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. Generation of active immunotoxins containing recombinant restrictocin.

    PubMed

    Rathore, D; Batra, J K

    1996-05-01

    Restrictocin, a toxin produced by the fungus Aspergillus restrictus, is a potent inhibitor of eukaryotic protein synthesis. Recombinant restrictocin was made in Escherichia coli and purified to homogeneity in large amounts. The recombinant protein was found to be poorly immunogenic in mice with low toxicity, when injected intraperitoneally. Two immunotoxins were constructed by coupling the recombinant restrictocin to an antibody to the human transferrin receptor, using a cleavable and a stable linkage. The immunotoxins so generated showed specific cytotoxic activity toward receptor bearing cells in tissue culture. Immunotoxin with a cleavable linkage, however, was more active than that containing a stable linkage. Restrictocin appears to be a promising candidate to be developed as a chimeric toxin for targeted therapy. PMID:8630074

  4. Pattern Generation by Dissipative Parametric Instability

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  5. Pattern Generation by Dissipative Parametric Instability.

    PubMed

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

    2016-01-15

    Nonlinear instabilities are responsible for spontaneous pattern formation in a vast number of natural and engineered systems, ranging from biology to galaxy buildup. We propose a new instability mechanism leading to pattern formation in spatially extended nonlinear systems, which is based on a periodic antiphase modulation of spectrally dependent losses arranged in a zigzag way: an effective filtering is imposed at symmetrically located wave numbers k and -k in alternating order. The properties of the dissipative parametric instability differ from the features of both key classical concepts of modulation instabilities, i.e., the Benjamin-Feir instability and the Faraday instabiltyity. We demonstrate how the dissipative parametric instability can lead to the formation of stable patterns in one- and two-dimensional systems. The proposed instability mechanism is generic and can naturally occur or can be implemented in various physical systems. PMID:26824573

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

    SciTech Connect

    Schild, David; Wiese, Claudia

    2009-10-15

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

  7. Generation of instability waves at a leading edge

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1982-01-01

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

  8. 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)

  9. Pump instability phenomena generated by fluid forces

    NASA Technical Reports Server (NTRS)

    Gopalakrishnan, S.

    1985-01-01

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

  10. Topographically generated internal waves and boundary layer instabilities

    NASA Astrophysics Data System (ADS)

    Soontiens, Nancy; Stastna, Marek; Waite, Michael L.

    2015-08-01

    Flow over topography has been shown to generate finite amplitude internal waves upstream, over the topography and downstream. Such waves can interact with the viscous bottom boundary layer to produce vigorous instabilities. However, the strength and size of such instabilities depends on whether viscosity significantly modifies the wave generation process, which is usually treated using inviscid theory in the literature. In this work, we contrast cases in which boundary layer separation profoundly alters the wave generation process and cases for which the generated internal waves largely match inviscid theory. All results are generated using a numerical model that simulates stratified flow over topography. Several issues with using a wave-based Reynolds number to describe boundary layer properties are discussed by comparing simulations with modifications to the domain depth, background velocity, and viscosity. For hill-like topography, three-dimensional aspects of the instabilities are also discussed. Decreasing the Reynolds number by a factor of four (by increasing the viscosity), while leaving the primary two-dimensional instabilities largely unchanged, drastically affects their three-dimensionalization. Several cases at the laboratory scale with a depth of 1 m are examined in both two and three dimensions and a subset of the cases is scaled up to a field scale 10-m deep fluid while maintaining similar values for the background current and viscosity. At this scale, increasing the viscosity by an order of magnitude does not significantly change the wave properties but does alter the wave's interaction with the bottom boundary layer through the bottom shear stress. Finally, two subcritical cases for which disturbances are able to propagate upstream showcase a set of instabilities forming on the upstream slope of the elevated topography. The time scale over which these instabilities develop is related to but distinct from the advective time scale of the waves. At a

  11. Genomic instability in B-cells and diversity of recombinations that activate c-myc.

    PubMed

    Janz, S; Jones, G M; Müller, J R; Potter, M

    1995-01-01

    Genetic rearrangements activating the proto-oncogene c-myc comprise a mandatory oncogenic step in plasma cell tumor development in BALB/cAnPt mice. In the majority of plasmacytomas, c-myc activating rearrangements take the form of reciprocal chromosomal translocations t(12;15) that juxtapose c-myc to the immunoglobulin heavy chain alpha locus (IgH alpha) in particular the switch alpha region (S alpha). The genetic basis for the prevalence of S alpha/c-myc recombinations in BALB/cAnPt plasmacytomas is not known but may be related to a hypothetical regional genomic instability of the c-myc and IgH alpha loci in BALB/cAnPt mice. We wished to test whether the genomic instability of both loci might be revealed by the diversity of genetic recombinations that can be observed in IgH alpha and c-myc. We employed PCR methods to detect new recombinations of c-myc and IgH alpha in the preneoplastic stage of plasma cell tumor development and found that c-myc can be joined to more genes or genomic regions than known before. This is indicative but does not formally prove a particular genomic instability of c-myc and IgH alpha in BALB/cAnPt B cells. Since defective DNA repair provides a mechanistic explanation for genomic instability, we measured the efficiency of repair in IgH alpha and c-myc using an assay that quantitates the removal of UV-induced pyrimidine dimers within specific genomic regions. We used plasmacytoma XRPC 24 as a model system and found that both IgH alpha and c-myc were poorly repaired, whereas c-abl, a proto-oncogene not related to conventional pristane-induced plasmacytoma-genesis, was efficiently repaired. PMID:7895512

  12. Role of recombination activating genes in the generation of antigen receptor diversity and beyond.

    PubMed

    Nishana, Mayilaadumveettil; Raghavan, Sathees C

    2012-12-01

    V(D)J recombination is the process by which antibody and T-cell receptor diversity is attained. During this process, antigen receptor gene segments are cleaved and rejoined by non-homologous DNA end joining for the generation of combinatorial diversity. The major players of the initial process of cleavage are the proteins known as RAG1 (recombination activating gene 1) and RAG2. In this review, we discuss the physiological function of RAGs as a sequence-specific nuclease and its pathological role as a structure-specific nuclease. The first part of the review discusses the basic mechanism of V(D)J recombination, and the last part focuses on how the RAG complex functions as a sequence-specific and structure-specific nuclease. It also deals with the off-target cleavage of RAGs and its implications in genomic instability. PMID:23039142

  13. 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; Meulen, Jan Ter; 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

  14. 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

  15. Nernst advection and the field-generating thermal instability revisited

    NASA Astrophysics Data System (ADS)

    Bissell, J. J.

    2015-01-01

    It is widely held that the Nernst effect can drive instability in un-magnetised laser-plasmas by laterally compressing seed B-fields arising from the field-generating thermal instability [Tidman & Shanny, Phys. Fluids, 12:1207 (1974)]. Indeed, for wavelike perturbations, differential compression by the Nernst mechanism is thought to be most pronounced in the limit of low wave-number k -> 0, and is considered particularly important given that it can ostensibly lead to instability when the more usual field-generating mechanism is stable. However, as part of a recent article [Bissell et al., New J. Phys., 15:025017 (2013)] we noted some irregularities to the Nernst mechanism which obscure its operation. For example, by taking characteristic density and temperature length-scales ln and lT respectively, we observed that consistent analytical treatment of the instability requires kln,T >> 1, preventing the peak-growth limit k -> 0. Furthermore, the Nernst term-which compresses magnetic field perturbations-does not couple to a corresponding term acting on thermal perturbations, and as such does not describe an unstable feedback mechanism. In this article we probe the origin of such ambiguities more formally, and in so doing argue (contrary to reports existing elsewhere in the literature) that the Nernst effect does not drive instability in un-magnetised conditions, at least not in the fashion typically cited.

  16. Generation of instability waves at a leading edge

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1982-01-01

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

  17. 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.

  18. 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.

  19. Same-period emission and recombination in nonsequential double-recombination high-order-harmonic generation

    NASA Astrophysics Data System (ADS)

    Hansen, Kenneth K.; Madsen, Lars Bojer

    2016-05-01

    Nonsequential double-recombination (NSDR) high-order-harmonic generation (HHG) is studied in a molecular model system. We observe a unique molecular two-electron effect with a characteristic cutoff in the HHG spectrum at higher energies than what was previously seen for NSDR HHG in atoms. The effect is corroborated with a classical model where it is found that the effect is sensitive to the molecular potential and originates from same-period emission and recombination (SPEAR) of two electrons. The effect persists for intermediate nuclear distances of R ≳8.0 a.u.

  20. Instability studies in radial foil configurations on the COBRA generator

    NASA Astrophysics Data System (ADS)

    Gourdain, P.-A.; Greenly, J. B.; Hammer, D. A.; Knapp, P. F.; Kusse, B. R.; Pikuz, S. A.; Schrafel, P. C.; Shelkovenko, T. C.

    2010-11-01

    Radial foil configurations prove to be a very simple experimental set up to study high energy density plasmas. A 5-micron thin metallic foil lies flat over a stretcher which is connected to the anode of a pulsed power generator such as COBRA (1MA, 100 ns current rise time). The cathode contacts the foil at its geometrical center using a hollow stainless steel pin. As the foil ablates, JxB forces lift the foil leading to the formation a plasma bubble surrounding a central plasma column, which is a z-pinch. Force densities on this column should increase considerably as the initial pin diameter is diminished and we expect plasma properties to change accordingly. Based only on pin diameter considerations, radial foil explosions could produce magnetic pressures ranging from 160 kbar (for 2-mm pins) to 2.5 Mbar (for 0.5-mm pins). However, as the cathode diameter diminishes, instabilities appear earlier in the discharge, preventing the z-pinch implosion to occur at maximum current, de facto limiting plasma parameters. We investigate the cause of these instabilities, the possible means to reduce plasma instabilities and to improve plasma performances.

  1. 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

  2. GENERATION OF RECOMBINANT BACULOVIRUS VIA LIPOSOME MEDIATED TRANSFECTION

    EPA Science Inventory

    Baculovirus expression vectors have become a popular method of producing recombinant proteins. Production of recombinant virus requires the transfection of both the native viral DNA and a transfer plasmid into insect cells where recombination takes place. While several methods of...

  3. 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.

  4. Modulational-instability-induced supercontinuum generation with saturable nonlinear response

    SciTech Connect

    Raja, R. Vasantha Jayakantha; Porsezian, K.; Nithyanandan, K.

    2010-07-15

    We theoretically investigate the supercontinuum generation (SCG) on the basis of modulational instability (MI) in liquid-core photonic crystal fibers (LCPCF) with CS{sub 2}-filled central core. The effect of saturable nonlinearity of LCPCF on SCG in the femtosecond regime is studied using an appropriately modified nonlinear Schroedinger equation. We also compare the MI induced spectral broadening with SCG obtained by soliton fission. To analyze the quality of the pulse broadening, we study the coherence of the SC pulse numerically. It is evident from the numerical simulation that the response of the saturable nonlinearity suppresses the broadening of the pulse. We also observe that the MI induced SCG in the presence of saturable nonlinearity degrades the coherence of the SCG pulse when compared to unsaturated medium.

  5. Force-generation and dynamic instability of microtubule bundles

    PubMed Central

    Laan, Liedewij; Husson, Julien; Munteanu, E. Laura; Kerssemakers, Jacob W. J.; Dogterom, Marileen

    2008-01-01

    Individual dynamic microtubules can generate pushing or pulling forces when their growing or shrinking ends are in contact with cellular objects such as the cortex or chromosomes. These microtubules can operate in parallel bundles, for example when interacting with mitotic chromosomes. Here, we investigate the force-generating capabilities of a bundle of growing microtubules and study the effect that force has on the cooperative dynamics of such a bundle. We used an optical tweezers setup to study microtubule bundles growing against a microfabricated rigid barrier in vitro. We show that multiple microtubules can generate a pushing force that increases linearly with the number of microtubules present. In addition, the bundle can cooperatively switch to a shrinking state, due to a force-induced coupling of the dynamic instability of single microtubules. In the presence of GMPCPP, bundle catastrophes no longer occur, and high bundle forces are reached more effectively. We reproduce the observed behavior with a simple simulation of microtubule bundle dynamics that takes into account previously measured force effects on single microtubules. Using this simulation, we also show that a constant compressive force on a growing bundle leads to oscillations in bundle length that are of potential relevance for chromosome oscillations observed in living cells. PMID:18577596

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

    PubMed Central

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

    2000-01-01

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

  7. 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.

  8. Generation of instability waves in flows separating from smooth surfaces

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1984-01-01

    This paper analyses the coupling between an imposed disturbance and an instability wave that propagates downstream on a shear layer which emanates from a separation point on a smooth surface. Since the wavelengths of the most-amplified instability waves will generally be small compared with the streamwise body dimensions, the analysis is restricted to this 'high-frequency' limit and the solution is obtained by using matched asymptotic expansions. An 'inner' solution, valid near the separation point, is matched onto an outer solution, which represents an instability wave on a slowly diverging mean flow. The analysis relates the amplitude of this instability to that of the imposed disturbance.

  9. 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.

  10. 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.

  11. 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

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

    PubMed

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

    2015-04-30

    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

  13. 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...

  14. 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

  15. 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.

  16. 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.

  17. Targeting homologous recombination and telomerase in Barrett’s adenocarcinoma: Impact on telomere maintenance, genomic instability, and tumor growth

    PubMed Central

    Lu, Renquan; Pal, Jagannath; Buon, Leutz; Nanjappa, Puru; Shi, Jialan; Fulciniti, Mariateresa; Tai, Yu-Tzu; Guo, Lin; Yu, Min; Gryaznov, Sergei; Munshi, Nikhil C.; Shammas, Masood A.

    2014-01-01

    Homologous recombination (HR), a mechanism to accurately repair DNA in normal cells, is deregulated in cancer. Elevated/deregulated HR is implicated in genomic instability and telomere maintenance, which are critical lifelines of cancer cells. We have previously shown that HR activity is elevated and significantly contributes to genomic instability in BAC. The purpose of this study was to evaluate therapeutic potential of HR inhibition, alone and in combination with telomerase inhibition, in BAC. We demonstrate that telomerase inhibition in BAC cells increases HR activity, RAD51 expression, and association of RAD51 to telomeres. Suppression of HR leads to shorter telomeres as well as markedly reduced genomic instability in BAC cells over time. Combination of HR suppression (whether transgenic or chemical) with telomerase inhibition, causes a significant increase in telomere attrition and apoptotic death in all BAC cell lines tested, relative to either treatment alone. A subset of treated cells also stain positive for β-galactosidase, indicating senescence. The combined treatment is also associated with decline in S-phase and a strong G2/M arrest, indicating massive telomere attrition. In a subcutaneous tumor model, the combined treatment resulted in the smallest tumors, which were even smaller (P=0.001) than those resulted from either treatment alone. Even the tumors removed from these mice had significantly reduced telomeres and evidence of apoptosis. We therefore conclude that although telomeres are elongated by telomerase, elevated RAD51/HR assist in their maintenance/stabilization in BAC cells. Telomerase inhibitor prevents telomere elongation but induces RAD51/HR, which contribute to telomere maintenance/stabilization and prevention of apoptosis, reducing the efficacy of treatment. Combining HR inhibition with telomerase, makes telomeres more vulnerable to degradation and significantly increases/expedites their attrition, leading to apoptosis. We therefore

  18. Targeting homologous recombination and telomerase in Barrett's adenocarcinoma: impact on telomere maintenance, genomic instability and tumor growth.

    PubMed

    Lu, R; Pal, J; Buon, L; Nanjappa, P; Shi, J; Fulciniti, M; Tai, Y-T; Guo, L; Yu, M; Gryaznov, S; Munshi, N C; Shammas, M A

    2014-03-20

    Homologous recombination (HR), a mechanism to accurately repair DNA in normal cells, is deregulated in cancer. Elevated/deregulated HR is implicated in genomic instability and telomere maintenance, which are critical lifelines of cancer cells. We have previously shown that HR activity is elevated and significantly contributes to genomic instability in Barrett's esophageal adenocarcinoma (BAC). The purpose of this study was to evaluate therapeutic potential of HR inhibition, alone and in combination with telomerase inhibition, in BAC. We demonstrate that telomerase inhibition in BAC cells increases HR activity, RAD51 expression, and association of RAD51 to telomeres. Suppression of HR leads to shorter telomeres as well as markedly reduced genomic instability in BAC cells over time. Combination of HR suppression (whether transgenic or chemical) with telomerase inhibition, causes a significant increase in telomere attrition and apoptotic death in all BAC cell lines tested, relative to either treatment alone. A subset of treated cells also stain positive for β-galactosidase, indicating senescence. The combined treatment is also associated with decline in S-phase and a strong G2/M arrest, indicating massive telomere attrition. In a subcutaneous tumor model, the combined treatment resulted in the smallest tumors, which were even smaller (P=0.001) than those that resulted from either treatment alone. Even the tumors removed from these mice had significantly reduced telomeres and evidence of apoptosis. We therefore conclude that although telomeres are elongated by telomerase, elevated RAD51/HR assist in their maintenance/stabilization in BAC cells. Telomerase inhibitor prevents telomere elongation but induces RAD51/HR, which contributes to telomere maintenance/stabilization and prevention of apoptosis, reducing the efficacy of treatment. Combining HR inhibition with telomerase renders telomeres more vulnerable to degradation and significantly increases/expedites their

  19. Cytosines, but not purines, determine recombination activating gene (RAG)-induced breaks on heteroduplex DNA structures: implications for genomic instability.

    PubMed

    Naik, Abani Kanta; Lieber, Michael R; Raghavan, Sathees C

    2010-03-01

    The sequence specificity of the recombination activating gene (RAG) complex during V(D)J recombination has been well studied. RAGs can also act as structure-specific nuclease; however, little is known about the mechanism of its action. Here, we show that in addition to DNA structure, sequence dictates the pattern and efficiency of RAG cleavage on altered DNA structures. Cytosine nucleotides are preferentially nicked by RAGs when present at single-stranded regions of heteroduplex DNA. Although unpaired thymine nucleotides are also nicked, the efficiency is many fold weaker. Induction of single- or double-strand breaks by RAGs depends on the position of cytosines and whether it is present on one or both of the strands. Interestingly, RAGs are unable to induce breaks when adenine or guanine nucleotides are present at single-strand regions. The nucleotide present immediately next to the bubble sequence could also affect RAG cleavage. Hence, we propose "C((d))C((S))C((S))" (d, double-stranded; s, single-stranded) as a consensus sequence for RAG-induced breaks at single-/double-strand DNA transitions. Such a consensus sequence motif is useful for explaining RAG cleavage on other types of DNA structures described in the literature. Therefore, the mechanism of RAG cleavage described here could explain facets of chromosomal rearrangements specific to lymphoid tissues leading to genomic instability. PMID:20051517

  20. Laser-driven parametric instability and generation of entangled photon-plasmon states in graphene

    NASA Astrophysics Data System (ADS)

    Tokman, Mikhail; Wang, Yongrui; Oladyshkin, Ivan; Kutayiah, A. Ryan; Belyanin, Alexey

    2016-06-01

    We show that a strong 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 instability is due to a strong in-plane second-order nonlinear response of graphene which originates from its spatial dispersion. The parametric decay leads to efficient generation of THz plasmons and gives rise to quantum entanglement of idler photons and surface plasmon states.

  1. 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

  2. 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

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    Magnetic fields generated by the Rayleigh-Taylor instability were measured in laser-accelerated planar foils using ultrafast proton radiography. Thin plastic foils were irradiated with ˜4-kJ, 2.5-ns laser pulses focused to an intensity of ˜1014W/cm2 on the OMEGA EP Laser System. Target modulations were seeded by laser nonuniformities and amplified during target acceleration by the Rayleigh-Taylor instability. The experimental data show the hydrodynamic evolution of the target and MG-level magnetic fields generated in the broken foil. The experimental data are in good agreement with predictions from 2-D magnetohydrodynamic simulations.

  6. 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.

  7. High Harmonic Generation in Laser-Assisted Radiative Attachment or Recombination Processes

    NASA Astrophysics Data System (ADS)

    Flegel, Alexander V.; Zheltukhin, Alexander N.; Frolov, Mikhail V.; Manakov, Nikolai L.; Starace, Anthony F.

    2012-06-01

    Resonant enhancements are predicted in cross sections σn for laser-assisted radiative attachment or electron-ion recombination accompanied by absorption of n laser photons. These enhancements occur for incoming electron energies at which the electron can be attached or recombined by emitting μ laser photons followed by emission of a spontaneous photon upon absorbing n+μ laser photons. The close similarity between rescattering plateaus in spectra of resonant attachment/recombination and of high-order harmonic generation is shown based on a general parametrization for σn and on numerical results for e-H attachment.

  8. 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.

  9. 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.

  10. 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

  11. A method to generate recombinant Salmonella typhi Ty21a strains expressing multiple heterologous genes using an improved recombineering strategy.

    PubMed

    Yu, Bin; Yang, Mei; Wong, Ho Yin Bosco; Watt, Rory M; Song, Erwei; Zheng, Bo-Jian; Yuen, Kwok-Yung; Huang, Jian-Dong

    2011-07-01

    Live attenuated Salmonella enterica serovar Typhi Ty21a (Ty21a) is an important vaccine strain used in clinical studies for typhoid fever and as a vaccine vector for the expression of heterologous antigens. To facilitate the use of Ty21a in such studies, it is desirable to develop improved strategies that enable the stable chromosomal integration and expression of multiple heterologous antigens. The phage λ Red homologous recombination system has previously been used in various gram-negative bacteria species to mediate the accurate replacement of regions of chromosomal DNA with PCR-generated 'targeting cassettes' that contain flanking regions of shared homologous DNA sequence. However, the efficiency of λ Red-mediated recombineering in Ty21a is far lower than in Escherichia coli and other Salmonella typhimurium strains. Here, we describe an improved strategy for recombineering-based methods in Ty21a. Our reliable and efficient method involves the use of linear DNA-targeting cassettes that contain relatively long flanking 'arms' of sequence (ca. 1,000 bp) homologous to the chromosomal target. This enables multiple gene-targeting procedures to be performed on a single Ty21a chromosome in a straightforward, sequential manner. Using this strategy, we inserted three different influenza antigen expression cassettes as well as a green fluorescent protein gene reporter into four different loci on the Ty21a chromosome, with high efficiency and accuracy. Fluorescent microscopy and Western blotting analysis confirmed that strong inducible expression of all four heterologous genes could be achieved. In summary, we have developed an efficient, robust, and versatile method that may be used to construct recombinant Ty21a antigen-expressing strains. PMID:21611798

  12. 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.

  13. Design and generation of recombinant rabies virus vectors

    PubMed Central

    Osakada, Fumitaka; Callaway, Edward M.

    2014-01-01

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

  14. 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

  15. 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

  16. 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. PMID:24932318

  17. 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.

  18. 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

  19. Generation of χ(2) solitons from the Airy wave through the parametric instability.

    PubMed

    Mayteevarunyoo, Thawatchai; Malomed, Boris A

    2015-11-01

    Spontaneous creation of solitons in quadratic media by the downconversion (i.e., parametric instability against the generation of fundamental-frequency excitations) from the truncated Airy-wave (AW) mode in the second-harmonic component is studied. Parameter regions are identified for the generation of one, two, and three solitons, with additional small-amplitude "jets." Shares of the total power carried by individual solitons are found. Also considered are soliton patterns generated by the downconversion from a pair of AWs bending in opposite directions. PMID:26512490

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Thermodynamic Properties of Atmospheric Instability Associated With The Generation of Local Thunderstorms In Atmospheric Local Circulation

    NASA Astrophysics Data System (ADS)

    Nishiyama, K.; Jinno, K.; Kawamura, A.; Wakimizu, K.

    During a summer season after a rainy season in Japan, local thunderstorms occur in- land in the afternoon due to sun radiation and the subsequent development of local circulation including sea breeze or valley wind under the influence of the Pacific high pressure system. Some of the thunderstorms develop due to strong atmospheric in- stability and cause heavy precipitation and the resultant local flood. In our previous study, the observation of thunderstorms has been carried out using the meteorological radar and satellite images and, the Automated Meteorological Data Acquisition Sys- tem (AMeDAS), which is the ground observational network of the Japan Meteorolog- ical Agency, in the Northern Kyushu located in the west of Japan islands. AMeDAS consists of four elements, which are wind velocity and direction, temperature, rain- fall, duration of sunshine. Since AMeDAS has the fine resolution of approximately 20 km by 20 km and records these data every 10 minutes, it can be a useful tool for detecting the generation of local thunderstorms. These observations showed that tem- perature near the ground increased due to sun radiation and the subsequent sea breeze penetration towards inland formed convergence zone before the generation of local thunderstorms. It is inferred that the development of the atmospheric instability in the convergence zone around the sea breeze front was closely associated with the gen- eration of the local thunderstorms. This means that sea breeze circulation can trans- form atmospheric instability in the morning into more unstable situation. Therefore, it should be noted that the development of atmospheric instability with the movement and strength of sea breeze circulation is important factor for the generation of thun- derstorms. In this study, thermodynamic properties of atmospheric instability in a sea breeze circulation were investigated using a two-dimensional numerical model. Con- sequently, it could be confirmed that the increase of

  9. DNA shuffling method for generating highly recombined genes and evolved enzymes.

    PubMed

    Coco, W M; Levinson, W E; Crist, M J; Hektor, H J; Darzins, A; Pienkos, P T; Squires, C H; Monticello, D J

    2001-04-01

    We introduce a method of in vitro recombination or "DNA shuffling" to generate libraries of evolved enzymes. The approach relies on the ordering, trimming, and joining of randomly cleaved parental DNA fragments annealed to a transient polynucleotide scaffold. We generated chimeric libraries averaging 14.0 crossovers per gene, a several-fold higher level of recombination than observed for other methods. We also observed an unprecedented four crossovers per gene in regions of 10 or fewer bases of sequence identity. These properties allow generation of chimeras unavailable by other methods. We detected no unshuffled parental clones or duplicated "sibling" chimeras, and relatively few inactive clones. We demonstrated the method by molecular breeding of a monooxygenase for increased rate and extent of biodesulfurization on complex substrates, as well as for 20-fold faster conversion of a nonnatural substrate. This method represents a conceptually distinct and improved alternative to sexual PCR for gene family shuffling. PMID:11283594

  10. 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

  11. 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.

  12. Stability of periodic waves generated by long-wavelength instabilities in isotropic and anisotropic systems

    NASA Astrophysics Data System (ADS)

    Bar, Doron E.; Nepomnyashchy, Alexander A.

    1999-08-01

    We consider spontaneous generation of long waves in the presence of a conservation law in both cases of isotropic systems (e.g., Bénard-Marangoni waves) and anisotropic systems (e.g., waves in a film on an inclined plane). We found that near the instability threshold the problem is governed by the dissipation-modified Kadomtsev-Petviashvili equation in the former case and by the anisotropic dissipation-modified Korteweg-de Vries equation in the latter case. In frames of the derived 2+1-dimensional amplitude equations, we investigate the stability of one-dimensional waves. In isotropic systems the one-dimensional waves turned out to be always unstable with respect to a long-wave transverse modulation of the front. In anisotropic systems, only the one-dimensional periodic waves moving in the most preferred direction are found to be stable. Any deviation from this direction leads to instability of such an oblique wave.

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

    NASA Astrophysics Data System (ADS)

    Le, Chi Kien

    2016-06-01

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

  14. A protocol for construction of gene targeting vectors and generation of homologous recombinant ES cells

    PubMed Central

    Bouabe, Hicham; Okkenhaug, Klaus

    2015-01-01

    Summary The completion of human and mouse genome sequencing has confronted us with huge amount of data sequences that certainly need decades and many generations of scientists to be reasonably interpreted and assigned to physiological functions, and subsequently fruitfully translated into medical application. A means to assess the function of genes provides gene targeting in mouse embryonic stem (ES) cells that enables to introduce site-specific modifications in the mouse genome, and analyze their physiological consequences. Gene targeting enables almost any type of genetic modifications of interest, ranging from gene insertion (e.g. insertion of human-specific genes or reporter genes), gene disruption, point mutations, short and long range deletions, inversions. Site-specific modification into the genome of ES cells can be reached by homologous recombination using targeting vectors. Here, we describe a protocol to generate targeting constructs and homologous recombinant ES cells. PMID:23996269

  15. Rescattering effects in soft-x-ray generation by laser-assisted electron-ion recombination

    NASA Astrophysics Data System (ADS)

    Milošević, Dejan B.; Ehlotzky, Fritz

    2002-04-01

    Laser-assisted electron-ion recombination is investigated with an emphasis on the spectrum of the emitted high-energy photons and its modification due to the recollision of the incident electron and the ion. Numerical results for the soft-x-ray power spectra, added up over all intermediate laser photon channels, are presented as a function of the incident electron energy for different laser field intensities. For strong laser fields, maxima, and additional structures are found in these spectra for incident electron energies of the order of magnitude of the ponderomotive energy. We show that the laser-assisted electron-ion recombination, that includes the rescattering of the electron at the ion before the recombination, is a process complementary to the well-known processes of high-order harmonic generation and high-order above-threshold ionization. All these processes can be explained, using the three-step scenario. A semiclassical analysis is presented which shows that for the laser-assisted electron-ion recombination real solutions of the saddle-point equations exist, contrary to what is found with high-order harmonic generation and high-order above-threshold ionization when only complex solutions are permitted. For low incoming electron energies, the cutoff of the emitted soft-x-ray photon energies, including the process of rescattering, is higher than in the case of the direct recombination process. The height of the rescattering plateau is 6-7 orders of magnitude lower than that of the direct process. However, for higher incident electron energies we obtain the unexpected result that the difference between the height of the rescattering plateau and the height of the direct plateau can be less than one order of magnitude.

  16. Generation of cytotoxic and humoral immune responses by nonreplicative recombinant Semliki Forest virus.

    PubMed Central

    Zhou, X; Berglund, P; Zhao, H; Liljeström, P; Jondal, M

    1995-01-01

    The Semliki Forest virus (SFV) expression system can be used to package recombinant RNA into infectious suicide particles. Such RNA encodes only the SFV replicase and the heterologous protein but no structural proteins of SFV, and it is thus deficient in productive replication. We demonstrate here that infection of C57BL/6 (H-2b) and BALB/c (H-2d) mice with recombinant SFV expressing the nucleoprotein (NP) of influenza virus (SFV-NP) resulted in efficient priming of influenza virus-specific CD8+ cytotoxic T-cell (CTL) responses. The generated CTLs lysed both homologous (A/PR/8/34) and heterologous (A/HK/68) influenza virus-infected, or peptide-coated, target cells to a similar degree as CTLs induced by wild-type influenza virus in a major histocompatibility complex class I-restricted fashion. As few as 100 infectious units of virus induced a strong CTL response. Induction of CTL by SFV-NP could also be achieved in CD4 gene-targeted mice, demonstrating the independence of the primary CTL response of CD4+ helper T cells. One immunization generated a CTL response that peaked after 1 week, and an additional booster injection generated a CTL memory, which was still detectable after 40 days. SFV-NP immunizations also generated high-titered IgG humoral responses that remained significant after several months. These results demonstrate that the recombinant SFV suicide system is highly efficient in antigen presentation and suggest that it may have a potential as a recombinant vaccine. Images Fig. 1 PMID:7708765

  17. 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.

  18. 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.

  19. Generation of Recombinant Arenavirus for Vaccine Development in FDA-Approved Vero Cells

    PubMed Central

    de la Torre, Juan Carlos; Martínez-Sobrido, Luis

    2013-01-01

    The development and implementation of arenavirus reverse genetics represents a significant breakthrough in the arenavirus field 4. The use of cell-based arenavirus minigenome systems together with the ability to generate recombinant infectious arenaviruses with predetermined mutations in their genomes has facilitated the investigation of the contribution of viral determinants to the different steps of the arenavirus life cycle, as well as virus-host interactions and mechanisms of arenavirus pathogenesis 1, 3, 11 . In addition, the development of trisegmented arenaviruses has permitted the use of the arenavirus genome to express additional foreign genes of interest, thus opening the possibility of arenavirus-based vaccine vector applications 5 . Likewise, the development of single-cycle infectious arenaviruses capable of expressing reporter genes provides a new experimental tool to improve the safety of research involving highly pathogenic human arenaviruses 16 . The generation of recombinant arenaviruses using plasmid-based reverse genetics techniques has so far relied on the use of rodent cell lines 7,19 , which poses some barriers for the development of Food and Drug Administration (FDA)-licensed vaccine or vaccine vectors. To overcome this obstacle, we describe here the efficient generation of recombinant arenaviruses in FDA-approved Vero cells. PMID:23928556

  20. 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

  1. 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., III; 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.

  2. 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

  3. 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

  4. 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.

  5. Local generation of the strahl in the solar wind electrons via whistler instability

    NASA Astrophysics Data System (ADS)

    Seough, J.; Nariyuki, Y.; Yoon, P. H.; Saito, S.

    2015-12-01

    The present study put forth a possible explanation for the formation of the strahl component in the measured solar wind electron velocity distribution functions (VDFs). Based upon the observational fact that in the collisionless plasmas, the halo electrons possess a net drift speed with respect to the core, the present study carries out one-dimensional particle-in-cell simulation of the whistler instability driven by the anisotropic core in the presence of the isotropic drifting halo electrons. Pitch angle scattering of the halo electrons occurs by the enhanced whistler waves. The pitch angle scattering primarily affects the halo moving in the field-aligned direction, resulting in pitch angle diffusion across 90o gap in velocity space through nonlinear scattering process. This non-resonant interaction is accompanied by the reduction in a net drift speed of the halo, distinguishing the strahl feature from the halo electrons. Consequently, the remaining portion of the field-aligned moving halo, which is not affected by pitch angle scattering, simply appears to form the strahl in the electron velocity distribution. The core-halo-strahl feature shown in the numerical result is consistent with the observed electron VDF in the solar wind. The present scenario of local generation of the strahl suggests the new idea that the halo and strahl components might actually be one and the same, except that the strahl might simply be the remnant of pitch angle scattering of the anti-sunward moving halo by the whistler instability.

  6. Generation of genetically stable recombinant rotaviruses containing novel genome rearrangements and heterologous sequences by reverse genetics.

    PubMed

    Navarro, Aitor; Trask, Shane D; Patton, John T

    2013-06-01

    The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5' and 3' untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3' UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>10(7) PFU/ml) and remained genetically stable during serial passage. Despite their longer 3' UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein in vivo. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents. PMID:23536662

  7. Generation of a Chinese Hamster Ovary Cell Line Producing Recombinant Human Glucocerebrosidase

    PubMed Central

    Novo, Juliana Branco; Morganti, Ligia; Moro, Ana Maria; Paes Leme, Adriana Franco; Serrano, Solange Maria de Toledo; Raw, Isaias; Ho, Paulo Lee

    2012-01-01

    Impaired activity of the lysosomal enzyme glucocerebrosidase (GCR) results in the inherited metabolic disorder known as Gaucher disease. Current treatment consists of enzyme replacement therapy by administration of exogenous GCR. Although effective, it is exceptionally expensive, and patients worldwide have a limited access to this medicine. In Brazil, the public healthcare system provides the drug free of charge for all Gaucher's patients, which reaches the order of $ 84 million per year. However, the production of GCR by public institutions in Brazil would reduce significantly the therapy costs. Here, we describe a robust protocol for the generation of a cell line producing recombinant human GCR. The protein was expressed in CHO-DXB11 (dhfr−) cells after stable transfection and gene amplification with methotrexate. As expected, glycosylated GCR was detected by immunoblotting assay both as cell-associated (~64 and 59 kDa) and secreted (63–69 kDa) form. Analysis of subclones allowed the selection of stable CHO cells producing a secreted functional enzyme, with a calculated productivity of 5.14 pg/cell/day for the highest producer. Although being laborious, traditional methods of screening high-producing recombinant cells may represent a valuable alternative to generate expensive biopharmaceuticals in countries with limited resources. PMID:23091360

  8. COUPLING OF V(D)J RECOMBINATION TO THE CELL CYCLE SUPPRESSES GENOMIC INSTABILITY AND LYMPHOID TUMORIGENESIS

    PubMed Central

    Zhang, Li; Reynolds, Taylor L.; Shan, Xiaochuan

    2011-01-01

    Summary V(D)J gene segment recombination is linked to the cell cycle by the periodic phosphorylation and destruction of the RAG-2 protein at the G1-to-S cell cycle transition. To examine the function of this coupling, we constructed mice in which the phosphorylation site at threonine 490 of RAG-2 was mutated to alanine. The RAG-2 T490A mutation uncoupled DNA cleavage from cell cycle and promoted aberrant recombination. Similar aberrant recombination products were observed in mice deficient in the Skp2 ubiquitin ligase subunit, which is required for periodic destruction of RAG-2. On a p53-deficient background the RAG-2 T490A mutation induced lymphoid malignancies characterized by clonal chromosomal translocations involving antigen receptor genes. Taken together these observations provide a direct link between the periodic destruction of RAG-2 and lymphoid tumorigenesis. We infer that cell cycle control of the V(D)J recombinase limits the potential genomic damage that could otherwise result from RAG-mediated DNA cleavage. PMID:21349429

  9. Generation/recovery mechanism of defects responsible for the permanent component in negative bias temperature instability

    NASA Astrophysics Data System (ADS)

    Yonamoto, Yoshiki

    2013-04-01

    The defects responsible for the permanent component observed in negative bias temperature (NBT) stressed metal-oxide-semiconductor field effect transistors with an oxynitride gate insulator were investigated by using isochronal annealing experiments, spin dependent recombination (SDR), and spin dependent tunneling (SDT) technique. Two defects were found in the permanent component after light NBT stresses; interface states (Dit) and fixed positive charges (Dpc), which are closely related. The data support a model where hydrogen emitted from interfacial Si-H bonds by NBT stresses reacts with Si-X-Si structures (X = oxygen or nitrogen) in the gate insulator, which leaves silicon dangling bonds (Dit) and leads to the generation of Si-X+H-Si (overcoordinated oxygen or nitrogen, Dpc). Heavy NBT stresses simultaneously accelerate the formation and generation of new defects, which act as additional Dit and Dpc. Moreover, these defects cause stress-induced leakage current. Concerning their origin, defects similar to K- and E'γ-centers were detected by using SDR and SDT. They are unrelated to hydrogen and can be formed through the breaking of Si-X bonds. On the basis of these results, we propose a model for the generation and recovery behavior of defects and present a comparison with the previous studies.

  10. 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.

  11. Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques.

    PubMed

    Doxiadis, Gaby G M; de Groot, Nanine; Otting, Nel; de Vos-Rouweler, Annemiek J M; Bolijn, Maria J; Heijmans, Corrine M C; de Groot, Natasja G; van der Wiel, Marit K H; Remarque, Edmond J; Vangenot, Christelle; Nunes, José M; Sanchez-Mazas, Alicia; Bontrop, Ronald E

    2013-08-01

    The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated "new" haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population. PMID:23715823

  12. Exploring the transcriptome space of a recombinant BHK cell line through next generation sequencing.

    PubMed

    Johnson, Kathryn C; Yongky, Andrew; Vishwanathan, Nandita; Jacob, Nitya M; Jayapal, Karthik P; Goudar, Chetan T; Karypis, George; Hu, Wei-Shou

    2014-04-01

    Baby Hamster Kidney (BHK) cell lines are used in the production of veterinary vaccines and recombinant proteins. To facilitate transcriptome analysis of BHK cell lines, we embarked on an effort to sequence, assemble, and annotate transcript sequences from a recombinant BHK cell line and Syrian hamster liver and brain. RNA-seq data were supplemented with 6,170 Sanger ESTs from parental and recombinant BHK lines to generate 221,583 contigs. Annotation by homology to other species, primarily mouse, yielded more than 15,000 unique Ensembl mouse gene IDs with high coverage of KEGG canonical pathways. High coverage of enzymes and isoforms was seen for cell metabolism and N-glycosylation pathways, areas of highest interest for biopharmaceutical production. With the high sequencing depth in RNA-seq data, we set out to identify single-nucleotide variants in the transcripts. A majority of the high-confidence variants detected in both hamster tissue libraries occurred at a frequency of 50%, indicating their origin as heterozygous germline variants. In contrast, the cell line libraries' variants showed a wide range of occurrence frequency, indicating the presence of a heterogeneous population in cultured cells. The extremely high coverage of transcripts of highly abundant genes in RNA-seq enabled us to identify low-frequency variants. Experimental verification through Sanger sequencing confirmed the presence of two variants in the cDNA of a highly expressed gene in the BHK cell line. Furthermore, we detected seven potential missense mutations in the genes of the growth signaling pathways that may have arisen during the cell line derivation process. The development and characterization of a BHK reference transcriptome will facilitate future efforts to understand, monitor, and manipulate BHK cells. Our study on sequencing variants is crucial for improved understanding of the errors inherent in high-throughput sequencing and to increase the accuracy of variant calling in BHK or

  13. 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.

  14. 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). PMID:23909325

  15. 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.

  16. Utilization of site-specific recombination for generating therapeutic protein producing cell lines.

    PubMed

    Campbell, Margie; Corisdeo, Susanne; McGee, Clair; Kraichely, Denny

    2010-07-01

    The AttSite Recombinase Technology from Intrexon, Blacksburg, VA, utilizes specific DNA sequences and proprietary recombinase enzymes to catalyze the insertion of a gene of interest at a specific location in the host cell genome. Using this technology, we have developed Chinese Hamster Ovary (CHO) cell lines that have incorporated attB recombination sites at highly transcriptionally active loci or 'hot spots' within the cell genome. Subsequently, these attB site containing host cell lines could then be used for the expression of future Centocor products. Candidate production cell lines would be generated by a simple recombination event. Since the therapeutic gene of interest would preferentially integrate into the pre-selected high-expressing attB site, candidate cell lines would consistently express high levels of the gene of interest. We have been able to demonstrate that the AttSite Recombinase Technology could be a valid approach for the development of high-expressing production cell lines. PMID:20300883

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  18. 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.

  19. 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

  20. 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.

  1. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step

    PubMed Central

    Huang, Renhua; Gorman, Kevin T.; Vinci, Chris R.; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K.

    2015-01-01

    Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the “affinity maturation” step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402

  2. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step.

    PubMed

    Huang, Renhua; Gorman, Kevin T; Vinci, Chris R; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K

    2015-01-01

    Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402

  3. λ Recombination and Recombineering.

    PubMed

    Murphy, Kenan C

    2016-05-01

    The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics. PMID:27223821

  4. Diagnostic Potential of Recombinant scFv Antibodies Generated Against Hemagglutinin Protein of Influenza A Virus

    PubMed Central

    Rajput, Roopali; Sharma, Gaurav; Rawat, Varsha; Gautam, Anju; Kumar, Binod; Pattnaik, B.; Pradhan, H. K.; Khanna, Madhu

    2015-01-01

    Human influenza A viruses have been the cause of enormous socio-economic losses worldwide. In order to combat such a notorious pathogen, hemagglutinin protein (HA) has been a preferred target for generation of neutralizing-antibodies as potent therapeutic/diagnostic agents. In the present study, recombinant anti-HA single chain variable fragment antibodies were constructed using the phage-display technology to aid in diagnosis and treatment of human influenza A virus infections. Spleen cells of mice hyper-immunized with A/New Caledonia/20/99 (H1N1) virus were used as the source for recombinant antibody (rAb) production. The antigen-binding phages were quantified after six rounds of bio-panning against A/New Caledonia/20/99 (H1N1), A/California/07/2009 (H1N1)-like, or A/Udorn/307/72(H3N2) viruses. The maximum phage yield was for the A/New Caledonia/20/99 (H1N1), however, considerable cross-reactivity was observed for the other virus strains as well. The HA-specific polyclonal rAb preparation was subjected to selection of single clones for identification of high reactive relatively conserved epitopes. The high-affinity rAbs were tested against certain known conserved HA epitopes by peptide ELISA. Three recombinant mAbs showed reactivity with both the H1N1 strains and one (C5) showed binding with all the three viral strains. The C5 antibody was thus used for development of an ELISA test for diagnosis of influenza virus infection. Based on the sample size in the current analysis, the ELISA test demonstrated 83.9% sensitivity and 100% specificity. Thus, the ELISA, developed in our study, may prove as a cheaper alternative to the presently used real time RT–PCR test for detection of human influenza A viruses in clinical specimens, which will be beneficial, especially in the developing countries. PMID:26388868

  5. 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.

  6. 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. PMID:16486834

  7. 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.

  8. Generation and screening of recombinant inbred lines of rice for yellow stemborer resistance.

    PubMed

    Mohankumar, S; Thiruvengadam, V; Samiayyan, K; Shanmugasundaram, P

    2003-04-01

    Based on the results of studies on varietal screening, antixenosis (egg laying preference) and antibiosis (larval survival and adult emergence), rice varieties W1263 and CO43 were selected as resistant and susceptible parents, respectively, for yellow stemborer (YSB) infestation. A mapping population was developed using above parents following single seed descent method. Screening for YSB reaction in F1 and F2, generations under field and glasshouse conditions for both dead hearts and white ears, established the polygenic nature of inheritance for YSB resistance. Field screening for YSB resistance at F9 generation revealed the difference in the reactions among recombinant inbred lines (RILs) between vegetative and reproductive stages. The experiments under field and glasshouse screening of RILs for dead hearts showed significant positive association. However, the reaction was more towards susceptibility in glasshouse screening due to no choice test. Scoring of 250 RILs (F8) for various morphological traits showed wide range of variation indicating the suitability for QTL mapping. PMID:15255645

  9. High-Throughput Generation of P. falciparum Functional Molecules by Recombinational Cloning

    PubMed Central

    Aguiar, João Carlos; LaBaer, Joshua; Blair, Peter L.; Shamailova, Victoria Y.; Koundinya, Malvika; Russell, Joshua A.; Huang, Fengying; Mar, Wenhong; Anthony, Robert M.; Witney, Adam; Caruana, Sonia R.; Brizuela, Leonardo; Sacci, John B.; Hoffman, Stephen L.; Carucci, Daniel J.

    2004-01-01

    Large-scale functional genomics studies for malaria vaccine and drug development will depend on the generation of molecular tools to study protein expression. We examined the feasibility of a high-throughput cloning approach using the Gateway system to create a large set of expression clones encoding Plasmodium falciparum single-exon genes. Master clones and their ORFs were transferred en masse to multiple expression vectors. Target genes (n = 303) were selected using specific sets of criteria, including stage expression and secondary structure. Upon screening four colonies per capture reaction, we achieved 84% cloning efficiency. The genes were subcloned in parallel into three expression vectors: a DNA vaccine vector and two protein expression vectors. These transfers yielded a 100% success rate without any observed recombination based on single colony screening. The functional expression of 95 genes was evaluated in mice with DNA vaccine constructs to generate antibody against various stages of the parasite. From these, 19 induced antibody titers against the erythrocytic stages and three against sporozoite stages. We have overcome the potential limitation of producing large P. falciparum clone sets in multiple expression vectors. This approach represents a powerful technique for the production of molecular reagents for genome-wide functional analysis of the P. falciparum genome and will provide for a resource for the malaria resource community distributed through public repositories. PMID:15489329

  10. Generation of recombinant rabies viruses encoding NanoLuc luciferase for antiviral activity assays.

    PubMed

    Anindita, Paulina Duhita; Sasaki, Michihito; Nobori, Haruaki; Sato, Akihiko; Carr, Michael; Ito, Naoto; Sugiyama, Makoto; Orba, Yasuko; Sawa, Hirofumi

    2016-04-01

    Rabies is an invariably fatal disease caused by Rabies virus (RABV), a member of the family Rhabdoviridae, genus Lyssavirus. Once central nervous infection occurs and symptoms develop, the case fatality rate approaches 100% despite availability of post-exposure prophylaxis. Therefore, new antiviral therapies for rabies are urgently required. Antivirals which can inhibit virus replication can be identified through screening of small compounds, however, as RABV infection does not generate easily discernible cytopathic effects in vitro, cell viability assays may not be feasible to observe antiviral activity of small compounds against RABV. In this study, recombinant RABVs (rRABVs) encoding NanoLuc luciferase (NanoLuc) were generated to facilitate the screening of small compound libraries. NanoLuc expression was confirmed in single-step growth cures of virus infection and showed that the rRABVs were capable of viral replication without decrease of luciferase activity through ten serial passages. Furthermore, the rRABVs were able to quantify the antiviral activity of the nucleoside analogue ribavirin against RABV in vitro. These findings confirm the potential of the rRABV encoding NanoLuc system to facilitate screening of small compounds to inhibit RABV infection. PMID:26869397

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombination and reassortment of viral genomes are major processes contributing to 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 ...

  12. Strategies to generate high-titer, high-potency recombinant AAV3 serotype vectors

    PubMed Central

    Ling, Chen; Yin, Zifei; Li, Jun; Zhang, Daniel; Aslanidi, George; Srivastava, Arun

    2016-01-01

    Although recombinant adeno-associated virus serotype 3 (AAV3) vectors were largely ignored previously, owing to their poor transduction efficiency in most cells and tissues examined, our initial observation of the selective tropism of AAV3 serotype vectors for human liver cancer cell lines and primary human hepatocytes has led to renewed interest in this serotype. AAV3 vectors and their variants have recently proven to be extremely efficient in targeting human and nonhuman primate hepatocytes in vitro as well as in vivo. In the present studies, we wished to evaluate the relative contributions of the cis-acting inverted terminal repeats (ITRs) from AAV3 (ITR3), as well as the trans-acting Rep proteins from AAV3 (Rep3) in the AAV3 vector production and transduction. To this end, we utilized two helper plasmids: pAAVr2c3, which carries rep2 and cap3 genes, and pAAVr3c3, which carries rep3 and cap3 genes. The combined use of AAV3 ITRs, AAV3 Rep proteins, and AAV3 capsids led to the production of recombinant vectors, AAV3-Rep3/ITR3, with up to approximately two to fourfold higher titers than AAV3-Rep2/ITR2 vectors produced using AAV2 ITRs, AAV2 Rep proteins, and AAV3 capsids. We also observed that the transduction efficiency of Rep3/ITR3 AAV3 vectors was approximately fourfold higher than that of Rep2/ITR2 AAV3 vectors in human hepatocellular carcinoma cell lines in vitro. The transduction efficiency of Rep3/ITR3 vectors was increased by ~10-fold, when AAV3 capsids containing mutations in two surface-exposed residues (serine 663 and threonine 492) were used to generate a S663V+T492V double-mutant AAV3 vector. The Rep3/ITR3 AAV3 vectors also transduced human liver tumors in vivo approximately twofold more efficiently than those generated with Rep2/ITR2. Our data suggest that the transduction efficiency of AAV3 vectors can be significantly improved both using homologous Rep proteins and ITRs as well as by capsid optimization. Thus, the combined use of homologous Rep

  13. Observations of midlatitude ionospheric instabilities generating meter-scale waves at the magnetic equator

    NASA Astrophysics Data System (ADS)

    Makela, J. J.; Kelley, M. C.; Tsunoda, R. T.

    2009-01-01

    We present data from a spectacular low-latitude ionospheric event obtained using two ionospheric imaging systems located on the Haleakala Volcano on Maui, Hawaii (geographic: 20.7°N, 203.8°E geomagnetic: 21.0°N, 271.9°E), and a 50-MHz coherent scatter radar located on Christmas Island (geographic: 2.0°N, 202.6°E geomagnetic: 3.1°N, 273.6°E). During the event, structure is seen to develop in the imaging data, extending out of the northern edge of the imaging systems' fields of view. Using data from dual-frequency Global Positioning System receivers located throughout Hawaii, the structures are seen to evolve against an enhanced background of total electron content caused by an ongoing geomagnetic storm suggesting that the pertinent features in the event are electron density enhancements, rather than depletions that typify structure in the postsunset data from these instruments. Early in the evening, 3-m backscatter, as measured by the radar on Christmas Island, occurs at the magnetic equator on magnetic field lines that are connected to the edges on both sides of this enhanced structure seen in the images. We discuss how multiple irregularity processes must be responsible for this unusual facet of the radar data, as individual processes can only explain the development of irregularities on electron density gradients in one direction. We conclude that one of the processes responsible for the irregularities must occur in the local, off-equator ionosphere. The larger-scale electric fields associated with these irregularities map to the magnetic equator where they generate the instabilities observed by the radar.

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

  15. Laser-field-related recombination interference in high-order harmonic generation from CO{sub 2} molecules

    SciTech Connect

    Wei Pengfei; Liu Peng; Zeng Zhinan; Guo Xiaodong; Ge Xiaochun; Li Ruxin; Xu Zhizhan; Chen Jing

    2009-05-15

    We reinvestigate the modulation inversion of angular distribution of high-order harmonic generation (HHG) from impulsively aligned CO{sub 2} molecules. The angular distribution is found to be sensitive to both the harmonic order and the intensity of the driving laser pulse for HHG. The roles of intramolecular quantum interference and the laser intensity are clarified. A laser-field-related recombination interference model is proposed to explain the modulation inversion of harmonic yield with respect to the molecular alignment. We conclude that the two-center interference in the recombination process can be manipulated by changing the laser intensity.

  16. 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

  17. 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. PMID:25045718

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

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Ken; Kuwabara, Takuhito; Uda, Tsuyoshi

    2013-03-01

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

  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 meiomaps of genome-wide recombination and chromosome segregation in human oocytes.

    PubMed

    Ottolini, Christian S; Capalbo, Antonio; Newnham, Louise; Cimadomo, Danilo; Natesan, Senthilkumar A; Hoffmann, Eva R; Ubaldi, Filippo M; Rienzi, Laura; Handyside, Alan H

    2016-07-01

    We have developed a protocol for the generation of genome-wide maps (meiomaps) of recombination and chromosome segregation for the three products of human female meiosis: the first and second polar bodies (PB1 and PB2) and the corresponding oocyte. PB1 is biopsied and the oocyte is artificially activated by exposure to calcium ionophore, after which PB2 is biopsied and collected with the corresponding oocyte. The whole genomes of the polar bodies and oocytes are amplified by multiple displacement amplification and, together with maternal genomic DNA, genotyped for ∼300,000 single-nucleotide polymorphisms (SNPs) genome-wide by microarray. Informative maternal heterozygous SNPs are phased using a haploid PB2 or oocyte as a reference. A simple algorithm is then used to identify the maternal haplotypes for each chromosome, in all of the products of meiosis for each oocyte. This allows mapping of crossovers and analysis of chromosome segregation patterns. The protocol takes a minimum of 3-5 d and requires a clinical embryologist with micromanipulation experience and a molecular biologist with basic bioinformatic skills. It has several advantages over previous methods; importantly, the use of artificial oocyte activation avoids the creation of embryos for research purposes. In addition, compared with next-generation sequencing, targeted SNP genotyping is cost-effective and it simplifies the bioinformatic analysis, as only one haploid reference sample is required to establish phase for maternal haplotyping. Finally, meiomapping is more informative than copy-number analysis alone for analysis of chromosome segregation patterns. Using this protocol, we have provided new insights that may lead to improvements in assisted reproduction for the treatment of infertility. PMID:27310263

  1. 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.

  2. Modulational instability and generation of pulse trains in asymmetric dual-core nonlinear optical fibers

    NASA Astrophysics Data System (ADS)

    Ganapathy, R.; Malomed, Boris A.; Porsezian, K.

    2006-06-01

    Instability of continuous-wave (CW) states is investigated in a system of two parallel-coupled fibers, with a pumped (active) nonlinear dispersive core and a lossy (passive) linear one. Modulational instability (MI) conditions are found from linearized equations for small perturbations, the results being drastically different for the normal and anomalous group-velocity dispersion (GVD) in the active core. Simulations of the full system demonstrate that the development of the MI in the former regime leads to establishment of a regular or chaotic array of pulses, if the MI saturates, or a chain of well-separated peaks with continuously growing amplitudes if the instability does not saturate. In the anomalous-GVD regime, a chain of return-to-zero (RZ) peaks, or a single RZ peak emerge, also with growing amplitudes. The latter can be used as a source of RZ pulses for optical telecommunications.

  3. 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

  4. 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

  5. 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.

  6. DNA Delivery by Microinjection for the Generation of Recombinant Mammalian Cell Lines

    NASA Astrophysics Data System (ADS)

    Chenuet, Sebastien; Derouazi, Madiha; Hacker, David; Wurm, Florian

    Gene transfer methods for producing recombinant cell lines are often not very efficient. One reason is that the recombinant DNA is delivered into the cell cytoplasm and only a small fraction reaches the nucleus. This chapter describes a method for microinjecting DNA directly into the nucleus. Direct injection has several advantages including the ability to deliver a defined copy number into the nucleus, the avoidance of DNAses that are present in the cell cytoplasm, and the lack of a need for extensive subcloning to find the recombinant cells. The procedure is described for two cell lines, CHO DG44 and BHK-21, using green fluorescent protein as a reporter gene. However, this method could easily be adapted to other cells lines and using other recombinant genes.

  7. 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.

  8. 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

  9. [Generation and preliminary immunological efficacy of a recombinant human adenovirus-rabies virus glycoprotein].

    PubMed

    Wang, Ying; Zhang, Shou-Feng; Liu, Ye; Zhang, Fei; Zhang, Jin-Xia; Hu, Rong-Liang

    2011-09-01

    To construct a recombinant human adenovirus type 5 expressing glycoprotein (GP) of attenuated rabies virus SRV9 and testing immunological efficacy on the immunized mice. Open reading frame of rabies virus GP gene of SRV9 strain was cloned into the shuttle vector of adenovirus expression system in multiple cloning sites to construct the recombinant shuttle plasmid pacAd5 CMV-Gs9, cotransfection was performed into 293AD cells mediated by FuGENE Transfection Reagent with linearized backbone plasmid and recombinant shuttle plasmid, cell cultures were collected after CPE appearance and were identified by PCR and electronmicroscopy, virus titer was measured in 293AD cells. Kunming mice were intraperitoneally injected with 10(6) TCID50 adenovirus, blood for serum preparation was collected through caudal vein pre-immune and post-immune and tested for VNA appearance by fluorescent antibody virus neutralization test (FAVN) detection. Recombinant shuttle plasmid pacAd5 CMV-Gs9 was constructed correctly. A recombinant human adenovirus type 5 was obtained expressing GP protein of rabies virus SRV9. The virus titer reached 10(6) CFU/mL at the least. All mice developed a certain amount of the anti-rabies neutralizing antibody 14 days after intraperitoneal inoculation, while the effective protection rates were 90%. In conclusion, Recombinant adenovirus expressing the rabies virus GP was constructed successfully and a certain amount of neutralizing antibodies were induced in mice, which laid the material foundation for further development of new rabies vaccine. PMID:21998956

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

    PubMed Central

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

    2015-01-01

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

  11. Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China.

    PubMed

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

    2015-03-01

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

  12. On the generation of the pulsating aurora by the loss cone driven whistler instability in the equatorial region

    SciTech Connect

    Huang, L.; Hawkins, J.G.; Lee, L.C. )

    1990-04-01

    Whistler waves are believed to play an important role in the generation of the pulsating aurora. Calculations in the literature show that either a loss cone or a thermal anisotropy in the hot plasma component of the magnetosphere can lead to the generation of incoherent whistler waves. In this paper, the authors have calculated the characteristics of incoherent whistler mode waves generated along the L = 5 geomagnetic field line, and considered the implications for the pulsating aurora if these waves play an important role in the pulsation mechanism. For the loss cone driven whistler instability, the growth rate along the L = 5 field line is largest just above the ionosphere where the loss cone angle is also large. However, the total amplification factor is actually much larger near the equator due to the more gradual magnetospheric variations and the smaller group velocity in this region. Thus, the largest wave growth from this process is expected in the same location where pitch angle scattering is believed to occur during auroral pulsations. The peak growth rate at the equator occurs at approximately 100 Hz, corresponding to {approximately} 1% of the local electron cyclotron frequency. This frequency is much smaller than the peak growth rate frequency at altitudes nearer to the ionosphere on the L = 5 field line. It is also in contrast to the frequently stated assumption that the whistler instability results in wave generation near the electron cyclotron frequency.

  13. Generation of mature Nα-terminal acetylated thymosin α 1 by cleavage of recombinant prothymosin α.

    PubMed

    Liu, Bo; Gong, Xin; Chang, Shaohong; Sun, Peng; Wu, Jun

    2013-01-01

    N(α)-terminal acetylation of peptides plays an important biological role but is rarely observed in prokaryotes. N(α)-terminal acetylated thymosin α1 (Tα1), a 28-amino-acid peptide, is an immune modifier that has been used in the clinic to treat hepatitis B and C virus (HBV/HCV) infections. We previously documented N(α)-terminal acetylation of recombinant prothymosin α (ProTα) in E. coli. Here we present a method for production of N(α)-acetylated Tα1 from recombinant ProTα. The recombinant ProTα was cleaved by human legumain expressed in Pichia pastoris to release Tα1 in vitro. The N(α)-acetylated Tα1 peptide was subsequently purified by reverse phase and cation exchange chromatography. Mass spectrometry indicated that the molecular mass of recombinant N(α)-acetylated Tα1 was 3108.79 in, which is identical to the mass of N(α)-acetylated Tα1 produced by total chemical synthesis. This mass corresponded to the nonacetylated Tα1 mass with a 42 Da increment. The retention time of recombinant N(α)-acetylated Tα1 and chemosynthetic N(α)-acetylated Tα1 were both 15.4 min in RP-high performance liquid chromatography (HPLC). These data support the use of an E. coli expression system for the production of recombinant human N(α)-acetylated Tα1 and also will provide the basis for the preparation of recombinant acetylated peptides in E. coli. PMID:24288480

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

    PubMed

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

    2016-06-01

    Several naturally occurring vertebrate transposable elements have been genetically modified to enable the transposition of recombinant genes in mammalian cells. We compared three transposons-piggyBac, Tol2, and Sleeping Beauty-for their ability to generate cell pools (polyclonal cultures of recombinant cells) and clonal cell lines for the large-scale production of recombinant proteins using Chinese hamster ovary cells (CHO-DG44) as the host. Transfection with each of the dual-vector transposon systems resulted in cell pools with volumetric yields of tumor necrosis factor receptor-Fc fusion protein (TNFR:Fc) that were about ninefold higher than those from cell pools generated by conventional plasmid transfection. On average, the cell pools had 10-12 integrated copies of the transgene per cell. In the absence of selection, the volumetric productivity of the cell pools decreased by 50% over a 2-month cultivation period and then remained constant. The average volumetric TNFR:Fc productivity of clonal cell lines recovered from cell pools was about 25 times higher than that of cell lines generated by conventional transfection. In 14-day fed-batch cultures, TNFR:Fc levels up to 900 mg/L were obtained from polyclonal cell pools and up to 1.5 g/L from clonal cell lines using any of the three transposons. Biotechnol. Bioeng. 2016;113: 1234-1243. © 2015 Wiley Periodicals, Inc. PMID:26616356

  15. 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

  16. Generation of Periodic Signatures at Saturn Through Titan's Interaction with the Centrifugal Interchange Instability

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Due to 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. Multi-fluid/multi-scale simulations that include the heavy ions from the Enceladus plasma torus, the light ions of the solar wind and the interaction of Titan with the Kronian magnetosphere show that the rotational period is embedded in the development of the interchange instability but the planetary period is masked by high-frequency components of the instability. The presence of Titan is shown to damp the high-frequency components in association with the flapping of Titan's ion tail and this 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 5-7 large interchange fingers dominate to one where there are about 3 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 Saturn's kilometic radiation.

  17. Role of fluctuations in instability generation in gas-solid suspensions

    NASA Astrophysics Data System (ADS)

    Subramaniam, Shankar; Mehrabadi, Mohammad; Kolakaluri, Ravi; Tenneti, Sudheer

    2013-11-01

    Stability analysis of gas-solid suspensions using kinetic theory (Koch, Phys. Fluids, 1990) relies on a number density function (NDF) that is based on the canonical (constant number) ensemble. Euler-Lagrange simulations of a model problem are used to show that this approach does not accurately represent the scale-dependent interphase coupling between different realizations of the gas velocity field and fluctuations in the number of particles naturally occurring in fluidized beds. The grand-canonical (or variable number) ensemble is better suited to representing this coupling, and it is shown how the NDF can be related to this ensemble. The evolution of the grand-canonical NDF then leads to instabilities and growth of spatial fluctuations in the number density of a homogeneous suspension. This analysis leads to a different explanation for the growth of instabilities in homogeneous gas-solid suspensions that does not require perturbations in the average number density. Rather it is shown that the interaction of different realizations of the gas velocity field with individual realizations of the particle field leads to the growth of instabilities due to the dependence of drag on local volume fraction in each realization, that is extracted from particle-resolved DNS data. This work is partially supported by NSF CBET 1134500.

  18. Observation of Self-Similarity in the Magnetic Fields Generated by the Ablative Nonlinear Rayleigh-Taylor Instability

    NASA Astrophysics Data System (ADS)

    Gao, Lan

    2014-10-01

    The Rayleigh-Taylor (RT) instability has been extensively studied because of its relevance to ignition target designs in inertial confinement fusion, material strength studies in high energy density physics, and astrophysical systems. This talk presents the first measurements of magnetic field generation by the nonlinear RT instability in laser-accelerated planar foils using ultrafast proton radiography at the OMEGA EP Laser System. Thin plastic foils were irradiated with 4-kJ, 2.5-ns laser pulses at focused laser intensities of ~1014 W /cm2. Target modulations were seeded by laser nonuniformities and amplified during the target-acceleration phase by the RT instability growth. A high-energy proton beam tracked the hydrodynamic evolution of the target and mapped the magnetic field spatial distribution with high spatial and temporal resolution. The experimental data show self-similar behavior in the growing cellular magnetic field structures. The calculated magnetic cell-merging rate is consistent with the value determined by earlier x-ray measurements, linking the cellular magnetic field structures with the RT bubble and spike growth. The results are consistent with two-dimensional magnetohydrodynamic simulations, showing MG-level magnetic field generation in the laser-driven foil. The work could benefit the understanding of magnetic-seed-field generation in high energy density plasmas and the flow-driven processes that induce global magnetic structures prior to their turbulent amplification by the dynamo process. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  19. Modelling high angle wave instability and the generation of large scale shoreline sand waves

    NASA Astrophysics Data System (ADS)

    van den Berg, Niels; Falqués, Albert; Ribas, Francesca

    2010-05-01

    Sandy coasts are dynamic systems, shaped by the continuous interaction between hydrodynamics and morphology. On a large time and spacial scale it is commonly assumed that the diffusive action of alongshore wave driven sediment transport dominates and maintains a stable and straight shoreline. Ashton et. al. (2001) however showed with a cellular model that for high angle off-shore wave incidence a coastline can be unstable and that shoreline sand waves can develop due to the feedback of shoreline changes into the wave field. These shoreline undulations can migrate and merge to form large scale capes and spits. Falqués and Calvete (2005) confirmed the mechanism of shoreline instability and shoreline sand wave formation with a linear stability analysis. They found a typical wavelength in the range 4-15 km and a characteristic growth time of a few years. Both studies however have there limitations. Ashton et. al. (2001) assume rectilinear depth contours and an infinite cross-shore extent of shoreline changes in the bathymetry. The linear stability analysis by Falqués and Calvete (2005) can only be applied for small amplitude shoreline changes. Both studies neglect cross-shore dynamics as bathymetric changes associated to shoreline changes are assumed to be instantaneous. In the current study, a nonlinear morphodynamic model is used. In this model the bathymetric lines are curvilinear and the cross-shore extent of shoreline changes in the bathymetry is dynamic due to the introduction of cross-shore dynamics. The cross-shore dynamics are parameterized by assuming a relaxation to an equilibrium cross-shore profile. The relaxation is controlled by a diffusivity which is proportional to wave energy dissipation. The new model is equivalent to N-lines models but applies sediment conservation like 2DH models instead of just moving contour lines. The main objective of this study is to extend the work of Falqués and Calvete (2005) and to study in more detail the mechanism of

  20. 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.

  1. 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)

  2. Dissipative structures in the F-region of the equatorial ionosphere generated by Rayleigh-Taylor instability

    NASA Astrophysics Data System (ADS)

    Sazonov, S. V.

    1991-12-01

    The nonlinear regime of electrostatic perturbations of the equatorial ionospheric F-region generated by Rayleigh-Taylor instability has been discussed, taking into account conductivity along magnetic field lines. A closed nonlinear equation has been derived in the stationary limit for the polarization electric field potential. It coincides with the Karman equation of an ideal liquid. To solve the equation, the averaged variational Whitham method has been proposed. Some solutions localized along and across the geomagnetic field, B, as well as quasi-periodic solutions in the transverse direction, have been investigated. Nonlinear longitudinal localization of perturbations has been shown to be due to electron-ion collisions.

  3. 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

  4. 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. PMID:26458834

  5. Ion acceleration and coherent structures generated by lower hybrid shear-driven instabilities

    NASA Technical Reports Server (NTRS)

    Romero, H.; Ganguli, G.; Lee, Y. C.

    1992-01-01

    It is shown that if k = omega(S)/omega(LH) greater than 1 (omega(S) and omega(LH) are the shear and lower hybrid frequencies), a sheared electron cross-field flow excites the electron-ion-hybrid mode, causing significant perpendicular ion acceleration. The electric potential develops coherent structures (vortexlike) longer than the electron Larmor radius, rho(e). For k less than 1, a smooth transition occurs where the wavelength becomes of the order of rho(e), the lower hybrid drift instability dominates, and the formation of vortexlike structures is no longer observed. The results are relevant to laboratory, laser-produced, and space plasmas.

  6. 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.

  7. Variable opening angle of emission cone of Jovian decameter radiation generated by cyclotron maser instability

    NASA Astrophysics Data System (ADS)

    Galopeau, P. H. M.; Boudjada, M. Y.; Rucker, H. O.

    2015-10-01

    A recent study of the Io-controlled Jovian decameter radiation revealed that the radio emission is beamed in a hollow cone which presents a flattening in a specific direction linked to the local magnetic field in the source. We investigate some reasons for the existence of such a flattening. The Jovian decameter radiation, like the other auroral radio emissions emanating from the magnetized planets in the solar system, is known to be produced by the cyclotron maser instability (CMI). This mechanism allows the direct amplification of the waves through a resonant coupling between the electron population of the plasma and the electromagnetic.

  8. 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.

  9. 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.

  10. Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress

    PubMed Central

    Foijer, Floris; Xie, Stephanie Z.; Simon, Judith E.; Bakker, Petra L.; Conte, Nathalie; Davis, Stephanie H.; Kregel, Eva; Jonkers, Jos; Bradley, Allan; Sorger, Peter K.

    2014-01-01

    Aneuploidy is a hallmark of human solid cancers that arises from errors in mitosis and results in gain and loss of oncogenes and tumor suppressors. Aneuploidy poses a growth disadvantage for cells grown in vitro, suggesting that cancer cells adapt to this burden. To understand better the consequences of aneuploidy in a rapidly proliferating adult tissue, we engineered a mouse in which chromosome instability was selectively induced in T cells. A flanked by Lox mutation was introduced into the monopolar spindle 1 (Mps1) spindle-assembly checkpoint gene so that Cre-mediated recombination would create a truncated protein (Mps1DK) that retained the kinase domain but lacked the kinetochore-binding domain and thereby weakened the checkpoint. In a sensitized p53+/− background we observed that Mps1DK/DK mice suffered from rapid-onset acute lymphoblastic lymphoma. The tumors were highly aneuploid and exhibited a metabolic burden similar to that previously characterized in aneuploid yeast and cultured cells. The tumors nonetheless grew rapidly and were lethal within 3–4 mo after birth. PMID:25197064

  11. Generating energetic electrons through staged acceleration in the two-plasmon-decay instability in inertial confinement fusion.

    PubMed

    Yan, R; Ren, C; Li, J; Maximov, A V; Mori, W B; Sheng, Z-M; Tsung, F S

    2012-04-27

    A new hot-electron generation mechanism in two-plasmon-decay instabilities is described based on a series of 2D, long-term (~10 ps) particle-in-cell and fluid simulations under parameters relevant to inertial confinement fusion. The simulations show that significant laser absorption and hot-electron generation occur in the nonlinear stage. The hot electrons are stage accelerated from the low-density region to the high-density region. New modes with small phase velocities develop in the low-density region in the nonlinear stage and form the first stage for electron acceleration. Electron-ion collisions are shown to significantly reduce the efficiency of this acceleration mechanism. PMID:22680873

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

    PubMed

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

    2009-05-01

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

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

    PubMed Central

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

    2009-01-01

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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Generation of Antigenic Variants via Gene Conversion: Evidence for Recombination Fitness Selection at the Locus Level in Anaplasma marginale▿

    PubMed Central

    Futse, James E.; Brayton, Kelly A.; Nydam, Seth D.; Palmer, Guy H.

    2009-01-01

    Multiple bacterial and protozoal pathogens utilize gene conversion to generate antigenically variant surface proteins to evade immune clearance and establish persistent infection. Both the donor alleles that encode the variants following recombination into an expression site and the donor loci themselves are under evolutionary selection: the alleles that encode variants that are sufficiently antigenically unique yet retain growth fitness and the loci that allow efficient recombination. We examined allelic usage in generating Anaplasma marginale variants during in vivo infection in the mammalian reservoir host and identified preferential usage of specific alleles in the absence of immune selective pressure, consistent with certain individual alleles having a fitness advantage for in vivo growth. In contrast, the loci themselves appear to have been essentially equally selected for donor function in gene conversion with no significant effect of locus position relative to the expression site or origin of replication. This pattern of preferential allelic usage but lack of locus effect was observed independently for Msp2 and Msp3 variants, both generated by gene conversion. Furthermore, there was no locus effect observed when a single locus contained both msp2 and msp3 alleles in a tail-to-tail orientation flanked by a repeat. These experimental results support the hypothesis that predominance of specific variants reflects in vivo fitness as determined by the encoding allele, independent of locus structure and chromosomal position. Identification of highly fit variants provides targets for vaccines that will prevent the high-level bacteremia associated with acute disease. PMID:19487473

  1. 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.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    An extreme ultraviolet source having a tamper has been studied. This target scheme recombines forcedly lithium ions by low temperature electrons from the tamper, converting Li3+ rapidly to excited Li2+ which emit intense 1s-2p Lyman α emissions at 13.5nm. A strong 13.5nm emission appeared at 20-30ns after the time of laser peak within a small space volume near the tamper. The authors obtained an enhancement of extreme ultraviolet conversion efficiency by a factor of about 2 with the tamper against that of a target without the tamper at the same laser irradiation condition.

  4. The adaptive imbalance in base excision–repair enzymes generates microsatellite instability in chronic inflammation

    PubMed Central

    Hofseth, Lorne J.; Khan, Mohammed A.; Ambrose, Mark; Nikolayeva, Olga; Xu-Welliver, Meng; Kartalou, Maria; Hussain, S. Perwez; Roth, Richard B.; Zhou, Xiaoling; Mechanic, Leah E.; Zurer, Irit; Rotter, Varda; Samson, Leona D.; Harris, Curtis C.

    2003-01-01

    Chronic infection and associated inflammation are key contributors to human carcinogenesis. Ulcerative colitis (UC) is an oxyradical overload disease and is characterized by free radical stress and colon cancer proneness. Here we examined tissues from noncancerous colons of ulcerative colitis patients to determine (a) the activity of two base excision–repair enzymes , AAG, the major 3-methyladenine DNA glycosylase, and APE1, the major apurinic site endonuclease; and (b) the prevalence of microsatellite instability (MSI). AAG and APE1 were significantly increased in UC colon epithelium undergoing elevated inflammation and MSI was positively correlated with their imbalanced enzymatic activities. These latter results were supported by mechanistic studies using yeast and human cell models in which overexpression of AAG and/or APE1 was associated with frameshift mutations and MSI. Our results are consistent with the hypothesis that the adaptive and imbalanced increase in AAG and APE1 is a novel mechanism contributing to MSI in patients with UC and may extend to chronic inflammatory or other diseases with MSI of unknown etiology. PMID:14679184

  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. 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.

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

    PubMed

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

    2015-11-01

    Conductivity of methylammonium lead triiodide (MAPbI3) perovskite was measured on different mesoporous metal oxide scaffolds: TiO2, Al2O3, and ZrO2, as a function of incident light irradiation and temperature. It was found that MAPbI3 exhibits intrinsic charge separation, and its conductivity stems from a majority of free charge carriers. The crystal morphology of the MAPbI3 was found to significantly affect the photoconductivity, whereas in the dark the conductivity is governed by the perovskite in the pores of the mesoporous scaffold. The temperature-dependent conductivity measurements also indicate the presence of states within the band gap of the perovskite. Despite a relatively large amount of crystal defects in the measured material, the main recombination mechanism of the photogenerated charges is bimolecular (band-to-band), which suggests that the defect states are rather inactive in the recombination. This may explain the remarkable efficiencies obtained for perovskite solar cells prepared with wet-chemical methods. PMID:26538041

  8. Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation.

    PubMed

    Binder, Stephan; Siedler, Solvej; Marienhagen, Jan; Bott, Michael; Eggeling, Lothar

    2013-07-01

    Recombineering in bacteria is a powerful technique for genome reconstruction, but until now, it was not generally applicable for development of small-molecule producers because of the inconspicuous phenotype of most compounds of biotechnological relevance. Here, we establish recombineering for Corynebacterium glutamicum using RecT of prophage Rac and combine this with our recently developed nanosensor technology, which enables the detection and isolation of productive mutants at the single-cell level via fluorescence-activated cell sorting (FACS). We call this new technology RecFACS, which we use for genomic site-directed saturation mutagenesis without relying on pre-constructed libraries to directly isolate L-lysine-producing cells. A mixture of 19 different oligonucleotides was used targeting codon 81 in murE of the wild-type, at a locus where one single mutation is known to cause L-lysine production. Using RecFACS, productive mutants were screened and isolated. Sequencing revealed 12 different amino acid exchanges in the targeted murE codon, which caused different L-lysine production titers. Apart from introducing a rapid genome construction technology for C. glutamicum, the present work demonstrates that RecFACS is suitable to simply create producers as well as genetic diversity in one single step, thus establishing a new general concept in synthetic biology. PMID:23630315

  9. 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

  10. 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.

  11. 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.

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

    PubMed

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

    2016-06-01

    Yunnan seems to be a "hot spot" region of HIV-1 recombination. CRF01_AE and subtype CRF08_BC are two main HIV-1 clades circulating in Yunnan. We report here a novel HIV-1 second-generation recombinant form originated from CRF01_AE and CRF08_BC. The strain (12YN10551) was isolated from a HIV-positive male infected through heterosexual contact in Dali prefecture of Yunnan province, China. This is the first report of HIV-1 near full-length genomic sequence in Dali. Recombinant analysis shows that 12YN10551 was composed of two well-established circulating recombinant forms (CRF01_AE and CRF08_BC). Two CRF01_AE recombinant fragments were inserted into the CRF08_BC backbone genome in the pol/vif/vpr/tat/rev and nef gene regions, respectively. The discovery and characterization of this new recombinant indicate that intersubtype recombination is continuously generating new forms of HIV-1. More work is needed to better monitor the genetic diversity of HIV-1 in this region. PMID:26885777

  13. Generation of TALEN-Mediated GRdim Knock-In Rats by Homologous Recombination

    PubMed Central

    Ponce de León, Verónica; Mérillat, Anne-Marie; Tesson, Laurent; Anegón, Ignacio; Hummler, Edith

    2014-01-01

    Transcription Activator-Like Effector Nucleases (TALEN) are potential tools for precise genome engineering of laboratory animals. We report the first targeted genomic integration in the rat using TALENs (Transcription Activator-Like Effector Nucleases) by homology-derived recombination (HDR). We assembled TALENs and designed a linear donor insert targeting a pA476T mutation in the rat Glucocorticoid Receptor (Nr3c1) namely GRdim, that prevents receptor homodimerization in the mouse. TALEN mRNA and linear double-stranded donor were microinjected into rat one-cell embryos. Overall, we observed targeted genomic modifications in 17% of the offspring, indicating high TALEN cutting efficiency in rat zygotes. PMID:24523878

  14. A Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/07_BC) Among Heterosexuals in Nei Monggoi Autonomous Region in China.

    PubMed

    An, Minghui; Han, Xiaoxu; Zhao, Bin; Xu, Junjie; Chu, Zhenxing; Shang, Hong

    2016-08-01

    Increasing second-generation recombinant forms (CRF01_AE/07_BC) have been detected in China recently. Here, we isolated a novel CRF01_AE/07_BC second-generation recombinant form in HIV-1-positive Nei Monggoi's heterosexuals with one CRF07_BC inserted into the CRF01_AE backbone. Polygenetic analyses showed that the CRF01_AE region was grouped with the previously reported cluster 5 lineage, which spreads among the sexual population in north of China, inferring that this recombinant event occurred through heterosexual contact in the north of China possibly. The growing emergence of recombinant forms means coexistence of multiple strains and complexity of the HIV-1 epidemic, which reminds us of the urgent necessity to focus the HIV surveillance among the high-risk populations nationwide in China, particularly to enhance preventive measures in HIV-1 low-prevalence areas. PMID:27018546

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Lin, Shi-Zeng

    2016-07-01

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

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

    DOE PAGESBeta

    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)], 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

  18. 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.

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

    PubMed

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

    2015-07-01

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

  20. 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

  1. 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.

  2. 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.

  3. Generation of novel recombinant antibodies against nitrotyrosine by antibody phage display.

    PubMed

    Hof, Danielle; Cooksley-Decasper, Seraina; Moergeli, Sandra; von Eckardstein, Arnold

    2011-01-01

    Nitrotyrosine is a posttranslational protein modification that occurs under oxidative and nitrosative stress, and plays an important role in numerous pathological conditions. To analyse nitrotyrosine formation several commercial monoclonal and polyclonal antibodies reacting with 3-nitrotyrosine have been developed which however do not work properly in all required assays. Here, antibody phage display was used to select recombinant antibodies that specifically react with nitrotyrosine in various protein contexts. Nine initial selections were carried out, using synthetic peptides, peroxynitrite-modified proteins and conjugated proteins as antigens. Four antibodies were isolated that each exhibited a characteristic binding reactivity that greatly depended on the antigens that were used for their selections. In general, the selections using small, synthetic and biotinylated peptides were the most successful approach. Subsequently, antibody 11B1 was affinity matured by error prone mutagenesis, resulting in the isolation of two antibodies, designated 47A7 and 47B1. Competition ELISA and immunoblotting after treatment with sodium dithionite further demonstrated the specificity of antibody 47B1 for nitrotyrosine. The results presented here demonstrate that antibody phage display is a useful method to isolate antibodies against posttranslational modifications, which are powerful tools in the proteomic era. PMID:21558620

  4. Direct numerical simulations of trailing-edge noise generated by boundary-layer instabilities

    NASA Astrophysics Data System (ADS)

    Sandberg, R. D.; Sandham, N. D.; Joseph, P. F.

    2007-07-01

    Direct numerical simulations (DNS) are conducted of noise generated at an infinitely thin trailing edge (TE). The aim is to predict the far-field sound and the near-field hydrodynamics, thereby providing an insight into the physical mechanisms of sound generation at airfoil TEs and potentially helping to validate acoustic theories. One of the theories widely used is the classical inviscid theory of Amiet, where the far-field sound can be evaluated in closed form if the convecting surface pressure spectrum upstream of the TE is known. For the first time, data from DNS including viscous effects are compared to the classical inviscid TE noise theory. In the present investigation, Tollmien-Schlichting waves are introduced close to the inflow boundary. The disturbances propagate downstream producing pressure fluctuations at the TE. In conducting two-dimensional DNS the theoretical method requires modification to account for the radiation of the total pressure difference in two dimensions only, as opposed to the three-dimensional sound radiation originally considered by Amiet. The modified theoretical analysis and a comparison between DNS and theoretical results are presented, scrutinizing the assumptions made in the derivation. Amiet's surface pressure jump transfer function is found to predict the scattered pressure field accurately. Directivity plots of DNS data show that viscous effects appear to smear individual lobes and that a downstream pointing lobe is present at higher Mach number which is attributed to an additional wake source.

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

    PubMed

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

    2016-02-01

    Targeted cell- or region-specific gene recombination is widely used in the functional analysis of genes implicated in development and disease. In the brain, targeted gene recombination has become a mainstream approach to study neurodegeneration or tumorigenesis. The use of the Cre-loxP system to study tumorigenesis in the adult central nervous system (CNS) can be limited, when the promoter (such as GFAP) is also transiently expressed during development, which can result in the recombination of progenies of different lineages. Engineering of transgenic mice expressing Cre recombinase fused to a mutant of the human oestrogen receptor (ER) allows the circumvention of transient developmental Cre expression by inducing recombination in the adult organism. The recombination of loxP sequences occurs only in the presence of tamoxifen. Systemic administration of tamoxifen can, however, exhibit toxicity and might also recombine unwanted cell populations if the promoter driving Cre expression is active at the time of tamoxifen administration. Here, we report that a single site-specific injection of an active derivative of tamoxifen successfully activates Cre recombinase and selectively recombines tumour suppressor genes in neural progenitor cells of the subventricular zone in mice, and we demonstrate its application in a model for the generation of intrinsic brain tumours. PMID:26704996

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

    PubMed Central

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

    2016-01-01

    ABSTRACT Targeted cell- or region-specific gene recombination is widely used in the functional analysis of genes implicated in development and disease. In the brain, targeted gene recombination has become a mainstream approach to study neurodegeneration or tumorigenesis. The use of the Cre-loxP system to study tumorigenesis in the adult central nervous system (CNS) can be limited, when the promoter (such as GFAP) is also transiently expressed during development, which can result in the recombination of progenies of different lineages. Engineering of transgenic mice expressing Cre recombinase fused to a mutant of the human oestrogen receptor (ER) allows the circumvention of transient developmental Cre expression by inducing recombination in the adult organism. The recombination of loxP sequences occurs only in the presence of tamoxifen. Systemic administration of tamoxifen can, however, exhibit toxicity and might also recombine unwanted cell populations if the promoter driving Cre expression is active at the time of tamoxifen administration. Here, we report that a single site-specific injection of an active derivative of tamoxifen successfully activates Cre recombinase and selectively recombines tumour suppressor genes in neural progenitor cells of the subventricular zone in mice, and we demonstrate its application in a model for the generation of intrinsic brain tumours. PMID:26704996

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

    NASA Astrophysics Data System (ADS)

    Rossani, A.

    2016-04-01

    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.

  8. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  11. 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

  12. The Mitochondrial Genome Organization of a Maize Fertile Cmst Revertant Line Is Generated through Recombination between Two Sets of Repeats

    PubMed Central

    Fauron, CMR.; Havlik, M.; Brettell, RIS.

    1990-01-01

    The mitochondrial genome (mtDNA) organization from a fertile revertant line (V3) derived from the maize cytoplasmic male sterile type T (cmsT) callus tissue culture has been determined. We report that the sequence complexity can be mapped on to a circular ``master chromosome'' of 705 kb which includes a duplication of 165 kb of DNA when compared to its male sterile progenitor. Associated with this event is also a 0.423-kb deletion, which removed the cmsT-associated urf13 gene. As found for the maize normal type (N) and cmsT mitochondrial genomes, the V3 master chromosome also exists as a multipartite structure generated by recombination through repeated sequences. PMID:2307363

  13. Parametric chaos generator operating on a varactor diode with the instability limitation decay mechanism

    NASA Astrophysics Data System (ADS)

    Kuznetsov, S. P.

    2016-03-01

    Equations are derived for a parametric chaos generator containing three oscillatory circuits and a variable-capacitance diode (varactor) and are reduced to equations for slow amplitudes of parametrically interacting modes. With allowance for quadratic nonlinearity, the problem is reduced to a system of three first-order differential equations for Pikovsky-Rabinovich-Trakhtengerts real amplitudes with a Lorenz-type attractor. In a more accurate description of nonlinearity of the varactor, the equations for slow amplitudes are complex-valued, which leads to the loss of robustness of chaotic dynamics, which is typical of the Lorenz attractor. The results of numerical calculations (portraits of attractors and Lyapunov exponents) in models with different approximation levels are compared.

  14. 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.

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

    PubMed Central

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

    2009-01-01

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

  16. Characterization of Wild-Type Adeno-Associated Virus Type 2-Like Particles Generated during Recombinant Viral Vector Production and Strategies for Their Elimination

    PubMed Central

    Wang, Xu-Shan; Khuntirat, Benjawan; Qing, Keyun; Ponnazhagan, Selvarangan; Kube, Dagmar M.; Zhou, Shangzhen; Dwarki, Varavani J.; Srivastava, Arun

    1998-01-01

    The pSub201-pAAV/Ad plasmid cotransfection system was developed to eliminate homologous recombination which leads to generation of the wild-type (wt) adeno-associated virus type 2 (AAV) during recombinant vector production. The extent of contamination with wt AAV has been documented to range between 0.01 and 10%. However, the precise mechanism of generation of the contaminating wt AAV remains unclear. To characterize the wt AAV genomes, recombinant viral stocks were used to infect human 293 cells in the presence of adenovirus. Southern blot analyses of viral replicative DNA intermediates revealed that the contaminating AAV genomes were not authentic wt but rather wt AAV-like sequences derived from recombination between (i) AAV inverted terminal repeats (ITRs) in the recombinant plasmid and (ii) AAV sequences in the helper plasmid. Replicative AAV DNA fragments, isolated following amplification through four successive rounds of amplification in adenovirus-infected 293 cells, were molecularly cloned and subjected to nucleotide sequencing to identify the recombinant junctions. Following sequence analyses of 31 different ends of AAV-like genomes derived from two different recombinant vector stocks, we observed that all recombination events involved 10 nucleotides in the AAV D sequence distal to viral hairpin structures. We have recently documented that the first 10 nucleotides in the D sequence proximal to the AAV hairpin structures are essential for successful replication and encapsidation of the viral genome (X.-S. Wang et al., J. Virol. 71:3077–3082, 1997), and it was noteworthy that in each recombinant junction sequenced, the same 10 nucleotides were retained. We also observed that adenovirus ITRs in the helper plasmid were involved in illegitimate recombination with AAV ITRs, deletions of which significantly reduced the extent of wt AAV-like particles. Furthermore, the combined use of recombinant AAV plasmids lacking the distal 10 nucleotides in the D sequence

  17. 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.

  18. Generation of tendon-to-bone interface "enthesis" with use of recombinant BMP-2 in a rabbit model.

    PubMed

    Hashimoto, Yusuke; Yoshida, Gen; Toyoda, Hiromitsu; Takaoka, Kunio

    2007-11-01

    The anatomical structure at bone-tendon and bone-ligament interfaces is called the enthesis. Histologically, the enthesis is characterized by a transitional series of tissue layers from the end of the tendon to bone, including tendon, fibrocartilage, calcified fibrocartilage, and bone. This arrangement yields stronger direct connection of the soft tissues to bone. In surgical repair, the enthesis has proven difficult to reproduce, and the success of ligament-bone bonding has depended on the fibrous attachment that forms after any ligament reconstructions. In this study, we attempted to generate a direct-insertion enthesis in two stages. First, recombinant human bone morphogenetic protein-2 (rhBMP-2) was injected into the flexor digitorum communis tendon in the rabbit hind limb to induce ectopic ossicle formation. In a second step, the resultant tendon/ossicle complex was then surgically transferred onto the surface of the rabbit tibia to generate a stable tendon-bone junction. One month following surgery, histomorphological examination confirmed direct insertion of tendon-bone structures in the proximal tibia of the rabbit. Ultimate failure loads of the BMP-2-generated tendon-bone junction were significantly higher than in the control group (p < 0.01). These findings suggest that it is possible to successfully regenerate a direct tendon-to-bone enthesis. Use of this approach may enable successful reconstruction of joints rendered unstable after ligamentous rupture or laxity after anterior cruciate ligament injury. PMID:17557323

  19. 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.

  20. 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.

  1. 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.

  2. Generation of mink cell focus-forming viruses by Friend murine leukemia virus: recombination with specific endogenous proviral sequences.

    PubMed Central

    Evans, L H; Cloyd, M W

    1984-01-01

    A family of recombinant mink cell focus-forming viruses (MCF) was derived by inoculation of NFS mice with a Friend murine leukemia virus, and their genomes were analyzed by RNase T1-resistant oligonucleotide fingerprinting. The viruses were obtained from the thymuses and spleens of preleukemic and leukemic animals and were evaluated for dualtropism and oncogenicity. All these isolates induced cytopathic foci on mink cells but could be classified into two groups based on their relative infectivities for SC-1 (mouse) or mink (ATCC CCL64) cells. One group of Friend MCFs (F-MCFs) (group I) exhibited approximately equal infectivities for SC-1 and mink cells, whereas a second group (group II) infected mink cells 1,000- to 10,000-fold more efficiently than SC-1 cells. Structural analyses of the F-MCFs revealed that group I and group II viruses correlated with recombination of Friend murine leukemia virus with two distinct, but closely related, endogenous NFS proviral sequences. No correlation was found between the type of F-MCF and the tissue of origin or the disease state of the animal. Furthermore, none of the F-MCF isolates were found to be oncogenic in NFS/N or AKR/J mice. F-MCFs of both groups underwent extensive substitution of ecotropic sequences, involving much of the gag and env genes of group I F-MCFs and most of the gag, pol, and env genes of group II F-MCFs. All F-MCF isolates retained the 3' terminal U3 region of Friend murine leukemia virus. Comparison of the RNAs of the F-MCFs with RNAs of MCFs derived from NFS.Akv-1 or NFS.Akv-2 mice indicated that the F-MCFs were derived from NFS proviral sequences which are distinct from the sequences contained in NFS.Akv MCF isolates. This result suggested that recombination with particular endogenous proviral sequences to generate MCFs may be highly specific for a given murine leukemia virus. Images PMID:6422051

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

    PubMed

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

    2014-01-01

    Traditionally, cell line generation requires several months and involves screening of over several hundred cell clones for high productivity before dozens are selected as candidate cell lines. Here, we have designed a new strategy for the generation of stable and high-expression cell lines by combining homologous recombination (HR) and fluorescence-activated cell sorting (FACS). High expression was indicated by the expression of secreted green fluorescent protein (SEGFP). Parental cell lines with the highest expression of SEGFP were then selected by FACS and identified by stability analysis. Consequently, HR vectors were constructed using the cassette for SEGFP as the HR region. After transfecting the HR vector, the cells with negative SEGFP expression were enriched by FACS. The complete exchange between SEGFP and target gene (TNFR-Fc) cassettes was demonstrated by DNA analysis. Compared with the traditional method, by integrating the cassette containing the gene of interest into the pre-selected site, the highest producing cells secreted a more than 8-fold higher titer of target protein. Hence, this new strategy can be applied to isolated stable cell lines with desirable expression of any gene of interest. The stable cell lines can rapidly produce proteins for researching protein structure and function and are even applicable in drug discovery. PMID:24646904

  4. Generation of Recombinant Antibodies to Rat GABAA Receptor Subunits by Affinity Selection on Synthetic Peptides

    PubMed Central

    Koduvayur, Sujatha P.; Gussin, Hélène A.; Parthasarathy, Rajni; Hao, Zengping; Kay, Brian K.; Pepperberg, David R.

    2014-01-01

    The abundance and physiological importance of GABAA receptors in the central nervous system make this neurotransmitter receptor an attractive target for localizing diagnostic and therapeutic biomolecules. GABAA receptors are expressed within the retina and mediate synaptic signaling at multiple stages of the visual process. To generate monoclonal affinity reagents that can specifically recognize GABAA receptor subunits, we screened two bacteriophage M13 libraries, which displayed human scFvs, by affinity selection with synthetic peptides predicted to correspond to extracellular regions of the rat α1 and β2 GABAA subunits. We isolated three anti-β2 and one anti-α1 subunit specific scFvs. Fluorescence polarization measurements revealed all four scFvs to have low micromolar affinities with their cognate peptide targets. The scFvs were capable of detecting fully folded GABAA receptors heterologously expressed by Xenopus laevis oocytes, while preserving ligand-gated channel activity. Moreover, A10, the anti-α1 subunit-specific scFv, was capable of detecting native GABAA receptors in the mouse retina, as observed by immunofluorescence staining. In order to improve their apparent affinity via avidity, we dimerized the A10 scFv by fusing it to the Fc portion of the IgG. The resulting scFv-Fc construct had a Kd of ∼26 nM, which corresponds to an approximately 135-fold improvement in binding, and a lower detection limit in dot blots, compared to the monomeric scFv. These results strongly support the use of peptides as targets for generating affinity reagents to membrane proteins and encourage investigation of molecular conjugates that use scFvs as anchoring components to localize reagents of interest at GABAA receptors of retina and other neural tissues, for studies of receptor activation and subunit structure. PMID:24586298

  5. 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.

  6. 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

  7. 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.

  8. The PiggyBac transposon enhances the frequency of CHO stable cell line generation and yields recombinant lines with superior productivity and stability.

    PubMed

    Matasci, Mattia; Baldi, Lucia; Hacker, David L; Wurm, Florian M

    2011-09-01

    Generating stable, high-producing mammalian cell lines is a major bottleneck in the manufacture of recombinant therapeutic proteins. Conventional gene transfer methods for cell line generation rely on random plasmid integration, resulting in unpredictable and highly variable levels of transgene expression. As a consequence, a large number of stably transfected cells must be analyzed to recover a few high-producing clones. Here we present an alternative gene transfer method for cell line generation based on transgene integration mediated by the piggyBac (PB) transposon. Recombinant Chinese hamster ovary (CHO) cell lines expressing a tumor necrosis factor receptor:Fc fusion protein were generated either by PB transposition or by conventional transfection. Polyclonal populations and isolated clonal cell lines were characterized for the level and stability of transgene expression for up to 3 months in serum-free suspension culture. Pools of transposed cells produced up to fourfold more recombinant protein than did the pools generated by standard transfection. For clonal cell lines, the frequency of high-producers was greater following transposition as compared to standard transfection, and these clones had a higher volumetric productivity and a greater number of integrated transgenes than did those generated by standard transfection. In general, the volumetric productivity of the cell pools and individual cell lines generated by transposition was stable for up to 3 months in the absence of selection. Our results indicate that the PB transposon supports the generation of cell lines with high and stable transgene expression at an elevated frequency relative to conventional transfection. Thus, PB-mediated gene delivery is expected to reduce the extent of recombinant cell line screening. PMID:21495018

  9. A simple and efficient method for generating high-quality recombinant Mical enzyme for in vitro assays.

    PubMed

    Wu, Heng; Hung, Ruei-Jiun; Terman, Jonathan R

    2016-11-01

    We have recently identified a new family of multidomain oxidoreductase (redox) enzymes, the MICALs, that directly regulate the actin cytoskeletal elements necessary for the morphology, motility, and trajectory of cells. Our genetic assays reveal that Mical is both necessary and sufficient for actin organization and cellular effects in vivo and our biochemical assays with purified Mical protein reveal that Mical utilizes its redox activity to directly disassemble actin filaments. These results identify Mical proteins as novel actin disassembly factors and uncover a redox signaling mechanism that directly regulates the actin cytoskeleton. These results have also set the stage for in-depth characterization of the Mical enzyme. However, it has been difficult to obtain sufficient amounts of highly-pure Mical protein to conduct further biochemical, structural, imaging, catalytic, and other high-precision studies. Herein, we describe a means for expressing high levels of soluble recombinant Mical protein in bacteria. Likewise, we have designed a new purification strategy that enables the rapid and efficient purification of milligram quantities of highly-pure and >99% active Mical protein. This new strategy for generating large amounts of highly-pure and active Mical protein will aid research objectives designed to characterize the biochemical, enzymology, and structural biology of Mical and its effects on actin filament dynamics. PMID:27223600

  10. 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.

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

    PubMed

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

    2007-08-01

    In the present study hybridomas were produced from fusion with splenocytes of BALB/c mice immunized with the recombinant 31-kDa cell surface protein (r31CSP) specific for Brucella species. A set of eight stabilized hybridoma cell lines was generated against r31CSP. Monoclonal antibodies (MAbs) produced by all these clones exhibited reactivity for r31CSP as well as with the protein of 31-kDa, derived from whole-cell lysate of 31-kDa Brucella abortus 544. Four of eight MAbs were IgG1, two IgG2b, and two IgM in nature. These MAbs did not show any cross-reaction with whole-cell lysate of Yersinia enterocolitica O: 9, Vibrio cholerae, Salmonella typhimurium and Escherichia coli 0157 by Western blotting. Reactivity of these MAbs was further assessed with other organisms of Brucella species namely, B. abortus S99, B. canis, B. melitensis 16M, B. suis, and a clinical isolate of B. melitensis. Collectively, these data suggest that these MAbs may have the potential for use in the detection of Brucella species with high specificity. PMID:17725382

  12. 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

  13. 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. PMID:24654882

  14. Recombinant human activated protein C resets thrombin generation in patients with severe sepsis – a case control study

    PubMed Central

    de Pont, Anne-Cornélie JM; Bakhtiari, Kamran; Hutten, Barbara A; de Jonge, Evert; Vroom, Margreeth B; Meijers, Joost CM; Büller, Harry R; Levi, Marcel

    2005-01-01

    Introduction Recombinant human activated protein C (rhAPC) is the first drug for which a reduction of mortality in severe sepsis has been demonstrated. However, the mechanism by which this reduction in mortality is achieved is still not clearly defined. The aim of the present study was to evaluate the dynamics of the anticoagulant, anti-inflammatory and pro-fibrinolytic action of rhAPC in patients with severe sepsis, by comparing rhAPC-treated patients with case controls. Methods In this prospectively designed multicenter case control study, 12 patients who were participating in the ENHANCE study, an open-label study of rhAPC in severe sepsis, were treated intravenously with rhAPC at a constant rate of 24 μg/kg/h for a total of 96 h. Twelve controls with severe sepsis matching the inclusion criteria received standard therapy. The treatment was started within 48 h after the onset of organ failure. Blood samples were taken before the start of the infusion and at 4, 8, 24, 48, 96 and 168 h, for determination of parameters of coagulation and inflammation. Results Sepsis-induced thrombin generation as measured by thrombin-antithrombin complexes and prothrombin fragment F1+2, was reset by rhAPC within the first 8 h of infusion. The administration of rhAPC did not influence parameters of fibrinolysis and inflammation. There was no difference in outcome or occurrence of serious adverse events between the treatment group and the control group. Conclusion Sepsis-induced thrombin generation in severely septic patients is reset by rhAPC within the first 8 h of infusion without influencing parameters of fibrinolysis and inflammation. PMID:16277710

  15. 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

  16. 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

  17. Generation of recombinant canine interleukin-15 and evaluation of its effects on the proliferation and function of canine NK cells.

    PubMed

    Lee, Soo-Hyeon; Shin, Dong-Jun; Kim, Sang-Ki

    2015-05-15

    Interleukin-15 (IL-15) is a pleiotropic cytokine that plays a pivotal role in both innate and adaptive immunity. IL-15 is also a promising cytokine for treating cancer. Despite the growing importance of the clinical use of IL-15 for immunotherapy, no attempts have been made to generate a recombinant canine IL-15 (rcIL-15) and to examine its effects on the antitumor activities of immune effector cells in dogs. Here, we generated an rcIL-15 protein consisting of Asn-49-Ser-162 with a C-terminal His tag and examined its functions ex vivo in terms of the proliferation and antitumor effects on canine non-B, non-T, large granular natural killer (NK) cells. Non-B, non-T, large granular NK cells rapidly expanded in response to stimulation with rcIL-15 in the presence of IL-2, and a majority of the cells that selectively expanded over 21 days exhibited a CD3(-)CD5(-)CD4(-)CD8(+/-)CD21(-) phenotype. Purified rcIL-15 significantly enhanced the expansion rate of canine NK cells derived from peripheral blood mononuclear cells compared to human IL-15, or culture in the absence of IL-15 for 21 days (p<0.05). Purified rcIL-15 was superior at enhancing the effector function of NK cells compared to human IL-15. The cytotoxic activity against canine thyroid adenocarcinoma (CTAC) cells, interferon-γ production, and the mRNA expression levels of perforin and granzyme B of expanded NK cells cultured with rcIL-15 were significantly elevated compared to those cultured with human IL-15 or without IL-15 (p<0.05). Intravenous administration of rcIL-15 significantly increased the numbers of lymphocytes in the peripheral blood of dogs on days 6, 8, and 11 after injection compared to numbers before administration (p<0.05). The results of this study suggest that the rcIL-15 protein, consisting of Asn-49-Ser-162, enhanced the proliferation and antitumor effects of canine NK cells and promoted the generation of lymphocytes in dogs. PMID:25890849

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

    PubMed

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

    2015-05-01

    The anthrax protective antigen (PA) is the central component of the three-part anthrax toxin, and it is the primary immunogenic component in the approved AVA anthrax vaccine and the "next-generation" recombinant PA (rPA) anthrax vaccines. Animal models have indicated that PA-specific antibodies (AB) are sufficient to protect against infection with Bacillus anthracis. In this study, we investigated the PA domain specificity, affinity, mechanisms of neutralization, and synergistic effects of PA-specific antibodies from a single donor following vaccination with the rPA vaccine. Antibody-secreting cells were isolated 7 days after the donor received a boost vaccination, and 34 fully human monoclonal antibodies (hMAb) were identified. Clones 8H6, 4A3, and 22F1 were able to neutralize lethal toxin (LeTx) both in vitro and in vivo. Clone 8H6 neutralized LeTx by preventing furin cleavage of PA in a dose-dependent manner. Clone 4A3 enhanced degradation of nicked PA, thereby interfering with PA oligomerization. The mechanism of 22F1 is still unclear. A fourth clone, 2A6, that was protective only in vitro was found to be neutralizing in vivo in combination with a toxin-enhancing antibody, 8A7, which binds to domain 3 of PA and PA oligomers. These results provide novel insights into the antibody response elicited by the rPA vaccine and may be useful for PA-based vaccine and immunotherapeutic cocktail design. PMID:25787135

  19. Material property discontinuities in intervertebral disc porohyperelastic finite element models generate numerical instabilities due to volumetric strain variations.

    PubMed

    Ruiz, C; Noailly, J; Lacroix, D

    2013-10-01

    Numerical studies of the intervertebral disc (IVD) are important to better understand the load transfer and the mechanobiological processes within the disc. Among the relevant calculations, fluid-related outputs are critical to describe and explore accurately the tissue properties. Porohyperelastic finite element models of IVD can describe accurately the disc behaviour at the organ level and allow the inclusion of fluid effects. However, results may be affected by numerical instabilities when fast load rates are applied. We hypothesized that such instabilities would appear preferentially at material discontinuities such as the annulus-nucleus boundary and should be considered when testing mesh convergence. A L4-L5 IVD model including the nucleus, annulus and cartilage endplates were tested under pure rotational loads, with different levels of mesh refinement. The effect of load relaxation and swelling were also studied. Simulations indicated that fluid velocity oscillations appeared due to numerical instability of the pore pressure spatial derivative at material discontinuities. Applying local refinement only was not enough to eliminate these oscillations. In fact, mesh refinements had to be local, material-dependent, and supplemented by the creation of a material transition zone, including interpolated material properties. Results also indicated that oscillations vanished along load relaxation, and faster attenuation occurred with the incorporation of the osmotic pressure. We concluded that material discontinuities are a major cause of instability for poromechanical calculations in multi-tissue models when load velocities are simulated. A strategy was presented to address these instabilities and recommendations on the use of IVD porohyperelastic models were given. PMID:23796430

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

    PubMed

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

    1999-04-01

    To estimate the extent and position of homoeologous recombination during meiosis in an interspecific hybrid between two distantly related Alstroemeria species, the chromosome constitution of six first generation backcross (BC1) plants was analysed using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) analysis. Four different probes were used for the FISH analysis: two species-specific and two rDNA probes. The six BC1 plants were obtained from crosses between the hybrid A. aurea x A. inodora with its parent A. inodora. GISH clearly identified all chromosomes of both parental genomes as well as recombinant chromosomes. The sequential GISH and FISH analysis enabled the accurate identification of all individual chromosomes in the BC1 plants, resulting in the construction of detailed karyotypes of the plants. The identification of the recombinant chromosomes provided evidence which chromosomes of the two species are homoeologous. Two of the BC1 plants were aneuploid (2n=2x+1=17) and four triploid (2n=3x=24), indicating that both n and 2n gametes were functional in the F1 hybrid. Using GISH, it was possible to estimate homeologous recombination in two different types of gametes in the F1 hyrid. The positions of the crossover points ranged from highly proximal to distal and the maximum number of crossover points per chromosome arm was three. Compared with the aneuploid plants, the triploid plants (which received 2n gametes) clearly possessed fewer crossovers per chromosome, indicating reduced chromosome pairing/recombination prior to the formation of the 2n gametes. Besides homeologous recombination, evidence was found for the presence of structural rearrangements (inversion and translocation) between the chromosomes of the parental species. The presence of the ancient translocation was confirmed through FISH analysis of mitotic and meiotic chromosomes. PMID:10199956

  1. 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.

  2. 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.

  3. Shoulder Instability

    MedlinePlus

    ... Risk Factors Is shoulder instability the same as shoulder dislocation? No. The signs of dislocation and instability might ... the same to you--weakness and pain. However, dislocation occurs when your shoulder goes completely out of place. The shoulder ligaments ...

  4. Recombineering homologous recombination constructs in Drosophila.

    PubMed

    Carreira-Rosario, Arnaldo; Scoggin, Shane; Shalaby, Nevine A; Williams, Nathan David; Hiesinger, P Robin; Buszczak, Michael

    2013-01-01

    The continued development of techniques for fast, large-scale manipulation of endogenous gene loci will broaden the use of Drosophila melanogaster as a genetic model organism for human-disease related research. Recent years have seen technical advancements like homologous recombination and recombineering. However, generating unequivocal null mutations or tagging endogenous proteins remains a substantial effort for most genes. Here, we describe and demonstrate techniques for using recombineering-based cloning methods to generate vectors that can be used to target and manipulate endogenous loci in vivo. Specifically, we have established a combination of three technologies: (1) BAC transgenesis/recombineering, (2) ends-out homologous recombination and (3) Gateway technology to provide a robust, efficient and flexible method for manipulating endogenous genomic loci. In this protocol, we provide step-by-step details about how to (1) design individual vectors, (2) how to clone large fragments of genomic DNA into the homologous recombination vector using gap repair, and (3) how to replace or tag genes of interest within these vectors using a second round of recombineering. Finally, we will also provide a protocol for how to mobilize these cassettes in vivo to generate a knockout, or a tagged gene via knock-in. These methods can easily be adopted for multiple targets in parallel and provide a means for manipulating the Drosophila genome in a timely and efficient manner. PMID:23893070

  5. 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

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

    PubMed

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

    2016-01-01

    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

  7. X chromosomal recombination--a family study analysing 39 STR markers in German three-generation pedigrees.

    PubMed

    Hering, Sandra; Edelmann, Jeanett; Augustin, Christa; Kuhlisch, Eberhard; Szibor, Reinhard

    2010-09-01

    Typing of polymorphisms on the human chromosome X (ChrX) has become a standard technique in forensic genetics, and a growing number of short tandem repeats (STRs) has been established. Knowledge of marker recombination is of great significance especially when ChrX typing is used in forensic kinship testing. It is known that meiotic recombination is not a simple function of physical distance but crossing over events tend to be clustered. Information on genetic distances between markers can be gathered by family studies and by interpolation of gene bank data such as the Rutgers map. We typed DNA samples of pedigrees consisting of mothers with several sons and grandfather-mother-son constellations and report here the recombination characteristics of 39 ChrX STRs in up to 135 meioses. PMID:19936774

  8. 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

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

    PubMed

    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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. Properties of recombinant Staphylococcus haemolyticus cystathionine beta-lyase (metC) and its potential role in the generation of volatile thiols in axillary malodor.

    PubMed

    Troccaz, Myriam; Benattia, Faiza; Borchard, Gerrit; Clark, Anthony J

    2008-11-01

    Enzymes implicated in cysteine and methionine metabolism such as cystathionine beta-lyase (CBL; EC 4.4.1.8), a pyridoxal-5'-phosphate (PLP)-dependent carbon-sulfur lyase, have been shown to play a central role in the generation of sulfur compounds. This work describes the unprecedented cloning and characterization of the metC-cystathionine beta-lyase from the axillary-isolated strain Staphylococcus haemolyticus AX3, in order to determine its activity and its involvement in amino acid biosynthesis, and in the generation of sulfur compounds in human sweat. The gene contains a cysteine/methionine metabolism enzyme pattern, and also a sequence capable to effect beta-elimination. The recombinant enzyme was shown to cleave cystathionine into homocysteine and to convert methionine into methanethiol at low levels. No odor was generated after incubation of the recombinant enzyme with sterile human axillary secretions; sweat components were found to have an inhibitory effect. These results suggest that the generation of sulfur compounds by Staphylococci and the beta-lyase activity in human sweat are mediated by enzymes other than the metC gene or by the concerted activities of more than one enzyme. PMID:19035565

  16. 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.

  17. 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

  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. 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.

  20. 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.

  1. 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

  2. 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

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

    PubMed

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

    2016-04-01

    In this study, a new recombinant VHSV (rVHSV-Arfp-Bgfp) was generated by insertion of a red fluorescent protein (RFP) gene between N and P genes, a green fluorescent protein (GFP) gene between P and M genes of VHSV genome, the expression of each heterologous gene in infected cells, and effects of the lengthened recombinant VHSV's genome on the replication ability and in vivo virulence to olive flounder (Paralichthys olivaceus) fingerlings were compared with previously generated rVHSVs (rVHSV-wild, rVHSV-Arfp, and rVHSV-Brfp). The expression of RFP and GFP in cells infected with rVHSV-Arfp-Bgfp was verified through fluorescent microscopy and FACS analysis. In the viral growth analysis, rVHSV-Arfp and rVHSV-Brfp showed significantly lower viral titers than rVHSV-wild, and the replication of rVHSV-Arfp-Bgfp was significantly decreased compared to that of even rVHSV-Arfp or rVHSV-Brfp. These results suggest that the genome length is a critical factor for the determination of rVHSVs replication efficiency. In the in vivo virulence experiment, the cumulative mortalities of olive flounder fingerlings infected with each rVHSV were inversely proportional to the length of the viral genome, suggesting that decreased viral growth rate due to the lengthened viral genome is accompanied with the decrease of in vivo virulence of rVHSVs. Recombinant viruses expressing multiple foreign antigens can be used for the development of combined vaccines. However, as the present rVHSV-Arfp-Bgfp still possesses an ability to kill hosts (although very weakened), researches on the producing more attenuated viruses or propagation-deficient replicon particles are needed to solve safety-related problems. PMID:26921191

  4. 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

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

    PubMed Central

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

    2015-01-01

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

  6. The dock-and-lock method combines recombinant engineering with site-specific covalent conjugation to generate multifunctional structures.

    PubMed

    Rossi, Edmund A; Goldenberg, David M; Chang, Chien-Hsing

    2012-03-21

    Advances in recombinant protein technology have facilitated the production of increasingly complex fusion proteins with multivalent, multifunctional designs for use in various in vitro and in vivo applications. In addition, traditional chemical conjugation remains a primary choice for linking proteins with polyethylene glycol (PEG), biotin, fluorescent markers, drugs, and others. More recently, site-specific conjugation of two or more interactive modules has emerged as a valid approach to expand the existing repertoires produced by either recombinant engineering or chemical conjugation alone, thus advancing the range of potential applications. Five such methods, each involving a specific binding event, are highlighted in this review, with a particular focus on the Dock-and-Lock (DNL) method, which exploits the natural interaction between the dimerization and docking domain (DDD) of cAMP-dependent protein kinase (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP). The various enablements of DNL to date include trivalent, tetravalent, pentavalent, and hexavalent antibodies of monospecificity or bispecificity; immnocytokines comprising multiple copies of interferon-alpha (IFNα); and site-specific PEGylation. These achievements attest to the power of the DNL platform technology to develop novel therapeutic and diagnostic agents from both proteins and nonproteins for unmet medical needs. PMID:22168393

  7. Inhibition of Telomere Recombination by Inactivation of KEOPS Subunit Cgi121 Promotes Cell Longevity

    PubMed Central

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

    2015-01-01

    DNA double strand break (DSB) is one of the major damages that cause genome instability and cellular aging. The homologous recombination (HR)-mediated repair of DSBs plays an essential role in assurance of genome stability and cell longevity. Telomeres resemble DSBs and are competent for HR. Here we show that in budding yeast Saccharomyces cerevisiae telomere recombination elicits genome instability and accelerates cellular aging. Inactivation of KEOPS subunit Cgi121 specifically inhibits telomere recombination, and significantly extends cell longevity in both telomerase-positive and pre-senescing telomerase-negative cells. Deletion of CGI121 in the short-lived yku80tel mutant restores lifespan to cgi121Δ level, supporting the function of Cgi121 in telomeric single-stranded DNA generation and thus in promotion of telomere recombination. Strikingly, inhibition of telomere recombination is able to further slow down the aging process in long-lived fob1Δ cells, in which rDNA recombination is restrained. Our study indicates that HR activity at telomeres interferes with telomerase to pose a negative impact on cellular longevity. PMID:25822194

  8. 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. PMID:20956600

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

    PubMed

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

    2015-06-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2-lymphotropic human oncogenic herpesvirus associated with Kaposi's sarcoma (KS) and two B-cell lymphoproliferative diseases, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). KSHV establishes latency soon after infection in vivo and in vitro. Consequently, it is technically difficult to generate high-titre virus stocks required for infection experiments in tissue culture. Currently used methods of KSHV stock production involve induction of the lytic/productive cycle in PEL cell lines or in adherent cell lines harbouring recombinant KSHV genomes. In this study, the BJAB-derived B-cell line BrK.219, which is infected latently with a recombinant KSHV (rKSHV.219), is used to produce high-titre virus stocks. BrK.219 cells enter the lytic KSHV replication cycle upon cross-linking of B-cell receptors (BCRs) with anti-IgM antibodies without the need for additional, potentially toxic chemical inducers. High cell concentrations can be cultured and induced easily in spinner flasks, saving time and resources. The established protocol allows the generation of KSHV virus stocks with titres of up to 10(6) IU/ml in unconcentrated culture supernatants, representing a 10(3)-10(4)-fold improvement compared to conventional methods. PMID:25736227

  10. Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes

    PubMed Central

    2011-01-01

    We describe here a method to rapidly convert any desirable DNA fragment, as small as 100 bp, into long tandem DNA arrays up to 140 kb in size that are inserted into a microbe vector. This method includes rolling-circle phi29 amplification (RCA) of the sequence in vitro and assembly of the RCA products in vivo by homologous recombination in the yeast Saccharomyces cerevisiae. The method was successfully used for a functional analysis of centromeric and pericentromeric repeats and construction of new vehicles for gene delivery to mammalian cells. The method may have general application in elucidating the role of tandem repeats in chromosome organization and dynamics. Each cycle of the protocol takes ~ two weeks to complete. PMID:21982381