Site-directed mutagenesis of the proposed catalytic amino acids of the Sindbis virus capsid protein autoprotease

The structural proteins of Sindbis virus are translated as a polyprotein precursor that is cleaved upon translation. The capsid protein is postulated to be a serine protease that releases itself from the N terminus of the nascent polyprotein by autoproteolysis. We have tested the importance in autoproteolysis of His-141, Asp-147, and Ser-215, previously postulated to form the catalytic triad of the protease, and of Asp-163. Several site-specific mutations were constructed at each of these positions, and the release of the capsid protein during translation in a cell-free system was examined. Because proteolysis occurs in cis during translation, the kinetics of release cannot be determined in this system, but the extent of proteolysis can be ascertained. Ser-215 appears to be the catalytic serine of the proteinase. Cys or Thr could substitute inefficiently for Ser-215, but substitution with Ala or Ile led to complete loss of activity. His-141 was also important for proteolysis. Substitution with Ala or Pro led to total loss of activity. Surprisingly, substitution with Arg resulted in complete proteolysis in vitro. Changes at the two Asp residues resulted in complete proteolysis of the substrate in vitro. All mutations that resulted in at least partial cleavage in vitro were incorporated into a full-length clone of Sindbis virus and an attempt was made to recover mutant virus. All changes tested were lethal for the virus except Asp-163 to Asn. Thus, production of infectious virus is either a more sensitive measure of the catalytic rate than the extent of in vitro cleavage, or these residues have necessary functions in addition to their possible role in proteolysis

Photon molecules in atomic gases trapped near photonic crystal waveguides

Realizing systems that support robust, controlled interactions between individual photons is an exciting frontier of nonlinear optics. To this end, one approach that has emerged recently is to leverage atomic interactions to create strong and spatially non-local interactions between photons. In particular, effective interactions have been successfully created via interactions between atoms excited to Rydberg levels. Here, we investigate an alternative approach, in which atomic interactions arise via their common coupling to photonic crystal waveguides. This technique takes advantage of the ability to separately tailor the strength and range of interactions via the dispersion engineering of the structure itself, which can lead to qualitatively new types of phenomena. As an example, we discuss the formation of correlated transparency windows, in which photonic states of a certain number and shape selectively propagate through the system. Through this technique, we show in particular that one can create molecular-like potentials that lead to molecular bound states of photon pairs

Design and construction of an actively frequency-switchable RF coil for field-dependent Magnetisation Transfer Contrast MRI with fast field-cycling

Copyright © 2010 Elsevier Inc. All rights reserved.Peer reviewedPostprin

The near wall effect of synthetic jets in a boundary layer

Copyright @ 2007 Elsevier Inc. All rights reserved.An experimental investigation to analyse the qualitative near wall effect of synthetic jets in a laminar boundary layer has been undertaken for the purpose of identifying the types of vortical structures likely to have delayed separation on a 2D circular cylinder model described in this paper. In the first instance, dye visualisation of the synthetic jet was facilitated in conjunction with a stereoscopic imaging system to provide a unique quasi three-dimensional identification of the vortical structures. Secondly, the impact of synthetic jet structures along the wall was analysed using a thermochromic liquid crystal-based convective heat transfer sensing system in which, liquid crystals change colour in response to the thermal footprints of a passing flow structure. Of the different vortical structures produced as a result of varying actuator operating and freestream conditions, the footprints of hairpin vortices and stretched vortex rings revealed a marked similarity with the oil flow pattern of a vortex pair interacting with the separation line on the cylinder hence suggesting that either of these structures was responsible in delaying separation. Conditions were established for the formation of the different synthetic jet structures in non-dimensional parameter space

Sindbis virus ts103 has a mutation in glycoprotein E2 that leads to defective assembly of virions

Sindbis virus mutant ts103 is aberrant in the assembly of virus particles. During virus budding, proper nucleocapsid-glycoprotein interactions fail to occur such that particles containing many nucleocapsids are formed, and the final yield of virus is low. We have determined that a mutation in the external domain of glycoprotein E2, Ala-344-->Val, is the change that leads to this phenotype. Mapping was done by making recombinant viruses between ts103 and a parental strain of the virus, using a full-length cDNA clone of Sindbis virus from which infectious RNA can be transcribed, together with sequence analysis of the region of the genome shown in this way to contain the ts103 lesion. A partial revertant of ts103, called ts103R, was also mapped and sequenced and found to be a second-site revertant in which a change in glycoprotein E1 from lysine to methionine at position 227 partially suppresses the phenotypic effects of the change at E2 position 344. An analysis of revertants from ts103 mutants in which the Ala-->Val change had been transferred into a defined background showed that pseudorevertants were more likely to arise than were true revertants and that the ts103 change itself reverted very infrequently. The assembly defect in ts103 appeared to result from weakened interactions between the virus membrane glycoproteins or between these glycoproteins and the nucleocapsid during budding. Both the E2 mutation leading to the defect in virus assembly and the suppressor mutation in glycoprotein E1 are in the domains external to the lipid bilayer and thus in domains that cannot interact directly with the nucleocapsid. This suggests that in ts103, either the E1-E2 heterodimers or the trimeric spikes (consisting of three E1-E2 heterodimers) are unstable or have an aberrant configuration, and thus do not interact properly with the nucleocapsid, or cannot assembly correctly to form the proper icosahedral array on the surface of the virus

Electrostatic Modulation of the Electronic Properties of Dirac Semimetal Na3Bi

Large-area thin films of topological Dirac semimetal Na$_3$Bi are grown on amorphous SiO$_2$:Si substrates to realise a field-effect transistor with the doped Si acting as back gate. As-grown films show charge carrier mobilities exceeding 7,000 cm$^2$/Vs and carrier densities below 3 $\times$10$^{18}$ cm$^{-3}$, comparable to the best thin-film Na$_3$Bi. An ambipolar field effect and minimum conductivity are observed, characteristic of Dirac electronic systems. The results are quantitatively understood within a model of disorder-induced charge inhomogeneity in topological Dirac semimetals. Due to the inverted band structure, the hole mobility is significantly larger than the electron mobility in Na$_3$Bi, and when present, these holes dominate the transport properties.Comment: 5 pages, 4 figures; minor corrections and revisions for readabilit

Quantum dynamics of propagating photons with strong interactions: a generalized input-output formalism

There has been rapid development of systems that yield strong interactions between freely propagating photons in one dimension via controlled coupling to quantum emitters. This raises interesting possibilities such as quantum information processing with photons or quantum many-body states of light, but treating such systems generally remains a difficult task theoretically. Here, we describe a novel technique in which the dynamics and correlations of a few photons can be exactly calculated, based upon knowledge of the initial photonic state and the solution of the reduced effective dynamics of the quantum emitters alone. We show that this generalized "input-output" formalism allows for a straightforward numerical implementation regardless of system details, such as emitter positions, external driving, and level structure. As a specific example, we apply our technique to show how atomic systems with infinite-range interactions and under conditions of electromagnetically induced transparency enable the selective transmission of correlated multi-photon states

Intensity Mapping with Carbon Monoxide Emission Lines and the Redshifted 21 cm Line

We quantify the prospects for using emission lines from rotational transitions of the CO molecule to perform an `intensity mapping' observation at high redshift during the Epoch of Reionization (EoR). The aim of CO intensity mapping is to observe the combined CO emission from many unresolved galaxies, to measure the spatial fluctuations in this emission, and use this as a tracer of large scale structure at very early times in the history of our Universe. This measurement would help determine the properties of molecular clouds -- the sites of star formation -- in the very galaxies that reionize the Universe. We further consider the possibility of cross-correlating CO intensity maps with future observations of the redshifted 21 cm line. The cross spectrum is less sensitive to foreground contamination than the auto power spectra, and can therefore help confirm the high redshift origin of each signal. Furthermore, the cross spectrum measurement would help extract key information about the EoR, especially regarding the size distribution of ionized regions. We discuss uncertainties in predicting the CO signal at high redshift, and discuss strategies for improving these predictions. Under favorable assumptions, and feasible specifications for a CO survey mapping the CO(2-1) and CO(1-0) lines, the power spectrum of CO emission fluctuations and its cross spectrum with future 21 cm measurements from the MWA are detectable at high significance.Comment: 19 pages, 8 figures, submitted to Ap