Evaluation of the Influenza A Replicon for Transient Expression of Recombinant Proteins in Mammalian Cells

Recombinant protein expression in mammalian cells has become a very important technique over the last twenty years. It is mainly used for production of complex proteins for biopharmaceutical applications. Transient recombinant protein expression is a possible strategy to produce high quality material for preclinical trials within days. Viral replicon based expression systems have been established over the years and are ideal for transient protein expression. In this study we describe the evaluation of an influenza A replicon for the expression of recombinant proteins. We investigated transfection and expression levels in HEK-293 cells with EGFP and firefly luciferase as reporter proteins. Furthermore, we studied the influence of different influenza non-coding regions and temperature optima for protein expression as well. Additionally, we exploited the viral replication machinery for the expression of an antiviral protein, the human monoclonal anti-HIV-gp41 antibody 3D6. Finally we could demonstrate that the expression of a single secreted protein, an antibody light chain, by the influenza replicon, resulted in fivefold higher expression levels compared to the usually used CMV promoter based expression. We emphasize that the influenza A replicon system is feasible for high level expression of complex proteins in mammalian cells

Function and Assembly of a Chromatin-Associated RNase P that Is Required for Efficient Transcription by RNA Polymerase I

Human RNase P has been initially described as a tRNA processing enzyme, consisting of H1 RNA and at least ten distinct protein subunits. Recent findings, however, indicate that this catalytic ribonucleoprotein is also required for transcription of small noncoding RNA genes by RNA polymerase III (Pol III). Notably, subunits of human RNase P are localized in the nucleolus, thus raising the possibility that this ribonucleoprotein complex is implicated in transcription of rRNA genes by Pol I.By using biochemical and reverse genetic means we show here that human RNase P is required for efficient transcription of rDNA by Pol I. Thus, inactivation of RNase P by targeting its protein subunits for destruction by RNA interference or its H1 RNA moiety for specific cleavage causes marked reduction in transcription of rDNA by Pol I. However, RNase P restores Pol I transcription in a defined reconstitution system. Nuclear run on assays reveal that inactivation of RNase P reduces the level of nascent transcription by Pol I, and more considerably that of Pol III. Moreover, RNase P copurifies and associates with components of Pol I and its transcription factors and binds to chromatin of the promoter and coding region of rDNA. Strikingly, RNase P detaches from transcriptionally inactive rDNA in mitosis and reassociates with it at G1 phase through a dynamic and stepwise assembly process that is correlated with renewal of transcription.Our findings reveal that RNase P activates transcription of rDNA by Pol I through a novel assembly process and that this catalytic ribonucleoprotein determines the transcription output of Pol I and Pol III, two functionally coordinated transcription machineries

Function and Assembly of a Chromatin-Associated RNase P that Is Required for Efficient Transcription by RNA Polymerase I

Background: Human RNase P has been initially described as a tRNA processing enzyme, consisting of H1 RNA and at least ten distinct protein subunits. Recent findings, however, indicate that this catalytic ribonucleoprotein is also required for transcription of small noncoding RNA genes by RNA polymerase III (Pol III). Notably, subunits of human RNase P are localized in the nucleolus, thus raising the possibility that this ribonucleoprotein complex is implicated in transcription of rRNA genes by Pol I. Methodology/Principal Findings: By using biochemical and reverse genetic means we show here that human RNase P is required for efficient transcription of rDNA by Pol I. Thus, inactivation of RNase P by targeting its protein subunits for destruction by RNA interference or its H1 RNA moiety for specific cleavage causes marked reduction in transcription of rDNA by Pol I. However, RNase P restores Pol I transcription in a defined reconstitution system. Nuclear run on assays reveal that inactivation of RNase P reduces the level of nascent transcription by Pol I, and more considerably that of Pol III. Moreover, RNase P copurifies and associates with components of Pol I and its transcription factors and binds to chromatin of the promoter and coding region of rDNA. Strikingly, RNase P detaches from transcriptionally inactive rDNA in mitosis and reassociates with it at G1 phase through a dynamic and stepwise assembly process that is correlated with renewal of transcription

Searching for eV-scale sterile neutrinos with eight years of atmospheric neutrinos at the IceCube Neutrino Telescope

We report in detail on searches for eV-scale sterile neutrinos, in the context of a 3+1 model, using eight years of data from the IceCube Neutrino Telescope. By analyzing the reconstructed energies and zenith angles of 305,735 atmospheric νμ and ¯νμ events we construct confidence intervals in two analysis spaces: sin2(2θ$_{24}$) vs Δm2¦41 under the conservative assumption θ$_{34}$=0; and sin$^{2}$ (2θ$_{24}$) vs sin$^{2}$ (2θ$_{34}$) given sufficiently large Δm2¦41 that fast oscillation features are unresolvable. Detailed discussions of the event selection, systematic uncertainties, and fitting procedures are presented. No strong evidence for sterile neutrinos is found, and the best-fit likelihood is consistent with the no sterile neutrino hypothesis with a p value of 8% in the first analysis space and 19% in the second

Search for PeV gamma-ray emission from the southern hemisphere with 5 Yr of data from the IceCube observatory

The measurement of diffuse PeV gamma-ray emission from the Galactic plane would provide information about the energy spectrum and propagation of Galactic cosmic rays, and the detection of a pointlike source of PeV gamma-rays would be strong evidence for a Galactic source capable of accelerating cosmic rays up to at least a few PeV. This paper presents several unbinned maximum-likelihood searches for PeV gamma-rays in the Southern Hemisphere using 5 yr of data from the IceTop air shower surface detector and the in-ice array of the IceCube Observatory. The combination of both detectors takes advantage of the low muon content and deep shower maximum of gamma-ray air showers and provides excellent sensitivity to gamma-rays between similar to 0.6 and 100 PeV. Our measurements of pointlike and diffuse Galactic emission of PeV gamma-rays are consistent with the background, so we constrain the angle-integrated diffuse gamma-ray flux from the Galactic plane at 2 PeV to 2.61 x 10(-19) cm(-2) s(-1) TeV-1 at 90% confidence, assuming an E-3 spectrum, and we estimate 90% upper limits on pointlike emission at 2 PeV between 10(-21) and 10(-20) cm(-2) s(-1) TeV-1 for an E-2 spectrum, depending on decl. Furthermore, we exclude unbroken power-law emission up to 2 PeV for several TeV gamma-ray sources observed by the High Energy Spectroscopic System and calculate upper limits on the energy cutoffs of these sources at 90% confidence. We also find no PeV gamma-rays correlated with neutrinos from IceCube's high-energy starting event sample. These are currently the strongest constraints on PeV gamma-ray emission

IceCube Search for High-Energy Neutrino Emission from TeV Pulsar Wind Nebulae

Pulsar wind nebulae (PWNe) are the main gamma-ray emitters in the Galactic plane. They are diffuse nebulae that emit nonthermal radiation. Pulsar winds, relativistic magnetized outflows from the central star, shocked in the ambient medium produce a multiwavelength emission from the radio through gamma rays. Although the leptonic scenario is able to explain most PWNe emission, a hadronic contribution cannot be excluded. A possible hadronic contribution to the high-energy gamma-ray emission inevitably leads to the production of neutrinos. Using 9.5 yr of all-sky IceCube data, we report results from a stacking analysis to search for neutrino emission from 35 PWNe that are high-energy gamma-ray emitters. In the absence of any significant correlation, we set upper limits on the total neutrino emission from those PWNe and constraints on hadronic spectral components.Comment: 11 pages, 2 figures; matches the published version in Ap

eV-Scale Sterile Neutrino Search Using Eight Years of Atmospheric Muon Neutrino Data from the IceCube Neutrino Observatory

The results of a 3+1 sterile neutrino search using eight years of data from the IceCube Neutrino Observatory are presented. A total of 305 735 muon neutrino events are analyzed in reconstructed energy-zenith space to test for signatures of a matter-enhanced oscillation that would occur given a sterile neutrino state with a mass-squared differences between 0.01 and 100  eV$^{2}$. The best-fit point is found to be at sin$^{2}$ (2θ$_{24}$)=0.10 and Δm2/41 =4.5  eV$^{2}$, which is consistent with the no sterile neutrino hypothesis with a p value of 8.0%

IceCube Search for Neutrinos Coincident with Compact Binary Mergers from LIGO-Virgo's First Gravitational-Wave Transient Catalog

Using the IceCube Neutrino Observatory, we search for high-energy neutrino emission coincident with compact binary mergers observed by the LIGO and Virgo gravitational wave (GW) detectors during their first and second observing runs. We present results from two searches targeting emission coincident with the sky localization of each gravitational wave event within a 1000 second time window centered around the reported merger time. One search uses a model-independent unbinned maximum likelihood analysis, which uses neutrino data from IceCube to search for point-like neutrino sources consistent with the sky localization of GW events. The other uses the Low-Latency Algorithm for Multi-messenger Astrophysics, which incorporates astrophysical priors through a Bayesian framework and includes LIGO-Virgo detector characteristics to determine the association between the GW source and the neutrinos. No significant neutrino coincidence is seen by either search during the first two observing runs of the LIGO-Virgo detectors. We set upper limits on the time-integrated neutrino emission within the 1000 second window for each of the 11 GW events. These limits range from 0.02-0.7 $\mathrm{GeV~cm^{-2}}$. We also set limits on the total isotropic equivalent energy, $E_{\mathrm{iso}}$, emitted in high-energy neutrinos by each GW event. These limits range from 1.7 $\times$ 10$^{51}$ - 1.8 $\times$ 10$^{55}$ erg. We conclude with an outlook for LIGO-Virgo observing run O3, during which both analyses are running in real time

Characteristics of the diffuse astrophysical electron and tau neutrino flux with six years of IceCube high energy cascade data

We report on the first measurement of the astrophysical neutrino flux using particle showers (cascades) in IceCube data from 2010 -- 2015. Assuming standard oscillations, the astrophysical neutrinos in this dedicated cascade sample are dominated ($\sim 90 \%$) by electron and tau flavors. The flux, observed in the sensitive energy range from $16\,\mathrm{TeV}$ to $2.6\,\mathrm{PeV}$, is consistent with a single power-law model as expected from Fermi-type acceleration of high energy particles at astrophysical sources. We find the flux spectral index to be $\gamma=2.53\pm0.07$ and a flux normalization for each neutrino flavor of $\phi_{astro} = 1.66^{+0.25}_{-0.27}$ at $E_{0} = 100\, \mathrm{TeV}$, in agreement with IceCube's complementary muon neutrino results and with all-neutrino flavor fit results. In the measured energy range we reject spectral indices $\gamma\leq2.28$ at $\ge3\sigma$ significance level. Due to high neutrino energy resolution and low atmospheric neutrino backgrounds, this analysis provides the most detailed characterization of the neutrino flux at energies below $\sim100\,{\rm{TeV}}$ compared to previous IceCube results. Results from fits assuming more complex neutrino flux models suggest a flux softening at high energies and a flux hardening at low energies (p-value $\ge 0.06$). The sizable and smooth flux measured below $\sim 100\,{\rm{TeV}}$ remains a puzzle. In order to not violate the isotropic diffuse gamma-ray background as measured by the Fermi-LAT, it suggests the existence of astrophysical neutrino sources characterized by dense environments which are opaque to gamma-rays.Comment: 4 figures, 4 tables, includes supplementary materia