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Sample records for generation recombination instability

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

    PubMed Central

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

    2015-01-01

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

  2. Tidal instability and magnetic field generation

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  3. Recombination-generation currents in degenerate semiconductors

    NASA Technical Reports Server (NTRS)

    Von Roos, O.

    1978-01-01

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

  4. 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.

  5. Dynamo generated by the centrifugal instability

    NASA Astrophysics Data System (ADS)

    Marcotte, Florence; Gissinger, Christophe

    2016-10-01

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

  6. 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.

  7. 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.

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

    NASA Technical Reports Server (NTRS)

    Durbin, P. A.

    1987-01-01

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

  9. 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.

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

    PubMed Central

    Schild, David; Wiese, Claudia

    2010-01-01

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

  11. 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.

  12. Jeans instability of inhomogeneous dusty plasma with polarization force, ionization and recombination

    NASA Astrophysics Data System (ADS)

    Jain, Shweta; Sharma, Prerana; Chhajlani, R. K.

    2017-05-01

    The self-gravitational Jeans instability has been studied in dusty plasma containing significant background of neutral pressure and recombination of ions and electrons on the dust surface. The full dynamics of charged dust grains, ions and neutral species are employed considering the electrons as Maxwellian. We have derived the general dispersion relation for collisional dusty plasma with ionization, recombination and polarization force. The general dispersion relation describes the effects of considered parameters which are solved in different dusty plasma situations. Further, the dispersion relation is solved numerically. The present work is applicable to understand the structure formation of interstellar molecular clouds in astrophysical plasma.

  13. Recombination between defective tombusvirus RNAs generates functional hybrid genomes

    SciTech Connect

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

    1994-04-26

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

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

    PubMed

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

    2013-01-08

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

  15. 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.

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

    PubMed

    Kanemitsu, Yoshihiko

    2013-06-18

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

  17. 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.

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

    PubMed

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

    2016-01-01

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

  19. 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

  20. Magnetic Field Generation by the Stationary Accretion Shock Instability

    SciTech Connect

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

    2008-01-01

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

  1. Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe

    PubMed Central

    Yadav, Rajesh K; Jablonowski, Carolyn M; Fernandez, Alfonso G; Lowe, Brandon R; Henry, Ryan A; Finkelstein, David; Barnum, Kevin J; Pidoux, Alison L; Kuo, Yin-Ming; Huang, Jie; O’Connell, Matthew J; Andrews, Andrew J; Onar-Thomas, Arzu; Allshire, Robin C; Partridge, Janet F

    2017-01-01

    Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and have altered HR protein dynamics in both damaged and untreated cells. These data suggest H3-G34R slows resolution of HR-mediated repair and that unresolved replication intermediates impair chromosome segregation. This analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma. DOI: http://dx.doi.org/10.7554/eLife.27406.001 PMID:28718400

  2. Extreme waves generated by modulational instability on adverse currents

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  3. Efficient generation of recombinant adenoviral vectors by Cre-lox recombination in vitro.

    PubMed Central

    Aoki, K.; Barker, C.; Danthinne, X.; Imperiale, M. J.; Nabel, G. J.

    1999-01-01

    BACKGROUND: Although recombinant adenovirus vectors are attractive for use in gene expression studies and therapeutic applications, the construction of these vectors remains relatively time-consuming. We report here a strategy that simplifies the production of adenoviruses using the Cre-loxP system. MATERIALS AND METHODS: Full-length recombinant adenovirus DNA was generated in vitro by Cre-mediated recombination between loxP sites in a linearized shuttle plasmid containing a transgene and adenovirus genomic DNA. RESULTS: After transfection of Cre-treated DNA into 293 cells, replication-defective viral vectors were rapidly obtained without detectable wild-type virus. CONCLUSION: This system facilitates the development of recombinant adenoviral vectors for basic and clinical research. Images Fig. 1 Fig. 2 Fig. 4 PMID:10448644

  4. 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.

  5. 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.

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

    PubMed

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

    2010-10-01

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

  7. 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.

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

    PubMed Central

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

    1989-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Deng, Jian; Caulfield, C. P.

    2015-11-01

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

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

    SciTech Connect

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

    2010-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  14. 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.

  15. 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.

  16. 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

  17. Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins.

    PubMed

    Bedbrook, Claire N; Rice, Austin J; Yang, Kevin K; Ding, Xiaozhe; Chen, Siyuan; LeProust, Emily M; Gradinaru, Viviana; Arnold, Frances H

    2017-03-28

    Integral membrane proteins (MPs) are key engineering targets due to their critical roles in regulating cell function. In engineering MPs, it can be extremely challenging to retain membrane localization capability while changing other desired properties. We have used structure-guided SCHEMA recombination to create a large set of functionally diverse chimeras from three sequence-diverse channelrhodopsins (ChRs). We chose 218 ChR chimeras from two SCHEMA libraries and assayed them for expression and plasma membrane localization in human embryonic kidney cells. The majority of the chimeras express, with 89% of the tested chimeras outperforming the lowest-expressing parent; 12% of the tested chimeras express at even higher levels than any of the parents. A significant fraction (23%) also localize to the membrane better than the lowest-performing parent ChR. Most (93%) of these well-localizing chimeras are also functional light-gated channels. Many chimeras have stronger light-activated inward currents than the three parents, and some have unique off-kinetics and spectral properties relative to the parents. An effective method for generating protein sequence and functional diversity, SCHEMA recombination can be used to gain insights into sequence-function relationships in MPs.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

    Prado, Félix

    2014-01-01

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

  1. 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.

  2. Recombinant Enaction: Manipulatives Generate New Procedures in the Imagination, by Extending and Recombining Action Spaces.

    PubMed

    Rahaman, Jeenath; Agrawal, Harshit; Srivastava, Nisheeth; Chandrasekharan, Sanjay

    2017-08-27

    Manipulation of physical models such as tangrams and tiles is a popular approach to teaching early mathematics concepts. This pedagogical approach is extended by new computational media, where mathematical entities such as equations and vectors can be virtually manipulated. The cognitive and neural mechanisms supporting such manipulation-based learning-particularly how actions generate new internal structures that support problem-solving-are not understood. We develop a model of the way manipulations generate internal traces embedding actions, and how these action-traces recombine during problem-solving. This model is based on a study of two groups of sixth-grade students solving area problems. Before problem-solving, one group manipulated a tangram, the other group answered a descriptive test. Eye-movement trajectories during problem-solving were different between the groups. A second study showed that this difference required the tangram's geometrical structure, just manipulation was not enough. We propose a theoretical model accounting for these results, and discuss its implications. © 2017 Cognitive Science Society, Inc.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

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

    2009-09-01

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

  5. 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

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

    PubMed

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

    2015-01-01

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

  7. 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

  8. 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.

  9. Integrable turbulence generated from modulational instability of cnoidal waves

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. Magnetic field generation by the Rayleigh-Taylor instability in laser-driven planar plastic targets.

    PubMed

    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

    2012-09-14

    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 ∼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 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.

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

    PubMed

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

    2007-05-22

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

  13. Generation of long flavivirus expression cassettes by in vivo recombination and transient dominant selection.

    PubMed

    Yamshchikov, V F; Compans, R W

    1994-11-18

    Assembly of expression cassettes coding for large segments of viral polyproteins is often complicated or impossible due to the instability of the resulting recombinant (re-) plasmids during propagation in Escherichia coli. Using the transient dominant selection approach described for the construction of vaccinia virus recombinants (re-VV), we have constructed several intermediate vectors and developed a procedure which enables direct assembly of long expression cassettes in the VV genome by in vivo recombination and does not require preliminary assembly of long cassettes in intermediate plasmids, thus eliminating the instability problems. The procedure was used to construct re-VV carrying fragments of the West Nile (WN), Murray Valley encephalitis (MVE), tick-borne encephalitis (TBE) and dengue type-2 (DEN2) viral genomes. Using this procedure, we have assembled a WN expression cassette which represents 86% of the WN genome and codes for 91% of its polyprotein and constitutes the longest flavivirus (FV) expression cassette inserted so far into the VV genome. Analysis of FV protein expression from the obtained recombinants indicates that recombination occurs with a high degree of specificity and the ORF remains intact. The procedure described offers a possible approach for the assembly of infectious cDNA clones.

  14. 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.

  15. Topographic generation of submesoscale centrifugal instability and energy dissipation

    PubMed Central

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

    2016-01-01

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

  16. Topographic generation of submesoscale centrifugal instability and energy dissipation

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-09-29

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  20. 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

  1. Magnetic Field Generation and Its Nonlinear Evolution of the Weibel Instability

    NASA Astrophysics Data System (ADS)

    Mae, H.; Kazimura, Y.; Bulanov, S. V.; Sakai, J. I.

    The Weibel instability caused by anisotropic velocity distribution may play an important role for the generation of magnetic field in the laser produced plasmas. A three dimensional electromagnetic and relativistic particle-in-cell (PIC) code is used to show the generation of magnetic field and its nonlinear evolution. As a result, we confirm that strong magnetic fields are generated with coherent structures. Loop-like magnetic fields are generated in ``football-shaped" anisotropy and sheet-like magnetic fields are generated in ``pancake-shaped" anisotropy.

  2. 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.

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

    PubMed

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

    2010-12-01

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

  4. 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

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

    NASA Technical Reports Server (NTRS)

    Huba, J. D.

    1993-01-01

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

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

    SciTech Connect

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

    2015-10-15

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

  7. Repeat instability: mechanisms of dynamic mutations.

    PubMed

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

    2005-10-01

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

  8. Bombyx mori nucleopolyhedrovirus bacmid enabling rapid generation of recombinant virus by in vitro transposition.

    PubMed

    Tao, Xue Ying; Choi, Jae Young; Kim, Yang-Su; Lee, Seok Hee; An, Saes Byeol; Pang, Ying; Kim, Jong Hoon; Kim, Woo Jin; Je, Yeon Ho

    2015-03-01

    A novel recombinant bacmid, bEasyBm, that enables the easy and fast generation of pure recombinant baculovirus without any purification step was constructed. In bEasyBm, attR recombination sites were introduced to facilitate the generation of a recombinant viral genome by in vitro transposition. Moreover, the extracellular RNase gene from Bacillus amyloliquefaciens, barnase, was expressed under the control of the Cotesia plutellae bracovirus early promoter to negatively select against the nonrecombinant background. The bEasyBm bacmid could only replicate in host insect cells when the barnase gene was replaced with the gene of interest by in vitro transposition. When bEasyBm was transposed with pDualBac-EGFP, the resulting recombinant virus, EasyBm-EGFP, showed high levels of EGFP expression efficiency compared with that of non-purified recombinant virus BmGOZA-EGFP, which was constructed using the bBmGOZA system. In addition, nonrecombinant backgrounds were not detected in unpurified EasyBm-EGFP stocks. Based on these results, a high-throughput system for the generation of multiple recombinant viruses at a time was established.

  9. Generating recombinant antibodies to the complete human proteome.

    PubMed

    Dübel, Stefan; Stoevesandt, Oda; Taussig, Michael J; Hust, Michael

    2010-07-01

    In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded by the approximately 22,500 human protein-coding genes. Antibody selection in vitro offers properties not available in animal-based antibody generation methods. By adjusting the biochemical milieu during selection, it is possible to control the antigen conformation recognized, the antibody affinity or unwanted cross-reactivity. For larger-scale antibody generation projects, the handling, transport and storage logistics and bacterial production offer cost benefits. Because the DNA sequence encoding the antibody is available, modifications, such as site-specific in vivo biotinylation and multimerization, are only a cloning step away. This opinion article summarizes opportunities for the generation of antibodies for proteome research using in vitro technologies.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  12. 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.

  13. [Biosafety issues and public concerns on recombinant influenza viruses generated in the laboratories].

    PubMed

    Jia, Xiaojuan; Huang, Liqin; Liu, Wenjun

    2013-12-01

    Understanding inter-species transmission of influenza viruses is an important research topic. Scientists try to identify and evaluate the functional factors determining the host range of influenza viruses by generating the recombinant viruses through reverse genetics in laboratories, which reveals the viruses' molecular mechanisms of infection and transmission in different species. Therefore, the reverse genetic method is a very important tool for further understanding the biology of influenza viruses and will provide the insight for the prevention and treatment of infections and transmission. However, these recombinant influenza viruses generated in laboratories will become the potential threat to the public health and the environment. In this paper, we discussed the biological safety issues of recombinant influenza viruses and suggested we should set up protocols for risk management on research activities related to recombinant highly pathogenic influenza viruses.

  14. Use of natural instabilities for generation of streamwise vortices in a laminar channel flow

    NASA Astrophysics Data System (ADS)

    Moradi, H. V.; Budiman, A. C.; Floryan, J. M.

    2017-06-01

    An analysis of pressure-gradient-driven flows in channels with walls modified by transverse ribs has been carried out. The ribs have been introduced intentionally in order to generate streamwise vortices through centrifugally driven instabilities. The cost of their introduction, i.e. the additional pressure losses, have been determined. Linear stability theory has been used to determine conditions required for the formation of the vortices. It has been demonstrated that there exists a finite range of rib wave numbers capable of creating vortices. Within this range, there exists an optimal wave number which results in the minimum critical Reynolds number for the specified rib amplitude. The optimal wave numbers marginally depend on the rib positions and amplitudes. As the formation of the vortices can be interfered with by viscosity-driven instabilities, the critical conditions for the onset of such instabilities have also been determined. The rib geometries which result in the vortex formation with the smallest drag penalty and without interference from the viscosity-driven instabilities have been identified.

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

    PubMed

    Norkin, L C; Piatak, M

    1982-12-01

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

  16. A highly efficient recombineering-based method for generating conditional knockout mutations.

    PubMed

    Liu, Pentao; Jenkins, Nancy A; Copeland, Neal G

    2003-03-01

    Phage-based Escherichia coli homologous recombination systems have recently been developed that now make it possible to subclone or modify DNA cloned into plasmids, BACs, or PACs without the need for restriction enzymes or DNA ligases. This new form of chromosome engineering, termed recombineering, has many different uses for functional genomic studies. Here we describe a new recombineering-based method for generating conditional mouse knockout (cko) mutations. This method uses homologous recombination mediated by the lambda phage Red proteins, to subclone DNA from BACs into high-copy plasmids by gap repair, and together with Cre or Flpe recombinases, to introduce loxP or FRT sites into the subcloned DNA. Unlike other methods that use short 45-55-bp regions of homology for recombineering, our method uses much longer regions of homology. We also make use of several new E. coli strains, in which the proteins required for recombination are expressed from a defective temperature-sensitive lambda prophage, and the Cre or Flpe recombinases from an arabinose-inducible promoter. We also describe two new Neo selection cassettes that work well in both E. coli and mouse ES cells. Our method is fast, efficient, and reliable and makes it possible to generate cko-targeting vectors in less than 2 wk. This method should also facilitate the generation of knock-in mutations and transgene constructs, as well as expedite the analysis of regulatory elements and functional domains in or near genes.

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  18. Design and generation of recombinant rabies virus vectors

    PubMed Central

    Osakada, Fumitaka; Callaway, Edward M.

    2014-01-01

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

  19. [Recombinant antibodies: towards a new generation of antivenoms?].

    PubMed

    Aubrey, Nicolas; Muzard, Julien; Juste, Matthieu; Billiald, Philippe

    2006-01-01

    Poisoning by scorpion venoms is a major health hazard in tropical and subtropical regions and serum therapy, which was discovered in 1894, remains the only specific treatment. No real progress has been made since this time and the therapeutic use of antivenoms which still consists in polyclonal antibody fragments from the sera of immunized animals may be associated with major drawbacks. Protein engineering now allows to design novel recombinant antibody fragments which are superior to polyclonal antivenoms in homogeneity, specific activity and possibly safety. Several single-chain antibody fragments (scFvs) which neutralize scorpion toxins have been produced and characterized over the last few years. These scFvs can also be used as building blocks to engineer more complex structures including multivalent monospecific antibody fragments (diabodies, triabodies) and bispecific molecules (tandem-scFv). Some of these molecules neutralize scorpion neurotoxins and protect mice from experimental envenoming. Thus, research projects currently underway suggest that new strategies might soon be available to treat poisonings in the absence of socio-economic considerations.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Gotoda, Hiroshi; Kobayashi, Hiroaki; Hayashi, Kenta

    2017-02-01

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

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

    PubMed

    Gotoda, Hiroshi; Kobayashi, Hiroaki; Hayashi, Kenta

    2017-02-01

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

  3. Restrictions Limiting the Generation of DNA Double Strand Breaks during Chromosomal V(D)J Recombination

    PubMed Central

    Tillman, Robert E.; Wooley, Andrea L.; Hughes, Maureen M.; Wehrly, Tara D.; Swat, Wojciech; Sleckman, Barry P.

    2002-01-01

    Antigen receptor loci are composed of numerous variable (V), diversity (D), and joining (J) gene segments, each flanked by recombination signal sequences (RSSs). The V(D)J recombination reaction proceeds through RSS recognition and DNA cleavage steps making it possible for multiple DNA double strand breaks (DSBs) to be introduced at a single locus. Here we use ligation-mediated PCR to analyze DNA cleavage intermediates in thymocytes from mice with targeted RSS mutations at the endogenous TCRβ locus. We show that DNA cleavage does not occur at individual RSSs but rather must be coordinated between RSS pairs flanking gene segments that ultimately form coding joins. Coordination of the DNA cleavage step occurs over great distances in the chromosome and favors intra- over interchromosomal recombination. Furthermore, through several restrictions imposed on the generation of both nonpaired and paired DNA DSBs, this requirement promotes antigen receptor gene integrity and genomic stability in developing lymphocytes undergoing V(D)J recombination. PMID:11828005

  4. InGaAs-InP avalanche photodiodes with dark current limited by generation-recombination.

    PubMed

    Zhao, Yanli; Zhang, Dongdong; Qin, Long; Tang, Qi; Wu, Rui Hua; Liu, Jianjun; Zhang, Youping; Zhang, Hong; Yuan, Xiuhua; Liu, Wen

    2011-04-25

    Separate absorption grading charge multiplication avalanche photodiodes (SAGCM APDs) are widely accepted in photon starved optical communication systems due to the presence of large photocurrent gain. In this work, we present a detailed analysis of dark currents of planar-type SAGCM InGaAs-InP APDs with different thicknesses of multiplication layer. The effect of the diffusion process, the generation-recombination process, the tunneling process and the multiplication process on the total leakage current is discussed. A new empirical formula has been established to predict the optimal multiplication layer thickness of SAGCM APDs with dark current limited by generation-recombination at multiplication gain of 8.

  5. 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.

  6. 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.

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

    PubMed Central

    Tsuzuki, T; Rancourt, D E

    1998-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Shen, Meng; Liu, Yuming

    2015-11-01

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

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

    PubMed Central

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

    2014-01-01

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

  11. Using the longitudinal space charge instability for generation of vacuum ultraviolet and x-ray radiation

    NASA Astrophysics Data System (ADS)

    Schneidmiller, E. A.; Yurkov, M. V.

    2010-11-01

    Longitudinal space charge (LSC) driven microbunching instability in electron beam formation systems of x-ray free-electron lasers (FELs) is a recently discovered effect hampering beam instrumentation and FEL operation. The instability was observed in different facilities in infrared and visible wavelength ranges. In this paper we propose to use such an instability for generation of vacuum ultraviolet (VUV) and x-ray radiation. A typical longitudinal space charge amplifier (LSCA) consists of few amplification cascades (drift space plus chicane) with a short undulator behind the last cascade. If the amplifier starts up from the shot noise, the amplified density modulation has a wide band, on the order of unity. The bandwidth of the radiation within the central cone is given by an inverse number of undulator periods. A wavelength compression could be an attractive option for LSCA since the process is broadband, and a high compression stability is not required. LSCA can be used as a cheap addition to the existing or planned short-wavelength FELs. In particular, it can produce the second color for a pump-probe experiment. It is also possible to generate attosecond pulses in the VUV and x-ray regimes. Some user experiments can profit from a relatively large bandwidth of the radiation, and this is easy to obtain in the LSCA scheme. Finally, since the amplification mechanism is broadband and robust, LSCA can be an interesting alternative to the self-amplified spontaneous emission free-electron laser (SASE FEL) in the case of using laser-plasma accelerators as drivers of light sources.

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed

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

    2014-10-17

    Re-initiation of DNA replication at origins within a given cell cycle would result in DNA rereplication, which can lead to genome instability and tumorigenesis. DNA rereplication can be induced by loss of licensing control at cellular replication origins, or by viral protein-driven multiple rounds of replication initiation at viral origins. DNA double-strand breaks (DSBs) are generated during rereplication, but the mechanisms of how these DSBs are repaired to maintain genome stability and cell viability are poorly understood in mammalian cells. We generated novel EGFP-based DSB repair substrates, which specifically monitor the repair of rereplication-associated DSBs. We demonstrated that homologous recombination (HR) is an important mechanism to repair rereplication-associated DSBs, and sister chromatids are used as templates for such HR-mediated DSB repair. Micro-homology-mediated non-homologous end joining (MMEJ) can also be used but to a lesser extent compared to HR, whereas Ku-dependent classical non-homologous end joining (C-NHEJ) has a minimal role to repair rereplication-associated DSBs. In addition, loss of HR activity leads to severe cell death when rereplication is induced. Therefore, our studies identify HR, the most conservative repair pathway, as the primary mechanism to repair DSBs upon rereplication. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Comparison of two generation-recombination terms in the Poisson-Nernst-Planck model.

    PubMed

    Lelidis, I; Barbero, G; Sfarna, A

    2012-10-21

    Two phenomenological forms proposed to take into account the generation-recombination phenomenon of ions are investigated. The first form models the phenomenon as a chemical reaction, containing two coefficients describing the dissociation of neutral particles in ions, and the recombination of ions to give neutral particles. The second form is based on the assumption that in thermodynamical equilibrium, a well-defined density of ions is stable. Any deviation from the equilibrium density gives rise to a source term proportional to the deviation, whose phenomenological coefficient plays the role of a life time. The analysis is performed by evaluating the electrical response of an electrolytic cell to an external stimulus for both forms. For simplicity we assume that the electrodes are blocking, that there is only a group of negative and positive ions, and that the negative ions are immobile. For the second form, two cases are considered: (i) the generation-recombination phenomenon is due to an intrinsic mechanism, and (ii) the production of ions is triggered by an external source of energy, as in a solar cell. We show that the predictions of the two models are different at the impedance as well as at the admittance level. In particular, the first model predicts the existence of two plateaux for the real part of the impedance, whereas the second one predicts just one. It follows that impedance spectroscopy measurements could give information on the model valid for the generation-recombination of ions.

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Stoll, Moritz H. R.; Kley, Wilhelm

    2016-10-01

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

  17. 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

  18. Generation of Recombinant Antibodies Against Toxins and Viruses by Phage Display for Diagnostics and Therapy.

    PubMed

    Unkauf, Tobias; Miethe, Sebastian; Fühner, Viola; Schirrmann, Thomas; Frenzel, André; Hust, Michael

    2016-01-01

    Antibody phage display is an in vitro technology to generate recombinant antibodies. In particular for pathogens like viruses or toxins, antibody phage display is an alternative to hybridoma technology, since it circumvents the limitations of the immune system. Phage display allows the generation of human antibodies from naive antibody gene libraries when either immunized patients are not available or immunization is not ethically feasible. This technology also allows the construction of immune libraries to select in vivo affinity matured antibodies if immunized patients or animals are available.In this review, we describe the generation of human and human-like antibodies from naive antibody gene libraries and antibodies from immune antibody gene libraries. Furthermore, we give an overview about phage display derived recombinant antibodies against viruses and toxins for diagnostics and therapy.

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

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

    SciTech Connect

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

    2016-03-15

    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.

  2. 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.

  3. 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.

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

    DOE PAGES

    Fu, Xiangrong; Cowee, Misa M.; Gary, Stephen Peter; ...

    2016-03-17

    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 fields 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.more » the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. We find that 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 fields that propagate at the electron thermal speed, suggesting another potential explanation for the observations.« less

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2017-01-04

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

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

    PubMed Central

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

    2017-01-01

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

  8. A protocol for construction of gene targeting vectors and generation of homologous recombinant embryonic stem cells.

    PubMed

    Bouabe, Hicham; Okkenhaug, Klaus

    2013-01-01

    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 cells (ESCs) 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, and short- and long-range deletions, inversions. Site-specific modification into the genome of ESCs can be reached by homologous recombination using targeting vectors. Here, we describe a protocol to generate targeting constructs and homologous recombinant ESCs.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

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

    2013-12-20

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

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

    PubMed

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

    2013-08-01

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

  12. 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.

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

    PubMed

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

    2010-09-01

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

  14. Generation, characterization, and application in serodiagnosis of recombinant swine vesicular disease virus-like particles.

    PubMed

    Xu, Wanhong; Goolia, Melissa; Salo, Tim; Zhang, Zhidong; Yang, Ming

    2017-08-31

    Swine vesicular disease (SVD) is a highly contagious viral disease that causes vesicular disease in pigs. The importance of the disease is due to its indistinguishable clinical signs from those of foot-and-mouth disease, which prevents international trade of swine and related products. SVD-specific antibody detection via an enzyme-linked immunosorbent assay (ELISA) is the most versatile and commonly used method for SVD surveillance and export certification. Inactivated SVD virus is the commonly used antigen in SVD-related ELISA. A recombinant SVD virus-like particle (VLP) was generated by using a Bac-to-Bac baculovirus expression system. Results of SVD-VLP analyses from electron microscopy, western blotting, immunofluorescent assay, and mass spectrometry showed that the recombinant SVD-VLP morphologically resemble authentic SVD viruses. The SVD-VLP was evaluated as a replacement for inactivated whole SVD virus in competitive and isotype-specific ELISAs for the detection of antibodies against SVD virus. The recombinant SVD-VLP assay produced results similar to those from inactivated whole virus antigen ELISA. The VLP-based ELISA results were comparable to those from the virus neutralization test for antibody detection in pigs experimentally inoculated with SVD virus. Use of the recombinant SVD-VLP is a safe and valuable alternative to using SVD virus antigen in diagnostic assays.

  15. 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.

  16. 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.

  17. Generation of dark solitons and their instability dynamics in two-dimensional condensates

    NASA Astrophysics Data System (ADS)

    Verma, Gunjan; Rapol, Umakant D.; Nath, Rejish

    2017-04-01

    We analyze numerically the formation and the subsequent dynamics of two-dimensional matter wave dark solitons in a Thomas-Fermi rubidium condensate using various techniques. An initially imprinted sharp phase gradient leads to the dynamical formation of a stationary soliton as well as very shallow gray solitons, whereas a smooth gradient only creates gray solitons. The depth and hence, the velocity of the soliton is provided by the spatial width of the phase gradient, and it also strongly influences the snake-instability dynamics of the two-dimensional solitons. The vortex dipoles stemming from the unstable soliton exhibit rich dynamics. Notably, the annihilation of a vortex dipole via a transient dark lump or a vortexonium state, the exchange of vortices between either a pair of vortex dipoles or a vortex dipole and a single vortex, and so on. For sufficiently large width of the initial phase gradient, the solitons may decay directly into vortexoniums instead of vortex pairs, and also the decay rate is augmented. Later, we discuss alternative techniques to generate dark solitons, which involve a Gaussian potential barrier and time-dependent interactions, both linear and periodic. The properties of the solitons can be controlled by tuning the amplitude or the width of the potential barrier. In the linear case, the number of solitons and their depths are determined by the quench time of the interactions. For the periodic modulation, a transient soliton lattice emerges with its periodicity depending on the modulation frequency, through a wave number selection governed by the local Bogoliubov spectrum. Interestingly, for sufficiently low barrier potential, both Faraday pattern and soliton lattice coexist. The snake instability dynamics of the soliton lattice is characteristically modified if the Faraday pattern is present.

  18. Generating gene knockout rats by homologous recombination in embryonic stem cells

    PubMed Central

    Tong, Chang; Huang, Guanyi; Ashton, Charles; Li, Ping; Ying, Qi-Long

    2013-01-01

    We describe here a detailed protocol for generating gene knockout rats by homologous recombination in embryonic stem (ES) cells. This protocol comprises the following procedures: derivation and expansion of rat ES cells, construction of gene-targeting vectors, generation of gene-targeted rat ES cells and, finally, production of gene-targeted rats. The major differences between this protocol and the classical mouse gene-targeting protocol include ES cell culture methods, drug selection scheme, colony picking and screening strategies. This ES cell–based gene-targeting technique allows sophisticated genetic modifications to be performed in the rat, as many laboratories have been doing in the mouse for the past two decades. Recently we used this protocol to generate Tp53 (also known as p53) gene knockout rats. The entire process requires ~1 year to complete, from derivation of ES cells to generation of knockout rats. PMID:21637202

  19. Lobe-cleft instability in the buoyant gravity current generated by estuarine outflow

    NASA Astrophysics Data System (ADS)

    Horner-Devine, Alexander R.; Chickadel, C. Chris

    2017-05-01

    Gravity currents represent a broad class of geophysical flows including turbidity currents, powder avalanches, pyroclastic flows, sea breeze fronts, haboobs, and river plumes. A defining feature in many gravity currents is the formation of three-dimensional lobes and clefts along the front and researchers have sought to understand these ubiquitous geophysical structures for decades. The prevailing explanation is based largely on early laboratory and numerical model experiments at much smaller scales, which concluded that lobes and clefts are generated due to hydrostatic instability exclusively in currents propagating over a nonslip boundary. Recent studies suggest that frontal dynamics change as the flow scale increases, but no measurements have been made that sufficiently resolve the flow structure in full-scale geophysical flows. Here we use thermal infrared and acoustic imaging of a river plume to reveal the three-dimensional structure of lobes and clefts formed in a geophysical gravity current front. The observed lobes and clefts are generated at the front in the absence of a nonslip boundary, contradicting the prevailing explanation. The observed flow structure is consistent with an alternative formation mechanism, which predicts that the lobe scale is inherited from subsurface vortex structures.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  1. 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. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

  2. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.

    PubMed

    Mostowy, Rafal J; Croucher, Nicholas J; De Maio, Nicola; Chewapreecha, Claire; Salter, Susannah J; Turner, Paul; Aanensen, David M; Bentley, Stephen D; Didelot, Xavier; Fraser, Christophe

    2017-10-01

    Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and the target of the currently used pneumococcal vaccines-constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared with the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centered approach, we analyzed the evolutionary history of 12 major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to nonrandom associations between co-colonizing serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasize the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. 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.

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

    PubMed

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

    2016-11-17

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

  5. 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

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

    PubMed

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

    2015-01-01

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

  7. Impact of interfacial molecular orientation on radiative recombination and charge generation efficiency

    DOE PAGES

    Ran, Niva A.; Roland, Steffen; Love, John A.; ...

    2017-07-19

    Here, a long standing question in organic electronics concerns the effects of molecular orientation at donor/acceptor heterojunctions. Given a well-controlled donor/acceptor bilayer system, we uncover the genuine effects of molecular orientation on charge generation and recombination. These effects are studied through the point of view of photovoltaics—however, the results have important implications on the operation of all optoelectronic devices with donor/acceptor interfaces, such as light emitting diodes and photodetectors. Our findings can be summarized by two points. First, devices with donor molecules face-on to the acceptor interface have a higher charge transfer state energy and less non-radiative recombination, resulting inmore » larger open-circuit voltages and higher radiative efficiencies. Second, devices with donor molecules edge-on to the acceptor interface are more efficient at charge generation, attributed to smaller electronic coupling between the charge transfer states and the ground state, and lower activation energy for charge generation.« less

  8. Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display.

    PubMed

    Kuhn, Philipp; Fühner, Viola; Unkauf, Tobias; Moreira, Gustavo Marcal Schmidt Garcia; Frenzel, André; Miethe, Sebastian; Hust, Michael

    2016-10-01

    Antibodies are valuable molecules for the diagnostic and treatment of diseases caused by pathogens and toxins. Traditionally, these antibodies are generated by hybridoma technology. An alternative to hybridoma technology is the use of antibody phage display to generate recombinant antibodies. This in vitro technology circumvents the limitations of the immune system and allows-in theory-the generation of antibodies against all conceivable molecules. Phage display technology enables obtaining human antibodies from naïve antibody gene libraries when either patients are not available or immunization is not ethically feasible. On the other hand, if patients or immunized/infected animals are available, it is common to construct immune phage display libraries to select in vivo affinity-matured antibodies. Because the phage packaged DNA sequence encoding the antibodies is directly available, the antibodies can be smoothly engineered according to the requirements of the final application. In this review, an overview of phage display derived recombinant antibodies against bacterial, viral, and eukaryotic pathogens as well as toxins for diagnostics and therapy is given. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DTIC Science & Technology

    2011-01-01

    Haemost 2004;2:402–13. [20] Brummel Ziedins K, Rivard GE, Pouliot RL, Butenas S, Gissel M, Parhami-Seren B, et al. Factor VIIa replacement therapy in...coagulopathy in a porcine trauma model. J Trauma 2010;68:1151–7. [25] Gallistl S, Cvirn G, Muntean W . Recombinant factor VIIa does not induce...VIIa-induced thrombin generation in plasmas deficient in factors VIII, IX, XI. J Thromb Haemost 2006;4:192–200. [27] Streif W , Paes B, Berry L, Andrew

  10. Generation of the jovian radio emission by the maser cyclotron instability: first lessons from JUNO

    NASA Astrophysics Data System (ADS)

    Louarn, Philippe; Allegrini, Frederic; Kurth, WilliamS.; Valek, Philips. W.; McComas, Dave; Bagenal, Fran; Bolton, Scott; Connerney, John; Ebert, Robert W.; Levin, Steven; Szalay, Jamey; Wilson, Robert; Zink, Jenna; André, Nicolas; Imai, Masafumi

    2017-04-01

    Using JUNO plasma and wave observations (JADE and Waves instruments), the scenario for the generation of jovian auroral radio emissions are analyzed. The sources of radiation are identified by localized intensifications of the radio flux at frequencies close to the electron gyrofrequency. Not surprisingly, it is shown that the cyclotron maser instability is perfectly adapted to the plasma conditions prevailing in the radio sources. However, it appears that different forms of activation of the cyclotron maser are observed. For radiation at hectometric wavelengths (one of the main emissions), pronounced loss-cones in the electron distribution functions are likely the source of free energy. The sources would be extended over several thousand km in directions traverse to the magnetic field. The applications of the theory reveals that sufficient growth rates are obtained from the distributions functions that are actually measured by JADE. This differs from the Earth scenario for which 'trapped' distribution functions drive the maser. More localized sources are also observed, possibly linked to local acceleration process. These examples may present analogies with the 'Earth' scenario, with other forms of free energy than the loss-cone. A first lesson of these direct in-situ JADE and RPWS observations is thus to confirm the maser cyclotron scenario with, however, conditions for the wave amplification and detailed maser processes that appear to be different than at Earth.

  11. Generation and CRISPR/Cas9 editing of transformed progenitor B cells as a pseudo-physiological system to study DNA repair gene function in V(D)J recombination.

    PubMed

    Lenden Hasse, Hélène; Lescale, Chloé; Bianchi, Joy J; Yu, Wei; Bedora-Faure, Marie; Deriano, Ludovic

    2017-09-04

    Antigen receptor gene assembly is accomplished in developing lymphocytes by the V(D)J recombination reaction, which can be separated into two steps: DNA cleavage by the recombination-activating gene (RAG) nuclease and joining of DNA double strand breaks (DSBs) by components of the nonhomologous end joining (NHEJ) pathway. Deficiencies for NHEJ factors can result in immunodeficiency and a propensity to accumulate genomic instability, thus highlighting the importance of identifying all players in this process and deciphering their functions. Bcl2 transgenic v-Abl kinase-transformed pro-B cells provide a pseudo-physiological cellular system to study V(D)J recombination. Treatment of v-Abl/Bcl2 pro-B cells with the Abl kinase inhibitor Imatinib leads to G1 cell cycle arrest, the rapid induction of Rag1/2 gene expression and V(D)J recombination. In this system, the Bcl2 transgene alleviates Imatinib-induced apoptosis enabling the analysis of induced V(D)J recombination. Although powerful, the use of mouse models carrying the Bcl2 transgene for the generation of v-Abl pro-B cell lines is time and money consuming. Here, we describe a method for generating v-Abl/Bcl2 pro-B cell lines from wild type mice and for performing gene knock-out using episomal CRISPR/Cas9 targeting vectors. Using this approach, we generated distinct NHEJ-deficient pro-B cell lines and quantified V(D)J recombination levels in these cells. Furthermore, this methodology can be adapted to generate pro-B cell lines deficient for any gene suspected to play a role in V(D)J recombination, and more generally DSB repair. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2014-01-01

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

  13. 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.

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

    PubMed

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

    2003-09-01

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

  15. 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

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

    PubMed

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

    2016-11-29

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2013-12-01

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

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

    PubMed

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Movahed, Pooya

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

  1. 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.

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

    PubMed

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

    2014-06-01

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

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

    DTIC Science & Technology

    2007-11-02

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

  4. 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.

  5. 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.

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

    PubMed

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

    2016-11-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    PubMed

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

    2016-01-07

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

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

    PubMed

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

    2015-06-05

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

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Otobe, T.

    2016-12-01

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

  12. Mitigation of Hot Electrons from Laser-Plasma Instabilities in Laser-Generated X-Ray Sources

    NASA Astrophysics Data System (ADS)

    Fein, Jeffrey R.

    This thesis describes experiments to understand and mitigate energetic or "hot" electrons from laser-plasma instabilities (LPIs) in an effort to improve radiographic techniques using laser-generated x-ray sources. Initial experiments on the OMEGA-60 laser show evidence of an underlying background generated by x-rays with energies over 10 keV on radiographs using backlit pinhole radiography, whose source is consistent with hard x-rays from LPI-generated hot electrons. Mitigating this background can dramatically reduce uncertainties in measured object densities from radiographs and may be achieved by eliminating the target components in which LPIs are most likely to grow. Experiments were performed on the OMEGA-EP laser to study hot electron production from laser-plasma instabilities in high-Z plasmas relevant to laser-generated x-ray sources. Measurements of hard x-rays show a dramatic reduction in hot-electron energy going from low-Z CH to high-Z Au targets, in a manner that is consistent with steepening electron density profiles that were also measured. The profile-steepening, we infer, increased thresholds of LPIs and contributed to the reduced hot-electron production at higher Z. Possible mechanisms for generating hot electrons include the two-plasmon decay and stimulated Raman scattering instabilities driven by multiple laser beams. Radiation hydrodynamic simulations using the CRASH code predict that both of these instabilities were above threshold with linear threshold parameters that decreased with increasing Z due to steepening length-scales, as well as enhanced laser absorption and increased collisional and Landau damping of electron plasma waves. Another set of experiments were performed on the OMEGA-60 laser to test whether hard x-ray background could be mitigated in backlit pinhole imagers by controlling laser-plasma instabilities. Based on the results above, we hypothesized that LPIs and hot electrons that lead to hard x-ray background would be reduced

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

    PubMed

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

    2011-11-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    SciTech Connect

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

    1996-12-31

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

  16. 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

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

  18. Regulation of recombination and genomic maintenance.

    PubMed

    Heyer, Wolf-Dietrich

    2015-08-03

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

  19. Rac2-MRC-cIII–generated ROS cause genomic instability in chronic myeloid leukemia stem cells and primitive progenitors

    PubMed Central

    Nieborowska-Skorska, Margaret; Kopinski, Piotr K.; Ray, Regina; Hoser, Grazyna; Ngaba, Danielle; Flis, Sylwia; Cramer, Kimberly; Reddy, Mamatha M.; Koptyra, Mateusz; Penserga, Tyrone; Glodkowska-Mrowka, Eliza; Bolton, Elisabeth; Holyoake, Tessa L.; Eaves, Connie J.; Cerny-Reiterer, Sabine; Valent, Peter; Hochhaus, Andreas; Hughes, Timothy P.; van der Kuip, Heiko; Sattler, Martin; Wiktor-Jedrzejczak, Wieslaw; Richardson, Christine; Dorrance, Adrienne; Stoklosa, Tomasz; Williams, David A.

    2012-01-01

    Chronic myeloid leukemia in chronic phase (CML-CP) is induced by BCR-ABL1 oncogenic tyrosine kinase. Tyrosine kinase inhibitors eliminate the bulk of CML-CP cells, but fail to eradicate leukemia stem cells (LSCs) and leukemia progenitor cells (LPCs) displaying innate and acquired resistance, respectively. These cells may accumulate genomic instability, leading to disease relapse and/or malignant progression to a fatal blast phase. In the present study, we show that Rac2 GTPase alters mitochondrial membrane potential and electron flow through the mitochondrial respiratory chain complex III (MRC-cIII), thereby generating high levels of reactive oxygen species (ROS) in CML-CP LSCs and primitive LPCs. MRC-cIII–generated ROS promote oxidative DNA damage to trigger genomic instability, resulting in an accumulation of chromosomal aberrations and tyrosine kinase inhibitor–resistant BCR-ABL1 mutants. JAK2(V617F) and FLT3(ITD)–positive polycythemia vera cells and acute myeloid leukemia cells also produce ROS via MRC-cIII. In the present study, inhibition of Rac2 by genetic deletion or a small-molecule inhibitor and down-regulation of mitochondrial ROS by disruption of MRC-cIII, expression of mitochondria-targeted catalase, or addition of ROS-scavenging mitochondria-targeted peptide aptamer reduced genomic instability. We postulate that the Rac2-MRC-cIII pathway triggers ROS-mediated genomic instability in LSCs and primitive LPCs, which could be targeted to prevent the relapse and malignant progression of CML. PMID:22411871

  20. Rac2-MRC-cIII-generated ROS cause genomic instability in chronic myeloid leukemia stem cells and primitive progenitors.

    PubMed

    Nieborowska-Skorska, Margaret; Kopinski, Piotr K; Ray, Regina; Hoser, Grazyna; Ngaba, Danielle; Flis, Sylwia; Cramer, Kimberly; Reddy, Mamatha M; Koptyra, Mateusz; Penserga, Tyrone; Glodkowska-Mrowka, Eliza; Bolton, Elisabeth; Holyoake, Tessa L; Eaves, Connie J; Cerny-Reiterer, Sabine; Valent, Peter; Hochhaus, Andreas; Hughes, Timothy P; van der Kuip, Heiko; Sattler, Martin; Wiktor-Jedrzejczak, Wieslaw; Richardson, Christine; Dorrance, Adrienne; Stoklosa, Tomasz; Williams, David A; Skorski, Tomasz

    2012-05-03

    Chronic myeloid leukemia in chronic phase (CML-CP) is induced by BCR-ABL1 oncogenic tyrosine kinase. Tyrosine kinase inhibitors eliminate the bulk of CML-CP cells, but fail to eradicate leukemia stem cells (LSCs) and leukemia progenitor cells (LPCs) displaying innate and acquired resistance, respectively. These cells may accumulate genomic instability, leading to disease relapse and/or malignant progression to a fatal blast phase. In the present study, we show that Rac2 GTPase alters mitochondrial membrane potential and electron flow through the mitochondrial respiratory chain complex III (MRC-cIII), thereby generating high levels of reactive oxygen species (ROS) in CML-CP LSCs and primitive LPCs. MRC-cIII-generated ROS promote oxidative DNA damage to trigger genomic instability, resulting in an accumulation of chromosomal aberrations and tyrosine kinase inhibitor-resistant BCR-ABL1 mutants. JAK2(V617F) and FLT3(ITD)-positive polycythemia vera cells and acute myeloid leukemia cells also produce ROS via MRC-cIII. In the present study, inhibition of Rac2 by genetic deletion or a small-molecule inhibitor and down-regulation of mitochondrial ROS by disruption of MRC-cIII, expression of mitochondria-targeted catalase, or addition of ROS-scavenging mitochondria-targeted peptide aptamer reduced genomic instability. We postulate that the Rac2-MRC-cIII pathway triggers ROS-mediated genomic instability in LSCs and primitive LPCs, which could be targeted to prevent the relapse and malignant progression of CML.

  1. The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination.

    PubMed

    Delprat, Alejandra; Negre, Bàrbara; Puig, Marta; Ruiz, Alfredo

    2009-11-18

    Transposable elements (TEs) are responsible for the generation of chromosomal inversions in several groups of organisms. However, in Drosophila and other Dipterans, where inversions are abundant both as intraspecific polymorphisms and interspecific fixed differences, the evidence for a role of TEs is scarce. Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii. To assess the impact of TEs in Drosophila chromosomal evolution and shed light on the mechanism involved, we isolated and sequenced the two breakpoints of another widespread polymorphic inversion from D. buzzatii, 2z(3). In the non inverted chromosome, the 2z(3) distal breakpoint was located between genes CG2046 and CG10326 whereas the proximal breakpoint lies between two novel genes that we have named Dlh and Mdp. In the inverted chromosome, the analysis of the breakpoint sequences revealed relatively large insertions (2,870-bp and 4,786-bp long) including two copies of the transposon Galileo (subfamily Newton), one at each breakpoint, plus several other TEs. The two Galileo copies: (i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric. Our observations provide the best evidence gathered so far for the role of TEs in the generation of Drosophila inversions. In addition, they show unequivocally that ectopic recombination is the causative mechanism. The fact that the three polymorphic D. buzzatii inversions investigated so far were generated by the same transposon family is remarkable and is conceivably due to Galileo's unusual structure and current (or recent) transpositional activity.

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

    PubMed Central

    Delprat, Alejandra; Ruiz, Alfredo

    2009-01-01

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

  3. Cloning of an Avian Adeno-Associated Virus (AAAV) and Generation of Recombinant AAAV Particles

    PubMed Central

    Bossis, Ioannis; Chiorini, John A.

    2003-01-01

    Recent studies have proposed that adeno-associated viruses (AAVs) are not evolutionarily linked to other mammalian autonomous parvoviruses but are more closely linked to the autonomous parvoviruses of birds. To better understand the relationship between primate and avian AAVs (AAAVs), we cloned and sequenced the genome of an AAAV (ATCC VR-865) and generated recombinant AAAV particles. The genome of AAAV is 4,694 nucleotides in length and has organization similar to that of other AAVs. The entire genome of AAAV displays 56 to 65% identity at the nucleotide level with the other known AAVs. The AAAV genome has inverted terminal repeats of 142 nucleotides, with the first 122 forming the characteristic T-shaped palindromic structure. The putative Rep-binding element consists of a tandem (GAGY)4 repeat, and the putative terminal resolution site (trs), CCGGT/CG, contains a single nucleotide substitution relative to the AAV2 trs. The Rep open reading frame of AAAV displays 50 to 54% identity at the amino acid level with the other AAVs, with most of the diversity clustered at the carboxyl and amino termini. Comparison of the capsid proteins of AAAV and the primate dependoviruses indicate that divergent regions are localized to surface-exposed loops. Despite these sequence differences, we were able to produce recombinant AAAV particles carrying a lacZ reporter gene by cotransfection in 293T cells and were able to examine transduction efficiency in both chicken primary cells and several cell lines. Our findings indicate that AAAV is the most divergent AAV described to date but maintains all the characteristics unique to the genera of dependovirus. PMID:12768000

  4. Cloning of an avian adeno-associated virus (AAAV) and generation of recombinant AAAV particles.

    PubMed

    Bossis, Ioannis; Chiorini, John A

    2003-06-01

    Recent studies have proposed that adeno-associated viruses (AAVs) are not evolutionarily linked to other mammalian autonomous parvoviruses but are more closely linked to the autonomous parvoviruses of birds. To better understand the relationship between primate and avian AAVs (AAAVs), we cloned and sequenced the genome of an AAAV (ATCC VR-865) and generated recombinant AAAV particles. The genome of AAAV is 4,694 nucleotides in length and has organization similar to that of other AAVs. The entire genome of AAAV displays 56 to 65% identity at the nucleotide level with the other known AAVs. The AAAV genome has inverted terminal repeats of 142 nucleotides, with the first 122 forming the characteristic T-shaped palindromic structure. The putative Rep-binding element consists of a tandem (GAGY)(4) repeat, and the putative terminal resolution site (trs), CCGGT/CG, contains a single nucleotide substitution relative to the AAV(2) trs. The Rep open reading frame of AAAV displays 50 to 54% identity at the amino acid level with the other AAVs, with most of the diversity clustered at the carboxyl and amino termini. Comparison of the capsid proteins of AAAV and the primate dependoviruses indicate that divergent regions are localized to surface-exposed loops. Despite these sequence differences, we were able to produce recombinant AAAV particles carrying a lacZ reporter gene by cotransfection in 293T cells and were able to examine transduction efficiency in both chicken primary cells and several cell lines. Our findings indicate that AAAV is the most divergent AAV described to date but maintains all the characteristics unique to the genera of dependovirus.

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

    PubMed

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

    2016-12-01

    β-Lactoglobulin (BLG) is a dominant allergen present in the milk of goats and other ungulates, although it is not found in human breast milk. Thus, the presence of BLG restricts the consumption of goat's milk by humans. In the present study, we examined whether the disruption of the BLG gene in goats by homologous recombination (HR) reduced BLG content in goat's milk and decreased the allergic response to milk. In one approach, exon 2 of the BLG gene was efficiently targeted using HR with a BLG knockout vector. In a second approach to disrupt BLG gene expression and drive exogenous human α-lactalbumin (hLA) gene expression, two hLA knock-in constructs were used to target exons 1-4 of the BLG gene via HR, and expression of hLA was then confirmed in goat mammary epithelial cells in vitro. The recombinant clones from both approaches were then used for somatic cell nuclear transfer, generating two transgenic goats possessing a BLG knockout allele or site-specific hLA integration allele. Milk assays demonstrated a reduction in BLG levels in both the BLG knockout and hLA knock-in goats; furthermore, hLA was present in the hLA knock-in goat's milk. Allergenic analysis in mice indicated that the transgenic goat's milk was less allergenic than wild-type goat's milk. These results support the development of gene-targeted animals as an effective tool for reducing allergic reactions to milk and improving nutrition. © 2016 Federation of European Biochemical Societies.

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

    SciTech Connect

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

    1996-12-31

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

  7. 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.

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

    PubMed

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

    2012-06-22

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

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

    SciTech Connect

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

    1993-02-05

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

  10. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-02-01

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

  14. 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.

  15. 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)

  16. Ocular infection of mice with an avirulent recombinant HSV-1 expressing IL-4 and an attenuated HSV-1 strain generates virulent recombinants in vivo.

    PubMed

    Mott, Kevin R; Wechsler, Steven L; Ghiasi, Homayon

    2010-10-26

    To assess the relative impact of overexpression of interleukin 2 (IL-2), interleukin 4 (IL-4), and interferon gamma (IFN-γ) expressing recombinant herpes simplex virus type 1 (HSV-1) on altering immune responses in ocularly infected mice. BALB/c mice were co-infected ocularly with avirulent HSV-1 strain KOS and avirulent recombinant HSV-1 expressing murine IL-4 (HSV-IL-4). Controls mice were co-infected with KOS+HSV-IL-2 or KOS+HSV-IFNγ. Following ocular infection, virus replication in the eye, corneal scarring (CS), and survival were determined. We also isolated recombinant viruses from eye and trigeminal ganglia of KOS+HSV-IL-4 infected mice. In this study we found that ocular infection of BALB/c mice with a mixture of HSV-IL-4 and KOS resulted in increased death and increased eye disease. In contrast, when mice were infected in one eye with KOS and the other eye with HSV-IL-4 no death or eye disease was seen. Intraperitoneal co-infection of mice with KOS and HSV-IL-4 also did not result in HSV-1 induced death. Interestingly, ocular infection of mice with a mixture of HSV-IL-2 and KOS did not have any effect on severity of the disease in infected mice. We isolated recombinant viruses from KOS+HSV-IL-4 infected mice eye and trigeminal ganglia. Some of the isolated viruses were more neurovirulent then either parental virus. Infection of macrophages with IL-4 expressing virus down-regulated IL-12 production by macrophages. These results suggest a role for IL-4 in suppression of immune response and generation of virulent viruses in vivo.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Mehta, H.

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

  19. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.

    PubMed

    Soniat, Michael M; Myler, Logan R; Schaub, Jeffrey M; Kim, Yoori; Gallardo, Ignacio F; Finkelstein, Ilya J

    2017-01-01

    Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time. The DNA curtains platform facilitates high-throughput single-molecule imaging by organizing arrays of DNA molecules on the surface of a microfluidic flowcell. Here, we describe a second-generation UV lithography-based protocol for fabricating flowcells for DNA curtains. This protocol greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large datasets from individual single-molecule experiments. Drawing on our recent studies of human HR, we also provide an overview of how DNA curtains can be used for observing facilitated protein diffusion, processive enzyme translocation, and nucleoprotein filament dynamics on single-stranded DNA. Together, these protocols and case studies form a comprehensive introduction for other researchers that may want to adapt DNA curtains for high-throughput single-molecule studies of DNA replication, transcription, and repair. © 2017 Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. Characterization of a Novel HIV-1 Second-Generation Recombinant Form in Men Who Have Sex with Men in Beijing, China.

    PubMed

    Wang, Chen; Wang, Yan; Kong, Desheng; Xin, Ruolei; Xu, Weisi; Feng, Yi; Shao, Yiming; Ma, Liying

    2017-09-08

    Cocirculation of multiple subtypes in the same population contributes significantly to the emergence of recombinant viruses. BJ2015EU19, a novel CCR5-tropic human immunodeficiency virus (HIV)-1, second-generation recombinant virus, was isolated from a man who has sex with men in Beijing, China. Phylogenetic analysis of the near full-length genome showed that BJ2015EU19 consisted of seven fragments from CRF01_AE and CRF07_BC. There were six recombinant breakpoints in the pol, vpu, env, and nef genes of BJ2015EU19, which were different from the other circulating recombinant forms and unique recombinant forms (URFs). The new emergence of the URF increases the complexity of the HIV epidemic in the Chinese homosexual group, and the ongoing generation of recombinant viruses may provide an important basis for future analysis of the recombination mechanism of HIV-1.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Dennis, Graham R.; Johnsson, Mattias T.

    2010-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

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

    PubMed

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

    2015-11-02

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

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

    SciTech Connect

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

    2008-06-03

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

  9. 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.

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

    PubMed

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

    2013-11-01

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

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

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.; Giusti-Suzor, Annick

    1991-01-01

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

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

    PubMed

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

    2013-06-01

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

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

    SciTech Connect

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

    1993-11-15

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

  14. Nonsequential double-recombination high-order-harmonic generation in molecularlike systems

    NASA Astrophysics Data System (ADS)

    Hansen, Kenneth K.; Madsen, Lars Bojer

    2017-07-01

    We present a study of nonsequential double-recombination (NSDR) high-harmonic generation (HHG) in a molecularlike system. We have calculated the HHG spectrum for a wide range of internuclear distances, and using a Coulomb-corrected three-step model we are able to analyze and predict the observed NSDR HHG cutoffs precisely for all internuclear distances. It is shown through this Coulomb-corrected three-step (CC-TSM) model that there is an intrinsic dependence on the location of the nuclei in the NSDR HHG process not seen in one-electron HHG. This dependence originates from the strong electron correlation in the NSDR HHG process, and it modifies the classically allowed return energies which in return changes the cutoffs observed in the HHG spectra. It is observed that the CC-TSM correctly predicts cutoffs at all internuclear distances with differences of more than six harmonics being observed between the CC-TSM and the normal three-step model for the laser parameters used. We also observe that the NSDR HHG process changes for internuclear distances of R ≳8 -9 a.u., which is proposed to stem from a change in the charge-transfer dynamics within the molecule. For large internuclear distances of R ≳13 a.u., we observe a clear signature of the point of emission for the first electron emitted in the NSDR HHG signal and we also see signs of molecular exchange paths contributing to the HHG spectrum for these internuclear distances.

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

    NASA Astrophysics Data System (ADS)

    Schoeffler, Kevin

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  18. 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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  1. Retrovirus transduction: Generation of infectious retroviruses expressing dominant and selectable genes is associated with in vivo recombination and deletion events

    SciTech Connect

    Joyner, A.L.; Bernstein, A.

    1983-12-01

    The authors describe the generation of infectious retroviruses containing foreign genes by an in vivo recombination-deletion mechanism. Cotransfection into mouse cells of chimeric plasmids carrying a murine retrovirus 5' long terminal repeat and either the thymidine kinase (tk) gene of herpes virus or the dominant selectable bacterial gene for neomycin resistance (neo), along with a clone of Moloney murine leukemia virus, results in the generation of infectious thymidine kinase or neomycine-resistant viruses. Expression of the selectable marker in these viruses can be regulated by the homologous transcriptional promoter of the gene, by the promoter contained within the Friend spleen focus-forming virus long terminal repeat, or by the simian virus 40 early region promoter. In all cases, the rescued viruses appeared to arise by recombination in vivo with Moloney murine leukemia virus sequences, resulting in the acquisition of the Moloney 3' long terminal repeat and variable amounts of the 3' adjacent Moloney genome. In two of the thymidine kinase constructs where tk was inserted 200 base pairs downstream from the long terminal repeat, the rescued viruses acquired a large part of the murine leukemia virus genome, including the region involved in packaging genomic RNA into virions. The generation of infectious neomycin-resistant virus is associated with deletions of simian virus 40 splicing and polyadenylation sequences. These results demonstrate that nonhomologous recombination and deletion events can take place in animal cells, resulting in the acquisition or removal of cis-acting sequences required for, or inhibitory to, retrovirus infectivity.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Chen, Haifeng; Xie, Duan; Guo, Lixin

    2016-11-01

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

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

    SciTech Connect

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

    2011-03-15

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

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

    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.

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

    PubMed

    Morel, B; Hautier, C A

    2017-02-01

    The aim of this study was to evaluate the influence of the fatigue on the machine scrum pushing sagittal forces during repeated scrums and to determine the origin of the knee extensor fatigue. Twelve elite U23 rugby union front row players performed six 6-s scrums every 30 s against a dynamic scrum machine with passive or active recovery. The peak, average, and the standard deviation of the force were measured. A neuromuscular testing procedure of the knee extensors was carried out before and immediately after the repeated scrum protocol including maximal voluntary force, evoked force, and voluntary activation. The average and peak forces did not decrease after six scrums with passive recovery. The standard deviation of the force increased by 70.2 ± 42.7% (P < 0.001). Maximal voluntary/evoked force and voluntary activation decreased (respectively 25.1 ± 7.0%, 14.6 ± 5.5%, and 24 ± 9.9%; P < 0.001). The standard deviation of the force did not increase with active recovery and was associated with lower decrease of maximal voluntary/evoked force and voluntary activation (respectively 12.8 ± 7.9%, 4.9 ± 6.5%, and 7.6 ± 4.1%; all P < 0.01). As a conclusion repeated scrummaging induced an increased machine scrum pushing instability associated with central and peripheral fatigue of the knee extensors. Active recovery seems to limit all these manifestations of fatigue. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

    SciTech Connect

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

    2015-12-10

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

  8. 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

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

    PubMed

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

    2012-02-01

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

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

    PubMed

    Tilston-Lunel, Natasha L; Acrani, Gustavo Olszanski; Randall, Richard E; Elliott, Richard M

    2015-12-23

    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. 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 understanding this important yet

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

    SciTech Connect

    Lin, Shi -Zeng

    2016-07-05

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

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

    SciTech Connect

    Lin, Shi -Zeng

    2016-07-05

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

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

    PubMed

    Marín-López, Alejandro; Ortego, Javier

    2016-01-01

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

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

    SciTech Connect

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

    2012-10-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

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

    PubMed

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

    2010-11-01

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

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

    DOE PAGES

    Lin, Shi -Zeng

    2016-07-05

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

  18. 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.

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

    PubMed

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

    2016-01-22

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

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

    NASA Astrophysics Data System (ADS)

    Mueller, K.; Schmeling, H.

    2005-12-01

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

  1. How Expanded Ionospheres of Hot Jupiters Can Prevent Escape of Radio Emission Generated by the Cyclotron Maser Instability

    NASA Astrophysics Data System (ADS)

    Weber, Christof; Lammer, Helmut; Shaikhislamov, Ildar F.; Erkaev, Nikolai; Chadney, Joshua M.; Khodachenko, Maxim L.; Grießmeier, Jean-Mathias; Rucker, Helmut O.; Vocks, Christian; Macher, Wolfgang; Odert, Petra; Kislyakova, Kristina G.

    2017-04-01

    We present a study of the plasma conditions in the atmospheres of the Hot Jupiters HD 209458b and HD 189733b and for an HD 209458b-like planet at orbit locations between 0.2-1 AU around a Sun-like star. We discuss how these conditions influence the radio emission we expect from their planetary magnetospheres. We find that the environmental conditions for the cyclotron maser instability (CMI), the process which is responsible for the generation of radio waves at magnetic planets in the solar system, most likely will not operate at Hot Jupiters. The reason for that is that hydrodynamically expanding atmospheres possess extended ionospheres whose plasma densities within the magnetosphere are so large that the plasma frequency is much higher than the cyclotron frequency, which contradicts the necessary condition for the production of radio emission and prevents the escape of radio waves from close-in extrasolar planets at distances <0.05 AU from a Sun-like host star. The upper atmosphere structure of Hot Jupiters around stars similar to the Sun changes between 0.2 and 0.5 AU from the hydrodynamic to a hydrostatic regime and this results in conditions similar to solar system planets with a region of depleted plasma between the exobase and the magnetopause where the plasma frequency can be lower than the cyclotron frequency. In such an environment a beam of highly energetic electrons accelerated along the field lines towards the planet can produce radio emission. However, even if the CMI could operate the extended ionospheres of Hot Jupiters are too dense to let the radio emission escape from the planets. We also investigate the possible radio emission of the Hot Jupiter Tau Bootis b by placing it at different orbital distances from the host star, i.e. 0.1 and 0.2 AU. In particular we check if the atmosphere of Tau Bootis b at 0.046 AU is in the hydrostatic or in the hydrodynamic regime. If it is in the hydrodynamic regime it's ionosphere is extended and will constitute

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

    PubMed

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

    2013-11-01

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

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

    DTIC Science & Technology

    2005-04-01

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

  4. 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.

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

    PubMed

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

    2005-11-01

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

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

    PubMed Central

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

    1997-01-01

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

  7. 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.

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

    PubMed

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

    2016-02-04

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

  9. 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.

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

    PubMed Central

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

    2015-01-01

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

  11. Generation-recombination effects on dark currents in CdTe-passivated midwave infrared HgCdTe photodiodes

    NASA Astrophysics Data System (ADS)

    Jozwikowska, A.; Jozwikowski, K.; Antoszewski, J.; Musca, C. A.; Nguyen, T.; Sewell, R. H.; Dell, J. M.; Faraone, L.; Orman, Z.

    2005-07-01

    The effect of an abrupt CdTe /HgCdTe passivation heterointerface on generation recombination and dark currents in n-on-p midwave infrared photodiodes with 5.2-μm cut-off wavelength has been investigated. Experimentally, it was observed that the zero-bias-dynamic resistance, R0, at low temperatures scales with the perimeter of the n-on-p junction, rather than with the junction area, suggesting that surface effects are dominant. The diode current-voltage characteristics at low temperatures indicate significant contributions from tunneling effects, which is the dominant leakage current mechanism for reverse bias greater than approximately 30mV. These two observations suggest that the region where the junction terminates at the CdTe /HgCdTe abrupt interface is responsible for the above effects. A two-dimensional model has been developed to investigate the dark current mechanisms in the vicinity of the junction termination at CdTe /HgCdTe interface, which also takes into account the effect of dislocations on generation-recombination processes. Calculated profiles of the energy bands and electric field along different cross sections of the photodiode indicate that the electric field achieves a maximum value of the order of mid -105V/cm in the region where the junction terminates at the CdTe /HgCdTe interface. The presence of such a high localized electric field in this area decreases the ionization energy of trap levels in the band gap and, hence, increases efficiency of the Shockley-Read-Hall generation-recombination processes. In addition to diffusion, generation recombination, and trap-assisted tunneling mechanisms, the calculations of dynamic resistance include Poole-Frenkel and phonon-trap-assisted tunneling effects. The best fit to the zero bias dynamic resistance versus temperature results has been obtained using an aerial dislocation density in the bulk of the HgCdTe layer equal to 106cm-2. Although the direct band-to-band tunneling and impact ionization

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

    SciTech Connect

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

    2016-08-15

    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.

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

    NASA Astrophysics Data System (ADS)

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

    1986-07-01

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

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

    SciTech Connect

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

    2007-04-09

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

  15. Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi.

    PubMed

    Weatherly, D Brent; Peng, Duo; Tarleton, Rick L

    2016-09-13

    The protozoan parasite Trypanosoma cruzi, causative agent of Chagas disease, depends upon a cell surface-expressed trans-sialidase (ts) to avoid activation of complement-mediated lysis and to enhance intracellular invasion. However these functions alone fail to account for the size of this gene family in T. cruzi, especially considering that most of these genes encode proteins lacking ts enzyme activity. Previous whole genome sequencing of the CL Brener clone of T. cruzi identified ~1400 ts variants, but left many partially assembled sequences unannotated. In the current study we reevaluated the trans-sialidase-like sequences in this reference strain, identifying an additional 1779 full-length and partial ts genes with their important features annotated, and confirming the expression of previously annotated "pseudogenes" and newly annotated ts family members. Multiple EM for Motif Elicitation (MEME) analysis allowed us to generate a model T. cruzi ts (TcTS) based upon the most conserved motif patterns and demonstrated that a common motif order is highly conserved among ts family members. Using a newly developed pipeline for the analysis of recombination within large gene families, we further demonstrate that TcTS family members are undergoing frequent recombination, generating new variants from the thousands of functional and non-functional ts gene segments but retaining the overall structure of the core TcTS family members. The number and variety as well as high recombination frequency of TcTS family members supports strong evolutionary pressure, probably exerted by immune selection, for continued variation in ts sequences in T. cruzi, and thus for a unique immune evasion mechanism for the large ts gene family.

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

    PubMed Central

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

    2009-01-01

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

  17. Generation of Nanobodies against SlyD and development of tools to eliminate this bacterial contaminant from recombinant proteins.

    PubMed

    Hu, Yaozhong; Romão, Ema; Vertommen, Didier; Vincke, Cécile; Morales-Yánez, Francisco; Gutiérrez, Carlos; Liu, Changxiao; Muyldermans, Serge

    2017-09-01

    The gene for a protein domain, derived from a tumor marker, fused to His tag codons and under control of a T7 promotor was expressed in E. coli strain BL21 (DE3). The recombinant protein was purified from cell lysates through immobilized metal affinity chromatography and size-exclusion chromatography. A contaminating bacterial protein was consistently co-purified, even using stringent washing solutions containing 50 or 100 mM imidazole. Immunization of a dromedary with this contaminated protein preparation, and the subsequent generation and panning of the immune Nanobody library yielded several Nanobodies of which 2/3 were directed against the bacterial contaminant, reflecting the immunodominance of this protein to steer the dromedary immune response. Affinity adsorption of this contaminant using one of our specific Nanobodies followed by mass spectrometry identified the bacterial contaminant as FKBP-type peptidyl-prolyl cis-trans isomerase (SlyD) from E. coli. This SlyD protein contains in its C-terminal region 14 histidines in a stretch of 31 amino acids, which explains its co-purification on Ni-NTA resin. This protein is most likely present to varying extents in all recombinant protein preparations after immobilized metal affinity chromatography. Using our SlyD-specific Nb 5 we generated an immune-complex that could be removed either by immunocapturing or by size exclusion chromatography. Both methods allow us to prepare a recombinant protein sample where the SlyD contaminant was quantitatively eliminated. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2015-11-05

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

    Prado, Félix

    2014-05-01

    Homologous recombination (HR) is required to protect and restart stressed replication forks. Paradoxically, the Mrc1 branch of the S phase checkpoints, which is activated by replicative stress, prevents HR repair at breaks and arrested forks. Indeed, the mechanisms underlying HR can threaten genome integrity if not properly regulated. Thus, understanding how cells avoid genetic instability associated with replicative stress, a hallmark of cancer, is still a challenge. Here I discuss recent results that support a model by which HR responds to replication stress through replicative and repair activities that operate at different stages of the cell cycle (S and G2, respectively) and in distinct subnuclear structures. Remarkably, the replication checkpoint appears to control this scenario by inhibiting the assembly of HR repair centers at stressed forks during S phase, thereby avoiding genetic instability. © 2014 The Author. Bioessays published by WILEY Periodicals, Inc.

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

    SciTech Connect

    Pivi, M.

    2005-04-11

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

  2. 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.

  3. How expanded ionospheres of Hot Jupiters can prevent escape of radio emission generated by the cyclotron maser instability

    NASA Astrophysics Data System (ADS)

    Weber, C.; Lammer, H.; Shaikhislamov, I. F.; Chadney, J. M.; Khodachenko, M. L.; Grießmeier, J.-M.; Rucker, H. O.; Vocks, C.; Macher, W.; Odert, P.; Kislyakova, K. G.

    2017-08-01

    We present a study of plasma conditions in the atmospheres of the Hot Jupiters HD 209458b and HD 189733b and for an HD 209458b like planet at orbit locations between 0.2 and 1 au around a Sun-like star. We discuss how these conditions influence the radio emission we expect from their magnetospheres. We find that the environmental conditions are such that the cyclotron maser instability (CMI), the process responsible for the generation of radio waves at magnetic planets in the Solar system, most likely will not operate at Hot Jupiters. Hydrodynamically expanding atmospheres possess extended ionospheres whose plasma densities within the magnetosphere are so large that the plasma frequency is much higher than the cyclotron frequency, which contradicts the condition for the production of radio emission and prevents the escape of radio waves from close-in exoplanets at distances <0.05 au from a Sun-like host star. The upper atmosphere structure of gas giants around stars similar to the Sun changes between 0.2 and 0.5 au from the hydrodynamic to a hydrostatic regime, and this results in conditions similar to Solar system planets with a region of depleted plasma between the exobase and the magnetopause, where the plasma frequency can be lower than the cyclotron frequency. In such an environment, a beam of highly energetic electrons accelerated along the field lines towards the planet can produce radio emission. However, even if the CMI could operate, the extended ionospheres of Hot Jupiters are too dense to allow the radio emission to escape from the planets.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2017-01-01

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

  7. 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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Rossani, A.

    2016-11-01

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

  10. 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

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

    PubMed

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

    2014-04-23

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

  12. 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.

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

    PubMed

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

    2011-01-01

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

  14. 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

  15. Generation of recombinant single-chain antibodies neutralizing the cytolytic activity of vaginolysin, the main virulence factor of Gardnerella vaginalis.

    PubMed

    Pleckaityte, Milda; Mistiniene, Edita; Lasickiene, Rita; Zvirblis, Gintautas; Zvirbliene, Aurelija

    2011-11-03

    Gardnerella vaginalis is identified as the predominant colonist of the vaginal tract in women with bacterial vaginosis. Vaginolysin (VLY) is a protein toxin released by G. vaginalis. VLY possesses cytolytic activity and is considered as a main virulence factor of G. vaginalis. Inhibition of VLY-mediated cell lysis by antibodies may have important physiological relevance. Single-chain variable fragments of immunoglobulins (scFvs) were cloned from two hybridoma cell lines producing neutralizing antibodies against VLY and expressed as active proteins in E. coli. For each hybridoma, two variants of anti-VLY scFv consisting of either VL-VH or VH-VL linked with a 20 aa-long linker sequence (G₄S)₄ were constructed. Recovery of scFvs from inclusion bodies with subsequent purification by metal-chelate chromatography resulted in VLY-binding proteins that were predominantly monomeric. The antigen-binding activity of purified scFvs was verified by an indirect ELISA. The neutralizing activity was investigated by in vitro hemolytic assay and cytolytic assay using HeLa cell line. Calculated apparent Kd values and neutralizing potency of scFvs were in agreement with those of parental full-length antibodies. VH-VL and VL-VH variants of scFvs showed similar affinity and neutralizing potency. The anti-VLY scFvs derived from hybridoma clone 9B4 exhibited high VLY-neutralizing activity both on human erythrocytes and cervical epithelial HeLa cells. Hybridoma-derived scFvs with VLY-binding activity were expressed in E. coli. Recombinant anti-VLY scFvs inhibited VLY-mediated cell lysis. The monovalent scFvs showed reduced affinity and neutralizing potency as compared to the respective full-length antibodies. The loss of avidity could be restored by generating scFv constructs with multivalent binding properties. Generated scFvs is the first example of recombinant single-chain antibodies with VLY-neutralizing activity produced in prokaryote expression system. G. vaginalis caused

  16. 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.

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

    PubMed Central

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

    2016-01-01

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

  18. In vitro effects of recombinant activated factor VII on thrombin generation and coagulation following inhibition of platelet procoagulant activity by prasugrel.

    PubMed

    Mazzeffi, Michael; Szlam, Fania; Jakubowski, Joseph A; Tanaka, Kenichi A; Sugidachi, Atsuhiro; Levy, Jerrold H

    2013-07-01

    Prasugrel is a thienopyridyl P2Y12 antagonist with potent antiplatelet effects. At present, little is known about its effects on thrombin generation or what strategies may emergently reverse its anticoagulant effects. In the current study we evaluated whether recombinant activated factor VII may reverse prasugrel induced effects and increase thrombin generation in an in vitro model. The effect of prasugrel active metabolite, PAM (R-138727), was evaluated on platelet aggregation, thrombin generation, and rotational thromboelastometry parameters using blood from 20 healthy volunteers. Additionally, we evaluated the effects of adenosine diphosphate (ADP) and recombinant activated factor VII on restoring these parameters towards baseline values. PAM reduced maximum platelet aggregation and led to platelet disaggregation. It also decreased peak thrombin, increased lag time, and increased time to peak thrombin. Treatment with recombinant activated factor VII restored all three parameters of thrombin generation towards baseline. ADP decreased lag time and time to peak thrombin, but had no effect on peak thrombin. When recombinant activated factor VII and ADP were combined they had a greater effect on thrombin parameters than either drug alone. PAM also increased thromboelastometric clotting time and clot formation time, but had no effect on maximum clot firmness. Treatment with either recombinant activated factor VII or ADP restored these values towards baseline. Recombinant activated factor VII restores thrombin generation in the presence of PAM. In patients taking prasugrel with life-threatening refractory bleeding it has the potential to be a useful therapeutic approach. Additional clinical studies are needed to validate our findings. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2013-01-01

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

  20. 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

  1. Amphimeric mitochondrial genomes of petite mutants of yeast. III. Generation by linking two secondary-structure-dependent illegitimate recombination events.

    PubMed

    Rayko, E; Goursot, R

    1999-02-01

    The generation of amphimeric mitochondrial petite genomes of yeast can be explained by a process that links together two illegitimate recombination events, each involving a pair of short inverted repeats. Following "diagonal" double-strand breaks and inter-strand ligations at both possible stem-and-loop structures, a subgenomic single-stranded DNA circle can be excised. This circle comprises four building blocks organized in the so-called datA arrangement where d and t correspond, respectively, to the segments looped out by the upstream and the downstream pair of inverted repeats, a to the sequence separating the two loops, and A to the inverted duplication of segment a. Depending on the different possible "diagonal" recombinations at the inverted repeats, any of four isomeric circles can be excised, representing in its double-stranded form the nascent basic unit of an amphimeric mitochondrial petite genome of yeast. These isomeric basic units differ in the relative orientation of their sequences d and t (called D and T, respectively, when inverted), and are designated datA, DatA, daTA, and DaTA. Any one of these may be replicated to form the previously described regularly arrayed multimeric flip-flop genomes. Our new understanding of the amphimeric mitochondrial petite genomes of yeast emphasizes the role that topological features of DNA can play in mitochondrial genome dynamics. It also permits the re-interpretation of various observations reported in the literature. Some of them, including EtBr-mutagenesis in yeast, are discussed.

  2. 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.

  3. Combination of FACS and Homologous Recombination for the Generation of Stable and High-Expression Engineered Cell Lines

    PubMed Central

    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. Development and Characterization of Recombinant Virus Generated from a New World Zika Virus Infectious Clone.

    PubMed

    Weger-Lucarelli, James; Duggal, Nisha K; Bullard-Feibelman, Kristen; Veselinovic, Milena; Romo, Hannah; Nguyen, Chilinh; Rückert, Claudia; Brault, Aaron C; Bowen, Richard A; Stenglein, Mark; Geiss, Brian J; Ebel, Gregory D

    2017-01-01

    Zika virus (ZIKV; family Flaviviridae, genus Flavivirus) is a rapidly expanding global pathogen that has been associated with severe clinical manifestations, including devastating neurological disease in infants. There are currently no molecular clones of a New World ZIKV available that lack significant attenuation, hindering progress toward understanding determinants of transmission and pathogenesis. Here we report the development and characterization of a novel ZIKV reverse genetics system based on a 2015 isolate from Puerto Rico (PRVABC59). We generated a two-plasmid infectious clone system from which infectious virus was rescued that replicates in human and mosquito cells with growth kinetics representative of wild-type ZIKV. Infectious clone-derived virus initiated infection and transmission rates in Aedes aegypti mosquitoes comparable to those of the primary isolate and displayed similar pathogenesis in AG129 mice. This infectious clone system provides a valuable resource to the research community to explore ZIKV molecular biology, vaccine development, antiviral development, diagnostics, vector competence, and disease pathogenesis.

  5. Development and Characterization of Recombinant Virus Generated from a New World Zika Virus Infectious Clone

    PubMed Central

    Weger-Lucarelli, James; Duggal, Nisha K.; Bullard-Feibelman, Kristen; Veselinovic, Milena; Romo, Hannah; Nguyen, Chilinh; Rückert, Claudia; Brault, Aaron C.; Bowen, Richard A.; Stenglein, Mark

    2016-01-01

    ABSTRACT Zika virus (ZIKV; family Flaviviridae, genus Flavivirus) is a rapidly expanding global pathogen that has been associated with severe clinical manifestations, including devastating neurological disease in infants. There are currently no molecular clones of a New World ZIKV available that lack significant attenuation, hindering progress toward understanding determinants of transmission and pathogenesis. Here we report the development and characterization of a novel ZIKV reverse genetics system based on a 2015 isolate from Puerto Rico (PRVABC59). We generated a two-plasmid infectious clone system from which infectious virus was rescued that replicates in human and mosquito cells with growth kinetics representative of wild-type ZIKV. Infectious clone-derived virus initiated infection and transmission rates in Aedes aegypti mosquitoes comparable to those of the primary isolate and displayed similar pathogenesis in AG129 mice. This infectious clone system provides a valuable resource to the research community to explore ZIKV molecular biology, vaccine development, antiviral development, diagnostics, vector competence, and disease pathogenesis. IMPORTANCE ZIKV is a rapidly spreading mosquito-borne pathogen that has been linked to Guillain-Barré syndrome in adults and congenital microcephaly in developing fetuses and infants. ZIKV can also be sexually transmitted. The viral molecular determinants of any of these phenotypes are not well understood. There is no reverse genetics system available for the current epidemic virus that will allow researchers to study ZIKV immunity, develop novel vaccines, or develop antiviral drugs. Here we provide a novel infectious clone system generated from a recent ZIKV isolated from a patient infected in Puerto Rico. This infectious clone produces virus with in vitro and in vivo characteristics similar to those of the primary isolate, providing a critical tool to study ZIKV infection and disease. PMID:27795432

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

    PubMed

    Bayer, Sieglinde; Wirth, Matthias

    2017-01-01

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

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Erdmann, Michael; Horsfield, Brian

    2006-08-01

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

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

    PubMed Central

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

    2014-01-01

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

  10. Generation of a Uracil Auxotroph Strain of the Probiotic Yeast Saccharomyces boulardii as a Host for the Recombinant Protein Production

    PubMed Central

    Hamedi, Hassan; Misaghi, Ali; Modarressi, Mohammad Hossein; Salehi, Taghi Zahraei; Khorasanizadeh, Dorsa; Khalaj, Vahid

    2013-01-01

    Background Saccharomyces boulardii (S. boulardii) is the best known probiotic yeast. The genetic engineering of this probiotic strain requires the availability of appropriate mutants to accept various gene constructs carrying different selection markers. As the auxotrophy selection markers are under focus, we have generated a ura3 auxotroph mutant of S. boulardii for use in further genetic manipulations. Methods Classical UV mutagenesis was used for the generation of auxotroph mutants. The mutants were selected in the presence of 5-FOA (5-Fluoroorotic acid), uracil and uridine. Uracil auxotrophy phenotype was confirmed by the ability of mutants to grow in the presence of uracil and the lack of growth in the absence of this compound. To test whether the uracil auxotrophy phenotype is due to the inactivation of URA3, the mutants were transformed with a plasmid carrying the gene. An in vitro assay was used for the analysis of acid and bile resistance capacity of these mutants. Results Three mutants were found to be ura3 auxotroph as they were able to grow only in the presence of uracil. When the URA3 gene was added, these mutants were able to grow normally in the absence of uracil. Further in vitro analysis showed that the acid and bile resistance capacity of one of these mutants is intact and similar to the wild type. Conclusion A uracil auxotroph mutant of the probiotic yeast, S. boulardii, was generated and characterized. This auxotroph strain may have potential applications in the production and delivery of the recombinant pharmacuetics into the intestinal lumen. PMID:23626874

  11. Homologous recombination rescues ssDNA gaps generated by nucleotide excision repair and reduced translesion DNA synthesis in yeast G2 cells

    PubMed Central

    Ma, Wenjian; Westmoreland, James W.; Resnick, Michael A.

    2013-01-01

    Repair of DNA bulky lesions often involves multiple repair pathways such as nucleotide-excision repair, translesion DNA synthesis (TLS), and homologous recombination (HR). Although there is considerable information about individual pathways, little is known about the complex interactions or extent to which damage in single strands, such as the damage generated by UV, can result in double-strand breaks (DSBs) and/or generate HR. We investigated the consequences of UV-induced lesions in nonreplicating G2 cells of budding yeast. In contrast to WT cells, there was a dramatic increase in ssDNA gaps for cells deficient in the TLS polymerases η (Rad30) and ζ (Rev3). Surprisingly, repair in TLS-deficient G2 cells required HR repair genes RAD51 and RAD52, directly revealing a redundancy of TLS and HR functions in repair of ssDNAs. Using a physical assay that detects recombination between circular sister chromatids within a few hours after UV, we show an approximate three-fold increase in recombinants in the TLS mutants over that in WT cells. The recombination, which required RAD51 and RAD52, does not appear to be caused by DSBs, because a dose of ionizing radiation producing 20 times more DSBs was much less efficient than UV in producing recombinants. Thus, in addition to revealing TLS and HR functional redundancy, we establish that UV-induced recombination in TLS mutants is not attributable to DSBs. These findings suggest that ssDNA that might originate during the repair of closely opposed lesions or of ssDNA-containing lesions or from uncoupled replication may drive recombination directly in various species, including humans. PMID:23858457

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

    PubMed

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

    2014-06-01

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

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

    PubMed Central

    Domingue, Scott R.; Bartels, Randy A.

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Hyeon-Deuk, Kim; Prezhdo, Oleg V.

    2012-09-01

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

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

    PubMed

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

    2004-11-01

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

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

    PubMed

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

    2014-09-01

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

  17. 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.

  18. 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.

  19. The impact of three dimensional MHD instabilities on the generation of warm dense matter using a MA-class linear transformer driver

    NASA Astrophysics Data System (ADS)

    Gourdain, P.-A.; Seyler, C. E.

    2017-09-01

    Warm dense matter is difficult to generate since it corresponds to a state of matter which pressure is order of magnitude larger than can be handled by natural materials. A diamond anvil can be used to pressurize matter up to one Gbar, this matter is at high density but at room temperature. High power lasers and heavy ion beams can generate warm dense matter on time scales where measuring quasi-static transport coefficients such as viscosity or heat conduction proves difficult since both experimental techniques relies on inertial confinement. We present here a third method to generate warm dense matter. It uses a pulsed-power driver which current rise time is substantially shortened by using a plasma opening switch, limiting the development of electrothermal instabilities. The switch relies on the implosion of a gas puff Z-pinch which carries most of the discharge current until the pinch reaches the sample. After that, the sample is compressed until it reaches the warm dense matter regime. Three-dimensional magnetohydrodynamics computations show that if the density of the gas is low enough no detectable instabilities (e.g. kinks and sausages modes) impede the remainder of the implosion.

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

    PubMed

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

    2014-04-09

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

  1. On the Field Dependence of Free Charge Carrier Generation and Recombination in Blends of PCPDTBT/PC70BM: Influence of Solvent Additives.

    PubMed

    Albrecht, Steve; Schindler, Wolfram; Kurpiers, Jona; Kniepert, Juliane; Blakesley, James C; Dumsch, Ines; Allard, Sybille; Fostiropoulos, Konstantinos; Scherf, Ullrich; Neher, Dieter

    2012-03-01

    We have applied time-delayed collection field (TDCF) and charge extraction by linearly increasing voltage (CELIV) to investigate the photogeneration, transport, and recombination of charge carriers in blends composed of PCPDTBT/PC70BM processed with and without the solvent additive diiodooctane. The results suggest that the solvent additive has severe impacts on the elementary processes involved in the photon to collected electron conversion in these blends. First, a pronounced field dependence of the free carrier generation is found for both blends, where the field dependence is stronger without the additive. Second, the fate of charge carriers in both blends can be described with a rather high bimolecular recombination coefficients, which increase with decreasing internal field. Third, the mobility is three to four times higher with the additive. Both blends show a negative field dependence of mobility, which we suggest to cause bias-dependent recombination coefficients.

  2. 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.

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

    PubMed

    Wallace, David B; Viljoen, Gerrit J

    2005-04-27

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

  4. NGC 7385 - Generation of an H II region by thermal instability associated with the creation of a radio source

    NASA Astrophysics Data System (ADS)

    Hardee, P. E.; Eilek, J. A.; Owen, F. N.

    1980-12-01

    We have mapped the radio source NGC 7385 with the VLA at high resolution. The radio map suggests ejection of material from the galactic nucleus in directions parallel and antiparallel to the motion of the galaxy through the intergalactic medium. An optical knot detected by Simkin and Ekers is associated with the leading radio component. Our observations place the optical knot which is probably an H II region toward one edge of the radio lobe. The existence of an H II region in an elliptical galaxy and the position of the H II region in respect to the radio source suggest that more than coincidence is involved. We show that, for this particular galaxy, it is quite possible that an H II region may be produced in the interstellar medium (ISM) by interaction between the ISM and a jet ejected from the galactic nucleus, and thermal instabilities in the ISM. We also investigate the conditions for production of H II regions by thermal instability from a jet containing mixed relativistic and thermal material. Such processes may be important in other radio galaxies.

  5. Recombinative plasma in electron runaway discharge

    SciTech Connect

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

    2005-07-15

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

  6. 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.

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

    PubMed

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

    2015-05-01

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

  8. Effects of recombinant human prothrombin on thrombin generation in plasma from patients with hemophilia A and B.

    PubMed

    Hansson, K M; Gustafsson, D; Skärby, T; Frison, L; Berntorp, E

    2015-07-01

    The present study was carried out to investigate the impact of FII levels, and their increase, on the hemostatic potential in plasma from hemophilia A and B patients with and without inhibitors. Recombinant human factor (F) II (rhFII) was added ex vivo to plasma from 68 patients with hemophilia A and B, with or without inhibitors. The hemostatic potential as measured by thrombin generation (calibrated automated thrombogram [CAT]) was focused on the endogenous thrombin potential (ETP) as it has been shown to correlate with the clinical phenotype of bleeding in hemophilia patients and has also been used to guide bypassing therapy in hemophilia patients with inhibitors before elective surgery. The factor eight inhibitor bypassing agent (FEIBA(®) ) was used as a reference to the clinical situation. The study shows that rhFII concentration-dependently increased ETP by a similar magnitude in hemophilia A and B, both with and without inhibitors. Compared with FEIBA, rhFII showed a shallower concentration-response curve. In both types of hemophilia 100 mg L(-1) of rhFII roughly doubled the ETP. A corresponding response was obtained by 0.5 U mL(-1) of FEIBA. These data support the theory that FII is one of the major components responsible for the efficacy of FEIBA. The data also indicate that rhFII may be useful, alone or in combination with other coagulation factors, in some of the conditions for which FEIBA is used today, although more data are needed to substantiate this. © 2015 International Society on Thrombosis and Haemostasis.

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Sayag, Roiy; Tziperman, Eli

    2008-05-01

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay

    PubMed Central

    Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J.

    2011-01-01

    In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT. PMID:21629677

  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. [Intervertebral instability].

    PubMed

    Colaiacomo, M C; Tortora, A; Di Biasi, C; Polettini, E; Casciani, E; Gualdi, G F

    2009-01-01

    The clinic diagnosis of degenerative lumbar intervertebral instability is a controversial topic and have not yet been clarified clinical criteria for to define this condition with accuracy. Although the lumbar pain is the most common symptom in patients who have lumbar intervertebral instability its clinical presentation is not specific; moreover in patients with lumbar pain there are no agreed signs and symptoms that can be truly attributable to instability. Despite better imaging techniques of testing spinal instability there is not a clear relations between radiologic signs of instability and clinical symptoms. It is, however, still far from unanimous definition of degenerative lumbar intervertebral instability accepted from all specialists involved in diagnosis and treatment of this condition; however, seem there is most agree about suspected vertebral instability. Nevertheless this unresolved topic, it is possible to state that imaging play an increasing role in diagnosis and management of patients with suspected instability. The aim of this study is to investigate the different imaging modalities most indicated in diagnosis if vertebral instability and whether degenerative change can be associated with lower back pain.

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

    PubMed

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

    2016-04-05

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

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

    PubMed

    Parashar, Deepak; Satyanarayana, T

    2016-11-01

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

  2. 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

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

    PubMed Central

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

    1996-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

  6. 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

  7. 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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    PubMed

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

    2012-11-01

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

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

    SciTech Connect

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

    1996-08-09

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

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

    PubMed

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

    2015-06-01

    Pectate lyase (EC 4.2.2.2) gene from Bacillus subtilis RCK was cloned and expressed in Escherichia coli to maximize its production. In addition to soluble fraction, bioactive pectate lyase was also obtained from inclusion body aggregates by urea solubilization and refolding under in vitro conditions. Enzyme with specific activity ∼3194IU/mg and ∼1493IU/mg were obtained from soluble and inclusion bodies (IBs) fraction with recovery of 56% and 74% in terms of activity, respectively. The recombinant enzyme was moderately thermostable (t1/2 60min at 50°C) and optimally active in wider alkaline pH range (7.0-10.5). Interaction of protein with its cofactor CaCl2 was found to stimulate the change in tertiary structure as revealed by near UV CD spectra. Intrinsic tryptophan fluorescence spectra indicated that tryptophan is involved in substrate binding and there might be independent binding of Ca(2+) and polygalacturonic acid to the active site. The recombinant enzyme was found to be capable of degrading pectin and polygalacturonic acid. The work reports novel conditions for refolding to obtain active recombinant pectate lyase from inclusion bodies and elucidates the effect of ligand and substrate binding on protein conformation by circular dichroism (CD) and fluorescence spectrofluorometry. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Observation of self-similarity in the magnetic fields generated by the ablative nonlinear Rayleigh-Taylor instability.

    PubMed

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

    2013-05-03

    Magnetic fields generated by the nonlinear Rayleigh-Taylor growth of laser-seeded three-dimensional broadband perturbations were measured in laser-accelerated planar targets using ultrafast proton radiography. The experimental data show self-similar behavior in the growing cellular magnetic field structures. These observations are consistent with a bubble competition and merger model that predicts the time evolution of the number and size of the bubbles, linking the cellular magnetic field structures with the Rayleigh-Taylor bubble and spike growth.

  14. Generating novel recombinant prokaryotic lectins with altered carbohydrate binding properties through mutagenesis of the PA-IL protein from Pseudomonas aeruginosa.

    PubMed

    Keogh, Damien; Thompson, Roisin; Larragy, Ruth; McMahon, Kenneth; O'Connell, Michael; O'Connor, Brendan; Clarke, Paul

    2014-06-01

    Prokaryotic lectins offer significant advantages over eukaryotic lectins for the development of enhanced glycoselective tools. Amenability to recombinant expression in Escherichia coli simplifies their production and presents opportunities for further genetic manipulation to create novel recombinant prokaryotic lectins (RPLs) with altered or enhanced carbohydrate binding properties. This study explored the potential of the α-galactophilic PA-IL lectin from Pseudomonas aeruginosa for use as a scaffold structure for the generation of novel RPLs. Specific amino acid residues in the carbohydrate binding site of a recombinant PA-IL protein were randomly substituted by site-directed mutagenesis. The resulting expression clones were then functionally screened to identify clones expressing rPA-IL proteins with altered carbohydrate binding properties. This study generated RPLs exhibiting diverse carbohydrate binding activities including specificity and high affinity for β-linked galactose and N-acetyl-lactosamine (LacNAc) displayed by N-linked glycans on glycoprotein targets. Key amino acid substitutions were identified and linked with specific carbohydrate binding activities. Ultimately, the utility of these novel RPLs for glycoprotein analysis and for selective fractionation and isolation of glycoproteins and their glycoforms was demonstrated. The carbohydrate binding properties of the PA-IL protein can be significantly altered using site-directed mutagenesis strategies to generate novel RPLs with diverse carbohydrate binding properties. The novel RPLs reported would find a broad range of applications in glycobiology, diagnostics and in the analysis of biotherapeutics. The ability to readily produce these RPLs in gram quantities could enable them to find larger scale applications for glycoprotein or biotherapeutic purification. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2014-01-01

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

  16. An anti-amoebic vaccine: generation of the recombinant antigen LC3 from Entamoeba histolytica linked to mutated exotoxin A (PEΔIII) via the Pichia pastoris system.

    PubMed

    Martínez-Hernández, Sandra Luz; Cervantes-García, Daniel; Muñoz-Ortega, Martín; Aldaba-Muruato, Liseth R; Loera-Muro, Victor M; Ascacio-Martínez, Jorge A; de Jesús Loera-Arias, María; de Oca-Luna, Roberto Montes; Ventura-Juárez, Javier

    2017-08-01

    To generate an immunogenic chimeric protein containing the Entamoeba histolytica LC3 fragment fused to the retrograde delivery domains of exotoxin A of Pseudomonas aeruginosa and KDEL3 for use as an effective vaccine. A codon-optimized synthetic gene encoding the PEΔIII-LC3-KDEL3 fusion construct was designed for expression in Pichia pastoris. This transgene was subcloned into the plasmid pPIC9 for methanol-inducible expression. After transformation and selection of positive-transformed clones by PCR, the expression of the recombinant protein PEΔIII-LC3-KDEL3 was elicited. SDS-PAGE, protein glycosylation staining and western blot assays demonstrated a 67 kDa protein in the medium culture supernatant. The recombinant protein was detected with a polyclonal anti-6X His tag antibody and a polyclonal E. histolytica-specific antibody. A specific antibody response was induced in hamsters after immunization with this protein. We report for the first time the design and expression of the recombinant E. histolytica LC3 protein fused to PEΔIII and KDEL3, with potential application as an immunogen.

  17. Generation of a recombinant viral hemorrhagic septicemia virus (VHSV) expressing olive flounder (Paralichthys olivaceus) interferon-γ and its effects on type I interferon response and virulence.

    PubMed

    Kwak, Jun Soung; Kim, Min Sun; Kim, Ki Hong

    2017-09-01

    Rhabdoviruses including viral hemorrhagic septicemia virus (VHSV) are highly susceptible to type I interferon (IFN) responses, and IFN-γ that is belonging to the type II IFN has been known to enhance type I IFN responses in mammals. In this study, we generated a recombinant VHSV that can express olive flounder IFN-γ (rVHSV-A-IFNγ) using reverse genetics technology, and analyzed the effect of rVHSV-A-IFNγ infection on type I IFN response in Epithelioma papulosum cyprini (EPC) cells. Furthermore, the virulence of rVHSV-A-IFNγ was evaluated by infection to olive flounder (Paralichthys olivaceus). Using a recombinant VHSV full genome vector in which the olive flounder IFN-γ ORF was inserted between N and P genes, rVHSV-A-IFNγ was successfully rescued, and the recombinant virus was grown well in EPC cells. On the other hand, the growth of rVHSV-A-IFNγ rescued from EPC cells was severely retarded when infected into hirame natural embryo (HINAE) cells that were originated from olive flounder. These results indicate that the EPC cell's IFN-γ receptor could not bind to olive flounder IFN-γ, but the species-specific binding of IFN-γ in HINAE cells induced antiviral responses. The expression of Mx1 gene in EPC cells infected with rVHSV-A-IFNγ was not greatly different from cells infected with rVHSV-Arfp (a recombinant VHSV harboring red fluorescent protein gene between N and P genes of the genome), however, in HINAE cells, rVHSV-A-IFNγ infection induced distinctively higher Mx1 gene expression compared to other recombinant viruses. These results suggest that olive flounder IFN-γ produced from rVHSV-A-IFNγ effectively enhanced type I IFN response in HINAE cells. In the present study, the lowest mortality of olive flounder fingerlings was recorded in the group of fish challenged with rVHSV-A-IFNγ, suggesting that the recombinant VHSV was attenuated by production of IFN-γ by itself. However, although rVHSV-A-IFNγ induced significantly lower mortality, the

  18. Study of cavitating inducer instabilities

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  19. Instabilities in mimetic matter perturbations

    NASA Astrophysics Data System (ADS)

    Firouzjahi, Hassan; Gorji, Mohammad Ali; Mansoori, Seyed Ali Hosseini

    2017-07-01

    We study cosmological perturbations in mimetic matter scenario with a general higher derivative function. We calculate the quadratic action and show that both the kinetic term and the gradient term have the wrong sings. We perform the analysis in both comoving and Newtonian gauges and confirm that the Hamiltonians and the associated instabilities are consistent with each other in both gauges. The existence of instabilities is independent of the specific form of higher derivative function which generates gradients for mimetic field perturbations. It is verified that the ghost instability in mimetic perturbations is not associated with the higher derivative instabilities such as the Ostrogradsky ghost.

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

    PubMed Central

    2012-01-01

    Background Many viruses have evolved multiple strategies to prevent super infection of host cells by more than one virion. This phenomenon, known as super infection exclusion, may play an important role on virus evolution because it can affect the frequency of reassortment and/or recombination. Newcastle disease virus (NDV), a negative sense single-stranded RNA virus, is characterized by its continuous evolutionary dynamics and by a low frequency of recombination events. However, the mechanisms that contribute to the low recombination rates on NDV are still not completely understood. Methods In this study we assessed the ability of two NDV strains (LaSota and B1) to super infect host cells in vitro. We generated a recombinant NDV strain LaSota expressing the red fluorescent protein (RFP) and used it in co-infection assays with a related NDV strain B1 expressing the green fluorescent protein (GFP). DF-1 cells were inoculated with both viruses at the same time or at different intervals between primary infection and super infection. Results When both viruses were inoculated at the same time point, a 27% co-infection rate was observed, whereas when they were inoculated at different time points the super infection rates decreased to levels as low as 1.4%. Conclusions These results indicate that although different NDV strains can co-infect host cells in vitro, the super infection rates are low, specially as the time between the primary infection and super infection increases. These results confirm the occurrence of super infection exclusion between different strains of NDV. PMID:23034005

  1. Instabilities and generation of a quasistationary magnetic field by the interaction of relativistically intense electromagnetic wave with a plasma

    SciTech Connect

    Gillani, S. S. A.; Shah, H. A.; Tsintsadze, N. L.; Razzaq, M.

    2010-08-15

    It is shown that the interaction of the superstrong laser radiation with an isotropic plasma leads to the generation of low frequency electromagnetic (EM) waves and in particular a quasistationary magnetic field. When the relativistic circularly polarized transverse EM wave propagates along z-axis, it creates a ponderomotive force, which affects the motion of particles along the direction of its propagation. On the other hand, motion of the particles across the direction of propagation is defined by the ponderomotive potential. The dispersion relation for the transverse EM wave using a special distribution function, which has an anisotropic form, is derived. The dispersion relation is subsequently investigated for a number of special cases. In general, it is shown that the growth rate of the EM wave strongly depends upon its intensity.

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

    PubMed Central

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

    2011-01-01

    Vaccine production and initiation of mass vaccination is a key factor in rapid response to new influenza pandemic. During the 2009–2010 H1N1 pandemic, several bottlenecks were identified, including the delayed availability of vaccine potency reagents. Currently, antisera for the single-radial immunodiffusion (SRID) potency assay are generated in sheep immunized repeatedly with HA released and purified after bromelain-treatment of influenza virus grown in eggs. This approach was a major bottleneck for pandemic H1N1 (H1N1pdm09) potency reagent development in 2009. Alternative approaches are needed to make HA immunogens for generation of SRID reagents in the shortest possible time. In this study, we found that properly folded recombinant HA1 globular domain (rHA1) from several type A viruses including H1N1pdm09 and two H5N1 viruses could be produced efficiently by using a bacterial expression system and subsequent purification. The rHA1 proteins were shown to form functional oligomers of trimers, similar to virus derived HA, and elicited high titer of neutralizing antibodies in rabbits and sheep. Importantly, the immune sera formed precipitation rings with reference antigens in the SRID assay in a dose-dependent manner. The HA contents in multiple H1N1 vaccine products from different manufacturers (and in several lots) as determined with the rHA1-generated sheep sera were similar to the values obtained with a traditionally generated sheep serum from NIBSC. We conclude that bacterially-expressed recombinant HA1 proteins can be produced rapidly and used to generate SRID potency reagents shortly after new influenza strains with pandemic potential are identified. PMID:21704111

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    SciTech Connect

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

    2015-10-15

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

  5. A Nonlinear System Model of Wall Turbulence Generation Under Active Suppression and Enhancement of Streak Transient Growth Instability

    NASA Astrophysics Data System (ADS)

    Midya, Samaresh; Duong, Alan; Thomas, Flint; Corke, Thomas

    2016-11-01

    Schoppa and Hussain (1998, 2002) demonstrated streak transient growth (STG) as the dominant streamwise coherent structure generation mechanism required for wall turbulence production. A novel, flush surface-mounted pulsed-DC plasma actuator was recently developed at the University of Notre Dame to actively intervene in STG. In recent high Reynolds number, zero pressure gradient turbulent boundary layer experiments, drag reduction of up to 68% was achieved. This is due to a plasma-induced near-wall, spanwise mean flow sufficient in magnitude to prevent the lift-up of low-speed streaks. This limits their flanking wall-normal component vorticity-a critical parameter in STG. Experiments also show that sufficiently large plasma-induced spanwise flow can exacerbate STG and increase drag by 80%. The ability to significantly increase or decrease drag by near-wall actuation provides an unprecedented new tool for clarifying the open questions regarding the interaction between near-wall coherent structures and those in the logarithmic region. In the reported experiments this interaction is experimentally characterized by a second-order Volterra nonlinear system model under both active suppression and enhancement of STG. Supported by NASA Langley under NNX16CL27C.

  6. Dislocation motion and instability

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  7. 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.

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

    PubMed

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

    2016-09-07

    Human papillomavirus (HPV) infection is the most common sexually transmitted disease worldwide. HPVs are oncogenic small double-stranded DNA viruses that are the primary causal agent of cervical cancer and other types of cancers, including in the anus, oropharynx, vagina, vulva, and penis. Prophylactic vaccination against HPV is an attractive strategy for preventing cervical cancer and some other types of cancers. However, there are few safe and effective vaccines against HPV infections. Current first-generation commercial HPV vaccines are expensive to produce and deliver. The goal of this study was to develop an alternate potent HPV recombinant L1-based vaccines by producing HPV virus-like particles into a vaccine that is currently used worldwide. Live attenuated measles virus (MV) vaccines have a well-established safety and efficacy record, and recombinant MV (rMV) produced by reverse genetics may be useful for generating candidate HPV vaccines to meet the needs of the developing world. We studied in non-human primate rMV-vectored HPV vaccine in parallel with a classical alum adjuvant recombinant HPV16L1 and 18L1 protein vaccine produced in Pichia pastoris. A combined prime-boost approach using both vaccines was evaluated, as well as immune interference due to pre-existing immunity against the MV. The humoral immune response induced by the MV, Pichia-expressed vaccine, and their combination as priming and boosting approaches was found to elicit HPV16L1 and 18L1 specific total IgG and neutralizing antibody titres. Pre-existing antibodies against measles did not prevent the immune response against HPV16L1 and 18L1. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2009-06-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

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

    2015-01-01

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

  12. 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

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

    PubMed

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

    2015-11-26

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

  14. 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.

  15. RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator.

    PubMed

    Wardell, Kayleigh; Haldenby, Sam; Jones, Nathan; Liddell, Susan; Ngo, Greg H P; Allers, Thorsten

    2017-07-01

    Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination - it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination mediator, which it does by inducing a conformational change in RadA and thereby promoting its polymerisation on DNA. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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

    PubMed

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

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  18. Gene Therapy of mdx Mice With Large Truncated Dystrophins Generated by Recombination Using rAAV6

    PubMed Central

    Odom, Guy L; Gregorevic, Paul; Allen, James M; Chamberlain, Jeffrey S

    2011-01-01

    Recombinant adeno-associated viral (rAAV) vector-mediated gene transfer represents a promising approach for many diseases. However, the applicability of rAAV vectors has long been hindered by the small (~4.8 kb) DNA packaging capacity. This limitation can hamper the packaging and delivery of critical regulatory elements and/or larger coding sequences, such as the ~14-kb dystrophin complementary DNA (cDNA) that is of interest for gene therapy of Duchenne muscular dystrophy (DMD). Here, we have demonstrated reconstitution of an expression cassette (7.3 kb) encoding a highly functional “minidystrophin” protein (ΔH2–R19, 222 kd) in vivo following intravascular co-delivery of two independent rAAV6 vectors sharing a central homologous recombinogenic region of 372 nucleotides. Similar to previously reported trans-splicing approaches, one rAAV vector provides the promoter with the ~1/2 initial portion of minidystrophin, while the second vector provides the remaining minidystrophin cDNA followed by the polyadenylation signal. Significantly, administering a modest dose [2 × 1012 vector genomes (vg)] of the two minidystrophin-encoding rAAV vectors to dystrophic mice elicited an improvement of physiological performance indicative of prevention or amelioration of the disease state. These studies provide evidence that functional dystrophin transgenes larger than that typically carried by a single rAAV genome can be reconstituted in vivo by homologous recombination (HR) following intravascular co-delivery with rAAV6. PMID:20859263

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

    PubMed Central

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

    2015-01-01

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

  20. Current-driven plasma instabilities in superconductors

    SciTech Connect

    Kempa, K.; Cen, J.; Bakshi, P.

    1989-02-01

    We examine here the possibility of current-driven plasma instabilities in superconductors in two temperature regimes. At low temperatures (Tapprox. =0) an instability can be generated in a layered system. Near the critical temperature (Tapprox. =T/sub c/) an instability can occur in a single superconductor for sufficiently large drifts which might be achievable in the new high-T/sub c/ materials. These instabilities offer possibilities for new radiation-source device applications.

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

    PubMed

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

    2011-12-29

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

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

    PubMed

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

    2015-03-01

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

  3. Generation of a baculovirus recombinant prostate-specific membrane antigen and its use in the development of a novel protein biochip quantitative immunoassay.

    PubMed

    Xiao, Z; Jiang, X; Beckett, M L; Wright, G L

    2000-06-01

    Prostate-specific membrane antigen (PSMA) is a 100-kDa transmembrane glycoprotein identified by the monoclonal antibody 7E11-C5.3 from the human prostate tumor cell line LNCaP. Because of its significant upregulation in androgen refractory and metastatic prostate cancers, PSMA may be a useful prognostic biomarker and a target for developing novel therapeutic strategies. However, the lack of abundant pure PSMA protein and the low efficacy in immunoaffinity isolation from LNCaP cells have hampered the development of clinical assays. In order to obtain a renewable and reliable source of pure antigen, we used the baculovirus/insect cell system to express and purify a recombinant PSMA. A recombinant baculovirus containing a 6x histidine-tagged PSMA gene was generated, from which rPSMA was expressed and purified using cobalt-chelating affinity chromatography. The purity and correct molecular size of rPSMA were demonstrated by gel electrophoresis and mass spectrometry. Glycosidase digestions showed that the oligosaccharides on rPSMA are primarily N-linked high-mannose type. Although the glycosylation is different from the native PSMA, it did not affect the immunoreactivity of rPSMA to antibodies specific for either the intra- or the extracellular domains of PSMA. Finally, the purified rPSMA was successfully used to develop a quantitative PSMA immunoassay using the novel ProteinChip surface-enhanced laser desorption/ionization mass spectrometry technology. Copyright 2000 Academic Press.

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

    PubMed

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

    2015-05-04

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

  5. Norovirus recombination.

    PubMed

    Bull, Rowena A; Tanaka, Mark M; White, Peter A

    2007-12-01

    RNA recombination is a significant driving force in viral evolution. Increased awareness of recombination within the genus Norovirus of the family Calicivirus has led to a rise in the identification of norovirus (NoV) recombinants and they are now reported at high frequency. Currently, there is no classification system for recombinant NoVs and a widely accepted recombinant genotyping system is still needed. Consequently, there is duplication in reporting of novel recombinants. This has led to difficulties in defining the number and types of recombinants in circulation. In this study, 120 NoV nucleotide sequences were compiled from the current GenBank database and published literature. NoV recombinants and their recombination breakpoints were identified using three methods: phylogenetic analysis, SimPlot analysis and the maximum chi2 method. A total of 20 NoV recombinant types were identified in circulation worldwide. The recombination point is the ORF1/2 overlap in all isolates except one, which demonstrated a double recombination event within the polymerase region.

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

    PubMed

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

    2012-05-01

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

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

    PubMed

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

    2016-01-01

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

  8. Hybrid rocket instability

    NASA Technical Reports Server (NTRS)

    Greiner, B.; Frederick, R. A., Jr.

    1993-01-01

    The paper provides a brief review of theoretical and experimental studies concerned with hybrid rocket instability. The instabilities discussed include atomization and mixing instabilities, chuffing instabilities, pressure coupled combustion instabilities, and vortex shedding. It is emphasized that the future use of hybrid motor systems as viable design alternatives will depend on a better understanding of hybrid instability.

  9. Characterization of self-assembled virus-like particles of ferret hepatitis E virus generated by recombinant baculoviruses.

    PubMed

    Yang, Tingting; Kataoka, Michiyo; Ami, Yasushi; Suzaki, Yuriko; Kishida, Noriko; Shirakura, Masayuki; Imai, Masaki; Asanuma, Hideki; Takeda, Naokazu; Wakita, Takaji; Li, Tian-Cheng

    2013-12-01

    Ferret hepatitis E virus (HEV), a novel hepatitis E-like virus, has been identified in ferrets in The Netherlands. Due to the lack of a cell-culture system for ferret HEV, the antigenicity, pathogenicity and epidemiology of this virus have remained unclear. In the present study, we used a recombinant baculovirus expression system to express the 112-N-terminus and 47-C-terminus-amino-acid-truncated ferret HEV ORF2 protein in insect Tn5 cells, and found that a large amount of a 53 kDa protein (F-p53) was expressed and efficiently released into the supernatant. Electron microscopic analysis revealed that F-p53 was self-assembled into virus-like particles (ferret HEV-LPs). These ferret HEV-LPs were estimated to be 24 nm in diameter, which is similar to the size of G1, G3, G4 and rat HEV-LPs derived from both the N-terminus- and C-terminus-truncated constructs. Antigenic analysis demonstrated that ferret HEV-LPs were cross-reactive with G1, G3, G4 and rat HEVs, and rat HEV and ferret HEV showed a stronger cross-reactivity to each other than either did to human HEV genotypes. However, the antibody against ferret HEV-LPs does not neutralize G3 HEV, suggesting that the serotypes of these two HEVs are different. An ELISA for detection of anti-ferret HEV IgG and IgM antibodies was established using ferret HEV-LPs as antigen, and this assay system will be useful for monitoring ferret HEV infection in ferrets as well as other animals. In addition, analysis of ferret HEV RNA detected in ferret sera collected from a breeding colony in the USA revealed the genetic diversity of ferret HEV.

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

    PubMed Central

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

    1997-01-01

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

  11. A method for the generation of ectromelia virus (ECTV) recombinants: in vivo analysis of ECTV vCD30 deletion mutants.

    PubMed

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

    2009-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  13. Efficient generation of targeted and controlled mutational events in porcine cells using nuclease-directed homologous recombination.

    PubMed

    Butler, James R; Santos, Rafael M N; Martens, Gregory R; Ladowski, Joseph M; Wang, Zheng-Yu; Li, Ping; Tector, Matthew; Tector, A Joseph

    2017-05-15

    Nuclease-based genome editing has rapidly sped the creation of new models of human disease. These techniques also hold great promise for the future of clinical xenotransplantation and cell-based therapies for cancer or immunodeficient pathology. However, to fully realize the potential of nuclease editing tools, the efficiency and precision of their application must be optimized. The object of this study was to use nonintegrating selection and nuclease-directed homologous recombination to efficiently control the genetic modification of the porcine genome. Clustered randomly integrating spaced palindromic repeats and associated Cas9 protein (CRISPR/Cas9)-directed mutagenesis with a single-guide RNA target was designed to target the alpha-1,3-galactosyltransferase locus (GGTA1) of the porcine genome. A vector expressing a single-guide RNA, Cas9 protein, and green fluorescent protein was used to increase plasmid-delivered mutational efficiency when coupled with fluorescence sorting. Single and double-strand DNA oligonucleotides with a restriction site replacing the start codon were created with variable homology lengths surrounding the mutational event site. Finally, a transgene construct was flanked with 50 base pairs of homology directed immediately 5' to a nuclease cut site. These products were introduced to cells with a constant concentration of CRISPR/cas9 vector. Phenotype-specific mutational efficiency was measured by flow cytometer. Controlled homologous insertion was measured by Sanger sequence, restriction enzyme digest and flow cytometry. Expression of a fluorescence protein on the Cas9 vector functioned as a nonintegrating selection marker. Selection by this marker increased phenotype-silencing mutation rates from 3.5% to 82% (P = 0.0002). Insertion or deletion mutation increased from 11% to 96% (P = 0.0007). Co-transfection with homologous DNA oligonucleotides increased the aggregate phenotype-silencing mutation rates up to 22% and increased biallelic

  14. Analysis of the src gene of sarcoma viruses generated by recombination between transformation-defective mutants and quail cellular sequences.

    PubMed Central

    Wang, L H; Moscovici, C; Karess, R E; Hanafusa, H

    1979-01-01

    the resulting recombinant viruses genetic information for cell transformation. Images PMID:228078

  15. Hydrodynamic Instability of Ionization Fronts in HII Regions

    SciTech Connect

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

    2003-08-21

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

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

    PubMed

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

    2013-02-01

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

  17. Magnetohydrodynamic instability

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  18. Gravitational Instabilities in Circumstellar Disks

    NASA Astrophysics Data System (ADS)

    Kratter, Kaitlin; Lodato, Giuseppe

    2016-09-01

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

  19. Experimental characterization of next-generation expanded-bed adsorbents for capture of a recombinant protein expressed in high-cell-density yeast fermentation.

    PubMed

    Kelly, William; Garcia, Phillip; McDermott, Stefanie; Mullen, Peter; Kamguia, Guy; Jones, Gerard; Ubiera, Antonio; Göklen, Kent

    2013-01-01

    Expanded-bed adsorption (EBA) can be particularly useful in protein recovery from high-cell-density fermentation broth where conventional methods for harvest and clarification, such as continuous centrifugation and depth filtration, demand long processing times and are associated with high costs. In this work, the use of next-generation high-particle-density EBA adsorbents, including two mixed-mode resins, for the direct capture of a recombinant protein expressed in yeast at high cell densities is evaluated. Using classical experimental approaches and under different conditions (pH, salt, etc.), Langmuir isotherm parameters for these resins are obtained along with pore diffusivity values. Additional batch adsorption studies with Fastline® MabDirect, the resin that demonstrated the highest static binding capacity for the recombinant protein of interest under the conditions evaluated in this study, indicate competitive binding of nontarget proteins and approximately a 30% reduction in equilibrium binding capacity to 50 mg/mL settled bed in the presence of a 5%-10% cell concentration. Packed-bed (PB) dynamic binding capacities for the MabDirect resin (25-40 mg/mL PB) were significantly higher than for the Fastline® HSA resin and for the MabDirect MM resin in expanded-bed mode (5-10 mg/mL settled bed). Bed expansion behavior for the mMabDirect MM resin along with process yield and eluate purity are identified as a function of linear velocity and cell density, demonstrating process feasibility for pilot scale use. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

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

    PubMed

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

    2013-02-01

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

  1. Evaluation of Protective Potential of Yersinia pestis Outer Membrane Protein Antigens as Possible Candidates for a New-Generation Recombinant Plague Vaccine

    PubMed Central

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

    2013-01-01

    Plague caused by Yersinia pestis manifests itself in bubonic, septicemic, and pneumonic forms. Although the U.S. Food and Drug Administration recently approved levofloxacin, there is no approved human vaccine against plague. The capsular antigen F1 and the low-calcium-response V antigen (LcrV) of Y. pestis represent excellent vaccine candidates; however, the inability of the immune responses to F1 and LcrV to provide protection against Y. pestis F1− strains or those which harbor variants of LcrV is a significant concern. Here, we show that the passive transfer of hyperimmune sera from rats infected with the plague bacterium and rescued by levofloxacin protected naive animals against pneumonic plague. Furthermore, 10 to 12 protein bands from wild-type (WT) Y. pestis CO92 reacted with the aforementioned hyperimmune sera upon Western blot analysis. Based on mass spectrometric analysis, four of these proteins were identified as attachment invasion locus (Ail/OmpX), plasminogen-activating protease (Pla), outer membrane protein A (OmpA), and F1. The genes encoding these proteins were cloned, and the recombinant proteins purified from Escherichia coli for immunization purposes before challenging mice and rats with either the F1− mutant or WT CO92 in bubonic and pneumonic plague models. Although antibodies to Ail and OmpA protected mice against bubonic plague when challenged with the F1− CO92 strain, Pla antibodies were protective against pneumonic plague. In the rat model, antibodies to Ail provided protection only against pneumonic plague after WT CO92 challenge. Together, the addition of Y. pestis outer membrane proteins to a new-generation recombinant vaccine could provide protection against a wide variety of Y. pestis strains. PMID:23239803

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

    PubMed

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

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  4. Use of lambda Red-mediated recombineering and Cre/lox for generation of markerless chromosomal deletions in avian pathogenic Escherichia coli.

    PubMed

    Tuntufye, Huruma N; Goddeeris, Bruno M

    2011-12-01

    Avian pathogenic Escherichia coli (APEC) are bacteria associated with extraintestinal diseases in poultry. A method to generate markerless deletions of APEC genome is described. Lambda Red recombination is used to introduce a LoxP cassette (loxP-rpsL-neo-loxP) containing the rpsL gene for streptomycin sensitivity and the neo gene for kanamycin/neomycin resistance into the APEC genome, with attendant deletion of a desired chromosomal gene. The loxP sites are incorporated into primers used to amplify the rpsL-neo marker during the construction of the LoxP cassette, making the method rapid and efficient. The cassette is specifically integrated into the fiu gene or intergenic region 2051-52, and the Cre/lox system is used to remove the marker, hence deletion of the drug-resistance genes. The results demonstrate that the Cre/lox system can successfully be used to generate markerless deletions in APEC, and rpsL counter-selection can be used to select the deletions so that one does not have to pick and test to find the desired product. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

    PubMed

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

    2016-02-01

    Clostridium perfringens beta (CPB) and iota (CPI) toxaemias result in some of the most lethal forms of haemorrhagic and necrotic enteritis and sudden death syndrome affecting especially neonates. While CPB enterotoxemia is one of the most common forms of clostridial enterotoxemia, CPI enterotoxemia though putatively considered to be rare is an emerging cause of concern. The similarities in clinical manifestation, gross and histopathology findings of both types of toxaemias coupled to the infrequency of CPI toxaemia might lead to symptomatic misidentification with Type C resulting in therapeutic failure due to habitual administration of CPB anti-toxin which is ineffective against CPI. Therefore in the present study, to generate a composite anti-toxin capable of neutralizing both toxaemias, a novel bivalent chimera r-Cpib was constructed by splicing the non-toxic C terminal binding regions of CPB and CPI, via a flexible glycine linker (G4S) by overlap-extension PCR. The fusion protein was characterized for its therapeutic abilities toward CPI and CPB toxin neutralizations. The r-Cpib was found to be non-toxic and could competitively inhibit binding of CPB to host cell receptors thereby reducing its cytotoxicity. Immunization of mice with r-Cpib generated specific antibodies capable of neutralizing the above toxaemias both in vitro and in vivo. Caco-2 cells exposed to a mixture of anti-r-Cpib sera and native CPI or CPB, displayed significantly superior protection against the respective toxins while passive challenge of mice with a similar mixture resulted in 83 and 91% protection against CPI and CPB respectively. Alternatively, mice exposed to a mixture of sham sera and native toxins died within 2-3 days. This work thus demonstrates r-Cpib as a novel bivalent fusion protein capable of efficient immunotherapy against C. perfringens CPI and CPB toxaemia. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2014-06-26

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

  9. Specific identification of pathogenic Yersinia enterocolitica by monoclonal antibodies generated against recombinant attachment invasion locus (rAil) protein.

    PubMed

    Balakrishna, K; Radhika, M; Murali, H S; Batra, H V; Bawa, A S

    2012-02-01

    Classical pathogenic strains of Yersinia enterocolitica produce a 17 kDa outer membrane protein, Ail (attachment-invasion locus), which mediates bacterial attachment to some cultures epithelial cell lines and invasion of others. In the present study, hybridomas were developed for the production of monoclonal antibodies (MAbs) against Ail protein of Y. enterocolitica. A set of five stabilized hybridoma cell lines were generated, of which, two MAbs, YEA 302 and YEA 303, exhibited specific reaction to the native Ail protein (17 kDa) present in whole cell lysate of Y. enterocolitica strains beside having reaction with rAil. The other three MAbs, YEA 5, 17 and 32, had some cross reactions with proteins other than Ail. Two out of five MAbs were IgG1, two were IgG2b and one in IgM in nature. MAbs (YEA 302 and YEA 303) did not show any cross-reaction with whole cell lysate of Brucella abortus, Vibrio cholerae, Salmonella typhimurium and Escherichia coli and other species of Enterobacteriaceae including Y. pestis in ELISA and Western blot analysis. The presence of Ail protein among the strains recovered from pork and milk samples was evaluated by these sets of MAbs and the results were compared with the duplex PCR. Collectively, the data suggest that these MAbs may have the potential for their use in the detection of pathogenic Y. enterocolitica reliably, rapidly and at a relatively low cost.

  10. A highly sensitive thrombin generation assay for assessment of recombinant activated factor VII therapy in haemophilia patients with an inhibitor.

    PubMed

    Livnat, Tami; Martinowitz, Uri; Zivelin, Ariella; Rima, Dardik; Kenet, Gili

    2011-04-01

    Bypass agents are the common treatment for haemophilia patients who develop inhibitory antibodies. Laboratory assessment of the efficacy of bypassing agent therapy is a challenge. In the present work we modified the conditions triggering thrombin generation (TG) assay in order to find the most sensitive assay for detection of rFVIIa and its analogue NN1731 in haemophilic plasma. TG was measured in samples of normal plasma, plasma of haemophilia patient with inhibitors, as well as haemophilia induced plasma. Recalcification-induced TG was compared to tissue factor (TF) -induced TG in the presence and absence of rFVIIa and NN1731. Recalcification-induced TG (without TF) in haemophilic plasma yielded baseline flat curves, with increased TG as a consequence of spiking the plasma rFVIIa. Using our system, we observed both dose-dependence and time-dependence of rFVIIa effect on TG. Elevated concentrations of TF mask the difference between rFVIIa-treated and non-treated haemophilic plasma. NN1731 yielded normalisation of recalcification-induced TG curves (without TF) which may reflect high potency. In conclusion, we suggest that triggering TG by recalcification-only may be the most sensitive assay for determining the impact of bypassing agents in haemophilic plasma, and may serve as a caution surrogate safety marker in future studies.

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

    USDA-ARS?s Scientific Manuscript database

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

  12. Tex19.1 promotes Spo11-dependent meiotic recombination in mouse spermatocytes.

    PubMed

    Crichton, James H; Playfoot, Christopher J; MacLennan, Marie; Read, David; Cooke, Howard J; Adams, Ian R

    2017-07-01

    Meiosis relies on the SPO11 endonuclease to generate the recombinogenic DNA double strand breaks (DSBs) required for homologous chromosome synapsis and segregation. The number of meiotic DSBs needs to be sufficient to allow chromosomes to search for and find their homologs, but not excessive to the point of causing genome instability. Here we report that the mammal-specific gene Tex19.1 promotes Spo11-dependent recombination in mouse spermatocytes. We show that the chromosome asynapsis previously reported in Tex19.1-/- spermatocytes is preceded by reduced numbers of recombination foci in leptotene and zygotene. Tex19.1 is required for normal levels of early Spo11-dependent recombination foci during leptotene, but not for upstream events such as MEI4 foci formation or accumulation of H3K4me3 at recombination hotspots. Furthermore, we show that mice carrying mutations in Ubr2, which encodes an E3 ubiquitin ligase that interacts with TEX19.1, phenocopy the Tex19.1-/- recombination defects. These data suggest that Tex19.1 and Ubr2 are required for mouse spermatocytes to accumulate sufficient Spo11-dependent recombination to ensure that the homology search is consistently successful, and reveal a hitherto unknown genetic pathway promoting meiotic recombination in mammals.

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

    PubMed

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

    2011-03-01

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

  14. Evaporative instabilities in climbing films

    NASA Astrophysics Data System (ADS)

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

    2001-09-01

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

  15. Genetic Recombination

    ERIC Educational Resources Information Center

    Whitehouse, H. L. K.

    1973-01-01

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

  16. Genetic Recombination

    ERIC Educational Resources Information Center

    Whitehouse, H. L. K.

    1973-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Prange, R.; Bruston, P.

    1980-08-01

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

  1. Orientation Dependence in Homologous Recombination

    PubMed Central

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

    1996-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

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

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

    SciTech Connect

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

    2015-09-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  5. Generation of fatty acids from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cardiolipin liposomes that stabilize recombinant human serum albumin.

    PubMed

    Frahm, Grant E; Cameron, Brooke E; Smith, Jeffrey C; Johnston, Michael J W

    2013-06-01

    At elevated temperatures, studies have shown that serum albumin undergoes irreversible changes to its secondary structure. Anionic fatty acids and/or anionic surfactants have been shown to stabilize human serum albumin (HSA) against thermal denaturation through bridging hydrophobic domains and cationic amino acids residues of the protein. As albumin can readily interact with a variety of liposomes, this study proposes that cardiolipin delivered via 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes can improve the thermal stability of recombinant HSA produced in Saccharomyces cerevisiae (ScrHSA) in a similar manner to anionic fatty acids. Thermal stability and structure of ScrHSA in the absence and presence of DPPC/cardiolipin liposomes was assessed with U/V circular dichroism spectropolarimetry and protein thermal stability was confirmed with differential scanning calorimetry. Although freshly prepared DPPC/cardiolipin liposomes did not improve the stability of ScrHSA, DPPC/cardiolipin liposomes incubated at room temperature for 7 d (7dRT) dramatically improved the thermal stability of the protein. Mass spectrometry analysis identified the presence of fatty acids in the 7dRT liposomes, not identified in freshly prepared liposomes, to which the improved stability was attributed. The generation of fatty acids is attributed to either the chemical hydrolysis or oxidative cleavage of the unsaturated acyl chains of cardiolipin. By modulating the lipid composition through the introduction of lipids with higher acyl chain unsaturation, it may be possible to generate the stabilizing fatty acids in a more rapid manner.

  6. Generation and characterization of a unique reagent that recognizes a panel of recombinant human monoclonal antibody therapeutics in the presence of endogenous human IgG

    PubMed Central

    Wang, Xiangdan; Quarmby, Valerie; Ng, Carl; Chuntharapai, Anan; Shek, Theresa; Eigenbrot, Charles; Kelley, Robert F.; Shia, Steven; McCutcheon, Krista M; Lowe, John; Leddy, Cecilia; Coachman, Kyle; Cain, Gary; Chu, Felix; Hotzel, Isidro; Maia, Mauricio; Wakshull, Eric; Yang, Jihong

    2013-01-01

    Pharmacokinetic (PK) and immunohistochemistry (IHC) assays are essential to the evaluation of the safety and efficacy of therapeutic monoclonal antibodies (mAb) during drug development. These methods require reagents with a high degree of specificity because low concentrations of therapeutic antibody need to be detected in samples containing high concentrations of endogenous human immunoglobulins. Current assay reagent generation practices are labor-intensive and time-consuming. Moreover, these practices are molecule-specific and so only support one assay for one program at a time. Here, we describe a strategy to generate a unique assay reagent, 10C4, that preferentially recognizes a panel of recombinant human mAbs over endogenous human immunoglobulins. This “panel-specific” feature enables the reagent to be used in PK and IHC assays for multiple structurally-related therapeutic mAbs. Characterization revealed that the 10C4 epitope is conformational, extensive and mainly composed of non-CDR residues. Most key contact residues were conserved among structurally-related therapeutic mAbs, but the combination of these residues exists at low prevalence in endogenous human immunoglobulins. Interestingly, an indirect contact residue on the heavy chain of the therapeutic appears to play a critical role in determining whether or not it can bind to 10C4, but has no affect on target binding. This may allow us to improve the binding of therapeutic mAbs to 10C4 for assay development in the future. Here, for the first time, we present a strategy to develop a panel-specific reagent that can expedite the development of multiple clinical assays for structurally-related therapeutic mAbs. PMID:23774668

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

    PubMed

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

    2006-03-01

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

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

    PubMed

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

    2012-01-20

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

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

    PubMed Central

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

    1986-01-01

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

  10. Polygonal instabilities

    NASA Astrophysics Data System (ADS)

    Labousse, Matthieu

    2015-11-01

    The interaction of a vortex with a free surface is encountered in a series of experiments, the hydraulic jump, the hydraulic bump, the toroidal Leidenfrost experiment. All these experiments share in common an unstable configuration in which azimuthal perturbations give rise to polygonal patterns. We propose a unified theoretical framework to model the emergence of this instability by investigating the stability of a liquid torus with a poloidal motion. As simple as it is, we show that the model retains the necessary ingredients to account for the experimental observations. In this talk, I will first describe the model and compare it to the existing data. However this model is purely inviscid and reaches its limits when being applied to relatively moderate Reynolds flows. So in a second part, I will present a recent experimental and theoretical investigation in which polygonal patterns are now driven by Marangoni flows. To our great surprise, it extends the range of validity of the initial proposed framework, much more than initially expected.

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

    PubMed

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

    2014-08-01

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

  12. HLA-A3-B14 and the origin of the haemochromatosis C282Y mutation: founder effects and recombination events during 12 generations in a Scandinavian family with major iron overload.

    PubMed

    Olsson, K Sigvard; Ritter, Bernd; Raha-Chowdhury, Ruma

    2010-02-01

    The haemochromatosis mutation C282Y occurred once in a person who lived in Ireland or Scandinavia and carried either human leucocyte antigen (HLA)-A3-B7 or A3-B14. With time, recombinations are believed to have taken place introducing new HLA haplotypes. This evolution is mainly unknown. In this study, we tried to find a founder, possible recombination events and effect on the phenotype in descendants. A Swedish mountain population close to Norway, n = 3529, population density <1/km(2). Retrospective genealogy study of HLA haplotypes followed by extended haplotype studies. There were 34 probands (22 men, 12 women) where 31 (91%) shared a common founder origin 12 generations ago. The A3-B14 haplotype was the most common, 39%, in strong linkage disequilibrium (P < 0.0005) with controls, followed by A3-B7, 20% (P < 0.005), probably resulting from a centromeric recombination replacing the B14 allele with the common B7. Possible telomeric recombinations took place close to HLA-A and introduced the haplotypes AW19-B7 (n = 4), AW19-B27 (2), A1-B17 (5) and A2-B12 (4) supported by pedigree studies. Male homozygotes with two copies of HLA-A3 had significantly (P 0.001) higher mean serum ferritin values than those with one, and liver damage (fibrosis and cirrhosis) was also more common (P < 0.001) than in a population with a recombinant (A1-B8) haplotype. A3-B14 may well be the ancestral haplotype with A3B7, the result of centromeric recombinations introducing the common B7 allele. Telomeric recombinations were more common than expected. The ancestral HLA-A3 haplotype may be associated with a more severe phenotypic expression.

  13. Recombination and chromosome segregation.

    PubMed Central

    Sherratt, David J; Søballe, Britta; Barre, François-Xavier; Filipe, Sergio; Lau, Ivy; Massey, Thomas; Yates, James

    2004-01-01

    The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site-specific recombination system. Dimer resolution also requires FtsK, a division septum-located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination-associated proteins, RecQ and RarA, and specific genes within living Escherichia coli cells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated. PMID:15065657

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2013-12-01

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

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

    PubMed

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

    2009-12-10

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

  18. Recombinant polymorphic membrane protein D in combination with a novel, second-generation lipid adjuvant protects against intra-vaginal Chlamydia trachomatis infection in mice.

    PubMed

    Paes, Wayne; Brown, Naj; Brzozowski, Andrzej M; Coler, Rhea; Reed, Steve; Carter, Darrick; Bland, Martin; Kaye, Paul M; Lacey, Charles J N

    2016-07-29

    The development of a chlamydial vaccine that elicits protective mucosal immunity is of paramount importance in combatting the global spread of sexually transmitted Chlamydia trachomatis (Ct) infections. While the identification and prioritization of chlamydial antigens is a crucial prerequisite for efficacious vaccine design, it is likely that novel adjuvant development and selection will also play a pivotal role in the translational potential of preclinical Ct vaccines. Although the molecular nature of the immuno-modulatory component is of primary importance, adjuvant formulation and delivery systems may also govern vaccine efficacy and potency. Our study provides the first preclinical evaluation of recombinant Ct polymorphic membrane protein D (rPmpD) in combination with three different formulations of a novel second-generation lipid adjuvant (SLA). SLA was rationally designed in silico by modification of glucopyranosyl lipid adjuvant (GLA), a TLR4 agonistic precursor molecule currently in Phase II clinical development. We demonstrate robust protection against intra-vaginal Ct challenge in mice, evidenced by significantly enhanced resistance to infection and reduction in mean bacterial load. Strikingly, protection was found to correlate with the presence of robust anti-rPmpD serum and cervico-vaginal IgG titres, even in the absence of adjuvant-induced Th1-type cellular immune responses elicited by each SLA formulation, and we further show that anti-rPmpD antibodies recognize Ct EBs. These findings highlight the utility of SLA and rational molecular design of adjuvants in preclinical Ct vaccine development, but also suggest an important role for anti-rPmpD antibodies in protection against urogenital Ct infection. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  19. Mode-locking via dissipative Faraday instability.

    PubMed

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

    2016-08-09

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

  20. Mode-locking via dissipative Faraday instability

    PubMed Central

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

    2016-01-01

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

  1. Mode-locking via dissipative Faraday instability

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  2. Marangoni-B'enard instability in microgravity: PTV-analysis of the velocimetry data generated during the BAMBI - FOTON-M2 experiment

    NASA Astrophysics Data System (ADS)

    Dehaeck, Sam; Talvy, Samuel; Rednikov, Alexey; Queeckers, Patrick; Colinet, Pierre

    2010-11-01

    The BAMBI (Bifurcation Anomalies in Marangoni-B'enard Instabilities) experiment has been successfully flown onboard the FOTON-M2 satellite in June 2005. During the 4 days available for the experiment, a 5mm-thick 200 cSt silicone oil layer in a 10x10cm^2 wide container, and in contact with a similarly-sized helium gas layer was heated from "below" and cooled from "above." By varying the heating power applied at each experimental step, a range of temperature differences across the liquid and gas layers was scanned and the onset and evolution of the Marangoni-B'enard instability typical for this type of configuration was examined. The used optical diagnostics were Infrared Thermography of the liquid/gas interface, PTV (multiple views and heights in the liquid layer), Wollaston Interferometry and Electronic Speckle Pattern Interferometry. The present contribution focuses on the velocity results obtained by PTV in the interface plane, and discusses them in relation both with infrared images, and with theory/numerics.

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

    NASA Astrophysics Data System (ADS)

    Choi, Changhwan; Lee, Jack C.

    2011-02-01

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

  4. Recombinant allergens

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    SciTech Connect

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

    2016-03-28

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

  7. Interfacial Instability during Granular Erosion.

    PubMed

    Lefebvre, Gautier; Merceron, Aymeric; Jop, Pierre

    2016-02-12

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

  8. Interfacial Instabilities on a Droplet

    NASA Astrophysics Data System (ADS)

    Jalaal, Maziyar; Mehravaran, Kian

    2013-11-01

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

  9. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

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

  10. Recombinant gonadotropins.

    PubMed

    Lathi, R B; Milki, A A

    2001-10-01

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

  11. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

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

  12. Recombinant renewable polyclonal antibodies.

    PubMed

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

    2015-01-01

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

  13. Recombinant renewable polyclonal antibodies

    PubMed Central

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

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products. PMID:25530082

  14. Two-Fluid Interface Instability Being Studied

    NASA Technical Reports Server (NTRS)

    Niederhaus, Charles E.

    2003-01-01

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

  15. Electron heat flux instability

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  16. Kinesics of Affective Instability.

    ERIC Educational Resources Information Center

    Dil, Nasim

    1979-01-01

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

  17. Turbine instabilities: Case histories

    NASA Technical Reports Server (NTRS)

    Laws, C. W.

    1985-01-01

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

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

    PubMed

    Karpf, Adam R; Matsui, Sei-ichi

    2005-10-01

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

  19. Recombination between Homologous Chromosomes Induced by Unrepaired UV-Generated DNA Damage Requires Mus81p and Is Suppressed by Mms2p

    PubMed Central

    Yin, Yi; Petes, Thomas D.

    2015-01-01

    DNA lesions caused by UV radiation are highly recombinogenic. In wild-type cells, the recombinogenic effect of UV partially reflects the processing of UV-induced pyrimidine dimers into DNA gaps or breaks by the enzymes of the nucleotide excision repair (NER) pathway. In this study, we show that unprocessed pyrimidine dimers also potently induce recombination between homologs. In NER-deficient rad14 diploid strains, we demonstrate that unexcised pyrimidine dimers stimulate crossovers, noncrossovers, and break-induced replication events. The same dose of UV is about six-fold more recombinogenic in a repair-deficient strain than in a repair-proficient strain. We also examined the roles of several genes involved in the processing of UV-induced damage in NER-deficient cells. We found that the resolvase Mus81p is required for most of the UV-induced inter-homolog recombination events. This requirement likely reflects the Mus81p-associated cleavage of dimer-blocked replication forks. The error-free post-replication repair pathway mediated by Mms2p suppresses dimer-induced recombination between homologs, possibly by channeling replication-blocking lesions into recombination between sister chromatids. PMID:25738287

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

    PubMed Central

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. Analysis of Mycobacterium tuberculosis genoma and production of a recombinant protein containing specific B and T cell antigenic determinants--new approaches to second generation antituberculosis vaccines.

    PubMed

    Colizzi, V; Vismara, D; D'Urso, C; Mezzopreti, M F; Lombardi, G; Piccolella, E; Damiani, G; Marelli, P; Campa, M

    1989-01-01

    Tuberculosis is still a major health problem in almost all over the world. Thus, new directions in basic and applied research of tuberculosis are under investigation in several laboratories. In this paper, we provide recent data obtained in our laboratory with the recombinant DNA technology which allow a systematic survey of the microbial genome. Screening of the M. tuberculosis genomic DNA library in the phage lambda gt11 expression vector, using E. coli as surrogate host, has evidenced the possibility of producing recombinant M. tuberculosis proteins recognized by sera from tuberculosis patients and by specific monoclonal antibodies. Using this technology, we have isolated a recombinant protein (molecular weight 130 kilodaltons) which is identified by a murine monoclonal antibody recognizing a mycobacterial cell wall antigenic determinant present on a mycobacterial protein. This protein is only present on the mycobacterial species related to the tuberculosis complex (M. tuberculosis, M. bovis, M. africanum) and does not crossreact with nonpathogenic Mycobacteria. Since the immune response to mycobacterial infections is cell-mediated, the question arises about the use of M. tuberculosis-specific T lymphocytes to screen this gene bank. Thus, the recombinant mycobacterial protein isolated by antibodies has been then used to stimulate the proliferation of T lymphocytes from patients with tubercular pleuritis. This experiment indicates that the recombinant protein contains antigenic determinants recognized by T cells. Moreover, such protein is able to elicit delayed type hypersensitivity skin reaction in mice immunized or infected with M. tuberculosis and M. bovis. Finally, gene mapping and hybridization studies with native M. tuberculosis DNA confirme the mycobacterial nature of the recombinant DNA insert. Thus a good candidate for the prophylaxis and the immunodiagnosis of tuberculosis has been identified. The identification and selection of genes encoding antigenic

  3. Regulation of Meiotic Recombination

    SciTech Connect

    Gregory p. Copenhaver

    2011-11-09

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

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

    PubMed

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

    2012-09-07

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

  5. Analysis of nuclear reactor instability phenomena

    SciTech Connect

    Lahey, R.T. Jr.

    1993-01-01

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

  6. Instability of rectangular jets

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  7. Instability of rectangular jets

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  8. Recombineering linear BACs.

    PubMed

    Chen, Qingwen; Narayanan, Kumaran

    2015-01-01

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

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

    PubMed Central

    2011-01-01

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

  10. Generations.

    PubMed

    Chambers, David W

    2005-01-01

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

  11. Plasma, fluid instabilities in ionospheric holes

    SciTech Connect

    Bernhardt, P.A.

    1982-09-01

    Instabilities can be both triggered and quenched by chemical releases which generate ionospheric holes. Vapors, such as H/sub 2/O, H/sub 2/, and CO/sub 2/, rapidly react with the O/sup +/ ions in the upper atmosphere, producing polyatomic ions such as H/sub 2/O/sup +/, H/sub 3/O/sup +/, OH/sup +/ an O/sub 2//sup +/. These ions quickly combine with electrons, leaving natural species. The enhanced F region neutralization initially tends to quench the fluid instabilities in the modified region. After the injected vapors dissipate, chemical quenching becomes unimportant. At late times, the sides of the ionospheric hole may become unstable to fluid instabilities. The wind-driven gradient-drift instability, the current-convective instability, and the gravitational Rayleigh-Taylor instability are three classes of instabilities which may produce irregularities in ionospheric holes. These instabilities are investigated by using local, linear perturbation analysis. The removal of preexisting plasma irregularities by reactive chemical releases is also investigated.

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

    PubMed

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

    1999-12-01

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

  13. Baroclinic instability in stellar radiation zones

    SciTech Connect

    Kitchatinov, L. L.

    2014-03-20

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

  14. Aeroelastic instability in a jet plate interaction

    NASA Astrophysics Data System (ADS)

    Antoine, Maxime; Hémon, Pascal; de Langre, Emmanuel

    2007-11-01

    A flexible sheet subject to a normal impinging air jet can oscillate. We present a simple experiment that shows that added damping generated by the jet is responsible for this aeroelastic instability. The cases of planar jet and circular jet are studied. A model is presented to describe this instability and the results agree well with the experimental observations. The nozzle geometry is found to be a dominant parameter that drives the critical distance between the jet and the sheet, under which the instability develops. To cite this article: M. Antoine et al., C. R. Mecanique 335 (2007).

  15. Lending sociodynamics and economic instability

    NASA Astrophysics Data System (ADS)

    Hawkins, Raymond J.

    2011-11-01

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

  16. Weibel instability in relativistic quantum plasmas

    NASA Astrophysics Data System (ADS)

    Mendonça, J. T.; Brodin, G.

    2015-08-01

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

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

    SciTech Connect

    Bychenkov, V. Yu.; Rozmus, W.

    2015-08-15

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

  18. Primordial magnetogenesis before recombination

    NASA Astrophysics Data System (ADS)

    Fabre, Ophélia; Shankaranarayanan, S.

    2016-04-01

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

  19. Three spontaneous H-2Db mutants are generated by genetic micro- recombination (gene conversion) events. Impact on the H-2-restricted immune responsiveness

    PubMed Central

    1988-01-01

    Sequence analysis of the mutant Dbm13, Dbm14, and Dbm24 genes indicate that they differ from the parental Db gene by 4, 1, and 8 nucleotides, respectively. The mutant sequences substituted into Dbm13 and Dbm24 are identical to those found in the Kb gene, at the homologous positions. Thus, similar to the Kb gene, the Db gene is able to undergo micro- recombination (gene conversion) events with other class I genes. Such data suggest that micro-recombination events could be an important mechanism for the diversification of all H-2 genes. The Db mutant products share a common theme: the alterations in all occur at amino acid residues whose side chains in the homologous class I HLA-A2 molecule project into the postulated peptide antigen-binding cleft, and hence, would be expected to alter the binding of foreign or self peptides. Due to such changes, the bm14 mouse has become a nonresponder in the CTL response to Moloney murine leukemia virus (M-MuLV), as the alteration of one amino acid residue at position 70 (a Gln to His) is sufficient to entirely abrogate the cell-mediated response to the virus. On the other hand, the bm13 mouse has shifted the major part of its M-MuLV restriction to Kb, a profound alteration in CTL responsiveness due to the alteration of three amino acids (Leu to Gln at 114, Phe to Tyr at 116, and Glu to Asp at 119) in a peptide stretch of beta-pleated sheet structure lining the bottom of the antigen- binding cleft. Thus, study of these mutants reveals that, in one step, micro-recombination at the genetic level has resulted at the protein level in profound changes in the immune response to viral infection. Such a mechanism operating at the population level can be a driving force during evolution for modulating the character of CTL immunity. PMID:3199070

  20. Joint Instability and Osteoarthritis

    PubMed Central

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

    2015-01-01

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

  1. Ordinary electromagnetic mode instability

    NASA Technical Reports Server (NTRS)

    Cheng, C. Z.

    1974-01-01

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

  2. Generalities on combustion instabilities

    NASA Astrophysics Data System (ADS)

    Kuentzmann, Paul

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

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

    PubMed

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

    2009-04-01

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

  4. Generation of an HFRS patient-derived neutralizing recombinant antibody to Hantaan virus G1 protein and definition of the neutralizing domain.

    PubMed

    Liang, Mifang; Mahler, Michael; Koch, Joachim; Ji, Yan; Li, Dexin; Schmaljohn, Connie; Bautz, Ekkehard K F

    2003-01-01

    Hantaan virus (HTNV) in the Hantavirus genus, family Bunyaviridae, is the major cause of severe hemorrhagic fever with renal syndrome (HFRS). We prepared a combinatorial phage display library of human Fabs to HTNV from RNA extracted from the blood lymphocytes of a convalescent HFRS patient. We selected two G1 glycoprotein-specific clones and one nucleocapsid protein (N)-specific clone from the Fab library for further studies. The human Fab antibodies were converted to IgG form in baculovirus/insect cells system by using cassette vectors that we developed earlier. Characterization of the recombinant antibodies revealed that the two G1-specific IgGs, could bind to and neutralize HTNV but not Seoul virus (SEOV). The N-specific IgG did not neutralize either HTNV or SEOV. Sequence analysis revealed that the two G1-specific clones differed by only one predicted amino acid in their complementarity determining regions, CDR3. Epitope mapping studies were carried out with one of the two G1-specific clones and synthetic peptides representing portions of HTNV G1. Results indicated that the recombinant antibody recognizes the core amino acid sequence LTKTLVIGQ, which is found near the C-terminus of HTNV G1. These results are the first to define a neutralizing epitope on the G1 protein of HTNV using an antibody derived from an HFRS patient. Copyright 2003 Wiley-Liss, Inc.

  5. Numerical analysis of engine instability

    NASA Astrophysics Data System (ADS)

    Habiballah, M.; Dubois, I.

    Following a literature review on numerical analyses of combustion instability, to give the state of the art in the area, the paper describes the ONERA methodology used to analyze the combustion instability in liquid propellant engines. Attention is also given to a model (named Phedre) which describes the unsteady turbulent two-phase reacting flow in a liquid rocket engine combustion chamber. The model formulation includes axial or radial propellant injection, baffles, and acoustic resonators modeling, and makes it possible to treat different engine types. A numerical analysis of a cryogenic engine stability is presented, and the results of the analysis are compared with results of tests of the Viking engine and the gas generator of the Vulcain engine, showing good qualitative agreement and some general trends between experiments and numerical analysis.

  6. Circulation in blast driven instabilities

    NASA Astrophysics Data System (ADS)

    Henry de Frahan, Marc; Johnsen, Eric

    2016-11-01

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

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

    USDA-ARS?s Scientific Manuscript database

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

  8. Treatment of hip instability.

    PubMed

    Robbins, G M; Masri, B A; Garbuz, D S; Greidanus, N; Duncan, C P

    2001-10-01

    Instability after total hip arthroplasty is a major source of patient morbidity, second only to aseptic loosening. Certain patient groups have been identified as having a greater risk of instability, including patients undergoing revision arthroplasty as early or late treatment for proximal femoral fractures.

  9. Predictors for Surgery in Shoulder Instability

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Bohm, Lothar

    2006-01-01

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

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

    PubMed

    Bohm, Lothar

    2006-05-03

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

  12. Recombinant immunoglobulin variable domains generated from synthetic genes provide a system for in vitro characterization of light-chain amyloid proteins.

    PubMed Central

    Stevens, P. W.; Raffen, R.; Hanson, D. K.; Deng, Y. L.; Berrios-Hammond, M.; Westholm, F. A.; Murphy, C.; Eulitz, M.; Wetzel, R.; Solomon, A.

    1995-01-01

    The primary structural features that render human monoclonal light chains amyloidogenic are presently unknown. To gain further insight into the physical and biochemical factors that result in the pathologic deposition of these proteins as amyloid fibrils, we have selected for detailed study three closely homologous protein products of the light-chain variable-region single-gene family VkIV. Two of these proteins, REC and SMA, formed amyloid fibrils in vivo. The third protein, LEN, was excreted by the patient at levels of 50 g/day with no indication of amyloid deposits. Sequences of amyloidogenic proteins REC and SMA differed from the sequence of the nonpathogenic protein LEN at 14 and 8 amino acid positions, respectively, and these amino acid differences have been analyzed in terms of the three-dimensional structure of the LEN dimer. To provide a replenishable source of these human proteins, we constructed synthetic genes coding for the REC, SMA, and LEN variable domains and expressed these genes in Escherichia coli. Immunochemical and biophysical comparisons demonstrated that the recombinant VkIV products have tertiary structural features comparable to those of the patient-derived proteins. This well-defined set of three clinically characterized human kIV light chains, together with the capability to produce these kIV proteins recombinantly, provide a system for biophysical and structural comparisons of two different amyloidogenic light-chain proteins and a nonamyloidogenic protein of the same subgroup. This work lays the foundation for future investigations of the structural basis of light-chain amyloidogenicity. PMID:7795526

  13. Selection of Recombinant Human Antibodies.

    PubMed

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

    2016-01-01

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

  14. Controlling contractile instabilities in the actomyosin cortex

    PubMed Central

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

    2017-01-01

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

  15. An Experimental Study of Richtmyer-Meshkov Instability

    NASA Technical Reports Server (NTRS)

    Jacobs, Jeffrey W.; Niederhaus, Charles E.

    1996-01-01

    Richtmyer-Meshkov (RM) instability occurs when a planar interface separating two fluids of different density is impulsively accelerated In the direction of its normal. It is one of the most fundamental of fluid instabilities and is of importance in fields ranging from astrophysics to materials processing. Because RM instability experiments are normally carried out in shock tubes, where the generation of a sharp well controlled interface between gases is difficult, there is a scarcity of good experimental results. The experiments presented here utilize a novel technique which circumvents many of the experimental difficulties that have previously limited the study of RM instability. In this system, the instability is generated by bouncing a thin rectangular tank containing two liquids off of a fixed spring. Results obtained from these experiments yield particularly well visualized images of the nonlinear development of the instability. However, because the run time in these experiments is limited, new experiments capable of achieving longer run times are planned.

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

    SciTech Connect

    Morgan, William F.; Sowa, Marianne B.

    2007-03-30

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

  17. Improved packaging system for generation of high-level noncytotoxic HSV-1 amplicon vectors using Cre-loxP site-specific recombination to delete the packaging signals of defective helper genomes.

    PubMed

    Zaupa, Cécile; Revol-Guyot, Valerie; Epstein, Alberto L

    2003-07-20

    Amplicons are promising helper-dependent HSV-1-derived vectors that allow the transfer and expression of very large foreigner DNA into dividing and quiescent cells. We had already described an approach to prepare large amounts of high-titer amplicon vectors, using Cre-loxP site-specific recombination system to delete the packaging ("a") signals of an HSV-1 recombinant helper virus (HSV-1 LaL). Amplicon vectors prepared using such a system showed a level of contamination with helper particles lower than 1%. The residual helper particles generated by this system are, however, replication-competent, thus precluding their use in gene therapy. To avoid such potential spread of residual particles, we present here the development of a defective Cre-loxP-based helper virus (HSV-1 LaL Delta J), deleted of the genes encoding ICP4 and ICP34.5 proteins from the helper genome, in addition to the native "a" signals. HSV-1 LaL Delta J carries a single floxed "a" signal in gC locus. To produce HSV-1 LaL Delta J and to prepare the amplicon vectors, we have constructed two novel cell lines expressing the essential ICP4 protein, either alone or in combination with Cre recombinase. These cell lines were conceived to complement ICP4 while minimizing the probability of generating replication-competent particles. In this paper we present results demonstrating that the novel helper system allows ready production of large amounts of high-titer amplicon vectors. Residual helper particles generated still do not exceed 0.5% of the viral population and can grow only in cells expressing ICP4. Amplicon vectors produced with this method showed no cytotoxicty for infected cells.

  18. Dielectronic recombination lines of C{sup +}

    SciTech Connect

    Sochi, Taha Storey, Peter J.

    2013-11-15

    The present paper presents atomic data generated to investigate the recombination lines of C II in the spectra of planetary nebulae. These data include energies of bound and autoionizing states, oscillator strengths and radiative transition probabilities, autoionization probabilities, and recombination coefficients. The R-matrix method of electron scattering theory was used to describe the C{sup 2+} plus electron system.

  19. Soliton modulation instability in fiber lasers

    NASA Astrophysics Data System (ADS)

    Tang, D. Y.; Zhao, L. M.; Wu, X.; Zhang, H.

    2009-08-01

    We report experimental evidence of soliton modulation instability in erbium-doped fiber lasers. An alternate type of spectral sideband generation was always experimentally observed on the soliton spectrum of the erbium-doped soliton fiber lasers when energy of the formed solitons reached beyond a certain threshold value. Following this spectral sideband generation, if the pump power of the lasers was further increased, either a new soliton would be formed or the existing solitons would experience dynamical instabilities, such as the period-doubling bifurcations or period-doubling route to chaos. We point out that the mechanism for this soliton spectral sideband generation is the modulation instability of the solitons in the lasers. We further show that, owing to the internal energy balance of a dissipative soliton, modulation instability itself does not destroy the stable soliton evolution in a laser cavity. It is the strong resonant wave coupling between the soliton and dispersive waves that leads to the dynamic instability of the solitons.

  20. Site-specific DNA double-strand break generated by I-SceI endonuclease enhances ectopic homologous recombination in Pyricularia oryzae.

    PubMed

    Arazoe, Takayuki; Younomaru, Tetsuya; Ohsato, Shuichi; Kimura, Makoto; Arie, Tsutomu; Kuwata, Shigeru

    2014-03-01

    To evaluate the contribution of DNA double-strand breaks (DSBs) to somatic homologous recombination (HR) in Pyricularia oryzae, we established a novel detection/selection system of DSBs-mediated ectopic HR. This system consists of donor and recipient nonfunctional yellow fluorescent protein (YFP)/blasticidin S deaminase (BSD) fusion genes and the yeast endonuclease I-SceI gene as a recipient-specific DSB inducer. The system enables to detect and select ectopic HR events by the restoration of YFP fluorescence and blasticidin S resistance. The transformed lines with donor and recipient showed low frequencies of endogenous ectopic HR (> 2.1%). Compared with spontaneous HR, c. 20-fold increases in HR and absolute frequency of HR as high as 40% were obtained by integration of I-SceI gene, indicating that I-SceI-mediated DSB was efficiently repaired via ectopic HR. Furthermore, to validate the impact of DSB on targeted gene replacement (TGR), the transformed lines with a recipient gene were transfected with an exogenous donor plasmid in combination with the DSB inducer. TGR events were not observed without the DSB inducer, whereas hundreds of colonies resulting from TGR events were obtained with the DSB inducer. These results clearly demonstrated that the introduction of site-specific DSB promotes ectopic HR repair in P. oryzae.

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

    PubMed Central

    Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G.; Oropallo, Michael; Gaylord, Michelle; Ungaro, Ryan; Cunningham-Rundles, Charlotte; Alexandropoulos, Konstantina; Mucida, Daniel; Merad, Miriam; Cerutti, Andrea

    2016-01-01

    Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103+ and CD24+CD11b+ DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell–dependent or –independent pathways. Compared with lung DCs (LDC), lung CD64+ macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-β (TGF-β) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid–dependent up-regulation of α4β7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT–specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs. PMID:26712806

  2. Generation and characterization of a scFv against recombinant coat protein of the geminivirus tomato leaf curl New Delhi virus.

    PubMed

    Zakri, Adel M; Ziegler, Angelika; Torrance, Lesley; Fischer, Rainer; Commandeur, Ulrich

    2010-03-01

    We report the establishment of a hybridoma cell line secreting the monoclonal antibody (mAb) HAV, which recognizes the coat (AV1) protein of tomato leaf curl New Delhi virus (ToLCNDV), a begomovirus. The cell line was obtained following immunization of mice with purified recombinant AV1 fused to glutathione S-transferase (GST). A single-chain variable fragment (scFv-SAV) was assembled from hybridoma cDNA, but sequence analysis revealed a single nucleotide deletion causing a frame shift that resulted in a 21-residue N-terminal truncation. The missing nucleotide was restored by in vitro site-directed mutagenesis to create scFv-RWAV. The binding properties of mAb HAV and the corresponding scFvs were characterized by western blot, ELISA and surface plasmon resonance spectroscopy. MAb HAV bound to AV1 with nanomolar affinity but reacted neither with the N-terminal region of the protein nor with the GST fusion partner. This suggested that the antibody recognized a linear epitope in a region of the coat protein that is conserved among begomoviruses. Both scFvs retained the antigen specificity of mAb HAV, although the dissociation rate constant of scFv-RWAV was tenfold greater than that of scFv-SAV, showing the importance of restoring the 21 N-terminal amino acids.

  3. Generation of Recombinant Antibodies against the beta-(1,6)-Branched beta-(1,3)-D-Glucan Schizophyllan from Immunized Mice via Phage Display

    PubMed Central

    Buchmeier, Sabine; Frenzel, André; Tinnefeld, Philip

    2017-01-01

    beta-(1,6)-Branched beta-(1,3)-D-glucans like schizophyllan from the basidiomycete Schizophyllum commune excite various immunostimulatory effects and have been clinically tested as adjuvants. Some of the glucans are also applicable in food or petrol industry due to their viscosity and temperature stability in aqueous solution. Antibodies against these glucans could be used as tool for analysis of glucan preparations or for further research of its bioactivity. Therefore, an immune phage display library was constructed from mice immunized with schizophyllan. Three recombinant monoclonal antibodies were isolated from this library by affinity selection (panning) on schizophyllan. The half-maximal effective concentration (EC50) values for those antibodies varied between 16.4 ng mL−1 and 21.3 ng mL−1. The clones showed binding specificity not only for schizophyllan but also for other beta-(1,6)-branched beta-(1,3)-D-glucans of similar macromolecular structure. Denaturation of the secondary structure led to a reduced antibody binding, indicating an epitope requiring the correct conformation of the triple helical structure of the glucans. PMID:28620550

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

    PubMed

    Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G; Oropallo, Michael; Gaylord, Michelle; Ungaro, Ryan; Cunningham-Rundles, Charlotte; Alexandropoulos, Konstantina; Mucida, Daniel; Merad, Miriam; Cerutti, Andrea; Mehandru, Saurabh

    2016-01-11

    Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103(+) and CD24(+)CD11b(+) DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell-dependent or -independent pathways. Compared with lung DCs (LDC), lung CD64(+) macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-β (TGF-β) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid-dependent up-regulation of α4β7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT-specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs. © 2016 Ruane et al.

  5. Second-Generation Recombination-Based In Vivo Expression Technology for Large-Scale Screening for Vibrio cholerae Genes Induced during Infection of the Mouse Small Intestine

    PubMed Central

    Osorio, C. G.; Crawford, J. A.; Michalski, J.; Martinez-Wilson, H.; Kaper, J. B.; Camilli, A.

    2005-01-01

    We have constructed an improved recombination-based in vivo expression technology (RIVET) and used it as a screening method to identify Vibrio cholerae genes that are transcriptionally induced during infection of infant mice. The improvements include the introduction of modified substrate cassettes for resolvase that can be positively and negatively selected for, allowing selection of resolved strains from intestinal homogenates, and three different tnpR alleles that cover a range of translation initiation efficiencies, allowing identification of infection-induced genes that have low-to-moderate basal levels of transcription during growth in vitro. A transcriptional fusion library of 8,734 isolates of a V. cholerae El Tor strain that remain unresolved when the vibrios are grown in vitro was passed through infant mice, and 40 infection-induced genes were identified. Nine of these genes were inactivated by in-frame deletions, and their roles in growth in vitro and fitness during infection were measured by competition assays. Four mutant strains were attenuated >10-fold in vivo compared with the parental strain, demonstrating that infection-induced genes are enriched in genes essential for virulence. PMID:15664940

  6. Generation of recombinant monoclonal antibodies to study structure-function of envelope protein VP28 of white spot syndrome virus from shrimp

    SciTech Connect

    Wang Yuzhen; Zhang Xiaohua; Yuan Li; Xu Tao; Rao Yu; Li Jia; Dai Heping

    2008-08-08

    White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP28 is one of the most important envelope proteins of WSSV. In this study, a recombinant antibody library, as single-chain fragment variable (scFv) format, displayed on phage was constructed using mRNA from spleen cells of mice immunized with full-length VP28 expressed in Escherichia coli. After several rounds of panning, six scFv antibodies specifically binding to the epitopes in the N-terminal, middle, and C-terminal regions of VP28, respectively, were isolated from the library. Using these scFv antibodies as tools, the epitopes in VP28 were located on the envelope of the virion by immuno-electron microscopy. Neutralization assay with these antibodies in vitro suggested that these epitopes may not be the attachment site of WSSV to host cell receptor. This study provides a new way to investigate the structure and function of the envelope proteins of WSSV.

  7. Buckling instability in arteries.

    PubMed

    Vandiver, Rebecca M

    2015-04-21

    Arteries can become tortuous in response to abnormal growth stimuli, genetic defects and aging. It is suggested that a buckling instability is a mechanism that might lead to artery tortuosity. Here, the buckling instability in arteries is studied by examining asymmetric modes of bifurcation of two-layer cylindrical structures that are residually stressed. These structures are loaded by an axial force, internal pressure and have nonlinear, anisotropic, hyperelastic responses to stresses. Strain-softening and reduced opening angle are shown to lower the critical internal pressure leading to buckling. In addition, the ratio of the media thickness to the adventitia thickness is shown to have a dramatic impact on arterial instability.

  8. Demystified...recombinant antibodies.

    PubMed

    Smith, K A; Nelson, P N; Warren, P; Astley, S J; Murray, P G; Greenman, J

    2004-09-01

    Recombinant antibodies are important tools for biomedical research and are increasingly being used as clinical diagnostic/therapeutic reagents. In this article, a background to humanized antibodies is given, together with details of the generation of antibody fragments--for example, single chain Fv fragments. Phage antibody fragments are fast becoming popular and can be generated by simple established methods of affinity enrichment from libraries derived from immune cells. Phage display methodology can also be used for the affinity enrichment of existing antibody fragments to provide a reagent with a higher affinity. Here, phage antibodies are demystified to provide a greater understanding of the potential of these reagents and to engage clinicians and biomedical scientists alike to think about potential applications in pathology and clinical settings.

  9. Mirror Instability in the Turbulent Solar Wind

    NASA Astrophysics Data System (ADS)

    Hellinger, Petr; Landi, Simone; Matteini, Lorenzo; Verdini, Andrea; Franci, Luca

    2017-04-01

    The relationship between a decaying strong turbulence and the mirror instability in a slowly expanding plasma is investigated using two-dimensional hybrid expanding box simulations. We impose an initial ambient magnetic field perpendicular to the simulation box, and we start with a spectrum of large-scale, linearly polarized, random-phase Alfvénic fluctuations that have energy equipartition between kinetic and magnetic fluctuations and a vanishing correlation between the two fields. A turbulent cascade rapidly develops, magnetic field fluctuations exhibit a Kolmogorov-like power-law spectrum at large scales and a steeper spectrum at sub-ion scales. The imposed expansion (taking a strictly transverse ambient magnetic field) leads to the generation of an important perpendicular proton temperature anisotropy that eventually drives the mirror instability. This instability generates large-amplitude, nonpropagating, compressible, pressure-balanced magnetic structures in a form of magnetic enhancements/humps that reduce the perpendicular temperature anisotropy.

  10. Genetic instability in inherited and sporadic leukemias.

    PubMed

    Popp, Henning D; Bohlander, Stefan K

    2010-12-01

    Genetic instability due to increased DNA damage and altered DNA repair is of central significance in the initiation and progression of inherited and sporadic human leukemias. Although very rare, some inherited DNA repair insufficiency syndromes (e.g., Fanconi anemia, Bloom's syndrome) have added substantially to our understanding of crucial mechanisms of leukemogenesis in recent years. Conversely, sporadic leukemias account for the main proportion of leukemias and here DNA damaging reactive oxygen species (ROS) play a central role. Although the exact mechanisms of increased ROS production remain largely unknown and no single pathway has been detected thus far, some oncogenic proteins (e.g., the activated tyrosine kinases BCR-ABL1 and FLT3-ITD) seem to play a key role in driving genetic instability by increased ROS generation which influences the disease course (e.g., blast crisis in chronic myeloid leukemia or relapse in FLT3-ITD positive acute myeloid leukemia). Of course other mechanisms, which promote genetic instability in leukemia also exist. A newly emerging mechanism is the genome-wide alteration of epigenetic marks (e.g., hypomethylation of histone H3K79), which promotes chromosomal instability. Taken together genetic instability plays a critical role both in inherited and sporadic leukemias and emerges as a common theme in both inherited and sporadic leukemias. Beyond its theoretical impact, the analysis of genetic instability may lead the way to the development of innovative therapy strategies. © 2010 Wiley-Liss, Inc.

  11. Chronic Ankle Instability

    MedlinePlus

    ... Risk for Newly Active Baby Boomers The American College of Foot and Ankle Surgeons has a valuable lesson for Baby Boomers now getting back into fitness and sports: Get your ankles checked for chronic instability caused ...

  12. Evaporatively driven morphological instability

    NASA Astrophysics Data System (ADS)

    Style, Robert W.; Wettlaufer, J. S.

    2007-07-01

    Simple observations of evaporating solutions reveal a complex hierarchy of spatiotemporal instabilities. We analyze one such instability suggested by the qualitative observations of Du and Stone and find that it is driven by a variant of the classical morphological instability in alloy solidification. In the latter case a moving solid-liquid interface is accompanied by a solutally enriched boundary layer that is thermodynamically metastable due to constitutional supercooling. Here, we consider the evaporation of an impure film adjacent to a solid composed of the nonvolatile species. In this case, constitutional supercooling within the film is created by evaporation at the solution-vapor interface and this drives the corrugation of the solid-solution interface across the thickness of the film. The principal points of this simple theoretical study are to suggest an instability mechanism that is likely operative across a broad range of technological and natural systems and to focus future quantitative experimental searches.

  13. Bacteriophage recombination systems and biotechnical applications.

    PubMed

    Nafissi, Nafiseh; Slavcev, Roderick

    2014-04-01

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

  14. Current Trends of HIV Recombination Worldwide

    PubMed Central

    Lau, Katherine A.; Wong, Justin J.L.

    2013-01-01

    One of the major characteristics of HIV-1 is its high genetic variability and extensive heterogeneity. This characteristic is due to its molecular traits, which in turn allows it to vary, recombine, and diversify at a high frequency. As such, it generates complex molecular forms, termed recombinants, which evade the human immune system and so survive. There is no sequence constraint to the recombination pattern as it appears to occur at inter-group (between groups M and O), as well as interand intra-subtype within group M. Rapid emergence and active global transmission of HIV-1 recombinants, known as circulating recombinant forms (CRFs) and unique recombinant forms (URFs), requires urgent attention. To date, 55 CRFs have been reported around the world. The first CRF01_AE originated from Central Africa but spread widely in Asia. The most recent CRF; CRF55_01B is a recombinant form of CRF01_AE and subtype B, although its origin is yet to be publicly disclosed. HIV-1 recombination is an ongoing event and plays an indispensable role in HIV epidemics in different regions. Africa, Asia and South America are identified as recombination hot-spots. They are affected by continual emergence and cocirculation of newly emerging CRFs and URFs, which are now responsible for almost 20% of HIV-1 infections worldwide. Better understanding of recombinants is necessary to determine their biological and molecular attributes. PMID:24470968

  15. An alternative splicing event which occurs in mouse pachytene spermatocytes generates a form of DNA ligase III with distinct biochemical properties that may function in meiotic recombination.

    PubMed Central

    Mackey, Z B; Ramos, W; Levin, D S; Walter, C A; McCarrey, J R; Tomkinson, A E

    1997-01-01

    Three mammalian genes encoding DNA ligases have been identified. However, the role of each of these enzymes in mammalian DNA metabolism has not been established. In this study, we show that two forms of mammalian DNA ligase III, alpha and beta, are produced by a conserved tissue-specific alternative splicing mechanism involving exons encoding the C termini of the polypeptides. DNA ligase III-alpha cDNA, which encodes a 103-kDa polypeptide, is expressed in all tissues and cells, whereas DNA ligase III-beta cDNA, which encodes a 96-kDa polypeptide, is expressed only in the testis. During male germ cell differentiation, elevated expression of DNA ligase III-beta mRNA is restricted, beginning only in the latter stages of meiotic prophase and ending in the round spermatid stage. In 96-kDa DNA ligase III-beta, the C-terminal 77 amino acids of DNA ligase III-alpha are replaced by a different 17- to 18-amino acid sequence. As reported previously, the 103-kDa DNA ligase III-alpha interacts with the DNA strand break repair protein encoded by the human XRCC1 gene. In contrast, the 96-kDa DNA ligase III-beta does not interact with XRCC1, indicating that DNA ligase III-beta may play a role in cellular functions distinct from the DNA repair pathways involving the DNA ligase III-alpha x XRCC1 complex. The distinct biochemical properties of DNA ligase III-beta, in combination with the tissue- and cell-type-specific expression of DNA ligase III-beta mRNA, suggest that this form of DNA ligase III is specifically involved in the completion of homologous recombination events that occur during meiotic prophase. PMID:9001252

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

    PubMed

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

    2015-11-15

    Vaccination is the most cost-effective way to control infectious diseases in cattle. However, many infectious diseases leading to severe economical losses worldwide still remain for which a really effective and safe vaccine is not available. These diseases are most often due to intracellular pathogens such as bacteria or viruses, which are, by their localization, protected from antibiotics and/or CD4(+) T cell-dependent humoral responses. We therefore postulated that strategies leading to induction of not only CD4(+) T cell responses but also CD8(+) cytotoxic T lymphocyte (CTL) responses against infected cells should be privileged in the development of new vaccines against problematic intracellular pathogens in bovines. CD40 signaling in antigen-presenting cells may lead to the induction of robust CD4-independent CTL responses and several studies, especially in mice, have used CD40 stimulation to promote CD8(+) T cell-mediated immunity. For example, we have recently shown that immunization of mice with heat-killed Staphylococcus aureus (HKSA) and agonistic anti-CD40 monoclonal antibodies elicits strong CTL responses capable of protecting mice from subsequent staphylococcal mastitis. Unfortunately, there is at present no tool available to efficiently stimulate CD40 in cattle. In this study, we therefore first produced a soluble recombinant trimeric form of the natural bovine CD40 ligand (sboCD40LT). We then observed that sboCD40LT was able to potently stimulate bovine cells in vitro. Finally, we provide evidence that immunization of cows with sboCD40LT combined with HKSA was able to significantly increase the number of both HKSA-specific CD4(+) and CD8(+) T cells in the draining lymph nodes. In conclusion, we suggest that this new molecular tool could help in the development of vaccine strategies against bovine diseases caused by intracellular pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Generating controlled reducing environments in aerobic recombinant Escherichia coli fermentations: effects on cell growth, oxygen uptake, heat shock protein expression, and in vivo CAT activity.

    PubMed

    Gill, R T; Cha, H J; Jain, A; Rao, G; Bentley, W E

    1998-07-20

    The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/microgram total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/microgram CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (sigma32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/microgram CAT min. ) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations.

  18. Toxicity evaluation of e-juice and its soluble aerosols generated by electronic cigarettes using recombinant bioluminescent bacteria responsive to specific cellular damages.

    PubMed

    Bharadwaj, Shiv; Mitchell, Robert J; Qureshi, Anjum; Niazi, Javed H

    2017-04-15

    Electronic-cigarettes (e-cigarette) are widely used as an alternative to traditional cigarettes but their safety is not well established. Herein, we demonstrate and validate an analytical method to discriminate the deleterious effects of e-cigarette refills (e-juice) and soluble e-juice aerosol (SEA) by employing stress-specific bioluminescent recombinant bacterial cells (RBCs) as whole-cell biosensors. These RBCs carry luxCDABE-operon tightly controlled by promoters that specifically induced to DNA damage (recA), superoxide radicals (sodA), heavy metals (copA) and membrane damage (oprF). The responses of the RBCs following exposure to various concentrations of e-juice/SEA was recorded in real-time that showed dose-dependent stress specific-responses against both the e-juice and vaporized e-juice aerosols produced by the e-cigarette. We also established that high doses of e-juice (4-folds diluted) lead to cell death by repressing the cellular machinery responsible for repairing DNA-damage, superoxide toxicity, ion homeostasis and membrane damage. SEA also caused the cellular damages but the cells showed enhanced bioluminescence expression without significant growth inhibition, indicating that the cells activated their global defense system to repair these damages. DNA fragmentation assay also revealed the disintegration of total cellular DNA at sub-toxic doses of e-juice. Despite their state of matter, the e-juice and its aerosols induce cytotoxicity and alter normal cellular functions, respectively that raises concerns on use of e-cigarettes as alternative to traditional cigarette. The ability of RBCs in detecting both harmful effects and toxicity mechanisms provided a fundamental understanding of biological response to e-juice and aerosols. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. The Use of Recombinant Pseudotype Virus-Like Particles Harbouring Inserted Target Antigen to Generate Antibodies against Cellular Marker p16INK4A

    PubMed Central

    Lasickienė, Rita; Gedvilaite, Alma; Norkiene, Milda; Simanaviciene, Vaida; Sezaite, Indre; Dekaminaviciute, Dovile; Shikova, Evelina; Zvirbliene, Aurelija

    2012-01-01

    Protein engineering provides an opportunity to generate new immunogens with desired features. Previously, we have demonstrated that hamster polyomavirus major capsid protein VP1-derived virus-like particles (VLPs) are highly immunogenic and can be employed for the insertion of foreign epitopes at certain surface-exposed positions. In the current study, we have designed pseudotype VLPs consisting of an intact VP1 protein and VP2 protein fused with the target antigen—cellular marker p16INK4A—at its N terminus. Both proteins coexpressed in yeast were self-assembled to pseudotype VLPs harbouring the inserted antigen on the surface. The pseudotype VLPs were used for generation of antibodies against p16INK4A that represents a potential biomarker for cells transformed by high-risk human papillomavirus (HPV). The pseudotype VLPs induced in immunized mice a strong immune response against the target antigen. The antisera raised against pseudotype VLPs showed specific immunostaining of p16INK4A protein in malignant cervical tissue. Spleen cells of the immunized mice were used to generate monoclonal antibodies against p16INK4A protein. The specificity of antibodies was proven by the immunostaining of HPV-transformed cells. In conclusion, the current study demonstrates the potential of pseudotype VLPs with inserted target antigen as a new type of immunogens to generate antibodies of high diagnostic value. PMID:22629125

  20. Distal Radioulnar Joint Instability

    PubMed Central

    Mirghasemi, Ali R.; Lee, Daniel J.; Rahimi, Narges; Rashidinia, Shervin

    2015-01-01

    Distal radioulnar joint (DRUJ) instability is a common clinical condition but a frequently missed diagnosis. Both surgical and nonsurgical treatments are possible for chronic cases of DRUJ instability. Nonsurgical treatment can be considered as the primary therapy in less active patients, while surgery should be considered to recover bone and ligament injuries if nonsurgical treatment fails to restore forearm stability and function. The appropriate choice of treatment depends on the individual patient and specific derangement of the DRUJ PMID:26328241

  1. Rotor internal friction instability

    NASA Technical Reports Server (NTRS)

    Bently, D. E.; Muszynska, A.

    1985-01-01

    Two aspects of internal friction affecting stability of rotating machines are discussed. The first role of internal friction consists of decreasing the level of effective damping during rotor subsynchronous and backward precessional vibrations caused by some other instability mechanisms. The second role of internal frication consists of creating rotor instability, i.e., causing self-excited subsynchronous vibrations. Experimental test results document both of these aspects.

  2. State Instability and Terrorism

    DTIC Science & Technology

    2010-01-01

    terrorism is a form ( Durkheim , 1930 [1951]; Useem, 1998). In addit