Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses

RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that catalyzes the synthesis of their RNA(s). In the case of positive-stranded RNA viruses belonging to the order Nidovirales, the RdRp resides in a replicase subunit that is unusually large. Bioinformatics analysis of this non-structural protein has now revealed a nidoviral signature domain (genetic marker) that is N-terminally adjacent to the RdRp and has no apparent homologs elsewhere. Based on its conservation profile, this domain is proposed to have nucleotidylation activity. We used recombinant non-structural protein 9 of the arterivirus equine arteritis virus (EAV) and different biochemical assays, including irreversible labeling with a GTP analog followed by a proteomics analysis, to demonstrate the manganese-dependent covalent binding of guanosine and uridine phosphates to a lysine/histidine residue. Most likely this was the invariant lysine of the newly identified domain, named nidovirus RdRp-associated nucleotidyltransferase (NiRAN), whose substitution with alanine severely diminished the described binding. Furthermore, this mutation crippled EAV and prevented the replication of severe acute respiratory syndrome coronavirus (SARS-CoV) in cell culture, indicating that NiRAN is essential for nidoviruses. Potential functions supported by NiRAN may include nucleic acid ligation, mRNA capping and protein-primed RNA synthesis, possibilities that remain to be explored in future studies

Coronaviruses and the human airway: a universal system for virus-host interaction studies

Human coronaviruses (HCoVs) are large RNA viruses that infect the human respiratory tract. The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Various animal models have been established to investigate HCoV infection, including mice and non-human primates. To establish a link between the research conducted in animal models and humans, an organotypic human airway culture system, that recapitulates the human airway epithelium, has been developed. Currently, different cell culture systems are available to recapitulate the human airways, including the Air-Liquid Interface (ALI) human airway epithelium (HAE) model. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. These organotypic human airway cultures represent a universal platform to study respiratory virus-host interaction by offering more detailed insights compared to cell lines. Additionally, the epidemic potential of this virus family highlights the need for both vaccines and antivirals. No commercial vaccine is available but various effective antivirals have been identified, some with potential for human treatment. These morphological airway cultures are also well suited for the identification of antivirals, evaluation of compound toxicity and viral inhibition

Neutronic analysis of JET external neutron monitor response

The power output of fusion devices is measured in terms of the neutron yield which relates directly to the fusion yield. JET made a transition from Carbon wall to ITER-Like Wall (Beryllium/Tungsten/Carbon) during 2010–11. Absolutely calibrated measurement of the neutron yield by JET neutron monitors was ensured by direct measurements using a calibrated 252Cf neutron source (NS) deployed by the in-vessel remote handling system (RHS) inside the JET vacuum vessel. Neutronic calculations were required in order to understand the neutron transport from the source in the vacuum vessel to the fission chamber detectors mounted outside the vessel on the transformer limbs of the tokamak. We developed a simplified computational model of JET and the JET RHS in Monte Carlo neutron transport code MCNP and analyzed the paths and structures through which neutrons reach the detectors and the effect of the JET RHS on the neutron monitor response. In addition we performed several sensitivity studies of the effect of substantial massive structures blocking the ports on the external neutron monitor response. As the simplified model provided a qualitative picture of the process only, some calculations were repeated using a more detailed full 3D model of the JET tokamak

Radiation damage and nuclear heating studies in selected functional materials during the JET DT campaign

A new Deuterium-Tritium campaign (DTE2) is planned at JET in the next years, with a proposed 14MeV neutron budget of 1.7×1021, which is nearly an order of magnitude higher than any previous DT campaigns. The neutron and gamma ray fields inside the JET device during DT plasma operations at specific locations have previously been evaluated. It is estimated that a total neutron fluence on the first wall of JET of up to 1020 n/m2 could be achieved, which is comparable to the fluence occurring in ITER at the end of life in the rear part of the port plug, where several diagnostic components will be located.The purpose of the present work is to evaluate the radiation damage and nuclear heating in selected functional materials to be irradiated at JET during DT plasma operation. These quantities are calculated with the use of the MCNP6 code and the FISPACT II code. In particular the neutron and gamma ray fields at specific locations inside the JET device, dedicated to material damage studies, were characterized. The emphasis is on a potential long term irradiation station located close to the first wall at outboard midplane, offering the opportunity to irradiate samples of functional materials used in ITER diagnostics, to assess the degradation of the physical properties. The radiation damage and the nuclear heating were calculated for selected materials irradiated in these positions and for the neutron flux and fluence expected in DTE2. The studied candidate functional materials include, among others, Sapphire, YAG, ZnS, Spinel, Diamond. In addition the activation of the internal irradiation holder itself was calculated with FISPACT. Damage levels in the range of 10-5 dpa were found