have emerged as important technologies for efficiently sampling the natural antibody repertoire of immunized animals and humans. Having access to a range of methods to interrogate different B cell subsets provides an attractive option to ensure large and diverse panels of high quality antibody are produced. The generation of multiple antibodies and having the ability to find rare B cell clones producing IgG with unique and desirable characteristics facilitates the identification of fit-for-purpose molecules that can be developed into therapeutic agents or research reagents. Here, we describe a multi-parameter flow cytometry single-cell sorting technique for the generation of antigen-specific recombinant monoclonal antibodies from single IgG+ memory B cells. Both mouse splenocytes and rabbit PBMC from immunised animals were used as a source of B cells. Reagents staining both B cells and other unwanted cell types enabled efficient identification of class-switched IgG+ memory B cells. Concurrent staining with antigen labelled separately with two spectrally-distinct fluorophores enabled antigen-specific B cells to be identified, i.e. those which bind to both antigen conjugates (double-positive). These cells were then typically sorted at one cell per well using FACS directly into a 96-well plate containing reverse transcriptase reaction mix. Following production of cDNA, PCR was performed to amplify cognate heavy and light chain variable region genes and generate transcriptionally-active PCR (TAP) fragments. These linear expression cassettes were then used directly in a mammalian cell transfection to generate recombinant antibody for further testing. We were able to successfully generate antigen-specific recombinant antibodies from both the rabbit and mouse IgG+ memory B cell subset within one week. This included the generation of an anti-TNFR2 blocking antibody from mice

  1. 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.

  2. 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.

  3. 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.

  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. 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

  6. 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.

  7. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri.

    PubMed

    Timilsina, Sujan; Jibrin, Mustafa O; Potnis, Neha; Minsavage, Gerald V; Kebede, Misrak; Schwartz, Allison; Bart, Rebecca; Staskawicz, Brian; Boyer, Claudine; Vallad, Gary E; Pruvost, Olivier; Jones, Jeffrey B; Goss, Erica M

    2015-02-01

    Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations. PMID:25527544

  8. Generation-recombination processes in InGaAs/GaAs heterostructures with one-dimensional nanostructures

    NASA Astrophysics Data System (ADS)

    Kovalova, Marianna; Kondratenko, Serhiy; Yakovlev, Artem; Furrow, Colin; Kunets, Vasyl; Ware, Morgan; Salamo, Gregory

    2015-06-01

    Structures with one-dimensional quantum objects in intermediate band are promising for their application in solar cells and photodetectors. We present analysis of dark current-voltage characteristics, photo-voltage decay and photo-voltage spectra for this structures in comparison with reference GaAs based structures. It has been shown that InGaAs quantum wires make a significant influence on J-V dependences and photo-voltage spectra. InGaAs QWRS are additional recombination centers and transitions between them dominated over by Shockley-Read-Hall recombination at low bias. The InGaAs/GaAs sample shows a significantly higher photo-voltage in the spectral range of 1.25-1.37 eV, as compared to a reference GaAs p-n junction, due to intermediate band transitions in the quantum wires.

  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. Contribution of generation-recombination processes at inner interface of MBE-grown Hg1-xCdxTe heterostucture to dark current of small active area photodiode

    NASA Astrophysics Data System (ADS)

    Chekanova, Galina V.; Drugova, Albina A.; Kholodnov, Viacheslav; Nikitin, Mikhail S.

    2009-09-01

    Multilayer heterostructures of Hg1-xCdxTe alloy grown by Molecular Beam Epitaxy (MBE) on large size alternative substrates Si, GaAs and Ge are considered as one of productive alternative materials for issue of large format photovoltaic (PV) infrared (IR) focal plane arrays. However reaching of ultimate performance of small-pitched photodiode's (PD) covering spectral range from 8 to 12 μm depends on electronic properties of both individual layers and heterostructure interfaces. Due to small thickness of heterostructure layers, interfaces are located close to active regions of p-n junction and hence generation-recombination processes at interfaces will contribute to value of current flowing through junction. As usual measured dark current value of small-sized PD is higher than estimated from calculation and cannot be explained by discrepancy between real and estimated charge carriers concentration in absorption layers where p-n junction is formed. Objective of the present work was to calculate the contribution of recombination of charge carriers via electronic states on nearby inner interface to dark current of Hg1-xCdxTe LWIR PD (λco equals to 9.5-10.3 μm at Top=77 K) and its variation with absorption layer parameters and compare it to measured data on small-pitched arrays. We have concluded previously that at high recombination rate dark current can grow in orders of value.

  11. 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.

  12. 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.

  13. 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.

  14. Recombinant HA1 produced in E. coli forms functional oligomers and generates strain-specific SRID potency antibodies for pandemic influenza vaccines.

    PubMed

    Khurana, Surender; Larkin, Christopher; Verma, Swati; Joshi, Manju B; Fontana, Juan; Steven, Alasdair C; King, Lisa R; Manischewitz, Jody; McCormick, William; Gupta, Rajesh K; Golding, Hana

    2011-08-01

    Vaccine production and initiation of mass vaccination is a key factor in rapid response to new influenza pandemic. During the 2009-2010 H1N1 pandemic, several bottlenecks were identified, including the delayed availability of vaccine potency reagents. Currently, antisera for the single-radial immunodiffusion (SRID) potency assay are generated in sheep immunized repeatedly with HA released and purified after bromelain-treatment of influenza virus grown in eggs. This approach was a major bottleneck for pandemic H1N1 (H1N1pdm09) potency reagent development in 2009. Alternative approaches are needed to make HA immunogens for generation of SRID reagents in the shortest possible time. In this study, we found that properly folded recombinant HA1 globular domain (rHA1) from several type A viruses including H1N1pdm09 and two H5N1 viruses could be produced efficiently using a bacterial expression system and subsequent purification. The rHA1 proteins were shown to form functional oligomers of trimers, similar to virus derived HA, and elicited high titer of neutralizing antibodies in rabbits and sheep. Importantly, the immune sera formed precipitation rings with reference antigens in the SRID assay in a dose-dependent manner. The HA contents in multiple H1N1 vaccine products from different manufacturers (and in several lots) as determined with the rHA1-generated sheep sera were similar to the values obtained with a traditionally generated sheep serum from NIBSC. We conclude that bacterially expressed recombinant HA1 proteins can be produced rapidly and used to generate SRID potency reagents shortly after new influenza strains with pandemic potential are identified.

  15. 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

    2016-09-01

    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.

  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

    2016-09-01

    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. PMID:27523740

  17. 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

    2015-12-01

    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

  18. 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.

  19. Cross-resistance profile determination of two second-generation HIV-1 integrase inhibitors using a panel of recombinant viruses derived from raltegravir-treated clinical isolates.

    PubMed

    Van Wesenbeeck, L; Rondelez, E; Feyaerts, M; Verheyen, A; Van der Borght, K; Smits, V; Cleybergh, C; De Wolf, H; Van Baelen, K; Stuyver, L J

    2011-01-01

    The integrase inhibitor raltegravir (RAL) is currently used for the treatment of both treatment-naïve and treatment-experienced HIV-1-infected patients. Elvitegravir (EVG) is in late phases of clinical development. Since significant cross-resistance between RAL and EVG is observed, there is a need for second-generation integrase inhibitors (INIs) with a higher genetic barrier and limited cross-resistance to RAL/EVG. A panel of HIV-1 integrase recombinants, derived from plasma samples from raltegravir-treated patients (baseline and follow-up samples), were used to study the cross-resistance profile of two second-generation integrase inhibitors, MK-2048 and compound G. Samples with Q148H/R mutations had elevated fold change values with all compounds tested. Although samples with the Y143R/C mutation had reduced susceptibility to RAL, they remained susceptible to MK-2048 and compound G. Samples with the N155H mutation had no reduced susceptibility to compound G. In conclusion, our results allowed ranking of the INIs on the basis of the antiviral activities using recombinant virus stocks from RAL-treated patient viruses. The order according to decreasing susceptibility is compound G, MK-2048, and EVG.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. The bulk generation-recombination processes and the carrier lifetime in mid-wave infrared and long-wave infrared liquid nitrogen cooled HgCdTe alloys

    NASA Astrophysics Data System (ADS)

    Jóźwikowski, K.; Kopytko, M.; Rogalski, A.

    2012-08-01

    Comprehensive study of the bulk generation-recombination mechanisms and the carrier lifetime in long wavelength and mid wavelength infrared indium-doped as well as arsenic- and mercury vacancies-doped HgCdTe ternary alloys at liquid nitrogen temperature has been done. The excess minority carrier lifetime in HgCdTe materials has been calculated by solving the set of non-linear transport equations under conditions of small deviation from equilibrium. The results of numerical calculations of the carrier lifetime determined by the Auger 1, Auger 7, and Shockley-Read-Hall mechanisms related to mercury vacancies have been compared with experimental data available in the literature. We re-examine the carrier lifetime, including the impact of the electrical screening on Coulomb interaction of carriers in the Auger process to explain certain inconsistency between theoretical prediction and experimental data especially in highly doped p-type HgCdTe material. Moreover, the marginal significance of the interband radiative recombination has been indicated.

  6. Generation and characterization of a recombinant chimeric protein (rCpLi) consisting of B-cell epitopes of a dermonecrotic protein from Loxosceles intermedia spider venom.

    PubMed

    Mendes, T M; Oliveira, D; Figueiredo, L F M; Machado-de-Avila, R A; Duarte, C G; Dias-Lopes, C; Guimarães, G; Felicori, L; Minozzo, J C; Chávez-Olortegui, C

    2013-06-01

    A chimeric protein was constructed expressing three epitopes of LiD1, a dermonecrotic toxin from the venom of Loxosceles intermedia spider. This species is responsible for a large number of accidents involving spiders in Brazil. We demonstrated that the chimeric protein (rCpLi) generated is atoxic and that antibodies previously developed in rabbits against synthetic epitopes reactive with rCpLi in ELISA and immunoblot assays. The antibody response in rabbits against the rCpLi was evaluated by ELISA and we have detected an antibody response in all immunized animals. Overlapping peptides covering the amino acid sequence of the rCpLi were synthesized on a cellulose membrane, and their recognition by rabbit anti-rCpLi serum assessed. Three different antigenic regions were identified. The percentage of inhibition of the dermonecrotic, hemorrhagic and edematogenic activities caused by the recombinant protein LiD1r in naïve rabbits was assessed by pre-incubation with anti-rCpLi antibodies. Anti-rCpLi induced good dermonecrotic and hemorrhagic protection. The levels of protection were similar to the antiboides anti-LiD1r. In summary, we have developed a polyepitope recombinant chimeric protein capable of inducing multiple responses of neutralizing antibodies in a rabbit model. This engineered protein may be a promising candidate for therapeutic serum development or vaccination.

  7. 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

    2015-05-01

    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.

  8. Virus-like particles of porcine bocavirus generated by recombinant baculoviruses can be applied to sero-epidemic studies.

    PubMed

    Zhang, Wenjing; Sano, Natsuha; Kataoka, Michiyo; Ami, Yasushi; Suzaki, Yuriko; Wakita, Takaji; Ikeda, Hidetoshi; Li, Tian-Cheng

    2016-06-01

    Porcine bocaviruses (PBoVs), new members of the Bocavirus genus, have been identified in swine worldwide. However, the antigenicity and epidemiology of PBoVs are still unclear. Here we used a recombinant baculovirus expression system to express the main capsid protein VP2 of Japan strain JY31b in insect Tn5 cells, and successfully produced the virus-like particles of PBoV (PBoV-LPs). The diameter and densities of the PBoV-LPs were estimated to be 30nm and 1.300g/cm(3), respectively, which were similar to the values for the native virion of PBoV. Antigenic analysis demonstrated that the PBoV-LPs were not cross-reactive with porcine circovirus 2, but were cross-reactive with human bocavirus 1, 2, 3 and 4. An ELISA for detection of anti-PBoV IgG antibodies was established using PBoV-LPs as antigen, which proved to be useful for monitoring PBoV infection in both swine and wild boars. The preliminary epidemiology research showed that 90.7% of pigs and 59.5% of wild boars were positive for the anti-PBoV-IgG, suggesting that both species were also widely infected with PBoV. The seven PBoV strains detected in wild boars separated into four subgroups, demonstrating the genetic diversity of PBoV. PMID:26959654

  9. Generation of recombinant rabies Virus CVS-11 expressing eGFP applied to the rapid virus neutralization test.

    PubMed

    Xue, Xianghong; Zheng, Xuexing; Liang, Hongru; Feng, Na; Zhao, Yongkun; Gao, Yuwei; Wang, Hualei; Yang, Songtao; Xia, Xianzhu

    2014-04-01

    The determination of levels of rabies virus-neutralizing antibody (VNA) provides the foundation for the quantitative evaluation of immunity effects. The traditional fluorescent antibody virus neutralization test (FAVN) using a challenge virus standard (CVS)-11 strain as a detection antigen and staining infected cells with a fluorescein isothiocyanate (FITC)-labeled monoclonal antibody, is expensive and high-quality reagents are often difficult to obtain in developing countries. Indeed, it is essential to establish a rapid, economical, and specific rabies virus neutralization test (VNT). Here, we describe a recombinant virus rCVS-11-eGFP strain that stably expresses enhanced green fluorescent protein (eGFP) based on a reverse genetic system of the CVS-11 strain. Compared to the rCVS-11 strain, the rCVS-11-eGFP strain showed a similar growth property with passaging stability in vitro and pathogenicity in vivo. The rCVS-11-eGFP strain was utilized as a detection antigen to determine the levels of rabies VNAs in 23 human and 29 canine sera; this technique was termed the FAVN-eGFP method. The good reproducibility of FAVN-eGFP was tested with partial serum samples. Neutralization titers obtained from FAVN and FAVN-eGFP were not significantly different. The FAVN-eGFP method allows rapid economical, specific, and high-throughput assessment for the titration of rabies VNAs.

  10. Intragenic recombination generated two distinct Cf genes that mediate AVR9 recognition in the natural population of Lycopersicon pimpinellifolium

    PubMed Central

    Van der Hoorn, Renier A. L.; Kruijt, Marco; Roth, Ronelle; Brandwagt, Bas F.; Joosten, Matthieu H. A. J.; De Wit, Pierre J. G. M.

    2001-01-01

    Resistance gene Cf-9 of cultivated tomato (Lycopersicon esculentum) confers recognition of the AVR9 elicitor protein of the fungal pathogen Cladosporium fulvum. The Cf-9 locus, containing Cf-9 and four homologs (Hcr9s), originates from Lycopersicon pimpinellifolium (Lp). We examined naturally occurring polymorphism in Hcr9s that confer AVR9 recognition in the Lp population. AVR9 recognition occurs frequently throughout this population. In addition to Cf-9, we discovered a second gene in Lp, designated 9DC, which also confers AVR9 recognition. Compared with Cf-9, 9DC is more polymorphic, occurs more frequently, and is more widely spread throughout the Lp population, suggesting that 9DC is older than Cf-9. The sequences of Cf-9 and 9DC suggest that Cf-9 evolved from 9DC by intragenic recombination between 9DC and another Hcr9. The fact that the 9DC and Cf-9 proteins differ in 61 aa residues, and both mediate recognition of AVR9, shows that in nature Hcr9 proteins with the same recognitional specificity can vary significantly. PMID:11517316

  11. 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.

  12. Generation of New M2e-HA2 Fusion Chimeric Peptide to Development of a Recombinant Fusion Protein Vaccine

    PubMed Central

    Ameghi, Ali; Baradaran, Behzad; Aghaiypour, Khosrow; Barzegar, Abolfazl; Pilehvar-Soltanahmadi, Yones; Moghadampour, Masood; Taghizadeh, Morteza; Zarghami, Nosratollah

    2015-01-01

    Purpose: The purpose was to design a new construction containing influenza virus (H1N1) M2e gene and HA2 gene by bioinformatics approach, cloning the construct in to Escherichia coli and produce M2e-HA2 peptide. Methods: The procedure was done by virus cultivation in SPF eggs, hemagglutination assay (HA), RNA isolation, RT-PCR, primers designed (DNAMAN 4 and Oligo7), virtual fusion construction translation (ExPASy), N-Glycosylated sites prediction (Ensemblegly-Iowa), complete open reading frame (ORF), stop codon studied (NCBI ORF Finder), rare codon determination (GenScript), Solvent accessibility of epitopes (Swiss-PdbViewer), antigenic sites prediction (Protean), fusion PCR of M2e-HA2 gene, sequence analysis, nested PCR, gel electrophoresis, double digestion of pET22b(+) plasmid and the fusion construct, ligation of them, transformation of the ligated vector (pET22b-M2e-HA2) to E.coli (BL21), mass culture the cloned bacterium ,induction the expression by isopropyl-beta-D-thiogalactopyranoside (IPTG), sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), purification the fusion peptide by Ni-NTA column, western blot to verify the purification. Results: In this study we developed a new approach for fusion of Influenza virus M2e (96 nucleotides) and HA2 (663 nucleotides) genes based on fusion PCR strategy and produced a fused fragment with 793 nucleotides. The construct was successfully cloned and expressed. Conclusion: This construct is a 261 amino acid chimeric fusion peptide with about 30 KD molecular weight. According on the latest information; this is the first case of expression and purification M2e-HA2 fusion chimeric peptide, which could be used for development of a recombinant M2e-HA2 fusion protein vaccine. PMID:26793615

  13. The generation and analyses of a novel combination of recombinant adenovirus vaccines targeting three tumor antigens as an immunotherapeutic

    PubMed Central

    Gabitzsch, Elizabeth S.; Tsang, Kwong Yok; Palena, Claudia; David, Justin M.; Fantini, Massimo; Kwilas, Anna; Rice, Adrian E.; Latchman, Yvette; Hodge, James W.; Gulley, James L.; Madan, Ravi A.; Heery, Christopher R.; Balint, Joseph P.

    2015-01-01

    Phenotypic heterogeneity of human carcinoma lesions, including heterogeneity in expression of tumor-associated antigens (TAAs), is a well-established phenomenon. Carcinoembryonic antigen (CEA), MUC1, and brachyury are diverse TAAs, each of which is expressed on a wide range of human tumors. We have previously reported on a novel adenovirus serotype 5 (Ad5) vector gene delivery platform (Ad5 [E1-, E2b-]) in which regions of the early 1 (E1), early 2 (E2b), and early 3 (E3) genes have been deleted. The unique deletions in this platform result in a dramatic decrease in late gene expression, leading to a marked reduction in host immune response to the vector. Ad5 [E1-, E2b-]-CEA vaccine (ETBX-011) has been employed in clinical studies as an active vaccine to induce immune responses to CEA in metastatic colorectal cancer patients. We report here the development of novel recombinant Ad5 [E1-, E2b-]-brachyury and-MUC1 vaccine constructs, each capable of activating antigen-specific human T cells in vitro and inducing antigen-specific CD4+ and CD8+ T cells in vaccinated mice. We also describe the use of a combination of the three vaccines (designated Tri-Ad5) of Ad5 [E1-, E2b-]-CEA, Ad5 [E1-, E2b-]-brachyury and Ad5 [E1-, E2b-]-MUC1, and demonstrate that there is minimal to no “antigenic competition” in in vitro studies of human dendritic cells, or in murine vaccination studies. The studies reported herein support the rationale for the application of Tri-Ad5 as a therapeutic modality to induce immune responses to a diverse range of human TAAs for potential clinical studies. PMID:26374823

  14. 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

  15. [Carpal instability].

    PubMed

    Redeker, J; Vogt, P M

    2011-01-01

    Carpal instability can be understood as a disturbed anatomical alignment between bones articulating in the carpus. This disturbed balance occurs either only dynamically (with movement) under the effect of physiological force or even statically at rest. The most common cause of carpal instability is wrist trauma with rupture of the stabilizing ligaments and adaptive misalignment following fractures of the radius or carpus. Carpal collapse plays a special role in this mechanism due to non-healed fracture of the scaphoid bone. In addition degenerative inflammatory alterations, such as chondrocalcinosis or gout, more rarely aseptic bone necrosis of the lunate or scaphoid bones or misalignment due to deposition (Madelung deformity) can lead to wrist instability. Under increased pressure the misaligned joint surfaces lead to bone arrosion with secondary arthritis of the wrist. In order to arrest or slow down this irreversible process, diagnosis must occur as early as possible. Many surgical methods have been thought out to regain stability ranging from direct reconstruction of the damaged ligaments, through ligament replacement to partial stiffening of the wrist joint.

  16. BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks.

    PubMed

    Willis, Nicholas A; Chandramouly, Gurushankar; Huang, Bin; Kwok, Amy; Follonier, Cindy; Deng, Chuxia; Scully, Ralph

    2014-06-26

    Replication fork stalling can promote genomic instability, predisposing to cancer and other diseases. Stalled replication forks may be processed by sister chromatid recombination (SCR), generating error-free or error-prone homologous recombination (HR) outcomes. In mammalian cells, a long-standing hypothesis proposes that the major hereditary breast/ovarian cancer predisposition gene products, BRCA1 and BRCA2, control HR/SCR at stalled replication forks. Although BRCA1 and BRCA2 affect replication fork processing, direct evidence that BRCA gene products regulate homologous recombination at stalled chromosomal replication forks is lacking, due to a dearth of tools for studying this process. Here we report that the Escherichia coli Tus/Ter complex can be engineered to induce site-specific replication fork stalling and chromosomal HR/SCR in mouse cells. Tus/Ter-induced homologous recombination entails processing of bidirectionally arrested forks. We find that the Brca1 carboxy (C)-terminal tandem BRCT repeat and regions of Brca1 encoded by exon 11-two Brca1 elements implicated in tumour suppression-control Tus/Ter-induced homologous recombination. Inactivation of either Brca1 or Brca2 increases the absolute frequency of 'long-tract' gene conversions at Tus/Ter-stalled forks, an outcome not observed in response to a site-specific endonuclease-mediated chromosomal double-strand break. Therefore, homologous recombination at stalled forks is regulated differently from homologous recombination at double-strand breaks arising independently of a replication fork. We propose that aberrant long-tract homologous recombination at stalled replication forks contributes to genomic instability and breast/ovarian cancer predisposition in BRCA mutant cells.

  17. 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.

  18. Global Linear Instability

    NASA Astrophysics Data System (ADS)

    Theofilis, Vassilios

    2011-01-01

    This article reviews linear instability analysis of flows over or through complex two-dimensional (2D) and 3D geometries. In the three decades since it first appeared in the literature, global instability analysis, based on the solution of the multidimensional eigenvalue and/or initial value problem, is continuously broadening both in scope and in depth. To date it has dealt successfully with a wide range of applications arising in aerospace engineering, physiological flows, food processing, and nuclear-reactor safety. In recent years, nonmodal analysis has complemented the more traditional modal approach and increased knowledge of flow instability physics. Recent highlights delivered by the application of either modal or nonmodal global analysis are briefly discussed. A conscious effort is made to demystify both the tools currently utilized and the jargon employed to describe them, demonstrating the simplicity of the analysis. Hopefully this will provide new impulses for the creation of next-generation algorithms capable of coping with the main open research areas in which step-change progress can be expected by the application of the theory: instability analysis of fully inhomogeneous, 3D flows and control thereof.

  19. 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)

  20. Evaluation of protective potential of Yersinia pestis outer membrane protein antigens as possible candidates for a new-generation recombinant plague vaccine.

    PubMed

    Erova, Tatiana E; Rosenzweig, Jason A; Sha, Jian; Suarez, Giovanni; Sierra, Johanna C; Kirtley, Michelle L; van Lier, Christina J; Telepnev, Maxim V; Motin, Vladimir L; Chopra, Ashok K

    2013-02-01

    Plague caused by Yersinia pestis manifests itself in bubonic, septicemic, and pneumonic forms. Although the U.S. Food and Drug Administration recently approved levofloxacin, there is no approved human vaccine against plague. The capsular antigen F1 and the low-calcium-response V antigen (LcrV) of Y. pestis represent excellent vaccine candidates; however, the inability of the immune responses to F1 and LcrV to provide protection against Y. pestis F1(-) strains or those which harbor variants of LcrV is a significant concern. Here, we show that the passive transfer of hyperimmune sera from rats infected with the plague bacterium and rescued by levofloxacin protected naive animals against pneumonic plague. Furthermore, 10 to 12 protein bands from wild-type (WT) Y. pestis CO92 reacted with the aforementioned hyperimmune sera upon Western blot analysis. Based on mass spectrometric analysis, four of these proteins were identified as attachment invasion locus (Ail/OmpX), plasminogen-activating protease (Pla), outer membrane protein A (OmpA), and F1. The genes encoding these proteins were cloned, and the recombinant proteins purified from Escherichia coli for immunization purposes before challenging mice and rats with either the F1(-) mutant or WT CO92 in bubonic and pneumonic plague models. Although antibodies to Ail and OmpA protected mice against bubonic plague when challenged with the F1(-) CO92 strain, Pla antibodies were protective against pneumonic plague. In the rat model, antibodies to Ail provided protection only against pneumonic plague after WT CO92 challenge. Together, the addition of Y. pestis outer membrane proteins to a new-generation recombinant vaccine could provide protection against a wide variety of Y. pestis strains.

  1. Generation of a Recombinant Gag Virus-Like-Particle Panel for the Evaluation of p24 Antigen Detection by Diagnostic HIV Tests

    PubMed Central

    Vetter, Beatrice N.; Orlowski, Vanessa; Fransen, Katrien; Niederhauser, Christoph; Aubert, Vincent; Brandenberger, Marcel; Ciardo, Diana; Dollenmaier, Günter; Klimkait, Thomas; Regenass, Stephan; Schmid, Patrick; Schottstedt, Volkmar; Suter-Riniker, Franziska; Yerly, Sabine; Shah, Cyril; Böni, Jürg; Schüpbach, Jörg

    2014-01-01

    Background Detection of HIV-1 p24 antigen permits early identification of primary HIV infection and timely intervention to limit further spread of the infection. Principally, HIV screening should equally detect all viral variants, but reagents for a standardised test evaluation are limited. Therefore, we aimed to create an inexhaustible panel of diverse HIV-1 p24 antigens. Methods We generated a panel of 43 recombinantly expressed virus-like particles (VLPs), containing the structural Gag proteins of HIV-1 subtypes A-H and circulating recombinant forms (CRF) CRF01_AE, CRF02_AG, CRF12_BF, CRF20_BG and group O. Eleven 4th generation antigen/antibody tests and five antigen-only tests were evaluated for their ability to detect VLPs diluted in human plasma to p24 concentrations equivalent to 50, 10 and 2 IU/ml of the WHO p24 standard. Three tests were also evaluated for their ability to detect p24 after heat-denaturation for immune-complex disruption, a pre-requisite for ultrasensitive p24 detection. Results Our VLP panel exhibited an average intra-clade p24 diversity of 6.7%. Among the 4th generation tests, the Abbott Architect and Siemens Enzygnost Integral 4 had the highest sensitivity of 97.7% and 93%, respectively. Alere Determine Combo and BioRad Access were least sensitive with 10.1% and 40.3%, respectively. Antigen-only tests were slightly more sensitive than combination tests. Almost all tests detected the WHO HIV-1 p24 standard at a concentration of 2 IU/ml, but their ability to detect this input for different subtypes varied greatly. Heat-treatment lowered overall detectability of HIV-1 p24 in two of the three tests, but only few VLPs had a more than 3-fold loss in p24 detection. Conclusions The HIV-1 Gag subtype panel has a broad diversity and proved useful for a standardised evaluation of the detection limit and breadth of subtype detection of p24 antigen-detecting tests. Several tests exhibited problems, particularly with non-B subtypes. PMID:25343245

  2. Generation of Recombination Activating Gene-1-Deficient Neonatal Piglets: A Model of T and B Cell Deficient Severe Combined Immune Deficiency

    PubMed Central

    Ito, Tetsuya; Sendai, Yutaka; Yamazaki, Satoshi; Seki-Soma, Marie; Hirose, Kensuke; Watanabe, Motoo; Fukawa, Kazuo; Nakauchi, Hiromitsu

    2014-01-01

    Although severe combined immune deficiency (SCID) is a very important research model for mice and SCID mice are widely used, there are only few reports describing the SCID pig models. Therefore, additional research in this area is needed. In this study, we describe the generation of Recombination activating gene-1 (Rag-1)-deficient neonatal piglets in Duroc breed using somatic cell nuclear transfer (SCNT) with gene targeting and analysis using fluorescence-activated cell sorting (FACS) and histology. We constructed porcine Rag-1 gene targeting vectors for the Exon 2 region and obtained heterozygous/homozygous Rag-1 knockout cell colonies using SCNT. We generated two Rag-1-deficient neonatal piglets and compared them with wild-type neonatal piglets. FACS analysis showed that Rag-1 disruption causes a lack of Immunoglobulin M-positive B cells and CD3-positive T cells in peripheral blood mononuclear cells. Consistent with FACS analysis, histological analysis revealed structural defects and an absence of mature lymphocytes in the spleen, mesenteric lymph node (MLNs), and thymus in Rag-1-deficient piglets. These results confirm that Rag-1 is necessary for the generation of lymphocytes in pigs, and Rag-1-deficient piglets exhibit a T and B cell deficient SCID (T-B-SCID) phenotype similar to that of rodents and humans. The T-B-SCID pigs with Rag-1 deficiency generated in this study could be a suitably versatile model for laboratory, translational, and biomedical research, including the development of a humanized model and assessment of pluripotent stem cells. PMID:25437445

  3. 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.

  4. Woodchuck dendritic cells generated from peripheral blood mononuclear cells and transduced with recombinant human adenovirus serotype 5 induce antigen-specific cellular immune responses.

    PubMed

    Ochoa-Callejero, Laura; Berraondo, Pedro; Crettaz, Julien; Olagüe, Cristina; Vales, Africa; Ruiz, Juan; Prieto, Jesús; Tennant, Bud C; Menne, Stephan; González-Aseguinolaza, Gloria

    2007-05-01

    Woodchucks infected with the woodchuck hepatitis virus (WHV) is the best available animal model for testing the immunotherapeutic effects of dendritic cells (DCs) in the setting of a chronic infection, as woodchucks develop a persistent infection resembling that seen in humans infected with the hepatitis B virus. In the present study, DCs were generated from woodchuck peripheral blood mononuclear cells (wDCs) in the presence of human granulocyte macrophage colony-stimulating factor (hGM-CSF) and human interleukin 4 (hIL-4). After 7 days of culture, cells with morphology similar to DCs were stained positively with a cross-reactive anti-human CD86 antibody. Functional analysis showed that uptake of FITC-dextran by wDCs was very efficient and was partially inhibited after LPS-induced maturation. Furthermore, wDCs stimulated allogenic lymphocytes and induced proliferation. Moreover, wDCs were transduced efficiently with a human adenovirus serotype 5 for the expression of beta-galactosidase. Following transduction and in vivo administration of such DCs into woodchucks, an antigen-specific cellular immune response was induced. These results demonstrate that wDCs can be generated from the peripheral blood. Following transfection with a recombinant adenovirus wDCs can be used as a feasible and effective tool for eliciting WHV-specific T-cell responses indicating their potential to serve as prophylactic and therapeutic vaccines. PMID:17385694

  5. 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.

  6. Deletion of the carboxyl-terminal exons of K-sam/FGFR2 by short homology-mediated recombination, generating preferential expression of specific messenger RNAs.

    PubMed

    Ueda, T; Sasaki, H; Kuwahara, Y; Nezu, M; Shibuya, T; Sakamoto, H; Ishii, H; Yanagihara, K; Mafune, K; Makuuchi, M; Terada, M

    1999-12-15

    The K-sam gene was first identified as an amplified gene from human gastric cancer cell line KATOIII, and its product is identical to fibroblast growth factor receptor 2. The K-sam gene is located on human chromosome 10q26 and is preferentially amplified in the poorly differentiated types, especially in the scirrhous type, of gastric cancers. During the course of studies on the structural characterization of the amplification units, we found that the carboxyl-terminal exons of K-sam were deleted in three of four of the scirrhous type of gastric cancer cell lines. These deletions generate preferential expression of mRNAs encoding K-sam proteins lacking the carboxyl-terminal region containing the tyrosine residues at positions 780, 784, and 813. The carboxyl-terminal region has been reported to have a sequence required for the inhibition of NIH3T3 transformation, indicating that cells with amplification of the truncated K-sam gene have a growth advantage during the carcinogenic process for the scirrhous type of gastric cancers. This is the first report showing the deletion of the carboxyl-terminal exons of the receptor-type of the protein tyrosine kinase gene. Sequence analysis of the DNA sequences surrounding the deletion junctions shows the presence of unique sequences and indicates the involvement of short homology-mediated recombination in the generation of these deletions. PMID:10626794

  7. 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. PMID:26311244

  8. 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

  9. Generation and characterization of recombinant bivalent fusion protein r-Cpib for immunotherapy against Clostridium perfringens beta and iota toxemia.

    PubMed

    Das, Shreya; Majumder, Saugata; Kingston, Joseph J; Batra, Harsh V

    2016-02-01

    Clostridium perfringens beta (CPB) and iota (CPI) toxaemias result in some of the most lethal forms of haemorrhagic and necrotic enteritis and sudden death syndrome affecting especially neonates. While CPB enterotoxemia is one of the most common forms of clostridial enterotoxemia, CPI enterotoxemia though putatively considered to be rare is an emerging cause of concern. The similarities in clinical manifestation, gross and histopathology findings of both types of toxaemias coupled to the infrequency of CPI toxaemia might lead to symptomatic misidentification with Type C resulting in therapeutic failure due to habitual administration of CPB anti-toxin which is ineffective against CPI. Therefore in the present study, to generate a composite anti-toxin capable of neutralizing both toxaemias, a novel bivalent chimera r-Cpib was constructed by splicing the non-toxic C terminal binding regions of CPB and CPI, via a flexible glycine linker (G4S) by overlap-extension PCR. The fusion protein was characterized for its therapeutic abilities toward CPI and CPB toxin neutralizations. The r-Cpib was found to be non-toxic and could competitively inhibit binding of CPB to host cell receptors thereby reducing its cytotoxicity. Immunization of mice with r-Cpib generated specific antibodies capable of neutralizing the above toxaemias both in vitro and in vivo. Caco-2 cells exposed to a mixture of anti-r-Cpib sera and native CPI or CPB, displayed significantly superior protection against the respective toxins while passive challenge of mice with a similar mixture resulted in 83 and 91% protection against CPI and CPB respectively. Alternatively, mice exposed to a mixture of sham sera and native toxins died within 2-3 days. This work thus demonstrates r-Cpib as a novel bivalent fusion protein capable of efficient immunotherapy against C. perfringens CPI and CPB toxaemia. PMID:26774054

  10. The effect of processing additives for charge generation, recombination, and extraction in bulk heterojunction layers of all-polymer photovoltaics

    NASA Astrophysics Data System (ADS)

    Kim, Yu Jin; Ahn, Sunyong; Wang, Dong Hwan; Park, Chan Eon

    2015-08-01

    Bulk heterojunction all-polymer solar cells, fabricated with poly{[4,8-bis-(2-ethyl-hexyl-thiophene-5-yl)-benzo[1,2-b:4,5-b']dithiophene-2,6-diyl]-alt-[2-(2-ethyl-hexanoyl)-thieno[3,4-b']thiophen-4,6-diyl]} (PBDTTT-CT) as a donor polymer, and a acceptor polymer, poly{[N,N'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)} (P(NDI2OD-T2)), have been demonstrated and have achieved a power conversion efficiency exceeding 3.7% by using 1,8-diiodooctane (DIO) as a processing additive. Based on the analysis of charge carrier dynamics (charge generation, separation, and extraction), we found that the appropriate ratio of processing solvent additive (5 vol. % DIO) leads to enhanced device performance and favorable morphological characteristics. This research, therefore, indicates that the incorporation of a DIO additive in all-polymer blends is an effective way to form a morphologically ideal heterojunction network and thereby improve charge carrier kinetics for efficient photovoltaic devices.

  11. Generation and characterization of functional recombinant antibody fragments against tomato yellow leaf curl virus replication-associated protein.

    PubMed

    Safarnejad, M R; Fischer, R; Commandeur, U

    2008-01-01

    Tomato yellow leaf curl virus (TYLCV) is a complex of geminivirus species prevalent in the tropics and sub-tropics, which causes severe diseases in economically important crops such as tomato. Conventional strategies for disease management have shown little success and new approaches based on genetic engineering need to be considered. We generated two single-chain variable fragment antibodies (scFv-ScRep1 and scFv-ScRep2) that bound strongly to continuous epitopes within the TYLCV replication-associated protein (Rep). The TYLCV-Ir C1 gene (encoding Rep) was expressed as glutathione-S-transferase (GST) and maltose-binding protein (MBP) fusions. Purified MBP-Rep was used to immunize mice allowing the construction of naïve and pre-immunized scFv phage display libraries. Immunoassays showed that scFv-ScRep1 recognized an N-terminal epitope of Rep, whereas scFv-ScRep2 recognized a more central epitope. This is the first successful production of scFv antibodies against a geminivirus Rep, the initial step in the production of transgenic plants with resistance to TYLCV. PMID:19226769

  12. 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,...

  13. 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

  14. Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements

    PubMed Central

    Mohebi, Saed; Mizuno, Ken’Ichi; Watson, Adam; Carr, Antony M.; Murray, Johanne M.

    2015-01-01

    Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle. PMID:25721418

  15. 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.

  16. 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.

  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. PMID:24898110

  18. 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.

  19. 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.

  20. 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

  1. Generation of xylooligosaccharides from microwave irradiated agroresidues using recombinant thermo-alkali-stable endoxylanase of the polyextremophilic bacterium Bacillus halodurans expressed in Pichia pastoris.

    PubMed

    Kumar, Vikash; Satyanarayana, T

    2015-03-01

    The recombinant Pichia pastoris harboring the endoxylanase gene (TSEV1xyl) of Bacillus halodurans TSEV1 yielded a high titer of extracellular xylanase (502±23 U ml(-1)) on induction with methanol. The purified recombinant xylanase (TSEV1xyl) displayed optimal activity at 80°C and pH 9.0. The glycosylated recombinant xylanase exhibited higher thermostability (T1/2 of 45 min at 80°C) than the native enzyme (T1/2 of 35 min at 80°C). The agroresidues subjected to pretreatment (soaking in alkali followed by microwave irradiation) liberated xylooligosaccharides (XOS) upon hydrolysis with the recombinant xylanase. The removal of unhydrolyzed agroresidues, xylanase and xylose from the hydrolysate by two-step ultrafiltration led to the purification of XOS as confirmed by TLC as well as HPLC analysis.

  2. Recombinant Proapoptotic M. tuberculosis Generates CD8+ T-cell Responses Against Human Immunodeficiency Virus Type 1 Env and M. tuberculosis in Neonatal Mice

    PubMed Central

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

    2009-01-01

    M. 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 M. 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 (ΔlysA ΔpanCD Mtb and ΔRD1 ΔpanCD Mtb) failed to induce significant levels of HIV Env-specific CD8+ T cell responses. In striking contrast, an HIV-1-Env-expressing attenuated ΔlysA 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 ΔlysA ΔsecA2 Mtb expressing SIV Gag induced Gag- and Mtb-specific CD8+ T cells producing perforin or IFNγ, and Gag-specific CD4+ T cells producing IFNγ within 3 weeks after immunization in adult mice; in addition, IFNγ 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 ΔlysA ΔsecA2 Mtb is a promising vaccine platform to construct a safe combination HIV-TB vaccine for use in neonates. PMID:19808028

  3. The Energetics of Centrifugal Instability

    NASA Astrophysics Data System (ADS)

    Dewar, W. K.; Jiao, Y.

    2014-12-01

    A recent study has argued that the California Undercurrent, and poleward eastern boundary currents in general, generate mixing events through centrifugal instability (CI). Conditions favorable for CI are created by the strong horizontal shears developed in turbulent bottom layers of currents flowing in the direction of topographic waves. At points of abrupt topographic change, like promontories and capes, the coastal current separates from the boundary and injects gravitationally stable but dynamically unstable flow into the interior. The resulting finite amplitude development of the instability involves overturnings and diabatic mixing. The purpose of this study is to examine the energetics of CI in order to characterize it as has been done for other instabilities and develop a framework in which to estimate its regional and global impacts. We argue that CI is roughly twice as efficient at mixing as is Kelvin-Helmholtz instability, and that roughly 10% of the initial energy in a CUC-like current is lost to either local mixing or the generation of unbalanced flows. The latter probably leads to non-local mixing. Thus centrifugal instability is an effective process by which energy is lost from the balanced flow and spent in mixing neighboring water masses. We argue the importance of the mixing is regional in nature, but of less importance to the global budgets given its regional specificity.

  4. 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)

  5. 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

  6. 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.

  7. Mode-locking via dissipative Faraday instability.

    PubMed

    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

  8. 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.

  9. Columnar recombination for X-ray generated electron-holes in amorphous selenium and its significance in a-Se x-ray detectors

    NASA Astrophysics Data System (ADS)

    Bubon, O.; Jandieri, K.; Baranovskii, S. D.; Kasap, S. O.; Reznik, A.

    2016-03-01

    Although amorphous selenium (a-Se) has a long and successful history of application in optical and X-ray imaging, some of its fundamental properties are still puzzling. In particularly, the mechanism of carrier recombination following x-ray excitation and electric field and temperature dependences of the electron-hole pair creation energy (Wehp) remain unclear. Using the combination of X-ray photocurrent and pulse height spectroscopy measurements, we measure Wehp in a wide range of temperatures (218-320 K) and electric fields (10-100 V/µm) and show that the conventional columnar recombination model which assumes Langevin recombination within a column (a primary electron track) fails to explain experimental results in a wide range of electric fields and temperatures. The reason for the failure of the conventional model is revealed in this work, and the theory of the columnar recombination is modified to include the saturation of the recombination rate at high electric field in order to account for the experimental results in the entire range of fields and temperatures.

  10. 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

  11. Interfacial Instability during Granular Erosion

    NASA Astrophysics Data System (ADS)

    Lefebvre, Gautier; Merceron, Aymeric; Jop, Pierre

    2016-02-01

    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.

  12. 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. PMID:26919014

  13. 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.

  14. 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

  15. Recombination between homologous chromosomes induced by unrepaired UV-generated DNA damage requires Mus81p and is suppressed by Mms2p.

    PubMed

    Yin, Yi; Petes, Thomas D

    2015-03-01

    DNA lesions caused by UV radiation are highly recombinogenic. In wild-type cells, the recombinogenic effect of UV partially reflects the processing of UV-induced pyrimidine dimers into DNA gaps or breaks by the enzymes of the nucleotide excision repair (NER) pathway. In this study, we show that unprocessed pyrimidine dimers also potently induce recombination between homologs. In NER-deficient rad14 diploid strains, we demonstrate that unexcised pyrimidine dimers stimulate crossovers, noncrossovers, and break-induced replication events. The same dose of UV is about six-fold more recombinogenic in a repair-deficient strain than in a repair-proficient strain. We also examined the roles of several genes involved in the processing of UV-induced damage in NER-deficient cells. We found that the resolvase Mus81p is required for most of the UV-induced inter-homolog recombination events. This requirement likely reflects the Mus81p-associated cleavage of dimer-blocked replication forks. The error-free post-replication repair pathway mediated by Mms2p suppresses dimer-induced recombination between homologs, possibly by channeling replication-blocking lesions into recombination between sister chromatids.

  16. 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.

  17. Quantification of the effects of generation volume, surface recombination velocity, and diffusion length on the electron-beam-induced current and its derivative Determination of diffusion lengths in the low micron and submicron ranges

    NASA Technical Reports Server (NTRS)

    Luke, K. L.; Von Roos, O.; Cheng, L.-J.

    1985-01-01

    A systematic and quantitative analysis is carried out to investigate the effects of the shape (point, cube, Gaussian) and size of the generation volume, the surface recombination velocity, and the diffusion length on the electron-beam-induced current (EBIC) and its derivative (DEIC). Thick homogeneously doped samples exhibiting diffusion lengths in the low micron and submicron range are considered. The results are presented in computed EBIC curves as a function of scanning distance and of the ratio true diffusion length/effective diffusion length. Shown using these curves are: (1) a simple and yet rigorous method for the determination of the true diffusion length, taking into consideration all of the factors cited above, (2) a method for the rapid determination of the surface recombination velocity, (3) the condition under which the source shape becomes insignificant, and (4) a new value for the lower limit of the diffusion length which can be determined by the EBOC technique.

  18. Instability of canopy flows

    NASA Astrophysics Data System (ADS)

    Zampogna, Giuseppe A.; Pluvinage, Franck; Kourta, Azeddine; Bottaro, Alessandro

    2016-07-01

    Honami and monami waves are caused by large-scale coherent vortex structures which form in shear layers generated by canopies. In order to reach new insights on the onset of such waves, the instability of these shear layers is studied. Two different approaches are used. In the first approach, the presence of the canopy is modeled via a drag coefficient, taken to vary along the canopy as by experimental indications. The second approach considers the canopy as a porous medium and different governing equations for the fluid flow are deduced. In this second case, the anisotropy of the canopy, composed by rigid cylindrical elements, is accounted for via an apparent permeability tensor. The results obtained with the latter approach approximate better experimental correlations for the synchronous oscillations of the canopy.

  19. 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).

  20. 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

  1. Primordial magnetogenesis before recombination

    NASA Astrophysics Data System (ADS)

    Fabre, Ophélia; Shankaranarayanan, S.

    2016-04-01

    The origin of large magnetic fields in the Universe remains currently unknown. We investigate here a mechanism before recombination based on known physics. The source of the vorticity is due to the changes in the photon distribution function caused by the fluctuations in the background photons. We show that the magnetic field generated in the MHD limit, due to the Coulomb scattering, is of the order 10-49 G on a coherence scale of 10 kpc. We explicitly show that the magnetic fields generated from this process are sustainable and are not erased by resistive diffusion. We compare the results with current observations and discuss the implications. Our seed magnetic fields are generated on small scales whereas the main mechanisms studied in the literature are on scale bigger than 1 Mpc. However, compared to more exotic theories generating seed magnetic fields on similar scales, the strength of our fields are generally smaller.

  2. 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.

  3. Analysis of interchromosomal mitotic recombination.

    PubMed

    McGill, C B; Shafer, B K; Higgins, D R; Strathern, J N

    1990-07-01

    A novel synthetic locus is described that provides a simple assay system for characterizing mitotic recombinants. The locus consists of the TRP1 and HIS3 genes inserted into chromosome III of S. cerevisiae between the CRY1 and MAT loci. Defined trp1 and his3 alleles have been generated that allow the selection of interchromosomal recombinants in this interval. Trp+ or His+ recombinants can be divided into several classes based on coupling of the other alleles in the interval. The tight linkage of the CRY1 and MAT loci, combined with the drug resistance and cell type phenotypes that they respectively control, facilitates the classification of the recombinants without resorting to tetrad dissection. We present the distribution of spontaneous recombinants among the classes defined by this analysis. The data suggest that the recombination intermediate can have regions of symmetric strand exchange and that co-conversion tracts can extend over 1-3 kb. Continuous conversion tracts are favored over discontinuous tracts. The distribution among the classes defined by this analysis is altered in recombinants induced by UV irradiation.

  4. 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.

  5. Mating-induced recombination in fruit flies.

    PubMed

    Priest, Nicholas K; Roach, Deborah A; Galloway, Laura F

    2007-01-01

    In traditional deterministic models the conditions for the evolution of sex and sexual behavior are limited because their benefits are context dependent. In novel and adverse environments both multiple mating and recombination can help generate gene combinations that allow for rapid adaptation. Mating frequency often increases in conditions in which recombination might be beneficial; therefore, increased sexual behavior might evolve to act as a cue that stimulates recombination. We conducted two experiments in the fruit fly, Drosophila melanogaster, using linked phenotypic markers to determine how recent bouts of additional mating affect female recombination rate. The first experiment examined the effect of additional mating, mating history, and age on female recombination rate. The second experiment assessed the effect of recent mating events on recombination rate. Together, the experiments suggest that each additional bout of mating temporarily increases female recombination rate. These findings imply that the conditions favoring the evolution of sexual reproduction and multiple mating behaviors are broader than currently appreciated.

  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. Anatomy, pathophysiology, and biomechanics of shoulder instability.

    PubMed

    Doukas, W C; Speer, K P

    2001-07-01

    Instability in the athlete presents a unique challenge to the orthopaedic surgeon. A spectrum of both static and dynamic pathophysiology, as well as gross and microscopic histopathology, contribute to this complex clinical continuum. Biomechanical studies of the shoulder and ligament cutting studies in recent years have generated a more precise understanding of the individual contributions of the various ligaments and capsular regions to shoulder instability. An understanding of the underlying pathology and accurate assessment of degree and direction of the instability by clinical examination and history are essential to developing appropriate treatment algorithms.

  8. 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.

  9. 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...

  10. Flow instabilities in turbomachines

    NASA Astrophysics Data System (ADS)

    Greitzer, E. M.

    Instabilities occurring in systems involving the movement of a fluid through pipes, ducts, etc., by means of turbomachinery are discussed. While static instabilities may be inferred from system transient performance that is viewed as a sequence of quasi-steady states, such parameters as system interfaces and capacitances must be included in the prediction of dynamic instability, since they play an essential role in determining the transient response of the system to disturbances. A pumping system can be statically stable and still exhibit dynamic instability. Attention is given to rotating stall compressor instability, inlet distortion effects on axial compressor instability, the stability effects of downstream components, and the stability of centrifugal compressors and pumps.

  11. Joint Instability and Osteoarthritis

    PubMed Central

    Blalock, Darryl; Miller, Andrew; Tilley, Michael; Wang, Jinxi

    2015-01-01

    Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA). Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA. PMID:25741184

  12. Evolution of genetic instability in heterogeneous tumors.

    PubMed

    Asatryan, Ani D; Komarova, Natalia L

    2016-05-01

    Genetic instability is an important characteristic of cancer. While most cancers develop genetic instability at some stage of their progression, sometimes a temporary rise of instability is followed by the return to a relatively stable genome. Neither the reasons for these dynamics, nor, more generally, the role of instability in tumor progression, are well understood. In this paper we develop a class of mathematical models to study the evolutionary competition dynamics among different sub-populations in a heterogeneous tumor. We observe that despite the complexity of this multi-component and multi-process system, there is only a small number of scenarios expected in the context of the evolution of instability. If the penalty incurred by unstable cells (the decrease in the growth due to deleterious mutations) is high compared with the gain (the production rate of advantageous mutations), then instability does not evolve. In the opposite case, instability evolves and comes to dominate the system. In the intermediate parameter regime, instability is generated but later gives way to stable clones. Moreover, the model also informs us of the patterns of instability for cancer lineages corresponding to different stages of progression. It is predicted that mutations causing instability are merely "passengers" in tumors that have undergone only a small number of malignant mutations. Further down the path of carcinogenesis, however, unstable cells are more likely to give rise to the winning clonal wave that takes over the tumor and carries the evolution forward, thus conferring a causal role of the instability in such cases. Further, each individual clonal wave (i.e. cells harboring a fixed number of malignant driver mutations) experiences its own evolutionary history. It can fall under one of three types of temporal behavior: stable throughout, unstable to stable, or unstable throughout. Which scenario is realized depends on the subtle (but predictable) interplay among

  13. Evolution of genetic instability in heterogeneous tumors.

    PubMed

    Asatryan, Ani D; Komarova, Natalia L

    2016-05-01

    Genetic instability is an important characteristic of cancer. While most cancers develop genetic instability at some stage of their progression, sometimes a temporary rise of instability is followed by the return to a relatively stable genome. Neither the reasons for these dynamics, nor, more generally, the role of instability in tumor progression, are well understood. In this paper we develop a class of mathematical models to study the evolutionary competition dynamics among different sub-populations in a heterogeneous tumor. We observe that despite the complexity of this multi-component and multi-process system, there is only a small number of scenarios expected in the context of the evolution of instability. If the penalty incurred by unstable cells (the decrease in the growth due to deleterious mutations) is high compared with the gain (the production rate of advantageous mutations), then instability does not evolve. In the opposite case, instability evolves and comes to dominate the system. In the intermediate parameter regime, instability is generated but later gives way to stable clones. Moreover, the model also informs us of the patterns of instability for cancer lineages corresponding to different stages of progression. It is predicted that mutations causing instability are merely "passengers" in tumors that have undergone only a small number of malignant mutations. Further down the path of carcinogenesis, however, unstable cells are more likely to give rise to the winning clonal wave that takes over the tumor and carries the evolution forward, thus conferring a causal role of the instability in such cases. Further, each individual clonal wave (i.e. cells harboring a fixed number of malignant driver mutations) experiences its own evolutionary history. It can fall under one of three types of temporal behavior: stable throughout, unstable to stable, or unstable throughout. Which scenario is realized depends on the subtle (but predictable) interplay among

  14. Innovation by homologous recombination.

    PubMed

    Trudeau, Devin L; Smith, Matthew A; Arnold, Frances H

    2013-12-01

    Swapping fragments among protein homologs can produce chimeric proteins with a wide range of properties, including properties not exhibited by the parents. Computational methods that use information from structures and sequence alignments have been used to design highly functional chimeras and chimera libraries. Recombination has generated proteins with diverse thermostability and mechanical stability, enzyme substrate specificity, and optogenetic properties. Linear regression, Gaussian processes, and support vector machine learning have been used to model sequence-function relationships and predict useful chimeras. These approaches enable engineering of protein chimeras with desired functions, as well as elucidation of the structural basis for these functions.

  15. Nonlocal magnetorotational instability

    SciTech Connect

    Mikhailovskii, A. B.; Erokhin, N. N.; Lominadze, J. G.; Galvao, R. M. O.; Churikov, A. P.; Kharshiladze, O. A.; Amador, C. H. S.

    2008-05-15

    An analytical theory of the nonlocal magnetorotational instability (MRI) is developed for the simplest astrophysical plasma model. It is assumed that the rotation frequency profile has a steplike character, so that there are two regions in which it has constant different values, separated by a narrow transition layer. The surface wave approach is employed to investigate the MRI in this configuration. It is shown that the main regularities of the nonlocal MRI are similar to those of the local instability and that driving the nonaxisymmetric MRI is less effective than the axisymmetric one, also for the case of the nonlocal instability. The existence of nonlocal instabilities in nonmagnetized plasma is predicted.

  16. Recombinant snake venom prothrombin activators.

    PubMed

    Lövgren, Ann

    2013-01-01

    Three prothrombin activators; ecarin, which was originally isolated from the venom of the saw-scaled viper Echis carinatus, trocarin from the rough-scaled snake Tropidechis carinatus, and oscutarin from the Taipan snake Oxyuranus scutellatus, were expressed in mammalian cells with the purpose to obtain recombinant prothrombin activators that could be used to convert prothrombin to thrombin. We have previously reported that recombinant ecarin can efficiently generate thrombin without the need for additional cofactors, but does not discriminate non-carboxylated prothrombin from biologically active γ-carboxylated prothrombin. Here we report that recombinant trocarin and oscutarin could not efficiently generate thrombin without additional protein co-factors. We confirm that both trocarin and oscutarin are similar to human coagulation Factor X (FX), explaining the need for additional cofactors. Sequencing of a genomic fragment containing 7 out of the 8 exons coding for oscutarin further confirmed the similarity to human FX. PMID:23111318

  17. Reduced modeling of the magnetorotational instability

    NASA Astrophysics Data System (ADS)

    Jamroz, Ben F.

    2009-06-01

    Accretion describes the process by which matter in an astrophysical disk falls onto a central massive object. Accretion disks are present in many astrophysical situations including binary star systems, young stellar objects, and near black holes at the center of galaxies. Measurements from observations of these disks have shown that viscous processes are unable to transport the necessary levels of angular momentum needed for accretion. Therefore, accretion requires an efficient mechanism of angular momentum transport. Mixing by turbulent processes greatly enhances the level of angular momentum transport in a turbulent fluid. Thus, the generation of turbulence in these disks may provide the mechanism needed for accretion. A classical result of hydrodynamic theory is that typical accretion disks are hydrodynamically stable to shear instabilities, since the specific angular momentum increases outwards. Other processes of generating hydrodynamic turbulence (barotropic instability, baroclinic instability, sound wave, shock waves, finite amplitude instabilities) may be present in these disks, however, none of these mechanisms has been shown to produce the level of angular momentum transport needed for accretion. Hydrodynamical turbulence does not produce enough angular momentum transport to produce the level of accretion observed in astrophysical accretion disks. The leading candidate for the source of turbulence leading to the transport of angular momentum is the magnetorotational instability, a linear axisymmetric instability of electrically conducting fluid in the presence of an imposed magnetic field and shear (or differential rotation). This instability is an efficient mechanism of angular momentum transport generating the level of transport needed for accretion. The level of effective angular momentum transport is determined by the saturated state of sustained turbulence generated by the instability. The mechanism of nonlinear saturation of this instability is not

  18. 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. PMID:16623137

  19. Radiative heat transport instability in ICF plasmas

    NASA Astrophysics Data System (ADS)

    Rozmus, W.; Bychenkov, V. Yu.

    2015-11-01

    A laser produced high-Z plasma in which an energy balance is achieved due to radiation losses and radiative heat transfer supports ion acoustic wave instability. A linear dispersion relation is derived and instability is compared to the radiation cooling instability. This instability develops in the wide range of angles and wavenumbers with the typical growth rate on the order of cs/LT (cs is the sound speed, LT is the temperature scale length). In addition to radiation dominated systems, a similar thermal transport driven ion acoustic instability was found before in plasmas where the thermal transport coefficient depends on electron density. However, under conditions of indirect drive ICF 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 corresponding to a thermal conductivity coefficient that is inversely proportional to the square of local particle density. In the nonlinear regime this instability may lead to plasma jet formation and anisotropic x-ray generation.

  20. 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.

  1. Generation of eGFP expressing recombinant Zaire ebolavirus for analysis of early pathogenesis events and high-throughput antiviral drug screening.

    PubMed

    Towner, Jonathan S; Paragas, Jason; Dover, Jason E; Gupta, Manisha; Goldsmith, Cynthia S; Huggins, John W; Nichol, Stuart T

    2005-02-01

    Zaire ebolavirus causes large outbreaks of severe and usually fatal hemorrhagic disease in humans for which there is no effective treatment or cure. To facilitate examination of early critical events in viral pathogenesis and to identify antiviral compounds, a recombinant Zaire ebolavirus was engineered to express a foreign protein, eGFP, to provide a rapid and sensitive means to monitor virus replication in infected cells. This genetically engineered virus represents the first insertion of a foreign gene into ebolavirus. We show that Ebola-eGFP virus (EboZ-eGFP) infects known early targets of human infections and serves as an ideal model to screen antiviral compounds in less time than any previously published assay.

  2. 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

  3. High spontaneous intrachromosomal recombination rates in ataxia-telangiectasia

    SciTech Connect

    Meyn, M.S. )

    1993-05-28

    Ataxia-telangiectasia (A-T) is an inherited human disease associated with neurologic degeneration, immune dysfunctions, and high cancer risk. It has been proposed that the underlying abnormality in A-T is a defect in genetic recombination that interferes with immune gene rearrangements and the repair of DNA damage. Recombination was studied in A-T and control human fibroblast lines by means of two recombination vectors. Unexpectedly, spontaneous intrachromosomal recombination rates were 30 to 200 times higher in A-T fibroblast lines than in normal cells, whereas extrachromosomal recombination frequencies were near normal. Increased recombination is thus a component of genetic instability in A-T and may contribute to the cancer risk seen in A-T patients. 2 refs., 1 fig., 3 tabs.

  4. 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

  5. Preventing AID, a physiological mutator, from deleterious activation: regulation of the genomic instability that is associated with antibody diversity.

    PubMed

    Nagaoka, Hitoshi; Tran, Thinh Huy; Kobayashi, Maki; Aida, Masatoshi; Honjo, Tasuku

    2010-04-01

    Activation-induced cytidine deaminase (AID) is essential and sufficient to accomplish class-switch recombination and somatic hypermutation, which are two genetic events required for the generation of antibody-mediated memory responses. However, AID can also introduce genomic instability, giving rise to chromosomal translocation and/or mutations in proto-oncogenes. It is therefore important for cells to suppress AID expression unless B lymphocytes are stimulated by pathogens. The mechanisms for avoiding the accidental activation of AID and thereby avoiding genomic instability can be classified into three types: (i) transcriptional regulation, (ii) post-transcriptional regulation and (iii) target specificity. This review summarizes the recently elucidated comprehensive transcriptional regulation mechanisms of the AID gene and the post-transcriptional regulation that may be critical for preventing excess AID activity. Finally, we discuss why AID targets not only Igs but also other proto-oncogenes. AID targets many genes but it is not totally promiscuous and the criteria that specify its targets are unclear. A recent finding that a non-B DNA structure forms upon a decrease in topoisomerase 1 expression may explain this paradoxical target specificity determination. Evolution has chosen AID as a mutator of Ig genes because of its efficient DNA cleavage activity, even though its presence increases the risk of genomic instability. This is probably because immediate protection against pathogens is more critical for species survival than complete protection from the slower acting consequences of genomic instability, such as tumor formation.

  6. Towards Resolving Conflicting Reports of Radiation-Induced Genomic Instability in Populations Exposed to Ionizing Radiation: Implications for the Hibakusha

    SciTech Connect

    Morgan, William F.; Sowa, Marianne B.

    2007-03-30

    Radiation induced genomic instability has been described in a host of normal and transformed cells in vitro (Morgan 2003a). This instability can manifest as cell killing, micronuclei formation, transformation induction, di- and tri- nucleotide repeat instability, gene amplifications and mutations, and chromosomal rearrangements. Cytogenetic alterations are perhaps the best described of these endpoints following radiation exposures and will be the focus of this chapter. Chromosomal instability is characterized as either multiple sub populations of chromosomally rearranged metaphase chromosomes, or as newly arising chromatid and/or chromosomal aberrations occurring in the clonally expanded decedents of an irradiated cell. Some chromosomal changes appear to entail recombination events involving DNA repeat sequences within the genome, e.g., interstitial telomere-repeat like sequences (Day et al. 1998) and may be manifestations of telomere dysfunction in unstable clones of cells (Murnane and Sabatier 2004). Others, including the appearance of chromatid aberrations, indicate that DNA lesions can manifest in the preceding cell cycle multiple cell generations after the initial insult.

  7. Bacteriophage recombination systems and biotechnical applications.

    PubMed

    Nafissi, Nafiseh; Slavcev, Roderick

    2014-04-01

    Bacteriophage recombination systems have been widely used in biotechnology for modifying prokaryotic species, for creating transgenic animals and plants, and more recently, for human cell gene manipulation. In contrast to homologous recombination, which benefits from the endogenous recombination machinery of the cell, site-specific recombination requires an exogenous source of recombinase in mammalian cells. The mechanism of bacteriophage evolution and their coexistence with bacterial cells has become a point of interest ever since bacterial viruses' life cycles were first explored. Phage recombinases have already been exploited as valuable genetic tools and new phage enzymes, and their potential application to genetic engineering and genome manipulation, vectorology, and generation of new transgene delivery vectors, and cell therapy are attractive areas of research that continue to be investigated. The significance and role of phage recombination systems in biotechnology is reviewed in this paper, with specific focus on homologous and site-specific recombination conferred by the coli phages, λ, and N15, the integrase from the Streptomyces phage, ΦC31, the recombination system of phage P1, and the recently characterized recombination functions of Yersinia phage, PY54. Key steps of the molecular mechanisms involving phage recombination functions and their application to molecular engineering, our novel exploitations of the PY54-derived recombination system, and its application to the development of new DNA vectors are discussed. PMID:24442504

  8. Bacteriophage recombination systems and biotechnical applications.

    PubMed

    Nafissi, Nafiseh; Slavcev, Roderick

    2014-04-01

    Bacteriophage recombination systems have been widely used in biotechnology for modifying prokaryotic species, for creating transgenic animals and plants, and more recently, for human cell gene manipulation. In contrast to homologous recombination, which benefits from the endogenous recombination machinery of the cell, site-specific recombination requires an exogenous source of recombinase in mammalian cells. The mechanism of bacteriophage evolution and their coexistence with bacterial cells has become a point of interest ever since bacterial viruses' life cycles were first explored. Phage recombinases have already been exploited as valuable genetic tools and new phage enzymes, and their potential application to genetic engineering and genome manipulation, vectorology, and generation of new transgene delivery vectors, and cell therapy are attractive areas of research that continue to be investigated. The significance and role of phage recombination systems in biotechnology is reviewed in this paper, with specific focus on homologous and site-specific recombination conferred by the coli phages, λ, and N15, the integrase from the Streptomyces phage, ΦC31, the recombination system of phage P1, and the recently characterized recombination functions of Yersinia phage, PY54. Key steps of the molecular mechanisms involving phage recombination functions and their application to molecular engineering, our novel exploitations of the PY54-derived recombination system, and its application to the development of new DNA vectors are discussed.

  9. 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.

  10. 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

  11. Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal.

    PubMed

    Sauder, Christian J; Ngo, Laurie; Simonyan, Vahan; Cong, Yu; Zhang, Cheryl; Link, Malen; Malik, Tahir; Rubin, Steven A

    2015-08-01

    As a member of the family paramyxoviridae, subfamily paramyxovirinae, the genome of mumps virus (MuV) is postulated to be polyhexameric in length in order to be able to replicate efficiently. While all natural MuV strains sequenced so far obey to this "rule of six," we describe here the isolation of recombinant MuVs that appeared to contain an additional U residue in the homopolymeric tract of the F gene-end signal, resulting in a genome length of 6n + 1. Sequencing of several plaque-purified viruses from these preparations did not reveal the existence of length-correcting mutations, suggesting that they are violators of the rule of six. Employing high-throughput sequencing technology, we provide evidence that the insertion of an additional U residue is mainly the result of the rescue system used that relies on T7 RNA polymerase. Limited in vitro and in vivo testing of the viruses did not reveal any significant impact of the longer genome on virus replication or virulence, suggesting that the rule of six is not a strict requirement for MuV replication.

  12. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses.

    PubMed

    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; Mehandru, Saurabh

    2016-01-11

    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.

  13. 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. PMID:24517488

  14. Non-linear mirror instability

    NASA Astrophysics Data System (ADS)

    Rincon, F.; Schekochihin, A. A.; Cowley, S. C.

    2015-02-01

    Slow dynamical changes in magnetic-field strength and invariance of the particles' magnetic moments generate ubiquitous pressure anisotropies in weakly collisional, magnetized astrophysical plasmas. This renders them unstable to fast, small-scale mirror and firehose instabilities, which are capable of exerting feedback on the macroscale dynamics of the system. By way of a new asymptotic theory of the early non-linear evolution of the mirror instability in a plasma subject to slow shearing or compression, we show that the instability does not saturate quasi-linearly at a steady, low-amplitude level. Instead, the trapping of particles in small-scale mirrors leads to non-linear secular growth of magnetic perturbations, δB/B ∝ t2/3. Our theory explains recent collisionless simulation results, provides a prediction of the mirror evolution in weakly collisional plasmas and establishes a foundation for a theory of non-linear mirror dynamics with trapping, valid up to δB/B = O(1).

  15. 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.

  16. Generation of a soluble recombinant trimeric form of bovine CD40L and its potential use as a vaccine adjuvant in cows.

    PubMed

    Pujol, Julien; Bouillenne, Fabrice; Farnir, Frédéric; Dufrasne, Isabelle; Mainil, Jacques; Galleni, Moreno; Lekeux, Pierre; Bureau, Fabrice; Fiévez, Laurence

    2015-11-15

    Vaccination is the most cost-effective way to control infectious diseases in cattle. However, many infectious diseases leading to severe economical losses worldwide still remain for which a really effective and safe vaccine is not available. These diseases are most often due to intracellular pathogens such as bacteria or viruses, which are, by their localization, protected from antibiotics and/or CD4(+) T cell-dependent humoral responses. We therefore postulated that strategies leading to induction of not only CD4(+) T cell responses but also CD8(+) cytotoxic T lymphocyte (CTL) responses against infected cells should be privileged in the development of new vaccines against problematic intracellular pathogens in bovines. CD40 signaling in antigen-presenting cells may lead to the induction of robust CD4-independent CTL responses and several studies, especially in mice, have used CD40 stimulation to promote CD8(+) T cell-mediated immunity. For example, we have recently shown that immunization of mice with heat-killed Staphylococcus aureus (HKSA) and agonistic anti-CD40 monoclonal antibodies elicits strong CTL responses capable of protecting mice from subsequent staphylococcal mastitis. Unfortunately, there is at present no tool available to efficiently stimulate CD40 in cattle. In this study, we therefore first produced a soluble recombinant trimeric form of the natural bovine CD40 ligand (sboCD40LT). We then observed that sboCD40LT was able to potently stimulate bovine cells in vitro. Finally, we provide evidence that immunization of cows with sboCD40LT combined with HKSA was able to significantly increase the number of both HKSA-specific CD4(+) and CD8(+) T cells in the draining lymph nodes. In conclusion, we suggest that this new molecular tool could help in the development of vaccine strategies against bovine diseases caused by intracellular pathogens.

  17. Imaging in carpal instability.

    PubMed

    Ramamurthy, N K; Chojnowski, A J; Toms, A P

    2016-01-01

    Carpal instability is a complex and heterogeneous clinical condition. Management requires accurate identification of structural injury with an understanding of the resultant movement (kinematic) and load transfer (kinetic) failure. Static imaging techniques, such as plain film radiography, stress views, ultrasound, magnetic resonance, MR arthrography and computerized tomography arthrography, may accurately depict major wrist ligamentous injury. Dynamic ultrasound and videofluoroscopy may demonstrate dynamic instability and kinematic dysfunction. There is a growing evidence base for the diagnostic accuracy of these techniques in detecting intrinsic ligament tears, but there are limitations. Evidence of their efficacy and relevance in detection of non-dissociative carpal instability and extrinsic ligament tears is weak. Further research into the accuracy of existing imaging modalities is still required. Novel techniques, including four-dimensional computerized tomography and magnetic resonance, can evaluate both cross-sectional and functional carpal anatomy. This is a narrative review of level-III studies evaluating the role of imaging in carpal instability. PMID:26586689

  18. 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

  19. 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...

  20. 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.

  1. 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…

  2. mTORC1 in Thymic Epithelial Cells Is Critical for Thymopoiesis, T-Cell Generation, and Temporal Control of γδT17 Development and TCRγ/δ Recombination.

    PubMed

    Wang, Hong-Xia; Shin, Jinwook; Wang, Shang; Gorentla, Balachandra; Lin, Xingguang; Gao, Jimin; Qiu, Yu-Rong; Zhong, Xiao-Ping

    2016-02-01

    Thymus is crucial for generation of a diverse repertoire of T cells essential for adaptive immunity. Although thymic epithelial cells (TECs) are crucial for thymopoiesis and T cell generation, how TEC development and function are controlled is poorly understood. We report here that mTOR complex 1 (mTORC1) in TECs plays critical roles in thymopoiesis and thymus function. Acute deletion of mTORC1 in adult mice caused severe thymic involution. TEC-specific deficiency of mTORC1 (mTORC1KO) impaired TEC maturation and function such as decreased expression of thymotropic chemokines, decreased medullary TEC to cortical TEC ratios, and altered thymic architecture, leading to severe thymic atrophy, reduced recruitment of early thymic progenitors, and impaired development of virtually all T-cell lineages. Strikingly, temporal control of IL-17-producing γδT (γδT17) cell differentiation and TCRVγ/δ recombination in fetal thymus is lost in mTORC1KO thymus, leading to elevated γδT17 differentiation and rearranging of fetal specific TCRVγ/δ in adulthood. Thus, mTORC1 is central for TEC development/function and establishment of thymic environment for proper T cell development, and modulating mTORC1 activity can be a strategy for preventing thymic involution/atrophy. PMID:26889835

  3. mTORC1 in Thymic Epithelial Cells Is Critical for Thymopoiesis, T-Cell Generation, and Temporal Control of γδT17 Development and TCRγ/δ Recombination

    PubMed Central

    Wang, Hong-Xia; Shin, Jinwook; Wang, Shang; Gorentla, Balachandra; Lin, Xingguang; Gao, Jimin; Qiu, Yu-Rong; Zhong, Xiao-Ping

    2016-01-01

    Thymus is crucial for generation of a diverse repertoire of T cells essential for adaptive immunity. Although thymic epithelial cells (TECs) are crucial for thymopoiesis and T cell generation, how TEC development and function are controlled is poorly understood. We report here that mTOR complex 1 (mTORC1) in TECs plays critical roles in thymopoiesis and thymus function. Acute deletion of mTORC1 in adult mice caused severe thymic involution. TEC-specific deficiency of mTORC1 (mTORC1KO) impaired TEC maturation and function such as decreased expression of thymotropic chemokines, decreased medullary TEC to cortical TEC ratios, and altered thymic architecture, leading to severe thymic atrophy, reduced recruitment of early thymic progenitors, and impaired development of virtually all T-cell lineages. Strikingly, temporal control of IL-17-producing γδT (γδT17) cell differentiation and TCRVγ/δ recombination in fetal thymus is lost in mTORC1KO thymus, leading to elevated γδT17 differentiation and rearranging of fetal specific TCRVγ/δ in adulthood. Thus, mTORC1 is central for TEC development/function and establishment of thymic environment for proper T cell development, and modulating mTORC1 activity can be a strategy for preventing thymic involution/atrophy. PMID:26889835

  4. Heuristic explanation of journal bearing instability

    NASA Technical Reports Server (NTRS)

    Crandall, S. H.

    1982-01-01

    A fluid-filled journal bearing is viewed as a powerful pump circulating fluid around the annular space between the journal and the bearing. A small whirling motion of the journal generates a wave of thickness variation progressing around the channel. The hypothesis that the fluid flow drives the whirl whenever the mean of the pumped fluid velocity is greater than the peripheral speed of the thickness variation wave is discussed and compared with other simple explanations of journal bearing instability. It is shown that for non-cavitation long bearings the hypothesis predicts instability onset correctly for unloaded bearings but gradually overpredicts the onset speed as the load is increased.

  5. 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.

  6. Gauging magnetorotational instability

    NASA Astrophysics Data System (ADS)

    Herron, Isom; Goodman, Jeremy

    2010-08-01

    Previously (Z. Angew. Math. Phys. 57:615-622, 2006), we examined the axisymmetric stability of viscous resistive magnetized Couette flow with emphasis on flows that would be hydrodynamically stable according to Rayleigh’s criterion: opposing gradients of angular velocity and specific angular momentum. A uniform axial magnetic field permeates the fluid. In this regime, magnetorotational instability (MRI) may occur. It was proved that MRI is suppressed, in fact no instability at all occurs, with insulating boundary conditions, when a term multipling the magnetic Prandtl number is neglected. Likewise, in the current work, including this term, when the magnetic resistivity is sufficiently large, MRI is suppressed. This shows conclusively that small magnetic dissipation is a feature of this instability for all magnetic Prandtl numbers. A criterion is provided for the onset of MRI.

  7. The Walking Droplet Instability

    NASA Astrophysics Data System (ADS)

    Bostwick, Joshua; Steen, Paul

    2013-11-01

    A droplet of liquid that partially wets a solid substrate assumes a spherical-cap equilibrium shape. We show that the spherical-cap with a mobile contact-line is unstable to a non-axisymmetric disturbance and we characterize the instability mechanism, as it depends upon the wetting properties of the substrate. We then solve the hydrodynamic problem for inviscid motions showing that the flow associated with the instability correlates with horizontal motion of the droplet's center-of-mass. We calculate the resulting ``walking speed.'' A novel feature is that the energy conversion mechanism is not unique, so long as the contact-line is mobilized. Hence, the walking droplet instability is potentially significant to a number of industrial applications, such as self-cleansing surfaces or energy harvesting devices.

  8. 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.

  9. High efficiency recombineering in lactic acid bacteria

    PubMed Central

    van Pijkeren, Jan-Peter; Britton, Robert A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria. Mutations were incorporated in the chromosome of Lactobacillus reuteri and Lactococcus lactis without selection at frequencies ranging between 0.4% and 19%. Whole genome sequence analysis showed that ssDNA recombineering is specific and not hypermutagenic. To highlight the utility of ssDNA recombineering we reduced the intrinsic vancomymycin resistance of L. reuteri >100-fold. By creating a single amino acid change in the d-Ala-d-Ala ligase enzyme we reduced the minimum inhibitory concentration for vancomycin from >256 to 1.5 µg/ml, well below the clinically relevant minimum inhibitory concentration. Recombineering thus allows high efficiency mutagenesis in lactobacilli and lactococci, and may be used to further enhance beneficial properties and safety of strains used in medicine and industry. We expect that this work will serve as a blueprint for the adaptation of ssDNA recombineering to other Gram-positive bacteria. PMID:22328729

  10. Replication of a recombinant hepatitis E virus genome tagged with reporter genes and generation of a short-term cell line producing viral RNA and proteins.

    PubMed

    Thakral, Deepshi; Nayak, Baibaswata; Rehman, Shagufta; Durgapal, Hemlata; Panda, Subrat Kumar

    2005-04-01

    Hepatitis E virus (HEV) replication has been demonstrated in HepG2 cells transfected with full-length in vitro transcripts of an infectious cDNA clone. This cDNA clone was modified to generate several subgenomic HEV replicons with fused reporter genes. In vitro-transcribed capped RNAs generated from these were transfected into HepG2 cells. Negative-strand RNA was detected, indicating the occurrence of replication. The replicon containing an in-frame fusion of HEV ORF2 with enhanced green fluorescent protein (EGFP) was positive for fluorescence, whereas no signal was observed when the replicase domain was deleted. An HEV ORF3-EGFP in-frame fusion did not yield fluorescence. Deletions introduced into ORF2 did not affect the replication competency of the viral RNA. To explore the possibility of using a reporter-gene assay to monitor the synthesis of plus- and minus-strand RNA, the EGFP gene fused to the encephalomyocarditis virus internal ribosome entry site (IRES) was inserted into partially deleted ORF2 of HEV, in both the sense [HEV-IRES-EGFP(+)] and antisense [HEV-IRES-EGFP(-)] orientations. HepG2 cells transfected with HEV-IRES-EGFP(+) and HEV-IRES-EGFP(-) vectors were positive for EGFP fluorescence. To quantify HEV replication, EGFP was replaced with Renilla luciferase (RLuc). HEV-IRES-RLuc(+) showed approximately 10-fold higher luminescence than HEV-IRES-RLuc(-). There was complete loss of activity when the helicase-replicase domain in HEV-IRES-RLuc(-) was deleted. A short-term HepG2 cell line containing the full-length viral genome in the pcDNA3 vector was established. Viral RNA and proteins (RdRp, pORF2 and pORF3) could be detected in the geneticin-resistant cells, even after the seventh passage. In the absence of a reliable cell-culture system to study HEV biology, these reporter replicons, as well as the cell line, bestow immense utility.

  11. 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.

  12. 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.

  13. An electro-osmotic instability in biological cells

    NASA Astrophysics Data System (ADS)

    Leonetti, M.; Dubois-Violette, E.

    1997-01-01

    The development of ionic currents during the growth of biological cells contributes to the generation of spatial order. A new instability is proposed to describe such phenomenon. The mechanism triggering the instability is based on electro-osmosis flow which generates aggregation of channels or pumps. The onset of unstable modes and the dispersion relation are determined and a comparison with a biological cell is provided.

  14. The subcritical baroclinic instability in local accretion disc models

    NASA Astrophysics Data System (ADS)

    Lesur, G.; Papaloizou, J. C. B.

    2010-04-01

    Context. The presence of vortices in accretion discs has been debated for more than a decade. Baroclinic instabilities might be a way to generate these vortices in the presence of a radial entropy gradient. However, the nature of these instabilities is still unclear and 3D parametric instabilities can lead to the rapid destruction of these vortices. Aims: We present new results exhibiting a subcritical baroclinic instability (SBI) in local shearing box models. We describe the 2D and 3D behaviour of this instability using numerical simulations and we present a simple analytical model describing the underlying physical process. Methods: We investigate the SBI in local shearing boxes, using either the incompressible Boussinesq approximation or a fully compressible model. We explore the parameter space varying several local dimensionless parameters and we isolate the regime relevant for the SBI. 3D shearing boxes are also investigated using high resolution spectral methods to resolve both the SBI and 3D parametric instabilities. Results: A subcritical baroclinic instability is observed in flows stable for the Solberg-Hoïland criterion using local simulations. This instability is found to be a nonlinear (or subcritical) instability, which cannot be described by ordinary linear approaches. It requires a radial entropy gradient weakly unstable for the Schwartzchild criterion and a strong thermal diffusivity (or equivalently a short cooling time). In compressible simulations, the instability produces density waves which transport angular momentum outward with typically α ⪉ 3 × 10-3, the exact value depending on the background temperature profile. Finally, the instability survives in 3D, vortex cores becoming turbulent due to parametric instabilities. Conclusions: The subcritical baroclinic instability is a robust phenomenon, which can be captured using local simulations. The instability survives in 3D thanks to a balance between the 2D SBI and 3D parametric

  15. Consistency and stability of recombinant fermentations.

    PubMed

    Wiebe, M E; Builder, S E

    1994-01-01

    Production of proteins of consistent quality in heterologous, genetically-engineered expression systems is dependent upon identifying the manufacturing process parameters which have an impact on product structure, function, or purity, validating acceptable ranges for these variables, and performing the manufacturing process as specified. One of the factors which may affect product consistency is genetic instability of the primary product sequence, as well as instability of genes which code for proteins responsible for post-translational modification of the product. Approaches have been developed for mammalian expression systems to assure that product quality is not changing through mechanisms of genetic instability. Sensitive protein analytical methods, particularly peptide mapping, are used to evaluate product structure directly, and are more sensitive in detecting genetic instability than is direct genetic analysis by nucleotide sequencing of the recombinant gene or mRNA. These methods are being employed to demonstrate that the manufacturing process consistently yields a product of defined structure from cells cultured through the range of cell ages used in the manufacturing process and well beyond the maximum cell age defined for the process. The combination of well designed validation studies which demonstrate consistent product quality as a function of cell age, and rigorous quality control of every product lot by sensitive protein analytical methods provide the necessary assurance that product structure is not being altered through mechanisms of mutation and selection.

  16. Targets for, and consequences of, radiation-induced chromosomal instability

    NASA Astrophysics Data System (ADS)

    Kaplan, Mark Isaac

    Chromosomal instability has been demonstrated in a human- hamster hybrid cell line, GM10115, 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. Labeling cells with 125I-iododeoxyuridine, which caused radiation damage to the DNA and associated nuclear structures, did induce 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. Incorporation of an 125I-labeled protein, 125I-succinyl- concanavalin A, into either the plasma membrane or the cytoplasm, failed to elicit chromosomal instability. These results show that radiation damage to the nucleus, and not to extranuclear regions, contributes to the induction of chromosomal instability. To determine the role of DNA strand breaks as a molecular lesion responsible for initiating chromosomal instability, cells were treated with a variety of DNA strand breaking agents. Agents capable of producing complex DNA double strand breaks, including X-rays, Neocarzinostatin and bleomycin, were able to induce chromosomal instability. In contrast, double strand breaks produced by restriction endonucleases as well as DNA strand breaks produced by hydrogen peroxide failed to induce chromosomal instability. This demonstrates that the type of DNA breakage is important in the eventual manifestation of chromosomal instability. In order to understand the relationship between chromosomal instability and other end points of genomic instability, chromosomally stable and unstable clones were analyzed for sister chromatid exchange, delayed reproductive cell death, delayed mutation, mismatch repair and delayed gene amplification

  17. 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

  18. Capillary instability of jets

    NASA Astrophysics Data System (ADS)

    Chauhan, Anuj

    This thesis studies the capillary instability of a compound jet. A compound jet comprises an inner core of a primary fluid surrounded by an annulus of an immiscible secondary fluid. The compound jet is unstable due to capillarity. A compound jet finds applications in a variety of fields, such as, ink jet printing, particle sorting, extrusion, molding, particle production etc. In some of these applications such as molding, the disturbances that could cause the jet breakup start as periodic spatial disturbances of Fourier wave number k and grow in time. This is the temporal instability. In some other applications, such as, ink-jet printing, the disturbances initiate at the edge of the nozzle from which the jet issues out. These disturbances grow in space. This is the spatial instability. At small velocities, even if the initial disturbances are periodic in time, they grow exponentially in time. This is the absolute instability. We perform the temporal, spatial and the absolute stability analysis of an inviscid compound jet in a unified framework using the theory of transforms. Further, we solve the temporal instability problem for a viscous jet to understand the effect of viscosity on breakup dynamics. In the temporal analysis, we show that each interface of the compound jet contributes one mode to the instability. The modes contributed by the inner and outer interfaces grow for waves longer than the inner and the outer circumference of the undisturbed jet, respectively. The inner interface mode has a higher growth rate and hence dominates the breakup. The two interfaces grow exactly in phase in this mode and hence it is refereed to as the stretching mode. The other mode is the squeezing mode because the two interfaces grow exactly out of phase. The same two modes are also present in the spatial analysis. At high Weber numbers the predictions of the spatial theory reduce to those of the temporal theory because the waves simply convect with the jet velocity and there

  19. 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.

  20. Active Suppression of Instabilities in Engine Combustors

    NASA Technical Reports Server (NTRS)

    Kopasakis, George

    2004-01-01

    A method of feedback control has been proposed as a means of suppressing thermo-acoustic instabilities in a liquid- fueled combustor of a type used in an aircraft engine. The basic principle of the method is one of (1) sensing combustor pressure oscillations associated with instabilities and (2) modulating the rate of flow of fuel to the combustor with a control phase that is chosen adaptively so that the pressure oscillations caused by the modulation oppose the sensed pressure oscillations. The need for this method arises because of the planned introduction of advanced, lean-burning aircraft gas turbine engines, which promise to operate with higher efficiencies and to emit smaller quantities of nitrogen oxides, relative to those of present aircraft engines. Unfortunately, the advanced engines are more susceptible to thermoacoustic instabilities. These instabilities are hard to control because they include large dead-time phase shifts, wide-band noise characterized by amplitudes that are large relative to those of the instabilities, exponential growth of the instabilities, random net phase walks, and amplitude fluctuations. In this method (see figure), the output of a combustion-pressure sensor would be wide-band-pass filtered and then further processed to generate a control signal that would be applied to a fast-actuation valve to modulate the flow of fuel. Initially, the controller would rapidly take large phase steps in order to home in, within a fraction of a second, to a favorable phase region within which the instability would be reduced. Then the controller would restrict itself to operate within this phase region and would further restrict itself to operate within a region of stability, as long as the power in the instability signal was decreasing. In the phase-shifting scheme of this method, the phase of the control vector would be made to continuously bounce back and forth from one boundary of an effective stability region to the other. Computationally

  1. Instabilities in coaxial rotating jets

    NASA Astrophysics Data System (ADS)

    Ivanic, Tanja; Foucault, Eric; Pecheux, Jean; Gilard, Virginie

    2000-12-01

    The aim of this study is the characterization of the cylindrical mixing layer resulting from the interaction of two coaxial swirling jets. The experimental part of this study was performed in a cylindrical water tunnel, permitting an independent rotation of two coaxial jets. The rotations are generated by means of 2×36 blades localized in two swirling chambers. As expected, the evolution of the main instability modes presents certain differences compared to the plane-mixing-layer case. Experimental results obtained by tomography showed the existence of vortex rings and streamwise vortex pairs in the near field region. This method also permitted the observation of the evolution and interaction of different modes. PIV velocity measurements realized in the meridian plans and the plans perpendicular to the jet axis show that rotation distorts the typical top-hat axial velocity profile. The transition of the axial velocity profile from jet-like into wake-like is also observed.

  2. 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.

  3. 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. PMID:23276922

  4. 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.

  5. Instability of Magnetized Ionization Fronts Surrounding H II Regions

    NASA Astrophysics Data System (ADS)

    Kim, Jeong-Gyu; Kim, Woong-Tae

    2014-12-01

    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}_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/(2β1) compared to the unmagnetized case, with β1 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 α1/2. 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}_M22 < 2/(2β 1 - 1). When the front experiences an acceleration, the IF instability cooperates with the Rayleigh-Taylor instability to make the front more unstable.

  6. DNA damage tolerance by recombination: Molecular pathways and DNA structures.

    PubMed

    Branzei, Dana; Szakal, Barnabas

    2016-08-01

    Replication perturbations activate DNA damage tolerance (DDT) pathways, which are crucial to promote replication completion and to prevent fork breakage, a leading cause of genome instability. One mode of DDT uses translesion synthesis polymerases, which however can also introduce mutations. The other DDT mode involves recombination-mediated mechanisms, which are generally accurate. DDT occurs prevalently postreplicatively, but in certain situations homologous recombination is needed to restart forks. Fork reversal can function to stabilize stalled forks, but may also promote error-prone outcome when used for fork restart. Recent years have witnessed important advances in our understanding of the mechanisms and DNA structures that mediate recombination-mediated damage-bypass and highlighted principles that regulate DDT pathway choice locally and temporally. In this review we summarize the current knowledge and paradoxes on recombination-mediated DDT pathways and their workings, discuss how the intermediate DNA structures may influence genome integrity, and outline key open questions for future research. PMID:27236213

  7. Mutagenic roles of DNA "repair" proteins in antibody diversity and disease-associated trinucleotide repeat instability.

    PubMed

    Slean, Meghan M; Panigrahi, Gagan B; Ranum, Laura P; Pearson, Christopher E

    2008-07-01

    While DNA repair proteins are generally thought to maintain the integrity of the whole genome by correctly repairing mutagenic DNA intermediates, there are cases where DNA "repair" proteins are involved in causing mutations instead. For instance, somatic hypermutation (SHM) and class switch recombination (CSR) require the contribution of various DNA repair proteins, including UNG, MSH2 and MSH6 to mutate certain regions of immunoglobulin genes in order to generate antibodies of increased antigen affinity and altered effector functions. Another instance where "repair" proteins drive mutations is the instability of gene-specific trinucleotide repeats (TNR), the causative mutations of numerous diseases including Fragile X mental retardation syndrome (FRAXA), Huntington's disease (HD), myotonic dystrophy (DM1) and several spinocerebellar ataxias (SCAs) all of which arise via various modes of pathogenesis. These healthy and deleterious mutations that are induced by repair proteins are distinct from the genome-wide mutations that arise in the absence of repair proteins: they occur at specific loci, are sensitive to cis-elements (sequence context and/or epigenetic marks) and transcription, occur in specific tissues during distinct developmental windows, and are age-dependent. Here we review and compare the mutagenic role of DNA "repair" proteins in the processes of SHM, CSR and TNR instability.

  8. Transverse electron-scale instability in relativistic shear flows.

    PubMed

    Alves, E P; Grismayer, T; Fonseca, R A; Silva, L O

    2015-08-01

    Electron-scale surface waves are shown to be unstable in the transverse plane of a sheared flow in an initially unmagnetized collisionless plasma, not captured by (magneto)hydrodynamics. It is found that these unstable modes have a higher growth rate than the closely related electron-scale Kelvin-Helmholtz instability in relativistic shears. Multidimensional particle-in-cell simulations verify the analytic results and further reveal the emergence of mushroomlike electron density structures in the nonlinear phase of the instability, similar to those observed in the Rayleigh Taylor instability despite the great disparity in scales and different underlying physics. This transverse electron-scale instability may play an important role in relativistic and supersonic sheared flow scenarios, which are stable at the (magneto)hydrodynamic level. Macroscopic (≫c/ωpe) fields are shown to be generated by this microscopic shear instability, which are relevant for particle acceleration, radiation emission, and to seed magnetohydrodynamic processes at long time scales.

  9. Genomic Instability and Cancer

    PubMed Central

    Yao, Yixin; Dai, Wei

    2014-01-01

    Genomic instability is a characteristic of most cancer cells. It is an increased tendency of genome alteration during cell division. Cancer frequently results from damage to multiple genes controlling cell division and tumor suppressors. It is known that genomic integrity is closely monitored by several surveillance mechanisms, DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. A defect in the regulation of any of these mechanisms often results in genomic instability, which predisposes the cell to malignant transformation. Posttranslational modifications of the histone tails are closely associated with regulation of the cell cycle as well as chromatin structure. Nevertheless, DNA methylation status is also related to genomic integrity. We attempt to summarize recent developments in this field and discuss the debate of driving force of tumor initiation and progression. PMID:25541596

  10. A trickle instability

    NASA Astrophysics Data System (ADS)

    Bossa, Benjamin

    2005-11-01

    We address the problem of the free fall of a long, horizontal and narrow liquid layer squeezed in a vertical open Hele-Shaw cell. The layer destabilizes as it falls down, evolving into a series of liquid blobs linked together by thin bridges, which ultimately break, leaving the initially connex fluid layer as a set a disjointed drops. The mechanism of this instability is the onset of a vertical pressure gradient due to the curvature difference of the moving contact line between the advancing interface and the rear interface. This instability, whose growth rate scales with a non-trivial power of the capillary number, amplifies indifferently a broad band of wavenumbers because of the flat shape of its dispersion relation in the thin layer limit. We will finally comment on the nature of the final fragmentation process and drop size distributions.

  11. Sessile Rayleigh drop instability

    NASA Astrophysics Data System (ADS)

    Steen, Paul; Bostwick, Josh

    2012-11-01

    Rayleigh (1879) determined the mode shapes and frequencies of the inviscid motion of a free drop held by surface tension. We study the inviscid motions of a sessile Rayleigh drop - a drop which rests on a planar solid and whose contact-line is free to move. Linear stability analysis gives the modes and frequencies of the droplet motions. In this talk, we focus on the ``walking instability,'' an unstable mode wherein the drop moves across a planar substrate in an inviscid rocking-like motion. The mode shape is non-axisymmetric. Although the experimental literature has hinted at such a mode, this is the first prediction from linear stability analysis, as far as we are aware. The ``walking instability'' of the drop converts energy stored in the liquid shape into the energy of liquid motion - which represents a heretofore unknown pathway of energy conversion of potentially wide significance for a broad range of applications.

  12. 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.}

  13. 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.

  14. 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.

  15. Recombinant baculovirus isolation.

    PubMed

    King, Linda A; Hitchman, Richard; Possee, Robert D

    2007-01-01

    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. Additionally, many systems require a plaque-assay to separate parental and recombinant virus prior to amplification and use of the recombinant virus. 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. 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.

  16. Genetic recombination. [Escherichia coli

    SciTech Connect

    Stahl, F.W.

    1987-02-01

    The molecular pathways of gene recombination are explored and compared in studies of the model organisms, Escherichia coli and phase lambda. In the discussion of data from these studies it seems that recombination varies with the genetic idiosyncrasies of the organism and may also vary within a single organism.

  17. Robust dynamic mitigation of instabilities

    NASA Astrophysics Data System (ADS)

    Kawata, S.; Karino, T.

    2015-04-01

    A dynamic mitigation mechanism for instability growth was proposed and discussed in the paper [S. Kawata, Phys. Plasmas 19, 024503 (2012)]. In the present paper, the robustness of the dynamic instability mitigation mechanism is discussed further. The results presented here show that the mechanism of the dynamic instability mitigation is rather robust against changes in the phase, the amplitude, and the wavelength of the wobbling perturbation applied. Generally, instability would emerge from the perturbation of the physical quantity. Normally, the perturbation phase is unknown so that the instability growth rate is discussed. However, if the perturbation phase is known, the instability growth can be controlled by a superposition of perturbations imposed actively: If the perturbation is induced by, for example, a driving beam axis oscillation or wobbling, the perturbation phase could be controlled, and the instability growth is mitigated by the superposition of the growing perturbations.

  18. Robust dynamic mitigation of instabilities

    SciTech Connect

    Kawata, S.; Karino, T.

    2015-04-15

    A dynamic mitigation mechanism for instability growth was proposed and discussed in the paper [S. Kawata, Phys. Plasmas 19, 024503 (2012)]. In the present paper, the robustness of the dynamic instability mitigation mechanism is discussed further. The results presented here show that the mechanism of the dynamic instability mitigation is rather robust against changes in the phase, the amplitude, and the wavelength of the wobbling perturbation applied. Generally, instability would emerge from the perturbation of the physical quantity. Normally, the perturbation phase is unknown so that the instability growth rate is discussed. However, if the perturbation phase is known, the instability growth can be controlled by a superposition of perturbations imposed actively: If the perturbation is induced by, for example, a driving beam axis oscillation or wobbling, the perturbation phase could be controlled, and the instability growth is mitigated by the superposition of the growing perturbations.

  19. Instabilities of twisted strings

    NASA Astrophysics Data System (ADS)

    Forgács, Péter; Lukács, Árpád

    2009-12-01

    A linear stability analysis of twisted flux-tubes (strings) in an SU(2) semilocal theory — an Abelian-Higgs model with two charged scalar fields with a global SU(2) symmetry — is carried out. Here the twist refers to a relative phase between the two complex scalars (with linear dependence on, say, the z coordinate), and importantly it leads to a global current flowing along the the string. Such twisted strings bifurcate with the Abrikosov-Nielsen-Olesen (ANO) solution embedded in the semilocal theory. Our numerical investigations of the small fluctuation spectrum confirm previous results that twisted strings exhibit instabilities whose amplitudes grow exponentially in time. More precisely twisted strings with a single magnetic flux quantum admit a continuous family of unstable eigenmodes with harmonic z dependence, indexed by a wavenumber kin[-km, km]. Carrying out a perturbative semi-analytic analysis of the bifurcation, it is found that the purely numerical results are very well reproduced. This way one obtains not only a good qualitative description of the twisted solutions themselves as well as of their instabilities, but also a quantitative description of the numerical results. Our semi-analytic results indicate that in close analogy to the known instability of the embedded ANO vortex a twisted string is also likely to expand in size caused by the spreading out of its magnetic flux.

  20. 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.

  1. Instabilities and constitutive modelling.

    PubMed

    Wilson, Helen J

    2006-12-15

    The plastics industry today sees huge wastage through product defects caused by unstable flows during the manufacturing process. In addition, many production lines are throughput-limited by a flow speed threshold above which the process becomes unstable. Therefore, it is critically important to understand the mechanisms behind these instabilities. In order to investigate the flow of a molten plastic, the first step is a model of the liquid itself, a relation between its current stress and its flow history called a constitutive relation. These are derived in many ways and tested on several benchmark flows, but rarely is the stability of the model used as a criterion for selection. The relationship between the constitutive model and the stability properties of even simple flows is not yet well understood. We show that in one case a small change to the model, which does not affect the steady flow behaviour, entirely removes a known instability. In another, a change that makes a qualitative difference to the steady flow makes only tiny changes to the stability.The long-term vision of this research is to exactly quantify what are the important properties of a constitutive relation as far as stability is concerned. If we could understand that, not only could very simple stability experiments be used to choose the best constitutive models for a particular material, but our ability to predict and avoid wasteful industrial instabilities would also be vastly improved.

  2. Carpal instability nondissociative.

    PubMed

    Wolfe, Scott W; Garcia-Elias, Marc; Kitay, Alison

    2012-09-01

    Carpal instability nondissociative (CIND) represents a spectrum of conditions characterized by kinematic dysfunction of the proximal carpal row, often associated with a clinical "clunk." CIND is manifested at the midcarpal and/or radiocarpal joints, and it is distinguished from carpal instability dissociative (CID) by the lack of disruption between bones within the same carpal row. There are four major subcategories of CIND: palmar, dorsal, combined, and adaptive. In palmar CIND, instability occurs across the entire proximal carpal row. When nonsurgical management fails, surgical options include arthroscopic thermal capsulorrhaphy, soft-tissue reconstruction, or limited radiocarpal or intercarpal fusions. In dorsal CIND, the capitate subluxates dorsally from its reduced resting position. Dorsal CIND usually responds to nonsurgical management; refractory cases respond to palmar ligament reefing and/or dorsal intercarpal capsulodesis. Combined CIND demonstrates signs of both palmar and dorsal CIND and can be treated with soft-tissue or bony procedures. In adaptive CIND, the volar carpal ligaments are slackened and are less capable of inducing the physiologic shift of the proximal carpal row from flexion into extension as the wrist ulnarly deviates. Treatment of choice is a corrective osteotomy to restore the normal volar tilt of the distal radius.

  3. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  4. 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.

  5. Modulational instability in optical-microwave interaction

    NASA Astrophysics Data System (ADS)

    Bubke, K.; Hutchings, D. C.; Peschel, U.; Lederer, F.

    2002-09-01

    The stability of continuous optical and microwave fields is studied in the presence of dispersion and second order nonlinearity. The cascade combination of optical rectification and the electro-optic effect induces modulational instability (MI) in a wide range of system parameters. It is demonstrated that MI can lead potentially to filamentation of high power optical pulses as well as the generation of terahertz radiation.

  6. 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.

  7. Resonant instability of supersonic shear layers

    NASA Technical Reports Server (NTRS)

    Tam, C. K. W.; Lele, S. K.

    1990-01-01

    A computer simulation of possible resonant instability of a supersonic shear layer is carried out. The resonance of two acoustic duct modes of the flow induced by periodic Mach waves generated by a wavy wall is sought. Results of the simulations are reported. Simulations are unable to document a resonant instability and the mixing characteristics remain unchanged. Possible weakness of the present simulations are discussed. A second set of simulations involving a mixing layer separating a supersonic and a subsonic stream were performed. A wavy wall placed adjacent to the supersonic stream to produce a set of periodic Mach waves terminating at the shear layer is modelled. The entire flow field is similar to that of an imperfectly expanded supersonic jet discharging into a subsonic coflowing stream for which enhanced mixing due to the onset of screech (feedback instability) is known to occur. The purpose of these simulations is to see if enhanced mixing and feedback instability would, indeed, take place. Some evidence of feedback oscillations is found in the simulated flow.

  8. 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.

  9. Patents in therapeutic recombinant protein production using mammalian cells.

    PubMed

    Picanco-Castro, Virginia; de Freitas, Marcela Cristina Correa; Bomfim, Aline de Sousa; de Sousa Russo, Elisa Maria

    2014-01-01

    The industrial production of recombinant proteins preferentially requires the generation of stable cell lines expressing proteins in a quick, relatively facile, and a reproducible manner. Different methods are used to insert exogenous DNA into the host cell, and choosing the appropriate producing cell is of paramount importance for the efficient production and quality of the recombinant protein. This review addresses the advances in recombinant protein production in mammalian cell lines, according to key patents from the last 30 years.

  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. Crossing over is rarely associated with mitotic intragenic recombination in Schizosaccharomyces pombe.

    PubMed Central

    Virgin, J B; Bailey, J P; Hasteh, F; Neville, J; Cole, A; Tromp, G

    2001-01-01

    Chromosomal rearrangements can result from crossing over during ectopic homologous recombination between dispersed repetitive DNA. We have previously shown that meiotic ectopic recombination between artificially dispersed ade6 heteroalleles in the fission yeast Schizosaccharomyces pombe frequently results in chromosomal rearrangements. The same recombination substrates have been studied in mitotic recombination. Ectopic recombination rates in haploids were approximately 1-4 x 10(-6) recombinants per cell generation, similar to allelic recombination rates in diploids. In contrast, ectopic recombination rates in heterozygous diploids were 2.5-70 times lower than allelic recombination or ectopic recombination in haploids. These results suggest that diploid-specific factors inhibit ectopic recombination. Very few crossovers occurred in ade6 mitotic recombination, either allelic or ectopic. Allelic intragenic recombination was associated with 2% crossing over, and ectopic recombination between multiple different pairing partners showed 1-7% crossing over. These results contrast sharply with the 35-65% crossovers associated with meiotic ade6 recombination and suggest either differential control of resolution of recombination intermediates or alternative pathways of recombination in mitosis and meiosis. PMID:11139492

  12. [Oncovirus-induced permanent genetic instability in Drosophila melanogaster].

    PubMed

    Mit', N V; Dzhansugurova, L B; Bersimbaev, R I

    2000-08-01

    Mutant alleles of a system of genetic instability induced by oncoviral DNAs were shown to demonstrate an unstable manifestation 500 generations after their emergence. A cytogenetic analysis of oncovirus-induced unstable lines has revealed numerous chromosome rearrangements. For the Lobe alleles of this system, a specific chromosome rearrangement, Df(2L) = 35C-36B, was found on the left arm of chromosome 2. We used recessive lethal mutations involving DNA rearrangements in a successful construction of cross systems for "explosive" instability.

  13. Recombination and Replication

    PubMed Central

    Syeda, Aisha H.; Hawkins, Michelle; McGlynn, Peter

    2014-01-01

    The links between recombination and replication have been appreciated for decades and it is now generally accepted that these two fundamental aspects of DNA metabolism are inseparable: Homologous recombination is essential for completion of DNA replication and vice versa. This review focuses on the roles that recombination enzymes play in underpinning genome duplication, aiding replication fork movement in the face of the many replisome barriers that challenge genome stability. These links have many conserved features across all domains of life, reflecting the conserved nature of the substrate for these reactions, DNA. PMID:25341919

  14. Recombination Pattern Reanalysis of Some HIV-1 Circulating Recombination Forms Suggest the Necessity and Difficulty of Revision

    PubMed Central

    Jia, Lei; Li, Lin; Li, Hanping; Liu, Siyang; Wang, Xiaolin; Bao, Zuoyi; Li, Tianyi; Zhuang, Daomin; Liu, Yongjian; Li, Jingyun

    2014-01-01

    Background Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. Methods Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. Results The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. Conclusion Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also

  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. The cosmic Doppler instability

    NASA Technical Reports Server (NTRS)

    Hogan, Craig J.

    1993-01-01

    The equations governing the behavior of perturbations of a mixture of nearly homogeneous and isotropic matter and radiation are derived, using a diffusion approximation where spatial perturbations in the radiation spectrum are allowed to vary with frequency. A simple model of line opacity leads to dispersion relations which display a new bulk instability. The model is used to derive an approximate dispersion relation for radiation interacting via resonance scattering opacity in atomic hydrogen at low density and low temperature. Possible applications to cosmology are briefly discussed.

  17. Gas turbine combustion instability

    SciTech Connect

    Richards, G.A.; Lee, G.T.

    1996-09-01

    Combustion oscillations are a common problem in development of LPM (lean premix) combustors. Unlike earlier, diffusion style combustors, LPM combustors are especially susceptible to oscillations because acoustic losses are smaller and operation near lean blowoff produces a greater combustion response to disturbances in reactant supply, mixing, etc. In ongoing tests at METC, five instability mechanisms have been identified in subscale and commercial scale nozzle tests. Changes to fuel nozzle geometry showed that it is possible to stabilize combustion by altering the timing of the feedback between acoustic waves and the variation in heat release.

  18. Chemically Driven Hydrodynamic Instabilities

    NASA Astrophysics Data System (ADS)

    Almarcha, C.; Trevelyan, P. M. J.; Grosfils, P.; de Wit, A.

    2010-01-01

    In the gravity field, density changes triggered by a kinetic scheme as simple as A+B→C can induce or affect buoyancy-driven instabilities at a horizontal interface between two solutions containing initially the scalars A and B. On the basis of a general reaction-diffusion-convection model, we analyze to what extent the reaction can destabilize otherwise buoyantly stable density stratifications. We furthermore show that, even if the underlying nonreactive system is buoyantly unstable, the reaction breaks the symmetry of the developing patterns. This is demonstrated both numerically and experimentally on the specific example of a simple acid-base neutralization reaction.

  19. Booming Dune Instability

    NASA Astrophysics Data System (ADS)

    Andreotti, B.; Bonneau, L.

    2009-12-01

    Sand avalanches flowing down the leeward face of some desert dunes spontaneously produce a loud sound with a characteristic vibrato around a well-defined frequency, a phenomenon called the “song of dunes.” Here, we show through theory that a homogenous granular surface flow is linearly unstable towards growing elastic waves when a localized shear band forms at the interface between the avalanche and the static part of the dune. We unravel the nature of the acoustic amplifying mechanism at the origin of this booming instability. The dispersion relation and the shape of the most unstable modes are computed and compared to field measurements.

  20. Booming dune instability.

    PubMed

    Andreotti, B; Bonneau, L

    2009-12-01

    Sand avalanches flowing down the leeward face of some desert dunes spontaneously produce a loud sound with a characteristic vibrato around a well-defined frequency, a phenomenon called the "song of dunes." Here, we show through theory that a homogenous granular surface flow is linearly unstable towards growing elastic waves when a localized shear band forms at the interface between the avalanche and the static part of the dune. We unravel the nature of the acoustic amplifying mechanism at the origin of this booming instability. The dispersion relation and the shape of the most unstable modes are computed and compared to field measurements. PMID:20366176

  1. 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.

  2. 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

  3. Shilnikov instabilities in laser systems

    SciTech Connect

    Swetits, J.J.; Buoncristiani, A.M.

    1988-11-15

    Experiments on a CO/sub 2/ laser with feedback (F. T. Arecchi, R. Meucci, and W. Gadomski, Phys. Rev. Lett. 58, 2205 (1987)) displayed an extraordinary set of instabilities, identified as Shilnikov chaos. We have investigated the stability structure of a theoretical model developed to describe this laser system and carried out an extensive numerical search for the Shilnikov instability. No computational evidence to support the claim of a Shilnikov instability for model parameters corresponding to the experimental region can be found.

  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. 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.

  6. Activated recombinant adenovirus proteinases

    SciTech Connect

    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.

  7. 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.

  8. Recombinant expression of the precursor of the hemorrhagic metalloproteinase HF3 and its non-catalytic domains using a cell-free synthesis system.

    PubMed

    Menezes, Milene C; Imbert, Lionel; Kitano, Eduardo S; Vernet, Thierry; Serrano, Solange M T

    2016-09-01

    Snake venom metalloproteinases (SVMPs) participate in snakebite pathology such as hemorrhage, inflammation, and necrosis. They are synthesized as latent multi-domain precursors whose processing generates either catalytically active enzymes or free non-enzymatic domains. Recombinant expression of the precursor of P-III class SVMPs has failed due to the instability of the multi-domain polypeptide structure. Conversely, functional recombinant non-catalytic domains were obtained by prokaryotic expression systems. Here, we show for the first time the recombinant expression of the precursor of HF3, a highly hemorrhagic SVMP from Bothrops jararaca, and its non-catalytic domains, using an E. coli-based cell-free synthesis system. The precursor of HF3, composed of pro-, metalloproteinase-, disintegrin-like-, and cysteine-rich domains, and containing 38 Cys residues, was successfully expressed and purified. A protein composed of the disintegrin-like and cysteine-rich domains (DC protein) and the cysteine-rich domain alone (C protein) were expressed in vitro individually and purified. Both proteins were shown to be functional in assays monitoring the interaction with matrix proteins and in modulating the cleavage of fibrinogen by HF3. These data indicate that recombinant expression using prokaryotic-based cell-free synthesis emerges as an attractive alternative for the study of the structure and function of multi-domain proteins with a high content of Cys residues. PMID:27209197

  9. Trypanosoma brucei BRCA2 acts in antigenic variation and has undergone a recent expansion in BRC repeat number that is important during homologous recombination.

    PubMed

    Hartley, Claire L; McCulloch, Richard

    2008-06-01

    Antigenic variation in Trypanosoma brucei has selected for the evolution of a massive archive of silent Variant Surface Glycoprotein (VSG) genes, which are activated by recombination into specialized expression sites. Such VSG switching can occur at rates substantially higher than background mutation and is dependent on homologous recombination, a core DNA repair reaction. A key regulator of homologous recombination is BRCA2, a protein that binds RAD51, the enzyme responsible for DNA strand exchange. Here, we show that T. brucei BRCA2 has undergone a recent, striking expansion in the number of BRC repeats, a sequence element that mediates interaction with RAD51. T. brucei BRCA2 mutants are shown to be significantly impaired in antigenic variation and display genome instability. By generating BRCA2 variants with reduced BRC repeat numbers, we show that the BRC expansion is crucial in determining the efficiency of T. brucei homologous recombination and RAD51 localization. Remarkably, however, this appears not to be a major determinant of the activation of at least some VSG genes.

  10. Turbulence and instabilities

    NASA Astrophysics Data System (ADS)

    Belotserkovskii, Oleg

    2001-06-01

    The main principles for constructing of mathematical models for fully developed free shear turbulence and hydrodynamic instabilities are considered in the report. Such a “rational” modeling is applied for a variety of unsteady multidimensional problems. For the wide class of phenomena, by the large Reynolds numbers within the low-frequency and inertial intervals of turbulent motion, the effect of molecular viscosity and of the small elements of flow in the largest part of perturbation domain are not practically essential neither for the general characteristics of macroscopic structures of the flow developed, nor the flow pattern as a whole. This makes it possible not to take into consideration the effects of molecular viscosity when studying the dynamics of large vortices, and to implement the study of those on the basis of models of the ideal gas (using the methods of “rational” averaging, but without application of semi-empirical models of turbulence). Among the problems, which have been studied by such a way, there are those of the jet-type flow in the wake behind the body, the motions of ship frames with stern shearing, the formation of anterior stalling zones by the flow about blunted bodies with jets or needles directed to meet the flow, etc. As applications the problems of instability development and of spreading of smoke cloud from large-scale source of the fire are considered.

  11. [Aspirin suppresses microsatellite instability].

    PubMed

    Wallinger, S; Dietmaier, W; Beyser, K; Bocker, T; Hofstädter, F; Fishel, R; Rüschoff, J

    1999-01-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) exhibit cancer preventive effects and have been shown to induce regression of adenomas in FAP patients. In order to elucidate the probable underlying mechanism, the effect of NSAIDs on mismatch repair related microsatellite instability was investigated. Six colorectal cancer cell lines all but one deficient for human mismatch repair (MMR) genes were examined for microsatellite instability (MSI) prior and after treatment with Aspirin or Sulindac. For rapid in vitro analysis of MSI a microcloning assay was developed by combining Laser microdissection and random (PEP-) PCR prior to specific MSI-PCR. Effects of NSAIDs on cell cycle and apoptosis were systematically investigated by using flow cytometry and cell-sorting. MSI frequency in cells deficient of MMR genes (hMSH2, hMLH1, hMSH6) was markedly reduced after long-term (> 10 weeks) NSAID treatment. This effect was reversible, time- and concentration dependent. However, in the hPMS2 deficient endometrial cancer cell line (HEC-1-A) the MSI phenotype kept unchanged. According to cell sorting, non-apoptotic cells were stable and apoptotic cells were unstable. These results suggest that aspirin/sulindac induces a genetic selection for microsatellite stability in a subset of MMR-deficient cells and may thus provide an effective prophylactic therapy for HNPCC related colorectal carcinomas.

  12. Evidence of structural genomic region recombination in Hepatitis C virus

    PubMed Central

    Cristina, Juan; Colina, Rodney

    2006-01-01

    Background/Aim Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there have been few studies reporting recombination on natural populations of HCV. Recombination break-points have been identified in non structural proteins of the HCV genome. Given the implications that recombination has for RNA virus evolution, it is clearly important to determine the extent to which recombination plays a role in HCV evolution. In order to gain insight into these matters, we have performed a phylogenetic analysis of 89 full-length HCV strains from all types and sub-types, isolated all over the world, in order to detect possible recombination events. Method Putative recombinant sequences were identified with the use of SimPlot program. Recombination events were confirmed by bootscaning, using putative recombinant sequence as a query. Results Two crossing over events were identified in the E1/E2 structural region of an intra-typic (1a/1c) recombinant strain. Conclusion Only one of 89 full-length strains studied resulted to be a recombinant HCV strain, revealing that homologous recombination does not play an extensive roll in HCV evolution. Nevertheless, this mechanism can not be denied as a source for generating genetic diversity in natural populations of HCV, since a new intra-typic recombinant strain was found. Moreover, the recombination break-points were found in the structural region of the HCV genome. PMID:16813646

  13. PEP-X IMPEDANCE AND INSTABILITY CALCULATIONS

    SciTech Connect

    Bane, K.L.F.; Lee, L.-Q.; Ng, C.; Stupakov, G.; au Wang, L.; Xiao, L.; /SLAC

    2010-08-25

    PEP-X, a next generation, ring-based light source is designed to run with beams of high current and low emittance. Important parameters are: energy 4.5 GeV, circumference 2.2 km, beam current 1.5 A, and horizontal and vertical emittances, 185 pm by 8 pm. In such a machine it is important that impedance driven instabilities not degrade the beam quality. In this report they study the strength of the impedance and its effects in PEP-X. For the present, lacking a detailed knowledge of the vacuum chamber shape, they create a straw man design comprising important vacuum chamber objects to be found in the ring, for which they then compute the wake functions. From the wake functions they generate an impedance budget and a pseudo-Green function wake representing the entire ring, which they, in turn, use for performing microwave instability calculations. In this report they, in addition, consider in PEP-X the transverse mode-coupling, multi-bunch transverse, and beam-ion instabilities.

  14. BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks

    PubMed Central

    Willis, Nicholas A.; Chandramouly, Gurushankar; Huang, Bin; Kwok, Amy; Follonier, Cindy; Deng, Chuxia; Scully, Ralph

    2014-01-01

    Replication fork stalling can promote genomic instability, predisposing to cancer and other diseases1–3. Stalled replication forks may be processed by sister chromatid recombination (SCR), generating error-free or error-prone homologous recombination (HR) outcomes4–8. In mammalian cells, a long-standing hypothesis proposes that the major hereditary breast/ovarian cancer predisposition gene products, BRCA1 and BRCA2, control HR/SCR at stalled replication forks9. Although BRCA1 and BRCA2 affect replication fork processing10–12, direct evidence that BRCA genes regulate HR at stalled chromosomal replication forks is lacking due to a dearth of tools for studying this process. We report that the Escherichia coli Tus/Ter complex13–16 can be engineered to induce site-specific replication fork stalling and chromosomal HR/SCR in mammalian cells. Tus/Ter-induced HR entails processing of bidirectionally arrested forks. We find that the BRCA1 C-terminal tandem BRCT repeat and regions of BRCA1 encoded by exon 11—two BRCA1 elements implicated in tumor suppression—control Tus/Ter-induced HR. Inactivation of either BRCA1 or BRCA2 increases the absolute frequency of “long-tract” gene conversions at Tus/Ter-stalled forks—an outcome not observed in response to a restriction endonuclease-mediated chromosomal double strand break (DSB). Therefore, HR at stalled forks is regulated differently from HR at DSBs arising independently of a fork. We propose that aberrant long-tract HR at stalled replication forks contributes to genomic instability and breast/ovarian cancer predisposition in BRCA mutant cells. PMID:24776801

  15. 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.

  16. 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

  17. Relativistic electromagnetic ion cyclotron instabilities.

    PubMed

    Chen, K R; Huang, R D; Wang, J C; Chen, Y Y

    2005-03-01

    The relativistic instabilities of electromagnetic ion cyclotron waves driven by MeV ions are analytically and numerically studied. As caused by wave magnetic field and in sharp contrast to the electrostatic case, interesting characteristics such as Alfve nic behavior and instability transition are discovered and illuminated in detail. The instabilities are reactive and are raised from the coupling of slow ions' first-order resonance and fast ions' second-order resonance, that is an essential extra mechanism due to relativistic effect. Because of the wave magnetic field, the nonresonant plasma dielectric is usually negative and large, that affects the instability conditions and scaling laws. A negative harmonic cyclotron frequency mismatch between the fast and slow ions is required for driving a cubic (and a coupled quadratic) instability; the cubic (square) root scaling of the peak growth rate makes the relativistic effect more important than classical mechanism, especially for low fast ion density and Lorentz factor being close to unity. For the cubic instability, there is a threshold (ceiling) on the slow ion temperature and density (the external magnetic field and the fast ion energy); the Alfve n velocity is required to be low. This Alfve nic behavior is interesting in physics and important for its applications. The case of fast protons in thermal deuterons is numerically studied and compared with the analytical results. When the slow ion temperature or density (the external magnetic field or the fast ion energy) is increased (reduced) to about twice (half) the threshold (ceiling), the same growth rate peak transits from the cubic instability to the coupled quadratic instability and a different cubic instability branch appears. The instability transition is an interesting new phenomenon for instability. PMID:15903591

  18. Feedback control of coupled-bunch instabilities

    SciTech Connect

    Fox, J.D.; Eisen, N.; Hindi, H.; Linscott, I.; Oxoby, G.; Sapozhnikov, L.; Serio, M.

    1993-05-01

    The next generation of synchrotron light sources and particle accelerators will require active feedback systems to control multi-bunch instabilities. Stabilizing hundreds or thousands of potentially unstable modes in these accelerator designs presents many technical challenges. Feedback systems to stabilize coupled-bunch instabilities may be understood in the frequency domain (mode-based feedback) or in the time domain (bunch-by-bunch feedback). In both approaches an external amplifier system is used to create damping fields that prevent coupled-bunch oscillations from growing without bound. The system requirements for transverse (betatron) and longitudinal (synchrotron) feedback are presented, and possible implementation options developed. Feedback system designs based on digital signal-processing techniques are described. Experimental results are shown from a synchrotron oscillation damper in the SSRL/SLAC storage ring SPEAR that uses digital signal-processing techniques.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Elastic instabilities in planar elongational flow of monodisperse polymer solutions.

    PubMed

    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

  4. Episodic Instabilities of Thick Continental Lithosphere (Invited)

    NASA Astrophysics Data System (ADS)

    Jaupart, C. P.; Fourel, L.; Farnetani, C. G.

    2009-12-01

    Although continental interiors are commonly described as stable, many have been subjected to major perturbations. The North American continent, for example, saw the formation or reactivation of four intracratonic basins (Williston, Hudson Bay, Illinois and Michigan) in the Paleozoic about 500 million years ago. These events occurred far from ocean basins and are not related to other tectonic events, and hence have usually been explained as late consequences of earlier orogenies or of mantle plumes impinging the base of the lithosphere. Why and how subsidence affected four neighbouring basins simultaneously in the Paleozoic has not been explained, however. Other important observations are that intracratonic basins and subsidence events tend to recur at the same locations, and that subsidence is rarely preceded by domal uplift. These observations can be explained by the behaviour of thick compositionally buoyant lithosphere that becomes unstable because it is being cooled from above. Laboratory analog experiments, stability theory and numerical simulations in 2-D and 3-D have been conducted to specify the necessary conditions for instability and to illustrate how flow develops and deforms the lithosphere. Numerical solutions accounting for temperature-dependent viscosity show that the compositional viscosity contrast between the lithospheric mantle and the underlying asthenosphere has only a weak effect on flow and deformation. Lithosphere behaviour depends on the Rayleigh number and the buoyancy ratio, which is equal to the ratio of compositional density contrast over the thermal density contrast through the unstable part of the lithosphere. Episodic instabilities are generated at small buoyancy numbers appropriate for geological conditions. Scaling laws for temperature-dependent viscosity fluids will be presented. Little uplift is generated by the instability because the hot upwelling asthenospheric mantle displaces compositionally buoyant colder lithospheric

  5. 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.

  6. 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.

  7. 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.

  8. Cohabitation and Children's Family Instability

    ERIC Educational Resources Information Center

    Kelly Raley, R.; Wildsmith, Elizabeth

    2004-01-01

    This study estimates how much children's family instability is missed when we do not count transitions into and out of cohabitation, and examines early life course trajectories of children to see whether children who experience maternal cohabitation face more family instability than children who do not. Using data from the 1995 National Survey of…

  9. 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

  10. The booming dune instability

    NASA Astrophysics Data System (ADS)

    Andreotti, B.; Bonneau, L.

    2009-12-01

    Sand avalanches flowing down the leeward face of some desert dunes spontaneously produce a loud sound with a characteristic vibrato around a well defined frequency, a phenomenon called the "song of dunes". Here, we show theoretically that an homogenous granular surface flow is linearly unstable towards growing elastic waves when a localized shear band form at the interface between the avalanche and the static part of the dune. We unravel the nature of the acoustic amplifying mechanism at the origin of this booming instability. The dispersion relation and the shape of the most unstable modes are computed and compared to field records performed in the Atlantic Sahara. We finally show that several characteristics predicted by the model and observed in the field allow to dismiss former hypothesis based on resonances or the synchronisation of sand grain collisions.

  11. Inhomogeneity driven by Higgs instability in a gapless superconductor

    SciTech Connect

    Giannakis, Ioannis; Hou Defu; Huang Mei; Ren Haicang

    2007-01-01

    The fluctuations of the Higgs and pseudo Nambu-Goldstone fields in the 2-flavor color superconductivity (2SC) phase with mismatched pairing are described in the nonlinear realization framework of the gauged Nambu-Jona-Lasinio model. In the gapless 2SC phase, not only Nambu-Goldstone currents can be spontaneously generated, but also the Higgs field exhibits instablity. The Nambu-Goldstone currents generation indicates the formation of the single plane wave Larkin-Ovchinnikov-Fulde-Ferrel state and breaks rotation symmetry, while the Higgs instability favors spatial inhomogeneity and breaks translation invariance. In this paper, we focus on the Higgs instability which has not drawn much attention yet. The Higgs instability cannot be removed without a long range force, thus it persists in the gapless superfluidity and induces phase separation. In the case of gapless 2-flavor color superconductivity state, the Higgs instability can only be partially removed by the electric Coulomb energy. However, it is not excluded that the Higgs instability might be completely removed in the charge neutral gapless color-flavor locked phase by the color Coulomb energy.

  12. 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.

  13. 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.

  14. 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

  15. Shear instabilities in a fully compressible polytropic atmosphere

    NASA Astrophysics Data System (ADS)

    Witzke, V.; Silvers, L. J.; Favier, B.

    2015-05-01

    Shear flows have a significant impact on the dynamics in an assortment of different astrophysical objects, including accretion discs and stellar interiors. Investigating shear flow instabilities in a polytropic atmosphere provides a fundamental understanding of the motion in stellar interiors where turbulent motions, mixing processes, and magnetic field generation take place. Here, a linear stability analysis for a fully compressible fluid in a two-dimensional Cartesian geometry is carried out. Our study focuses on determining the critical Richardson number for different Mach numbers and the destabilising effects of high thermal diffusion. We find that there is a deviation in the predicted stability threshold for moderate Mach number flows, along with a significant effect on the growth rate of the linear instability for small Péclet numbers. We show that in addition to a Kelvin-Helmholtz instability, a Holmboe instability can appear, and we discuss the implication of this in stellar interiors.

  16. 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

    2016-01-01

    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

  17. 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

  18. Single-stranded DNA as a recombination substrate in plants as assessed by stable and transient recombination assays.

    PubMed Central

    Bilang, R; Peterhans, A; Bogucki, A; Paszkowski, J

    1992-01-01

    Two separate assays, one that requires stable integration of recombination products and one that does not, were employed to elucidate the role of single-stranded DNA in extrachromosomal homologous recombination in Nicotiana tabacum. Both assays revealed that single-stranded DNA in linear and in circular forms was an efficient substrate for recombination, provided that the cotransformed recombination substrates were of complementary sequence, so that direct annealing was possible. Recombination was inefficient when both single-stranded recombination partners contained homologous regions of identical sequence and generation of a double-stranded DNA was required prior to heteroduplex formation. These results indicate that direct annealing of single strands is an important initial step for intermolecular recombination in tobacco cells. Annealed cotransformed single-stranded molecules yielded intermediates that could be further processed by either continuous or discontinuous second-strand synthesis. The type of intermediate had no influence on the recombination efficiency. Double-stranded circles were unable to recombine efficiently either with each other or with single-stranded DNA. Our results suggest that a helicase activity is involved in the initial steps of double-stranded DNA recombination which unwinds duplex molecules at the site of double-strand breaks. Images PMID:1729608

  19. 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

  20. 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.

  1. Is homologous recombination really an error-free process?

    PubMed Central

    Guirouilh-Barbat, Josée; Lambert, Sarah; Bertrand, Pascale; Lopez, Bernard S.

    2014-01-01

    Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR. First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO) and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here. We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic) or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be “Dr. Jekyll” in maintaining genome stability/variability and “Mr. Hyde” in jeopardizing genome integrity. PMID:24966870

  2. Is homologous recombination really an error-free process?

    PubMed

    Guirouilh-Barbat, Josée; Lambert, Sarah; Bertrand, Pascale; Lopez, Bernard S

    2014-01-01

    Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR. First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO) and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here. We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic) or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be "Dr. Jekyll" in maintaining genome stability/variability and "Mr. Hyde" in jeopardizing genome integrity. PMID:24966870

  3. 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.

  4. Tumor hypoxia as a driving force in genetic instability

    PubMed Central

    2013-01-01

    Sub-regions of hypoxia exist within all tumors and the presence of intratumoral hypoxia has an adverse impact on patient prognosis. Tumor hypoxia can increase metastatic capacity and lead to resistance to chemotherapy and radiotherapy. Hypoxia also leads to altered transcription and translation of a number of DNA damage response and repair genes. This can lead to inhibition of recombination-mediated repair of DNA double-strand breaks. Hypoxia can also increase the rate of mutation. Therefore, tumor cell adaptation to the hypoxic microenvironment can drive genetic instability and malignant progression. In this review, we focus on hypoxia-mediated genetic instability in the context of aberrant DNA damage signaling and DNA repair. Additionally, we discuss potential therapeutic approaches to specifically target repair-deficient hypoxic tumor cells. PMID:24152759

  5. 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.

  6. Meiotic recombination mechanisms.

    PubMed

    Grelon, Mathilde

    2016-01-01

    Meiosis is a specialized cell division at the origin of the haploid cells that eventually develop into the gametes. It therefore lies at the heart of Mendelian heredity. Recombination and redistribution of the homologous chromosomes arising during meiosis constitute an important source of genetic diversity, conferring to meiosis a particularly important place in the evolution and the diversification of the species. Our understanding of the molecular mechanisms governing meiotic recombination has considerably progressed these last decades, benefiting from complementary approaches led on various model species. An overview of these mechanisms will be provided as well as a discussion on the implications of these recent discoveries. PMID:27180110

  7. Temperature anisotropy and beam type whistler instabilities

    NASA Technical Reports Server (NTRS)

    Hashimoto, K.; Matsumoto, H.

    1976-01-01

    Whistler instabilities have been investigated for two different types; i.e., a temperature-anisotropy type instability and a beam-type instability. A comparison between the two types of whistler instabilities is made within the framework of linear theory. A transition from one type to the other is also discussed, which is an extension of the work on electrostatic beam and Landau instabilities performed by O'Neil and Malmberg (1968) for electromagnetic whistler instabilities. It is clarified that the essential source of the whistler instability is not beam kinetic energy but a temperature anisotropy, even for the beam-type whistler instability.

  8. Yet another instability in glasma

    NASA Astrophysics Data System (ADS)

    Tsutsui, Shoichiro; Iida, Hideaki; Kunihiro, Teiji; Ohnishi, Akira

    2014-09-01

    In relativistic heavy ion collisions (HIC), hydrodynamic models can describe many experimental data and suggest that the quark-gluon plasma formed at RHIC and LHC is almost perfect fluid. We need very short thermalization time and far-from-equilibrium dynamics may be important in thermalization processes of HIC. In the earliest stages of HIC, classical gluon dynamics is dominant and many types of instabilities emerge there. These instabilities may strongly affect the later stages of dynamics; realization of chaoticity and field-particle conversions. We investigate instabilities of classical gluon fields under the homogeneous, but time dependent background color magnetic fields. The background field become periodic function of time and we can analyze the stability of fluctuations based on the Floquet theory which consists the basis of the Bloch theory. As a result, we get the complete structure of instability bands for physical degrees of freedom appearing from parametric resonance. We also find that the parametric instabilities considered here have different natures from the several known instabilities; Weibel and Nielsen-Olesen instabilities. We also discuss some implications of parametric resonance to the particle productions in HIC.

  9. 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.

  10. 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

  11. Stable Expression of Lentiviral Antigens by Quality-Controlled Recombinant Mycobacterium bovis BCG Vectors.

    PubMed

    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; Frothingham, Richard

    2015-07-01

    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 10(24)-fold amplification in vitro and following 60 days of growth in mice. A second vaccine lot expressed full-length SIV Gag for >10(68)-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

  12. 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.

  13. Astrophysical Weibel instability in counterstreaming laser-produced plasmas

    NASA Astrophysics Data System (ADS)

    Fox, William; Fiksel, Gennady; Bhattacharjee, Amitava; Change, Po-Yu; Germaschewski, Kai; Hu, Suxing; Nilson, Philip

    2014-06-01

    Astrophysical shock waves play diverse roles, including energizing cosmic rays in the blast waves of astrophysical explosions, and generating primordial magnetic fields during the formation of galaxies and clusters. These shocks are typically collisionless and require collective electromagnetic fields to couple the upstream and downstream plasmas. The Weibel instability has been proposed to provide the requisite interaction mechanism for shock formation in weakly-magnetized shocks by generating turbulent electric and magnetic fields in the shock front. This work presents the first laboratory identification of this Weibel instability between counterstreaming supersonic plasma flows and confirms its basic features, a significant step towards understanding these shocks. In the experiments, conducted on the OMEGA EP laser facility at the University of Rochester, a pair of plasmas plumes are generated by irradiating of a pair of opposing parallel plastic (CH) targets. The ion-ion interaction between the two plumes is collisionless, so as the plumes interpenetrate, supersonic, counterstreaming ion flow conditions are obtained. Electromagnetic fields formed in the interaction of the two plumes were probed with an ultrafast laser-driven proton beam, and we observed the growth of a highly striated, transverse instability with extended filaments parallel to the flows. The instability is identified as an ion-driven Weibel instability through agreement with analytic theory and particle-in-cell simulations, paving the way for further detailed laboratory study of this instability and its consequences for particle energization and shock formation.[1] W. Fox, G. Fiksel, A. Bhattacharjee, P. Y. Chang, K. Germaschewski, S. X. Hu, and P. M. Nilson, “Filamentation instability of counterstreaming laser-driven plasmas,” Phys. Rev. Lett. 111, 225002 (2013).

  14. Microbunching Instability in Velocity Bunching

    SciTech Connect

    Xiang, D; Wu, J.; /SLAC

    2009-05-26

    Microbunching instability is one of the most challenging threats to FEL performances. The most effective ways to cure the microbunching instability include suppression of the density modulation sources and suppression of the amplification process. In this paper we study the microbunching instability in velocity bunching. Our simulations show that the initial current and energy modulations are suppressed in velocity bunching process, which may be attributed to the strong plasma oscillation and Landau damping from the relatively low beam energy and large relative slice energy spread. A heating effect that may be present in a long solenoid is also preliminarily analyzed.

  15. Longitudinal instability of the forearm.

    PubMed

    Phadnis, J; Watts, A C

    2016-10-01

    The Essex Lopresti lesion is a rare triad of injury to the radial head, interosseous membrane of the forearm and distal radio-ulnar joint, which results in longitudinal instability of the radius. If unrecognized this leads to chronic pain and disability which is difficult to salvage. Early recognition and appropriate treatment is therefore desirable to prevent long-term problems. The aim of this article is to review the pathoanatomy of longitudinal radius instability and use the existing literature and authors' experience to provide recommendations for recognition and treatment of acute and chronic forearm instability, including description of the author's technique for interosseous membrane reconstruction. PMID:27628434

  16. Hydrodynamic instability modeling for ICF

    SciTech Connect

    Haan, S.W.

    1993-03-31

    The intent of this paper is to review how instability growth is modeled in ICF targets, and to identify the principal issues. Most of the material has been published previously, but is not familiar to a wide audience. Hydrodynamic instabilities are a key issue in ICF. Along with laser-plasma instabilities, they determine the regime in which ignition is possible. At higher laser energies, the same issues determine the achievable gain. Quantitative predictions are therefore of the utmost importance to planning the ICF program, as well as to understanding current Nova results. The key fact that underlies all this work is the stabilization of short wavelengths.

  17. New instability of Saturn's ring

    SciTech Connect

    Goertz, C.K.; Morfill, G.

    1988-05-01

    Perturbations in the Saturn ring's mass density are noted to be prone to instabilities through the sporadic elevation of submicron-size dust particles above the rings, which furnishes an effective angular momentum exchange between the rings and Saturn. The dust thus elevated from the ring settles back onto it at a different radial distance. The range of wavelength instability is determinable in light of the dust charge, the average radial displacement of the dust, and the fluctuation of these quantities. It is suggested that at least some of the B-ring's ringlets may arise from the instability.

  18. 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.

  19. Recombinant production of spider silk proteins.

    PubMed

    Heidebrecht, Aniela; Scheibel, Thomas

    2013-01-01

    Natural spider silk fibers combine extraordinary properties such as stability and flexibility which results in a toughness superseding that of all other fiber materials. As the spider's aggressive territorial behavior renders their farming not feasible, the biotechnological production of spider silk proteins (spidroins) is essential in order to investigate and employ them for applications. In order to accomplish this task, two approaches have been tested: firstly, the expression of partial cDNAs, and secondly, the expression of synthetic genes in several host organisms, including bacteria, yeast, plants, insect cells, mammalian cells, and transgenic animals. The experienced problems include genetic instability, limitations of the translational and transcriptional machinery, and low solubility of the produced proteins. Here, an overview of attempts to recombinantly produce spidroins will be given, and advantages and disadvantages of the different approaches and host organisms will be discussed. PMID:23415154

  20. Instabilities in counterstreaming plasmas

    NASA Astrophysics Data System (ADS)

    Park, Hye-Sook

    2013-10-01

    We are performing high power laser experiments showing large, stable, reproducible electromagnetic field structures that arise in counter-streaming interpenetrating supersonic plasma flows in the laboratory. Self organization, whereby energy progressively transfers from smaller to larger scales in an inverse cascade, is widely observed in fluid flows, such as in the nonlinear evolution of multimode Rayleigh-Taylor and Kelvin-Helmholtz instabilities. There are many scenarios in astrophysics where self organization involving magnetic or electric fields in collisionless settings is observed. These surprising structures, predominantly oriented transverse to the primary flow direction, extend for much larger distances than the intrinsic plasma spatial scales, and persist for much longer than the plasma kinetic timescales. Their origin may be magnetic field advection from the recompression of the Biermann battery fields in the midplane. Understanding interactions of high velocity plasma flows is interests to the ICF and astrophysics. This paper will present experimental results and interpretation of these counterstreaming plasma experiments. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

  1. 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.

  2. 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.

  3. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  4. Recombineering Pseudomonas syringae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we report the identification of functions that promote genomic recombination of linear DNA introduced into Pseudomonas cells by electroporation. The genes encoding these functions were identified in Pseudomonas syringae pv. syringae B728a based on similarity to the lambda Red Exo/Beta and RecE...

  5. A Heritable Recombination system for synthetic Darwinian evolution in yeast.

    PubMed

    Romanini, Dante W; Peralta-Yahya, Pamela; Mondol, Vanessa; Cornish, Virginia W

    2012-12-21

    Genetic recombination is central to the generation of molecular diversity and enhancement of evolutionary fitness in living systems. Methods such as DNA shuffling that recapitulate this diversity mechanism in vitro are powerful tools for engineering biomolecules with useful new functions by directed evolution. Synthetic biology now brings demand for analogous technologies that enable the controlled recombination of beneficial mutations in living cells. Thus, here we create a Heritable Recombination system centered around a library cassette plasmid that enables inducible mutagenesis via homologous recombination and subsequent combination of beneficial mutations through sexual reproduction in Saccharomyces cerevisiae. Using repair of nonsense codons in auxotrophic markers as a model, Heritable Recombination was optimized to give mutagenesis efficiencies of up to 6% and to allow successive repair of different markers through two cycles of sexual reproduction and recombination. Finally, Heritable Recombination was employed to change the substrate specificity of a biosynthetic enzyme, with beneficial mutations in three different active site loops crossed over three continuous rounds of mutation and selection to cover a total sequence diversity of 10(13). Heritable Recombination, while at an early stage of development, breaks the transformation barrier to library size and can be immediately applied to combinatorial crossing of beneficial mutations for cell engineering, adding important features to the growing arsenal of next generation molecular biology tools for synthetic biology. PMID:23412545

  6. Thin-shell instability in collisionless plasma.

    PubMed

    Dieckmann, M E; Ahmed, H; Doria, D; Sarri, G; Walder, R; Folini, D; Bret, A; Ynnerman, A; Borghesi, M

    2015-09-01

    Thin-shell instability is one process which can generate entangled structures in astrophysical plasma on collisional (fluid) scales. It is driven by a spatially varying imbalance between the ram pressure of the inflowing upstream plasma and the downstream's thermal pressure at a nonplanar shock. Here we show by means of a particle-in-cell simulation that an analog process can destabilize a thin shell formed by two interpenetrating, unmagnetized, and collisionless plasma clouds. The amplitude of the shell's spatial modulation grows and saturates after about ten inverse proton plasma frequencies, when the shell consists of connected piecewise linear patches.

  7. 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.

  8. Cycles of chromosome instability are associated with a fragilesite and are increased by defects in DNA replication and checkpointcontrols in yeast

    SciTech Connect

    Admire, Anthony; Shanks, Lisa; Danzl, Nicole; Wang, Mei; Weier,Ulli; Stevens, William; Hunt, Elizabeth; Weinert, Ted

    2005-11-22

    We report here that a normal budding yeast chromosome (ChrVII) can undergo remarkable cycles of chromosome instability. The events associated with cycles of instability caused a distinctive ''sectoring'' of colonies on selective agar plates. We found that instability initiated at any of several sites on ChrVII, and was sharply increased by the disruption of DNA replication or by defects in checkpoint controls. We studied in detail the cycles of instability associated with one particular chromosomal site (the ''403 site''). This site contained multiple tRNA genes known to stall replication forks, and when deleted, the overall frequency of sectoring was reduced. Instability of the 403 site involved multiple nonallelic recombination events that led to the formation of amonocentric translocation. This translocation remained unstable, frequently undergoing either loss or recombination events linked to the translocation junction. These results suggest a model in which instability initiates at specific chromosomal sites that stall replication forks. Forks not stabilized by checkpoint proteins break and undergo multiple rounds of nonallelic recombination to form translocations. Some translocations remain unstable because they join two ''incompatible'' chromosomal regions. Cycles of instability of this normal yeast chromosome may be relevant to chromosome instability of mammalian fragile sites and of chromosomes in cancer cells.

  9. Coupling of Kelvin-Helmholtz instability and buoyancy instability in a thermally laminar plasma

    SciTech Connect

    Ren Haijun; Wu Zhengwei; Cao Jintao; Dong Chao; Chu, Paul K.

    2011-02-15

    Thermal convective instability is investigated in a thermally stratified plasma in the presence of shear flow, which is known to give rise to the Kelvin-Helmholtz (KH) instability. We examine how the KH instability and magnetothermal instability (MTI) affect each other. Based on the sharp boundary model, the KH instability coupled with the MTI is studied. We present the growth rate and instability criteria. The shear flow is shown to significantly alter the critical condition for the occurrence of thermal convective instability.

  10. 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.

  11. 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.

  12. Nonaxisymmetric linear instability of cylindrical magnetohydrodynamic Taylor-Couette flow.

    PubMed

    Child, Adam; Kersalé, Evy; Hollerbach, Rainer

    2015-09-01

    We consider the nonaxisymmetric modes of instability present in Taylor-Couette flow under the application of helical magnetic fields, mainly for magnetic Prandtl numbers close to the inductionless limit, and conduct a full examination of marginal stability in the resulting parameter space. We allow for the azimuthal magnetic field to be generated by a combination of currents in the inner cylinder and fluid itself and introduce a parameter governing the relation between the strength of these currents. A set of governing eigenvalue equations for the nonaxisymmetric modes of instability are derived and solved by spectral collocation with Chebyshev polynomials over the relevant parameter space, with the resulting instabilities examined in detail. We find that by altering the azimuthal magnetic field profiles the azimuthal magnetorotational instability, nonaxisymmetric helical magnetorotational instability, and Tayler instability yield interesting dynamics, such as different preferred mode types and modes with azimuthal wave number m>1. Finally, a comparison is given to the recent WKB analysis performed by Kirillov et al. [Kirillov, Stefani, and Fukumoto, J. Fluid Mech. 760, 591 (2014)JFLSA70022-112010.1017/jfm.2014.614] and its validity in the linear regime.

  13. Cosmic instability from radiation pressure

    NASA Technical Reports Server (NTRS)

    Hogan, Craig J.

    1990-01-01

    The Cosmic Background Explorer has recently confirmed the blackbody character of the microwave background to high accuracy (Mather et al., 1990), and will have the capability to detect other cosmic backgrounds throughout the infrared. A detection of cosmic background radiation dating from the pregalactic era would have important consequences for theories of cosmic structure. During the creation of such a background the pressure of the radiation itself causes an instability which leads inevitably to the growth of large-scale structure in the matter distribution. In contrast to conventional gravitational-instability models, the statistical properties of this structure are determined primarily by the self-organizing dynamics of the instability rather than details of cosmological initial conditions. The behavior of the instability is described here.

  14. Instabilities of High Temperature Superconductors

    PubMed Central

    Matthias, B. T.; Corenzwit, E.; Cooper, A. S.; Longinotti, L. D.

    1971-01-01

    We have observed the transition temperature of both the cubic and tetragonal phases of several high-temperature β-W superconductors. The instability of the cubic lattice appears to be characteristic of high-temperature superconductors. PMID:16591897

  15. Instability-driven quantum dots

    NASA Astrophysics Data System (ADS)

    Aqua, Jean-Noël; Frisch, Thomas

    2015-10-01

    When a film is strained in two dimensions, it can relax by developing a corrugation in the third dimension. We review here the resulting morphological instability that occurs by surface diffusion, called the Asaro-Tiller-Grinfel'd instability (ATG), especially on the paradigmatic silicon/germanium system. The instability is dictated by the balance between the elastic relaxation induced by the morphological evolution, and its surface energy cost. We focus here on its development at the nanoscales in epitaxial systems when a crystal film is coherently deposited on a substrate with a different lattice parameter, thence inducing epitaxial stresses. It eventually leads to the self-organization of quantum dots whose localization is dictated by the instability long-time dynamics. In these systems, new effects, such as film/substrate wetting or crystalline anisotropy, come into play and lead to a variety of behaviors. xml:lang="fr"

  16. 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).

  17. Genomic homologous recombination in planta.

    PubMed Central

    Gal, S; Pisan, B; Hohn, T; Grimsley, N; Hohn, B

    1991-01-01

    A system for monitoring intrachromosomal homologous recombination in whole plants is described. A multimer of cauliflower mosaic virus (CaMV) sequences, arranged such that CaMV could only be produced by recombination, was integrated into Brassica napus nuclear DNA. This set-up allowed scoring of recombination events by the appearance of viral symptoms. The repeated homologous regions were derived from two different strains of CaMV so that different recombinant viruses (i.e. different recombination events) could be distinguished. In most of the transgenic plants, a single major virus species was detected. About half of the transgenic plants contained viruses of the same type, suggesting a hotspot for recombination. The remainder of the plants contained viruses with cross-over sites distributed throughout the rest of the homologous sequence. Sequence analysis of two recombinant molecules suggest that mismatch repair is linked to the recombination process. Images PMID:2026150

  18. 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.

  19. 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.

  20. Aerodynamic instability: A case history

    NASA Technical Reports Server (NTRS)

    Eisenmann, R. C.

    1985-01-01

    The identification, diagnosis, and final correction of complex machinery malfunctions typically require the correlation of many parameters such as mechanical construction, process influence, maintenance history, and vibration response characteristics. The progression is reviewed of field testing, diagnosis, and final correction of a specific machinery instability problem. The case history presented addresses a unique low frequency instability problem on a high pressure barrel compressor. The malfunction was eventually diagnosed as a fluidic mechanism that manifested as an aerodynamic disturbance to the rotor assembly.

  1. Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination

    PubMed Central

    Ross, Joseph A.; Koboldt, Daniel C.; Staisch, Julia E.; Chamberlin, Helen M.; Gupta, Bhagwati P.; Baird, Scott E.; Haag, Eric S.

    2011-01-01

    The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes. PMID:21779179

  2. Pattern Formation in Convective Instabilities

    NASA Astrophysics Data System (ADS)

    Friedrich, R.; Bestehorn, M.; Haken, H.

    The present article reviews recent progress in the study of pattern formation in convective instabilities. After a brief discussion of the relevant basic hydrodynamic equations as well as a short outline of the mathematical treatment of pattern formation in complex systems the self-organization of spatial and spatio-temporal structures due to convective instabilities is considered. The formation of various forms of convective patterns arising in the Bénard experiment, i.e. in a horizontal fluid layer heated from below, is discussed. Then the review considers pattern formation in the Bénard instability in spherical geometries. In that case it can be demonstrated how the interaction among several convective cells may lead to time dependent as well as chaotic evolution of the spatial structures. Finally, the convective instability in a binary fluid mixture is discussed. In contrast to the instability in a single component fluid the instability may be oscillatory. In that case convection sets in in the form of travelling wave patterns which in addition to a complicated and chaotic temporal behaviour exhibit more or less spatial irregularity already close to threshold.

  3. 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.

  4. Recombination and the maintenance of plant organelle genome stability.

    PubMed

    Maréchal, Alexandre; Brisson, Normand

    2010-04-01

    Like their nuclear counterpart, the plastid and mitochondrial genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain organelle genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of organelle genomes. Revealingly, deregulation of recombination in organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their organelle genomes intact. These new features presumably optimized the protection of plastid and mitochondrial genomes against the particular genotoxic stresses they face.

  5. Conjugational Recombination in Escherichia Coli: Genetic Analysis of Recombinant Formation in Hfr X F(-) Crosses

    PubMed Central

    Lloyd, R. G.; Buckman, C.

    1995-01-01

    The formation of recombinants during conjugation between Hfr and F(-) strains of Escherichia coli was investigated using unselected markers to monitor integration of Hfr DNA into the circular recipient chromosome. In crosses selecting a marker located ~500 kb from the Hfr origin, 60-70% of the recombinants appeared to inherit the Hfr DNA in a single segment, with the proximal exchange located >300 kb from the selected marker. The proportion of recombinants showing multiple exchanges increased in matings selecting more distal markers located 700-2200 kb from the origin, but they were always in the minority. This effect was associated with decreased linkage of unselected proximal markers. Mutation of recB, or recD plus recJ, in the recipient reduced the efficiency of recombination and shifted the location of the proximal exchange (s) closer to the selected marker. Mutation of recF, recO or recQ produced recombinants in which this exchange tended to be closer to the origin, though the effect observed was rather small. Up to 25% of recombinant colonies in rec(+) crosses showed segregation of both donor and recipient alleles at a proximal unselected locus. Their frequency varied with the distance between the selected and unselected markers and was also related directly to the efficiency of recombination. Mutation of recD increased their number by twofold in certain crosses to a value of 19%, a feature associated with an increase in the survival of linear DNA in the absence of RecBCD exonuclease. Mutation of recN reduced sectored recombinants in these crosses to ~1% in all the strains examined, including recD. A model for conjugational recombination is proposed in which recombinant chromosomes are formed initially by two exchanges that integrate a single piece of duplex Hfr DNA into the recipient chromosome. Additional pairs of exchanges involving the excised recipient DNA, RecBCD enzyme and RecN protein, can subsequently modify the initial product to generate the

  6. 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.

  7. Warburg effect and translocation-induced genomic instability: two yeast models for cancer cells

    PubMed Central

    Tosato, Valentina; Grüning, Nana-Maria; Breitenbach, Michael; Arnak, Remigiusz; Ralser, Markus; Bruschi, Carlo V.

    2013-01-01

    Yeast has been established as an efficient model system to study biological principles underpinning human health. In this review we focus on yeast models covering two aspects of cancer formation and progression (i) the activity of pyruvate kinase (PK), which recapitulates metabolic features of cancer cells, including the Warburg effect, and (ii) chromosome bridge-induced translocation (BIT) mimiking genome instability in cancer. Saccharomyces cerevisiae is an excellent model to study cancer cell metabolism, as exponentially growing yeast cells exhibit many metabolic similarities with rapidly proliferating cancer cells. The metabolic reconfiguration includes an increase in glucose uptake and fermentation, at the expense of respiration and oxidative phosphorylation (the Warburg effect), and involves a broad reconfiguration of nucleotide and amino acid metabolism. Both in yeast and humans, the regulation of this process seems to have a central player, PK, which is up-regulated in cancer, and to occur mostly on a post-transcriptional and post-translational basis. Furthermore, BIT allows to generate selectable translocation-derived recombinants (“translocants”), between any two desired chromosomal locations, in wild-type yeast strains transformed with a linear DNA cassette carrying a selectable marker flanked by two DNA sequences homologous to different chromosomes. Using the BIT system, targeted non-reciprocal translocations in mitosis are easily inducible. An extensive collection of different yeast translocants exhibiting genome instability and aberrant phenotypes similar to cancer cells has been produced and subjected to analysis. In this review, we hence provide an overview upon two yeast cancer models, and extrapolate general principles for mimicking human disease mechanisms in yeast. PMID:23346549

  8. Sex recombination, and reproductive fitness: an experimental study using Paramecium

    SciTech Connect

    Nyberg, D.

    1982-08-01

    The effect of sex and recombination on reproductive fitness are measured using five wild stocks of Paramecium primaurelia. Among the wild stocks there were highly significant differences in growth rates. No hybrid had as low a fitness as the least fit parental stock. Recombination produced genotypes of higher fitness than those of either parent only in the cross between the two stocks of lowest fitness. The increase in variance of fitness as a result of recombination was almost exclusively attributable to the generation lines with low fitness. The fitness consequences of sexuality and mate choice were stock specific; some individuals leaving the most descendants by inbreeding, others by outcrossing. For most crosses the short-term advantage of sex, if any, accrue from the fusion of different gametes (hybrid vigor) and not from recombination. Since the homozygous genotype with the highest fitnes left the most progeny by inbreeding (no recombination), the persistence of conjugation in P. primaurelia is paradoxical. (JMT)

  9. CRISPR-directed mitotic recombination enables genetic mapping without crosses.

    PubMed

    Sadhu, Meru J; Bloom, Joshua S; Day, Laura; Kruglyak, Leonid

    2016-05-27

    Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR (clustered, regularly interspaced, short palindromic repeats) to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.

  10. Production and secretion of recombinant proteins in Dictyostelium discoideum.

    PubMed

    Dittrich, W; Williams, K L; Slade, M B

    1994-06-01

    We have expressed useful amounts of three recombinant proteins in a new eukaryotic host/vector system. The cellular slime mold Dictyostelium discoideum efficiently secreted two recombinant products, a soluble form of the normally cell surface associated D. discoideum glycoprotein (PsA) and the heterologous protein glutathione-S-transferase (GST) from Schistosoma japonicum, while the enzyme beta-glucuronidase (GUS) from Escherichia coli was cell associated. Up to 20mg/l of recombinant PsA and 1mg/l of GST were obtained after purification from a standard, peptone based growth medium. The secretion signal peptide was correctly cleaved from the recombinant GST- and PsA-proteins and the expression of recombinant PsA was shown to be stable for at least one hundred generations in the absence of selection. PMID:7764951

  11. 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.

  12. Site directed recombination

    DOEpatents

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  13. Weibel Instability Of Counter-Streaming Dust Beams

    SciTech Connect

    Dahamni, M.S.; Fentazi, S.; Annou, R.

    2005-10-31

    A study of the excitation via Weibel instability, of electromagnetic waves in a plasma where counter-streaming grain beams propagate, is conducted. Agglomeration of dust grains is taken into account. The dispersion relation is obtained and analytically solved. New modes are generated.

  14. Radiation induced genome instability: multiscale modelling and data analysis

    NASA Astrophysics Data System (ADS)

    Andreev, Sergey; Eidelman, Yuri

    2012-07-01

    Genome instability (GI) is thought to be an important step in cancer induction and progression. Radiation induced GI is usually defined as genome alterations in the progeny of irradiated cells. The aim of this report is to demonstrate an opportunity for integrative analysis of radiation induced GI on the basis of multiscale modelling. Integrative, systems level modelling is necessary to assess different pathways resulting in GI in which a variety of genetic and epigenetic processes are involved. The multilevel modelling includes the Monte Carlo based simulation of several key processes involved in GI: DNA double strand breaks (DSBs) generation in cells initially irradiated as well as in descendants of irradiated cells, damage transmission through mitosis. Taking the cell-cycle-dependent generation of DNA/chromosome breakage into account ensures an advantage in estimating the contribution of different DNA damage response pathways to GI, as to nonhomologous vs homologous recombination repair mechanisms, the role of DSBs at telomeres or interstitial chromosomal sites, etc. The preliminary estimates show that both telomeric and non-telomeric DSB interactions are involved in delayed effects of radiation although differentially for different cell types. The computational experiments provide the data on the wide spectrum of GI endpoints (dicentrics, micronuclei, nonclonal translocations, chromatid exchanges, chromosome fragments) similar to those obtained experimentally for various cell lines under various experimental conditions. The modelling based analysis of experimental data demonstrates that radiation induced GI may be viewed as processes of delayed DSB induction/interaction/transmission being a key for quantification of GI. On the other hand, this conclusion is not sufficient to understand GI as a whole because factors of DNA non-damaging origin can also induce GI. Additionally, new data on induced pluripotent stem cells reveal that GI is acquired in normal mature

  15. 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.

  16. 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.

  17. The recombination epoch revisited

    NASA Technical Reports Server (NTRS)

    Krolik, Julian H.

    1989-01-01

    Previous studies of cosmological recombination have shown that this process produces as a by-product a highly superthermal population of Ly-alpha photons which retard completion of recombination. Cosmological redshifting was thought to determine the frequency distribution of the photons, while two-photon decay of hydrogen's 2s state was thought to control their numbers. It is shown here that frequency diffusion due to photon scattering dominate the cosmological redshift in the frequency range near line center which fixes the ratio of ground state to excited state population, while incoherent scattering into the far-red damping wing effectively destroys Ly-alpha photons as a rate which is competitive with two-photon decay. The former effect tends to hold back recombination, while the latter tends to accelerate it; the net results depends on cosmological parameters, particularly the combination Omega(b) h/sq rt (2q0), where Omega(b) is the fraction of the critical density provided by baryons.

  18. Electrohydrodynamic instabilities in thin liquid trilayer films

    DOE PAGES

    Roberts, Scott A.; Kumar, Satish

    2010-12-09

    Experiments by Dickey and Leach show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DCmore » field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.« less

  19. Electrohydrodynamic instabilities in thin liquid trilayer films

    SciTech Connect

    Roberts, Scott A.; Kumar, Satish

    2010-12-09

    Experiments by Dickey and Leach show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DC field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.

  20. Ancestries of a recombining diploid population.

    PubMed

    Sainudiin, R; Thatte, B; Véber, A

    2016-01-01

    We derive the exact one-step transition probabilities of the number of lineages that are ancestral to a random sample from the current generation of a bi-parental population that is evolving under the discrete Wright-Fisher model with n diploid individuals. Our model allows for a per-generation recombination probability of r . When r = 1, our model is equivalent to Chang's (Adv Appl Probab 31:1002-1038, 1999) model for the karyotic pedigree. When r = 0, our model is equivalent to Kingman's (Stoch Process Appl 13:235-248, 1982) discrete coalescent model for the cytoplasmic tree or sub-karyotic tree containing a DNA locus that is free of intra-locus recombination. When 0 < r < 1 our model can be thought to track a sub-karyotic ancestral graph containing a DNA sequence from an autosomal chromosome that has an intra-locus recombination probability r . Thus, our family of models indexed by r ∈ [0, 1] connects Kingman's discrete coalescent to Chang's pedigree in a continuous way as r goes from 0 to 1. For large populations, we also study three properties of the ancestral process corresponding to a given r ∈ (0, 1): the time Tn to a most recent common ancestor (MRCA) of the population, the time Un at which all individuals are either common ancestors of all present day individuals or ancestral to none of them, and the fraction of individuals that are common ancestors at time Un. These results generalize the three main results of Chang's (Adv Appl Probab 31:1002-1038, 1999). When we appropriately rescale time and recombination probability by the population size, our model leads to the continuous time Markov chain called the ancestral recombination graph of Hudson (Theor Popul Biol 23:183-201, 1983) and Griffiths (The two-locus ancestral graph, Institute of Mathematical Statistics 100-117, 1991). PMID:25925241

  1. Rayleigh-Taylor instability at ionization fronts: perturbation analysis

    NASA Astrophysics Data System (ADS)

    Ricotti, Massimo

    2014-01-01

    The linear growth rate of the Rayleigh-Taylor instability (RTI) at ionization fronts is investigated via perturbation analysis in the limit of incompressible fluids. In agreement with previous numerical studies, it is found that absorption of ionizing radiation inside the H II region due to hydrogen recombinations suppresses the growth of instabilities. In the limit of a large density contrast at the ionization front, the RTI growth rate has the simple analytical solution n=-ν _rec+(ν _rec^2+gk)^{1/2}, where νrec is the hydrogen recombination rate inside the H II region, k is the perturbation's wavenumber and g is the effective acceleration in the frame of reference of the front. Therefore, the growth of surface perturbations with wavelengths λ ≫ λ _cr ≡ 2π g/ν _rec^2 is suppressed by a factor ˜(λcr/4λ)1/2 with respect to the non-radiative incompressible RTI. Implications on stellar and black hole feedback are briefly discussed.

  2. Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates.

    PubMed Central

    Balasubramanian, V; Pavelka, M S; Bardarov, S S; Martin, J; Weisbrod, T R; McAdam, R A; Bloom, B R; Jacobs, W R

    1996-01-01

    Genetic studies of Mycobacterium tuberculosis have been greatly hampered by the inability to introduce specific chromosomal mutations. Whereas the ability to perform allelic exchanges has provided a useful method of gene disruption in other organisms, in the clinically important species of mycobacteria, such as M. tuberculosis and Mycobacterium bovis, similar approaches have thus far been unsuccessful. In this communication, we report the development of a shuttle mutagenesis strategy that involves the use of long linear recombination substrates to reproducibly obtain recombinants by allelic exchange in M. tuberculosis. Long linear recombination substrates, approximately 40 to 50 kb in length, were generated by constructing libraries in the excisable cosmid vector pYUB328. The cosmid vector could be readily excised from the recombinant cosmids by digestion with PacI, a restriction endonuclease for which there exist few, if any, sites in mycobacterial genomes. A cosmid containing the mycobacterial leuD gene was isolated, and a selectable marker conferring resistance to kanamycin was inserted into the leuD gene in the recombinant cosmid by interplasmid recombination in Escherichia coli. A long linear recombination substrate containing the insertionally mutated leuD gene was generated by PacI digestion. Electroporation of this recombination substrate containing the insertionally mutated leuD allele resulted in the generation of leucine auxotrophic mutants by homologous recombination in 6% of the kanamycin-resistant transformants for both the Erdman and H37Rv strains of M. tuberculosis. The ability to perform allelic exchanges provides an important approach for investigating the biology of this pathogen as well as developing new live-cell M. tuberculosis-based vaccines. PMID:8550428

  3. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.

    PubMed

    Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Palero, Ferran; González-Candelas, Fernando

    2015-03-01

    Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure. PMID:25541518

  4. Genomic complexity profiling reveals that HORMAD1 overexpression contributes to homologous recombination deficiency in triple-negative breast cancers

    PubMed Central

    Watkins, Johnathan; Weekes, Daniel; Shah, Vandna; Gazinska, Patrycja; Joshi, Shalaka; Sidhu, Bhavna; Gillett, Cheryl; Pinder, Sarah; Vanoli, Fabio; Jasin, Maria; Mayrhofer, Markus; Isaksson, Anders; Cheang, Maggie C.U.; Mirza, Hasan; Frankum, Jessica; Lord, Christopher J.; Ashworth, Alan; Vinayak, Shaveta; Ford, James M.; Telli, Melinda L.; Grigoriadis, Anita; Tutt, Andrew N.J.

    2015-01-01

    Triple-negative breast cancers (TNBCs) are characterised by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that Allelic-imbalanced Copy Number Aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs as well as sensitising cancer cells to HR targeting therapies. Our data therefore provides a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability and an association with response to platinum-based chemotherapy in TNBC. PMID:25770156

  5. Planetary Diversity through Instability and Consolidation of High Multiplicity STIPs

    NASA Astrophysics Data System (ADS)

    Granados-Contreras, Agueda Paula; Boley, Aaron C.

    2016-10-01

    In previous work, we conducted a series of simulations to demonstrate the feasibility of in situ formation of giant planets at short orbital periods through the consolidation of planets in high multiplicity STIPs. The resulting planet-planet collisions can generate planetary diversity, depending on the timing of instability in the system. If instability occurs while significant gas is still present, then consolidation can produce critical cores massive enough to initiate runaway gas accretion within the lifetime of the gaseous disk. At the time, however, we did not include gas damping effects. Here, we explore how eccentricity and inclination damping can affect the outcomes of STIP metastability

  6. Hose-Modulation Instability of Laser Pulses in Plasmas

    SciTech Connect

    Sprangle, P.; Krall, J.; Esarey, E. )

    1994-12-26

    A laser pulse propagating in a uniform plasma or a preformed plasma density channel is found to undergo a combination of hose and modulation instabilities, provided the pulse centroid has an initial tilt. Coupled equations for the laser centroid and envelope are derived and solved for a finite-length laser pulse. Significant coupling between the centroid and the envelope, harmonic generation in the envelope, and strong modification of the wake field can occur. Methods to reduce the growth rate of the laser hose instability are demonstrated.

  7. A replication-competent retrovirus arising from a split-function packaging cell line was generated by recombination events between the vector, one of the packaging constructs, and endogenous retroviral sequences.

    PubMed

    Chong, H; Starkey, W; Vile, R G

    1998-04-01

    Previously we reported the presence of a replication-competent retrovirus in supernatant from a vector-producing line derived from a widely used split-function amphotropic packaging cell line. Rigorous routine screening of all retroviral stocks produced in our laboratory has not, previously or since, indicated the presence of such a virus. Replication-competent retroviruses have never previously been used in our laboratory, and stringent screening of all routinely used cell lines has not revealed the presence of any helper viruses. Therefore, it is highly unlikely that this virus represents an adventitious cross-contaminant or had been imported unknowingly with our cell line stocks. PCR studies with DNA from infected cell lines and Northern blot analysis and reverse transcriptase PCR with RNA from infected cells suggest that the helper virus arose by recombination events, at sites of partial homology, between sequences in the vector, one of the packaging constructs, and endogenous retroviral elements. These recombinations were not present in stocks of the packaging cell line or in an initial stock of the vector-producing line, indicating that these events occurred while the vector-producing line was being passaged for harvest of supernatant stocks. PMID:9525583

  8. Kekule-distortion-induced exciton instability in graphene

    SciTech Connect

    Dillenschneider, Raoul

    2008-09-15

    Effects of a Kekule distortion on exciton instability in single-layer graphene are discussed. In the framework of quantum electrodynamics the mass of the electron generated dynamically is worked out using a Schwinger-Dyson equation. For homogeneous lattice distortion it is shown that the generated mass is independent of the amplitude of the lattice distortion at the one-loop approximation. Formation of excitons induced by the homogeneous Kekule distortion could appear only through direct dependence of the lattice distortion.

  9. Recombinant protein blends: silk beyond natural design.

    PubMed

    Dinjaski, Nina; Kaplan, David L

    2016-06-01

    Recombinant DNA technology and new material concepts are shaping future directions in biomaterial science for the design and production of the next-generation biomaterial platforms. Aside from conventionally used synthetic polymers, numerous natural biopolymers (e.g., silk, elastin, collagen, gelatin, alginate, cellulose, keratin, chitin, polyhydroxyalkanoates) have been investigated for properties and manipulation via bioengineering. Genetic engineering provides a path to increase structural and functional complexity of these biopolymers, and thereby expand the catalog of available biomaterials beyond that which exists in nature. In addition, the integration of experimental approaches with computational modeling to analyze sequence-structure-function relationships is starting to have an impact in the field by establishing predictive frameworks for determining material properties. Herein, we review advances in recombinant DNA-mediated protein production and functionalization approaches, with a focus on hybrids or combinations of proteins; recombinant protein blends or 'recombinamers'. We highlight the potential biomedical applications of fibrous protein recombinamers, such as Silk-Elastin Like Polypeptides (SELPs) and Silk-Bacterial Collagens (SBCs). We also discuss the possibility for the rationale design of fibrous proteins to build smart, stimuli-responsive biomaterials for diverse applications. We underline current limitations with production systems for these proteins and discuss the main trends in systems/synthetic biology that may improve recombinant fibrous protein design and production. PMID:26686863

  10. Fundamental Studies of Recombinant Hydrogenases

    SciTech Connect

    Adams, Michael W

    2014-01-25

    This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

  11. Hydrodynamick instabilities on ICF capsules

    SciTech Connect

    Haan, S.W.

    1991-06-07

    This article summarizes our current understanding of hydrodynamic instabilities as relevant to ICF. First we discuss classical, single mode Rayleigh-Taylor instability, and nonlinear effects in the evolution of a single mode. Then we discuss multimode systems, considering: (1) the onset of nonlinearity; (2) a second order mode coupling theory for weakly nonlinear effects, and (3) the fully nonlinear regime. Two stabilization mechanisms relevant to ICF are described next: gradient scale length and convective stabilization. Then we describe a model which is meant to estimate the weakly nonlinear evolution of multi-mode systems as relevant to ICF, given the short-wavelength stabilization. Finally, we discuss the relevant code simulation capability, and experiments. At this time we are quite optimistic about our ability to estimate instability growth on ICF capsules, but further experiments and simulations are needed to verify the modeling. 52 refs.

  12. Instability of EDS maglev systems

    SciTech Connect

    Cai, Y.; Chen, S.S.

    1993-09-01

    Instabilities of an EDS maglev suspension system with 3 D.O.F. and 5 D.O.F. vehicles traveling on a double L-shaped set of guideway conductors have been investigated with various experimentally measured magnetical force data incorporated into the theoretical models. Divergence and flutter are obtained from both analytical and numerical solutions for coupled vibration of the 3 D.O.F. maglev vehicle model. Instabilities of five direction motions (heave, slip, rill, pitch and yaw) are observed for the 4 D.O.F. vehicle model. It demonstrates that system parameters, such as, system damping, vehicle geometry and coupling effects among five different motions play very important roles in the occurrence of dynamic instabilities of maglev vehicles.

  13. Performance through Deformation and Instability

    NASA Astrophysics Data System (ADS)

    Bertoldi, Katia

    2015-03-01

    Materials capable of undergoing large deformations like elastomers and gels are ubiquitous in daily life and nature. An exciting field of engineering is emerging that uses these compliant materials to design active devices, such as actuators, adaptive optical systems and self-regulating fluidics. Compliant structures may significantly change their architecture in response to diverse stimuli. When excessive deformation is applied, they may eventually become unstable. Traditionally, mechanical instabilities have been viewed as an inconvenience, with research focusing on how to avoid them. Here, I will demonstrate that these instabilities can be exploited to design materials with novel, switchable functionalities. The abrupt changes introduced into the architecture of soft materials by instabilities will be used to change their shape in a sudden, but controlled manner. Possible and exciting applications include materials with unusual properties such negative Poisson's ratio, phononic crystals with tunable low-frequency acoustic band gaps and reversible encapsulation systems.

  14. Faraday instability in deformable domains

    NASA Astrophysics Data System (ADS)

    Pucci, Giuseppe; Ben Amar, Martine; Couder, Yves

    2014-11-01

    We investigate the Faraday instability in floating liquid lenses, as an example of hydrodynamic instability that develops in a domain with flexible boundaries. We show that a mutual adaptation of the instability pattern and the domain shape occurs, as a result of the competition between the wave radiation pressure and the capillary response of the lens border. Two archetypes of behaviour are observed. In the first, stable shapes are obtained experimentally and predicted theoretically as the exact solutions of a Riccati equation, and they result from the equilibrium between wave radiation pressure and capillarity. In the second, the radiation pressure exceeds the capillary response of the lens border and leads to non-equilibrium behaviours, with breaking into smaller domains that have a complex dynamics including spontaneous propagation. The authors are grateful to Université Franco-Italienne (UFI) for financial support.

  15. Interfacial instabilities and Kapitsa pendula

    NASA Astrophysics Data System (ADS)

    Krieger, Madison

    2015-11-01

    Determining the critera for onset and amplitude growth of instabilities is one of the central problems of fluid mechanics. We develop a parallel between the Kapitsa effect, in which a pendulum subject to high-frequency low-amplitude vibrations becomes stable in the inverted position, and interfaces separating fluids of different density. It has long been known that such interfaces can be stabilized by vibrations, even when the denser fluid is on top. We demonstrate that the stability diagram for these fluid interfaces is identical to the stability diagram for an appopriate Kapitsa pendulum. We expand the robust, ``dictionary''-type relationship between Kapitsa pendula and interfacial instabilities by considering the classical Rayleigh-Taylor, Kelvin-Helmholtz and Plateau instabilities, as well as less-canonical examples ranging in scale from the micron to the width of a galaxy.

  16. Stellar explosions, instabilities, and turbulence

    SciTech Connect

    Drake, R. P.; Kuranz, C. C.; Miles, A. R.; Muthsam, H. J.; Plewa, T.

    2009-04-15

    It has become very clear that the evolution of structure during supernovae is centrally dependent on the pre-existing structure in the star. Modeling of the pre-existing structure has advanced significantly, leading to improved understanding and to a physically based assessment of the structure that will be present when a star explodes. It remains an open question whether low-mode asymmetries in the explosion process can produce the observed effects or whether the explosion mechanism somehow produces jets of material. In any event, the workhorse processes that produce structure in an exploding star are blast-wave driven instabilities. Laboratory experiments have explored these blast-wave-driven instabilities and specifically their dependence on initial conditions. Theoretical work has shown that the relative importance of Richtmyer-Meshkov and Rayleigh-Taylor instabilities varies with the initial conditions and does so in ways that can make sense of a range of astrophysical observations.

  17. Gravitational instabilities in protostellar disks

    NASA Technical Reports Server (NTRS)

    Tohline, J. E.

    1994-01-01

    The nonaxisymmetric stability of self-gravitating, geometrically thick accretion disks has been studied for protostellar systems having a wide range of disk-to-central object mass ratios. Global eigenmodes with four distinctly different characters were identified using numerical, nonlinear hydrodynamic techniques. The mode that appears most likely to arise in normal star formation settings, however, resembles the 'eccentric instability' that was identified earlier in thin, nearly Keplerian disks: It presents an open, one-armed spiral pattern that sweeps continuously in a trailing direction through more than 2-pi radians, smoothly connecting the inner and outer edges of the disk, and requires cooperative motion of the point mass for effective amplification. This particular instability promotes the development of a single, self-gravitating clump of material in orbit about the point mass, so its routine appearance in our simulations supports the conjecture that the eccentric instability provides a primary route to the formation of short-period binaries in protostellar systems.

  18. Chondral Injury in Patellofemoral Instability

    PubMed Central

    Lustig, Sébastien; Servien, Elvire; Neyret, Philippe

    2014-01-01

    Objective: Patellofemoral instability is common and affects a predominantly young age group. Chondral injury occurs in up to 95%, and includes osteochondral fractures and loose bodies acutely and secondary degenerative changes in recurrent cases. Biomechanical abnormalities, such as trochlear dysplasia, patella alta, and increased tibial tuberosity-trochlear groove distance, predispose to both recurrent dislocations and patellofemoral arthrosis. Design: In this article, we review the mechanisms of chondral injury in patellofemoral instability, diagnostic modalities, the distribution of lesions seen in acute and episodic dislocation, and treatments for articular cartilage lesions of the patellofemoral joint. Results: Little specific evidence exists for cartilage treatments in patellofemoral instability. In general, the results of reparative and restorative procedures in the patellofemoral joint are inferior to those observed in other compartments of the knee. Conclusion: Given the increased severity of chondral lesions and progression to osteoarthritis seen with recurrent dislocations, careful consideration should be given to early stabilisation in patients with predisposing factors. PMID:26069693

  19. Laboratory blast wave driven instabilities

    NASA Astrophysics Data System (ADS)

    Kuranz, Carolyn

    2008-11-01

    This presentation discusses experiments involving the evolution of hydrodynamic instabilities in the laboratory under high-energy-density (HED) conditions. These instabilities are driven by blast waves, which occur following a sudden, finite release of energy, and consist of a shock front followed by a rarefaction wave. When a blast wave crosses an interface with a decrease in density, hydrodynamic instabilities will develop. Instabilities evolving under HED conditions are relevant to astrophysics. These experiments include target materials scaled in density to the He/H layer in SN1987A. About 5 kJ of laser energy from the Omega Laser facility irradiates a 150 μm plastic layer that is followed by a low-density foam layer. A blast wave structure similar to those in supernovae is created in the plastic layer. The blast wave crosses an interface having a 2D or 3D sinusoidal structure that serves as a seed perturbation for hydrodynamic instabilities. This produces unstable growth dominated by the Rayleigh-Taylor (RT) instability in the nonlinear regime. We have detected the interface structure under these conditions using x-ray backlighting. Recent advances in our diagnostic techniques have greatly improved the resolution of our x-ray radiographic images. Under certain conditions, the improved images show some mass extending beyond the RT spike and penetrating further than previously observed or predicted by current simulations. The observed effect is potentially of great importance as a source of mass transport to places not anticipated by current theory and simulation. I will discuss the amount of mass in these spike extensions, the associated uncertainties, and hypotheses regarding their origin We also plan to show comparisons of experiments using single mode and multimode as well as 2D and 3D initial conditions. This work is sponsored by DOE/NNSA Research Grants DE-FG52-07NA28058 (Stewardship Sciences Academic Alliances) and DE-FG52-04NA00064 (National Laser User

  20. The Role of Thermal Instability in Interstellar Medium

    NASA Astrophysics Data System (ADS)

    Inutsuka, Shu-Ichiro; Koyama, Hiroshi; Inoue, Tsuyoshi

    2005-09-01

    Our understanding on the physical processes in the transition between warm neutral medium (WNM) and cold neutral medium (CNM) is dramatically increased in the last few years. This article reviews the role of thermal instability in interstellar medium. First we explain the basic property of thermal instability in terms of linear stability analysis. Then we analyze the propagation of a shock wave into WNM or CNM by taking into account radiative heating/cooling, thermal conduction, and physical viscosity, in one-, two-, and three-dimensional magnetohydrodynamical simulations. The results show that the thermal instability in the post-shock gas produces high-density molecular cloudlets embedded in warm neutral medium. The molecular cloudlets have velocity dispersion which is supersonic with respect to the sound speed of the cold medium but is sub-sonic with respect to the warm medium. The dynamical evolution driven by thermal instability in the post-shock layer is an important basic process for the transition from warm gases to cold molecular gases, because the shock waves are frequently generated by supernovae in the Galaxy. The mechanism for maintaining the turbulent motion in two-phase medium is analyzed further by identifying the dynamical instability of the transition layer between WNM and CNM, that has analogy to Darrieus-Landau Instability of flame fronts and the corrugation instability of MHD slow shocks. Once the total column density of the ensemble of cold clouds becomes larger than the critical value (~ 1021cm-2), the two-phase medium is expected to become one phase medium with the cooling timescale. This process is not well understood and remains to be studied. Attempts to compare the numerical results of dynamical calculations with observation are suggested.