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

DTIC Science & Technology

2011-01-01

Regular Article Kinetic modeling sheds light on the mode of action of recombinant factor VIIa on thrombin generation Alexander Y. Mitrophanov...its effects on the quantitative parameters of thrombin generation. For recombinant activated factor VII (rFVIIa) ― a promising hemostasis-inducing...modulate thrombin production , it is necessary to identify rFVIIa-induced effects that are compatible with the available biochemical knowledge about

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.

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

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.

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...

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.

Insights into the chicken IgY with emphasis on the generation and applications of chicken recombinant monoclonal antibodies.

PubMed

Lee, Warren; Syed Atif, Ali; Tan, Soo Choon; Leow, Chiuan Herng

2017-08-01

The advantages of chicken (Gallus gallus domesticus) antibodies as immunodiagnostic and immunotherapeutic biomolecules has only been recently recognized. Even so, chicken antibodies remain less-well characterized than their mammalian counterparts. This review aims at providing a current overview of the structure, function, development and generation of chicken antibodies. Additionally, brief but comprehensive insights into current knowledge pertaining to the immunogenetic framework and diversity-generation of the chicken immunoglobulin repertoire which have contributed to the establishment of recombinant chicken mAb-generating methods are discussed. Focus is provided on the current methods used to generate antibodies from chickens with added emphasis on the generation of recombinant chicken mAbs and its derivative formats. The advantages and limitations of established protocols for the generation of chicken mAbs are highlighted. The various applications of recombinant chicken mAbs and its derivative formats in immunodiagnostics and immunotherapy are further detailed. Copyright © 2017 Elsevier B.V. All rights reserved.

Subcritical saturation of the magnetorotational instability through mean magnetic field generation

NASA Astrophysics Data System (ADS)

Xie, Jin-Han; Julien, Keith; Knobloch, Edgar

2018-03-01

The magnetorotational instability is widely believed to be responsible for outward angular momentum transport in astrophysical accretion discs. The efficiency of this transport depends on the amplitude of this instability in the saturated state. We employ an asymptotic expansion based on an explicit, astrophysically motivated time-scale separation between the orbital period, Alfvén crossing time and viscous or resistive dissipation time-scales, originally proposed by Knobloch and Julien, to formulate a semi-analytical description of the saturated state in an incompressible disc. In our approach a Keplerian shear flow is maintained by the central mass but the instability saturates via the generation of a mean vertical magnetic field. The theory assumes that the time-averaged angular momentum flux and the radial magnetic flux are constant and determines both self-consistently. The results predict that, depending on parameters, steady saturation may be supercritical or subcritical, and in the latter case that the upper (lower) solution branch is always stable (unstable). The angular momentum flux is always outward, consistent with the presence of accretion, and for fixed wavenumber peaks in the subcritical regime. The limit of infinite Reynolds number at large but finite magnetic Reynolds number is also discussed.

Generation of a Recombinant Akabane Virus Expressing Enhanced Green Fluorescent Protein

PubMed Central

Takenaka-Uema, Akiko; Murata, Yousuke; Gen, Fumihiro; Ishihara-Saeki, Yukari; Watanabe, Ken-ichi; Uchida, Kazuyuki; Kato, Kentaro; Murakami, Shin; Haga, Takeshi

2015-01-01

ABSTRACT We generated a recombinant Akabane virus (AKAV) expressing enhanced green fluorescence protein (eGFP-AKAV) by using reverse genetics. We artificially constructed an ambisense AKAV S genome encoding N/NSs on the negative-sense strand, and eGFP on the positive-sense strand with an intergenic region (IGR) derived from the Rift Valley fever virus (RVFV) S genome. The recombinant virus exhibited eGFP fluorescence and had a cytopathic effect in cell cultures, even after several passages. These results indicate that the gene encoding eGFP in the ambisense RNA could be stably maintained. Transcription of N/NSs and eGFP mRNAs of eGFP-AKAV was terminated within the IGR. The mechanism responsible for this appears to be different from that in RVFV, where the termination sites for N and NSs are determined by a defined signal sequence. We inoculated suckling mice intraperitoneally with eGFP-AKAV, which resulted in neurological signs and lethality equivalent to those seen for the parent AKAV. Fluorescence from eGFP in frozen brain slices from the eGFP-AKAV-infected mice was localized to the cerebellum, pons, and medulla oblongata. Our approach to producing a fluorescent virus, using an ambisense genome, helped obtain eGFP-AKAV, a fluorescent bunyavirus whose viral genes are intact and which can be easily visualized. IMPORTANCE AKAV is the etiological agent of arthrogryposis-hydranencephaly syndrome in ruminants, which causes considerable economic loss to the livestock industry. We successfully generated a recombinant enhanced green fluorescent protein-tagged AKAV containing an artificial ambisense S genome. This virus could become a useful tool for analyzing AKAV pathogenesis in host animals. In addition, our approach of using an ambisense genome to generate an orthobunyavirus stably expressing a foreign gene could contribute to establishing alternative vaccine strategies, such as bivalent vaccine virus constructs, for veterinary use against infectious diseases. PMID

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.

The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

PubMed Central

Wahba, Lamia; Gore, Steven K; Koshland, Douglas

2013-01-01

Genome instability in yeast and mammals is caused by RNA–DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation requires Rad51p and Rad52p. These proteins normally promote DNA–DNA strand exchange in homologous recombination. We suggest they also directly promote the DNA–RNA strand exchange necessary for hybrid formation since we observed accumulation of Rad51p at a model hybrid-forming locus. Furthermore, we provide evidence that Rad51p mediates hybridization of transcripts to homologous chromosomal loci distinct from their site of synthesis. This hybrid formation in trans amplifies the genome-destabilizing potential of RNA and broadens the exclusive co-transcriptional models that pervade the field. The deleterious hybrid-forming activity of Rad51p is counteracted by Srs2p, a known Rad51p antagonist. Thus Srs2p serves as a novel anti-hybrid mechanism in vivo. DOI: http://dx.doi.org/10.7554/eLife.00505.001 PMID:23795288

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Shimin, E-mail: gsm861@126.com; Mei, Liquan, E-mail: lqmei@mail.xjtu.edu.cn

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 numericallymore » 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.« less

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

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

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

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.

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

Enhanced homologous recombination is induced by alpha-particle radiation in somatic cells of Arabidopsis thaliana

NASA Astrophysics Data System (ADS)

Bian, Po; Liu, Ping; Wu, Yuejin

Almost 9 percent of cosmic rays which strike the earth's atmosphere are alpha particles. As one of the ionizing radiations (IR), its biological effects have been widely studied. However, the plant genomic instability induced by alpha-particle radiation was not largely known. In this research, the Arabidopsis thaliana transgenic for GUS recombination substrate was used to evaluate the genomic instability induced by alpha-particle radiation (3.3MeV). The pronounced effects of systemic exposure to alpha-particle radiation on the somatic homologous recombination frequency (HRF) were found at different doses. The 10Gy dose of radiation induced the maximal HRF which was 1.9-fold higher than the control. The local radiation of alpha-particle (10Gy) on root also resulted in a 2.5-fold increase of somatic HRF in non-radiated aerial plant, indicating that the signal(s) of genomic instability was transferred to non-radiated parts and initiated their genomic instability. Concurrent treatment of seedlings of Arabidopsis thaliana with alpha-particle and DMSO(ROS scavenger) both in systemic and local radiation signifi- cantly suppressed the somatic HR, indicating that the free radicals produced by alpha-particle radiation took part in the production of signal of genomic instability rather than the signal transfer. Key words: alpha-particle radiation, somatic homologous recombination, genomic instability

Ultra wide band supercontinuum generation in air-silica holey fibers by SHG-induced modulation instabilities.

PubMed

Tombelaine, Vincent; Lesvigne, Christelle; Leproux, Philippe; Grossard, Ludovic; Couderc, Vincent; Auguste, Jean-Louis; Blondy, Jean-Marc; Huss, Guillaume; Pioger, Paul-Henri

2005-09-19

Second harmonic generation in an air-silica microstructured optical fiber pumped by subnanosecond pulses is used in order to initiate modulation instability processes in normal and anomalous dispersion regimes. This allows us to generate an ultra wide and flat supercontinuum (350-1750 nm), covering the entire transparency window of silica and exhibiting a singlemode transverse profile in visible range.

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.

Wave-Kinetic Simulations of the Nonlinear Generation of Electromagnetic VLF Waves through Velocity Ring Instabilities

NASA Astrophysics Data System (ADS)

Ganguli, G.; Crabtree, C. E.; Rudakov, L.; Mithaiwala, M.

2014-12-01

Velocity ring instabilities are a common naturally occuring magnetospheric phenomenon that can also be generated by man made ionospheric experiments. These instabilities are known to generate lower-hybrid waves, which generally cannot propagte out of the source region. However, nonlinear wave physics can convert these linearly driven electrostatic lower-hybrid waves into electromagnetic waves that can escape the source region. These nonlinearly generated waves can be an important source of VLF turbulence that controls the trapped electron lifetime in the radiation belts. We develop numerical solutions to the wave-kinetic equation in a periodic box including the effects of nonlinear (NL) scattering (nonlinear Landau damping) of Lower-hybrid waves giving the evolution of the wave-spectra in wavenumber space. Simultaneously we solve the particle diffusion equation of both the background plasma particles and the ring ions, due to both linear and nonlinear Landau resonances. At initial times for cold ring ions, an electrostatic beam mode is excited, while the kinetic mode is stable. As the instability progresses the ring ions heat, the beam mode is stabilized, and the kinetic mode destabilizes. When the amplitude of the waves becomes sufficient the lower-hybrid waves are scattered (by either nearly unmagnetized ions or magnetized electrons) into electromagnetic magnetosonic waves [Ganguli et al 2010]. The effect of NL scattering is to limit the amplitude of the waves, slowing down the quasilinear relaxation time and ultimately allowing more energy from the ring to be liberated into waves [Mithaiwala et al. 2011]. The effects of convection out of the instability region are modeled, additionally limiting the amplitude of the waves, allowing further energy to be liberated from the ring [Scales et al., 2012]. Results are compared to recent 3D PIC simulations [Winske and Duaghton 2012].

Reevaluation of the Reliability and Usefulness of the Somatic Homologous Recombination Reporter Lines

PubMed Central

Ülker, Bekir; Hommelsheim, Carl Maximilian; Berson, Tobias; Thomas, Stefan; Chandrasekar, Balakumaran; Olcay, Ahmet Can; Berendzen, Kenneth Wayne; Frantzeskakis, Lamprinos

2012-01-01

A widely used approach for assessing genome instability in plants makes use of somatic homologous recombination (SHR) reporter lines. Here, we review the published characteristics and uses of SHR lines. We found a lack of detailed information on these lines and a lack of sufficient evidence that they report only homologous recombination. We postulate that instead of SHR, these lines might be reporting a number of alternative stress-induced stochastic events known to occur at transcriptional, posttranscriptional, and posttranslational levels. We conclude that the reliability and usefulness of the somatic homologous recombination reporter lines requires revision. Thus, more detailed information about these reporter lines is needed before they can be used with confidence to measure genome instability, including the complete sequences of SHR constructs, the genomic location of reporter genes and, importantly, molecular evidence that reconstituted gene expression in these lines is indeed a result of somatic recombination. PMID:23144181

Bypass of lethality with mosaic mice generated by Cre-loxP-mediated recombination.

PubMed

Betz, U A; Vosshenrich, C A; Rajewsky, K; Müller, W

1996-10-01

The analysis of gene function based on the generation of mutant mice by homologous recombination in embryonic stem cells is limited if gene disruption results in embryonic lethality. Mosaic mice, which contain a certain proportion of mutant cells in all organs, allow lethality to be circumvented and the potential of mutant cells to contribute to different cell lineages to be analyzed. To generate mosaic animals, we used the bacteriophage P1-derived Cre-loxP recombination system, which allows gene alteration by Cre-mediated deletion of loxP-flanked gene segments. We generated nestin-cre transgenic mouse lines, which expressed the Cre recombinase under the control of the rat nestin promoter and its second intron enhancer. In crosses to animals carrying a loxP-flanked target gene, partial deletion of the loxP-flanked allele occurred before day 10.5 post coitum and was detectable in all adult organs examined, including germ-line cells. Using this approach, we generated mosaic mice containing cells deficient in the gamma-chain of the interleukin-2 receptor (IL-2R gamma); in these animals, the IL-2R gamma-deficient cells were underrepresented in the thymus and spleen. Because mice deficient in DNA polymerase beta die perinatally, we studied the effects of DNA polymerase beta deficiency in mosaic animals. We found that some of the mosaic polymerase beta-deficient animals were viable, but were often reduced in size and weight. The fraction of DNA polymerase beta-deficient cells in mosaic embryos decreased during embryonic development, presumably because wild-type cells had a competitive advantage. The nestin-cre transgenic mice can be used to generate mosaic animals in which target genes are mutated by Cre-mediated recombination of loxP-flanked target genes. By using mosaic animals, embryonic lethality can be bypassed and cell lineages for whose development a given target gene is critical can be identified. In the case of DNA polymerase beta, deficient cells are already

Genome instabilities arising from ribonucleotides in DNA.

PubMed

Klein, Hannah L

2017-08-01

Genomic DNA is transiently contaminated with ribonucleotide residues during the process of DNA replication through misincorporation by the replicative DNA polymerases α, δ and ε, and by the normal replication process on the lagging strand, which uses RNA primers. These ribonucleotides are efficiently removed during replication by RNase H enzymes and the lagging strand synthesis machinery. However, when ribonucleotides remain in DNA they can distort the DNA helix, affect machineries for DNA replication, transcription and repair, and can stimulate genomic instabilities which are manifest as increased mutation, recombination and chromosome alterations. The genomic instabilities associated with embedded ribonucleotides are considered here, along with a discussion of the origin of the lesions that stimulate particular classes of instabilities. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Generation and purification of recombinant fimbrillin from Porphyromonas (Bacteroides) gingivalis 381.

PubMed Central

Washington, O R; Deslauriers, M; Stevens, D P; Lyford, L K; Haque, S; Yan, Y; Flood, P M

1993-01-01

Fimbrillin is the major subunit protein of fimbriae from the human periodontal pathogen Porphyromonas (Bacteroides) gingivalis. We describe here the generation and initial characterization of recombinant fimbrillin (r-fimbrillin) isolated from P. gingivalis 381. A fragment of DNA encoding the gene for fimbrillin was generated by polymerase chain reaction and cloned into the expression vector pET11b. Plasmids containing the recombinant gene were transfected into Escherichia coli. Clones were selected on plates for ampicillin resistance and individually screened by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for protein production after activation with IPTG (isopropyl-beta-D- thiogalactopyranoside). One clone, OW0.2, produced significant amounts of a 42-kDa protein after induction with IPTG. This clone contained the pET11b plasmid with a 1-kb insert that had sequence homology to the gene encoding fimbrillin. The majority of recombinant protein from clone OW0.2 was found in the cytoplasm within inclusion bodies. Protein aggregates were solubilized in 8 M urea, and SDS-PAGE analysis showed two major protein bands, one at 42 kDa and the other at 17 kDa. These two proteins coeluted from a DEAE-Sepharose column at 0.15 M NaCl and were reactive to rabbit antiserum to fimbrillin in a Western blot (immunoblot). A preparation giving a single protein band at 42 kDa in SDS-PAGE was obtained by size fractionation by using continuous-elution electrophoresis. Lymph node cells from animals immunized with either fimbrillin from P. gingivalis or r-fimbrillin showed antigen-specific proliferation to both P. gingivalis fimbrillin and r-fimbrillin in an in vitro recall assay. Therefore, it appears that r-fimbrillin is chemically, antigenically, and serologically identical to fimbrillin isolated from P. gingivalis 381. Images PMID:8094377

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

Longitudinal instabilities of the experimentally generated laser accelerated ion beam relevant to fast ignition

NASA Astrophysics Data System (ADS)

Khoshbinfar, S.

2017-11-01

The advent of laser-assisted ion acceleration technology promises an alternative candidate to conventional accelerator drivers used in inertial confinement fusion. The experimental generation of quasi-monoenergetic heavier ion species i.e. carbon and aluminum, applicable to fast ignition studies has been recently reported. The propagation of these energetic ions may impact on the proper ignition phase through growing of micro-instabilities of beam-plasma system. The growth of flow-aligned instabilities is much more important for heavier ions transport in the dense plasma. Here, we have presented a general non-relativistic one-dimensional dispersion relation of cold fluid model as well as corresponding kinetic theory of incident ion beam with atomic number, Zb enters into a fast ignition DT plasma. The longitudinal instabilities of some selected average energies of experimentally generated C6+ (EC=50, 100 and 200 MeV with δE/E ∼ 10 %) and Al11+ (EAl=150 and 300 MeV with δE/E ∼25%) quasi-monoenergetic beams were examined and beam-plasma system stable configuration have been then derived. It has been shown that in the kinetic theory framework, carbon and aluminum ions may be completely stabilized by the combination of beam to plasma density ratio (αb) and plasma temperature (Tp) of ignition phase parameters. Moreover, in complete stabilization, αb parameter of aluminum beam is an order of magnitude lower than carbon.

The typical RB76 recombination breakpoint of the invasive recombinant tomato yellow leaf curl virus of Morocco can be generated experimentally but is not positively selected in tomato.

PubMed

Belabess, Z; Urbino, C; Granier, M; Tahiri, A; Blenzar, A; Peterschmitt, M

2018-01-02

TYLCV-IS76 is an unusual recombinant between the highly recombinogenic tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), two Mediterranean begomoviruses (Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, it has a TYLCSV derived fragment of only 76 nucleotides, and has replaced its parental viruses in natural conditions (Morocco, Souss region). The viral population shift coincided with the deployment of the popular Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in such resistant plants. However, although Ty-1 cultivars were extensively used in Mediterranean countries, TYLCV-IS76 was not reported outside Morocco. This, in combination with its unusual recombination pattern suggests that it was generated through a rare and possibly multistep process. The potential generation of a recombination breakpoint (RB) at locus 76 (RB76) was investigated over time in 10 Ty-1 resistant and 10 nearly isogenic susceptible tomato plants co-inoculated with TYLCV and TYLCSV clones. RB76 could not be detected in the recombinant progeny using the standard PCR/sequencing approach that was previously designed to monitor the emergence of TYLCV-IS76 in Morocco. Using a more sensitive PCR test, RB76 was detected in one resistant and five susceptible plants. The results are consistent with a very low intra-plant frequency of RB76 bearing recombinants throughout the test and support the hypothesis of a rare emergence of TYLCV-IS76. More generally, RBs were more scattered in resistant than in susceptible plants and an unusual RB at position 141 (RB141) was positively selected in the resistant cultivar; interestingly, RB141 bearing recombinants were detected in resistant tomato plants from the field. Scenarios of TYLCV-IS76 pre-emergence are proposed. Copyright © 2017 Elsevier B.V. All rights reserved.

Supersonic jet noise generated by large scale instabilities

NASA Technical Reports Server (NTRS)

Seiner, J. M.; Mclaughlin, D. K.; Liu, C. H.

1982-01-01

The role of large scale wavelike structures as the major mechanism for supersonic jet noise emission is examined. With the use of aerodynamic and acoustic data for low Reynolds number, supersonic jets at and below 70 thousand comparisons are made with flow fluctuation and acoustic measurements in high Reynolds number, supersonic jets. These comparisons show that a similar physical mechanism governs the generation of sound emitted in he principal noise direction. These experimental data are further compared with a linear instability theory whose prediction for the axial location of peak wave amplitude agrees satisfactorily with measured phased averaged flow fluctuation data in the low Reynolds number jets. The agreement between theory and experiment in the high Reynolds number flow differs as to the axial location for peak flow fluctuations and predicts an apparent origin for sound emission far upstream of the measured acoustic data.

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

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.

Modulational-instability-induced supercontinuum generation with saturable nonlinear response

NASA Astrophysics Data System (ADS)

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

2010-07-01

We theoretically investigate the supercontinuum generation (SCG) on the basis of modulational instability (MI) in liquid-core photonic crystal fibers (LCPCF) with CS2-filled central core. The effect of saturable nonlinearity of LCPCF on SCG in the femtosecond regime is studied using an appropriately modified nonlinear Schrödinger equation. We also compare the MI induced spectral broadening with SCG obtained by soliton fission. To analyze the quality of the pulse broadening, we study the coherence of the SC pulse numerically. It is evident from the numerical simulation that the response of the saturable nonlinearity suppresses the broadening of the pulse. We also observe that the MI induced SCG in the presence of saturable nonlinearity degrades the coherence of the SCG pulse when compared to unsaturated medium.

Modulational-instability-induced supercontinuum generation with saturable nonlinear response

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2010-07-15

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

A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs.

PubMed

Maye, Peter; Stover, Mary Louise; Liu, Yaling; Rowe, David W; Gong, Shiaochin; Lichtler, Alexander C

2009-03-13

Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP) reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1) subclone genes of interest into BAC linking vectors, (2) insert desired reporter genes into respective genes and (3) link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

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

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.

Characterization of Helper Virus-Independent Cytopathogenic Classical Swine Fever Virus Generated by an In Vivo RNA Recombination System

PubMed Central

Gallei, Andreas; Rümenapf, Till; Thiel, Heinz-Jürgen; Becher, Paul

2005-01-01

Molecular analyses revealed that most cytopathogenic (cp) pestivirus strains evolve from noncytopathogenic (noncp) viruses by nonhomologous RNA recombination. In contrast to bovine viral diarrhea virus (BVDV), cp classical swine fever virus (CSFV) field isolates were rarely detected and always represented helper virus-dependent subgenomes. To investigate RNA recombination in more detail, we recently established an in vivo system allowing the efficient generation of recombinant cp BVDV strains in cell culture after transfecting a synthetic subgenomic and nonreplicatable transcript into cells being infected with noncp BVDV (A. Gallei, A. Pankraz, H.-J. Thiel, and P. Becher, J. Virol. 78:6271-6281, 2004). Using an analogous approach, the first helper virus-independent cp CSFV strain (CP G1) has now been generated by RNA recombination. Accordingly, this study demonstrates the applicability of RNA recombination for designing new viral RNA genomes. The genomic RNA of CP G1 has a calculated size of 18.139 kb, almost 6 kb larger than all previously described CSFV genomes. It contains cellular sequences encoding a polyubiquitin fragment directly upstream of the nonstructural protein NS3 coding gene together with a duplication of viral sequences. CP G1 induces a cytopathic effect on different tissue culture cell lines from pigs and cattle. Subsequent analyses addressed growth kinetics, expression of NS3, and genetic stability of CP G1. PMID:15681445

Recombinant Modified Vaccinia Virus Ankara Generating Ebola Virus-Like Particles.

PubMed

Schweneker, Marc; Laimbacher, Andrea S; Zimmer, Gert; Wagner, Susanne; Schraner, Elisabeth M; Wolferstätter, Michael; Klingenberg, Marieken; Dirmeier, Ulrike; Steigerwald, Robin; Lauterbach, Henning; Hochrein, Hubertus; Chaplin, Paul; Suter, Mark; Hausmann, Jürgen

2017-06-01

There are currently no approved therapeutics or vaccines to treat or protect against the severe hemorrhagic fever and death caused by Ebola virus (EBOV). Ebola virus-like particles (EBOV VLPs) consisting of the matrix protein VP40, the glycoprotein (GP), and the nucleoprotein (NP) are highly immunogenic and protective in nonhuman primates against Ebola virus disease (EVD). We have constructed a modified vaccinia virus Ankara-Bavarian Nordic (MVA-BN) recombinant coexpressing VP40 and GP of EBOV Mayinga and the NP of Taï Forest virus (TAFV) (MVA-BN-EBOV-VLP) to launch noninfectious EBOV VLPs as a second vaccine modality in the MVA-BN-EBOV-VLP-vaccinated organism. Human cells infected with either MVA-BN-EBOV-VLP or MVA-BN-EBOV-GP showed comparable GP expression levels and transport of complex N-glycosylated GP to the cell surface. Human cells infected with MVA-BN-EBOV-VLP produced large amounts of EBOV VLPs that were decorated with GP spikes but excluded the poxviral membrane protein B5, thus resembling authentic EBOV particles. The heterologous TAFV NP enhanced EBOV VP40-driven VLP formation with efficiency similar to that of the homologous EBOV NP in a transient-expression assay, and both NPs were incorporated into EBOV VLPs. EBOV GP-specific CD8 T cell responses were comparable between MVA-BN-EBOV-VLP- and MVA-BN-EBOV-GP-immunized mice. The levels of EBOV GP-specific neutralizing and binding antibodies, as well as GP-specific IgG1/IgG2a ratios induced by the two constructs, in mice were also similar, raising the question whether the quality rather than the quantity of the GP-specific antibody response might be altered by an EBOV VLP-generating MVA recombinant. IMPORTANCE The recent outbreak of Ebola virus (EBOV), claiming more than 11,000 lives, has underscored the need to advance the development of safe and effective filovirus vaccines. Virus-like particles (VLPs), as well as recombinant viral vectors, have proved to be promising vaccine candidates. Modified

Homologous Recombination Repair Protects Against Particulate Chromate-induced Chromosome Instability in Chinese Hamster Cells

PubMed Central

Stackpole, Megan M.; Wise, Sandra S.; Duzevik, Eliza Grlickova; Munroe, Ray C.; Thompson, W. Douglas; Thacker, John; Thompson, Larry H.; Hinz, John M.; Wise, John Pierce

2008-01-01

Particulate hexavalent chromium [Cr(VI)] compounds are well-established human carcinogens. Cr(VI)-induced tumors are characterized by chromosomal instability (CIN); however, the mechanisms of this effect are unknown. We investigated the hypothesis that homologous recombination (HR) repair of DNA double strand breaks protect cells from Cr(VI)-induced CIN by focusing on the XRCC3 and RAD51C genes, which play an important role in cellular resistance to DNA double strand breaks. We used Chinese hamster cells defective in each HR gene (irs3 for RAD51C and irs1SF for XRCC3) and compared with their wildtype parental and cDNA-complemented controls. We found that the intracellular Cr ion levels varied among the cell lines after particulate chromate treatment. Importantly, accounting for differences in Cr ion levels, we discovered that XRCC3 and RAD51C cells treated with lead chromate had increased cytotoxicity and chromosomal aberrations, relative to wild-type and cDNA-complimented cells. We also observed the emergence of high levels of chromatid exchanges in the two mutant cell lines. For example, 1 ug/cm2 lead chromate induced 20 and 32 exchanges in XRCC3- and RAD51C-deficient cells, respectively, whereas no exchanges were detected in the wildtype and cDNA-complemented cells. These observations suggest that HR protects cells from Cr(VI)-induced CIN, consistent with the ability of particulate Cr(VI) to induce double strand breaks. PMID:17662313

Functional bottlenecks for generation of HIV-1 intersubtype Env recombinants.

PubMed

Bagaya, Bernard S; Vega, José F; Tian, Meijuan; Nickel, Gabrielle C; Li, Yuejin; Krebs, Kendall C; Arts, Eric J; Gao, Yong

2015-05-23

Intersubtype recombination is a powerful driving force for HIV evolution, impacting both HIV-1 diversity within an infected individual and within the global epidemic. This study examines if viral protein function/fitness is the major constraint shaping selection of recombination hotspots in replication-competent HIV-1 progeny. A better understanding of the interplay between viral protein structure-function and recombination may provide insights into both vaccine design and drug development. In vitro HIV-1 dual infections were used to recombine subtypes A and D isolates and examine breakpoints in the Env glycoproteins. The entire env genes of 21 A/D recombinants with breakpoints in gp120 were non-functional when cloned into the laboratory strain, NL4-3. Likewise, cloning of A/D gp120 coding regions also produced dead viruses with non-functional Envs. 4/9 replication-competent viruses with functional Env's were obtained when just the V1-V5 regions of these same A/D recombinants (i.e. same A/D breakpoints as above) were cloned into NL4-3. These findings on functional A/D Env recombinants combined with structural models of Env suggest a conserved interplay between the C1 domain with C5 domain of gp120 and extracellular domain of gp41. Models also reveal a co-evolution within C1, C5, and ecto-gp41 domains which might explain the paucity of intersubtype recombination in the gp120 V1-V5 regions, despite their hypervariability. At least HIV-1 A/D intersubtype recombination in gp120 may result in a C1 from one subtype incompatible with a C5/gp41 from another subtype.

Local shear instabilities in weakly ionized, weakly magnetized disks

NASA Technical Reports Server (NTRS)

Blaes, Omer M.; Balbus, Steven A.

1994-01-01

We extend the analysis of axisymmetric magnetic shear instabilities from ideal magnetohydrodynamic (MHD) flows to weakly ionized plasmas with coupling between ions and neutrals caused by collisions, ionization, and recombination. As part of the analysis, we derive the single-fluid MHD dispersion relation without invoking the Boussinesq approximation. This work expands the range of applications of these instabilities from fully ionized accretion disks to molecular disks in galaxies and, with somewhat more uncertainty, to protostellar disks. Instability generally requires the angular velocity to decrease outward, the magnetic field strengths to be subthermal, and the ions and neutrals to be sufficiently well coupled. If ionization and recombination processes can be neglected on an orbital timescale, adequate coupling is achieved when the collision frequency of a given neutral with the ions exceeds the local epicyclic freqency. When ionization equilibrium is maintained on an orbital timescale, a new feature is present in the disk dynamics: in contrast to a single-fluid system, subthermal azimuthal fields can affect the axisymmetric stability of weakly ionized two-fluid systems. We discuss the underlying causes for this behavior. Azimuthal fields tend to be stabilizing under these circumstances, and good coupling between the neutrals and ions requires the collision frequency to exceed the epicyclic frequency by a potentially large secant factor related to the magnetic field geometry. When the instability is present, subthermal azimuthal fields may also reduce the growth rate unless the collision frequency is high, but this is important only if the field strengths are very subthermal and/or the azimuthal field is the dominant field component. We briefly discuss our results in the context of the Galactic center circumnuclear disk, and suggest that the shear instability might be present there, and be responsible for the observed turbulent motions.

Evidence for Secondary Flux Rope Generated by the Electron Kelvin-Helmholtz Instability in a Magnetic Reconnection Diffusion Region

NASA Astrophysics Data System (ADS)

Zhong, Z. H.; Tang, R. X.; Zhou, M.; Deng, X. H.; Pang, Y.; Paterson, W. R.; Giles, B. L.; Burch, J. L.; Tobert, R. B.; Ergun, R. E.; Khotyaintsev, Y. V.; Lindquist, P.-A.

2018-02-01

Secondary flux ropes are suggested to play important roles in energy dissipation and particle acceleration during magnetic reconnection. However, their generation mechanism is not fully understood. In this Letter, we present the first direct evidence that a secondary flux rope was generated due to the evolution of an electron vortex, which was driven by the electron Kelvin-Helmholtz instability in an ion diffusion region as observed by the Magnetospheric Multiscale mission. The subion scale (less than the ion inertial length) flux rope was embedded within the electron vortex, which contained a secondary electron diffusion region at the trailing edge of the flux rope. We propose that intense electron shear flow produced by reconnection generated the electron Kelvin-Helmholtz vortex, which induced a secondary reconnection in the exhaust of the primary X line and then led to the formation of the flux rope. This result strongly suggests that secondary electron Kelvin-Helmholtz instability is important for reconnection dynamics.

Evidence for Secondary Flux Rope Generated by the Electron Kelvin-Helmholtz Instability in a Magnetic Reconnection Diffusion Region.

PubMed

Zhong, Z H; Tang, R X; Zhou, M; Deng, X H; Pang, Y; Paterson, W R; Giles, B L; Burch, J L; Tobert, R B; Ergun, R E; Khotyaintsev, Y V; Lindquist, P-A

2018-02-16

Secondary flux ropes are suggested to play important roles in energy dissipation and particle acceleration during magnetic reconnection. However, their generation mechanism is not fully understood. In this Letter, we present the first direct evidence that a secondary flux rope was generated due to the evolution of an electron vortex, which was driven by the electron Kelvin-Helmholtz instability in an ion diffusion region as observed by the Magnetospheric Multiscale mission. The subion scale (less than the ion inertial length) flux rope was embedded within the electron vortex, which contained a secondary electron diffusion region at the trailing edge of the flux rope. We propose that intense electron shear flow produced by reconnection generated the electron Kelvin-Helmholtz vortex, which induced a secondary reconnection in the exhaust of the primary X line and then led to the formation of the flux rope. This result strongly suggests that secondary electron Kelvin-Helmholtz instability is important for reconnection dynamics.

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.

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.

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.

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.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Xiangrong, E-mail: xrfu@lanl.gov; Cowee, Misa M.; Winske, Dan

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 electronmore » 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.« less

Generation Dependent Ultrafast Charge Separation and Recombination in a Pyrene-Viologen Family of Dendrons.

PubMed

Gong, Zheng; Bao, Jianhua; Nagai, Keiji; Iyoda, Tomokazu; Kawauchi, Takehiro; Piotrowiak, Piotr

2016-05-12

The ability of a dendritic network to intercept electrons and extend the lifetime of a short-lived photoinduced charge separated (CS) state was investigated in a homologous family of methyl viologen (MV(2+)) dendrons spanning four generations, G0 through G3. The CS state in the parent pyrene-methylene-viologen G0 system with a single acceptor exhibits an extremely short lifetime of τ = 0.72 ps. The expansion of the viologen network introduces slower components to the recombination kinetics by allowing the injected electron to migrate further away from the donor. The long-lived fraction of the population increases monotonically in the order G3 > G2 > G1 > G0, while the respective recombination rates decrease. In the highest generation of the dendron ∼14% of the CS state population experiences a 10-fold or greater lifetime extension. Long range tunneling across multiple viologen units and sequential site-to-site hopping both contribute to the overall effect. The large excess energy deposited in the apical viologen upon charge separation and the presence of an extended network of low lying π-orbitals likely facilitate shuttling the electron further down the dendron.

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

NASA Technical Reports Server (NTRS)

Leib, S. J.

1985-01-01

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

First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing

PubMed Central

Haas, Bernhard; Bauer, Bernd; Zhang, Sherry; Fiss, Ellen H.; Hillman, Grantland; Hamilton, Aaron T.; Mehta, Rochak; Heil, Marintha L.; Marins, Ed G.; Santner, Brigitte I.; Kessler, Harald H.

2017-01-01

Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189–3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2) and Azerbaijan (n = 1), the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment. PMID:28742818

First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing.

PubMed

Stelzl, Evelyn; Haas, Bernhard; Bauer, Bernd; Zhang, Sherry; Fiss, Ellen H; Hillman, Grantland; Hamilton, Aaron T; Mehta, Rochak; Heil, Marintha L; Marins, Ed G; Santner, Brigitte I; Kessler, Harald H

2017-01-01

Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189-3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2) and Azerbaijan (n = 1), the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment.

Kinase-dead ATM protein causes genomic instability and early embryonic lethality in mice.

PubMed

Yamamoto, Kenta; Wang, Yunyue; Jiang, Wenxia; Liu, Xiangyu; Dubois, Richard L; Lin, Chyuan-Sheng; Ludwig, Thomas; Bakkenist, Christopher J; Zha, Shan

2012-08-06

Ataxia telangiectasia (A-T) mutated (ATM) kinase orchestrates deoxyribonucleic acid (DNA) damage responses by phosphorylating numerous substrates implicated in DNA repair and cell cycle checkpoint activation. A-T patients and mouse models that express no ATM protein undergo normal embryonic development but exhibit pleiotropic DNA repair defects. In this paper, we report that mice carrying homozygous kinase-dead mutations in Atm (Atm(KD/KD)) died during early embryonic development. Atm(KD/-) cells exhibited proliferation defects and genomic instability, especially chromatid breaks, at levels higher than Atm(-/-) cells. Despite this increased genomic instability, Atm(KD/-) lymphocytes progressed through variable, diversity, and joining recombination and immunoglobulin class switch recombination, two events requiring nonhomologous end joining, at levels comparable to Atm(-/-) lymphocytes. Together, these results reveal an essential function of ATM during embryogenesis and an important function of catalytically inactive ATM protein in DNA repair.

Reduced modeling of the magnetorotational instability

NASA Astrophysics Data System (ADS)

Jamroz, Ben F.

2009-06-01

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

An improved Red/ET recombineering system and mouse ES cells culture conditions for the generation of targeted mutant mice.

PubMed

Kumagai, Katsuyoshi; Takanashi, Masakatsu; Ohno, Shin-Ichiro; Kuroda, Masahiko; Sudo, Katsuko

2017-05-03

Targeted mutant mice generated on a C57BL/6 background are powerful tools for analysis of the biological functions of genes, and gene targeting technologies using mouse embryonic stem (ES) cells have been used to generate such mice. Recently, a bacterial artificial chromosome (BAC) recombineering system was established for the construction of targeting vectors. However, gene retrieval from BACs for the generation of gene targeting vectors using this system remains difficult. Even when construction of a gene targeting vector is successful, the efficiency of production of targeted mutant mice from ES cells derived from C57BL/6 mice are poor. Therefore, in this study, we first improved the strategy for the retrieval of genes from BACs and their transfer into a DT-A plasmid, for the generation of gene targeting vectors using the BAC recombineering system. Then, we attempted to generate targeted mutant mice from ES cell lines derived from C57BL/6 mice, by culturing in serum-free medium. In conclusion, we established an improved strategy for the efficient generation of targeted mutant mice on a C57BL/6 background, which are useful for the in vivo analysis of gene functions and regulation.

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.

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.

Targeting vector construction through recombineering.

PubMed

Malureanu, Liviu A

2011-01-01

Gene targeting in mouse embryonic stem cells is an essential, yet still very expensive and highly time-consuming, tool and method to study gene function at the organismal level or to create mouse models of human diseases. Conventional cloning-based methods have been largely used for generating targeting vectors, but are hampered by a number of limiting factors, including the variety and location of restriction enzymes in the gene locus of interest, the specific PCR amplification of repetitive DNA sequences, and cloning of large DNA fragments. Recombineering is a technique that exploits the highly efficient homologous recombination function encoded by λ phage in Escherichia coli. Bacteriophage-based recombination can recombine homologous sequences as short as 30-50 bases, allowing manipulations such as insertion, deletion, or mutation of virtually any genomic region. The large availability of mouse genomic bacterial artificial chromosome (BAC) libraries covering most of the genome facilitates the retrieval of genomic DNA sequences from the bacterial chromosomes through recombineering. This chapter describes a successfully applied protocol and aims to be a detailed guide through the steps of generation of targeting vectors through recombineering.

P53 Suppression of Homologous Recombination and Tumorigenesis

DTIC Science & Technology

2012-01-01

mutation acted on both rad51 dependent gene conversion events and deletion events (6). Willers et al. also showed an increase in recombination...suffer from sarcomas. MEFs from these mice show aneuploidy, allelic loss and gene amplification. Most of these germline mutations are missense...the absence of tumor suppressor gene activity, such as p53, results in increased genomic instability and increased cancer predisposition

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

On the variances of generation-recombination noise in a three-level system

NASA Astrophysics Data System (ADS)

Hooge, F. N.; Ren, L.

1994-01-01

A statistical treatment is given of the generation-recombination noise in a semiconductor with a conduction band and two traps X and Y. The system is described in terms of x and y, where x is half the harmonic mean of the numbers of occupied and empty traps X. A corresponding definition is given for y. The use of x and y makes the formalism very transparent. Simple, explicit relations are easily found, which can be further simplified by approximations depending on the ratios between N, x and y. We consider correlations and Burgess' theorem; time dependence and spectra are not discussed.

On the conservative nature of intragenic recombination

PubMed Central

Drummond, D. Allan; Silberg, Jonathan J.; Meyer, Michelle M.; Wilke, Claus O.; Arnold, Frances H.

2005-01-01

Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function. Here, we compare recombination of the distantly related β-lactamases PSE-4 and TEM-1 to mutation of PSE-4. We show that, among β-lactamase variants containing the same number of amino acid substitutions, variants created by recombination retain function with a significantly higher probability than those generated by random mutagenesis. We present a simple model that accurately captures the differing effects of mutation and recombination in real and simulated proteins with only four parameters: (i) the amino acid sequence distance between parents, (ii) the number of substitutions, (iii) the average probability that random substitutions will preserve function, and (iv) the average probability that substitutions generated by recombination will preserve function. Our results expose a fundamental functional enrichment in regions of protein sequence space accessible by recombination and provide a framework for evaluating whether the relative rates of mutation and recombination observed in nature reflect the underlying imbalance in their effects on protein function. PMID:15809422

On the conservative nature of intragenic recombination.

PubMed

Drummond, D Allan; Silberg, Jonathan J; Meyer, Michelle M; Wilke, Claus O; Arnold, Frances H

2005-04-12

Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function. Here, we compare recombination of the distantly related beta-lactamases PSE-4 and TEM-1 to mutation of PSE-4. We show that, among beta-lactamase variants containing the same number of amino acid substitutions, variants created by recombination retain function with a significantly higher probability than those generated by random mutagenesis. We present a simple model that accurately captures the differing effects of mutation and recombination in real and simulated proteins with only four parameters: (i) the amino acid sequence distance between parents, (ii) the number of substitutions, (iii) the average probability that random substitutions will preserve function, and (iv) the average probability that substitutions generated by recombination will preserve function. Our results expose a fundamental functional enrichment in regions of protein sequence space accessible by recombination and provide a framework for evaluating whether the relative rates of mutation and recombination observed in nature reflect the underlying imbalance in their effects on protein function.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Djidjou, T. K.; Basel, Tek; Rogachev, A.

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 magnitudemore » 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.« less

Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability.

PubMed

Bonnet, Amandine; Grosso, Ana R; Elkaoutari, Abdessamad; Coleno, Emeline; Presle, Adrien; Sridhara, Sreerama C; Janbon, Guilhem; Géli, Vincent; de Almeida, Sérgio F; Palancade, Benoit

2017-08-17

Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage. Copyright © 2017 Elsevier Inc. All rights reserved.

Thermal instability in the inner coma of a comet

NASA Technical Reports Server (NTRS)

Milikh, G. M.; Sharma, A. S.

1995-01-01

The spacecraft and ground based observations of comet Halley inner coma showed a localized ion density depletion region whose origin is not well understood. Although it has been linked to a thermal instability associated with negative ions, the photodetachment lifetime of negative ions (approximately 1 sec) is too short compared to the electron attachment time scale (approximately 100 sec) for this process to have a significant effect. A mechanism for the ion density depletion based on the thermal instability of the cometary plasma due to the excitation of rotational and vibrational levels of water molecules is proposed. The electron energy losses due to these processes peak near 4000 K (0.36 eV) and at temperatures higher than this value a localized cooling leads to further cooling (thermal instability) due to the increased radiation loss. The resulting increase in recombination leads to an ion density depletion and the estimates for this depletion at comet Halley agree with the observations.

Msh1p counteracts oxidative lesion-induced instability of mtDNA and stimulates mitochondrial recombination in Saccharomyces cerevisiae.

PubMed

Kaniak, Aneta; Dzierzbicki, Piotr; Rogowska, Agata T; Malc, Ewa; Fikus, Marta; Ciesla, Zygmunt

2009-03-01

The proximity of the mitochondrial genome to the respiratory chain, a major source of ROS (radical oxygen species), makes mtDNA more vulnerable to oxidative damage than nuclear DNA. Mitochondrial BER (base excision repair) is generally considered to be the main pathway involved in the prevention of oxidative lesion-induced mutations in mtDNA. However, we previously demonstrated that the increased frequency of mitochondrial Oli(r) mutants in an ogg1Delta strain, lacking the activity of a crucial mtBER glycosylase, is reduced in the presence of plasmids encoding Msh1p, the mitochondrial homologue of the bacterial mismatch protein MutS. This finding suggested that Msh1p might be involved in the prevention of mitochondrial mutagenesis induced by oxidative stress. Here we show that a double mutant carrying the msh1-R813W allele, encoding a variant of the protein defective in the ATP hydrolysis activity, combined with deletion of SOD2, encoding the mitochondrial superoxide dismutase, displays a synergistic effect on the frequency of Oli(r) mutants, indicating that Msh1p prevents generation of oxidative lesion-induced mitochondrial mutations. We also show that double mutants carrying the msh1-R813W allele, combined with deletion of either OGG1 or APN1, the latter resulting in deficiency of the Apn1 endonuclease, exhibit a synergistic effect on the frequency of respiration-defective mutants having gross rearrangements of the mitochondrial genome. This suggests that Msh1p, Ogg1p and Apn1p play overlapping functions in maintaining the stability of mtDNA. In addition, we demonstrate, using a novel ARG8(m) recombination assay, that a surplus of Msh1p results in enhanced mitochondrial recombination. Interestingly, the mutant forms of the protein, msh1p-R813W and msh1p-G776D, fail to stimulate recombination. We postulate that the Msh1p-enhanced homologous recombination may play an important role in the prevention of oxidative lesion-induced rearrangements of the mitochondrial

The analysis of harmonic generation coefficients in the ablative Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Lu, Yan; Fan, Zhengfeng; Lu, Xinpei; Ye, Wenhua; Zou, Changlin; Zhang, Ziyun; Zhang, Wen

2017-10-01

In this research, we use the numerical simulation method to investigate the generation coefficients of the first three harmonics and the zeroth harmonic in the Ablative Rayleigh-Taylor Instability. It is shown that the interface shifts to the low temperature side during the ablation process. In consideration of the third-order perturbation theory, the first three harmonic amplitudes of the weakly nonlinear regime are calculated and then the harmonic generation coefficients are obtained by curve fitting. The simulation results show that the harmonic generation coefficients changed with time and wavelength. Using the higher-order perturbation theory, we find that more and more harmonics are generated in the later weakly nonlinear stage, which is caused by the negative feedback of the later higher harmonics. Furthermore, extending the third-order theory to the fifth-order theory, we find that the second and the third harmonics coefficients linearly depend on the wavelength, while the feedback coefficients are almost constant. Further analysis also shows that when the fifth-order theory is considered, the normalized effective amplitudes of second and third harmonics can reach about 25%-40%, which are only 15%-25% in the frame of the previous third-order theory. Therefore, the third order perturbation theory is needed to be modified by the higher-order theory when ηL reaches about 20% of the perturbation wavelength.

Investigation of geminate recombination of radical ion pairs generated by dissociation of exciplexes in moderately polar solvents using the photoconductivity technique

NASA Astrophysics Data System (ADS)

Lukin, Leonid V.

2009-06-01

A new approach to determination of the recombination rate of radical ion pairs in moderately polar solvents is presented. It is based on an investigation of transient photocurrents caused by dissociation of exciplexes generated in photoinduced electron transfer reactions. It has been shown that the recombination rate of geminate ion pairs can be found from the photocurrent rise time. We have applied such an approach to transient photocurrents observed by Hirata et al. [Y. Hirata, Y. Kanda, N. Mataga, J. Phys. Chem. 87 (1983) 1659] for the pyrene/dicyanobenzene system in solvents of moderate polarity. The increase of the obtained recombination rate of photogenerated ions with increasing polarity of solvent testifies that ions recombine mainly by the backward electron transfer from the dicyanobenzene anions to solvent-separated cations of pyrene.

Vortex-Surface Interactions: Vortex Dynamics and Instabilities

DTIC Science & Technology

2015-10-16

31 May 2015 4. TITLE AND SUBTITLE VORTEX -SURFACE INTERACTIONS: VORTEX DYNAMICS AND INSTABILITIES Sa. CONTRACT NUMBER Sb. GRANT NUMBER N00014-12...new natural instabilities coming from vortex - vortex or vortex -surface interactions, but also ultimately the possibility to control these flows...design of vortex generators to modify surface pressures. We find a short wave instability of the secondary vortices that are created by the

Precise identification of endogenous proviruses of NFS/N mice participating in recombination with moloney ecotropic murine leukemia virus (MuLV) to generate polytropic MuLVs.

PubMed

Alamgir, A S M; Owens, Nick; Lavignon, Marc; Malik, Frank; Evans, Leonard H

2005-04-01

Polytropic murine leukemia viruses (MuLVs) are generated by recombination of ecotropic MuLVs with env genes of a family of endogenous proviruses in mice, resulting in viruses with an expanded host range and greater virulence. Inbred mouse strains contain numerous endogenous proviruses that are potential donors of the env gene sequences of polytropic MuLVs; however, the precise identification of those proviruses that participate in recombination has been elusive. Three different structural groups of proviruses in NFS/N mice have been described and different ecotropic MuLVs preferentially recombine with different groups of proviruses. In contrast to other ecotropic MuLVs such as Friend MuLV or Akv that recombine predominantly with a single group of proviruses, Moloney MuLV (M-MuLV) recombines with at least two distinct groups. In this study, we determined that only three endogenous proviruses, two of one group and one of another group, are major participants in recombination with M-MuLV. Furthermore, the distinction between the polytropic MuLVs generated by M-MuLV and other ecotropic MuLVs is the result of recombination with a single endogenous provirus. This provirus exhibits a frameshift mutation in the 3' region of the surface glycoprotein-encoding sequences that is excluded in recombinants with M-MuLV. The sites of recombination between the env genes of M-MuLV and endogenous proviruses were confined to a short region exhibiting maximum homology between the ecotropic and polytropic env sequences and maximum stability of predicted RNA secondary structure. These observations suggest a possible mechanism for the specificity of recombination observed for different ecotropic MuLVs.

Noncytopathogenic Pestivirus Strains Generated by Nonhomologous RNA Recombination: Alterations in the NS4A/NS4B Coding Region

PubMed Central

Gallei, Andreas; Orlich, Michaela; Thiel, Heinz-Juergen; Becher, Paul

2005-01-01

Several studies have demonstrated that cytopathogenic (cp) pestivirus strains evolve from noncytopathogenic (noncp) viruses by nonhomologous RNA recombination. In addition, two recent reports showed the rapid emergence of noncp Bovine viral diarrhea virus (BVDV) after a few cell culture passages of cp BVDV strains by homologous recombination between identical duplicated viral sequences. To allow the identification of recombination sites from noncp BVDV strains that evolve from cp viruses, we constructed the cp BVDV strains CP442 and CP552. Both harbor duplicated viral sequences of different origin flanking the cellular insertion Nedd8*; the latter is a prerequisite for their cytopathogenicity. In contrast to the previous studies, isolation of noncp strains was possible only after extensive cell culture passages of CP442 and CP552. Sequence analysis of 15 isolated noncp BVDVs confirmed that all recombinant strains lack at least most of Nedd8*. Interestingly, only one strain resulted from homologous recombination while the other 14 strains were generated by nonhomologous recombination. Accordingly, our data suggest that the extent of sequence identity between participating sequences influences both frequency and mode (homologous versus nonhomologous) of RNA recombination in pestiviruses. Further analyses of the noncp recombinant strains revealed that a duplication of 14 codons in the BVDV nonstructural protein 4B (NS4B) gene does not interfere with efficient viral replication. Moreover, an insertion of viral sequences between the NS4A and NS4B genes was well tolerated. These findings thus led to the identification of two genomic loci which appear to be suited for the insertion of heterologous sequences into the genomes of pestiviruses and related viruses. PMID:16254361

Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination

PubMed Central

Nicolas, Laura; Cols, Montserrat; Choi, Jee Eun; Chaudhuri, Jayanta; Vuong, Bao

2018-01-01

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity. PMID:29744038

Many-body instabilities and mass generation in slow Dirac materials

NASA Astrophysics Data System (ADS)

Triola, Christopher; Zhu, Jianxin; Migliori, Albert; Balatsky, Alexander

2015-03-01

Some Kondo insulators are expected to possess topologically protected surface states with linear Dirac spectrum, the topological Kondo insulators. Because the bulk states of these systems typically have heavy effective electron masses, the surface states may exhibit extraordinarily small Fermi velocities that could force the effective fine structure constant of the surface states into the strong coupling regime. Using a tight-binding model we study the many-body instabilities of these systems and identify regions of parameter space for which antiferromagnetic, ferromagnetic and charge density wave instabilities occur. Work Supported by USDOE BES E304.

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

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.

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.

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.

RTEL1 maintains genomic stability by suppressing homologous recombination.

PubMed

Barber, Louise J; Youds, Jillian L; Ward, Jordan D; McIlwraith, Michael J; O'Neil, Nigel J; Petalcorin, Mark I R; Martin, Julie S; Collis, Spencer J; Cantor, Sharon B; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C; Rose, Ann M; Boulton, Simon J

2008-10-17

Homologous recombination (HR) is an important conserved process for DNA repair and ensures maintenance of genome integrity. Inappropriate HR causes gross chromosomal rearrangements and tumorigenesis in mammals. In yeast, the Srs2 helicase eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has been elusive. Here, we identify C. elegans RTEL-1 as a functional analog of Srs2 and describe its vertebrate counterpart, RTEL1, which is required for genome stability and tumor avoidance. We find that rtel-1 mutant worms and RTEL1-depleted human cells share characteristic phenotypes with yeast srs2 mutants: lethality upon deletion of the sgs1/BLM homolog, hyperrecombination, and DNA damage sensitivity. In vitro, purified human RTEL1 antagonizes HR by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. We propose that loss of HR control after deregulation of RTEL1 may be a critical event that drives genome instability and cancer.

Observation of astrophysical Weibel instability in counterstreaming laser-produced plasmas

NASA Astrophysics Data System (ADS)

Fox, W.; Fiksel, G.; Bhattacharjee, A.; Germaschewski, K.; Chang, P.-Y.; Hu, S. X.; Nilson, P. M.

2013-10-01

Astrophysical shocks are typically collisionless and require collective electromagnetic fields to couple the upstream and downstream plasmas. The Weibel instability has been proposed to be one of such collective mechanism. Here we present laboratory tests of this process through observations of the Weibel instability generated between two counterstreaming, supersonic plasma flows, generated on the OMEGA EP laser facility by irradiating of a pair of opposing parallel CH targets by UV laser pulses (0.351 μm, 1.8 kJ, 2 ns). The Weibel-generated electromagnetic fields were probed with an ultrafast proton beam, generated with a high-intensity laser pulse (1.053 μm, 800 J, 10 ps) focused to >1018 W/cm2 onto a thin Cu disk. Growth of a striated, transverse instability is observed at the midplane as the two plasmas interpenetrate, which is identified as the Weibel instability through agreement with analytic theory and particle-in-cell simulations. These laboratory observations directly demonstrate the existence of this astrophysical process, and pave the way for further detailed laboratory study of this instability and its consequences for particle energization and shock formation. This work was supported by DOE grant DE-SC0007168.

Instabilities in mimetic matter perturbations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Firouzjahi, Hassan; Gorji, Mohammad Ali; Mansoori, Seyed Ali Hosseini, E-mail: firouz@ipm.ir, E-mail: gorji@ipm.ir, E-mail: shosseini@shahroodut.ac.ir, E-mail: shossein@ipm.ir

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 instabilitiesmore » such as the Ostrogradsky ghost.« less

In vitro V(D)J recombination: signal joint formation.

PubMed

Cortes, P; Weis-Garcia, F; Misulovin, Z; Nussenzweig, A; Lai, J S; Li, G; Nussenzweig, M C; Baltimore, D

1996-11-26

The first step of V(D)J recombination, specific cleavage at the recombination signal sequence (RSS), can be carried out by the recombination activating proteins RAG1 and RAG2. In vivo, the cleaved coding and signal ends must be rejoined to generate functional antigen receptors and maintain chromosomal integrity. We have investigated signal joint formation using deletion and inversion substrates in a cell free system. RAG1 and RAG2 alone or in combination were unable to generate signal joints. However, RAG1 and RAG2 complemented with nuclear extracts were able to recombine an extrachromosomal substrate and form precise signal joints. The in vitro reaction resembled authentic V(D)J recombination in being Ku-antigen-dependent.

Strategy to approach stable production of recombinant nattokinase in Bacillus subtilis.

PubMed

Chen, Po Ting; Chiang, Chung-Jen; Chao, Yun-Peng

2007-01-01

Bacillus subtilis (B. subtilis) is widely accepted as an excellent host cell for the secretory production of recombinant proteins. In this study, a shuttle vector was constructed by fusion of Staphylococcus aureus (S. aureus) plasmid pUB110 with Escherichia coli (E. coli) plasmid pUC18 and used for the expression of nattokinase in B. subtilis. The pUB110/pUC-based plasmid was found to exhibit high structural instability with the identification of a DNA deletion between two repeated regions. An initial attempt was made to eliminate the homologous site in the plasmid, whereas the stability of the resulting plasmid was not improved. In an alternative way, the pUC18-derived region in this hybrid vector was replaced by the suicidal R6K plasmid origin of E. coli. As a consequence, the pUB110/R6K-based plasmid displayed full structural stability, leading to a high-level production of recombinant nattokinase in the culture broth. This was mirrored by the detection of a very low level of high molecular weight DNAs generated by the plasmid. Moreover, 2-fold higher nattokinase production was obtained by B. subtilis strain carrying the pUB110/R6K-based plasmid as compared to the cell with the pAMbeta1-derived vector, a plasmid known to have high structural stability. Overall, it indicates the feasibility of the approach by fusing two compatible plasmid origins for stable and efficient production of recombinant nattokinase in B. subtilis.

RNA Recombination In Vivo in the Absence of Viral Replication

PubMed Central

Gallei, Andreas; Pankraz, Alexander; Thiel, Heinz-Jürgen; Becher, Paul

2004-01-01

To study fundamental aspects of RNA recombination, an in vivo RNA recombination system was established. This system allowed the efficient generation of recombinant cytopathogenic pestiviruses after transfection of synthetic, nonreplicatable, subgenomic transcripts in cells infected with a replicating noncytopathogenic virus. Studies addressing the interplay between RNA recombination and replication revealed that cotransfection of noninfected cells with various pairs of nonreplicatable RNA derivatives also led to the emergence of recombinant viral genomes. Remarkably, homologous and nonhomologous recombination occurred between two overlapping transcripts, each lacking different essential parts of the viral RNA-dependent RNA polymerase (RdRp) gene. Apart from the generally accepted viral replicative copy choice recombination, our results prove the existence of a viral RdRp-independent mechanism of RNA recombination that occurs in vivo. It appears likely that such a mechanism not only contributes to the evolution of RNA viruses but also leads to the generation of recombinant cellular RNAs. PMID:15163720

Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability.

PubMed

Stirling, Peter C; Hieter, Philip

2017-10-27

DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial factories for recombinant pharmaceuticals

PubMed Central

Ferrer-Miralles, Neus; Domingo-Espín, Joan; Corchero, José Luis; Vázquez, Esther; Villaverde, Antonio

2009-01-01

Most of the hosts used to produce the 151 recombinant pharmaceuticals so far approved for human use by the Food and Drug Administration (FDA) and/or by the European Medicines Agency (EMEA) are microbial cells, either bacteria or yeast. This fact indicates that despite the diverse bottlenecks and obstacles that microbial systems pose to the efficient production of functional mammalian proteins, namely lack or unconventional post-translational modifications, proteolytic instability, poor solubility and activation of cell stress responses, among others, they represent convenient and powerful tools for recombinant protein production. The entering into the market of a progressively increasing number of protein drugs produced in non-microbial systems has not impaired the development of products obtained in microbial cells, proving the robustness of the microbial set of cellular systems (so far Escherichia coli and Saccharomyces cerevisae) developed for protein drug production. We summarize here the nature, properties and applications of all those pharmaceuticals and the relevant features of the current and potential producing hosts, in a comparative way. PMID:19317892

Diffusion controlled initial recombination

NASA Astrophysics Data System (ADS)

Christen, T.; Büttiker, M.

1998-08-01

This work addresses nucleation rates in systems with strong initial recombination. Initial (or ``geminate'') recombination is a process where a dissociated structure (anion, vortex, kink, etc.) recombines with its twin brother (cation, antivortex, antikink) generated in the same nucleation event. Initial recombination is important if there is an asymptotically vanishing interaction force instead of a generic saddle-type activation barrier. At low temperatures, initial recombination strongly dominates homogeneous recombination. In a first part, we discuss the effect in one-, two-, and three-dimensional diffusion controlled systems with spherical symmetry. Since there is no well-defined saddle, we introduce a threshold which is to some extent arbitrary but which is restricted by physically reasonable conditions. We show that the dependence of the nucleation rate on the specific choice of this threshold is strongest for one-dimensional systems and decreases in higher dimensions. We also discuss the influence of a weak driving force, and show that the transport current is directly determined by the imbalance of the activation rate in the direction of the field and the rate against this direction. In a second part, we apply the results to the overdamped sine-Gordon system at equilibrium. It turns out that diffusive initial recombination is the essential mechanism which governs the equilibrium kink nucleation rate. We emphasize analogies between the single particle problem with initial recombination and the multidimensional kink-antikink nucleation problem.

Generation of dark and bright spin wave envelope soliton trains through self-modulational instability in magnetic films.

PubMed

Wu, Mingzhong; Kalinikos, Boris A; Patton, Carl E

2004-10-08

The generation of dark spin wave envelope soliton trains from a continuous wave input signal due to spontaneous modulational instability has been observed for the first time. The dark soliton trains were formed from high dispersion dipole-exchange spin waves propagated in a thin yttrium iron garnet film with pinned surface spins at frequencies situated near the dipole gaps in the dipole-exchange spin wave spectrum. Dark and bright soliton trains were generated for one and the same film through placement of the input carrier frequency in regions of negative and positive dispersion, respectively. Two unreported effects in soliton dynamics, hysteresis and period doubling, were also observed.

Generation and characterization of koi herpesvirus recombinants lacking viral enzymes of nucleotide metabolism.

PubMed

Fuchs, Walter; Fichtner, Dieter; Bergmann, Sven M; Mettenleiter, Thomas C

2011-06-01

Koi herpesvirus (KHV) causes a fatal disease in koi and common carp, but no reliable and genetically characterized vaccines are available up to now. Therefore, we generated KHV recombinants possessing deletions within the viral ribonucleotide reductase (RNR), thymidine kinase (TK), dUTPase, or TK and dUTPase genes, and their corresponding rescuants. All KHV mutants were replication competent in cultured cells. Whereas plaque sizes and titers of RNR-negative KHV were reduced, replication of the other mutants was not affected. Experimental infection of carp indicated attenuation of TK- or dUTPase-deleted KHV, and PCR analysis of tissue samples permitted differentiation of mutant from wild-type virus.

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.

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.

Transposable Elements and Genetic Instabilities in Crop Plants

DOE R&D Accomplishments Database

Burr, B.; Burr, F.

1981-04-10

Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro

PubMed Central

Williams, Jonathan D.; Fleetwood, Sara; Berroyer, Alexandra; Kim, Nayun; Larson, Erik D.

2015-01-01

The formation of highly stable four-stranded DNA, called G-quadruplex (G4), promotes site-specific genome instability. G4 DNA structures fold from repetitive guanine sequences, and increasing experimental evidence connects G4 sequence motifs with specific gene rearrangements. The human transcription factor 3 (TCF3) gene (also termed E2A) is subject to genetic instability associated with severe disease, most notably a common translocation event t(1;19) associated with acute lymphoblastic leukemia. The sites of instability in TCF3 are not randomly distributed, but focused to certain sequences. We asked if G4 DNA formation could explain why TCF3 is prone to recombination and mutagenesis. Here we demonstrate that sequences surrounding the major t(1;19) break site and a region associated with copy number variations both contain G4 sequence motifs. The motifs identified readily adopt G4 DNA structures that are stable enough to interfere with DNA synthesis in physiological salt conditions in vitro. When introduced into the yeast genome, TCF3 G4 motifs promoted gross chromosomal rearrangements in a transcription-dependent manner. Our results provide a molecular rationale for the site-specific instability of human TCF3, suggesting that G4 DNA structures contribute to oncogenic DNA breaks and recombination. PMID:26029241

RECG Maintains Plastid and Mitochondrial Genome Stability by Suppressing Extensive Recombination between Short Dispersed Repeats

PubMed Central

Odahara, Masaki; Masuda, Yuichi; Sato, Mayuko; Wakazaki, Mayumi; Harada, Chizuru; Toyooka, Kiminori; Sekine, Yasuhiko

2015-01-01

Maintenance of plastid and mitochondrial genome stability is crucial for photosynthesis and respiration, respectively. Recently, we have reported that RECA1 maintains mitochondrial genome stability by suppressing gross rearrangements induced by aberrant recombination between short dispersed repeats in the moss Physcomitrella patens. In this study, we studied a newly identified P. patens homolog of bacterial RecG helicase, RECG, some of which is localized in both plastid and mitochondrial nucleoids. RECG partially complements recG deficiency in Escherichia coli cells. A knockout (KO) mutation of RECG caused characteristic phenotypes including growth delay and developmental and mitochondrial defects, which are similar to those of the RECA1 KO mutant. The RECG KO cells showed heterogeneity in these phenotypes. Analyses of RECG KO plants showed that mitochondrial genome was destabilized due to a recombination between 8–79 bp repeats and the pattern of the recombination partly differed from that observed in the RECA1 KO mutants. The mitochondrial DNA (mtDNA) instability was greater in severe phenotypic RECG KO cells than that in mild phenotypic ones. This result suggests that mitochondrial genomic instability is responsible for the defective phenotypes of RECG KO plants. Some of the induced recombination caused efficient genomic rearrangements in RECG KO mitochondria. Such loci were sometimes associated with a decrease in the levels of normal mtDNA and significant decrease in the number of transcripts derived from the loci. In addition, the RECG KO mutation caused remarkable plastid abnormalities and induced recombination between short repeats (12–63 bp) in the plastid DNA. These results suggest that RECG plays a role in the maintenance of both plastid and mitochondrial genome stability by suppressing aberrant recombination between dispersed short repeats; this role is crucial for plastid and mitochondrial functions. PMID:25769081

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albariño, César G., E-mail: calbarino@cdc.gov; Wiggleton Guerrero, Lisa; Lo, Michael K.

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 usefulnessmore » 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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nekrasov, Anatoly K.; Shadmehri, Mohsen, E-mail: anekrasov@ifz.ru, E-mail: nekrasov.anatoly@gmail.com, E-mail: m.shadmehri@gu.ac.ir

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 notmore » 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.« less

A Novel Behavior of Pump Power in the Instability Induced Supercontinuum Generation of Saturable Nonlinear Media

NASA Astrophysics Data System (ADS)

Nithyanandan, K.; Porsezian, K.

2015-04-01

We investigate the modulational instability (MI) induced Supercontinuum generation (SCG) in exponential saturable nonlinearity. The pump power (P) is observed to behave in a unique way such that unlike the conventional Kerr case, the effective nonlinearity of saturable nonlinear system does not monotonously increases with an increase in power. The supercontinuum is observed at the shortest distance of propagation at power equal to the saturation power (Ps), whereas for all combinations of powers (P < Ps or P > Ps) spectral broadening occurs at longer distance.

SPAR1/RTEL1 maintains genomic stability by suppressing homologous recombination

PubMed Central

Barber, Louise J.; Youds, Jillian L.; Ward, Jordan D.; McIlwraith, Michael J.; O’Neil, Nigel J.; Petalcorin, Mark I.R.; Martin, Julie S.; Collis, Spencer J.; Cantor, Sharon B.; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C.; Rose, Ann M.; Boulton, Simon J.

2013-01-01

SUMMARY Inappropriate homologous recombination (HR) can cause gross chromosomal rearrangements that in mammalian cells may lead to tumorigenesis. In yeast, the Srs2 protein is an anti-recombinase that eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has proven to be elusive. In this work, we identify C. elegans SPAR-1 as a functional analogue of Srs2 and describe its vertebrate counterpart, SPAR1/RTEL1, which is required for genome stability and tumour avoidance. We find that spar-1 mutant worms and SPAR1 knockdown human cells share characteristic phenotypes with yeast srs2 mutants, including inviability upon deletion of the sgs1/BLM homologue, hyper-recombination, and DNA damage sensitivity. In vitro, purified human SPAR1 antagonises HR by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. We propose that loss of HR control following deregulation of SPAR1/RTEL1 may be a critical event that drives genome instability and cancer. PMID:18957201

Instabilities of Internal Gravity Wave Beams

NASA Astrophysics Data System (ADS)

Dauxois, Thierry; Joubaud, Sylvain; Odier, Philippe; Venaille, Antoine

2018-01-01

Internal gravity waves play a primary role in geophysical fluids: They contribute significantly to mixing in the ocean, and they redistribute energy and momentum in the middle atmosphere. Until recently, most studies were focused on plane wave solutions. However, these solutions are not a satisfactory description of most geophysical manifestations of internal gravity waves, and it is now recognized that internal wave beams with a confined profile are ubiquitous in the geophysical context. We discuss the reason for the ubiquity of wave beams in stratified fluids, which is related to the fact that they are solutions of the nonlinear governing equations. We focus more specifically on situations with a constant buoyancy frequency. Moreover, in light of recent experimental and analytical studies of internal gravity beams, it is timely to discuss the two main mechanisms of instability for those beams: (a) the triadic resonant instability generating two secondary wave beams and (b) the streaming instability corresponding to the spontaneous generation of a mean flow.

Centrifugally Driven Rayleigh-Taylor Instability

NASA Astrophysics Data System (ADS)

Scase, Matthew; Hill, Richard

2017-11-01

The instability that develops at the interface between two fluids of differing density due to the rapid rotation of the system may be considered as a limit of high-rotation rate Rayleigh-Taylor instability. Previously the authors have considered the effect of rotation on a gravitationally dominated Rayleigh-Taylor instability and have shown that some growth modes of instability may be suppressed completely by the stabilizing effect of rotation (Phys. Rev. Fluids 2:024801, Sci. Rep. 5:11706). Here we consider the case of very high rotation rates and a negligible gravitational field. The initial condition is of a dense inner cylinder of fluid surrounded by a lighter layer of fluid. As the system is rotated about the generating axis of the cylinder, the dense inner fluid moves away from the axis and the familiar bubbles and spikes of Rayleigh-Taylor instability develop at the interface. The system may be thought of as a ``fluid-fluid centrifuge''. By developing a model based on an Orr-Sommerfeld equation, we consider the effects of viscosity, surface tension and interface diffusion on the growth rate and modes of instability. We show that under particular circumstances some modes may be stabilized. School of Mathematical Sciences.

A targeted neuroglial reporter line generated by homologous recombination in human embryonic stem cells.

PubMed

Xue, Haipeng; Wu, Sen; Papadeas, Sophia T; Spusta, Steve; Swistowska, Anna Maria; MacArthur, Chad C; Mattson, Mark P; Maragakis, Nicholas J; Capecchi, Mario R; Rao, Mahendra S; Zeng, Xianmin; Liu, Ying

2009-08-01

In this study, we targeted Olig2, a basic helix-loop-helix transcription factor that plays an important role in motoneuron and oligodendrocyte development, in human embryonic stem cell (hESC) line BG01 by homologous recombination. One allele of Olig2 locus was replaced by a green fluorescent protein (GFP) cassette with a targeting efficiency of 5.7%. Targeted clone R-Olig2 (like the other clones) retained pluripotency, typical hESC morphology, and a normal parental karyotype 46,XY. Most importantly, GFP expression recapitulated endogenous Olig2 expression when R-Olig2 was induced by sonic hedgehog and retinoic acid, and GFP-positive cells could be purified by fluorescence-activated cell sorting. Consistent with previous reports on rodents, early GFP-expressing cells appeared biased to a neuronal fate, whereas late GFP-expressing cells appeared biased to an oligodendrocytic fate. This was corroborated by myoblast coculture, transplantation into the rat spinal cords, and whole genome expression profiling. The present work reports an hESC reporter line generated by homologous recombination targeting a neural lineage-specific gene, which can be differentiated and sorted to obtain pure neural progenitor populations.

Genomic instability in human lymphoid cells exposed to 1 GeV/amu Fe ions

NASA Technical Reports Server (NTRS)

Grosovsky, A.; Bethel, H.; Parks, K.; Ritter, L.; Giver, C.; Gauny, S.; Wiese, C.; Kronenberg, A.

2001-01-01

The goal of this study was to assess whether charged particle radiations of importance to spaceflight elicit genomic instability in human TK6 lymphoblasts. The incidence of genomic instability in TK6 cells was assessed 21 days after exposure to 2, 4, or 6 Fe ions (1 GeV/amu, LET= 146 keV/micrometers). Three indices of instability were used: intraclonal karyotypic heterogeneity, mutation rate analysis at the thymidine kinase (TK1) locus, and re-cloning efficiency. Fifteen of sixty clones demonstrated karyotypic heterogeneity. Five clones had multiple indicators of karyotypic change. One clone was markedly hypomutable and polyploid. Six clones were hypomutable, while 21 clones were mutators. Of these, seven were karyotypically unstable. Six clones had low re-cloning efficiencies, one of which was a mutator. All had normal karyotypes. In summary, many clones that survived exposure to a low fluence of Fe ions manifested one or more forms of genomic instability that may hasten the development of neoplasia through deletion or by recombination.

Genomic instability in human lymphoid cells exposed to 1 GeV/amu Fe ions.

PubMed

Grosovsky, A; Bethel, H; Parks, K; Ritter, L; Giver, C; Gauny, S; Wiese, C; Kronenberg, A

2001-01-01

The goal of this study was to assess whether charged particle radiations of importance to spaceflight elicit genomic instability in human TK6 lymphoblasts. The incidence of genomic instability in TK6 cells was assessed ~21 days after exposure to 2, 4, or 6 Fe ions (1 GeV/amu, LET= 146 keV/micrometers). Three indices of instability were used: intraclonal karyotypic heterogeneity, mutation rate analysis at the thymidine kinase (TK1) locus, and re-cloning efficiency. Fifteen of sixty clones demonstrated karyotypic heterogeneity. Five clones had multiple indicators of karyotypic change. One clone was markedly hypomutable and polyploid. Six clones were hypomutable, while 21 clones were mutators. Of these, seven were karyotypically unstable. Six clones had low re-cloning efficiencies, one of which was a mutator. All had normal karyotypes. In summary, many clones that survived exposure to a low fluence of Fe ions manifested one or more forms of genomic instability that may hasten the development of neoplasia through deletion or by recombination.

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

Recombination within the nonstructural genes of the parvovirus minute virus of mice (MVM) generates functional levels of wild-type NS1, which can be detected in the absence of selective pressure following transfection of nonreplicating plasmids.

PubMed

Pearson, J L; Pintel, D J

2000-03-30

Recombination within the coding region of the nonstructural genes of minute virus of mice (MVM), which generates functional levels of wild-type NS1, was observed in the absence of selective pressure following cotransfection of nonreplicating plasmids. P38 activity was used as a measure of recombinant NS1 production, which, together with direct detection of recombinant-generated products by RT-PCR, allowed an estimation of recombination efficiency. In addition, we show that very low levels of wild-type NS1 were able to significantly transactivate P38. Given that recombination following cotransfection can generate NS1 at these levels, our observations have implications for the study of parvoviral genetics, the construction of recombinant parvoviral vectors for gene therapy applications, and perhaps other systems using cotransfection of plasmids that share homologous sequences. Copyright 2000 Academic Press.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safari, S.; Jazi, B., E-mail: jaziada@kashanu.ac.ir; 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 electronmore » beam plays a stabilizing role.« less

Exploiting translational coupling for the selection of cells producing toxic recombinant proteins from expression vectors.

PubMed

Tagliavia, Marcello; Cuttitta, Angela

2016-01-01

High rates of plasmid instability are associated with the use of some expression vectors in Escherichia coli, resulting in the loss of recombinant protein expression. This is due to sequence alterations in vector promoter elements caused by the background expression of the cloned gene, which leads to the selection of fast-growing, plasmid-containing cells that do not express the target protein. This phenomenon, which is worsened when expressing toxic proteins, results in preparations containing very little or no recombinant protein, or even in clone loss; however, no methods to prevent loss of recombinant protein expression are currently available. We have exploited the phenomenon of translational coupling, a mechanism of prokaryotic gene expression regulation, in order to select cells containing plasmids still able to express recombinant proteins. Here we designed an expression vector in which the cloned gene and selection marker are co-expressed. Our approach allowed for the selection of the recombinant protein-expressing cells and proved effective even for clones encoding toxic proteins.

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.

Molecular simulation study of cavity-generated instabilities in the superheated Lennard-Jones liquid

NASA Astrophysics Data System (ADS)

Torabi, Korosh; Corti, David S.

2010-10-01

Previous equilibrium-based density-functional theory (DFT) analyses of cavity formation in the pure component superheated Lennard-Jones (LJ) liquid [S. Punnathanam and D. S. Corti, J. Chem. Phys. 119, 10224 (2003); M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007)] revealed that a thermodynamic limit of stability appears in which no liquidlike density profile can develop for cavity radii greater than some critical size (being a function of temperature and bulk density). The existence of these stability limits was also verified using isothermal-isobaric Monte Carlo (MC) simulations. To test the possible relevance of these limits of stability to a dynamically evolving system, one that may be important for homogeneous bubble nucleation, we perform isothermal-isobaric molecular dynamics (MD) simulations in which cavities of different sizes are placed within the superheated LJ liquid. When the impermeable boundary utilized to generate a cavity is removed, the MD simulations show that the cavity collapses and the overall density of the system remains liquidlike, i.e., the system is stable, when the initial cavity radius is below some certain value. On the other hand, when the initial radius is large enough, the cavity expands and the overall density of the system rapidly decreases toward vaporlike densities, i.e., the system is unstable. Unlike the DFT predictions, however, the transition between stability and instability is not infinitely sharp. The fraction of initial configurations that generate an instability (or a phase separation) increases from zero to unity as the initial cavity radius increases over a relatively narrow range of values, which spans the predicted stability limit obtained from equilibrium MC simulations. The simulation results presented here provide initial evidence that the equilibrium-based stability limits predicted in the previous DFT and MC simulation studies may play some role, yet to be fully determined, in the homogeneous

Design and Fabrication of a Hele-Shaw Apparatus for Observing Instabilities of Diffusion Flames

NASA Technical Reports Server (NTRS)

Wichman, I. S.; Oravecz-Simpkins, L.; Olson, S.

2001-01-01

Examinations of flame fronts spreading over solid fuels in an opposed flow of oxidizer have shown that the flame front fragments into smaller (cellular) flames. These 'flamelets' will oscillate, recombine, or extinguish, indicating that they are in the near extinction limit regime (i.e., to one side of the quenching branch of the flammability map). Onset of unstable cellular flamelet formation for flame spread over thin fuels occurs when a heat-sink substrate is placed a small distance from the underside of the fuel. This heat-sink substrate (or backing) displaces the quenching branch of the flammability map in a direction that causes the instabilities to occur at higher air velocities. Similar near-limit behavior has been observed in other works using different fuels, thus suggesting that these dynamic mechanisms are fuel-independent and therefore fundamental attributes of flames in this near-limit flame spread regime. The objective of this project is to determine the contributions of the hydrodynamic and thermodiffusive mechanisms to the observed formation of flame instabilities. From this, a model of diffusion flame instabilities shall be generated. Previously, experiments were conducted in NASA drop towers, thereby limiting observation time to O(1-5 sec). The NASA tests exhibited flamelet survival for the entire drop time, suggesting that flamelets (i.e., small cellular flames) might exist, if permitted, for longer time periods. By necessity, experiments were limited to thermally thin cellulose fuels (approximately 0.001 in thick): instabilities could form by virtue of faster spread rates over thin fuels. Unstable behavior was unlikely in the short drop time for thicker fuels. In the International Space Station (ISS), microgravity time is unlimited, so both thin and thick fuels can be tested.

A colloquium on the influence of versatile class of saturable nonlinear responses in the instability induced supercontinuum generation

NASA Astrophysics Data System (ADS)

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

2013-08-01

We investigate the modulational instability induced supercontinuum generation (MI-SCG) under versatile saturable nonlinear (SNL) responses. We identify and discuss the salient features of saturable nonlinear responses of various functional forms such as exponential, conventional and coupled type on modulational instability (MI) and the subsequent supercontinuum (SC) process. Firstly, we analyze the impact of SNL on the MI spectrum and found both analytically and numerically that MI gain and bandwidth is maximum for exponential nonlinearity in comparison to other types of SNL's. We also reported the unique behavior of the SNL system in the MI dynamics. Following the MI analysis, the proceeding section deals with the supercontinuum generation (SCG) process by virtue of MI. We examine exclusively the impact of each form of SNL on the SC spectrum and predicted numerically that exponential case attains the phase matching earlier and thus enable to achieve broad spectrum at a relatively shorter distance of propagation than the other cases of SNL's. Thus a direct evidence of SCG from MI is emphasized and the impact of SNL in MI-SCG is highlighted. To analyze the quality of the output continuum spectrum, we performed the coherence analysis for MI-SCG in the presence of SNL.

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

Direct Measurements of the Baroclinic Instability in the Ocean

NASA Astrophysics Data System (ADS)

Sadek, Mahmoud; Aluie, Hussein; Hecht, Matthew; Vallis, Geoffrey

2016-11-01

The ocean is mechanically driven by wind and buoyancy at the surface which produce sloping isopycnals with a reservoir of available potential energy (APE). Large scale APE can be converted to kinetic energy via the baroclinic instability, which produces mesoscale eddies. Mesoscale eddies are ubiquitous in mid- and high-latitudes, and play a primary role in determining the strength and trajectories of currents and in generating intrinsic climate variability. The widespread belief that mesoscale eddies are generated through baroclinic instability is based on general accord between observations and linear stability analysis and the predicted behavior of nonlinear models. However, these models are unable to give us quantitative evidence of the extent to which the instability is responsible for eddy generation at various locations in the ocean. To this end, we implement a new coarse-graining framework, recently developed to study flow on a sphere, to directly analyze the baroclinic instability as a function of scale and geographic location, and implement it using strongly eddying high-resolution simulations in the North Atlantic and in the Southern Ocean. The results give us new information about location and intensity of the instability in both physical and spectral space. Partial support was provided by National Science Foundation (NSF) Grant OCE-1259794, US Department of Energy (US DOE) Grant DE-SC0014318, and the LANL LDRD program through Project Number 20150568ER.

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.

[Induced germ line genomic instability at mini- and micro-satellites in animals].

PubMed

Bezlepkin, V G; Gaziev, A I

2001-01-01

The recent data on the phenomenon of the induced germline genomic instability at mini- and microsatellites in animals were considered. Natural hypervariability of the minisatellites and microsatellites and their abundance in eukaryotic genome provide it's utility as the useful genetic markers for evaluation of the germline mutation frequency induced by treatment with different type of genotoxic factors at the low doses. High sensitivity of assays and possibility for direct determinations of the mutations, without the necessity to use extrapolation, are ensured. Some discussion is presented on the role of non-targeted mechanisms for the radiation-prone DNA lesions in the induction of germline genomic instability and also on the involving in this process the recombination events upon meiosis or during the early development stages of embryos. It is proposed that quantitative determination of germline genomic instability rate may be used as an acceptable variant for the genetic risk assessment and as indicator of increased probability for cancer and other pathologies at the offspring born to irradiated parents.

Self-Induced Faraday Instability Laser

NASA Astrophysics Data System (ADS)

Perego, A. M.; Smirnov, S. V.; Staliunas, K.; Churkin, D. V.; Wabnitz, S.

2018-05-01

We predict the onset of self-induced parametric or Faraday instabilities in a laser, spontaneously caused by the presence of pump depletion, which leads to a periodic gain landscape for light propagating in the cavity. As a result of the instability, continuous wave oscillation becomes unstable even in the normal dispersion regime of the cavity, and a periodic train of pulses with ultrahigh repetition rate is generated. Application to the case of Raman fiber lasers is described, in good quantitative agreement between our conceptual analysis and numerical modeling.

Self-Induced Faraday Instability Laser.

PubMed

Perego, A M; Smirnov, S V; Staliunas, K; Churkin, D V; Wabnitz, S

2018-05-25

We predict the onset of self-induced parametric or Faraday instabilities in a laser, spontaneously caused by the presence of pump depletion, which leads to a periodic gain landscape for light propagating in the cavity. As a result of the instability, continuous wave oscillation becomes unstable even in the normal dispersion regime of the cavity, and a periodic train of pulses with ultrahigh repetition rate is generated. Application to the case of Raman fiber lasers is described, in good quantitative agreement between our conceptual analysis and numerical modeling.

A role for chromosomal instability in the development of and selection for radioresistant cell variants

NASA Technical Reports Server (NTRS)

Limoli, C. L.; Corcoran, J. J.; Jordan, R.; Morgan, W. F.; Schwartz, J. L.

2001-01-01

Chromosome instability is a common occurrence in tumour cells. We examined the hypothesis that the elevated rate of mutation formation in unstable cells can lead to the development of clones of cells that are resistant to the cancer therapy. To test this hypothesis, we compared chromosome instability to radiation sensitivity in 30 independently isolated clones of GM10115 human-hamster hybrid cells. There was a broader distribution of radiosensitivity and a higher mean SF(2)in chromosomally unstable clones. Cytogenetic and DNA double-strand break rejoining assays suggest that sensitivity was a function of DNA repair efficiency. In the unstable population, the more radioresistant clones also had significantly lower plating efficiencies. These observations suggest that chromosome instability in GM10115 cells can lead to the development of cell variants that are more resistant to radiation. In addition, these results suggest that the process of chromosome breakage and recombination that accompanies chromosome instability might provide some selective pressure for more radioresistant variants. Copyright 2001 Cancer Research Campaign.

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).

Recombinant production and film properties of full-length hornet silk proteins.

PubMed

Kambe, Yusuke; Sutherland, Tara D; Kameda, Tsunenori

2014-08-01

Full-length versions of the four main components of silk cocoons of Vespa simillima hornets, Vssilk1-4, were produced as recombinant proteins in Escherichia coli. In shake flasks, the recombinant Vssilk proteins yielded 160-330mg recombinant proteinl(-1). Films generated from solutions of single Vssilk proteins had a secondary structure similar to that of films generated from native hornet silk. The films made from individual recombinant hornet silk proteins had similar or enhanced mechanical performance compared with films generated from native hornet silk, possibly reflecting the homogeneity of the recombinant proteins. The pH-dependent changes in zeta (ζ) potential of each Vssilk film were measured, and isoelectric points (pI) of Vssilk1-4 were determined as 8.9, 9.1, 5.0 and 4.2, respectively. The pI of native hornet silk, a combination of the four Vssilk proteins, was 4.7, a value similar to that of Bombyx mori silkworm silk. Films generated from Vssilk1 and 2 had net positive charge under physiological conditions and showed significantly higher cell adhesion activity. It is proposed that recombinant hornet silk is a valuable new material with potential for cell culture applications. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Synchrophasor-Assisted Prediction of Stability/Instability of a Power System

NASA Astrophysics Data System (ADS)

Saha Roy, Biman Kumar; Sinha, Avinash Kumar; Pradhan, Ashok Kumar

2013-05-01

This paper presents a technique for real-time prediction of stability/instability of a power system based on synchrophasor measurements obtained from phasor measurement units (PMUs) at generator buses. For stability assessment the technique makes use of system severity indices developed using bus voltage magnitude obtained from PMUs and generator electrical power. Generator power is computed using system information and PMU information like voltage and current phasors obtained from PMU. System stability/instability is predicted when the indices exceeds a threshold value. A case study is carried out on New England 10-generator, 39-bus system to validate the performance of the technique.

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.

The potential of shifting recombination hotspots to increase genetic gain in livestock breeding.

PubMed

Gonen, Serap; Battagin, Mara; Johnston, Susan E; Gorjanc, Gregor; Hickey, John M

2017-07-04

This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance. Our results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain. Shifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended

Pair-instability supernovae of fast rotating stars

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung

2015-01-01

We present 2D simulations of pair-instability supernovae considering rapid rotation during their explosion phases. Recent studies of the Population III (Pop III) star formation suggested that these stars could be born with a mass scale about 100 M⊙ and with a strong rotation. Based on stellar evolution models, these massive Pop III stars might have died as highly energetic pair-instability supernovae. We perform 2D calculations to investigate the impact of rotation on pair-instability supernovae. Our results suggest that rotation leads to an aspherical explosion due to an anisotropic collapse. If the first stars have a 50% of keplerian rotational rate of the oxygen core before their pair-instability explosions, the overall 56Ni production can be significantly reduced by about two orders of magnitude. An extreme case of 100% keplerian rotational rate shows an interesting feature of fluid instabilities along the equatorial plane caused by non-synchronized and non-isotropic ignitions of explosions, so that the shocks run into the in-falling gas and generate the Richtmyer-Meshkov instability.

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.

Mirror Instability in the Turbulent Solar Wind

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hellinger, Petr; Landi, Simone; Verdini, Andrea

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) leadsmore » 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.« less

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.

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.

Electron Debye scale Kelvin-Helmholtz instability: Electrostatic particle-in-cell simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sang-Yun; Lee, Ensang, E-mail: eslee@khu.ac.kr; Kim, Khan-Hyuk

2015-12-15

In this paper, we investigated the electron Debye scale Kelvin-Helmholtz (KH) instability using two-dimensional electrostatic particle-in-cell simulations. We introduced a velocity shear layer with a thickness comparable to the electron Debye length and examined the generation of the KH instability. The KH instability occurs in a similar manner as observed in the KH instabilities in fluid or ion scales producing surface waves and rolled-up vortices. The strength and growth rate of the electron Debye scale KH instability is affected by the structure of the velocity shear layer. The strength depends on the magnitude of the velocity and the growth ratemore » on the velocity gradient of the shear layer. However, the development of the electron Debye scale KH instability is mainly determined by the electric field generated by charge separation. Significant mixing of electrons occurs across the shear layer, and a fraction of electrons can penetrate deeply into the opposite side fairly far from the vortices across the shear layer.« less

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.

The Utilization during Mitotic Cell Division of Loci Controlling Meiotic Recombination and Disjunction in DROSOPHILA MELANOGASTER

PubMed Central

Baker, Bruce S.; Carpenter, Adelaide T. C.; Ripoll, P.

1978-01-01

To inquire whether the loci identified by recombination-defective and disjunction-defective meiotic mutants in Drosophila are also utilized during mitotic cell division, the effects of 18 meiotic mutants (representing 13 loci) on mitotic chromosome stability have been examined genetically. To do this, meiotic-mutant-bearing flies heterozygous for recessive somatic cell markers were examined for the frequencies and types of spontaneous clones expressing the cell markers. In such flies, marked clones can arise via mitotic recombination, mutation, chromosome breakage, nondisjunction or chromosome loss, and clones from these different origins can be distinguished. In addition, meiotic mutants at nine loci have been examined for their effects on sensitivity to killing by UV and X rays.—Mutants at six of the seven recombination-defective loci examined (mei-9, mei-41, c(3)G, mei-W68, mei-S282, mei-352, mei-218) cause mitotic chromosome instability in both sexes, whereas mutants at one locus (mei-218) do not affect mitotic chromosome stability. Thus many of the loci utilized during meiotic recombination also function in the chromosomal economy of mitotic cells.—The chromosome instability produced by mei-41 alleles is the consequence of chromosome breakage, that of mei-9 alleles is primarily due to chromosome breakage and, to a lesser extent, to an elevated frequency of mitotic recombination, whereas no predominant mechanism responsible for the instability caused by c(3)G alleles is discernible. Since these three loci are defective in their responses to mutagen damage, their effects on chromosome stability in nonmutagenized cells are interpreted as resulting from an inability to repair spontaneous lesions. Both mei-W68 and mei-S282 increase mitotic recombination (and in mei-W68, to a lesser extent, chromosome loss) in the abdomen but not the wing. In the abdomen, the primary effect on chromosome stability occurs during the larval period when the abdominal histoblasts

3D Stagnation instabilities in MagLIF loads on the Z Generator

NASA Astrophysics Data System (ADS)

Jennings, Christopher

2017-10-01

Experiments with Magnetized Liner Inertial Fusion (MagLIF) loads have successfully demonstrated the premise of magnetized fusion. While these experiments are increasingly well diagnosed, many of the measurements (particularly during stagnation) are time integrated, limited in spatial resolution or require additional assumptions to interpret in the context of a structured, rapidly evolving system. As such, there is some ambiguity over what may be limiting performance. Poor laser coupling in preheating the fuel prior to implosion has been suggested as a mechanism. Mix of high Z contaminants that cool the fuel is also a significant concern. In addition, time integrated crystal imaging has shown significant structure in the final fuel assembly indicating potential disruption from instabilities. Understanding the balance between these degradation mechanisms is vital to progress with MagLif. We compare several sets of experimental data with synthetically generated data from systematically varied 3D resistive-MHD simulations to gain insight into the relative contributions of different degradation mechanisms. We demonstrate how some measurements strongly indicate disruption from liner material penetrating into the fuel at stagnation, and discuss the implications this has for how MagLif targets work and scale to larger drive currents. We then explore the extent to which different combinations of instability development, current delivery, high-Z mix into the fuel and initial laser deposition can be differentiated in our existing measurements. Better determining the dominant degradation mechanisms can directly influence the direction we take to improve performance, or our confidence in scaling these targets to higher currents. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. DoE's NNSA under contract DE-NA0003525.

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.

Feline immunodeficiency virus (FIV) env recombinants are common in natural infections.

PubMed

Bęczkowski, Paweł M; Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J; Hosie, Margaret J

2014-09-17

Recombination is a common feature of retroviral biology and one of the most important factors responsible for generating viral diversity at both the intra-host and the population levels. However, relatively little is known about rates and molecular processes of recombination for retroviruses other than HIV, including important model viruses such as feline immunodeficiency virus (FIV). We investigated recombination in complete FIV env gene sequences (n = 355) isolated from 43 naturally infected cats. We demonstrated that recombination is abundant in natural FIV infection, with over 41% of the cats being infected with viruses containing recombinant env genes. In addition, we identified shared recombination breakpoints; the most significant hotspot occurred between the leader/signal fragment and the remainder of env. Our results have identified the leader/signal fragment of env as an important site for recombination and highlight potential limitations of the current phylogenetic classification of FIV based on partial env sequences. Furthermore, the presence of abundant recombinant FIV in the USA poses a significant challenge for commercial diagnostic tests and should inform the development of the next generation of FIV vaccines.

Properties of the surface generation-recombination noise in 1.94 μm GaSb-based laser diodes

NASA Astrophysics Data System (ADS)

Glemža, Justinas; Palenskis, Vilius; Pralgauskaitė, Sandra; Vyšniauskas, Juozas; Matukas, Jonas

2018-06-01

A detail investigation of generation-recombination (g-r) noise in 1.94 μm GaSb-based type-I ridge waveguide laser diodes (LDs) has been performed in a temperature range (230-295) K. Lorentzian-type noise spectra have been observed in the current range below the threshold at the forward and reverse biases of the LDs with the same characteristic time (3.7 μs) and activation energy (≈0.37 eV) of charge carriers transitions associated with the g-r processes. An equivalent electrical circuit possessing the voltage noise source is presented, which allows the description of both the current-voltage characteristic and the voltage fluctuation spectral density of the laser diode. Results indicate that the origin of the g-r noise in the investigated samples is the surface recombination caused by the surface leakage current channel between n+GaSb and p+GaSb contacts, which is practically independent from the applied bias polarity.

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, 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. 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

Characterization of recombination features and the genetic basis in multiple cattle breeds.

PubMed

Shen, Botong; Jiang, Jicai; Seroussi, Eyal; Liu, George E; Ma, Li

2018-04-27

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds. Collectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an

RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence.

PubMed

Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone; Acevedo, Ashley; Goldstein, Elizabeth Faul; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

2016-04-13

Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations. Copyright © 2016 Elsevier Inc. All rights reserved.

Topographic-driven instabilities in terrestrial bodies

NASA Astrophysics Data System (ADS)

Vantieghem, S.; Cebron, D.; Herreman, W.; Lacaze, L.

2013-12-01

Models of internal planetary fluid layers (core flows, subsurface oceans) commonly assume that these fluid envelopes have a spherical shape. This approximation however entails a serious restriction from the fluid dynamics point of view. Indeed, in the presence of mechanical forcings (precession, libration, nutation or tides) due to gravitational interaction with orbiting partners, boundary topography (e.g. of the core-mantle boundary) may excite flow instabilities and space-filling turbulence. These phenomena may affect heat transport and dissipation at the main order. Here, we focus on instabilities driven by longitudinal libration. Using a suite of theoretical tools and numerical simulations, we are able to discern a parameter range for which instability may be excited. We thereby consider deformations of different azimuthal order. This study gives the first numerical evidence of the tripolar instability. Furthermore, we explore the non-linear regime and investigate the amplitude as well as the dissipation of the saturated instability. Indeed, these two quantities control the torques on the solid layers and the thermal transport. Furthermore, based on this results, we address the issue of magnetic field generation associated with these flows (by induction or by dynamo process). This instability mechanism applies to both synchronized as non-synchronized bodies. As such, our results show that a tripolar instability might be present in various terrestrial bodies (Early Moon, Gallilean moons, asteroids, etc.), where it could participate in dynamo action. Simulation of a libration-driven tripolar instability in a deformed spherical fluid layer: snapshot of the velocity magnitude, where a complex 3D flow pattern is established.

Instability Coupling Experiments*

NASA Astrophysics Data System (ADS)

Chrien, R. E.; Hoffman, N. M.; Magelssen, G. R.; Schappert, G. T.; Smitherman, D. P.

1996-11-01

The coupling of Richtmyer-Meshkov (RM) and ablative Rayleigh-Taylor (ART) instabilities is being studied with indirectly-driven planar foil experiments on the Nova laser at Livermore. The foil is attached to a 1.6-mm-diameter, 2.75-mm-long Au hohlraum driven by a 2.2-ns long, 1:5-contrast-ratio shaped laser pulse. A shock is generated in 35-μm or 86-μm thick Al foils with a 50-μm-wavelength, 4-μm-amplitude sinusoidal perturbation on its rear surface. In some experiments, the perturbation is applied to a 10-μm Be layer on the Al. A RM instability develops when the shock encounters the perturbed surface. The flow field of the RM instability can ``feed out'' to the ablation surface of the foil and provide the seed for ART perturbation growth. Face-on and side-on x-radiography are used to observe areal density perturbations in the foil. For the 86-μm foil, the perturbation arrives at the ablation surface while the hohlraum drive is dropping and the data are consistent with RM instability alone. For the 35-μm foil, the perturbation feeds out while the hohlraum drive is close to its peak and the data appear to show strong ART perturbation growth. Comparisons with LASNEX simulations will be presented. *This work supported under USDOE contract W-7405-ENG-36.

Radiation-induced genomic instability and its implications for radiation carcinogenesis

NASA Technical Reports Server (NTRS)

Huang, Lei; Snyder, Andrew R.; Morgan, William F.

2003-01-01

Radiation-induced genomic instability is characterized by an increased rate of genetic alterations including cytogenetic rearrangements, mutations, gene amplifications, transformation and cell death in the progeny of irradiated cells multiple generations after the initial insult. Chromosomal rearrangements are the best-characterized end point of radiation-induced genomic instability, and many of the rearrangements described are similar to those found in human cancers. Chromosome breakage syndromes are defined by chromosome instability, and individuals with these diseases are cancer prone. Consequently, chromosomal instability as a phenotype may underlie some fraction of those changes leading to cancer. Here we attempt to relate current knowledge regarding radiation-induced chromosome instability with the emerging molecular information on the chromosome breakage syndromes. The goal is to understand how genetic and epigenetic factors might influence the onset of chromosome instability and the role of chromosomal instability in carcinogenesis.

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

PubMed Central

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

2016-01-01

Despite being intensely studied for more than 50 years, a complete understanding of the enterovirus replication cycle remains elusive. Specifically, only a handful of cellular proteins have been shown to be involved in the RNA replication cycle of these viruses. In an effort to isolate and identify additional cellular proteins that function in enteroviral RNA replication, we have generated multiple recombinant polioviruses containing RNA affinity tags within the 3′ or 5′ noncoding region of the genome. These recombinant viruses retained RNA affinity sequences within the genome while remaining viable and infectious over multiple passages in cell culture. Further characterization of these viruses demonstrated that viral protein production and growth kinetics were unchanged or only slightly altered relative to wild type poliovirus. However, attempts to isolate these genetically-tagged viral genomes from infected cells have been hindered by high levels of co-purification of nonspecific proteins and the limited matrix-binding efficiency of RNA affinity sequences. Regardless, these recombinant viruses represent a step toward more thorough characterization of enterovirus ribonucleoprotein complexes involved in RNA replication. PMID:26861382

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.

Bimolecular recombination quenching in Langmuir Blodgett multilayers

NASA Astrophysics Data System (ADS)

Elliott, J. E.; Jeong, I. S.; Scott, K.; Donovan, K. J.; Wilson, E. G.

2000-11-01

A model is developed that describes bimolecular recombination of photogenerated carriers in two dimensional systems. Carriers are free to diffuse in two dimensions and undergo bimolecular recombination, while drifting under the influence of an electric field in the third dimension. The model describes a competition between carrier loss due to transiting and loss due to bimolecular recombination. This model of recombination quenching is then used to obtain information on microscopic parameters associated with photogeneration efficiency and charge transport in organic quantum wells formed from Langmuir Blodgett films of conjugated molecules. The ratio of the intralayer to interlayer tunneling rates is found along with the quantum efficiency for photocarrier generation for two bis-phthalocyanine amphiphilic molecules.

Heterogeneous recombination among Hepatitis B virus genotypes.

PubMed

Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

2017-10-01

The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

An Experimental Investigation of Incompressible Richtmyer-Meshkov Instability

NASA Technical Reports Server (NTRS)

Jacobs, J. W.; Niederhaus, C. E.

2002-01-01

Richtmyer-Meshkov (RM) instability occurs when two different density fluids are impulsively accelerated in the direction normal to their nearly planar interface. The instability causes small perturbations on the interface to grow and eventually become a turbulent flow. It is closely related to Rayleigh-Taylor instability, which is the instability of a planar interface undergoing constant acceleration, such as caused by the suspension of a heavy fluid over a lighter one in the earth's gravitational field. Like the well-known Kelvin-Helmholtz instability, RM instability is a fundamental hydrodynamic instability which exhibits many of the nonlinear complexities that transform simple initial conditions into a complex turbulent flow. Furthermore, the simplicity of RM instability (in that it requires very few defining parameters), and the fact that it can be generated in a closed container, makes it an excellent test bed to study nonlinear stability theory as well as turbulent transport in a heterogeneous system. However, the fact that RM instability involves fluids of unequal densities which experience negligible gravitational force, except during the impulsive acceleration, requires RM instability experiments to be carried out under conditions of microgravity. This experimental study investigates the instability of an interface between incompressible, miscible liquids with an initial sinusoidal perturbation. The impulsive acceleration is generated by bouncing a rectangular tank containing two different density liquids off a retractable vertical spring. The initial perturbation is produced prior to release by oscillating the tank in the horizontal direction to produce a standing wave. The instability evolves in microgravity as the tank travels up and then down the vertical rails of a drop tower until hitting a shock absorber at the bottom. Planar Laser Induced Fluorescence (PLIF) is employed to visualize the flow. PLIF images are captured by a video camera that travels

Characterization of recombination features and the genetic basis in multiple cattle breeds

USDA-ARS?s Scientific Manuscript database

Background: Crossover generated by meiotic recombination is a fundamental event which facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination between species, but the characterization of recombination between bovine breeds remains elusive. Cattle p...

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...

Generation of insulin-producing human mesenchymal stem cells using recombinant adeno-associated virus.

PubMed

Kim, Jeong Hwan; Park, Si-Nae; Suh, Hwal

2007-02-28

The purpose of current experiment is the generation of insulin-producing human mesenchymal stem cells as therapeutic source for the cure of type 1 diabetes. Type 1 diabetes is generally caused by insulin deficiency accompanied by the destruction of islet beta-cells. In various trials for the treatment of type 1 diabetes, cell-based gene therapy using stem cells is considered as one of the most useful candidate for the treatment. In this experiment, human mesenchymal stem cells were transduced with AAV which is containing furin-cleavable human preproinsulin gene to generate insulin-producing cells as surrogate beta-cells for the type 1 diabetes therapy. In the rAAV production procedure, rAAV was generated by transfection of AD293 cells. Human mesenchymal stems cells were transduced using rAAV with a various multiplicity of infection. Transduction of recombinant AAV was also tested using beta-galactosidse expression. Cell viability was determined by using MTT assay to evaluate the toxicity of the transduction procedure. Expression and production of Insulin were tested using reverse transcriptase-polymerase chain reaction and immunocytochemistry. Secretion of human insulin and C-peptide from the cells was assayed using enzyme-linked immunosorbent assay. Production of insulin and C-peptide from the test group represented a higher increase compared to the control group. In this study, we examined generation of insulin-producing cells from mesenchymal stem cells by genetic engineering for diabetes therapy. This work might be valuable to the field of tissue engineering for diabetes treatment.

Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

PubMed Central

Chen, Yue; Hora, Bhavna; DeMarco, Todd; Shah, Sharaf Ali; Ahmed, Manzoor; Sanchez, Ana M.; Su, Chang; Carter, Meredith; Stone, Mars; Hasan, Rumina; Hasan, Zahra; Busch, Michael P.; Denny, Thomas N.; Gao, Feng

2016-01-01

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan. PMID:27973597

Resonant Drag Instabilities in protoplanetary disks: the streaming instability and new, faster-growing instabilities

NASA Astrophysics Data System (ADS)

Squire, Jonathan; Hopkins, Philip F.

2018-04-01

We identify and study a number of new, rapidly growing instabilities of dust grains in protoplanetary disks, which may be important for planetesimal formation. The study is based on the recognition that dust-gas mixtures are generically unstable to a Resonant Drag Instability (RDI), whenever the gas, absent dust, supports undamped linear modes. We show that the "streaming instability" is an RDI associated with epicyclic oscillations; this provides simple interpretations for its mechanisms and accurate analytic expressions for its growth rates and fastest-growing wavelengths. We extend this analysis to more general dust streaming motions and other waves, including buoyancy and magnetohydrodynamic oscillations, finding various new instabilities. Most importantly, we identify the disk "settling instability," which occurs as dust settles vertically into the midplane of a rotating disk. For small grains, this instability grows many orders of magnitude faster than the standard streaming instability, with a growth rate that is independent of grain size. Growth timescales for realistic dust-to-gas ratios are comparable to the disk orbital period, and the characteristic wavelengths are more than an order of magnitude larger than the streaming instability (allowing the instability to concentrate larger masses). This suggests that in the process of settling, dust will band into rings then filaments or clumps, potentially seeding dust traps, high-metallicity regions that in turn seed the streaming instability, or even overdensities that coagulate or directly collapse to planetesimals.

SequenceLDhot: detecting recombination hotspots.

PubMed

Fearnhead, Paul

2006-12-15

There is much local variation in recombination rates across the human genome--with the majority of recombination occurring in recombination hotspots--short regions of around approximately 2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease genes. Population genetic data, such as that generated by the HapMap project, can be used to infer the location of these hotspots. We present a new, efficient and powerful method for detecting recombination hotspots from population data. We compare our method with four current methods for detecting hotspots. It is orders of magnitude quicker, and has greater power, than two related approaches. It appears to be more powerful than HotspotFisher, though less accurate at inferring the precise positions of the hotspot. It was also more powerful than LDhot in some situations: particularly for weaker hotspots (10-40 times the background rate) when SNP density is lower (< 1/kb). Program, data sets, and full details of results are available at: http://www.maths.lancs.ac.uk/~fearnhea/Hotspot.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kukushkin, V. A., E-mail: vakuk@appl.sci-nnov.ru

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 bemore » used to generate picosecond pulses of ultraviolet and soft X-ray electromagnetic field at a wavelength of 235 nm.« less

Transverse electron-scale instability in relativistic shear flows.

PubMed

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

2015-08-01

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

The Electric Honeycomb; an investigation of the Rose window instability

NASA Astrophysics Data System (ADS)

Niazi, Muhammad Shaheer

2017-10-01

The Rose window instability is a little-explored electrohydrodynamic instability that manifests when a layer of low-conducting oil is placed in an electric field generated by corona discharge in a point-to-plane configuration. Above a critical voltage, the instability starts as a single dimple in the oil layer right below the point electrode and subsequently evolves into a characteristic pattern of polygonal cells. In this study, we experimentally explore governing parameters that guide the instability and document geometric attributes of the characteristic cellular pattern. The driving force for the instability has been attributed to the buildup of charged ions which in turn apply an electric pressure on the oil surface. We confirm the charged surface distribution using thermal imaging and demonstrate that the instability can be locally inhibited by preventing charge buildup under an ion shadow.

The Electric Honeycomb; an investigation of the Rose window instability

PubMed Central

2017-01-01

The Rose window instability is a little-explored electrohydrodynamic instability that manifests when a layer of low-conducting oil is placed in an electric field generated by corona discharge in a point-to-plane configuration. Above a critical voltage, the instability starts as a single dimple in the oil layer right below the point electrode and subsequently evolves into a characteristic pattern of polygonal cells. In this study, we experimentally explore governing parameters that guide the instability and document geometric attributes of the characteristic cellular pattern. The driving force for the instability has been attributed to the buildup of charged ions which in turn apply an electric pressure on the oil surface. We confirm the charged surface distribution using thermal imaging and demonstrate that the instability can be locally inhibited by preventing charge buildup under an ion shadow. PMID:29134066

Space-Charge Waves and Instabilities in Intense Beams

NASA Astrophysics Data System (ADS)

Wang, J. G.

1997-11-01

Advancced accelerator applications, such as drivers for heavy ion inertial fusion, high-intensity synchrotrons for spallation neutron sources, high energy boosters, free electron lasers, high-power microwave generators, etc., require ever-increasing beam intensity. An important beam dynamics issue in such beams is the collective behavior of charged particles due to their space charge effects. This includes the phenomena of space-charge waves and instabilities excited on beams by external perturbations. It is very crucial to fully understand these phenomena in order to develop advanced accelerators for various applications. At the University of Maryland we have been conducting experimental programs to study space-charge waves and longitudinal instabilities by employing low-energy, high-current, space-charge dominated electron beams. Localized perturbations on the beams are generated from a gridded electron gun. In a conducting transport channel focused by short solenoids, these perturbations evolve into space-charge waves propagating on the beams. The wave speed is measured and many beam parameters are determined with this technique. The reflection of space-charge waves at the shoulder of an initially rectangular beam bunch is also observed. In a resistive-wall channel focused by a uniform long solenoid, the space-charge waves suffer longitudinal instability. The properties of the instabilities are studied in detail in the long wavelength range. In this talk we review our experimental results on the waves and instabilities and compare with theory.

Mammalian chiasma frequencies as a test of two theories of recombination.

PubMed

Burt, A; Bell, G

A broad survey of asexuality in the animal kingdom is sufficient to reject all theories of sex and recombination except two: the Red Queen and the Tangled Bank. The Red Queen theory states that an organism's biotic environment tends to be 'contrary', consistently evolving to the detriment of the organism; sex and recombination result in progeny genetically distinct from their parents and grandparents and thus less susceptible to the antagonistic advances made during the previous generations, particularly by their parasites. The alternative theory, the Tangled Bank, states that sex and recombination function to diversify the progeny from each other, thus reducing competition between them. An extensive survey of mammalian recombination shows that the total number of chiasmata in excess of one per bivalent is strongly correlated with generation time but uncorrelated with fecundity. We conclude that crossing-over may function to combat antagonists with short generation times but does not function to reduce sib competition. Chromosome number is selectively neutral with respect to these factors.

In vivo production of recombinant proteins using occluded recombinant AcMNPV-derived baculovirus vectors.

PubMed

Guijarro-Pardo, Eva; Gómez-Sebastián, Silvia; Escribano, José M

2017-12-01

Trichoplusia ni insect larvae infected with vectors derived from the Autographa californica multiple nucleopolyhedrovirus (AcMNPV), are an excellent alternative to insect cells cultured in conventional bioreactors to produce recombinant proteins because productivity and cost-efficiency reasons. However, there is still a lot of work to do to reduce the manual procedures commonly required in this production platform that limit its scalability. To increase the scalability of this platform technology, a current bottleneck to be circumvented in the future is the need of injection for the inoculation of larvae with polyhedrin negative baculovirus vectors (Polh-) because of the lack of oral infectivity of these viruses, which are commonly used for production in insect cell cultures. In this work we have developed a straightforward alternative to obtain orally infective vectors derived from AcMNPV and expressing recombinant proteins that can be administered to the insect larvae (Trichoplusia ni) by feeding, formulated in the insect diet. The approach developed was based on the use of a recombinant polyhedrin protein expressed by a recombinant vector (Polh+), able to co-occlude any recombinant Polh- baculovirus vector expressing a recombinant protein. A second alternative was developed by the generation of a dual vector co-expressing the recombinant polyhedrin protein and the foreign gene of interest to obtain the occluded viruses. Additionally, by the incorporation of a reporter gene into the helper Polh+ vector, it was possible the follow-up visualization of the co-occluded viruses infection in insect larvae and will help to homogenize infection conditions. By using these methodologies, the production of recombinant proteins in per os infected larvae, without manual infection procedures, was very similar in yield to that obtained by manual injection of recombinant Polh- AcMNPV-based vectors expressing the same proteins. However, further analyses will be required for a

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

USDA-ARS?s Scientific Manuscript database

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

Direct Simulation of Evolution and Control of Nonlinear Instabilities in Attachment-Line Boundary Layers

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.

2004-01-01

The unsteady, incompressible Navier-Stokes equations are used for the direct numerical simulation (DNS) of spatially evolving disturbances in a three-dimensional (3-D) attachment-line boundary layer. Two-dimensional (2-D) disturbances are introduced either by forcing at the in ow or by harmonic-source generators at the wall; 3-D disturbances are introduced by harmonic-source generators at the wall. The DNS results are in good agreement with both 2-D non-parallel theory (for small-amplitude disturbances) and weakly nonlinear theory (for finite-amplitude disturbances), which validates the two theories. The 2-D DNS results indicate that nonlinear disturbance growth occurs near branch II of the neutral stability curve; however, steady suction can be used to stabilize this disturbance growth. For 3-D instabilities that are generated o the attachment line, spreading both toward and away from the attachment line causes energy transfer to the attachment-line and downstream instabilities; suction stabilizes these instabilities. Furthermore, 3-D instabilities are more stable than 2-D or quasi-2-D instabilities.

Electromechanical instability in soft materials: Theory, experiments and applications

NASA Astrophysics Data System (ADS)

Suo, Zhigang

2013-03-01

Subject to a voltage, a membrane of a dielectric elastomer reduces thickness and expands area, possibly straining over 100%. The phenomenon is being developed as transducers for broad applications, including soft robots, adaptive optics, Braille displays, and electric generators. The behavior of dielectric elastomers is closely tied to electromechanical instability. This instability may limit the performance of devices, and may also be used to achieve giant actuation strains. This talk reviews the theory of dielectric elastomers, coupling large deformation and electric potential. The theory is developed within the framework of continuum mechanics and thermodynamics. The theory attempts to answer commonly asked questions. How do mechanics and electrostatics work together to generate large deformation? How efficiently can a material convert energy from one form to another? How do molecular processes affect macroscopic behavior? The theory is used to describe electromechanical instability, and is related to recent experiments.

A hydrodynamic instability for rip currents

NASA Astrophysics Data System (ADS)

Yu, J.; Chen, S.

2012-12-01

In Yu (2006), it is shown that on a planar beach a hydrodynamic instability can occur, leading to the generation of circulations that are related to rip currents. This instability depends on the mutual interaction of waves and evolving currents. In this study, we extend the analysis to non-planar profiles, include barred beaches. Both propagating and non-propagating unstable solutions are found. The oscillatory nature (in space and in time) of the propagating solutions may provide one explanation of the episodic events of rip currents on some beaches. Support from National Science Foundation (Grant CBET-0845957) is acknowledged.

High-efficiency generation of induced pluripotent mesenchymal stem cells from human dermal fibroblasts using recombinant proteins.

PubMed

Chen, Fanfan; Zhang, Guoqiang; Yu, Ling; Feng, Yanye; Li, Xianghui; Zhang, Zhijun; Wang, Yongting; Sun, Dapeng; Pradhan, Sriharsa

2016-07-30

Induced pluripotent mesenchymal stem cells (iPMSCs) are novel candidates for drug screening, regenerative medicine, and cell therapy. However, introduction of transcription factor encoding genes for induced pluripotent stem cell (iPSC) generation which could be used to generate mesenchymal stem cells is accompanied by the risk of insertional mutations in the target cell genome. We demonstrate a novel method using an inactivated viral particle to package and deliver four purified recombinant Yamanaka transcription factors (Sox2, Oct4, Klf4, and c-Myc) resulting in reprogramming of human primary fibroblasts. Whole genome bisulfite sequencing was used to analyze genome-wide CpG methylation of human iPMSCs. Western blot, quantitative PCR, immunofluorescence, and in-vitro differentiation were used to assess the pluripotency of iPMSCs. The resulting reprogrammed fibroblasts show high-level expression of stem cell markers. The human fibroblast-derived iPMSC genome showed gains in DNA methylation in low to medium methylated regions and concurrent loss of methylation in previously hypermethylated regions. Most of the differentially methylated regions are close to transcription start sites and many of these genes are pluripotent pathway associated. We found that DNA methylation of these genes is regulated by the four iPSC transcription factors, which functions as an epigenetic switch during somatic reprogramming as reported previously. These iPMSCs successfully differentiate into three embryonic germ layer cells, both in vitro and in vivo. Following multipotency induction in our study, the delivered transcription factors were degraded, leading to an improved efficiency of subsequent programmed differentiation. Recombinant transcription factor based reprogramming and derivatization of iPMSC offers a novel high-efficiency approach for regenerative medicine from patient-derived cells.

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.

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

Differences between selection on sex versus recombination in red queen models with diploid hosts.

PubMed

Agrawal, Aneil F

2009-08-01

The Red Queen hypothesis argues that parasites generate selection for genetic mixing (sex and recombination) in their hosts. A number of recent papers have examined this hypothesis using models with haploid hosts. In these haploid models, sex and recombination are selectively equivalent. However, sex and recombination are not equivalent in diploids because selection on sex depends on the consequences of segregation as well as recombination. Here I compare how parasites select on modifiers of sexual reproduction and modifiers of recombination rate. Across a wide set of parameters, parasites tend to select against both sex and recombination, though recombination is favored more often than is sex. There is little correspondence between the conditions favoring sex and those favoring recombination, indicating that the direction of selection on sex is often determined by the effects of segregation, not recombination. Moreover, when sex was favored it is usually due to a long-term advantage whereas short-term effects are often responsible for selection favoring recombination. These results strongly indicate that Red Queen models focusing exclusively on the effects of recombination cannot be used to infer the type of selection on sex that is generated by parasites on diploid hosts.

FANCD2 limits replication stress and genome instability in cells lacking BRCA2

PubMed Central

Buffa, Francesca M.; McDermott, Ultan; Tarsounas, Madalena

2016-01-01

The tumor suppressor BRCA2 plays a key role in genome integrity by promoting replication fork stability and homologous recombination (HR) DNA repair. Here we report that human cancer cells lacking BRCA2 rely on the Fanconi anemia protein FANCD2 to limit replication fork progression and genomic instability. Our results identify a novel role for FANCD2 in limiting constitutive replication stress in BRCA2-deficient cells, which impacts on cell survival and treatment responses. PMID:27322732

A versatile microsatellite instability reporter system in human cells.

PubMed

Koole, Wouter; Schäfer, Henning S; Agami, Reuven; van Haaften, Gijs; Tijsterman, Marcel

2013-09-01

Here, we report the investigation of microsatellite instability (MSI) in human cells with a newly developed reporter system based on fluorescence. We composed a vector into which microsatellites of different lengths and nucleotide composition can be introduced between a functional copy of the fluorescent protein mCherry and an out-of-frame copy of EGFP; in vivo frameshifting will lead to EGFP expression, which can be quantified by fluorescence activated cell sorting (FACS). Via targeted recombineering, single copy reporters were introduced in HEK293 and MCF-7 cells. We found predominantly -1 and +1 base pair frameshifts, the levels of which are kept in tune by mismatch repair. We show that tract length and composition greatly influences MSI. In contrast, a tracts' potential to form a G-quadruplex structure, its strand orientation or its transcriptional status is not affecting MSI. We further validated the functionality of the reporter system for screening microsatellite mutagenicity of compounds and for identifying modifiers of MSI: using a retroviral miRNA expression library, we identified miR-21, which targets MSH2, as a miRNA that induces MSI when overexpressed. Our data also provide proof of principle for the strategy of combining fluorescent reporters with next-generation sequencing technology to identify genetic factors in specific pathways.

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.

Correlated Template-Switching Events during Minus-Strand DNA Synthesis: a Mechanism for High Negative Interference during Retroviral Recombination

PubMed Central

Anderson, Jeffrey A.; Teufel, Ronald J.; Yin, Philip D.; Hu, Wei-Shau

1998-01-01

Two models for the mechanism of retroviral recombination have been proposed: forced copy choice (minus-strand recombination) and strand displacement-assimilation (plus-strand recombination). Each minus-strand recombination event results in one template switch, whereas each plus-strand recombination event results in two template switches. Recombinant proviruses with one and more than one template switches were previously observed. Recombinants with one template switch were generated by minus-strand recombination, while recombinants containing more than one template switch may have been generated by plus-strand recombination or by correlated minus-strand recombination. We recently observed that retroviral recombination exhibits high negative interference whereby the frequency of recombinants containing multiple template-switching events is higher than expected. To delineate the mechanism that generates recombinants with more than one template switch, we devised a system that permits only minus-strand recombination. Two highly homologous vectors, WH204 and WH221, containing eight different restriction site markers were used. The primer binding site (PBS) of WH221 was deleted; although reverse transcription cannot initiate from WH221 RNA, it can serve as a template for DNA synthesis in heterozygotic virions. After one round of retroviral replication, the structures of the recombinant proviruses were examined. Recombinants containing two, three, four, and five template switches were observed at 1.4-, 10-, 65-, and 50-fold-higher frequencies, respectively, than expected. This indicates that minus-strand recombination events are correlated and can generate proviruses with multiple template switches efficiently. The frequencies of recombinants containing multiple template switches were similar to those observed in the previous system, which allowed both minus- and plus-strand recombination. Thus, the previously reported high negative interference during retroviral

Mitochondrial Recombination Reveals Mito-Mito Epistasis in Yeast.

PubMed

Wolters, John F; Charron, Guillaume; Gaspary, Alec; Landry, Christian R; Fiumera, Anthony C; Fiumera, Heather L

2018-05-01

Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mito-nuclear interactions. Recombinant mtDNAs were generated to determine fitness components within high- and low-fitness mtDNAs. Based on phenotypic distributions of isogenic strains containing recombinant mtDNAs, we found that multiple loci contributed to mitotype fitness differences. These mitochondrial loci interacted in epistatic, nonadditive ways in certain environmental conditions. Mito-mito epistasis ( i.e. , nonadditive interactions between mitochondrial loci) influenced fitness in progeny from four different crosses, suggesting that mito-mito epistasis is a widespread phenomenon in yeast and other systems with recombining mtDNAs. Furthermore, we found that interruption of coadapted mito-mito interactions produced recombinant mtDNAs with lower fitness. Our results demonstrate that mito-mito epistasis results in functional variation through mitochondrial recombination in fungi, providing modes for adaptive evolution and the generation of mito-mito incompatibilities. Copyright © 2018 by the Genetics Society of America.

Inferring Strength of Tantalum from Hydrodynamic Instability Recovery Experiments

NASA Astrophysics Data System (ADS)

Sternberger, Z.; Maddox, B.; Opachich, Y.; Wehrenberg, C.; Kraus, R.; Remington, B.; Randall, G.; Farrell, M.; Ravichandran, G.

2018-05-01

Hydrodynamic instability experiments allow access to material properties at extreme conditions, where strain rates exceed 105 s-1 and pressures reach 100 GPa. Current hydrodynamic instability experimental methods require in-flight radiography to image the instability growth at high pressure and high strain rate, limiting the facilities where these experiments can be performed. An alternate approach, recovering the sample after loading, allows measurement of the instability growth with profilometry. Tantalum samples were manufactured with different 2D and 3D initial perturbation patterns and dynamically compressed by a blast wave generated by laser ablation. The samples were recovered from peak pressures between 30 and 120 GPa and strain rates on the order of 107 s-1, providing a record of the growth of the perturbations due to hydrodynamic instability. These records are useful validation points for hydrocode simulations using models of material strength at high strain rate. Recovered tantalum samples were analyzed, providing an estimate of the strength of the material at high pressure and strain rate.

The rise and fall of a human recombination hot spot.

PubMed

Jeffreys, Alec J; Neumann, Rita

2009-05-01

Human meiotic crossovers mainly cluster into narrow hot spots that profoundly influence patterns of haplotype diversity and that may also affect genome instability and sequence evolution. Hot spots also seem to be ephemeral, but processes of hot-spot activation and their subsequent evolutionary dynamics remain unknown. We now analyze the life cycle of a recombination hot spot. Sperm typing revealed a polymorphic hot spot that was activated in cis by a single base change, providing evidence for a primary sequence determinant necessary, though not sufficient, to activate recombination. This activating mutation occurred roughly 70,000 y ago and has persisted to the present, most likely fortuitously through genetic drift despite its systematic elimination by biased gene conversion. Nonetheless, this self-destructive conversion will eventually lead to hot-spot extinction. These findings define a subclass of highly transient hot spots and highlight the importance of understanding hot-spot turnover and how it influences haplotype diversity.

Kinetic modeling sheds light on the mode of action of recombinant factor VIIa on thrombin generation.

PubMed

Mitrophanov, Alexander Y; Reifman, Jaques

2011-10-01

The therapeutic potential of a hemostatic agent can be assessed by investigating its effects on the quantitative parameters of thrombin generation. For recombinant activated factor VII (rFVIIa)--a promising hemostasis-inducing biologic--experimental studies addressing its effects on thrombin generation yielded disparate results. To elucidate the inherent ability of rFVIIa to modulate thrombin production, it is necessary to identify rFVIIa-induced effects that are compatible with the available biochemical knowledge about thrombin generation mechanisms. The existing body of knowledge about coagulation biochemistry can be rigorously represented by a computational model that incorporates the known reactions and parameter values constituting the biochemical network. We used a thoroughly validated numerical model to generate activated factor VII (FVIIa) titration curves in the cases of normal blood composition, hemophilia A and B blood, blood lacking factor VII, blood lacking tissue factor pathway inhibitor, and diluted blood. We utilized the generated curves to perform systematic fold-change analyses for five quantitative parameters characterizing thrombin accumulation. The largest fold changes induced by increasing FVIIa concentration were observed for clotting time, thrombin peak time, and maximum slope of the thrombin curve. By contrast, thrombin peak height was much less affected by FVIIa titrations, and the area under the thrombin curve stayed practically unchanged. Comparisons with experimental data demonstrated that the computationally derived patterns can be observed in vitro. rFVIIa modulates thrombin generation primarily by accelerating the process, without significantly affecting the total amount of generated thrombin. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2014-01-01

ABSTRACT Interleukin 18 (IL-18) plays an important role in the T-helper-cell type 1 immune response against intracellular parasites, bacteria and viral infections. It has been widely used as an adjuvant for vaccines and as an anticancer agent. However, IL-18 protein lacks a typical signal sequence and requires cleavage into its mature active form by caspase 1. In this study, we constructed mammalian expression vectors carrying cDNA encoding mature canine IL-18 (cIL-18) or mouse IL-18 (mIL-18) fused to the human IL-2 (hIL-2) signal sequence. The expressed proIL-18 proteins were processed to their mature forms in the cells. The supernatants of cells transfected with these plasmids induced high interferon-γ production in canine peripheral blood mononuclear cells or mouse splenocytes, respectively, indicating the secretion of bioactive IL-18. Using reverse genetics, we also generated a recombinant canine distemper virus that expresses cIL-18 or mIL-18 fused to the hIL-2 signal sequence. As expected, both recombinant viruses produced mature IL-18 in the infected cells, which secreted bioactive IL-18. These results indicate that the signal sequence from hIL-2 is suitable for the secretion of mature IL-18. These recombinant viruses can also potentially be used as immunoadjuvants and agents for anticancer therapies in vivo. PMID:24898077

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.

Phosphorylation of Exo1 modulates homologous recombination repair of DNA double-strand breaks

PubMed Central

Bolderson, Emma; Tomimatsu, Nozomi; Richard, Derek J.; Boucher, Didier; Kumar, Rakesh; Pandita, Tej K.; Burma, Sandeep; Khanna, Kum Kum

2010-01-01

DNA double-strand break (DSB) repair via the homologous recombination pathway is a multi-stage process, which results in repair of the DSB without loss of genetic information or fidelity. One essential step in this process is the generation of extended single-stranded DNA (ssDNA) regions at the break site. This ssDNA serves to induce cell cycle checkpoints and is required for Rad51 mediated strand invasion of the sister chromatid. Here, we show that human Exonuclease 1 (Exo1) is required for the normal repair of DSBs by HR. Cells depleted of Exo1 show chromosomal instability and hypersensitivity to ionising radiation (IR) exposure. We find that Exo1 accumulates rapidly at DSBs and is required for the recruitment of RPA and Rad51 to sites of DSBs, suggesting a role for Exo1 in ssDNA generation. Interestingly, the phosphorylation of Exo1 by ATM appears to regulate the activity of Exo1 following resection, allowing optimal Rad51 loading and the completion of HR repair. These data establish a role for Exo1 in resection of DSBs in human cells, highlighting the critical requirement of Exo1 for DSB repair via HR and thus the maintenance of genomic stability. PMID:20019063

Regulation of Meiotic Recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory p. Copenhaver

facile system 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« less

Recombinant Allergens in Structural Biology, Diagnosis, and Immunotherapy

PubMed Central

Tscheppe, Angelika; Breiteneder, Heimo

2017-01-01

The years 1988–1995 witnessed the beginning of allergen cloning and the generation of recombinant allergens, which opened up new avenues for the diagnosis and research of human allergic diseases. Most crystal and solution structures of allergens have been obtained using recombinant allergens. Structural information on allergens allows insights into their evolutionary biology, illustrates clinically observed cross-reactivities, and makes the design of hypoallergenic derivatives for allergy vaccines possible. Recombinant allergens are widely used in molecule-based allergy diagnosis such as protein microarrays or suspension arrays. Recombinant technologies have been used to produce well-characterized, noncontaminated vaccine components with known biological activities including a variety of allergen derivatives with reduced IgE reactivity. Such recombinant hypoallergens as well as wild-type recombinant allergens have been used successfully in several immunotherapy trials for more than a decade to treat birch and grass pollen allergy. As a more recent application, the development of antibody repertoires directed against conformational epitopes during immunotherapy has been monitored by recombinant allergen chimeras. Although much progress has been made, the number and quality of recombinant allergens will undoubtedly increase and keep improving our knowledge in basic scientific investigations, diagnosis, and therapy of human allergic diseases. PMID:28467993

Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus

PubMed Central

Thor, Sharmi W.; Hilt, Deborah A.; Kissinger, Jessica C.; Paterson, Andrew H.; Jackwood, Mark W.

2011-01-01

Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus. PMID:21994806

The evolution of recombination in a heterogeneous environment.

PubMed Central

Lenormand, T; Otto, S P

2000-01-01

Most models describing the evolution of recombination have focused on the case of a single population, implicitly assuming that all individuals are equally likely to mate and that spatial heterogeneity in selection is absent. In these models, the evolution of recombination is driven by linkage disequilibria generated either by epistatic selection or drift. Models based on epistatic selection show that recombination can be favored if epistasis is negative and weak compared to directional selection and if the recombination modifier locus is tightly linked to the selected loci. In this article, we examine the joint effects of spatial heterogeneity in selection and epistasis on the evolution of recombination. In a model with two patches, each subject to different selection regimes, we consider the cases of mutation-selection and migration-selection balance as well as the spread of beneficial alleles. We find that including spatial heterogeneity extends the range of epistasis over which recombination can be favored. Indeed, recombination can be favored without epistasis, with negative and even with positive epistasis depending on environmental circumstances. The selection pressure acting on recombination-modifier loci is often much stronger with spatial heterogeneity, and even loosely linked modifiers and free linkage may evolve. In each case, predicting whether recombination is favored requires knowledge of both the type of environmental heterogeneity and epistasis, as none of these factors alone is sufficient to predict the outcome. PMID:10978305

Oscillatory interfacial instability between miscible fluids

NASA Astrophysics Data System (ADS)

Shevtsova, Valentina; Gaponenko, Yuri; Mialdun, Aliaksandr; Torregrosa, Marita; Yasnou, Viktar

Interfacial instabilities occurring between two fluids are of fundamental interest in fluid dynamics, biological systems and engineering applications such as liquid storage, solvent extraction, oil recovery and mixing. Horizontal vibrations applied to stratified layers of immiscible liquids may generate spatially periodic waving of the interface, stationary in the reference frame of the vibrated cell, referred to as a "frozen wave". We present experimental evidence that frozen wave instability exists between two ordinary miscible liquids of similar densities and viscosities. At the experiments and at the numerical model, two superimposed layers of ordinary liquids, water-alcohol of different concentrations, are placed in a closed cavity in a gravitationally stable configuration. The density and viscosity of these fluids are somewhat similar. Similar to the immiscible fluids this instability has a threshold. When the value of forcing is increased the amplitudes of perturbations grow continuously displaying a saw-tooth structure. The decrease of gravity drastically changes the structure of frozen waves.

Vaccine instability in the cold chain: mechanisms, analysis and formulation strategies.

PubMed

Kumru, Ozan S; Joshi, Sangeeta B; Smith, Dawn E; Middaugh, C Russell; Prusik, Ted; Volkin, David B

2014-09-01

Instability of vaccines often emerges as a key challenge during clinical development (lab to clinic) as well as commercial distribution (factory to patient). To yield stable, efficacious vaccine dosage forms for human use, successful formulation strategies must address a combination of interrelated topics including stabilization of antigens, selection of appropriate adjuvants, and development of stability-indicating analytical methods. This review covers key concepts in understanding the causes and mechanisms of vaccine instability including (1) the complex and delicate nature of antigen structures (e.g., viruses, proteins, carbohydrates, protein-carbohydrate conjugates, etc.), (2) use of adjuvants to further enhance immune responses, (3) development of physicochemical and biological assays to assess vaccine integrity and potency, and (4) stabilization strategies to protect vaccine antigens and adjuvants (and their interactions) during storage. Despite these challenges, vaccines can usually be sufficiently stabilized for use as medicines through a combination of formulation approaches combined with maintenance of an efficient cold chain (manufacturing, distribution, storage and administration). Several illustrative case studies are described regarding mechanisms of vaccine instability along with formulation approaches for stabilization within the vaccine cold chain. These include live, attenuated (measles, polio) and inactivated (influenza, polio) viral vaccines as well as recombinant protein (hepatitis B) vaccines. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Morphology of single Shockley-type stacking faults generated by recombination enhanced dislocation glide in 4H-SiC

NASA Astrophysics Data System (ADS)

Matsuhata, Hirofumi; Sekiguchi, Takashi

2018-04-01

Morphology of single Shockley-type stacking faults (SFs) generated by recombination enhanced dislocation glide (REDG) in 4H-SiC are discussed and analysed. A complete set of the 12 different dissociated states of basal-plane dislocation loops is obtained using the crystallographic space group operations. From this set, six different double rhombic-shaped SFs are derived. These tables indicate the rules that connect shapes of SFs with the locations of partial dislocations having different core structures, the positions of slip planes in a unit cell, and the Burgers vectors of partial dislocations. We applied these tables for the analysis of SFs generated by the REDG effect reported in the past articles. Shapes, growing process of SFs and perfect dislocations for origins of SFs were well analysed systematically.

phiC31 Integrase-Mediated Site-Specific Recombination in Barley

PubMed Central

Rubtsova, Myroslava; Kumlehn, Jochen; Gils, Mario

2012-01-01

The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity. PMID:23024817

Recombination rate plasticity: revealing mechanisms by design

PubMed Central

Sefick, Stephen; Rushton, Chase

2017-01-01

For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

Temporal Instabilities in Amblyopic Perception: A Quantitative Approach.

PubMed

Thiel, Aylin; Iftime, Adrian

2016-04-01

The purpose of this study is to quantify the temporal characteristics of spatial misperceptions in human amblyopia. Twenty-two adult participants with strabismus, strabismic, anisometropic, or mixed amblyopia were asked to describe their subjective percept of static geometrical patterns with different spatial frequencies and shapes, as seen with their non-dominant eye. We generated digital reconstructions of their perception (static images or movies) that were subsequently validated by the subjects using consecutive matching sessions. We calculated the Shannon entropy variation in time for each recorded movie, as a measure of temporal instability. Nineteen of the 22 subjects perceived temporal instabilities that can be broadly classified in two categories. We found that the average frequency of the perceived temporal instabilities is ∼1 Hz. The stimuli with higher spatial frequencies yielded more often temporally unstable perceptions with higher frequencies. We suggest that type and amount of temporal instabilities in amblyopic vision are correlated with the etiology and spatial frequency of the stimulus.

Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

PubMed Central

Throop, Andrea L.; LaBaer, Joshua

2015-01-01

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates this method from the classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular recombinational cloning technologies, including the commercially available Gateway® (Life Technologies) and In-Fusion® (Clontech) cloning technologies. PMID:25827088

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.

New Developments on the PSR Instability

NASA Astrophysics Data System (ADS)

Macek, Robert

2000-04-01

A strong, fast, transverse instability has long been observed at the Los Alamos Proton Storage Ring (PSR) where it is a limiting factor on peak intensity. Most of the characteristics and experimental data are consistent with a two-stream instability (e-p) arising from coupled oscillations of the proton beam and an electron cloud. In past operations, where the average intensity was limited by beam losses, the instability was controlled by sufficient rf voltage in the ring. The need for higher beam intensity has motivated new work to better understand and control the instability. Results will be presented from studies of the production and characteristics of the electron cloud at various locations in the ring for both stable and unstable beams and suppression of electron cloud generation by TiN coatings. Studies of additional or alternate controls include application of dual harmonic rf, damping of the instability by higher order multipoles, damping by X,Y coupling from skew quadrupoles and the use of inductive inserts to compensate longitudinal space charge forces. Use of a skew quadrupole, heated inductive inserts and higher rf voltage from a refurbished rf buncher has enabled the PSR to accumulate stable beam intensity up to 9.7 micro-Coulombs (6 E13 protons) per macropulse, a significant increase (60over the previous maximum of 6 micro-Coulombs (3.7 E13 protons). However, slow losses were rather high and must be reduced for routine operation at repetition rates of 20 Hz or higher.

Nonhomologous Recombination between Defective Poliovirus and Coxsackievirus Genomes Suggests a New Model of Genetic Plasticity for Picornaviruses

PubMed Central

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line

2014-01-01

ABSTRACT Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3′ end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. PMID:25096874

CRISPR-directed mitotic recombination enables genetic mapping without crosses.

PubMed

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

2016-05-27

Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR (clustered, regularly interspaced, short palindromic repeats) to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences. Copyright © 2016, American Association for the Advancement of Science.

The nucleus is the target for radiation-induced chromosomal instability

NASA Technical Reports Server (NTRS)

Kaplan, M. I.; Morgan, W. F.

1998-01-01

We have previously described chromosomal instability in cells of a human-hamster hybrid cell line after exposure to X rays. Chromosomal instability in these cells is characterized by the appearance of novel chromosomal rearrangements multiple generations after exposure to ionizing radiation. To identify the cellular target(s) for radiation-induced chromosomal instability, cells were treated with 125I-labeled compounds and frozen. Radioactive decays from 125I cause damage to the cell primarily at the site of their decay, and freezing the cells allows damage to accumulate in the absence of other cellular processes. We found that the decay of 125I-iododeoxyuridine, which is incorporated into the DNA, caused chromosomal instability. While cell killing and first-division chromosomal rearrangements increased with increasing numbers of 125I decays, the frequency of chromosomal instability was independent of dose. Chromosomal instability could also be induced from incorporation of 125I-iododeoxyuridine without freezing the cells for accumulation of decays. This indicates that DNA double-strand breaks in frozen cells resulting from 125I decays failed to lead to instability. Incorporation of an 125I-labeled protein (125I-succinyl-concanavalin A), which was internalized into the cell and/or bound to the plasma membrane, neither caused chromosomal instability nor potentiated chromosomal instability induced by 125I-iododeoxyuridine. These results show that the target for radiation-induced chromosomal instability in these cells is the nucleus.

AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination

PubMed Central

Vaidyanathan, Bharat; Yen, Wei-Feng; Pucella, Joseph N.; Chaudhuri, Jayanta

2014-01-01

Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe. PMID:24734031

Dissociation of recombinant prion autocatalysis from infectivity.

PubMed

Noble, Geoffrey P; Supattapone, Surachai

2015-01-01

Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication--that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and non-infectious pair of autocatalytic recombinant PrP conformers derived from the same initial prion strain. (1) We identified restricted, C-terminal structural differences between these 2 conformers and provided evidence that these relatively subtle differences prevent the non-infectious conformer from templating the conversion of native PrP(C) substrates containing a glycosylphosphatidylinositol (GPI) anchor. (1) In this article we discuss a model, consistent with these findings, in which recombinant PrP, lacking post-translational modifications and associated folding constraints, is capable of adopting a wide variety of autocatalytic conformations. Only a subset of these recombinant conformers can be adopted by post-translationally modified native PrP(C), and this subset represents the recombinant conformers with high specific infectivity. We examine this model's implications for the generation of highly infectious recombinant prions and the protein-only hypothesis of prion replication.

Multifaceted regulation of V(D)J recombination

NASA Astrophysics Data System (ADS)

Wang, Guannan

V(D)J recombination is responsible for generating an enormous repertoire of immunoglobulins and T cell receptors, therefore it is a centerpiece to the formation of the adaptive immune system. The V(D)J recombination process proceeds through two steps, site-specific cleavage at RSS (Recombination Signal Sequence) site mediated by the RAG recombinase (RAG1/2) and the subsequent imprecise resolution of the DNA ends, which is carried out by the ubiquitous non-homologous end joining pathway (NHEJ). The V(D)J recombination reaction is obliged to be tightly controlled under all circumstances, as it involves generations of DNA double strand breaks, which are considered the most dangerous lesion to a cell. Multifaceted regulatory mechanisms have been evolved to create great diversity of the antigen receptor repertoire while ensuring genome stability. The RAG-mediated cleavage reaction is stringently regulated at both the pre-cleavage stage and the post-cleavage stage. Specifically, RAG1/2 first forms a pre-cleavage complex assembled at the boarder of RSS and coding flank, which ensures the appropriate DNA targeting. Subsequently, this complex initiates site-specific cleavage, generating two types of double stranded DNA breaks, hairpin-ended coding ends (HP-CEs) and blunt signal ends (SEs). After the cleavage, RAG1/2 proteins bind and retain the recombination ends to form post-cleavage complexes (PCC), which collaborates with the NHEJ machinery for appropriate transfer of recombination ends to NHEJ for proper end resolution. However, little is known about the molecular basis of this collaboration, partly attributed to the lack of sensitive assays to reveal the interaction of PCC with HP-CEs. Here, for the first time, by using two complementary fluorescence-based techniques, fluorescence anisotropy and fluorescence resonance energy transfer (FRET), I managed to monitor the RAG1/2-catalyzed cleavage reaction in real time, from the pre-cleavage to the post-cleavage stages. By

The Zombie Instability: Using Numerical Simulation to Design a Laboratory Experiment

NASA Astrophysics Data System (ADS)

Wang, Meng; Pei, Suyang; Jiang, Chung-Hsiang; Hassanzadeh, Pedram; Marcus, Philip

2014-11-01

A new type of finite amplitude-instability has been found in numerical simulations of stratified, rotating, shear flows. The instability occurs via baroclinic critical layers that create linearly unstable vortex layers, which roll-up into vortices. Under the right conditions, those vortices can form a new generation of vortices, resulting in ``vortex self-replication'' that fills the fluid with vortices. Creating this instability in a laboratory would provide further evidence for the existence of the instability, which we first found in numerical simulations of protoplanetary disks. To design a laboratory experiment we need to know how the flow parameters-- shear, rotation and stratification, etc. affect the instability. To build an experiment economically, we also need to know how the finite-amplitude trigger of the instability scales with viscosity and the size of the domain. In this talk, we summarize our findings. We present a map, in terms of the experimentally controllable parameters, that shows where the instability occurs and whether the instability creates a few isolated transient vortices, a few long-lived vortices, or long-lived, self-replicating vortices that fill the entire flow.

Hydrodynamic Model for Density Gradients Instability in Hall Plasmas Thrusters

NASA Astrophysics Data System (ADS)

Singh, Sukhmander

2017-10-01

There is an increasing interest for a correct understanding of purely growing electromagnetic and electrostatic instabilities driven by a plasma gradient in a Hall thruster devices. In Hall thrusters, which are typically operated with xenon, the thrust is provided by the acceleration of ions in the plasma generated in a discharge chamber. The goal of this paper is to study the instabilities due to gradients of plasma density and conditions for the growth rate and real part of the frequency for Hall thruster plasmas. Inhomogeneous plasmas prone a wide class of eigen modes induced by inhomogeneities of plasma density and called drift waves and instabilities. The growth rate of the instability has a dependences on the magnetic field, plasma density, ion temperature and wave numbers and initial drift velocities of the plasma species.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

PubMed

Ma, Li; O'Connell, Jeffrey R; VanRaden, Paul M; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M; Cole, John B; Null, Daniel J; Liu, George E; Da, Yang; Wiggans, George R

2015-11-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

PubMed Central

Ma, Li; O'Connell, Jeffrey R.; VanRaden, Paul M.; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M.; Cole, John B.; Null, Daniel J.; Liu, George E.; Da, Yang; Wiggans, George R.

2015-01-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination. PMID:26540184

Suppression of the Rayleigh Taylor instability and its implication for the impact ignition

NASA Astrophysics Data System (ADS)

Azechi, H.; Shiraga, H.; Nakai, M.; Shigemori, K.; Fujioka, S.; Sakaiya, T.; Tamari, Y.; Ohtani, K.; Murakami, M.; Sunahara, A.; Nagatomo, H.; Nishihara, K.; Miyanaga, N.; Izawa, Y.

2004-12-01

The Rayleigh Taylor (RT) instability with material ablation through an unstable interface is the key physics that determines the success or failure of inertial fusion energy (IFE) generation, as the RT instability potentially quenches ignition and burn by disintegrating the IFE target. We present two suppression schemes of the RT growth without significant degradation of the target density. The first scheme is to generate a double ablation structure in high-Z doped plastic targets. In addition to the electron ablation surface, a new ablation surface is created by x-ray radiation from the high-Z ions. Contrary to the previous thought, the electron ablation surface is almost completely stabilized by extremely high flow velocity. On the other hand, the RT instability on the radiative ablation surface is significantly moderated. The second is to enhance the nonlocal nature of the electron heat transport by illuminating the target with long wavelength laser light, whereas the high ablation pressure is generated by irradiating with short wavelength laser light. The significant suppression of the RT instability may increase the possibility of impact ignition which uses a high-velocity fuel colliding with a preformed main fuel.

Strings, vortex rings, and modes of instability

DOE PAGES

Gubser, Steven S.; Nayar, Revant; Parikh, Sarthak

2015-01-12

We treat string propagation and interaction in the presence of a background Neveu–Schwarz three-form field strength, suitable for describing vortex rings in a superfluid or low-viscosity normal fluid. A circular vortex ring exhibits instabilities which have been recognized for many years, but whose precise boundaries we determine for the first time analytically in the small core limit. Two circular vortices colliding head-on exhibit stronger instabilities which cause splitting into many small vortices at late times. We provide an approximate analytic treatment of these instabilities and show that the most unstable wavelength is parametrically larger than a dynamically generated length scalemore » which in many hydrodynamic systems is close to the cutoff. We also summarize how the string construction we discuss can be derived from the Gross–Pitaevskii Lagrangian, and also how it compares to the action for giant gravitons.« less

Generation of 2A-linked multicistronic cassettes by recombinant PCR.

PubMed

Szymczak-Workman, Andrea L; Vignali, Kate M; Vignali, Dario A A

2012-02-01

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18-22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector. This protocol describes the use of recombinant polymerase chain reaction (PCR) to connect multiple 2A-linked protein sequences. The final construct is subcloned into an expression vector.

Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

PubMed

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line; Delpeyroux, Francis

2014-08-05

Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3' end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. Importance: The multiplication of circulating vaccine-derived polioviruses (cVDPVs) in poorly immunized human populations can render these viruses pathogenic, causing poliomyelitis outbreaks. Most cVDPVs are intertypic recombinants between a poliovirus (PV) strain and another human enterovirus, such as type 17 coxsackie A viruses (CA17). For further studies of the genetic exchanges

A Protein Chimera Strategy Supports Production of a Model "Difficult-to-Express" Recombinant Target.

PubMed

Hussain, Hirra; Fisher, David I; Roth, Robert G; Abbott, W Mark; Carballo-Amador, Manuel Alejandro; Warwicker, Jim; Dickson, Alan J

2018-06-22

Due in part to the needs of the biopharmaceutical industry, there has been an increased drive to generate high quality recombinant proteins in large amounts. However, achieving high yields can be a challenge as the novelty and increased complexity of new targets often makes them 'difficult-to-express'. This study aimed to define the molecular features that restrict the production of a model 'difficult-to-express' recombinant protein, Tissue Inhibitor Metalloproteinase-3 (TIMP-3). Building from experimental data, computational approaches were used to rationalise the re-design of this recombinant target to generate a chimera with enhanced secretion. The results highlight the importance of early identification of unfavourable sequence attributes, enabling the generation of engineered protein forms that bypass 'secretory' bottlenecks and result in efficient recombinant protein production. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Construction of human artificial chromosome vectors by recombineering.

PubMed

Kotzamanis, George; Cheung, Wing; Abdulrazzak, Hassan; Perez-Luz, Sara; Howe, Steven; Cooke, Howard; Huxley, Clare

2005-05-23

Human artificial chromosomes (HACs) can be formed de novo by transfection of large fragments of cloned alphoid DNA into human HT1080 cells in tissue culture. In order to generate HACs carrying a gene of interest, one can either co-transfect the alphoid DNA and the gene of interest, or one can clone both into a single vector prior to transfection. Here we describe linking approximately 70 kb of alphoid DNA onto a 156-kb BAC carrying the human HPRT gene using Red homologous recombination in the EL350 Escherichia coli host [Lee et al., Genomics 73 (2001) 56-65]. A selectable marker and EGFP marker were then added by loxP/Cre recombination using the arabinose inducible cre gene in the EL350 bacteria. The final construct generates minichromosomes in HT1080 cells and the HPRT gene is expressed. The retrofitting vector can be used to add the approximately 70 kb of alphoid DNA to any BAC carrying a gene of interest to generate a HAC vector. The method can also be used to link any unrelated BAC or PAC insert onto another BAC clone. The EL350 bacteria are an excellent host for building up complex vectors by a combination of homologous and loxP/Cre recombination.

Genetic recombination pathways and their application for genome modification of human embryonic stem cells.

PubMed

Nieminen, Mikko; Tuuri, Timo; Savilahti, Harri

2010-10-01

Human embryonic stem cells are pluripotent cells derived from early human embryo and retain a potential to differentiate into all adult cell types. They provide vast opportunities in cell replacement therapies and are expected to become significant tools in drug discovery as well as in the studies of cellular and developmental functions of human genes. The progress in applying different types of DNA recombination reactions for genome modification in a variety of eukaryotic cell types has provided means to utilize recombination-based strategies also in human embryonic stem cells. Homologous recombination-based methods, particularly those utilizing extended homologous regions and those employing zinc finger nucleases to boost genomic integration, have shown their usefulness in efficient genome modification. Site-specific recombination systems are potent genome modifiers, and they can be used to integrate DNA into loci that contain an appropriate recombination signal sequence, either naturally occurring or suitably pre-engineered. Non-homologous recombination can be used to generate random integrations in genomes relatively effortlessly, albeit with a moderate efficiency and precision. DNA transposition-based strategies offer substantially more efficient random strategies and provide means to generate single-copy insertions, thus potentiating the generation of genome-wide insertion libraries applicable in genetic screens. 2010 Elsevier Inc. All rights reserved.

Novel canine circovirus strains from Thailand: Evidence for genetic recombination.

PubMed

Piewbang, Chutchai; Jo, Wendy K; Puff, Christina; van der Vries, Erhard; Kesdangsakonwut, Sawang; Rungsipipat, Anudep; Kruppa, Jochen; Jung, Klaus; Baumgärtner, Wolfgang; Techangamsuwan, Somporn; Ludlow, Martin; Osterhaus, Albert D M E

2018-05-14

Canine circoviruses (CanineCV's), belonging to the genus Circovirus of the Circoviridae family, were detected by next generation sequencing in samples from Thai dogs with respiratory symptoms. Genetic characterization and phylogenetic analysis of nearly complete CanineCV genomes suggested that natural recombination had occurred among different lineages of CanineCV's. Similarity plot and bootscaning analyses indicated that American and Chinese viruses had served as major and minor parental viruses, respectively. Positions of recombination breakpoints were estimated using maximum-likelihood frameworks with statistical significant testing. The putative recombination event was located in the Replicase gene, intersecting with open reading frame-3. Analysis of nucleotide changes confirmed the origin of the recombination event. This is the first description of naturally occurring recombinant CanineCV's that have resulted in the circulation of newly emerging CanineCV lineages.

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

Recombination between bacteriophage lambda and plasmid pBR322 in Escherichia coli.

PubMed Central

Pogue-Geile, K L; Dassarma, S; King, S R; Jaskunas, S R

1980-01-01

Recombinant lambda phages were isolated that resulted from recombination between the lambda genome and plasmid pBR322 in Escherichia coli, even though these deoxyribonucleic acids (DNAs) did not share extensive regions of homology. The characterization of these recombinant DNAs by heteroduplex analysis and restriction endonucleases is described. All but one of the recombinants appeared to have resulted from reciprocal recombination between a site on lambda DNA and a site on the plasmid. In general, there were two classes of recombinants. One class appeared to have resulted from recombination at the phage attachment site that probably resulted from lambda integration into secondary attachment sites on the plasmid. Seven different secondary attachment sites on pBR322 were found. The other class resulted from plasmid integration at other sites that were widely scattered on the lambda genome. For this second class of recombinants, more than one site on the plasmid could recombine with lambda DNA. Thus, the recombination did not appear to be site specific with respect to lambda or the plasmid. Possible mechanisms for generating these recombinants are discussed. Images PMID:6247334

Suppression of Instabilities Generated by an Anti-Damper with a Nonlinear Magnetic Element in IOTA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stern, E.

The Integrable Optics Test Accelerator (IOTA) storage ring is being constructed at Fermilab as a testbed for new accelerator concepts. One important series of experiments tests the use of a novel nonlinear magnetic insert to damp coherent instabilities. To test the damping power of the element, an instability of desired strength may be intentionally excited with an anti-damper. We report on simulations of beam stabilization using the Synergia modeling framework over ranges of driving and damping strengths.

Microsatellite instability in prostate cancer by PCR or next-generation sequencing.

PubMed

Hempelmann, Jennifer A; Lockwood, Christina M; Konnick, Eric Q; Schweizer, Michael T; Antonarakis, Emmanuel S; Lotan, Tamara L; Montgomery, Bruce; Nelson, Peter S; Klemfuss, Nola; Salipante, Stephen J; Pritchard, Colin C

2018-04-17

Microsatellite instability (MSI) is now being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Yet current molecular diagnostic tests for MSI have not been evaluated for use in prostate cancer. We evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus (18 markers) and MSI by Large Panel NGS (> 60 markers), and compared the performance of each NGS method to the most widely used 5-marker MSI-PCR detection system. All methods were evaluated by comparison to targeted whole gene sequencing of DNA mismatch-repair genes, and immunohistochemistry for mismatch repair genes, where available. In a set of 91 prostate tumors with known mismatch repair status (29-deficient and 62-intact mismatch-repair) MSIplus had a sensitivity of 96.6% (28/29) and a specificity of 100% (62/62), MSI by Large Panel NGS had a sensitivity of 93.1% (27/29) and a specificity of 98.4% (61/62), and MSI-PCR had a sensitivity of 72.4% (21/29) and a specificity of 100% (62/62). We found that the widely used 5-marker MSI-PCR panel has inferior sensitivity when applied to prostate cancer and that NGS testing with an expanded panel of markers performs well. In addition, NGS methods offer advantages over MSI-PCR, including no requirement for matched non-tumor tissue and an automated analysis pipeline with quantitative interpretation of MSI-status.

A Recombinant Human Anti-Platelet scFv Antibody Produced in Pichia pastoris for Atheroma Targeting

PubMed Central

Vallet-Courbin, Amelie; Larivière, Mélusine; Hocquellet, Agnès; Hemadou, Audrey; Parimala, Sarjapura-Nagaraja; Laroche-Traineau, Jeanny; Santarelli, Xavier; Clofent-Sanchez, Gisèle; Jacobin-Valat, Marie-Josée; Noubhani, Abdelmajid

2017-01-01

Cells of the innate and adaptive immune system are key factors in the progression of atherosclerotic plaque, leading to plaque instability and rupture, potentially resulting in acute atherothrombotic events such as coronary artery disease, cerebrovascular disease and peripheral arterial disease. Here, we describe the cloning, expression, purification, and immunoreactivity assessment of a recombinant single-chain variable fragment (scFv) derived from a human anti-αIIbβ3 antibody (HuAb) selected to target atheromatous lesions for the presence of platelets. Indeed, platelets within atheroma plaques have been shown to play a role in inflammation, in platelet-leucocyte aggregates and in thrombi formation and might thus be considered relevant biomarkers of atherosclerotic progression. The DNA sequence that encodes the anti-αIIbβ3 TEG4 scFv previously obtained from a phage-display selection on activated platelets, was inserted into the eukaryote vector (pPICZαA) in fusion with a tag sequence encoding 2 cysteines useable for specific probes grafting experiments. The recombinant protein was expressed at high yields in Pichia pastoris (30 mg/L culture). The advantage of P. pastoris as an expression system is the production and secretion of recombinant proteins in the supernatant, ruling out the difficulties encountered when scFv are produced in the cytoplasm of bacteria (low yield, low solubility and reduced affinity). The improved conditions allowed for the recovery of highly purified and biologically active scFv fragments ready to be grafted in a site-directed way to nanoparticles for the imaging of atherosclerotic plaques involving inflammatory processes and thus at high risk of instability. PMID:28125612

Elastic instabilities in planar elongational flow of monodisperse polymer solutions

PubMed Central

Haward, Simon J.; McKinley, Gareth H.; Shen, Amy Q.

2016-01-01

We investigate purely elastic flow instabilities in the almost ideal planar stagnation point elongational flow field generated by a microfluidic optimized-shape cross-slot extensional rheometer (OSCER). We use time-resolved flow velocimetry and full-field birefringence microscopy to study the behavior of a series of well-characterized viscoelastic polymer solutions under conditions of low fluid inertia and over a wide range of imposed deformation rates. At low deformation rates the flow is steady and symmetric and appears Newtonian-like, while at high deformation rates we observe the onset of a flow asymmetry resembling the purely elastic instabilities reported in standard-shaped cross-slot devices. However, for intermediate rates, we observe a new type of elastic instability characterized by a lateral displacement and time-dependent motion of the stagnation point. At the onset of this new instability, we evaluate a well-known dimensionless criterion M that predicts the onset of elastic instabilities based on geometric and rheological scaling parameters. The criterion yields maximum values of M which compare well with critical values of M for the onset of elastic instabilities in viscometric torsional flows. We conclude that the same mechanism of tension acting along curved streamlines governs the onset of elastic instabilities in both extensional (irrotational) and torsional (rotational) viscoelastic flows. PMID:27616181

Two-stage continuous operation of recombinant Escherichia coli using the bacteriophage lambda Q- vector.

PubMed

Oh, Jeong Seok; Cho, Daechul; Park, Tai Hyun

2005-11-01

A two-stage continuous culture of Escherichia coli in combination with a bacteriophage lambda system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. A phage lambda vector with a Q(-) mutation was used to enhance the expression of the lambda system. The optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned gene were determined in both batch and continuous cultures. For all culturing modes, the full induction of the cloned gene was observed 4 h after the temperature shift. In the two stage continuous culture, the overproduction reached their maxima at D=0.25 h(-1) with 1.5 S(0) of the medium supply. The maximum productivity of the total beta-galactosidase was 16.3x10(6) U l(-1) h(-1), which was approximately seven times higher than that in the single-copy lysogenic stage. The recombinant cells were stable in the lysogenic state for more than 260 h, while they were stable for 40 h in the lytic state. The instability that developed rapidly in the second tank is believed to be due to the accumulation of lysis proteins as a result of vector leakage during the operation.

Population-specific recombination sites within the human MHC region.

PubMed

Lam, T H; Shen, M; Chia, J-M; Chan, S H; Ren, E C

2013-08-01

Genetic rearrangement by recombination is one of the major driving forces for genome evolution, and recombination is known to occur in non-random, discreet recombination sites within the genome. Mapping of recombination sites has proved to be difficult, particularly, in the human MHC region that is complicated by both population variation and highly polymorphic HLA genes. To overcome these problems, HLA-typed individuals from three representative populations: Asian, European and African were used to generate phased HLA haplotypes. Extended haplotype homozygosity (EHH) plots constructed from the phased haplotype data revealed discreet EHH drops corresponding to recombination events and these signatures were observed to be different for each population. Surprisingly, the majority of recombination sites detected are unique to each population, rather than being common. Unique recombination sites account for 56.8% (21/37 of total sites) in the Asian cohort, 50.0% (15/30 sites) in Europeans and 63.2% (24/38 sites) in Africans. Validation carried out at a known sperm typing recombination site of 45 kb (HLA-F-telomeric) showed that EHH was an efficient method to narrow the recombination region to 826 bp, and this was further refined to 660 bp by resequencing. This approach significantly enhanced mapping of the genomic architecture within the human MHC, and will be useful in studies to identify disease risk genes.

Prolonged Particulate Hexavalent Chromium Exposure Suppresses Homologous Recombination Repair in Human Lung Cells

PubMed Central

Browning, Cynthia L.; Qin, Qin; Kelly, Deborah F.; Prakash, Rohit; Vanoli, Fabio; Jasin, Maria

2016-01-01

Abstract Genomic instability is one of the primary models of carcinogenesis and a feature of almost all cancers. Homologous recombination (HR) repair protects against genomic instability by maintaining high genomic fidelity during the repair of DNA double strand breaks. The defining step of HR repair is the formation of the Rad51 nucleofilament, which facilitates the search for a homologous sequence and invasion of the template DNA strand. Particulate hexavalent chromium (Cr(VI)), a human lung carcinogen, induces DNA double strand breaks and chromosome instability. Since the loss of HR repair increases Cr(VI)-induced chromosome instability, we investigated the effect of extended Cr(VI) exposure on HR repair. We show acute (24 h) Cr(VI) exposure induces a normal HR repair response. In contrast, prolonged (120 h) exposure to particulate Cr(VI) inhibited HR repair and Rad51 nucleofilament formation. Prolonged Cr(VI) exposure had a profound effect on Rad51, evidenced by reduced protein levels and Rad51 mislocalization to the cytoplasm. The response of proteins involved in Rad51 nuclear import and nucleofilament formation displayed varying responses to prolonged Cr(VI) exposure. BRCA2 formed nuclear foci after prolonged Cr(VI) exposure, while Rad51C foci formation was suppressed. These results suggest that particulate Cr(VI), a major chemical carcinogen, inhibits HR repair by targeting Rad51, causing DNA double strand breaks to be repaired by a low fidelity, Rad51-independent repair pathway. These results further enhance our understanding of the underlying mechanism of Cr(VI)-induced chromosome instability and thus, carcinogenesis. PMID:27449664

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.

Mus81 and Yen1 promote reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast

PubMed Central

Ho, Chu Kwen; Mazón, Gerard; Lam, Alicia F.; Symington, Lorraine S.

2010-01-01

Holliday junction (HJ) resolution is required for segregation of chromosomes and for formation of crossovers during homologous recombination. The identity of the resolvase(s) that functions in vivo has yet to be established, although several proteins able to cut HJs in vitro have been identified as candidates in yeasts and mammals. Using an assay to detect unselected products of mitotic recombination we found a significant decrease in crossovers in the Saccharomyces cerevisiae mus81Δ mutant. Yen1 serves a back-up function responsible for resolving intermediates in mus81Δ mutants, or when conversion tracts are short. In the absence of both Mus81 and Yen1 intermediates are not channeled exclusively to non-crossover recombinants, but instead are processed by Pol32-dependent break-induced replication (BIR). The channeling of recombination from reciprocal exchange to BIR results in greatly increased spontaneous loss of heterozygosity (LOH) and chromosome mis-segregation in the mus81Δ yen1Δ mutant, typical of the genomic instability found in tumor cells. PMID:21172663

Strategy to overcome recombination limited photocurrent generation in CsPbX3 nanocrystal arrays

NASA Astrophysics Data System (ADS)

Mir, Wasim J.; Livache, Clément; Goubet, Nicolas; Martinez, Bertille; Jagtap, Amardeep; Chu, Audrey; Coutard, Nathan; Cruguel, Hervé; Barisien, Thierry; Ithurria, Sandrine; Nag, Angshuman; Dubertret, Benoit; Ouerghi, Abdelkarim; Silly, Mathieu G.; Lhuillier, Emmanuel

2018-03-01

We discuss the transport properties of CsPbBrxI3-x perovskite nanocrystal arrays as a model ensemble system of caesium lead halide-based perovskite nanocrystal arrays. While this material is very promising for the design of light emitting diodes, laser, and solar cells, very little work has been devoted to the basic understanding of their (photo)conductive properties in an ensemble system. By combining DC and time-resolved photocurrent measurements, we demonstrate fast photodetection with time response below 2 ns. The photocurrent generation in perovskite nanocrystal-based arrays is limited by fast bimolecular recombination of the material, which limits the lifetime of the photogenerated electron-hole pairs. We propose to use nanotrench electrodes as a strategy to ensure that the device size fits within the obtained diffusion length of the material in order to boost the transport efficiency and thus observe an enhancement of the photoresponse by a factor of 1000.

Instability timescale for the inclination instability in the solar system

NASA Astrophysics Data System (ADS)

Zderic, Alexander; Madigan, Ann-Marie; Fleisig, Jacob

2018-04-01

The gravitational influence of small bodies is often neglected in the study of solar system dynamics. However, this is not always an appropriate assumption. For example, mutual secular torques between low mass particles on eccentric orbits can result in a self-gravity instability (`inclination instability'; Madigan & McCourt 2016). During the instability, inclinations increase exponentially, eccentricities decrease (detachment), and orbits cluster in argument of perihelion. In the solar system, the orbits of the most distant objects show all three of these characteristics (high inclination: Volk & Malhotra (2017), detachment: Delsanti & Jewitt (2006), and argument of perihelion clustering: Trujillo & Sheppard (2014)). The inclination instability is a natural explanation for these phenomena.Unfortunately, full N-body simulations of the solar system are unfeasible (N ≈ O(1012)), and the behavior of the instability depends on N, prohibiting the direct application of lower N simulations. Here we present the instability timescale's functional dependence on N, allowing us to extrapolate our simulation results to that appropriate for the solar system. We show that ~5 MEarth of small icy bodies in the Sedna region is sufficient for the inclination instability to occur in the outer solar system.

The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo.

PubMed

MacAlpine, D M; Perlman, P S; Butow, R A

1998-06-09

Abf2p is a high mobility group (HMG) protein found in yeast mitochondria that is required for the maintenance of wild-type (rho+) mtDNA in cells grown on fermentable carbon sources, and for efficient recombination of mtDNA markers in crosses. Here, we show by two-dimensional gel electrophoresis that Abf2p promotes or stabilizes Holliday recombination junction intermediates in rho+ mtDNA in vivo but does not influence the high levels of recombination intermediates readily detected in the mtDNA of petite mutants (rho-). mtDNA recombination junctions are not observed in rho+ mtDNA of wild-type cells but are elevated to detectable levels in cells with a null allele of the MGT1 gene (Deltamgt1), which codes for a mitochondrial cruciform-cutting endonuclease. The level of recombination intermediates in rho+ mtDNA of Deltamgt1 cells is decreased about 10-fold if those cells contain a null allele of the ABF2 gene. Overproduction of Abf2p by >/= 10-fold in wild-type rho+ cells, which leads to mtDNA instability, results in a dramatic increase in mtDNA recombination intermediates. Specific mutations in the two Abf2p HMG boxes required for DNA binding diminishes these responses. We conclude that Abf2p functions in the recombination of rho+ mtDNA.

Robustness of the filamentation instability for asymmetric plasma shells collision in arbitrarily oriented magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bret, A.

2013-10-15

The filamentation instability triggered when two counter streaming plasma shells overlap appears to be the main mechanism by which collisionless shocks are generated. It has been known for long that a flow aligned magnetic field can completely suppress this instability. In a recent paper [Phys. Plasmas 18, 080706 (2011)], it was demonstrated in two dimensions that for the case of two cold, symmetric, relativistically colliding shells, such cancellation cannot occur if the field is not perfectly aligned. Here, this result is extended to the case of two asymmetric shells. The filamentation instability appears therefore as an increasingly robust mechanism tomore » generate shocks.« less

Many-body instabilities and mass generation in slow Dirac materials

NASA Astrophysics Data System (ADS)

Triola, Christopher; Zhu, Jian-Xin; Migliori, Albert; Balatsky, Alexander V.

2015-07-01

Some Kondo insulators are expected to possess topologically protected surface states with linear Dirac spectrum: the topological Kondo insulators. Because the bulk states of these systems typically have heavy effective electron masses, the surface states may exhibit extraordinarily small Fermi velocities that could force the effective fine structure constant of the surface states into the strong coupling regime. Using a tight-binding model, we study the many-body instabilities of these systems and identify regions of parameter space in which the system exhibits spin density wave and charge density wave order.

Numerical Simulations of Instabilities in Single-Hole Office Elements

NASA Technical Reports Server (NTRS)

Ahuja, Vineet; Hosangadi, Ashvin; Hitt, Matthew A.; Lineberry, David M.

2013-01-01

An orifice element is commonly used in liquid rocket engine test facilities either as a flow metering device, a damper for acoustic resonance or to provide a large reduction in pressure over a very small distance in the piping system. While the orifice as a device is largely effective in stepping down pressure, it is also susceptible to a wake-vortex type instability that generates pressure fluctuations that propagate downstream and interact with other elements of the test facility resulting in structural vibrations. Furthermore in piping systems an unstable feedback loop can exist between the vortex shedding and acoustic perturbations from upstream components resulting in an amplification of the modes convecting downstream. Such was the case in several tests conducted at NASA as well as in the Ariane 5 strap-on P230 engine in a static firing test where pressure oscillations of 0.5% resulted in 5% thrust oscillations. Exacerbating the situation in cryogenic test facilities, is the possibility of the formation of vapor clouds when the pressure in the wake falls below the vapor pressure leading to a cavitation instability that has a lower frequency than the primary wake-vortex instability. The cavitation instability has the potential for high amplitude fluctuations that can cause catastrophic damage in the facility. In this paper high-fidelity multi-phase numerical simulations of an orifice element are used to characterize the different instabilities, understand the dominant instability mechanisms and identify the tonal content of the instabilities.

FIRE HOSE INSTABILITY DRIVEN BY ALPHA PARTICLE TEMPERATURE ANISOTROPY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matteini, L.; Schwartz, S. J.; Hellinger, P.

We investigate properties of a solar wind-like plasma, including a secondary alpha particle population exhibiting a parallel temperature anisotropy with respect to the background magnetic field, using linear and quasi-linear predictions and by means of one-dimensional hybrid simulations. We show that anisotropic alpha particles can drive a parallel fire hose instability analogous to that generated by protons, but that, remarkably, can also be triggered when the parallel plasma beta of alpha particles is below unity. The wave activity generated by the alpha anisotropy affects the evolution of the more abundant protons, leading to their anisotropic heating. When both ion speciesmore » have sufficient parallel anisotropies, both of them can drive the instability, and we observe the generation of two distinct peaks in the spectra of the fluctuations, with longer wavelengths associated to alphas and shorter ones to protons. If a non-zero relative drift is present, the unstable modes propagate preferentially in the direction of the drift associated with the unstable species. The generated waves scatter particles and reduce their temperature anisotropy to a marginally stable state, and, moreover, they significantly reduce the relative drift between the two ion populations. The coexistence of modes excited by both species leads to saturation of the plasma in distinct regions of the beta/anisotropy parameter space for protons and alpha particles, in good agreement with in situ solar wind observations. Our results confirm that fire hose instabilities are likely at work in the solar wind and limit the anisotropy of different ion species in the plasma.« less

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

PubMed Central

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

2014-01-01

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. PMID:24945141

B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass.

PubMed

Harper, John; Phillips, Dylan; Thomas, Ann; Gasior, Dagmara; Evans, Caron; Powell, Wayne; King, Julie; King, Ian; Jenkins, Glyn; Armstead, Ian

2018-04-09

Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.

Tidal excitation of elliptical instability in the Martian core: Possible mechanism for generating the core dynamo

NASA Astrophysics Data System (ADS)

Arkani-Hamed, J.; Seyed-Mahmoud, B.; Aldridge, K. D.; Baker, R. E.

2008-06-01

We propose a causal relationship between the creation of the giant impact basins on Mars by a large asteroid, ruptured when it entered the Roche limit, and the excitation of the Martian core dynamo. Our laboratory experiments indicate that the elliptical instability of the Martian core can be excited if the asteroid continually exerts tidal forces on Mars for ~20,000 years. Our numerical experiments suggest that the growth-time of the instability was 5,000-15,000 years when the asteroid was at a distance of 50,000-75,000 km. We demonstrate the stability of the orbital motion of an asteroid captured by Mars at a distance of 100,000 km in the presence of the Sun and Jupiter. We also present our results for the tidal interaction of the asteroid with Mars. An asteroid captured by Mars in prograde fashion can survive and excite the elliptical instability of the core for only a few million years, whereas a captured retrograde asteroid can excite the elliptical instability for hundreds of millions of years before colliding with Mars. The rate at which tidal energy dissipates in Mars during this period is over two orders of magnitude greater than the rate at which magnetic energy dissipates. If only 1% of the tidal energy dissipation is partitioned to the core, sufficient energy would be available to maintain the core dynamo. Accordingly, a retrograde asteroid is quite capable of exciting an elliptical instability in the Martian core, thus providing a candidate process to drive a core dynamo.

Recombinational Repair of DNA Damage in Escherichia coli and Bacteriophage λ

PubMed Central

Kuzminov, Andrei

1999-01-01

Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage λ recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation. PMID:10585965

Recombinant protein production from stable mammalian cell lines and pools.

PubMed

Hacker, David L; Balasubramanian, Sowmya

2016-06-01

We highlight recent developments for the production of recombinant proteins from suspension-adapted mammalian cell lines. We discuss the generation of stable cell lines using transposons and lentivirus vectors (non-targeted transgene integration) and site-specific recombinases (targeted transgene integration). Each of these methods results in the generation of cell lines with protein yields that are generally superior to those achievable through classical plasmid transfection that depends on the integration of the transfected DNA by non-homologous DNA end-joining. This is the main reason why these techniques can also be used for the generation of stable cell pools, heterogenous populations of recombinant cells generated by gene delivery and genetic selection without resorting to single cell cloning. This allows the time line from gene transfer to protein production to be reduced. Copyright © 2016 Elsevier Ltd. All rights reserved.

A low-frequency noise model with carrier generation-recombination process for pentacene organic thin-film transistor

NASA Astrophysics Data System (ADS)

Han, C. Y.; Qian, L. X.; Leung, C. H.; Che, C. M.; Lai, P. T.

2013-07-01

By including the generation-recombination process of charge carriers in conduction channel, a model for low-frequency noise in pentacene organic thin-film transistors (OTFTs) is proposed. In this model, the slope and magnitude of power spectral density for low-frequency noise are related to the traps in the gate dielectric and accumulation layer of the OTFT for the first time. The model can well fit the measured low-frequency noise data of pentacene OTFTs with HfO2 or HfLaO gate dielectric, which validates this model, thus providing an estimate on the densities of traps in the gate dielectric and accumulation layer. It is revealed that the traps in the accumulation layer are much more than those in the gate dielectric, and so dominate the low-frequency noise of pentacene OTFTs.

Correlation of mutations and recombination with growth kinetics of poliovirus vaccine strains.

PubMed

Pliaka, V; Kyriakopoulou, Z; Tsakogiannis, D; Ruether, I G A; Gartzonika, C; Levidiotou-Stefanou, S; Krikelis, A; Markoulatos, P

2010-12-01

Attenuated strains of Sabin poliovirus vaccine replicate in the human gut and, in rare cases, may cause vaccine-associated paralytic poliomyelitis (VAPP). The genetic instability of Sabin strains constitutes one of the main causes of VAPP, a disease that is most frequently associated with type 3 and type 2 Sabin strains, and more rarely with type 1 Sabin strains. In the present study, the growth phenotype of eight oral poliovirus vaccine (OPV) isolates (two non-recombinants and six recombinants), as well as of Sabin vaccine strains, was evaluated using two different assays, the reproductive capacity at different temperatures (Rct) test and the one-step growth curve test in Hep-2 cells at two different temperatures (37°C and 40°C). The growth phenotype of isolates was correlated with genomic modifications in order to identify the determinants and mechanisms of reversion towards neurovirulence. All of the recombinant OPV isolates showed a thermoresistant phenotype in the Rct test. Moreover, both recombinant Sabin-3 isolates showed significantly higher viral yield than Sabin 3 vaccine strain at 37°C and 40°C in the one-step growth curve test. All of the OPV isolates displayed mutations at specific sites of the viral genome, which are associated with the attenuated and temperature-sensitive phenotype of Sabin strains. The results showed that both mutations and recombination events could affect the phenotype traits of Sabin derivatives and may lead to the reversion of vaccinal strains to neurovirulent ones. The use of phenotypic markers along with the genomic analysis may shed additional light on the molecular determinants of the reversed neurovirulent phenotype of Sabin derivatives.

Collective instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Bayesian Inference of Shared Recombination Hotspots Between Humans and Chimpanzees

PubMed Central

Wang, Ying; Rannala, Bruce

2014-01-01

Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies. PMID:25261696

Bayesian inference of shared recombination hotspots between humans and chimpanzees.

PubMed

Wang, Ying; Rannala, Bruce

2014-12-01

Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies. Copyright © 2014 by the Genetics Society of America.

[Shoulder instability].

PubMed

Sailer, J; Imhof, H

2004-06-01

Shoulder instability is a common clinical feature leading to recurrent pain and limited range of motion within the glenohumeral joint. Instability can be due a single traumatic event, general joint laxity or repeated episodes of microtrauma. Differentiation between traumatic and atraumatic forms of shoulder instability requires careful history and a systemic clinical examination. Shoulder laxity has to be differentiated from true instability followed by the clinical assessment of direction and degree of glenohumeral translation. Conventional radiography and CT are used for the diagnosis of bony lesions. MR imaging and MR arthrography help in the detection of soft tissue affection, especially of the glenoid labrum and the capsuloligamentous complex. The most common lesion involving the labrum is the anterior labral tear, associated with capsuloperiostal stripping (Bankart lesion). A number of variants of the Bankart lesion have been described, such as ALPSA, SLAP or HAGL lesions. The purpose of this review is to highlight different forms of shoulder instability and its associated radiological findings with a focus on MR imaging.

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

PubMed Central

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

2009-01-01

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

Effect of manipulating recombination rates on response to selection in livestock breeding programs.

PubMed

Battagin, Mara; Gorjanc, Gregor; Faux, Anne-Michelle; Johnston, Susan E; Hickey, John M

2016-06-22

In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. We carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %. Increasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination. Higher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in

Three-dimensional doubly diffusive convectons: instability and transition to complex dynamics

NASA Astrophysics Data System (ADS)

Knobloch, Edgar; Beaume, Cedric; Bergeon, Alain

2017-11-01

Doubly diffusive convection in a closed vertically extended 3D container driven by competing horizontal temperature and concentration gradients is studied. No-slip boundary conditions are imposed. The buoyancy number N = - 1 to ensure the presence of a conduction state. The primary instability is subcritical and generates two families of spatially localised steady states known as convectons. The convectons bifurcate directly from the conduction state and are organized in a pair of primary branches that snake within a well-defined range of Rayleigh numbers as the convectons grow in length. Secondary instabilities generating twist result in secondary snaking branches of twisted convectons. These destabilize the primary convectons and are responsible for the absence of stable steady states, localized or otherwise, in the subcritical regime. As a result, once the Rayleigh number for the primary instability of the conduction state is exceeded, the system exhibits an abrupt transition to large amplitude spatio-temporal chaos that arises whenever the twist instability leading to collapse is faster than the nucleation time for new rolls. These numerical results are confirmed by determining the stability properties of all convecton states as well as spatially extended convection. Supported in part by the National Science Foundation under Grant DMS-1613132.

Photoionization and Recombination

NASA Technical Reports Server (NTRS)

Nahar, Sultana N.

2000-01-01

Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

Evidence of locally enhanced target heating due to instabilities of counter-streaming fast electron beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koester, Petra; Cecchetti, Carlo A.; Booth, Nicola

2015-02-15

The high-current fast electron beams generated in high-intensity laser-solid interactions require the onset of a balancing return current in order to propagate in the target material. Such a system of counter-streaming electron currents is unstable to a variety of instabilities such as the current-filamentation instability and the two-stream instability. An experimental study aimed at investigating the role of instabilities in a system of symmetrical counter-propagating fast electron beams is presented here for the first time. The fast electron beams are generated by double-sided laser-irradiation of a layered target foil at laser intensities above 10{sup 19 }W/cm{sup 2}. High-resolution X-ray spectroscopy ofmore » the emission from the central Ti layer shows that locally enhanced energy deposition is indeed achieved in the case of counter-propagating fast electron beams.« less

Kinetic-MHD simulations of gyroresonance instability driven by CR pressure anisotropy

NASA Astrophysics Data System (ADS)

Lebiga, O.; Santos-Lima, R.; Yan, H.

2018-05-01

The transport of cosmic rays (CRs) is crucial for the understanding of almost all high-energy phenomena. Both pre-existing large-scale magnetohydrodynamic (MHD) turbulence and locally generated turbulence through plasma instabilities are important for the CR propagation in astrophysical media. The potential role of the resonant instability triggered by CR pressure anisotropy to regulate the parallel spatial diffusion of low-energy CRs (≲100 GeV) in the interstellar and intracluster medium of galaxies has been shown in previous theoretical works. This work aims to study the gyroresonance instability via direct numerical simulations, in order to access quantitatively the wave-particle scattering rates. For this, we employ a 1D PIC-MHD code to follow the growth and saturation of the gyroresonance instability. We extract from the simulations the pitch-angle diffusion coefficient Dμμ produced by the instability during the linear and saturation phases, and a very good agreement (within a factor of 3) is found with the values predicted by the quasi-linear theory (QLT). Our results support the applicability of the QLT for modelling the scattering of low-energy CRs by the gyroresonance instability in the complex interplay between this instability and the large-scale MHD turbulence.

Posterior Shoulder Instability

PubMed Central

Antosh, Ivan J.; Tokish, John M.; Owens, Brett D.

2016-01-01

Context: Posterior shoulder instability has become more frequently recognized and treated as a unique subset of shoulder instability, especially in the military. Posterior shoulder pathology may be more difficult to accurately diagnose than its anterior counterpart, and commonly, patients present with complaints of pain rather than instability. “Posterior instability” may encompass both dislocation and subluxation, and the most common presentation is recurrent posterior subluxation. Arthroscopic and open treatment techniques have improved as understanding of posterior shoulder instability has evolved. Evidence Acquisition: Electronic databases including PubMed and MEDLINE were queried for articles relating to posterior shoulder instability. Study Design: Clinical review. Level of Evidence: Level 4. Results: In low-demand patients, nonoperative treatment of posterior shoulder instability should be considered a first line of treatment and is typically successful. Conservative treatment, however, is commonly unsuccessful in active patients, such as military members. Those patients with persistent shoulder pain, instability, or functional limitations after a trial of conservative treatment may be considered surgical candidates. Arthroscopic posterior shoulder stabilization has demonstrated excellent clinical outcomes, high patient satisfaction, and low complication rates. Advanced techniques may be required in select cases to address bone loss, glenoid dysplasia, or revision. Conclusion: Posterior instability represents about 10% of shoulder instability and has become increasingly recognized and treated in military members. Nonoperative treatment is commonly unsuccessful in active patients, and surgical stabilization can be considered in patients who do not respond. Isolated posterior labral repairs constitute up to 24% of operatively treated labral repairs in a military population. Arthroscopic posterior stabilization is typically considered as first-line surgical

Genome-wide variation in recombination rate in Eucalyptus.

PubMed

Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

2016-08-09

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = -0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = -0.75). The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst

Assessing Spontaneous Combustion Instability with Nonlinear Time Series Analysis

NASA Technical Reports Server (NTRS)

Eberhart, C. J.; Casiano, M. J.

2015-01-01

Considerable interest lies in the ability to characterize the onset of spontaneous instabilities within liquid propellant rocket engine (LPRE) combustion devices. Linear techniques, such as fast Fourier transforms, various correlation parameters, and critical damping parameters, have been used at great length for over fifty years. Recently, nonlinear time series methods have been applied to deduce information pertaining to instability incipiency hidden in seemingly stochastic combustion noise. A technique commonly used in biological sciences known as the Multifractal Detrended Fluctuation Analysis has been extended to the combustion dynamics field, and is introduced here as a data analysis approach complementary to linear ones. Advancing, a modified technique is leveraged to extract artifacts of impending combustion instability that present themselves a priori growth to limit cycle amplitudes. Analysis is demonstrated on data from J-2X gas generator testing during which a distinct spontaneous instability was observed. Comparisons are made to previous work wherein the data were characterized using linear approaches. Verification of the technique is performed by examining idealized signals and comparing two separate, independently developed tools.

Gas recombination assembly for electrochemical cells

DOEpatents

Levy, Isaac; Charkey, Allen

1989-01-01

An assembly for recombining gases generated in electrochemical cells wherein a catalyst strip is enveloped within a hydrophobic, gas-porous film which, in turn, is encased between gas-porous, metallic layers. The sandwich construction of metallic layers and film is formed into a spiral with a tab for connection to the cell.

Collisionless shock experiments with lasers and observation of Weibel instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, H.-S., E-mail: park1@llnl.gov; Huntington, C. M.; Fiuza, F.

2015-05-15

Astrophysical collisionless shocks are common in the universe, occurring in supernova remnants, gamma ray bursts, and protostellar jets. They appear in colliding plasma flows when the mean free path for ion-ion collisions is much larger than the system size. It is believed that such shocks could be mediated via the electromagnetic Weibel instability in astrophysical environments without pre-existing magnetic fields. Here, we present laboratory experiments using high-power lasers and investigate the dynamics of high-Mach-number collisionless shock formation in two interpenetrating plasma streams. Our recent proton-probe experiments on Omega show the characteristic filamentary structures of the Weibel instability that are electromagneticmore » in nature with an inferred magnetization level as high as ∼1% [C. M. Huntington et al., “Observation of magnetic field generation via the weibel instability in interpenetrating plasma flows,” Nat. Phys. 11, 173–176 (2015)]. These results imply that electromagnetic instabilities are significant in the interaction of astrophysical conditions.« less

Extended mimetic gravity: Hamiltonian analysis and gradient instabilities

NASA Astrophysics Data System (ADS)

Takahashi, Kazufumi; Kobayashi, Tsutomu

2017-11-01

We propose a novel class of degenerate higher-order scalar-tensor theories as an extension of mimetic gravity. By performing a noninvertible conformal transformation on "seed" scalar-tensor theories which may be nondegenerate, we can generate a large class of theories with at most three physical degrees of freedom. We identify a general seed theory for which this is possible. Cosmological perturbations in these extended mimetic theories are also studied. It is shown that either of tensor or scalar perturbations is plagued with gradient instabilities, except for a special case where the scalar perturbations are presumably strongly coupled, or otherwise there appear ghost instabilities.

Effects of Ion Magnetization on the Farley–Buneman Instability in the Solar Chromosphere

NASA Astrophysics Data System (ADS)

Fletcher, Alex C.; Dimant, Yakov S.; Oppenheim, Meers M.; Fontenla, Juan M.

2018-04-01

Intense heating in the quiet-Sun chromosphere raises the temperature from 4000 to 6500 K but, despite decades of study, the underlying mechanism remains a mystery. This study continues to explore the possibility that the Farley–Buneman instability contributes to chromospheric heating. This instability occurs in weakly ionized collisional plasmas in which electrons are magnetized, but ions are not. A mixture of metal ions generate the plasma density in the coolest parts of the chromosphere; while some ions are weakly magnetized, others are demagnetized by neutral collisions. This paper incorporates the effects of multiple, arbitrarily magnetized species of ions to the theory of the Farley–Buneman instability and examines the ramifications on instability in the chromosphere. The inclusion of magnetized ions introduces new restrictions on the regions in which the instability can occur in the chromosphere—in fact, it confines the instability to the regions in which heating is observed. For a magnetic field of 30 G, the minimum ambient electric field capable of driving the instability is 13.5 V/m at the temperature minimum.

Cre recombinase-mediated site-specific recombination between plant chromosomes.

PubMed Central

Qin, M; Bayley, C; Stockton, T; Ow, D W

1994-01-01

We report the use of the bacteriophage P1 Cre-lox system for generating conservative site-specific recombination between tobacco chromosomes. Two constructs, one containing a promoterless hygromycin-resistance gene preceded by a lox site (lox-hpt) and the other containing a cauliflower mosaic virus 35S promoter linked to a lox sequence and the cre coding region (35S-lox-cre), were introduced separately into tobacco plants. Crosses between plants harboring either construct produced plants with the two constructs situated on different chromosomes. Plants with recombination events were identified by selecting for hygromycin resistance, a phenotype expressed upon recombination. Molecular analysis showed that these recombination events occurred specifically at the lox sites and resulted in the reciprocal exchange of flanking host DNA. Progenies of these plants showed 67-100% cotransmission of the new transgenes, 35S-lox-hpt and lox-cre, consistent with the preferential cosegregation of translocated chromosomes. These results illustrate that site-specific recombination systems can be useful tools for the large-scale manipulation of eukaryotic chromosomes in vivo. Images PMID:8127869

Design and Construction of a Shock Tube Experiment for Multiphase Instability Experiments

NASA Astrophysics Data System (ADS)

Middlebrooks, John; Black, Wolfgang; Avgoustopoulos, Constantine; Allen, Roy; Kathakapa, Raj; Guo, Qiwen; McFarland, Jacob

2016-11-01

Hydrodynamic instabilities are important phenomena that have a wide range of practical applications in engineering and physics. One such instability, the shock driven multiphase instability (SDMI), arises when a shockwave accelerates an interface between two particle-gas mixtures with differing multiphase properties. The SDMI is present in high energy explosives, scramjets, and supernovae. A practical way of studying shock wave driven instabilities is through experimentation in a shock tube laboratory. This poster presentation will cover the design and data acquisition process of the University of Missouri's Fluid Mixing Shock Tube Laboratory. In the shock tube, a pressure generated shockwave is passed through a multiphase interface, creating the SDMI instability. This can be photographed for observation using high speed cameras, lasers, and advance imaging techniques. Important experimental parameters such as internal pressure and temperature, and mass flow rates of gases can be set and recorded by remotely controlled devices. The experimental facility provides the University of Missouri's Fluid Mixing Shock Tube Laboratory with the ability to validate simulated experiments and to conduct further inquiry into the field of shock driven multiphase hydrodynamic instabilities. Advisor.

A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations.

PubMed

Rueppell, Olav; Kuster, Ryan; Miller, Katelyn; Fouks, Bertrand; Rubio Correa, Sara; Collazo, Juan; Phaincharoen, Mananya; Tingek, Salim; Koeniger, Nikolaus

2016-12-01

Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species.

Inertial Wave Turbulence Driven by Elliptical Instability.

PubMed

Le Reun, Thomas; Favier, Benjamin; Barker, Adrian J; Le Bars, Michael

2017-07-21

The combination of elliptical deformation of streamlines and vorticity can lead to the destabilization of any rotating flow via the elliptical instability. Such a mechanism has been invoked as a possible source of turbulence in planetary cores subject to tidal deformations. The saturation of the elliptical instability has been shown to generate turbulence composed of nonlinearly interacting waves and strong columnar vortices with varying respective amplitudes, depending on the control parameters and geometry. In this Letter, we present a suite of numerical simulations to investigate the saturation and the transition from vortex-dominated to wave-dominated regimes. This is achieved by simulating the growth and saturation of the elliptical instability in an idealized triply periodic domain, adding a frictional damping to the geostrophic component only, to mimic its interaction with boundaries. We reproduce several experimental observations within one idealized local model and complement them by reaching more extreme flow parameters. In particular, a wave-dominated regime that exhibits many signatures of inertial wave turbulence is characterized for the first time. This regime is expected in planetary interiors.

Inertial Wave Turbulence Driven by Elliptical Instability

NASA Astrophysics Data System (ADS)

Le Reun, Thomas; Favier, Benjamin; Barker, Adrian J.; Le Bars, Michael

2017-07-01

The combination of elliptical deformation of streamlines and vorticity can lead to the destabilization of any rotating flow via the elliptical instability. Such a mechanism has been invoked as a possible source of turbulence in planetary cores subject to tidal deformations. The saturation of the elliptical instability has been shown to generate turbulence composed of nonlinearly interacting waves and strong columnar vortices with varying respective amplitudes, depending on the control parameters and geometry. In this Letter, we present a suite of numerical simulations to investigate the saturation and the transition from vortex-dominated to wave-dominated regimes. This is achieved by simulating the growth and saturation of the elliptical instability in an idealized triply periodic domain, adding a frictional damping to the geostrophic component only, to mimic its interaction with boundaries. We reproduce several experimental observations within one idealized local model and complement them by reaching more extreme flow parameters. In particular, a wave-dominated regime that exhibits many signatures of inertial wave turbulence is characterized for the first time. This regime is expected in planetary interiors.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nyberg, D.

1982-08-01

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

Polarity of recombination in transformation of Streptococcus pneumoniae.

PubMed

Pasta, F; Sicard, M A

1999-03-16

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

Age at migration, family instability, and timing of sexual onset.

PubMed

Goldberg, Rachel E; Tienda, Marta; Adserà, Alícia

2017-03-01

This study builds on and extends previous research on nativity variations in adolescent health and risk behavior by addressing three questions: (1) whether and how generational status and age at migration are associated with timing of sexual onset among U.S. adolescents; (2) whether and how family instability mediates associations between nativity and sexual debut; and (3) whether and how these associations vary by gender. We find that first- and second-generation immigrant youth initiate sexual activity later than native youth. Foreign-born youth who migrate after the start of adolescence exhibit the latest sexual onset; boys' sexual behavior is particularly sensitive to age at migration. Parental union stability is protective for first- and second-generation youth, especially boys; however, instability in co-residence with parents accelerates sexual debut for foreign-born girls, and dilutes protections from parental marital stability. Use of a non-English language at home delays sexual onset for immigrant girls, but not boys. Copyright © 2016 Elsevier Inc. All rights reserved.

A novel system for constructing a recombinant highly-attenuated vaccinia virus strain (LC16m8) expressing foreign genes and its application for the generation of LC16m8-based vaccines against herpes simplex virus 2.

PubMed

Omura, Natsumi; Yoshikawa, Tomoki; Fujii, Hikaru; Shibamura, Miho; Inagaki, Takuya; Kato, Hirofumi; Egawa, Kazutaka; Harada, Shizuko; Yamada, Souichi; Takeyama, Haruko; Saijo, Masayuki

2018-04-27

A novel system was developed for generating a highly-attenuated vaccinia virus LC16m8 (m8, third generation smallpox vaccine) that expresses foreign genes. The innovations in this system are its excisable selection marker, specificity of the integration site of a gene of interest, and easy identification of clones with the fluorescent signal. Using this system, recombinant m8s, which expressed either herpes simplex virus 2 (HSV-2) glycoprotein B (gB)-, gD-, or both gB and gD (gB+gD) were developed, and their efficacy was evaluated. First, the induction of a specific IgG against these HSV-2 glycoproteins in mice infected with each of these recombinant m8s was confirmed with an immunofluorescence assay. Next, mice pre-infected with each of the recombinant m8s were infected with HSV-2 at the lethal dose to examine the vaccine efficacy. The fatality rate in mice pre-infected with either of the recombinant gB+gD- or gD-expressing m8s significantly decreased in comparison with that of the control. The survival rate in both male and female mice pre-infected with either of the recombinant gB+gD- and gD-expressing m8s increased to 100 % and 60 %, respectively, while most of the control mice died. In summary, this new system might be applicable for generating a novel m8-based vaccine.

A network approach to analyzing highly recombinant malaria parasite genes.

PubMed

Larremore, Daniel B; Clauset, Aaron; Buckee, Caroline O

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences.

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

PubMed Central

Larremore, Daniel B.; Clauset, Aaron; Buckee, Caroline O.

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. PMID:24130474

Electrokinetic instability in microchannel ferrofluid/water co-flows

PubMed Central

Song, Le; Yu, Liandong; Zhou, Yilong; Antao, Asher Reginald; Prabhakaran, Rama Aravind; Xuan, Xiangchun

2017-01-01

Electrokinetic instability refers to unstable electric field-driven disturbance to fluid flows, which can be harnessed to promote mixing for various electrokinetic microfluidic applications. This work presents a combined numerical and experimental study of electrokinetic ferrofluid/water co-flows in microchannels of various depths. Instability waves are observed at the ferrofluid and water interface when the applied DC electric field is beyond a threshold value. They are generated by the electric body force that acts on the free charge induced by the mismatch of ferrofluid and water electric conductivities. A nonlinear depth-averaged numerical model is developed to understand and simulate the interfacial electrokinetic behaviors. It considers the top and bottom channel walls’ stabilizing effects on electrokinetic flow through the depth averaging of three-dimensional transport equations in a second-order asymptotic analysis. This model is found accurate to predict both the observed electrokinetic instability patterns and the measured threshold electric fields for ferrofluids of different concentrations in shallow microchannels. PMID:28406228

Preparative SDS PAGE as an Alternative to His-Tag Purification of Recombinant Amelogenin

PubMed Central

Gabe, Claire M.; Brookes, Steven J.; Kirkham, Jennifer

2017-01-01

Recombinant protein technology provides an invaluable source of proteins for use in structure-function studies, as immunogens, and in the development of therapeutics. Recombinant proteins are typically engineered with “tags” that allow the protein to be purified from crude host cell extracts using affinity based chromatography techniques. Amelogenin is the principal component of the developing enamel matrix and a frequent focus for biomineralization researchers. Several groups have reported the successful production of recombinant amelogenins but the production of recombinant amelogenin free of any tags, and at single band purity on silver stained SDS PAGE is technically challenging. This is important, as rigorous structure-function research frequently demands a high degree of protein purity and fidelity of protein sequence. Our aim was to generate His-tagged recombinant amelogenin at single band purity on silver stained SDS PAGE for use in functionality studies after His-tag cleavage. An acetic acid extraction technique (previously reported to produce recombinant amelogenin at 95% purity directly from E. coli) followed by repeated rounds of nickel column affinity chromatography, failed to generate recombinant amelogenin at single band purity. This was because following an initial round of nickel column affinity chromatography, subsequent cleavage of the His-tag was not 100% efficient. A second round of nickel column affinity chromatography, used in attempts to separate the cleaved His-tag free recombinant from uncleaved His-tagged contaminants, was still unsatisfactory as cleaved recombinant amelogenin exhibited significant affinity for the nickel column. To solve this problem, we used preparative SDS PAGE to successfully purify cleaved recombinant amelogenins to single band purity on silver stained SDS PAGE. The resolving power of preparative SDS PAGE was such that His-tag based purification of recombinant amelogenin becomes redundant. We suggest that acetic

Recombineering: A Homologous Recombination-Based Method of Genetic Engineering

PubMed Central

Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G.; Court, Donald L.

2009-01-01

Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in E. coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraints being imposed by restriction enzyme site location. Bacteriophage homologous recombination proteins catalyze these recombineering reactions using double- and single-strand linear DNA substrates, so-called targeting constructs, introduced by electroporation. Gene knockouts, deletions and point mutations are readily made, gene tags can be inserted, and regions of bacterial artificial chromosomes (BACs) or the E. coli genome can be subcloned by gene retrieval using recombineering. Most of these constructs can be made within about a week's time. PMID:19180090

Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria

PubMed Central

Cahoon, Laty A.; Seifert, H. Steven

2011-01-01

Summary Some pathogenic microbes utilize homologous recombination to generate antigenic variability in targets of immune surveillance. These specialized systems rely on the cellular recombination machinery to catalyze dedicated, high-frequency reactions that provide extensive diversity in the genes encoding surface antigens. A description of the specific mechanisms that allow unusually high rates of recombination without deleterious effects on the genome in the well characterized pilin antigenic variation systems of Neisseria gonorrhoeae and Neisseria meningitidis is presented. We will also draw parallels to selected bacterial and eukaryotic antigenic variation systems, and suggest the most pressing unanswered questions related to understanding these important processes. PMID:21812841

Shoulder Instability

MedlinePlus

... as bad as the pain of a sudden injury. Your shoulder might be sore when you move it. It ... Treatment How is shoulder instability treated? Treatment for shoulder instability depends on how bad your injury is and how important it is for you ...

A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination.

PubMed

León-Ortiz, Ana María; Panier, Stephanie; Sarek, Grzegorz; Vannier, Jean-Baptiste; Patel, Harshil; Campbell, Peter J; Boulton, Simon J

2018-01-18

Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Recombinant Protein Containing B-Cell Epitopes of Different Loxosceles Spider Toxins Generates Neutralizing Antibodies in Immunized Rabbits

PubMed Central

Lima, Sabrina de Almeida; Guerra-Duarte, Clara; Costal-Oliveira, Fernanda; Mendes, Thais Melo; Figueiredo, Luís F. M.; Oliveira, Daysiane; Machado de Avila, Ricardo A.; Ferrer, Valéria Pereira; Trevisan-Silva, Dilza; Veiga, Silvio S.; Minozzo, João C.; Kalapothakis, Evanguedes; Chávez-Olórtegui, Carlos

2018-01-01

Loxoscelism is the most important form of araneism in South America. The treatment of these accidents uses heterologous antivenoms obtained from immunization of production animals with crude loxoscelic venom. Due to the scarcity of this immunogen, new alternatives for its substitution in antivenom production are of medical interest. In the present work, three linear epitopes for Loxosceles astacin-like protease 1 (LALP-1) (SLGRGCTDFGTILHE, ENNTRTIGPFDYDSIMLYGAY, and KLYKCPPVNPYPGGIRPYVNV) and two for hyaluronidase (LiHYAL) (NGGIPQLGDLKAHLEKSAVDI and ILDKSATGLRIIDWEAWR) from Loxosceles intermedia spider venom were identified by SPOT-synthesis technique. One formerly characterized linear epitope (DFSGPYLPSLPTLDA) of sphingomyelinase D (SMase D) SMase-I from Loxosceles laeta was also chosen to constitute a new recombinant multiepitopic protein. These epitopes were combined with a previously produced chimeric multiepitopic protein (rCpLi) composed by linear and conformational B-cell epitopes from SMase D from L. intermedia venom, generating a new recombinant multiepitopic protein derived from loxoscelic toxins (rMEPLox). We demonstrated that rMEPLox is non-toxic and antibodies elicited in rabbits against this antigen present reactivity in ELISA and immunoblot assays with Brazilian L. intermedia, L. laeta, L. gaucho, and L. similis spider venoms. In vivo and in vitro neutralization assays showed that anti-rMEPLox antibodies can efficiently neutralize the sphingomyelinase, hyaluronidase, and metalloproteinase activity of L. intermedia venom. This study suggests that this multiepitopic protein can be a suitable candidate for experimental vaccination approaches or for antivenom production against Loxosceles spp. venoms. PMID:29666624

Recombinant Protein Containing B-Cell Epitopes of Different Loxosceles Spider Toxins Generates Neutralizing Antibodies in Immunized Rabbits.

PubMed

Lima, Sabrina de Almeida; Guerra-Duarte, Clara; Costal-Oliveira, Fernanda; Mendes, Thais Melo; Figueiredo, Luís F M; Oliveira, Daysiane; Machado de Avila, Ricardo A; Ferrer, Valéria Pereira; Trevisan-Silva, Dilza; Veiga, Silvio S; Minozzo, João C; Kalapothakis, Evanguedes; Chávez-Olórtegui, Carlos

2018-01-01

Loxoscelism is the most important form of araneism in South America. The treatment of these accidents uses heterologous antivenoms obtained from immunization of production animals with crude loxoscelic venom. Due to the scarcity of this immunogen, new alternatives for its substitution in antivenom production are of medical interest. In the present work, three linear epitopes for Loxosceles astacin-like protease 1 (LALP-1) (SLGRGCTDFGTILHE, ENNTRTIGPFDYDSIMLYGAY, and KLYKCPPVNPYPGGIRPYVNV) and two for hyaluronidase (LiHYAL) (NGGIPQLGDLKAHLEKSAVDI and ILDKSATGLRIIDWEAWR) from Loxosceles intermedia spider venom were identified by SPOT-synthesis technique. One formerly characterized linear epitope (DFSGPYLPSLPTLDA) of sphingomyelinase D (SMase D) SMase-I from Loxosceles laeta was also chosen to constitute a new recombinant multiepitopic protein. These epitopes were combined with a previously produced chimeric multiepitopic protein (rCpLi) composed by linear and conformational B-cell epitopes from SMase D from L. intermedia venom, generating a new recombinant multiepitopic protein derived from loxoscelic toxins (rMEPLox). We demonstrated that rMEPLox is non-toxic and antibodies elicited in rabbits against this antigen present reactivity in ELISA and immunoblot assays with Brazilian L. intermedia, L. laeta, L. gaucho , and L. similis spider venoms. In vivo and in vitro neutralization assays showed that anti-rMEPLox antibodies can efficiently neutralize the sphingomyelinase, hyaluronidase, and metalloproteinase activity of L. intermedia venom. This study suggests that this multiepitopic protein can be a suitable candidate for experimental vaccination approaches or for antivenom production against Loxosceles spp. venoms.

Genetic Analysis of Recombinant Inbred Lines For Sorghum Bicolor x Perennial S. Propinquum.

USDA-ARS?s Scientific Manuscript database

From an annual S. bicolor x perennial S. propinquum F2 population used in early-generation genetic analysis, we have produced and describe here a recombinant inbred line (RIL) population of 161 F5 genotypes that segregates for rhizomatousness and many other traits. The genetic map of the recombinant...

Spatial Instability of the Linearly Polarized Plane Wave in a Cubic Crystal

NASA Astrophysics Data System (ADS)

Kuz'mina, M. S.; Khazanov, E. A.

2016-12-01

We study theoretically the development of a small-scale spatial instability of a plane wave in a cubic crystal with [111], [001] and [101] orientations. It is shown that in the [111] oriented crystals the instability develops at lower intensities than in the [001] and [101] oriented crystals. In the latter two crystals, the instability can significantly be suppressed by choosing the optimal radiation polarization. It is found that in the case of a small B integral, the method of temporal contrast enhancement of laser pulses by generating an orthogonal polarization achieves the largest efficiency with the [101] orientation, while the [001] orientation is more preferable for B > 3.

Instability of rectangular jets

NASA Technical Reports Server (NTRS)

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

1993-01-01

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. It is demonstrated that the boundary element method can be used to calculate the dispersion relations and eigenfunctions of these instability wave modes. The method is robust and efficient. 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.

Nonlinear Interaction of Detuned Instability Waves in Boundary-Layer Transition: Resonant-Triad Interaction

NASA Technical Reports Server (NTRS)

Lee, Sang Soo

1998-01-01

The non-equilibrium critical-layer analysis of a system of frequency-detuned resonant-triads is presented using the generalized scaling of Lee. It is shown that resonant-triads can interact nonlinearly within the common critical layer when their (fundamental) Strouhal numbers are different by a factor whose magnitude is of the order of the growth rate multiplied by the wavenumber of the instability wave. Since the growth rates of the instability modes become larger and the critical layers become thicker as the instability waves propagate downstream, the frequency-detuned resonant-triads that grow independently of each other in the upstream region can interact nonlinearly in the later downstream stage. In the final stage of the non-equilibrium critical-layer evolution, a wide range of instability waves with the scaled frequencies differing by almost an Order of (l) can nonlinearly interact. Low-frequency modes are also generated by the nonlinear interaction between oblique waves in the critical layer. The system of partial differential critical-layer equations along with the jump equations are presented here. The amplitude equations with their numerical solutions are given in Part 2. The nonlinearly generated low-frequency components are also investigated in Part 2.

Chitosan-plasmid nanoparticle formulations for IM and SC delivery of recombinant FGF-2 and PDGF-BB or generation of antibodies.

PubMed

Jean, M; Smaoui, F; Lavertu, M; Méthot, S; Bouhdoud, L; Buschmann, M D; Merzouki, A

2009-09-01

Growth factor therapy is an emerging treatment modality that enhances tissue vascularization, promotes healing and regeneration and can treat a variety of inflammatory diseases. Both recombinant human growth factor proteins and their gene therapy are in human clinical trials to heal chronic wounds. As platelet-derived growth factor-bb (PDGF-BB) and fibroblast growth factor-2 (FGF-2) are known to induce chemotaxis, proliferation, differentiation, and matrix synthesis, we investigated a non-viral means for gene delivery of these factors using the cationic polysaccharide chitosan. Chitosan is a polymer of glucosamine and N-acetyl-glucosamine, in which the percentage of the residues that are glucosamine is called the degree of deacetylation (DDA). The purpose of this study was to express PDGF-BB and FGF-2 genes in mice using chitosan-plasmid DNA nanoparticles for the controlled delivery of genetic material in a specific, efficient, and safe manner. PDGF-BB and FGF-2 genes were amplified from human tissues by RT-PCR. To increase the secretion of FGF-2, a recombinant 4sFGF-2 was constructed bearing eight amino-acid residues of the signal peptide of FGF-4. PCR products were inserted into the expression vector pVax1 to produce recombinant plasmids pVax1-4sFGF2 and pVax1-PDGF-BB, which were then injected into BALB/C mice in the format of polyelectrolyte nanocomplexes with specific chitosans of controlled DDA and molecular weight, including 92-10, 80-10, and 80-80 (DDA-number average molecular weight or M(n) in kDa). ELISA assays on mice sera showed that recombinant FGF-2 and PDGF-BB proteins were efficiently expressed and specific antibodies to these proteins could be identified in sera of injected mice, but with levels that were clearly dependent on the specific chitosan used. We found high DDA low molecular weight chitosans to be efficient protein expressors with minimal or no generation of neutralizing antibodies, while lowering DDA resulted in greater antibody levels

On the 'flip-flop' instability of Bondi-Hoyle accretion flows

NASA Technical Reports Server (NTRS)

Livio, Mario; Soker, Noam; Matsuda, Takuya; Anzer, Ulrich

1991-01-01

A simple physical interpretation is advanced by means of an analysis of the shock cone in the accretion flows past a compact object and with an examination of the accretion-line stability analyses. The stability of the conical shock is examined against small angular deflections with attention given to several simplifying assumptions. A line instability is identified in the Bondi-Hoyle accretion flows that leads to the formation of a large opening-angle shock. When the opening angle becomes large the instability becomes irregular oscillation. The analytical methodology is compared to previous numerical configurations that demonstrate different shock morphologies. The Bondi-Hoyle accretion onto a compact object is concluded to generate a range of nonlinear instabilities in both homogeneous and inhomogeneous cases with a quasiperiodic oscillation in the linear regime.

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

PubMed Central

Lee, Kyubin; Kolb, Aaron W.; Sverchkov, Yuriy; Cuellar, Jacqueline A.; Craven, Mark

2015-01-01

ABSTRACT Herpes simplex virus 1 (HSV-1) causes recurrent mucocutaneous ulcers and is the leading cause of infectious blindness and sporadic encephalitis in the United States. HSV-1 has been shown to be highly recombinogenic; however, to date, there has been no genome-wide analysis of recombination. To address this, we generated 40 HSV-1 recombinants derived from two parental strains, OD4 and CJ994. The 40 OD4-CJ994 HSV-1 recombinants were sequenced using the Illumina sequencing system, and recombination breakpoints were determined for each of the recombinants using the Bootscan program. Breakpoints occurring in the terminal inverted repeats were excluded from analysis to prevent double counting, resulting in a total of 272 breakpoints in the data set. By placing windows around the 272 breakpoints followed by Monte Carlo analysis comparing actual data to simulated data, we identified a recombination bias toward both high GC content and intergenic regions. A Monte Carlo analysis also suggested that recombination did not appear to be responsible for the generation of the spontaneous nucleotide mutations detected following sequencing. Additionally, kernel density estimation analysis across the genome found that the large, inverted repeats comprise a recombination hot spot. IMPORTANCE Herpes simplex virus 1 (HSV-1) virus is the leading cause of sporadic encephalitis and blinding keratitis in developed countries. HSV-1 has been shown to be highly recombinogenic, and recombination itself appears to be a significant component of genome replication. To date, there has been no genome-wide analysis of recombination. Here we present the findings of the first genome-wide study of recombination performed by generating and sequencing 40 HSV-1 recombinants derived from the OD4 and CJ994 parental strains, followed by bioinformatics analysis. Recombination breakpoints were determined, yielding 272 breakpoints in the full data set. Kernel density analysis determined that the large

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

PubMed Central

Fritsch, Emilie S.; Chabbert, Christophe D.; Klaus, Bernd; Steinmetz, Lars M.

2014-01-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome

A genome-wide map of mitochondrial DNA recombination in yeast.

PubMed

Fritsch, Emilie S; Chabbert, Christophe D; Klaus, Bernd; Steinmetz, Lars M

2014-10-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome

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

PubMed

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

2004-10-01

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

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

Progress Toward Kelvin-Helmholtz instabilities in a High-Energy-Density Plasma on the Nike Laser

NASA Astrophysics Data System (ADS)

Harding, E. C.; Drake, R. P.; Aglitskiy, Y.; Dwarkadas, V. V.; Gillespie, R. S.; Grosskopf, M. J.; Huntington, C. M.; Gjeci, N.; Campbell, D. A.; Marion, D. C.

2007-11-01

In the realm of high-energy-density (HED) plasmas, there exist three primary hydrodynamic instabilities: Rayleigh-Taylor (RT), Richtmyer-Meshkov (RM), and Kelvin-Helmholtz (KH). Although the RT and the RM instabilities have been observed in the laboratory, no experiment to our knowledge has cleanly diagnosed the KH instability. While the RT instability results from the acceleration of a more dense fluid into a less dense fluid and the RM instability is due to shock deposited vorticity onto an interface, the KH instability is driven by a lifting force generated by velocity shear at a perturbed fluid interface. Understanding the KH instability mechanism in HED plasmas will provide essential insight into detailed RT-spike development, mass stripping, many astrophysical processes, as well as laying the groundwork for future transition to turbulence experiments. We present 2D simulations and data from our initial attempts to create a pure KH system using the Nike laser at the Naval Research Laboratory.

The Effect of Dopant-Free Hole-Transport Polymers on Charge Generation and Recombination in Cesium-Bismuth-Iodide Solar Cells.

PubMed

Zhu, Huimin; Johansson, Malin B; Johansson, Erik M J

2018-03-22

The photovoltaic characteristics of CsBi 3 I 10 -based solar cells with three dopant-free hole-conducting polymers are investigated. The effect on charge generation and charge recombination in the solar cells using the different polymers is studied and the results indicate that the choice of polymer strongly affects the device properties. Interestingly, for the solar cell with poly[[2,3-bis(3-octyloxyphenyl)-5,8-quinoxalinediyl]-2,5-thiophenediyl] (TQ1), the photon-to-current conversion spectrum is highly improved in the red wavelength region, suggesting that the polymer also contributes to the photocurrent generation in this case. This report provides a new direction for further optimization of Bi-halide solar cells by using dopant-free hole-transporting polymers and shows that the energy levels and the interaction between the Bi-halide and the conducting polymers are very important for solar cell performance. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prolonged Particulate Hexavalent Chromium Exposure Suppresses Homologous Recombination Repair in Human Lung Cells.

PubMed

Browning, Cynthia L; Qin, Qin; Kelly, Deborah F; Prakash, Rohit; Vanoli, Fabio; Jasin, Maria; Wise, John Pierce

2016-09-01

Genomic instability is one of the primary models of carcinogenesis and a feature of almost all cancers. Homologous recombination (HR) repair protects against genomic instability by maintaining high genomic fidelity during the repair of DNA double strand breaks. The defining step of HR repair is the formation of the Rad51 nucleofilament, which facilitates the search for a homologous sequence and invasion of the template DNA strand. Particulate hexavalent chromium (Cr(VI)), a human lung carcinogen, induces DNA double strand breaks and chromosome instability. Since the loss of HR repair increases Cr(VI)-induced chromosome instability, we investigated the effect of extended Cr(VI) exposure on HR repair. We show acute (24 h) Cr(VI) exposure induces a normal HR repair response. In contrast, prolonged (120 h) exposure to particulate Cr(VI) inhibited HR repair and Rad51 nucleofilament formation. Prolonged Cr(VI) exposure had a profound effect on Rad51, evidenced by reduced protein levels and Rad51 mislocalization to the cytoplasm. The response of proteins involved in Rad51 nuclear import and nucleofilament formation displayed varying responses to prolonged Cr(VI) exposure. BRCA2 formed nuclear foci after prolonged Cr(VI) exposure, while Rad51C foci formation was suppressed. These results suggest that particulate Cr(VI), a major chemical carcinogen, inhibits HR repair by targeting Rad51, causing DNA double strand breaks to be repaired by a low fidelity, Rad51-independent repair pathway. These results further enhance our understanding of the underlying mechanism of Cr(VI)-induced chromosome instability and thus, carcinogenesis. © The Author 2016. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability

PubMed Central

Germann, Susanne M.; Schramke, Vera; Pedersen, Rune Troelsgaard; Gallina, Irene; Eckert-Boulet, Nadine; Oestergaard, Vibe H.

2014-01-01

DNA anaphase bridges are a potential source of genome instability that may lead to chromosome breakage or nondisjunction during mitosis. Two classes of anaphase bridges can be distinguished: DAPI-positive chromatin bridges and DAPI-negative ultrafine DNA bridges (UFBs). Here, we establish budding yeast Saccharomyces cerevisiae and the avian DT40 cell line as model systems for studying DNA anaphase bridges and show that TopBP1/Dpb11 plays an evolutionarily conserved role in their metabolism. Together with the single-stranded DNA binding protein RPA, TopBP1/Dpb11 binds to UFBs, and depletion of TopBP1/Dpb11 led to an accumulation of chromatin bridges. Importantly, the NoCut checkpoint that delays progression from anaphase to abscission in yeast was activated by both UFBs and chromatin bridges independently of Dpb11, and disruption of the NoCut checkpoint in Dpb11-depleted cells led to genome instability. In conclusion, we propose that TopBP1/Dpb11 prevents accumulation of anaphase bridges via stimulation of the Mec1/ATR kinase and suppression of homologous recombination. PMID:24379413

TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability.

PubMed

Germann, Susanne M; Schramke, Vera; Pedersen, Rune Troelsgaard; Gallina, Irene; Eckert-Boulet, Nadine; Oestergaard, Vibe H; Lisby, Michael

2014-01-06

DNA anaphase bridges are a potential source of genome instability that may lead to chromosome breakage or nondisjunction during mitosis. Two classes of anaphase bridges can be distinguished: DAPI-positive chromatin bridges and DAPI-negative ultrafine DNA bridges (UFBs). Here, we establish budding yeast Saccharomyces cerevisiae and the avian DT40 cell line as model systems for studying DNA anaphase bridges and show that TopBP1/Dpb11 plays an evolutionarily conserved role in their metabolism. Together with the single-stranded DNA binding protein RPA, TopBP1/Dpb11 binds to UFBs, and depletion of TopBP1/Dpb11 led to an accumulation of chromatin bridges. Importantly, the NoCut checkpoint that delays progression from anaphase to abscission in yeast was activated by both UFBs and chromatin bridges independently of Dpb11, and disruption of the NoCut checkpoint in Dpb11-depleted cells led to genome instability. In conclusion, we propose that TopBP1/Dpb11 prevents accumulation of anaphase bridges via stimulation of the Mec1/ATR kinase and suppression of homologous recombination.

Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA.

PubMed

Ladoukakis, E D; Zouros, E

2001-07-01

The assumption that animal mitochondrial DNA (mtDNA) does not undergo homologous recombination is based on indirect evidence, yet it has had an important influence on our understanding of mtDNA repair and mutation accumulation (and thus mitochondrial disease and aging) and on biohistorical inferences made from population data. Recently, several studies have suggested recombination in primate mtDNA on the basis of patterns of frequency distribution and linkage associations of mtDNA mutations in human populations, but others have failed to produce similar evidence. Here, we provide direct evidence for homologous mtDNA recombination in mussels, where heteroplasmy is the rule in males. Our results indicate a high rate of mtDNA recombination. Coupled with the observation that mammalian mitochondria contain the enzymes needed for the catalysis of homologous recombination, these findings suggest that animal mtDNA molecules may recombine regularly and that the extent to which this generates new haplotypes may depend only on the frequency of biparental inheritance of the mitochondrial genome. This generalization must, however, await evidence from animal species with typical maternal mtDNA inheritance.

Polarity of recombination in transformation of Streptococcus pneumoniae

PubMed Central

Pasta, Franck; Sicard, Michel A.

1999-01-01

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5′- and 3′-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami− transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5′ to the deletion, showing that, in vivo, the 5′ side is strongly favored by recombination. Further results suggest that exchanges occurring from 5′ to 3′ relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5′ preference. PMID:10077616

R-loops: targets for nuclease cleavage and repeat instability.

PubMed

Freudenreich, Catherine H

2018-01-11

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

Instability-driven electromagnetic fields in coronal plasmas

DOE PAGES

Manuel, M. J.-E.; Li, C. K.; Seguin, F. H.; ...

2013-04-15

Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. S eguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of 210 lm throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature andmore » density profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.« less

Active Suppression of Instabilities in Engine Combustors

NASA Technical Reports Server (NTRS)

Kopasakis, George

2004-01-01

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

Magnetic field production via the Weibel instability in interpenetrating plasma flows

DOE PAGES

Huntington, C. M.; Manuel, M. J. -E.; Ross, J. S.; ...

2017-04-26

Here, many astrophysical systems are effectively “collisionless,” that is, the mean free path for collisions between particles is much longer than the size of the system. The absence of particle collisions does not preclude shock formation, however, as shocks can be the result of plasma instabilities that generate and amplify electromagnetic fields. The magnetic fields required for shock formation may either be initially present, for example, in supernova remnants or young galaxies, or they may be self-generated in systems such as gamma-ray bursts (GRBs). In the case of GRB outflows, the Weibel instability is a candidate mechanism for the generationmore » of sufficiently strong magnetic fields to produce shocks. In experiments on the OMEGA Laser, we have demonstrated a quasi-collisionless system that is optimized for the study of the non-linear phase of Weibel instability growth. Using a proton probe to directly image electromagnetic fields, we measure Weibel-generated magnetic fields that grow in opposing, initially unmagnetized plasma flows. The collisionality of the system is determined from coherent Thomson scattering measurements, and the data are compared to similar measurements of a fully collisionless system. The strong, persistent Weibel growth observed here serves as a diagnostic for exploring large-scale magnetic field amplification and the microphysics present in the collisional–collisionless transition.« less

Minimal model for a hydrodynamic fingering instability in microroller suspensions

NASA Astrophysics Data System (ADS)

Delmotte, Blaise; Donev, Aleksandar; Driscoll, Michelle; Chaikin, Paul

2017-11-01

We derive a minimal continuum model to investigate the hydrodynamic mechanism behind the fingering instability recently discovered in a suspension of microrollers near a floor [M. Driscoll et al., Nat. Phys. 13, 375 (2017), 10.1038/nphys3970]. Our model, consisting of two continuous lines of rotlets, exhibits a linear instability driven only by hydrodynamic interactions and reproduces the length-scale selection observed in large-scale particle simulations and in experiments. By adjusting only one parameter, the distance between the two lines, our dispersion relation exhibits quantitative agreement with the simulations and qualitative agreement with experimental measurements. Our linear stability analysis indicates that this instability is caused by the combination of the advective and transverse flows generated by the microrollers near a no-slip surface. Our simple model offers an interesting formalism to characterize other hydrodynamic instabilities that have not been well understood, such as size scale selection in suspensions of particles sedimenting adjacent to a wall, or the recently observed formations of traveling phonons in systems of confined driven particles.

Electromagnetic ion beam instabilities - Growth at cyclotron harmonic wave numbers

NASA Technical Reports Server (NTRS)

Smith, Charles W.; Gary, S. Peter

1987-01-01

The linear theory of electromagnetic ion beam instabilities for arbitrary angles of propagation is studied, with an emphasis on the conditions necessary to generate unstable modes at low harmonics of the ion cyclotron resonance condition. The present results extend the analysis of Smith et al. (1985). That paper considered only the plasma parameters at a time during which harmonic wave modes were observed in the earth's foreshock. The parameters of that paper are used as the basis of parametric variations here to establish the range of beam properties which may give rise to observable harmonic spectra. It is shown that the growth rates of both left-hand and right-hand cyclotron harmonic instabilities are enhanced by an increase in the beam temperature anisotropy and/or the beam speed. Decreases in the beam density and/or the core-ion beta reduce the overall growth of the cyclotron harmonic instabilities but favor the growth of these modes over the growth of the nonresonant instability and thereby enhance the observability of the harmonics.

The temporal interplay of self-esteem instability and affective instability in borderline personality disorder patients' everyday lives.

PubMed

Santangelo, Philip S; Reinhard, Iris; Koudela-Hamila, Susanne; Bohus, Martin; Holtmann, Jana; Eid, Michael; Ebner-Priemer, Ulrich W

2017-11-01

Borderline personality disorder (BPD) is defined by a pervasive pattern of instability. Although there is ample empirical evidence that unstable self-esteem is associated with a myriad of BPD-like symptoms, self-esteem instability and its temporal dynamics have received little empirical attention in patients with BPD. Even worse, the temporal interplay of affective instability and self-esteem instability has been neglected completely, although it has been hypothesized recently that the lack of specificity of affective instability in association with BPD might be explained by the highly intertwined temporal relationship between affective and self-esteem instability. To investigate self-esteem instability, its temporal interplay with affective instability, and its association with psychopathology, 60 patients with BPD and 60 healthy controls (HCs) completed electronic diaries for 4 consecutive days during their everyday lives. Participants reported their current self-esteem, valence, and tense arousal levels 12 times a day in approximately one-hr intervals. We used multiple state-of-the-art statistical techniques and graphical approaches to reveal patterns of instability, clarify group differences, and examine the temporal interplay of self-esteem instability and affective instability. As hypothesized, instability in both self-esteem and affect was clearly elevated in the patients with BPD. In addition, self-esteem instability and affective instability were highly correlated. Both types of instability were related to general psychopathology. Because self-esteem instability could not fully explain affective instability and vice versa and neither affective instability nor self-esteem instability was able to explain psychopathology completely, our findings suggest that these types of instability represent unique facets of BPD. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Acceleration Techniques for Recombination of Gases in Electrolysis Microactuators with Nafion®-Coated Electrocatalyst

PubMed Central

Sheybani, Roya; Meng, Ellis

2015-01-01

Recombination of electrolysis gases (oxidation of hydrogen and reduction of oxygen) is an important factor in operation efficiency of devices employing electrolysis such as actuators and also unitized regenerative fuel cells. Several methods of improving recombination speed and repeatability were developed for application to electrolysis microactuators with Nafion®-coated catalytic electrodes. Decreasing the electrolysis chamber volume increased the speed, consistency, and repeatability of the gas recombination rate. To further improve recombination performance, methods to increase the catalyst surface area, hydrophobicity, and availability were developed and evaluated. Of these, including in the electrolyte pyrolyzed-Nafion®-coated Pt segments contained in the actuator chamber accelerated recombination by increasing the catalyst surface area and decreasing the gas transport diffusion path. This approach also reduced variability in recombination encountered under varying actuator orientation (resulting in differing catalyst/gas bubble proximity) and increased the rate of recombination by 2.3 times across all actuator orientations. Repeatability of complete recombination for different generated gas volumes was studied through cycling. PMID:26251561

Recombination in Eukaryotic Single Stranded DNA Viruses

PubMed Central

Martin, Darren P.; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

2011-01-01

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. PMID:21994803

Activation of Dun1 in response to nuclear DNA instability accounts for the increase in mitochondrial point mutations in Rad27/FEN1 deficient S. cerevisiae.

PubMed

Kaniak-Golik, Aneta; Kuberska, Renata; Dzierzbicki, Piotr; Sledziewska-Gojska, Ewa

2017-01-01

Rad27/FEN1 nuclease that plays important roles in the maintenance of DNA stability in the nucleus has recently been shown to reside in mitochondria. Accordingly, it has been established that Rad27 deficiency causes increased mutagenesis, but decreased microsatellite instability and homologous recombination in mitochondria. Our current analysis of mutations leading to erythromycin resistance indicates that only some of them arise in mitochondrial DNA and that the GC→AT transition is a hallmark of the mitochondrial mutagenesis in rad27 null background. We also show that the mitochondrial mutator phenotype resulting from Rad27 deficiency entirely depends on the DNA damage checkpoint kinase Dun1. DUN1 inactivation suppresses the mitochondrial mutator phenotype caused by Rad27 deficiency and this suppression is eliminated at least in part by subsequent deletion of SML1 encoding a repressor of ribonucleotide reductase. We conclude that Rad27 deficiency causes a mitochondrial mutator phenotype via activation of DNA damage checkpoint kinase Dun1 and that a Dun1-mediated increase of dNTP pools contributes to this phenomenon. These results point to the nuclear DNA instability as the source of mitochondrial mutagenesis. Consistently, we show that mitochondrial mutations occurring more frequently in yeast devoid of Rrm3, a DNA helicase involved in rDNA replication, are also dependent on Dun1. In addition, we have established that overproduction of Exo1, which suppresses DNA damage sensitivity and replication stress in nuclei of Rad27 deficient cells, but does not enter mitochondria, suppresses the mitochondrial mutagenesis. Exo1 overproduction restores also a great part of allelic recombination and microsatellite instability in mitochondria of Rad27 deficient cells. In contrast, the overproduction of Exo1 does not influence mitochondrial direct-repeat mediated deletions in rad27 null background, pointing to this homologous recombination pathway as the direct target of Rad27

Recombination era magnetic fields from axion dark matter

DOE PAGES

Banik, Nilanjan; Christopherson, Adam J.

2016-02-04

We introduce a new mechanism for generating magnetic fields in the recombination era. This Harrison-like mechanism utilizes vorticity in baryons that is sourced through the Bose-Einstein condensate of axions via gravitational interactions. The magnetic fields generated are on galactic scales ~10 kpc and have a magnitude of the order of B~10 –23G today. Lastly, the field has a greater magnitude than those generated from other mechanisms relying on second-order perturbation theory, and is sufficient to provide a seed for battery mechanisms.

Experimental Investigation of Cavitation Induced Feedline Instability from an Orifice

NASA Technical Reports Server (NTRS)

Hitt, Matthew A.; Lineberry, David M.; Ahuja, Vineet; Frederick, Robert A,

2012-01-01

This paper details the results of an experimental investigation into the cavitation instabilities created by a circular orifice conducted at the University of Alabama in Huntsville Propulsion Research Center. This experiment was conducted in concert with a computational simulation to serve as a reference point for the simulation. Testing was conducted using liquid nitrogen as a cryogenic propellant simulant. A 1.06 cm diameter thin orifice with a rounded inlet was tested in an approximately 1.25 kg/s flow with inlet pressures ranging from 504.1 kPa to 829.3 kPa. Pressure fluctuations generated by the orifice were measured using a high frequency pressure sensor located 0.64 tube diameters downstream of the orifice. Fast Fourier Transforms were performed on the high frequency data to determine the instability frequency. Shedding resulted in a primary frequency with a cavitation related subharmonic frequency. For this experiment, the cavitation instability ranged from 153 Hz to 275 Hz. Additionally, the strength of the cavitation occur red as a function of cavitation number. At lower cavitation numbers, the strength of the cavitation instability ranged from 2.4 % to 7 % of the inlet pressure. However, at higher cavitation numbers, the strength of the cavitation instability ranged from 0.6 % to 1 % of the inlet pressure.

Kelvin-Helmholtz instability in a single-component atomic superfluid

NASA Astrophysics Data System (ADS)

Baggaley, A. W.; Parker, N. G.

2018-05-01

We demonstrate an experimentally feasible method for generating the classical Kelvin-Helmholtz instability in a single-component atomic Bose-Einstein condensate. By progressively reducing a potential barrier between two counterflowing channels, we seed a line of quantized vortices, which precede to form progressively larger clusters, mimicking the classical roll-up behavior of the Kelvin-Helmholtz instability. This cluster formation leads to an effective superfluid shear layer, formed through the collective motion of many quantized vortices. From this we demonstrate a straightforward method to measure the effective viscosity of a turbulent quantum fluid in a system with a moderate number of vortices, within the range of current experimental capabilities.

Interchromosomal recombination in Zea mays.

PubMed Central

Hu, W; Timmermans, M C; Messing, J

1998-01-01

A new allele of the 27-kD zein locus in maize has been generated by interchromosomal recombination between chromosomes of two different inbred lines. A continuous patch of at least 11,817 bp of inbred W64A, containing the previously characterized Ra allele of the 27-kD zein gene, has been inserted into the genome of A188 by a single crossover. While both junction sequences are conserved, sequences of the two homologs between these junctions differ considerably. W64A contains the 7313-bp-long retrotransposon, Zeon-1. A188 contains a second copy of the 27-kD zein gene and a 2-kb repetitive element. Therefore, recombination results in a 7.3-kb insertion and a 14-kb deletion compared to the original S+A188 allele. If nonpairing sequences are looped out, 206 single base changes, frequently clustered, are present. The structure of this allele may explain how a recently discovered example of somatic recombination occurred in an A188/W64A hybrid. This would indicate that despite these sequence differences, pairing between these alleles could occur early during plant development. Therefore, such a somatically derived chimeric chromosome can also be heritable and give rise to new alleles. PMID:9799274

Thermonuclear instabilities and plasma edge transport in tokamaks

NASA Astrophysics Data System (ADS)

Fulop, Tunde Maria

High-energy ions generated by fusion reactions in a burning fusion plasma may give rise to different types of wave instabilities. The present thesis investigates two types of such instabilities which recently have been observed in fusion experiments: the Toroidal Alfvén Eigenmode (TAE) instability and the magnetoacoustic cyclotron instability (MCI) which is predicted to give rise to ion cyclotron emission (ICE). The TAE instability may degrade the confinement of fusion-produced high energy alpha particles and adversely affect the possibilities of reaching ignition. The present work derives it generalized expression for the linear growth rate of the instability, by including the effects of finite orbit width and finite Larmor radius of energetic particles, as well as the effects of mode localization and the possible mode excitation by both passing and trapped energetic ions. ICE does not threaten the plasma performance, but it might be useful as a fast ion diagnostic. The ICE originates from the MCI involving fast magnetoacoustic waves driven unstable by toroidicity-affected cyclotron resonance with fast ions. In the present thesis a detailed numerical and analytical investigation of this instability is presented, that explains most of the experimental ICE features observed in JET and TFTR. Moreover, the radial and poloidal localization of the fast magnetoacoustic eigenmodes is investigated, including the effects of toroidicity, ellipticity, the presence of a subpopulation of high energy ions and various profiles of the bulk ion density. In a fusion reactor, the transport of the particles near the edge have a strong influence on the global confinement of the plasma. In the edge region, where neutral atoms and impurity ions are abundant and the temperature and density gradients are large, the assumptions of the standard neoclassical theory break down. In this thesis, we explore the effect of neutral particles on the ion flow shear in the edge region. Furthermore

Progress toward Kelvin-Helmholtz instabilities in a High-Energy-Density Plasma on the Nike laser

NASA Astrophysics Data System (ADS)

Harding, E. C.; Drake, R. P.; Gillespie, R. S.; Grosskopf, M. J.; Huntington, C. M.; Aglitskiy, Y.; Weaver, J. L.; Velikovich, A. L.; Plewa, T.; Dwarkadas, V. V.

2008-04-01

In the realm of high-energy-density (HED) plasmas, there exist three primary hydrodynamic instabilities of concern: Rayleigh-Taylor (RT), Richtmyer-Meshkov (RM), and Kelvin-Helmholtz (KH). Although the RT and the RM instabilities have been readily observed and diagnosed in the laboratory, the KH instability remains relatively unexplored in HED plasmas. Unlike the RT and RM instabilities, the KH instability is driven by a lifting force generated by a strong velocity gradient in a stratified fluid. Understanding the KH instability mechanism in HED plasmas will provide essential insight into oblique shock systems, jets, mass stripping, and detailed RT-spike development. In addition, our KH experiment will help provide the groundwork for future transition to turbulence experiments. We present 2D FLASH simulations and experimental data from our initial attempts to create a pure KH system using the Nike laser at the Naval Research Laboratory.

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

Joint instability and osteoarthritis.

PubMed

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.

Electrostatic Solitary Waves in the Solar Wind: Evidence for Instability at Solar Wind Current Sheets

NASA Technical Reports Server (NTRS)

Malaspina, David M.; Newman, David L.; Wilson, Lynn Bruce; Goetz, Keith; Kellogg, Paul J.; Kerstin, Kris

2013-01-01

A strong spatial association between bipolar electrostatic solitary waves (ESWs) and magnetic current sheets (CSs) in the solar wind is reported here for the first time. This association requires that the plasma instabilities (e.g., Buneman, electron two stream) which generate ESWs are preferentially localized to solar wind CSs. Distributions of CS properties (including shear angle, thickness, solar wind speed, and vector magnetic field change) are examined for differences between CSs associated with ESWs and randomly chosen CSs. Possible mechanisms for producing ESW-generating instabilities at solar wind CSs are considered, including magnetic reconnection.

The Kelvin-Helmholtz instability in National Ignition Facility hohlraums as a source of gold-gas mixing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vandenboomgaerde, M.; Bonnefille, M.; Gauthier, P.

Highly resolved radiation-hydrodynamics FCI2 simulations have been performed to model laser experiments on the National Ignition Facility. In these experiments, cylindrical gas-filled hohlraums with gold walls are driven by a 20 ns laser pulse. For the first time, simulations show the appearance of Kelvin-Helmholtz (KH) vortices at the interface between the expanding wall material and the gas fill. In this paper, we determine the mechanisms which generate this instability: the increase of the gas pressure around the expanding gold plasma leads to the aggregation of an over-dense gold layer simultaneously with shear flows. At the surface of this layer, all themore » conditions are met for a KH instability to grow. Later on, as the interface decelerates, the Rayleigh-Taylor instability also comes into play. A potential scenario for the generation of a mixing zone at the gold-gas interface due to the KH instability is presented. Our estimates of the Reynolds number and the plasma diffusion width at the interface support the possibility of such a mix. The key role of the first nanosecond of the laser pulse in the instability occurrence is also underlined.« less

Real world ocean rogue waves explained without the modulational instability.

PubMed

Fedele, Francesco; Brennan, Joseph; Ponce de León, Sonia; Dudley, John; Dias, Frédéric

2016-06-21

Since the 1990s, the modulational instability has commonly been used to explain the occurrence of rogue waves that appear from nowhere in the open ocean. However, the importance of this instability in the context of ocean waves is not well established. This mechanism has been successfully studied in laboratory experiments and in mathematical studies, but there is no consensus on what actually takes place in the ocean. In this work, we question the oceanic relevance of this paradigm. In particular, we analyze several sets of field data in various European locations with various tools, and find that the main generation mechanism for rogue waves is the constructive interference of elementary waves enhanced by second-order bound nonlinearities and not the modulational instability. This implies that rogue waves are likely to be rare occurrences of weakly nonlinear random seas.

Real world ocean rogue waves explained without the modulational instability

PubMed Central

Fedele, Francesco; Brennan, Joseph; Ponce de León, Sonia; Dudley, John; Dias, Frédéric

2016-01-01

Since the 1990s, the modulational instability has commonly been used to explain the occurrence of rogue waves that appear from nowhere in the open ocean. However, the importance of this instability in the context of ocean waves is not well established. This mechanism has been successfully studied in laboratory experiments and in mathematical studies, but there is no consensus on what actually takes place in the ocean. In this work, we question the oceanic relevance of this paradigm. In particular, we analyze several sets of field data in various European locations with various tools, and find that the main generation mechanism for rogue waves is the constructive interference of elementary waves enhanced by second-order bound nonlinearities and not the modulational instability. This implies that rogue waves are likely to be rare occurrences of weakly nonlinear random seas. PMID:27323897

Particle acceleration and magnetic field generation in SNR shocks

NASA Astrophysics Data System (ADS)

Suslov, M.; Diamond, P. H.; Malkov, M. A.

2006-04-01

We discuss the diffusive acceleration mechanism in SNR shocks in terms of its potential to accelerate CRs to 10^18 eV, as observations imply. One possibility, currently discussed in the literature, is to resonantly generate a turbulent magnetic field via accelerated particles in excess of the background field. We analyze some problems of this scenario and suggest a different mechanism, which is based on the generation of Alfven waves at the gyroradius scale at the background field level, with a subsequent transfer to longer scales via interaction with strong acoustic turbulence in the shock precursor. The acoustic turbulence in turn, may be generated by Drury instability or by parametric instability of the Alfven (A) waves. The essential idea is an A->A+S decay instability process, where one of the interacting scatterers (i.e. the sound, or S-waves) are driven by the Drury instability process. This rapidly generates longer wavelength Alfven waves, which in turn resonate with high energy CRs thus binding them to the shock and enabling their further acceleration.

MHD instabilities in astrophysical plasmas: very different from MHD instabilities in tokamaks!

NASA Astrophysics Data System (ADS)

Goedbloed, J. P.

2018-01-01

The extensive studies of MHD instabilities in thermonuclear magnetic confinement experiments, in particular of the tokamak as the most promising candidate for a future energy producing machine, have led to an ‘intuitive’ description based on the energy principle that is very misleading for most astrophysical plasmas. The ‘intuitive’ picture almost directly singles out the dominant stabilizing field line bending energy of the Alfvén waves and, consequently, concentrates on expansion schemes that minimize that contribution. This happens when the wave vector {{k}}0 of the perturbations, on average, is perpendicular to the magnetic field {B}. Hence, all macroscopic instabilities of tokamaks (kinks, interchanges, ballooning modes, ELMs, neoclassical tearing modes, etc) are characterized by satisfying the condition {{k}}0 \\perp {B}, or nearly so. In contrast, some of the major macroscopic instabilities of astrophysical plasmas (the Parker instability and the magneto-rotational instability) occur when precisely the opposite condition is satisfied: {{k}}0 \\parallel {B}. How do those instabilities escape from the dominance of the stabilizing Alfvén wave? The answer to that question involves, foremost, the recognition that MHD spectral theory of waves and instabilities of laboratory plasmas could be developed to such great depth since those plasmas are assumed to be in static equilibrium. This assumption is invalid for astrophysical plasmas where rotational and gravitational accelerations produce equilibria that are at best stationary, and the associated spectral theory is widely, and incorrectly, believed to be non-self adjoint. These complications are addressed, and cured, in the theory of the Spectral Web, recently developed by the author. Using this method, an extensive survey of instabilities of astrophysical plasmas demonstrates how the Alfvén wave is pushed into insignificance under these conditions to give rise to a host of instabilities that do not

Wavenumber distribution in Hopf-wave instability: the reversible Selkov model of glycolytic oscillation.

PubMed

Dutt, Arun K

2005-09-22

We have investigated the short-wave instability due to Hopf bifurcation in a reaction-diffusion model of glycolytic oscillations. Very low values of the ratio d of the diffusion coefficient of the inhibitor (ATP) and that of the activator (ADP) do help to create short waves, whereas high values of the ratio d and the complexing reaction of the activator ADP reduces drastically the wave-instability domain, generating much longer wavelengths.

Recombinant aequorin and recombinant semi-synthetic aequorins. Cellular Ca2+ ion indicators.

PubMed Central

Shimomura, O; Inouye, S; Musicki, B; Kishi, Y

1990-01-01

Properties of a recombinant aequorin were investigated in comparison with those of natural aequorin. In chromatographic behaviour the recombinant aequorin did not match any of ten isoaequorins tested, although it was very similar to aequorin J. Its sensitivity to Ca2+ was found to be higher than that of any isoaequorin except aequorin D. The recombinant aequorin exhibited no toxicity when tested in various kinds of cells, even where samples of natural aequorin had been found to be toxic. Properties of four recombinant semi-synthetic aequorins (fch-, hcp-, e- and n-types), prepared from the recombinant apo-aequorin and synthetic analogues of coelenterazine, were approximately parallel with those of corresponding semi-synthetic aequorins prepared from natural apo-aequorin. Both recombinant e-aequorin and natural e-aequorin J luminesced with high values of the luminescence intensity ratio I400/I465, although the ratios were not pCa-dependent. The recombinant aequorin and recombinant semi-synthetic aequorins are highly suited for monitoring cellular Ca2+. PMID:2400391

Targeted mutagenesis of dengue virus type 2 replicon RNA by yeast in vivo recombination.

PubMed

Manzano, Mark; Padmanabhan, Radhakrishnan

2014-01-01

The use of cDNA infectious clones or subgenomic replicons is indispensable in studying flavivirus biology. Mutating nucleotides or amino acid residues gives important clues to their function in the viral life cycle. However, a major challenge to the establishment of a reverse genetics system for flaviviruses is the instability of their nucleotide sequences in Escherichia coli. Thus, direct cloning using conventional restriction enzyme-based procedures usually leads to unwanted rearrangements of the construct. In this chapter, we discuss a cloning strategy that bypasses traditional cloning procedures. We take advantage of the observations from previous studies that (1) unstable sequences in bacteria can be cloned in eukaryotic systems and (2) Saccharomyces cerevisiae has a well-studied genetics system to introduce sequences using homologous recombination. We describe a protocol to perform targeted mutagenesis in a subgenomic dengue virus 2 replicon. Our method makes use of homologous recombination in yeast using a linearized replicon and a PCR product containing the desired mutation. Constructs derived from this method can be propagated in E. coli with improved stability. Thus, yeast in vivo recombination provides an excellent strategy to genetically engineer flavivirus infectious clones or replicons because this system is compatible with inherently unstable sequences of flaviviruses and is not restricted by the limitations of traditional cloning procedures.

Immortal, telomerase-negative cell lines derived from a Li-Fraumeni syndrome patient exhibit telomere length variability and chromosomal and minisatellite instabilities.

PubMed

Tsutsui, Takeki; Kumakura, Shin-Ichi; Tamura, Yukiko; Tsutsui, Takeo W; Sekiguchi, Mizuki; Higuchi, Tokihiro; Barrett, J Carl

2003-05-01

Five immortal cell lines derived from a Li-Fraumeni syndrome patient (MDAH 087) with a germline mutant p53 allele were characterized with respect to telomere length and genomic instability. The remaining wild-type p53 allele is lost in the cell lines. Telomerase activity was undetectable in all immortal cell lines. Five subclones of each cell line and five re-subclones of each of the subclones also showed undetectable telomerase activity. All five immortal cell lines exhibited variability in the mean length of terminal restriction fragments (TRFs). Subclones of each cell line, and re-subclones of the subclones also showed TRF variability, indicating that the variability is owing to clonal heterogeneity. Chromosome aberrations were observed at high frequencies in these cell lines including the subclones and re-subclones, and the principal types of aberrations were breaks, double minute chromosomes and dicentric chromosomes. In addition, minisatellite instability detected by DNA fingerprints was observed in the immortal cell lines. However, all of the cell lines were negative for microsatellite instability. As minisatellite sequences are considered recombinogenic in mammalian cells, these results suggest that recombination rates can be increased in these cell lines. Tumor-derived human cell lines, HT1080 cells and HeLa cells that also lack p53 function, exhibited little genomic instability involving chromosomal and minisatellite instabilities, indicating that chromosomal and minisatellite instabilities observed in the immortal cell lines lacking telomerase activity could not result from loss of p53 function.

Production of recombinant dengue non-structural 1 (NS1) proteins from clinical virus isolates.

PubMed

Yohan, Benediktus; Wardhani, Puspa; Aryati; Trimarsanto, Hidayat; Sasmono, R Tedjo

2017-01-01

Dengue is a febrile disease caused by infection of dengue virus (DENV). Early diagnosis of dengue infection is important for better management of the disease. The DENV Non-Structural Protein 1 (NS1) antigen has been routinely used for the early dengue detection. In dengue epidemic countries such as Indonesia, clinicians are increasingly relying on the NS1 detection for confirmation of dengue infection. Various NS1 diagnostic tests are commercially available, however different sensitivities and specificities were observed in various settings. This study was aimed to generate dengue NS1 recombinant protein for the development of dengue diagnostic tests. Four Indonesian DENV isolates were used as the source of the NS1 gene cloning, expression, and purification in bacterial expression system. Recombinant NS1 proteins were successfully purified and their antigenicities were assessed. Immunization of mice with recombinant proteins observed the immunogenicity of the NS1 protein. The generated recombinant proteins can be potentially used in the development of NS1 diagnostic test. With minimal modifications, this method can be used for producing NS1 recombinant proteins from isolates obtained from other geographical regions. Copyright © 2016 Elsevier Inc. All rights reserved.

DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions.

PubMed

Shibata, Takehiko; Ling, Feng

2007-01-01

Homoplasmy is a basic genetic state of mitochondria, in which all of the hundreds to thousands of mitochondrial (mt)DNA copies within a cell or an individual have the same nucleotide-sequence. It was recently found that "vegetative segregation" to generate homoplasmic cells is an active process under genetic control. In the yeast Saccharomyces cerevisiae, the Mhr1 protein which catalyzes a key reaction in mtDNA homologous recombination, plays a pivotal role in vegetative segregation. Conversely, within the nuclear genome, homologous DNA recombination causes genetic diversity. Considering these contradictory roles of this key reaction in DNA recombination, possible functions of homoplasmy are discussed.

Resonant Drag Instability of Grains Streaming in Fluids

NASA Astrophysics Data System (ADS)

Squire, J.; Hopkins, P. F.

2018-03-01

We show that grains streaming through a fluid are generically unstable if their velocity, projected along some direction, matches the phase velocity of a fluid wave (linear oscillation). This can occur whenever grains stream faster than any fluid wave. The wave itself can be quite general—sound waves, magnetosonic waves, epicyclic oscillations, and Brunt–Väisälä oscillations each generate instabilities, for example. We derive a simple expression for the growth rates of these “resonant drag instabilities” (RDI). This expression (i) illustrates why such instabilities are so virulent and generic and (ii) allows for simple analytic computation of RDI growth rates and properties for different fluids. As examples, we introduce several new instabilities, which could see application across a variety of physical systems from atmospheres to protoplanetary disks, the interstellar medium, and galactic outflows. The matrix-based resonance formalism we introduce can also be applied more generally in other (nonfluid) contexts, providing a simple means for calculating and understanding the stability properties of interacting systems.

Cosmic microwave background bispectrum from recombination.

PubMed

Huang, Zhiqi; Vernizzi, Filippo

2013-03-08

We compute the cosmic microwave background temperature bispectrum generated by nonlinearities at recombination on all scales. We use CosmoLib2nd, a numerical Boltzmann code at second order to compute cosmic microwave background bispectra on the full sky. We consistently include all effects except gravitational lensing, which can be added to our result using standard methods. The bispectrum is peaked on squeezed triangles and agrees with the analytic approximation in the squeezed limit at the few percent level for all the scales where this is applicable. On smaller scales, we recover previous results on perturbed recombination. For cosmic-variance limited data to l(max)=2000, its signal-to-noise ratio is S/N=0.47, corresponding to f(NL)(eff)=-2.79, and will bias a local signal by f(NL)(loc) ~/= 0.82.

Viscoelastic Taylor-Couette instability as analog of the magnetorotational instability.

PubMed

Bai, Yang; Crumeyrolle, Olivier; Mutabazi, Innocent

2015-09-01

A linear stability analysis and an experimental study of a viscoelastic Taylor-Couette flow corotating in the Keplerian ratio allow us to elucidate the analogy between the viscoelastic instability and the magnetorotational instability (MRI). A generalized Rayleigh criterion allows us to determine the potentially unstable zone to pure-elasticity-driven perturbations. Experiments with a viscoelastic polymer solution yield four modes: one pure-elasticity mode and three elastorotational instability (ERI) modes that represent the MRI-analog modes. The destabilization by the polymer viscosity is evidenced for the ERI modes.

Enhanced production of recombinant proteins with Corynebacterium glutamicum by deletion of insertion sequences (IS elements).

PubMed

Choi, Jae Woong; Yim, Sung Sun; Kim, Min Jeong; Jeong, Ki Jun

2015-12-29

In most bacteria, various jumping genetic elements including insertion sequences elements (IS elements) cause a variety of genetic rearrangements resulting in harmful effects such as genome and recombinant plasmid instability. The genetic stability of a plasmid in a host is critical for high-level production of recombinant proteins, and in this regard, the development of an IS element-free strain could be a useful strategy for the enhanced production of recombinant proteins. Corynebacterium glutamicum, which is a workhorse in the industrial-scale production of various biomolecules including recombinant proteins, also has several IS elements, and it is necessary to identify the critical IS elements and to develop IS element deleted strain. From the cultivation of C. glutamicum harboring a plasmid for green fluorescent protein (GFP) gene expression, non-fluorescent clones were isolated by FACS (fluorescent activated cell sorting). All the isolated clones had insertions of IS elements in the GFP coding region, and two major IS elements (ISCg1 and ISCg2 families) were identified. By co-cultivating cells harboring either the isolated IS element-inserted plasmid or intact plasmid, it was clearly confirmed that cells harboring the IS element-inserted plasmids became dominant during the cultivation due to their growth advantage over cells containing intact plasmids, which can cause a significant reduction in recombinant protein production during cultivation. To minimize the harmful effects of IS elements on the expression of heterologous genes in C. glutamicum, two IS element free C. glutamicum strains were developed in which each major IS element was deleted, and enhanced productivity in the engineered C. glutamicum strain was successfully demonstrated with three models: GFP, poly(3-hydroxybutyrate) [P(3HB)] and γ-aminobutyrate (GABA). Our findings clearly indicate that the hopping of IS elements could be detrimental to the production of recombinant proteins in C

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

PubMed Central

Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

2014-01-01

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

A systematic investigation of production of synthetic prions from recombinant prion protein.

PubMed

Schmidt, Christian; Fizet, Jeremie; Properzi, Francesca; Batchelor, Mark; Sandberg, Malin K; Edgeworth, Julie A; Afran, Louise; Ho, Sammy; Badhan, Anjna; Klier, Steffi; Linehan, Jacqueline M; Brandner, Sebastian; Hosszu, Laszlo L P; Tattum, M Howard; Jat, Parmjit; Clarke, Anthony R; Klöhn, Peter C; Wadsworth, Jonathan D F; Jackson, Graham S; Collinge, John

2015-12-01

According to the protein-only hypothesis, infectious mammalian prions, which exist as distinct strains with discrete biological properties, consist of multichain assemblies of misfolded cellular prion protein (PrP). A critical test would be to produce prion strains synthetically from defined components. Crucially, high-titre 'synthetic' prions could then be used to determine the structural basis of infectivity and strain diversity at the atomic level. While there have been multiple reports of production of prions from bacterially expressed recombinant PrP using various methods, systematic production of high-titre material in a form suitable for structural analysis remains a key goal. Here, we report a novel high-throughput strategy for exploring a matrix of conditions, additives and potential cofactors that might generate high-titre prions from recombinant mouse PrP, with screening for infectivity using a sensitive automated cell-based bioassay. Overall, approximately 20,000 unique conditions were examined. While some resulted in apparently infected cell cultures, this was transient and not reproducible. We also adapted published methods that reported production of synthetic prions from recombinant hamster PrP, but again did not find evidence of significant infectious titre when using recombinant mouse PrP as substrate. Collectively, our findings are consistent with the formation of prion infectivity from recombinant mouse PrP being a rare stochastic event and we conclude that systematic generation of prions from recombinant PrP may only become possible once the detailed structure of authentic ex vivo prions is solved. © 2015 The Authors.

A systematic investigation of production of synthetic prions from recombinant prion protein

PubMed Central

Schmidt, Christian; Fizet, Jeremie; Properzi, Francesca; Batchelor, Mark; Sandberg, Malin K.; Edgeworth, Julie A.; Afran, Louise; Ho, Sammy; Badhan, Anjna; Klier, Steffi; Linehan, Jacqueline M.; Brandner, Sebastian; Hosszu, Laszlo L. P.; Tattum, M. Howard; Jat, Parmjit; Clarke, Anthony R.; Klöhn, Peter C.; Wadsworth, Jonathan D. F.; Jackson, Graham S.; Collinge, John

2015-01-01

According to the protein-only hypothesis, infectious mammalian prions, which exist as distinct strains with discrete biological properties, consist of multichain assemblies of misfolded cellular prion protein (PrP). A critical test would be to produce prion strains synthetically from defined components. Crucially, high-titre ‘synthetic' prions could then be used to determine the structural basis of infectivity and strain diversity at the atomic level. While there have been multiple reports of production of prions from bacterially expressed recombinant PrP using various methods, systematic production of high-titre material in a form suitable for structural analysis remains a key goal. Here, we report a novel high-throughput strategy for exploring a matrix of conditions, additives and potential cofactors that might generate high-titre prions from recombinant mouse PrP, with screening for infectivity using a sensitive automated cell-based bioassay. Overall, approximately 20 000 unique conditions were examined. While some resulted in apparently infected cell cultures, this was transient and not reproducible. We also adapted published methods that reported production of synthetic prions from recombinant hamster PrP, but again did not find evidence of significant infectious titre when using recombinant mouse PrP as substrate. Collectively, our findings are consistent with the formation of prion infectivity from recombinant mouse PrP being a rare stochastic event and we conclude that systematic generation of prions from recombinant PrP may only become possible once the detailed structure of authentic ex vivo prions is solved. PMID:26631378

Mode selection of magneto-Rayleigh-Taylor instability from the point of view of Landau phase transition theory

NASA Astrophysics Data System (ADS)

Dan, Jia Kun; Huang, Xian Bin; Ren, Xiao Dong; Wei, Bing

2017-08-01

A theoretical model referring to mode selection of Z-pinch-driven magneto-Rayleigh-Taylor (MRT) instability, which explains the generation of fundamental instability mode and evolution of fundamental wavelength in experiments, is proposed on the basis of the Landau theory of phase transition. The basic idea of this phase transition model lies in that the appearance of MRT instability pattern can be considered as a consequence of the spontaneous generation of interfacial structure like the spontaneous magnetization in a ferromagnetic system. It is demonstrated that the amplitude of instability is responsible for the order parameter in the Landau theory of phase transition and the fundamental wavelength appears to play a role analogous to inverse temperature in thermodynamics. Further analysis indicates that the MRT instability is characterized by first order phase transition and the fundamental wavelength is proportional to the square root of energy entering into the system from the driving source. The theory predicts that the fundamental wavelength grows rapidly and saturates reaching a limiting wavelength of the order of the liner's final outer radius. The results given by this theory show qualitative agreement with the available experimental data of MRT instability of liner implosions conducted on the Sandia Z machine as well as Primary Test Stand facility at the Institute of Fluid Physics.

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination

PubMed Central

Uringa, Evert-Jan; Youds, Jillian L.; Lisaingo, Kathleen; Lansdorp, Peter M.; Boulton, Simon J.

2011-01-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron–sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1’s enzymatic activity to its function in telomere maintenance and DNA repair. PMID:21097466

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

PubMed

Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

2011-03-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

Patellar Instability Management: A Survey of the International Patellofemoral Study Group.

PubMed

Liu, Joseph N; Steinhaus, Michael E; Kalbian, Irene L; Post, William R; Green, Daniel W; Strickland, Sabrina M; Shubin Stein, Beth E

2017-10-01

Although patellofemoral instability is among the most prevalent knee disorders, the management of patients with this condition is complex and remains variable, given the lack of long-term, high-level clinical outcome studies to compare various operative and nonoperative modalities. To discover a consensus within treatment controversies in patellofemoral instability among experienced knee surgeons with a specific interest in the patellofemoral joint. Expert opinion; Level of evidence, 5. A 3-step modified Delphi technique was used to establish a consensus. A 34-question, case-based online survey regarding patellofemoral instability was distributed to all active members of the International Patellofemoral Study Group. Consensus statements were generated if at least 66% of the respondents agreed and then redistributed to the same panel. Modifications to the consensus statements were made based on the iterative feedback process until no discordance was encountered in the third stage. Eight consensus statements were achieved. Nonoperative management is the current standard of care for a first-time dislocation in the absence of an osteochondral fragment or loose body requiring excision (100% agreement). In patients with a first-time dislocation with an operative osteochondral fracture requiring excision or repair, patellar instability should be addressed concurrently (89% agreement). Recurrent instability should be treated surgically, with most surgeons favoring medial reconstruction (77%-86% agreement). While there is general agreement that bony procedures should be performed to correct underlying bony deformities, there is no consensus regarding the most appropriate type of procedure performed. Lateral release should not be performed in isolation for the treatment of patellar instability (89% agreement). Despite the consensus generated in this study, our current understanding remains limited by a lack of high-level evidence as well as the numerous complex variables

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability.

PubMed

Wang, Guliang; Vasquez, Karen M

2017-01-05

Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

PubMed Central

Wang, Guliang; Vasquez, Karen M.

2017-01-01

Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease. PMID:28067787

Hydrodynamic Instabilities in High-Energy-Density Settings

NASA Astrophysics Data System (ADS)

Smalyuk, Vladimir

2016-10-01

Our understanding of hydrodynamic instabilities, such as the Rayleigh-Taylor (RT), Richtmyer-Meshkov (RM), and Kelvin-Helmholtz (KH) instabilities, in high-energy-density (HED) settings over past two decades has progressed enormously. The range of conditions where hydrodynamic instabilities are experimentally observed now includes direct and indirect drive inertial confinement fusion (ICF) where surprises continue to emerge, linear and nonlinear regimes, classical interfaces vs. stabilized ablation fronts, tenuous ideal plasmas vs. high density Fermi degenerate plasmas, bulk fluid interpenetration vs. mixing down to the atomic level, in the presence of magnetic fields and/or intense radiation, and in solid state plastic flow at high pressures and strain rates. Regimes in ICF can involve extreme conditions of matter with temperatures up to kilovolts, densities of a thousand times solid densities, and time scales of nanoseconds. On the other hand, scaled conditions can be generated that map to exploding stars (supernovae) with length and time scales of millions of kilometers and hours to days or even years of instability evolution, planetary formation dynamics involving solid-state plastic flow which severely modifies the RT growth and continues to challenge reliable theoretical descriptions. This review will look broadly at progress in probing and understanding hydrodynamic instabilities in these very diverse HED settings, and then will examine a few cases in more depth to illustrate the detailed science involved. Experimental results on large-scale HED facilities such as the Omega, Nike, Gekko, and Shenguang lasers will be reviewed and the latest developments at the National Ignition Facility (NIF) and Z machine will be covered. Finally, current overarching questions and challenges will be summarized to motivate research directions for future. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

Introduction to the Focus Issue: Chemo-Hydrodynamic Patterns and Instabilities

NASA Astrophysics Data System (ADS)

De Wit, A.; Eckert, K.; Kalliadasis, S.

2012-09-01

Pattern forming instabilities are often encountered in a wide variety of natural phenomena and technological applications, from self-organization in biological and chemical systems to oceanic or atmospheric circulation and heat and mass transport processes in engineering systems. Spatio-temporal structures are ubiquitous in hydrodynamics where numerous different convective instabilities generate pattern formation and complex spatiotemporal dynamics, which have been much studied both theoretically and experimentally. In parallel, reaction-diffusion processes provide another large family of pattern forming instabilities and spatio-temporal structures which have been analyzed for several decades. At the intersection of these two fields, "chemo-hydrodynamic patterns and instabilities" resulting from the coupling of hydrodynamic and reaction-diffusion processes have been less studied. The exploration of the new instability and symmetry-breaking scenarios emerging from the interplay between chemical reactions, diffusion and convective motions is a burgeoning field in which numerous exciting problems have emerged during the last few years. These problems range from fingering instabilities of chemical fronts and reactive fluid-fluid interfaces to the dynamics of reaction-diffusion systems in the presence of chaotic mixing. The questions to be addressed are at the interface of hydrodynamics, chemistry, engineering or environmental sciences to name a few and, as a consequence, they have started to draw the attention of several communities including both the nonlinear chemical dynamics and hydrodynamics communities. The collection of papers gathered in this Focus Issue sheds new light on a wide range of phenomena in the general area of chemo-hydrodynamic patterns and instabilities. It also serves as an overview of the current research and state-of-the-art in the field.

Parametric instabilities of rotor-support systems with application to industrial ventilators

NASA Technical Reports Server (NTRS)

Parszewski, Z.; Krodkiemski, T.; Marynowski, K.

1980-01-01

Rotor support systems interaction with parametric excitation is considered for both unequal principal shaft stiffness (generators) and offset disc rotors (ventilators). Instability regions and types of instability are computed in the first case, and parametric resonances in the second case. Computed and experimental results are compared for laboratory machine models. A field case study of parametric vibrations in industrial ventilators is reported. Computed parametric resonances are confirmed in field measurements, and some industrial failures are explained. Also the dynamic influence and gyroscopic effect of supporting structures are shown and computed.

Expression of Recombinant Antibodies

PubMed Central

Frenzel, André; Hust, Michael; Schirrmann, Thomas

2013-01-01

Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with “human-like” post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications. PMID:23908655

Inhibition of electron thermal conduction by electromagnetic instabilities. [in stellar coronas

NASA Technical Reports Server (NTRS)

Levinson, Amir; Eichler, David

1992-01-01

Heat flux inhibition by electromagnetic instabilities in a hot magnetized plasma is investigated. Low-frequency electromagnetic waves become unstable due to anisotropy of the electron distribution function. The chaotic magnetic field thus generated scatters the electrons with a specific effective mean free path. Saturation of the instability due to wave-wave interaction, nonlinear scattering, wave propagation, and collisional damping is considered. The effective mean free path is found self-consistently, using a simple model to estimate saturation level and scattering, and is shown to decrease with the temperature gradient length. The results, limited to the assumptions of the model, are applied to astrophysical systems. For some interstellar clouds the instability is found to be important. Collisional damping stabilizes the plasma, and the heat conduction can be dominated by superthermal electrons.

The shear-Hall instability in newborn neutron stars

NASA Astrophysics Data System (ADS)

Kondić, T.; Rüdiger, G.; Hollerbach, R.

2011-11-01

Aims: In the first few minutes of a newborn neutron star's life the Hall effect and differential rotation may both be important. We demonstrate that these two ingredients are sufficient for generating a "shear-Hall instability" and for studying its excitation conditions, growth rates, and characteristic magnetic field patterns. Methods: We numerically solve the induction equation in a spherical shell, with a kinematically prescribed differential rotation profile Ω(s), where s is the cylindrical radius. The Hall term is linearized about an imposed uniform axial field. The linear stability of individual azimuthal modes, both axisymmetric and non-axisymmetric, is then investigated. Results: For the shear-Hall instability to occur, the axial field must be parallel to the rotation axis if Ω(s) decreases outward, whereas if Ω(s) increases outward it must be anti-parallel. The instability draws its energy from the differential rotation, and occurs on the short rotational timescale rather than on the much longer Hall timescale. It operates most efficiently if the Hall time is comparable to the diffusion time. Depending on the precise field strengths B0, either axisymmetric or non-axisymmetric modes may be the most unstable. Conclusions: Even if the differential rotation in newborn neutron stars is quenched within minutes, the shear-Hall instability may nevertheless amplify any seed magnetic fields by many orders of magnitude.

[Advances of consolidated bioprocessing based on recombinant strategy].

PubMed

Zheng, Zongbao; Zhao, Meina; Chen, Tao; Zhao, Xueming

2013-10-01

Lignocellulosic biomass represents an abundant, low-cost and renewable source of potentially fermentable sugars. It is acandidate besides petroleum as feedstock for fuel and chemical production. Recent researches on utilizing lignocellulosicsas feedstock boost development of numerous-promising processes for a variety of fuels and chemicals, such as biodiesel, biohydrogen and ethanol. However, high cost in depolymerization is a primary obstacle preventing the use of lignocellulosic biomass as feedstock. Consolidated bioprocessing (CBP), refers to the bioprocess without any exogenous cellulolyotic enzymes added, converting the lignocellulosic material into biochemicals directly, which could potentially avoid the cost of the dedicated enzyme generation step by incorporating enzyme-generating, biomass-degrading and bioproduct-producing capabilities into a single organism through genetic engineering. There are two CBP strategies, native strategy and recombinant strategy. We mainly introduce the recombinant strategy, including its principle, the two responding styles, the contributions of synthetic biology and metabolic engineering and the future challenges.

Rayleigh-Taylor instability and mushroom-pattern formation in a two-component Bose-Einstein condensate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sasaki, Kazuki; Suzuki, Naoya; Saito, Hiroki

2009-12-15

The Rayleigh-Taylor instability at the interface in an immiscible two-component Bose-Einstein condensate is investigated using the mean field and Bogoliubov theories. Rayleigh-Taylor fingers are found to grow from the interface and mushroom patterns are formed. Quantized vortex rings and vortex lines are then generated around the mushrooms. The Rayleigh-Taylor instability and mushroom-pattern formation can be observed in a trapped system.

Signatures of Sex-Antagonistic Selection on Recombining Sex Chromosomes

PubMed Central

Kirkpatrick, Mark; Guerrero, Rafael F.

2014-01-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. PMID:24578352

Signatures of sex-antagonistic selection on recombining sex chromosomes.

PubMed

Kirkpatrick, Mark; Guerrero, Rafael F

2014-06-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. Copyright © 2014 by the Genetics Society of America.

The kinetochore prevents centromere-proximal crossover recombination during meiosis

PubMed Central

Vincenten, Nadine; Kuhl, Lisa-Marie; Lam, Isabel; Oke, Ashwini; Kerr, Alastair RW; Hochwagen, Andreas; Fung, Jennifer; Keeney, Scott; Vader, Gerben; Marston, Adèle L

2015-01-01

During meiosis, crossover recombination is essential to link homologous chromosomes and drive faithful chromosome segregation. Crossover recombination is non-random across the genome, and centromere-proximal crossovers are associated with an increased risk of aneuploidy, including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub-complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. The Ctf19 complex independently drives the enrichment of cohesin throughout the broader pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer of functionality by which the kinetochore prevents the incidence of chromosome segregation errors that generate aneuploid gametes. DOI: http://dx.doi.org/10.7554/eLife.10850.001 PMID:26653857

Generation of mesoscale magnetic fields and the dynamics of Cosmic Ray acceleration

NASA Astrophysics Data System (ADS)

Diamond, P. H.; Malkov, M. A.

The problem of the cosmic ray origin is discussed in connection with their acceleration in supernova remnant shocks. The diffusive shock acceleration mechanism is reviewed and its potential to accelerate particles to the maximum energy of (presumably) galactic cosmic rays (1018eV ) is considered. It is argued that to reach such energies, a strong magnetic field at scales larger than the particle gyroradius must be created as a result of the acceleration process, itself. One specific mechanism suggested here is based on the generation of Alfven wave at the gyroradius scale with a subsequent transfer to longer scales via interaction with strong acoustic turbulence in the shock precursor. The acoustic turbulence in turn, may be generated by Drury instability or by parametric instability of the Alfven waves. The generation mechanism is modulational instability of CR generated Alfven wave packets induced, in turn, by scattering off acoustic fluctuations in the shock precursor which are generated by Drury instability.

Cattle sex-specific recombination and genetic control from a very large pedigree

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is an essential biological process that generates novel genetic variants and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified ov...

Imaging of shoulder instability

PubMed Central

Martínez Martínez, Alberto; Tomás Muñoz, Pablo; Pozo Sánchez, José; Zarza Pérez, Antonio

2017-01-01

This extended review tries to cover the imaging findings of the wide range of shoulder injuries secondary to shoulder joint instability. Usefulness of the different imaging methods is stressed, including radiography, computed tomography (CT) and magnetic resonance. The main topics to be covered include traumatic, atraumatic and minor instability syndromes. Radiography may show bone abnormalities associated to instability, including developmental and post-traumatic changes. CT is the best technique depicting and quantifying skeletal changes. MR-arthrography is the main tool in diagnosing the shoulder instability injuries. PMID:28932699

Direct Simulation of Evolution and Control of Three-Dimensional Instabilities in Attachment-Line Boundary Layers

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.

1995-01-01

The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic- source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in at-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

Three-dimensional instability analysis of boundary layers perturbed by streamwise vortices

NASA Astrophysics Data System (ADS)

Martín, Juan A.; Paredes, Pedro

2017-12-01

A parametric study is presented for the incompressible, zero-pressure-gradient flat-plate boundary layer perturbed by streamwise vortices. The vortices are placed near the leading edge and model the vortices induced by miniature vortex generators (MVGs), which consist in a spanwise-periodic array of small winglet pairs. The introduction of MVGs has been experimentally proved to be a successful passive flow control strategy for delaying laminar-turbulent transition caused by Tollmien-Schlichting (TS) waves. The counter-rotating vortex pairs induce non-modal, transient growth that leads to a streaky boundary layer flow. The initial intensity of the vortices and their wall-normal distances to the plate wall are varied with the aim of finding the most effective location for streak generation and the effect on the instability characteristics of the perturbed flow. The study includes the solution of the three-dimensional, stationary, streaky boundary layer flows by using the boundary region equations, and the three-dimensional instability analysis of the resulting basic flows by using the plane-marching parabolized stability equations. Depending on the initial circulation and positioning of the vortices, planar TS waves are stabilized by the presence of the streaks, resulting in a reduction in the region of instability and shrink of the neutral stability curve. For a fixed maximum streak amplitude below the threshold for secondary instability (SI), the most effective wall-normal distance for the formation of the streaks is found to also offer the most stabilization of TS waves. By setting a maximum streak amplitude above the threshold for SI, sinuous shear layer modes become unstable, as well as another instability mode that is amplified in a narrow region near the vortex inlet position.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

PubMed

Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

2014-01-01

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

Genome-wide recombination rate variation in a recombination map of cotton.

PubMed

Shen, Chao; Li, Ximei; Zhang, Ruiting; Lin, Zhongxu

2017-01-01

Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species' genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.

Genome-wide recombination rate variation in a recombination map of cotton

PubMed Central

Shen, Chao; Li, Ximei; Zhang, Ruiting

2017-01-01

Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species’ genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton. PMID:29176878

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.

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

PubMed Central

Stukenbrock, Eva H.; Dutheil, Julien Y.

2018-01-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. PMID:29263029

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

PubMed

Stukenbrock, Eva H; Dutheil, Julien Y

2018-03-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

Recombination monitor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, S. Y.; Blaskiewicz, M.

This is a brief report on LEReC recombination monitor design considerations. The recombination produced Au 78+ ion rate is reviewed. Based on this two designs are discussed. One is to use the large dispersion lattice. It is shown that even with the large separation of the Au 78+ beam from the Au 79+ beam, the continued monitoring of the recombination is not possible. Accumulation of Au 78+ ions is needed, plus collimation of the Au79+ beam. In another design, it is shown that the recombination monitor can be built based on the proposed scheme with the nominal lattice. From machinemore » operation point of view, this design is preferable. Finally, possible studies and the alternative strategies with the basic goal of the monitor are discussed.« less

About the influence of phase mixing process and current neutralization on the resistive sausage instability dynamics of a relativistic electron beam

NASA Astrophysics Data System (ADS)

Kolesnikov, E. K.; Manuilov, A. S.; Petrov, V. S.; Zelensky, A. G.

2018-05-01

The resistive sausage instability of the relativistic electron beam in dense gas-plasma medium in the case of the generation of equilibrium return plasma current is investigated. In this situation the eigenvalue equation of this instability is obtained. The stabilizing and destabilizing effects of the phase mixing and generation of the return plasma current respectively have been shown.

Robust dynamic mitigation of instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawata, S.; Karino, T.

2015-04-15

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

Chronic ankle instability: Current perspectives

PubMed Central

Al-Mohrej, Omar A.; Al-Kenani, Nader S.

2016-01-01

Ankle sprain is reported to be among the most common recurrent injuries. About 20% of acute ankle sprain patients develop chronic ankle instability. The failure of functional rehabilitation after acute ankle sprain leads to the development of chronic ankle instability. Differentiation between functional and anatomical ankle instability is very essential to guide the proper treatment. Stability testing by varus stress test and anterior drawer test should be carried out. Subtalar instability is an important pathology that is commonly by passed during the assessment of chronic ankle instability. Unlike acute ankle sprain, chronic ankle instability might require surgical intervention. The surgical and conservative management options can be very much developed by in-depth knowledge of the ankle anatomy, biomechanics, and pathology. Anatomical repair, augmentation by tendon, or both are the basic methods of surgical intervention. Arthroscopy is becoming more popular in the management of chronic ankle instability. PMID:27843798

Suppression of the Transit -Time Instability in Large-Area Electron Beam Diodes

NASA Astrophysics Data System (ADS)

Myers, Matthew C.; Friedman, Moshe; Swanekamp, Stephen B.; Chan, Lop-Yung; Ludeking, Larry; Sethian, John D.

2002-12-01

Experiment, theory, and simulation have shown that large-area electron-beam diodes are susceptible to the transit-time instability. The instability modulates the electron beam spatially and temporally, producing a wide spread in electron energy and momentum distributions. The result is gross inefficiency in beam generation and propagation. Simulations indicate that a periodic, slotted cathode structure that is loaded with resistive elements may be used to eliminate the instability. Such a cathode has been fielded on one of the two opposing 60 cm × 200 cm diodes on the NIKE KrF laser at the Naval Research Laboratory. These diodes typically deliver 600 kV, 500 kA, 250 ns electron beams to the laser cell in an external magnetic field of 0.2 T. We conclude that the slotted cathode suppressed the transit-time instability such that the RF power was reduced by a factor of 9 and that electron transmission efficiency into the laser gas was improved by more than 50%.

Ablative Rayleigh-Taylor and Richtmyer-Meshkov Instabilities in Laser-Accelerated Colliding Foils

NASA Astrophysics Data System (ADS)

Aglitskiy, Y.; Metzler, N.; Karasik, M.; Serlin, V.; Weaver, J.; Obenschain, S. P.; Oh, J.; Schmitt, A. J.; Velikovich, A. L.; Zalesak, S. T.; Gardner, J. H.; Harding, E. C.

2008-11-01

In our experiments done on the Nike KrF laser, we study instability growth at shock-decelerated interfaces in planar colliding-foil experiments. We use streaked monochromatic (1.86 keV) x-ray face-on imaging diagnostics to measure the areal mass modulation growth caused by the instability. Higher x-ray energies up to 5.25 keV are used to follow the shock propagation as well as the 1D dynamics of the collision. While a laser-driven foil is accelerated towards the stationary low-density foam layer, an ablative RT instability develops. Having reached a high velocity, the foil hits the foam layer. The impact generates strong shocks in the plastic and in the foam. The reflected shock wave re-shocks the ablation front, its acceleration stops, and so does the observed RT growth. This is followed by areal mass oscillations due to the ablative RM instability and feedout mechanisms, of which the latter dominates.

Low power generation of equalized broadband CW supercontinua using a novel technique incorporating modulation instability of line broadened pump

NASA Astrophysics Data System (ADS)

Prakash, Roopa; Choudhury, Vishal; Arun, S.; Supradeepa, V. R.

2018-02-01

Continuous-wave(CW) supercontinuum sources find applications in various domains such as imaging, spectroscopy, test and measurement. They are generated by pumping an optical fiber with a CW laser in the anomalous-dispersion region close to its zero-dispersion wavelength. Modulation instability(MI) sidebands are created, and further broadened and equalized by additional nonlinear processes generating the supercontinuum. This necessitates high optical powers and at lower powers, only MI sidebands can be seen without the formation of the supercontinuum. Obtaining a supercontinuum at low, easily manageable optical powers is attractive for many applications, but current techniques cannot achieve this. In this work, we propose a new mechanism for low power supercontinuum generation utilizing the modified MI gain spectrum for a line-broadened, decorrelated pump. A novel two-stage generation mechanism is demonstrated, where the first stage constituting standard telecom fiber slightly broadens the input pump linewidth. However, this process in the presence of dispersion, acts to de-correlate the different spectral components of the pump signal. When this is sent through highly nonlinear fiber near its zero-dispersion wavelength, the shape of the MI gain spectrum is modified, and this process naturally results in the generation of a broadband, equalized supercontinuum source at much lower powers than possible using conventional single stage spectral broadening. Here, we demonstrate a 0.5W supercontinuum source pumped using a 4W Erbium-Ytterbium co-doped fiber laser with a bandwidth spanning from 1300nm to 2000nm. We also demonstrate an interesting behaviour of this technique of relative insensitivity to the pump wavelength vis-a-vis zero-dispersion wavelength of the fiber.

Reactions of chicken sera to recombinant Campylobacter jejuni flagellar proteins.

PubMed

Yeh, Hung-Yueh; Hiett, Kelli L; Line, John E

2015-03-01

Campylobacter jejuni is a Gram-negative spiral rod bacterium and is the leading but underreported bacterial food-borne pathogen that causes human campylobacteriosis worldwide. Raw or undercooked poultry products are regarded as a major source for human infection. C. jejuni flagella have been implicated in colonization and adhesion to the mucosal surface of chicken gastrointestinal tracts. Therefore, flagellar proteins would be the excellent targets for further investigation. In this report, we used the recombinant technology to generate a battery of C. jejuni flagellar proteins, which were purified by His tag affinity chromatography and determined antigenic profiles of these recombinant flagellar proteins using sera from chickens older than 6 weeks of age. The immunoblot results demonstrate that each chicken serum reacted to various numbers of recombinant flagellar proteins. Among these recombinant proteins, chicken sera reacted predominantly to the FlgE1, FlgK, FlhF, FliG and FliY proteins. These antibody screening results provide a rationale for further evaluation of these recombinant flagellar proteins as potential vaccines for chickens to improve food safety as well as investigation of host immune response to C. jejuni.

Genetic diversity and recombination analysis of sweepoviruses from Brazil

PubMed Central

2012-01-01

Background Monopartite begomoviruses (genus Begomovirus, family Geminiviridae) that infect sweet potato (Ipomoea batatas) around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses. Results This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV). Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR) and in the middle of the C1 open reading frame (ORF). Conclusions The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses. PMID:23082767

Recombinant protective antigen 102 (rPA102): profile of a second-generation anthrax vaccine.

PubMed

Keitel, Wendy A

2006-08-01

Recent terrorist attacks involving the use of Bacillus anthracis spores have stimulated interest in the development of new vaccines for anthrax prevention. Studies of the pathogenesis of anthrax and of the immune responses following infection and immunization underscore the pivotal role that antibodies to the protective antigen play in protection. The most promising vaccine candidates contain purified recombinant protective antigen. Clinical trials of one of these, recombinant protective antigen (rPA)102, are underway. Initial results suggest that rPA102 is well tolerated and immunogenic. Additional trials are necessary to identify optimal formulations and immunization regimens for pre- and postexposure prophylaxis. Future licensure of these and other candidate vaccines will depend on their safety and immunogenicity profiles in humans, and their ability to confer protection in animal models of inhalational anthrax.

A novel reverse genetics system for production of infectious West Nile virus using homologous recombination in mammalian cells.

PubMed

Kobayashi, Shintaro; Yoshii, Kentaro; Hirano, Minato; Muto, Memi; Kariwa, Hiroaki

2017-02-01

Reverse genetics systems facilitate investigation of many aspects of the life cycle and pathogenesis of viruses. However, genetic instability in Escherichia coli has hampered development of a reverse genetics system for West Nile virus (WNV). In this study, we developed a novel reverse genetics system for WNV based on homologous recombination in mammalian cells. Introduction of the DNA fragment coding for the WNV structural protein together with a DNA-based replicon resulted in the release of infectious WNV. The growth rate and plaque size of the recombinant virus were almost identical to those of the parent WNV. Furthermore, chimeric WNV was produced by introducing the DNA fragment coding for the structural protein and replicon plasmid derived from various strains. Here, we report development of a novel system that will facilitate research into WNV infection. Copyright © 2016 Elsevier B.V. All rights reserved.

Nuclear delivery of recombinant OCT4 by chitosan nanoparticles for transgene-free generation of protein-induced pluripotent stem cells.

PubMed

Tammam, Salma; Malak, Peter; Correa, Daphne; Rothfuss, Oliver; Azzazy, Hassan M E; Lamprecht, Alf; Schulze-Osthoff, Klaus

2016-06-21

Protein-based reprogramming of somatic cells is a non-genetic approach for the generation of induced pluripotent stem cells (iPSCs), whereby reprogramming factors, such as OCT4, SOX2, KLF4 and c-MYC, are delivered as functional proteins. The technique is considered safer than transgenic methods, but, unfortunately, most protein-based protocols provide very low reprogramming efficiencies. In this study, we developed exemplarily a nanoparticle (NP)-based delivery system for the reprogramming factor OCT4. To this end, we expressed human OCT4 in Sf9 insect cells using a baculoviral expression system. Recombinant OCT4 showed nuclear localization in Sf9 cells indicating proper protein folding. In comparison to soluble OCT4 protein, encapsulation of OCT4 in nuclear-targeted chitosan NPs strongly stabilized its DNA-binding activity even under cell culture conditions. OCT4-loaded NPs enabled cell treatment with high micromolar concentrations of OCT4 and successfully delivered active OCT4 into human fibroblasts. Chitosan NPs therefore provide a promising tool for the generation of transgene-free iPSCs.

Experimental evolution of recombination and crossover interference in Drosophila caused by directional selection for stress-related traits.

PubMed

Aggarwal, Dau Dayal; Rashkovetsky, Eugenia; Michalak, Pawel; Cohen, Irit; Ronin, Yefim; Zhou, Dan; Haddad, Gabriel G; Korol, Abraham B

2015-11-27

Population genetics predicts that tight linkage between new and/or pre-existing beneficial and deleterious alleles should decrease the efficiency of natural selection in finite populations. By decoupling beneficial and deleterious alleles and facilitating the combination of beneficial alleles, recombination accelerates the formation of high-fitness genotypes. This may impose indirect selection for increased recombination. Despite the progress in theoretical understanding, interplay between recombination and selection remains a controversial issue in evolutionary biology. Even less satisfactory is the situation with crossover interference, which is a deviation of double-crossover frequency in a pair of adjacent intervals from the product of recombination rates in the two intervals expected on the assumption of crossover independence. Here, we report substantial changes in recombination and interference in three long-term directional selection experiments with Drosophila melanogaster: for desiccation (~50 generations), hypoxia, and hyperoxia tolerance (>200 generations each). For all three experiments, we found a high interval-specific increase of recombination frequencies in selection lines (up to 40-50% per interval) compared to the control lines. We also discovered a profound effect of selection on interference as expressed by an increased frequency of double crossovers in selection lines. Our results show that changes in interference are not necessarily coupled with increased recombination. Our results support the theoretical predictions that adaptation to a new environment can promote evolution toward higher recombination. Moreover, this is the first evidence of selection for different recombination-unrelated traits potentially leading, not only to evolution toward increased crossover rates, but also to changes in crossover interference, one of the fundamental features of recombination.

POD analysis of the instability mode of a low-speed streak in a laminar boundary layer

NASA Astrophysics Data System (ADS)

Deng, Si-Chao; Pan, Chong; Wang, Jin-Jun; Rinoshika, Akira

2017-12-01

The instability of one single low-speed streak in a zero-pressure-gradient laminar boundary layer is investigated experimentally via both hydrogen bubble visualization and planar particle image velocimetry (PIV) measurement. A single low-speed streak is generated and destabilized by the wake of an interference wire positioned normal to the wall and in the upstream. The downstream development of the streak includes secondary instability and self-reproduction process, which leads to the generation of two additional streaks appearing on either side of the primary one. A proper orthogonal decomposition (POD) analysis of PIV measured velocity field is used to identify the components of the streak instability in the POD mode space: for a sinuous/varicose type of POD mode, its basis functions present anti-symmetric/symmetric distributions about the streak centerline in the streamwise component, and the symmetry condition reverses in the spanwise component. It is further shown that sinuous mode dominates the turbulent kinematic energy (TKE) through the whole streak evolution process, the TKE content first increases along the streamwise direction to a saturation value and then decays slowly. In contrast, varicose mode exhibits a sustained growth of the TKE content, suggesting an increasing competition of varicose instability against sinuous instability.

Antigenic Variation in the Lyme Spirochete: Insights into Recombinational Switching with a Suggested Role for Error-Prone Repair.

PubMed

Verhey, Theodore B; Castellanos, Mildred; Chaconas, George

2018-05-29

The Lyme disease spirochete, Borrelia burgdorferi, uses antigenic variation as a strategy to evade the host's acquired immune response. New variants of surface-localized VlsE are generated efficiently by unidirectional recombination from 15 unexpressed vls cassettes into the vlsE locus. Using algorithms to analyze switching from vlsE sequencing data, we characterize a population of over 45,000 inferred recombination events generated during mouse infection. We present evidence for clustering of these recombination events within the population and along the vlsE gene, a role for the direct repeats flanking the variable region in vlsE, and the importance of sequence homology in determining the location of recombination, despite RecA's dispensability. Finally, we report that non-templated sequence variation is strongly associated with recombinational switching and occurs predominantly at the 5' end of conversion tracts. This likely results from an error-prone repair mechanism operational during recombinational switching that elevates the mutation rate > 5,000-fold in switched regions. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

RAC-tagging: Recombineering And Cas9-assisted targeting for protein tagging and conditional analyses

PubMed Central

Baker, Oliver; Gupta, Ashish; Obst, Mandy; Zhang, Youming; Anastassiadis, Konstantinos; Fu, Jun; Stewart, A. Francis

2016-01-01

A fluent method for gene targeting to establish protein tagged and ligand inducible conditional loss-of-function alleles is described. We couple new recombineering applications for one-step cloning of gRNA oligonucleotides and rapid generation of short-arm (~1 kb) targeting constructs with the power of Cas9-assisted targeting to establish protein tagged alleles in embryonic stem cells at high efficiency. RAC (Recombineering And Cas9)-tagging with Venus, BirM, APEX2 and the auxin degron is facilitated by a recombineering-ready plasmid series that permits the reuse of gene-specific reagents to insert different tags. Here we focus on protein tagging with the auxin degron because it is a ligand-regulated loss-of-function strategy that is rapid and reversible. Furthermore it includes the additional challenge of biallelic targeting. Despite high frequencies of monoallelic RAC-targeting, we found that simultaneous biallelic targeting benefits from long-arm (>4 kb) targeting constructs. Consequently an updated recombineering pipeline for fluent generation of long arm targeting constructs is also presented. PMID:27216209

EMAST is a Form of Microsatellite Instability That is Initiated by Inflammation and Modulates Colorectal Cancer Progression.

PubMed

Carethers, John M; Koi, Minoru; Tseng-Rogenski, Stephanie S

2015-03-31

DNA mismatch repair (MMR) function is critical for correcting errors coincident with polymerase-driven DNA replication, and its proteins are frequent targets for inactivation (germline or somatic), generating a hypermutable tumor that drives cancer progression. The biomarker for defective DNA MMR is microsatellite instability-high (MSI-H), observed in ~15% of colorectal cancers, and defined by mono- and dinucleotide microsatellite frameshift mutations. MSI-H is highly correlated with loss of MMR protein expression, is commonly diploid, is often located in the right side of the colon, prognosticates good patient outcome, and predicts poor efficacy with 5-fluorouracil treatment. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is another form of MSI at tetranucleotide repeats that has been observed in multiple cancers, but its etiology and clinical relevance to patient care has only been recently illuminated. Specifically, EMAST is an acquired somatic defect observed in up to 60% of colorectal cancers and caused by unique dysfunction of the DNA MMR protein MSH3 (and its DNA MMR complex MutSβ, a heterodimer of MSH2-MSH3), and in particular a loss-of-function phenotype due to a reversible shift from its normal nuclear location into the cytosol in response to oxidative stress and the pro-inflammatory cytokine interleukin-6. Tumor hypoxia may also be a contributor. Patients with EMAST colorectal cancers show diminished prognosis compared to patients without the presence of EMAST in their cancer. In addition to defective DNA MMR recognized by tetranucleotide (and di- and tri-nucleotide) frameshifts, loss of MSH3 also contributes to homologous recombination-mediated repair of DNA double stranded breaks, indicating the MSH3 dysfunction is a complex defect for cancer cells that generates not only EMAST but also may contribute to chromosomal instability and aneuploidy. Areas for future investigation for this most common DNA MMR defect among

EMAST is a Form of Microsatellite Instability That is Initiated by Inflammation and Modulates Colorectal Cancer Progression

PubMed Central

Carethers, John M.; Koi, Minoru; Tseng-Rogenski, Stephanie S.

2015-01-01

DNA mismatch repair (MMR) function is critical for correcting errors coincident with polymerase-driven DNA replication, and its proteins are frequent targets for inactivation (germline or somatic), generating a hypermutable tumor that drives cancer progression. The biomarker for defective DNA MMR is microsatellite instability-high (MSI-H), observed in ~15% of colorectal cancers, and defined by mono- and dinucleotide microsatellite frameshift mutations. MSI-H is highly correlated with loss of MMR protein expression, is commonly diploid, is often located in the right side of the colon, prognosticates good patient outcome, and predicts poor efficacy with 5-fluorouracil treatment. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is another form of MSI at tetranucleotide repeats that has been observed in multiple cancers, but its etiology and clinical relevance to patient care has only been recently illuminated. Specifically, EMAST is an acquired somatic defect observed in up to 60% of colorectal cancers and caused by unique dysfunction of the DNA MMR protein MSH3 (and its DNA MMR complex MutSβ, a heterodimer of MSH2-MSH3), and in particular a loss-of-function phenotype due to a reversible shift from its normal nuclear location into the cytosol in response to oxidative stress and the pro-inflammatory cytokine interleukin-6. Tumor hypoxia may also be a contributor. Patients with EMAST colorectal cancers show diminished prognosis compared to patients without the presence of EMAST in their cancer. In addition to defective DNA MMR recognized by tetranucleotide (and di- and tri-nucleotide) frameshifts, loss of MSH3 also contributes to homologous recombination-mediated repair of DNA double stranded breaks, indicating the MSH3 dysfunction is a complex defect for cancer cells that generates not only EMAST but also may contribute to chromosomal instability and aneuploidy. Areas for future investigation for this most common DNA MMR defect among

Recombinant protein blends: silk beyond natural design.

PubMed

Dinjaski, Nina; Kaplan, David L

2016-06-01

Recombinant DNA technology and new material concepts are shaping future directions in biomaterial science for the design and production of the next-generation biomaterial platforms. Aside from conventionally used synthetic polymers, numerous natural biopolymers (e.g., silk, elastin, collagen, gelatin, alginate, cellulose, keratin, chitin, polyhydroxyalkanoates) have been investigated for properties and manipulation via bioengineering. Genetic engineering provides a path to increase structural and functional complexity of these biopolymers, and thereby expand the catalog of available biomaterials beyond that which exists in nature. In addition, the integration of experimental approaches with computational modeling to analyze sequence-structure-function relationships is starting to have an impact in the field by establishing predictive frameworks for determining material properties. Herein, we review advances in recombinant DNA-mediated protein production and functionalization approaches, with a focus on hybrids or combinations of proteins; recombinant protein blends or 'recombinamers'. We highlight the potential biomedical applications of fibrous protein recombinamers, such as Silk-Elastin Like Polypeptides (SELPs) and Silk-Bacterial Collagens (SBCs). We also discuss the possibility for the rationale design of fibrous proteins to build smart, stimuli-responsive biomaterials for diverse applications. We underline current limitations with production systems for these proteins and discuss the main trends in systems/synthetic biology that may improve recombinant fibrous protein design and production. Copyright © 2016. Published by Elsevier Ltd.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors.

PubMed

Skamagki, Maria; Correia, Cristina; Yeung, Percy; Baslan, Timour; Beck, Samuel; Zhang, Cheng; Ross, Christian A; Dang, Lam; Liu, Zhong; Giunta, Simona; Chang, Tzu-Pei; Wang, Joye; Ananthanarayanan, Aparna; Bohndorf, Martina; Bosbach, Benedikt; Adjaye, James; Funabiki, Hironori; Kim, Jonghwan; Lowe, Scott; Collins, James J; Lu, Chi-Wei; Li, Hu; Zhao, Rui; Kim, Kitai

2017-09-01

Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS-glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients' own cells that are safe for transplantation.

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

PubMed Central

Skamagki, Maria; Correia, Cristina; Yeung, Percy; Baslan, Timour; Beck, Samuel; Zhang, Cheng; Ross, Christian A.; Dang, Lam; Liu, Zhong; Giunta, Simona; Chang, Tzu-Pei; Wang, Joye; Ananthanarayanan, Aparna; Bohndorf, Martina; Bosbach, Benedikt; Adjaye, James; Funabiki, Hironori; Kim, Jonghwan; Lowe, Scott; Collins, James J.; Lu, Chi-Wei; Li, Hu; Zhao, Rui; Kim, Kitai

2018-01-01

Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS–glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients’ own cells that are safe for transplantation. PMID:28846095

Harnessing the relativistic Buneman instability for laser-ion acceleration in the transparency regime

NASA Astrophysics Data System (ADS)

Stark, D. J.; Yin, L.; Albright, B. J.

2018-06-01

We examine the relativistic Buneman instability in systems relevant to high-intensity laser-plasma interactions under conditions of relativistically-induced transparency, as this instability can generate large-amplitude electrostatic waves at low frequencies that are pertinent to ion dynamics in these systems. Ion flows are shown to significantly alter the range of unstable wave numbers and to increase the phase velocities of the unstable modes; we particularly highlight the relativistic effects from both the ion and electron (with transverse motion) populations. These findings are related to the mode structure seen in particle-in-cell simulation results of a short-pulse laser breaking through an initially opaque target with the onset of relativistic transparency. Additionally, driving mechanisms from free energy present in density and velocity gradients are shown to be capable of significantly enhancing the growth rates, and these instabilities furthermore extend the breadth of the unstable wave number range. Lastly, we discuss how the transverse self-generated magnetic fields characteristic of short-pulse interactions can potentially constrain the unstable wave numbers in a non-trivial manner.

The TP53 dependence of radiation-induced chromosome instability in human lymphoblastoid cells

NASA Technical Reports Server (NTRS)

Schwartz, Jeffrey L.; Jordan, Robert; Evans, Helen H.; Lenarczyk, Marek; Liber, Howard

2003-01-01

The dose and TP53 dependence for the induction of chromosome instability were examined in cells of three human lymphoblastoid cell lines derived from WIL2 cells: TK6, a TP53-normal cell line, NH32, a TP53-knockout created from TK6, and WTK1, a WIL2-derived cell line that spontaneously developed a TP53 mutation. Cells of each cell line were exposed to (137)Cs gamma rays, and then surviving clones were isolated and expanded in culture for approximately 35 generations before the frequency and characteristics of the instability were analyzed. The presence of dicentric chromosomes, formed by end-to-end fusions, served as a marker of chromosomal instability. Unexposed TK6 cells had low levels of chromosomal instability (0.002 +/- 0.001 dicentrics/cell). Exposure of TK6 cells to doses as low as 5 cGy gamma rays increased chromosome instability levels nearly 10-fold to 0.019 +/- 0.008 dicentrics/cell. There was no further increase in instability levels beyond 5 cGy. In contrast to TK6 cells, unexposed cultures of WTK1 and NH32 cells had much higher levels of chromosome instability of 0.034 +/- 0.007 and 0.041 +/- 0.009, respectively, but showed little if any effect of radiation on levels of chromosome instability. The results suggest that radiation exposure alters the normal TP53-dependent cell cycle checkpoint controls that recognize alterations in telomere structure and activate apoptosis.

Genome instability in Novel Lolium multiflorum x L. arundinaceum hybrids

USDA-ARS?s Scientific Manuscript database

We have identified a method whereby Lolium multiflorum (Lm) or L. arundinaceum (Fa) genomes are preferentially eliminated through a mitotic loss behavior in interspecific Lm x Fa F1 hybrids,generating either dihaploid Lm lines or Fa lines. The genome instability has been visualized phenotypically an...

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen

PubMed Central

Croll, Daniel; Lendenmann, Mark H.; Stewart, Ethan; McDonald, Bruce A.

2015-01-01

Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host. PMID:26392286

Relativistic electromagnetic ion cyclotron instabilities

NASA Astrophysics Data System (ADS)

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

2005-03-01

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

Three-dimensional instabilities of mantle convection with multiple phase transitions

NASA Technical Reports Server (NTRS)

Honda, S.; Yuen, D. A.; Balachandar, S.; Reuteler, D.

1993-01-01

The effects of multiple phase transitions on mantle convection are investigated by numerical simulations that are based on three-dimensional models. These simulations show that cold sheets of mantle material collide at junctions, merge, and form a strong downflow that is stopped temporarily by the transition zone. The accumulated cold material gives rise to a strong gravitational instability that causes the cold mass to sink rapidly into the lower mantle. This process promotes a massive exchange between the lower and upper mantles and triggers a global instability in the adjacent plume system. This mechanism may be cyclic in nature and may be linked to the generation of superplumes.

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)

Recombinant Immunotoxin Therapy of Solid Tumors: Challenges and Strategies.

PubMed

Shan, Liang; Liu, Yuanyi; Wang, Paul

2013-01-01

Immunotoxins are a group of protein-based therapeutics, basically comprising two functional moieties: one is the antibody or antibody Fv fragment that allows the immunotoxin to bind specifically to target cells; another is the plant or bacterial toxin that kills the cells upon internalization. Immunotoxins have several unique features which are superior to conventional chemotherapeutics, including high specificity, extraordinary potency, and no known drug resistance. Development of immunotoxins evolves with time and technology, but significant progress has been achieved in the past 20 years after introduction of recombinant DNA technique and generation of the first single-chain variable fragment of monoclonal antibodies. Since then, more than 1,000 recombinant immunotoxins have been generated against cancer. However, most success in immunotoxin therapy has been achieved against hematological malignancies, several issues persist to be significant barriers for effective therapy of human solid tumors. Further development of immunotoxins will largely focus on the improvement of penetration capability to solid tumor mass and elimination of immunogenicity occurred when given repeatedly to patients. Promising strategies may include construction of recombinant antibody fragments with higher binding affinity and stability, elimination of immunodominant T- and B-cell epitopes of toxins, modification of immunotoxins with macromolecules like poly(ethylene glycol) and liposomes, and generation of immunotoxins with humanized antibody fragments and human endogenous cytotoxic enzymes. In this paper, we briefly reviewed the evolution of immunotoxin development and then discussed the challenges of immunotoxin therapy for human solid tumors and the potential strategies we may seek to overcome the challenges.

Excitation correlation photoluminescence in the presence of Shockley-Read-Hall recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borgwardt, M., E-mail: mario.borgwardt@helmholtz-berlin.de; Sippel, P.; Eichberger, R.

Excitation correlation photoluminescence (ECPL) measurements are often analyzed in the approximation of a cross correlation of charge carrier populations generated by the two delayed pulses. In semiconductors, this approach is valid for a linear non-radiative recombination path, but not for a non-linear recombination rate as in the general Shockley-Read-Hall recombination scenario. Here, the evolution of the ECPL signal was studied for deep trap recombination following Shockley-Read-Hall statistics. Analytic solutions can be obtained for a fast minority trapping regime and steady state recombination. For the steady state case, our results show that the quadratic radiative term plays only a minor role,more » and that the shape of the measured signal is mostly determined by the non-linearity of the recombination itself. We find that measurements with unbalanced intense pump and probe pulses can directly provide information about the dominant non-radiative recombination mechanism. The signal traces follow the charge carrier concentrations, despite the complex origins of the signal, thus showing that ECPL can be applied to study charge carrier dynamics in semiconductors without requiring elaborate calculations. The model is compared with measurements on a reference sample with alternating layers of InGaAs/InAlAs that were additionally cross-checked with time resolved optical pump terahertz probe measurements and found to be in excellent agreement.« less

Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA.

PubMed

Chen, Xin Jie

2013-09-01

Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.

Mechanism of Homologous Recombination and Implications for Aging-Related Deletions in Mitochondrial DNA

PubMed Central

2013-01-01

SUMMARY Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells. PMID:24006472

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

Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome

PubMed Central

2010-01-01

Background The chromosome of Streptomyces has been shown to be unstable, frequently undergoing gross chromosomal rearrangements. However, the mechanisms underlying this phenomenon remain unclear, with previous studies focused on two chromosomal ends as targets for rearrangements. Here we investigated chromosomal instability of Streptomyces avermitilis, an important producer of avermectins, and characterized four gross chromosomal rearrangement events, including a major deletion in the central region. The present findings provide a valuable contribution to the mechanistic study of genetic instability in Streptomyces. Results Thirty randomly-selected "bald" mutants derived from the wild-type strain all contained gross chromosomal rearrangements of various types. One of the bald mutants, SA1-8, had the same linear chromosomal structure as the high avermectin-producing mutant 76-9. Chromosomes of both strains displayed at least three independent chromosomal rearrangements, including chromosomal arm replacement to form new 88-kb terminal inverted repeats (TIRs), and two major deletions. One of the deletions eliminated the 36-kb central region of the chromosome, but surprisingly did not affect viability of the cells. The other deletion (74-kb) was internal to the right chromosomal arm. The chromosome of another bald mutant, SA1-6, was circularized with deletions at both ends. No obvious homology was found in all fusion sequences. Generational stability analysis showed that the chromosomal structure of SA1-8 and SA1-6 was stable. Conclusions Various chromosomal rearrangements, including chromosomal arm replacement, interstitial deletions and chromosomal circularization, occurred in S. avermitilis by non-homologous recombination. The finding of an inner deletion involving in the central region of S. avermitilis chromosome suggests that the entire Streptomyces chromosome may be the target for rearrangements, which are not limited, as previously reported, to the two

Inertial instabilities in a mixing-separating microfluidic device

NASA Astrophysics Data System (ADS)

Domingues, Allysson; Poole, Robert; Dennis, David

2017-11-01

Combining and separating fluids has many industrial and biomedical applications. This numerical and experimental study explores inertial instabilities in a so-called mixing-separating cell micro-geometry which could potentiality be used to enhance mixing. Our microfluidic mixing-separating cell consists of two straight square parallel channels with flow from opposite directions with a central gap that allows the streams to interact, mix or remain separate (often referred to as the `H' geometry). A stagnation point is generated at the centre of symmetry due to the two opposed inlets and outlets. Under creeping flow conditions (Reynolds number [ Re 0 ]) the flow is steady, two-dimensional and produces a sharp symmetric boundary between fluids stream entering the geometry from opposite directions. For Re > 30 , an inertial instability appears which leads to the generation of a central vortex and the breaking of symmetry, although the flow remains steady. As Re increases the central vortex divides into two vortices. Our experimental and numerical investigations both show the same phenomena. The results suggest that the effect observed can be exploited to enhance mixing in biomedical or other applications. Work supported by CNPq Grant 203195/2014-0.

Thin-film-induced morphological instabilities over calcite surfaces

PubMed Central

Vesipa, R.; Camporeale, C.; Ridolfi, L.

2015-01-01

Precipitation of calcium carbonate from water films generates fascinating calcite morphologies that have attracted scientific interest over past centuries. Nowadays, speleothems are no longer known only for their beauty but they are also recognized to be precious records of past climatic conditions, and research aims to unveil and understand the mechanisms responsible for their morphological evolution. In this paper, we focus on crenulations, a widely observed ripple-like instability of the the calcite–water interface that develops orthogonally to the film flow. We expand a previous work providing new insights about the chemical and physical mechanisms that drive the formation of crenulations. In particular, we demonstrate the marginal role played by carbon dioxide transport in generating crenulation patterns, which are indeed induced by the hydrodynamic response of the free surface of the water film. Furthermore, we investigate the role of different environmental parameters, such as temperature, concentration of dissolved ions and wall slope. We also assess the convective/absolute nature of the crenulation instability. Finally, the possibility of using crenulation wavelength as a proxy of past flows is briefly discussed from a theoretical point of view. PMID:27547086

Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains.

PubMed

Lee, David J; Bingle, Lewis E H; Heurlier, Karin; Pallen, Mark J; Penn, Charles W; Busby, Stephen J W; Hobman, Jon L

2009-12-09

Homologous recombination mediated by the lambda-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the lambda-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these lambda-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains. Our goal was to develop a high-throughput recombineering system, primarily for the coupling of genes to epitope tags, which could also be used for deletion of genes in both pathogenic and K-12 E. coli strains. To that end we have designed a series of donor plasmids for use with the lambda-Red recombination system, which when cleaved in vivo by the I-SceI meganuclease generate a discrete linear DNA fragment, allowing for C-terminal tagging of chromosomal genes with a 6xHis, 3xFLAG, 4xProteinA or GFP tag or for the deletion of chromosomal regions. We have enhanced existing protocols and technologies by inclusion of a cassette conferring kanamycin resistance and, crucially, by including the sacB gene on the donor plasmid, so that all but true recombinants are counter-selected on kanamycin and sucrose containing media, thus eliminating the need for extensive screening. This method has the added advantage of limiting the exposure of cells to the potential damaging effects of the lambda-Red system, which can lead to unwanted secondary alterations to

The Time Scale of Recombination Rate Evolution in Great Apes

PubMed Central

Stevison, Laurie S.; Woerner, August E.; Kidd, Jeffrey M.; Kelley, Joanna L.; Veeramah, Krishna R.; McManus, Kimberly F.; Bustamante, Carlos D.; Hammer, Michael F.; Wall, Jeffrey D.

2016-01-01

Abstract We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10–15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives. PMID:26671457

Spatial Holmboe instability

NASA Astrophysics Data System (ADS)

Ortiz, Sabine; Chomaz, Jean-Marc; Loiseleux, Thomas

2002-08-01

In mixing-layers between two parallel streams of different densities, shear and gravity effects interplay; buoyancy acts as a restoring force and the Kelvin-Helmholtz mode is known to be stabilized by the stratification. If the density interface is sharp enough, two new instability modes, known as Holmboe modes, appear, propagating in opposite directions. This mechanism has been studied in the temporal instability framework. The present paper analyzes the associated spatial instability problem. It considers, in the Boussinesq approximation, two immiscible inviscid fluids with a piecewise linear broken-line velocity profile. We show how the classical scenario for transition between absolute and convective instability should be modified due to the presence of propagating waves. In the convective region, the spatial theory is relevant and the slowest propagating wave is shown to be the most spatially amplified, as suggested by intuition. Predictions of spatial linear theory are compared with mixing-layer [C. G. Koop and F. K. Browand, J. Fluid Mech. 93, 135 (1979)] and exchange flow [G. Pawlak and L. Armi, J. Fluid Mech. 376, 1 (1999)] experiments. The physical mechanism for Holmboe mode destabilization is analyzed via an asymptotic expansion that predicts the absolute instability domain at large Richardson number.

Spatial Holmboe Instability

NASA Astrophysics Data System (ADS)

Sabine, Ortiz; Marc, Chomaz Jean; Thomas, Loiseleux

2001-11-01

In mixing layers between two parallel streams of different densities, shear and gravity effects interplay. When the Roosby number, which compares the nonlinear acceleration terms to the Coriolis forces, is large enough, buoyancy acts as a restoring force, the Kelvin-Helmholtz mode is known to be stabilized by the stratification. If the density interface is sharp enough, two new instability modes, known as Holmboe modes, propagating in opposite directions appear. This mechanism has been study in the temporal instability framework. We analyze the associated spatial instability problem, in the Boussinesq approximation, for two immiscible inviscid fluids with broken-line velocity profile. We show how the classical scenario for transition between absolute and convective instability should be modified due to the presence of propagating waves. In convective region, the spatial theory is relevant and the slowest propagative wave is shown to be the most spatially amplified, as suggested by the intuition. Spatial theory is compared with mixing layer experiments (C.G. Koop and Browand J. Fluid Mech. 93, part 1, 135 (1979)), and wedge flows (G. Pawlak and L. Armi J. Fluid Mech. 376, 1 (1999)). Physical mechanism for the Holmboe mode destabilization is analyzed via an asymptotic expansion that explains precisely the absolute instability domain at large Richardson number.

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

PubMed

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

2013-12-06

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

Study on Influence of Tube Arrays on Fluid Elastic Instability

NASA Astrophysics Data System (ADS)

Ishihara, Kunihiko; Kitayama, Gen

The tube bank is used in boilers, heat exchangers in power plants and steam generators in nuclear plants. These tubes sometimes vibrate violently and come to the fatigue failure due to the flow induced vibration which is caused by the cross flow. This phenomenon is that the large vibrations arise at the critical flow velocity and it is called fluid elastic instability. However the relation between the onset velocity of fluid elastic instability and the tube array's geometry has not been clarified sufficiently. There is a few reference related to the relation between the pitch to diameter ratio and the onset velocity even in the lattice arrays. In this paper, the influence of tube arrays on fluid elastic instability is examined by experiments. As a result, it is clarified that the tube vibrations become large as T/D increases and L/D decreases, and the tube vibrations strongly depend on the dynamic characteristics of tubes such as the natural frequency and the damping ability.

Nonlinear spatial evolution of inviscid instabilities on hypersonic boundary layers

NASA Technical Reports Server (NTRS)

Wundrow, David W.

1996-01-01

The spatial development of an initially linear vorticity-mode instability on a compressible flat-plate boundary layer is considered. The analysis is done in the framework of the hypersonic limit where the free-stream Mach number M approaches infinity. Nonlinearity is shown to become important locally, in a thin critical layer, when sigma, the deviation of the phase speed from unity, becomes o(M(exp -8/7)) and the magnitude of the pressure fluctuations becomes 0(sigma(exp 5/2)M(exp 2)). The unsteady flow outside the critical layer takes the form of a linear instability wave but with its amplitude completely determined by the nonlinear flow within the critical layer. The coupled set of equations which govern the critical-layer dynamics reflect a balance between spatial-evolution, (linear and nonlinear) convection and nonlinear vorticity-generation terms. The numerical solution to these equations shows that nonlinear effects produce a dramatic reduction in the instability-wave amplitude.

Supersonic, shockwave-driven hydrodynamic instability experiments at OMEGA-EP

NASA Astrophysics Data System (ADS)

Wan, Willow

2016-10-01

Hydrodynamic instabilities play a dominant role in the transport of mass, momentum, and energy in nearly every plasma environment, governing the dynamics of natural and engineering systems such as solar convective zones, magnetospheric boundaries, and fusion experiments. In past decades, limitations in our understanding of hydrodynamic instabilities have led to discrepancies between observations and predictions. Since then, significant improvements have been made to our available experimental techniques, diagnostics, and simulation capabilities. Here, we present a novel experimental platform that can sustain a steady, supersonic flow across a precision-machined, well-characterized material interface for unprecedented durations We applied this platform to a series of Kelvin-Helmholtz instability experiments. The Kelvin-Helmholtz instability generates vortical structures and turbulence at an interface with shear flow. In a supersonic flow, the growth rate is inhibited and the instability structure is altered. The data were obtained at the OMEGA-EP facility by firing three laser beams in sequence to produce a 12 kJ, 28 ns stitched laser pulse. The ablation pressure sustained a steady shockwave for 70 ns over a foam-plastic, single-mode or dual-mode interface. A spherical crystal imager was used to measure the evolution of these modulations with high-resolution x-ray radiography using Cu Kα radiation at 8.0 keV. The observed structure was reproduced with 2D hydrodynamic simulations. Supported by the U.S. DOE, through NNSA Grants DE-NA0002956 (SSAA) and DE-NA0002719 (NLUF), by the LLE under DE-NA0001944, and by the LLNL under subcontract B614207 to DE-AC52-07NA27344.

Thermal shrinkage for shoulder instability.

PubMed

Toth, Alison P; Warren, Russell F; Petrigliano, Frank A; Doward, David A; Cordasco, Frank A; Altchek, David W; O'Brien, Stephen J

2011-07-01

Thermal capsular shrinkage was popular for the treatment of shoulder instability, despite a paucity of outcomes data in the literature defining the indications for this procedure or supporting its long-term efficacy. The purpose of this study was to perform a clinical evaluation of radiofrequency thermal capsular shrinkage for the treatment of shoulder instability, with a minimum 2-year follow-up. From 1999 to 2001, 101 consecutive patients with mild to moderate shoulder instability underwent shoulder stabilization surgery with thermal capsular shrinkage using a monopolar radiofrequency device. Follow-up included a subjective outcome questionnaire, discussion of pain, instability, and activity level. Mean follow-up was 3.3 years (range 2.0-4.7 years). The thermal capsular shrinkage procedure failed due to instability and/or pain in 31% of shoulders at a mean time of 39 months. In patients with unidirectional anterior instability and those with concomitant labral repair, the procedure proved effective. Patients with multidirectional instability had moderate success. In contrast, four of five patients with isolated posterior instability failed. Thermal capsular shrinkage has been advocated for the treatment of shoulder instability, particularly mild to moderate capsular laxity. The ease of the procedure makes it attractive. However, our retrospective review revealed an overall failure rate of 31% in 80 patients with 2-year minimum follow-up. This mid- to long-term cohort study adds to the literature lacking support for thermal capsulorrhaphy in general, particularly posterior instability. The online version of this article (doi:10.1007/s11420-010-9187-7) contains supplementary material, which is available to authorized users.

Artificial ion beam instabilities. I - Linear theory. II - Simulations

NASA Astrophysics Data System (ADS)

Scales, W. A.; Kintner, P. M.

1990-07-01

Some of the important plasma instabilities that result when an artificial ion beam is injected into the ionospheric F region are studied using linear Vlasov theory. The variation in wave spectra at the receiver as the receiver and plasma gun separate perpendicularly to the magnetic field is consistent with a beam density decrease at or near the receiver. At separation distances that are large fractions of the beam gyrodiameter, usually narrow-band waves near the background lower hybrid and H+ gyroharmonic frequencies are measured. These observations are consistent with waves expected to be generated by beam densities on the order of or less than a few percent of the background density. At smaller separation distances, broadband waves are usually observed with frequencies from zero up to and above the lower hybrid frequency. Electrostatic particle simulation studies of the plasma instabilities indicate that the broadband fluidlike lower hybrid instability is the most important for background particle heating. Perpendicular H+ heating is more efficient than perpendicular O+ or parallel electron heating for the drift velocity regime most relevant to past experiments.

Instability of liquid crystal elastomers

NASA Astrophysics Data System (ADS)

An, Ning; Li, Meie; Zhou, Jinxiong

2016-01-01

Nematic liquid crystal elastomers (LCEs) contract in the director direction but expand in other directions, perpendicular to the director, when heated. If the expansion of an LCE is constrained, compressive stress builds up in the LCE, and it wrinkles or buckles to release the stored elastic energy. Although the instability of soft materials is ubiquitous, the mechanism and programmable modulation of LCE instability has not yet been fully explored. We describe a finite element method (FEM) scheme to model the inhomogeneous deformation and instability of LCEs. A constrained LCE beam working as a valve for microfluidic flow, and a piece of LCE laminated with a nanoscale poly(styrene) (PS) film are analyzed in detail. The former uses the buckling of the LCE beam to occlude the microfluidic channel, while the latter utilizes wrinkling or buckling to measure the mechanical properties of hard film or to realize self-folding. Through rigorous instability analysis, we predict the critical conditions for the onset of instability, the wavelength and amplitude evolution of instability, and the instability patterns. The FEM results are found to correlate well with analytical results and reported experiments. These efforts shed light on the understanding and exploitation of the instabilities of LCEs.

Polyglutamine Disease Modeling: Epitope Based Screen for Homologous Recombination using CRISPR/Cas9 System.

PubMed

An, Mahru C; O'Brien, Robert N; Zhang, Ningzhe; Patra, Biranchi N; De La Cruz, Michael; Ray, Animesh; Ellerby, Lisa M

2014-04-15

We have previously reported the genetic correction of Huntington's disease (HD) patient-derived induced pluripotent stem cells using traditional homologous recombination (HR) approaches. To extend this work, we have adopted a CRISPR-based genome editing approach to improve the efficiency of recombination in order to generate allelic isogenic HD models in human cells. Incorporation of a rapid antibody-based screening approach to measure recombination provides a powerful method to determine relative efficiency of genome editing for modeling polyglutamine diseases or understanding factors that modulate CRISPR/Cas9 HR.

Shoulder instability in professional football players.

PubMed

Leclere, Lance E; Asnis, Peter D; Griffith, Matthew H; Granito, David; Berkson, Eric M; Gill, Thomas J

2013-09-01

Shoulder instability is a common problem in American football players entering the National Football League (NFL). Treatment options include nonoperative and surgical stabilization. This study evaluated how the method of treatment of pre-NFL shoulder instability affects the rate of recurrence and the time elapsed until recurrence in players on 1 NFL team. Retrospective cohort. Medical records from 1980 to 2008 for 1 NFL team were reviewed. There were 328 players included in the study who started their career on the team and remained on the team for at least 2 years (mean, 3.9 years; range, 2-14 years). The history of instability prior to entering the NFL and the method of treatment were collected. Data on the occurrence of instability while in the NFL were recorded to determine the rate and timing of recurrence. Thirty-one players (9.5%) had a history of instability prior to entering the NFL. Of the 297 players with no history of instability, 39 (13.1%) had a primary event at a mean of 18.4 ± 22.2 months (range, 0-102 months) after joining the team. In the group of players with prior instability treated with surgical stabilization, there was no statistical difference in the rate of recurrence (10.5%) or the timing to the instability episode (mean, 26 months) compared with players with no history of instability. Twelve players had shoulder instability treated nonoperatively prior to the NFL. Five of these players (41.7%) had recurrent instability at a mean of 4.4 ± 7.0 months (range, 0-16 months). The patients treated nonoperatively had a significantly higher rate of recurrence (P = 0.02) and an earlier time of recurrence (P = 0.04). The rate of contralateral instability was 25.8%, occurring at a mean of 8.6 months. Recurrent shoulder instability is more common in NFL players with a history of nonoperative treatment. Surgical stabilization appears to restore the rate and timing of instability to that of players with no prior history of instability.

Four Closely Related HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Identified in East China.

PubMed

Li, Fan; Li, Yuxueyun; Feng, Yi; Hu, Jing; Ruan, Yuhua; Xing, Hui; Shao, Yiming

2017-07-01

Five near full-length genomes of novel second-generation HIV-1 recombinant virus (JS150021, JS150029, JS150129, JS150132, and AH150183) were identified from five HIV-positive people in Jiangsu and Anhui province, east China. Phylogenic analyses showed that these five sequences are all composed of two well-established circulating recombinant forms (CRFs) CRF07_BC and CRF01_AE, grouped into four new discovered recombinant forms, which show several very similar but not identical recombinant breakpoints. The four recombinant forms are also identified to be a sort of family or related viruses, seems to be the results of different recombination events. The emergence of a serious new closely related CRF07_BC/CRF01_AE recombinant strain indicates the increasing complexity of sexual transmission of the HIV-1 epidemic in China.

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

PubMed Central

Deng, Shunzhou; Martin, Carly; Patil, Rasika; Zhu, Felix; Zhao, Bin; Xiang, Zuoshuang; He, Yongqun

2015-01-01

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development. PMID:26403370

LOX/Hydrocarbon Combustion Instability Investigation

NASA Technical Reports Server (NTRS)

Jensen, R. J.; Dodson, H. C.; Claflin, S. E.

1989-01-01

The LOX/Hydrocarbon Combustion Instability Investigation Program was structured to determine if the use of light hydrocarbon combustion fuels with liquid oxygen (LOX) produces combustion performance and stability behavior similar to the LOX/hydrogen propellant combination. In particular methane was investigated to determine if that fuel can be rated for combustion instability using the same techniques as previously used for LOX/hydrogen. These techniques included fuel temperature ramping and stability bomb tests. The hot fire program probed the combustion behavior of methane from ambient to subambient temperatures. Very interesting results were obtained from this program that have potential importance to future LOX/methane development programs. A very thorough and carefully reasoned documentation of the experimental data obtained is contained. The hot fire test logic and the associated tests are discussed. Subscale performance and stability rating testing was accomplished using 40,000 lb. thrust class hardware. Stability rating tests used both bombs and fuel temperature ramping techniques. The test program was successful in generating data for the evaluation of the methane stability characteristics relative to hydrogen and to anchor stability models. Data correlations, performance analysis, stability analyses, and key stability margin enhancement parameters are discussed.

Cyclotron maser instability and its applications

NASA Astrophysics Data System (ADS)

Wu, C. S.

The possible application of cyclotron maser theory to a variety of radio sources is considered, with special attention given to the theory of auroral kilometric radiation (AKR) of Wu and Lee (1979). The AKR model assumes a loss-cone distribution function for the reflected electrons, along with the depletion of low-energy electrons by the parallel electric field. Other topics considered include fundamental AKR, second-harmonic AKR, the generation of Z-mode radiation, and the application of maser instability to other sources than AKR.

Experimental evidence that RNA recombination occurs in the Japanese encephalitis virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuang, C.-K.; Chen, W.-J., E-mail: wjchen@mail.cgu.edu.t; Department of Public Health and Parasitology, Chang Gung University, Kwei-San, Tao-Yuan 33332, Taiwan

2009-11-25

Due to the lack of a proofreading function and error-repairing ability of genomic RNA, accumulated mutations are known to be a force driving viral evolution in the genus Flavivirus, including the Japanese encephalitis (JE) virus. Based on sequencing data, RNA recombination was recently postulated to be another factor associated with genomic variations in these viruses. We herein provide experimental evidence to demonstrate the occurrence of RNA recombination in the JE virus using two local pure clones (T1P1-S1 and CJN-S1) respectively derived from the local strains, T1P1 and CJN. Based on results from a restriction fragment length polymorphism (RFLP) assay onmore » the C/preM junction comprising a fragment of 868 nucleotides (nt 10-877), the recombinant progeny virus was primarily formed in BHK-21 cells that had been co-infected with the two clones used in this study. Nine of 20 recombinant forms of the JE virus had a crossover in the nt 123-323 region. Sequencing data derived from these recombinants revealed that no nucleotide deletion or insertion occurred in this region favoring crossovers, indicating that precisely, not aberrantly, homologous recombination was involved. With site-directed mutagenesis, three stem-loop secondary structures were destabilized and re-stabilized in sequence, leading to changes in the frequency of recombination. This suggests that the conformation, not the free energy, of the secondary structure is important in modulating RNA recombination of the virus. It was concluded that because RNA recombination generates genetic diversity in the JE virus, this must be considered particularly in studies of viral evolution, epidemiology, and possible vaccine safety.« less

Minor shoulder instability.

PubMed

Castagna, Alessandro; Nordenson, Ulf; Garofalo, Raffaele; Karlsson, Jon

2007-02-01

The wide spectrum of shoulder instability is difficult to include in 1 classification. The distinction between traumatic, unidirectional, and atraumatic multidirectional instability is still widely used, even though this classification is not sufficiently precise to include all the different pathological findings of shoulder instability. We present "minor instability," which is a pathological condition causing a dysfunction of the glenohumeral articulation, especially in combination with microtrauma, repetitive or not, or after a period of immobilization or inactivity. When "minor shoulder instability" is suspected, the patient's history and detailed clinical examination represent the most important factors when establishing the diagnosis. In particular, the apprehension test stressing the middle glenohumeral ligament (MGHL)/labral complex in the position of midabduction and external rotation may be painful and may even reveal anterior instability or subluxation. Conventional radiographs are negative in most cases, as is magnetic resonance imaging arthrography. It is only after an accurate arthroscopic assessment that the pathological lesion can be found. The major pathological process can be identified at the level of the anterior superior labrum, in particular the MGHL complex, and appears as hyperemia, fraying, stretching, loosening, thinning, hypoplasia, or even absence. It may, however, be difficult to distinguish between a normal variant and a pathological lesion. Clinical symptoms and examination should always be correlated with arthroscopic findings. Recommended treatment is to restore shoulder stability and thereby prevent shoulder pain secondary to the increase in laxity. A reduction in range of motion should be expected during the postoperative phase, at least up to six to nine months. External rotation is usually permanently reduced by a few degrees.

Nonlinear saturation of the Weibel instability