Inhibition of the RNA polymerase III-mediated dsDNA-sensing pathway of innate immunity by vaccinia virus protein E3.

The vaccinia virus E3 protein is an important intracellular modulator of innate immunity that can be split into distinct halves. The C terminus contains a well defined dsRNA-binding domain, whereas the N terminus contains a Z-DNA-binding domain, and both domains are required for virulence. In this study, we investigated whether the E3 Z-DNA-binding domain functions by sequestering cytoplasmic dsDNA thereby preventing the induction of type I interferon (IFN). In line with this hypothesis, expression of E3 ablated both IFN-beta expression and NF-kappaB activity in response to the dsDNA, poly(dA-dT). However, surprisingly, the ability of E3 to block poly(dA-dT) signalling was independent of the N terminus, whereas the dsRNA-binding domain was essential, suggesting that the Z-DNA-binding domain does not bind immunostimulatory dsDNA. This was confirmed by the failure of E3 to co-precipitate with biotinylated dsDNA, whereas the recruitment of several cytoplasmic DNA-binding proteins could be detected. Recently, AT-rich dsDNA was reported to be transcribed into 5'-triphosphate poly(A-U) RNA by RNA polymerase III, which then activates retinoic acid-inducible gene I (RIG-I). Consistent with this, RNA from poly(dA-dT) transfected cells induced IFN-beta and expression of the E3 dsRNA-binding domain was sufficient to ablate this response. Given the well documented function of the E3 dsRNA-binding domain we propose that E3 blocks signalling in response to poly(dA-dT) by binding to transcribed poly(A-U) RNA preventing RIG-I activation. This report describes a DNA virus-encoded inhibitor of the RNA polymerase III-dsDNA-sensing pathway and extends our knowledge of E3 as a modulator of innate immunity

Anisotropic focusing characteristics of micro-domain structures within crystalline Sr_0.61Ba_0.39Nb₂O₆ : the crystal ball

We report the anisotropic focusing characteristics of a spherically configured region of micro-domains that have been induced within a cubic shaped crystal of Ce:doped Sr0.61Ba0.39Nb2O6. The internal spherical structure focuses extraordinary polarised light, but not ordinary polarised. The spherical region, which is easily observed via scattering, is formed as the crystal cools down, after a repoling cycle through the Curie temperature, with an applied field. Analytic modelling of the thermal gradients that exist within the crystal during cooling reveals a small (< 1°) temperature difference between the central and outside regions. The similarity in shape between these temperature profiles and the observed scattering region suggests a possible mechanism for the growth of this spherical micro-domained structure

The steady-state repertoire of human SCF Ubiquitin ligase complexes does not require ongoing Nedd8 conjugation

The human genome encodes 69 different F-box proteins (FBPs), each of which can potentially assemble with Skp1-Cul1-RING to serve as the substrate specificity subunit of an SCF ubiquitin ligase complex. SCF activity is switched on by conjugation of the ubiquitin- like protein Nedd8 to Cul1. Cycles of Nedd8 conjugation and deconjugation acting in conjunction with the Cul1-sequestering factor Cand1 are thought to control dynamic cycles of SCF assembly and disassembly, which would enable a dynamic equilibrium between the Cul1- RING catalytic core of SCF and the cellular repertoire of FBPs. To test this hypothesis, we determined the cellular composition of SCF complexes and evaluated the impact of Nedd8 conjugation on this steady-state. At least 42 FBPs assembled with Cul1 in HEK 293 cells, and the levels of Cul1-bound FBPs varied by over two orders of magnitude. Unexpectedly, quantitative mass spectrometry revealed that blockade of Nedd8 conjugation led to a modest increase, rather than a decrease, in the overall level of most SCF complexes. We suggest that multiple mechanisms including FBP dissociation and turnover cooperate to maintain the cellular pool of SCF ubiquitin ligases

SimpleMOC - A performance abstraction for 3D MOC

The method of characteristics (MOC) is a popular method for efficiently solving two-dimensional reactor problems. Extensions to three dimensions have been attempted with mitigated success bringing into question the ability of performing efficient full core three-dimensional (3D) analysis. Although the 3D problem presents many computational difficulties, some simplifications can be made that allow for more efficient computation. In this investigation, we present SimpleMOC, a “mini-app” which mimics the computational performance of a full 3D MOC solver without involving the full physics perspective, allowing for a more straightforward analysis of the computational challenges. A variety of simplifications are implemented that are intended to increase the computational feasibility, including the formation axially-quadratic neutron sources. With the addition of the quadratic approximation to the neutron source, 3D MOC is cast as a CPU-intensive method with the potential for remarkable scalability on next generation computing architectures.United States. Dept. of Energy. Office of Nuclear Energy (Nuclear Energy University Programs Fellowship)United States. Dept. of Energy. Center for Exascale Simulation of Advanced ReactorUnited States. Dept. of Energy. Office of Advanced Scientific Computing Research (Contract DE-AC02-06CH11357

Cdc48/p97 Mediates UV-Dependent Turnover of RNA Pol II

Cdc48/p97 is an essential ATPase whose role in targeting substrates to the ubiquitin-proteasome system (UPS) remains unclear. Existing models posit that Cdc48 acts upstream of UPS receptors. To address this hypothesis, we examined the association of ubiquitin (Ub) conjugates with 26S proteasomes. Unexpectedly, proteasomes isolated from cdc48 mutants contain high levels of Ub conjugates, and mass spectrometry identified numerous nonproteasomal proteins, including Rpb1, the largest subunit of RNA Pol II. UV-induced turnover of Rpb1 depends upon Cdc48-Ufd1-Npl4, Ubx4, and the uncharacterized adaptor Ubx5. Ubiquitinated Rpb1, proteasomes, and Cdc48 accumulate on chromatin in UV-treated wild-type cells, and the former two accumulate to higher levels in mutant cells, suggesting that degradation of Rpb1 is facilitated by Cdc48 at sites of stalled transcription. These data reveal an intimate coupling of function between proteasomes and Cdc48 that we suggest is necessary to sustain processive degradation of unstable subunits of some macromolecular protein complexes

Selling Zoning: Do Density Bonus Incentives for Moderate-Cost Housing Work

This Article reviews the housing affordability problem, the California legislation, and previous research findings. The Article outlines our methods, presents our results, and recommends program improvements

Reducing 3D MOC Storage Requirements with Axial On-the-fly Ray Tracing

The Method of Characteristics (MOC) is a popular method to solve the multi-group neutron transport equation. While this method is most widely used in two dimensions, extension to three dimensions allows for more accurate calculation of axial leakage and reaction rates. However, the 3D form of MOC can be computationally prohibitive. One concern is the massive memory requirements imposed by storing all segments of 3D tracks. In this study, an alternative approach is presented for axially extruded geometries that only saves segments in two dimensions. This is accomplished by first creating a 2D xy-plane that incorporates all radial detail at every axial level. Then, standard 2D ray tracing is applied to this plane. Axial extruded regions are constructed during segmentation, each containing an axial mesh. During transport sweeps the 3D segments are reconstructed on-the-fly using 2D segment lengths and 1D axial meshes. This strategy implicitly transforms geometries into an axially extruded representation. The resulting algorithm consumes far less memory with minimal computational overhead for common reactor physics problems.United States. Office of the Assistant Secretary for Nuclear Energy (Nuclear Energy University Programs Fellowship)Center for Exascale Simulation of Advanced Reactors (U.S. Department of Energy Contract No. DE-AC02-06CH11357

Verification of the 3D Method of characteristics solver in OpenMOC

The Method of Characteristics (MOC) has seen wide interest in full-core reactor physics analysis due to its computational efficiency and ability to easily treat complex geometries. Recently, the OpenMOC reactor physics code was extended to include 3D MOC capability. In this study, we present verification for the 3D MOC solver in OpenMOC and sensitivity of 3D MOC to the axial geometry discretization and axial track laydown. Results for the Takeda Model 1 benchmark show excellent agreement with the reference eigenvalues. A sensitivity study was conducted on a UO [subscript 2] quarter-assembly extracted from the C5G7 3D unrodded benchmark geometry in order to show the effect of the axial MOC parameters on the solution eigenvalue for a heterogeneous problem. The sensitivity results demonstrated that the solution accuracy was highly dependent on the axial source region discretization, but insensitive to axial spacing between tracks below ~0.2 cm. Using the equal angle quadrature set, at least 10 and 18 polar angles were required to converge the problem to with 100 and 10 pcm, respectively. These results both verify the 3D MOC solver in OpenMOC and provide inUnited States. Office of the Assistant Secretary for Nuclear Energy (Nuclear Energy Uni- versity Programs Fellowship)Center for Exascale Simulation of Advanced Reactors (Contract No. DE-AC02-06CH11357

Theoretical Analysis of Track Generation in 3d Method of Characteristics

Generating the tracks to use in a 3D Method of Characteristics (MOC) simulation is not a trivial task. The method used to generate tracks has significant implications on the memory and compute requirements for a problem and the current track generation methods have shortcomings. In this study, we provide a detailed description and analysis of the current state of the art method to generate tracks for direct 3D MOC, the Modular Ray Tracing (MRT) method. Additionally, a new global method for generating tracks is presented that is generalizable to many geometries, domain decomposition schemes, and quadrature sets. The main difference between the global and modular track generation approaches is that the global approach does not require any knowledge of the underlying geometry discretization and is therefore more flexible in domain decomposing the geometry. Some considerations with memory requirements and general applicability that we and others have found are discussedUnited States. Dept. of Energy. Office of Nuclear Energy (Nuclear Energy University Programs Fellowship)United States. Department of Energy (Center for Exascale Simulation of Advanced Reactors (CESAR). Contract DE-AC02-06CH11357