The Structural Basis of Flaviviridae Interaction with Antibodies and Receptors

Flaviviridae are a family of enveloped, positive-stranded RNA viruses responsible for a variety of diseases including encephalitis, hemorrhagic fever and hepatocellular carcinoma. The envelope: E) proteins that coat the outer surface of these viruses provide the molecular machinery that drives receptor interaction and membrane fusion. The assignment of biological functions to specific structural elements of these E proteins has proven crucial to the understanding of viral entry into host cells. Clearance is dependent upon the presence of neutralizing antibodies that are able to disrupt several stages of this process. Given their fundamental role in the viral life cycle, we sought to determine the structural basis for envelope protein interaction with antibodies and receptors for human pathogens of the Flaviviridae family Japanese Encephalitis Virus, Hepatitis C Virus and St. Louis Encephalitis Virus. Viruses of the Flavivirus genus within Flaviviridae are grouped into serocomplexes with similar clinical manifestations that are defined by cross-neutralization tests with polysera from heterologous infections. Japanese Encephalitis Virus: JEV) is the leading cause of viral encephalitis and prototypical member of the JEV serocomplex. We determined the 2.1Ã… resolution crystal structure of the JEV E protein ectodomain to investigate whether structural features could contribute to our understanding of serocomplex-specific pathogenesis. JEV E possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies revealed residues localized to the domain I lateral ridge, fusion loop, domain III lateral ridge and domain I-II hinge. The dimer interface, however, is remarkably small and lacks several contacts present in other flavivirus E homodimers. Uniquely conserved histidines of the JEV serocomplex suggest that pH-mediated structural transitions may be assisted by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation of dimer structure and stability may influence the assembly, receptor interaction and uncoating of virions. St. Louis Encephalitis Virus: SLEV) is another member of the JEV serocomplex with similar pathogenesis to JEV. We determined the 4.0 Ã… structure of the SLEV E protein in the post-fusion trimer conformation to compare it with E trimer structures from other flavivirus serocomplexes. SLEV E crystallized as a trimer in the absence of lipids or detergents, requiring only low pH. However, its domain arrangement was nearly identical to other post-fusion structures. This suggests that viruses can alter dimer assembly but the structure of the activated, fusogenic conformation may be more strictly conserved. The only member of Flaviviridae known to chronically infect humans is Hepatitits C Virus: HCV). HCV is blood borne and carried by roughly 3 percent of the world\u27s population. Clinical manifestations include hepatitis, cirrhosis and hepatocellular carcinoma. HCV envelope protein E2 mediates interaction with host receptors CD81 and scavenger receptor BI: SR-BI) and is the primary target of neutralizing antibodies. To elucidate detailed biochemical roles for these receptors\u27 interactions with E2, we determined that the E2 ectodomain: sE2) interacts with soluble CD81 large extracellular loop: CD81-LEL) with 2:2 stoichiometry, and that this interaction inhibits subsequent engagement of SR-BI. We then evaluated the affinity and kinetics of sE2:CD81-LEL binding. Interaction between these proteins was enhanced by deletion of hypervariable region 1: HVR1) of E2 and modulated by the genotype from which sE2 was generated. Furthermore, neutralization of HVR1-deleted HCV by a cross-reactive antibody was enhanced in a genotype-specific manner that correlated with sE2:CD81-LEL affinity measurements. Our results suggest that E2 cannot engage CD81 and SR-BI simultaneously, that HVR1 obscures conserved CD81 and antibody binding sites, and that genotypic variation influences HCV host receptor preference

Absolute Single Ion Thermometry

We describe and experimentally implement a single-ion local thermometry technique with absolute sensitivity adaptable to all laser-cooled atomic ion species. The technique is based on the velocity-dependent spectral shape of a quasi-dark resonance tailored in a J $\rightarrow$ J transition such that the two driving fields can be derived from the same laser source leading to a negligible relative phase shift. We validated the method and tested its performances in an experiment on a single 88 Sr + ion cooled in a surface radio-frequency trap. We first applied the technique to characterise the heating-rate of the surface trap. We then measured the stationary temperature of the ion as a function of cooling laser detuning in the Doppler regime. The results agree with theoretical calculations, with an absolute error smaller than 100 $\mu$K at 500 $\mu$K, in a temperature range between 0.5 and 3 mK and in the absence of adjustable parameters. This simple-to-implement and reliable method opens the way to fast absolute measurements of single-ion temperatures in future experiments dealing with heat transport in ion chains or thermodynamics at the single-ion level

Energy-Efficient Power Control for Contention-Based Synchronization in OFDMA Systems with Discrete Powers and Limited Feedback

This work derives a distributed and iterative algorithm by which mobile terminals can selfishly control their transmit powers during the synchronization procedure specified by the IEEE 802.16m and the 3GPP-LTE standards for orthogonal frequency-division multiple-access technologies. The proposed solution aims at maximizing the energy efficiency of the network and is derived on the basis of a finite noncooperative game in which the players have discrete action sets of transmit powers. The set of Nash equilibria of the game is investigated, and a distributed power control algorithm is proposed to achieve synchronization in an energy-efficient manner under the assumption that the feedback from the base station is limited. Numerical results show that the proposed solution improves the energy efficiency as well as the timing estimation accuracy of the network compared to existing alternatives, while requiring a reasonable amount of information to be exchanged on the return channel

An Intuitive Automated Modelling Interface for Systems Biology

We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM

Optimisation of the pin cooler design for the megapie target using full 3D numerical simulations

The MEGAwatt PIlot Experiment (MEGAPIE) project has been recently proposed to demonstrate the feasibility of a liquid lead bismuth target for spallation facilities at a beam power level of 1 MW. The target will be put into operation at the Paul Scherrer Institut (PSI, Switzerland) in 2004 and will be used in the existing target block of SINQ. About 650 kW of thermal power has to be removed through a bunch of 12 pin-coolers. In order to improve the heat exchange, it was decided to investigate the possibility of accelerating the oil coolant by introducing a spiral in the oil cylindrical channel. This forces the flow to rotate while rising, thus increasing the Reynolds number and the heat transfer coefficient. We show some numerical simulations, which have supported the dimensioning of the pins as well as the choice of the secondary coolant, that is Diphyl THT. The spiral option has been confirmed. The spiral diameter must be a little smaller than the channel width, to allow the effective mechanical assemblage of the pin. The existence of a gap between the spiral and the external wall adds complexity to the numerical simulation, being fully 3D with several orders of magnitude of length scales involved. A single pin has been tested by Enea-Brasimone and entirely simulated by CRS4 for a matrix of various operational settings. Results are shown and compare

Benchmark calculation of the MEGAPIE target (M1)

The benchmark calculations performed by CRS4 with Star-CD on a reference geometry of the MEGAPIE target are presented in this report (benchmark M1). Scope of the benchmark is a comparison of the results obtained by the various partners involved in the MEGAPIE project using different codes and turbulence modelling approaches. The considered target geometry is the one with the final part of the guide tube slanted at an angle of about 9 degrees. The Pb-Bi flow in the last 2150 mm of the target have been simulated, including the calculation of the thermal field in all the solid structures (window, hull and flow guide). Due to geometrical symmetry, only half of the real domain was considered. Turbulence was simulated using a Chen k-ε model, combined with a Two-layer model in the most critical near-wall regions (window and flow guide in the spallation region) and with Wall Functions along the riser and the down-comer. Modified wall functions for low Prandtl number fluids were implemented. Results are presented for both cases with the beam footprint major axis parallel (benchmark M1.0) and normal (benchmark M1.1) to the guide-tube slant. In order to estimate the effect of the variation of the turbulent Prandtl number on the heat exchange, two calculation have been performed, one with Prt = 0.9 and one using a relationship Prt = f(Ret, Pr), yielding a locally variable turbulent Prandtl number. Results show a very complex flow pattern in the spallation region, with 3D vortex structures being generated in the reversing region and dragged along the rising duct. In case M1.0 with Prt = 0.9, results show maximum window temperatures of 521 °C and 487 °C in the external and internal side respectively, with a maximum Pb-Bi temperature of 486 °C located nearby the window centre. The maximum flow velocity is 1.35 m/s. A significant heat exchange takes place across the 1.5 mm thick flow guide, causing a mean temperature increase along the down-comer of about 34 °C. Due to the high Reynolds number of the flow, the effect of using a variable Prt is limited to near wall regions, where the heat exchange is slightly reduced. The combination of a lower heat exchange across the flow guide (resulting in a lower temperature increase of the Pb-Bi along the down-comer) and a worse window cooling yielded a maximum window temperature of 524°C, namely 3 °C more than in the case with Prt = 0.9. In case M1.1, maximum window temperatures of 447 °C and 414 oC were found using Prt = 0.9 with a maximum Pb-Bi temperature of 423 °C located in the central part of the spallation region. Using a variable Prt, window temperatures increased of about 2 °C while a 1 °C lower maximum Pb-Bi temperature was found