Host genetic regulation of immune-based and infectious diseases: Introduction to mammalian genome special issue: genetics of infectious disease

Infectious disease remains a leading cause of mortality worldwide and includes a wide range of ailments caused by a pathogen, typically a virus, bacterium, fungus or parasite, entering and living in the host body. For many decades, but particularly after the molecular biology revolution brought about by the advent of recombinant DNA techniques in the 1970s, the tenet for an infectious disease biologist was to identify genes on the microbe that might play a role in the pathogenic traits of that organism. By first cloning that gene, mutating it in a defined way, analysing the altered phenotype or function of the mutant strain then restoring the gene function to re-establish pathogenicity and satisfy Koch’s postulates, it was assumed this would lead to a complete understanding of disease. Koch’s postulates however imply that virulence traits reside solely in the microbe and are therefore independent of the host. It is now clear that this aspect of the postulate is erroneous and that indeed the susceptibility of the host is paramount and typically as important, if not more important, than the traits of the microbe in determining the outcome of infection and disease

Optimal Sizes of Dielectric Microspheres for Cavity QED with Strong Coupling

The whispering gallery modes (WGMs) of quartz microspheres are investigated for the purpose of strong coupling between single photons and atoms in cavity quantum electrodynamics (cavity QED). Within our current understanding of the loss mechanisms of the WGMs, the saturation photon number, n, and critical atom number, N, cannot be minimized simultaneously, so that an "optimal" sphere size is taken to be the radius for which the geometric mean, (n x N)^(1/2), is minimized. While a general treatment is given for the dimensionless parameters used to characterize the atom-cavity system, detailed consideration is given to the D2 transition in atomic Cesium (852nm) using fused-silica microspheres, for which the maximum coupling coefficient g/(2*pi)=750MHz occurs for a sphere radius a=3.63microns corresponding to the minimum for n=6.06x10^(-6). By contrast, the minimum for N=9.00x10^(-6) occurs for a sphere radius of a=8.12microns, while the optimal sphere size for which (n x N)^(1/2) is minimized occurs at a=7.83microns. On an experimental front, we have fabricated fused-silica microspheres with radii a=10microns and consistently observed quality factors Q=0.8x10^(7). These results for the WGMs are compared with corresponding parameters achieved in Fabry-Perot cavities to demonstrate the significant potential of microspheres as a tool for cavity QED with strong coupling.Comment: 12 pages, 14 figure

Loss of the homeostatic protein BPIFA1, leads to exacerbation of otitis media severity in the Junbo mouse model

Otitis Media (OM) is characterized by epithelial abnormalities and defects in innate immunity in the middle ear (ME). Although, BPIFA1, a member of the BPI fold containing family of putative innate defence proteins is abundantly expressed by the ME epithelium and SNPs in Bpifa1 have been associated with OM susceptibility, its role in the ME is not well characterized. We investigated the role of BPIFA1 in protection of the ME and the development of OM using murine models. Loss of Bpifa1 did not lead to OM development. However, deletion of Bpifa1 in Evi1Jbo/+mice, a model of chronic OM, caused significant exacerbation of OM severity, thickening of the ME mucosa and increased collagen deposition, without a significant increase in pro-inflammatory gene expression. Our data suggests that BPIFA1 is involved in maintaining homeostasis within the ME under steady state conditions and its loss in the presence of inflammation, exacerbates epithelial remodelling leading to more severe OM

Trapping of Single Atoms with Single Photons in Cavity QED

Two recent experiments have reported the trapping of individual atoms inside optical resonators by the mechanical forces associated with single photons [Hood et al., Science 287, 1447 (2000) and Pinkse et al., Nature 404, 365 (2000)]. Here we analyze the trapping dynamics in these settings, focusing on two points of interest. Firstly, we investigate the extent to which light-induced forces in these experiments are distinct from their free-space counterparts. Secondly, we explore the quantitative features of the resulting atomic motion and how these dynamics are mapped onto variations of the intracavity field. Not surprisingly, qualitatively distinct atomic dynamics arise as the coupling and dissipative rates are varied. For the experiment of Hood et al., we show that atomic motion is largely conservative and is predominantly in radial orbits transverse to the cavity axis. A comparison with the free-space theory demonstrates that the fluctuations of the dipole force are suppressed by an order of magnitude. This effect is based upon the Jaynes-Cummings eigenstates of the atom-cavity system and represents qualitatively new physics for optical forces at the single-photon level. By contrast, even in a regime of strong coupling in the experiment of Pinkse et al., there are only small quantitative distinctions between the free-space theory and the quantum theory, so it is not clear that description of this experiment as a novel single-quantum trapping effect is necessary. The atomic motion is strongly diffusive, leading to an average localization time comparable to the time for an atom to transit freely through the cavity and to a reduction in the ability to infer aspects of the atomic motion from the intracavity photon number.Comment: 19 pages, 22 figure files, REVTEX, corrected spelling, LaTeX now produces postscript which includes figures, minor changes to figures. Final version to be published in Physical Review A, expanded summary of results in introduction, minor changes to figures and tex

Quantum Communication with Phantom Photons

We show that quantum information may be transferred between atoms in different locations by using ``phantom photons'': the atoms are coupled through electromagnetic fields, but the corresponding field modes do not have to be fully populated. In the case where atoms are placed inside optical cavities, errors in quantum information processing due to photon absorption inside the cavity are diminished in this way. This effect persists up to intercavity distances of about a meter for the current levels of cavity losses, and may be useful for distributed quantum computing.Comment: 6 pages RevTex, 4 eps figures included. Revised calculation with more details about mode structure calculation and the introduction of losse

Trapping and cooling single atoms with far-off resonance intracavity doughnut modes

We investigate cooling and trapping of single atoms inside an optical cavity using a quasi-resonant field and a far-off resonant mode of the Laguerre-Gauss type. The far-off resonant doughnut mode provides an efficient trapping in the case when it shifts the atomic internal ground and excited state in the same way, which is particularly useful for quantum information applications of cavity quantum electrodynamics (QED) systems. Long trapping times can be achieved, as shown by full 3-D simulations of the quasi-classical motion inside the resonator.Comment: 18 pages, 18 figures, RevTe

Cooling of a single atom in an optical trap inside a resonator

We present detailed discussions of cooling and trapping mechanisms for an atom in an optical trap inside an optical cavity, as relevant to recent experiments. The interference pattern of cavity QED and trapping fields in space makes the trapping wells distinguishable from one another. This adds considerable flexibility to creating effective trapping and cooling conditions and to detection possibilities. Friction and diffusion coefficients are calculated in and beyond the low excitation limit and full 3-D simulations of the quasiclassical motion of a Cs atom are performed.Comment: One more figure and one more autho

All-optical switching and strong coupling using tunable whispering-gallery-mode microresonators

We review our recent work on tunable, ultrahigh quality factor whispering-gallery-mode bottle microresonators and highlight their applications in nonlinear optics and in quantum optics experiments. Our resonators combine ultra-high quality factors of up to Q = 3.6 \times 10^8, a small mode volume, and near-lossless fiber coupling, with a simple and customizable mode structure enabling full tunability. We study, theoretically and experimentally, nonlinear all-optical switching via the Kerr effect when the resonator is operated in an add-drop configuration. This allows us to optically route a single-wavelength cw optical signal between two fiber ports with high efficiency. Finally, we report on progress towards strong coupling of single rubidium atoms to an ultra-high Q mode of an actively stabilized bottle microresonator.Comment: 20 pages, 24 figures. Accepted for publication in Applied Physics B. Changes according to referee suggestions: minor corrections to some figures and captions, clarification of some points in the text, added references, added new paragraph with results on atom-resonator interactio

Flux-rope twist in eruptive flares and CMEs : due to zipper and main-phase reconnection

Funding: UK Science and Technology Facilities CouncilThe nature of three-dimensional reconnection when a twisted flux tube erupts during an eruptive flare or coronal mass ejection is considered. The reconnection has two phases: first of all, 3D “zipper reconnection” propagates along the initial coronal arcade, parallel to the polarity inversion line (PIL); then subsequent quasi-2D “main phase reconnection” in the low corona around a flux rope during its eruption produces coronal loops and chromospheric ribbons that propagate away from the PIL in a direction normal to it. One scenario starts with a sheared arcade: the zipper reconnection creates a twisted flux rope of roughly one turn (2π radians of twist), and then main phase reconnection builds up the bulk of the erupting flux rope with a relatively uniform twist of a few turns. A second scenario starts with a pre-existing flux rope under the arcade. Here the zipper phase can create a core with many turns that depend on the ratio of the magnetic fluxes in the newly formed flare ribbons and the new flux rope. Main phase reconnection then adds a layer of roughly uniform twist to the twisted central core. Both phases and scenarios are modeled in a simple way that assumes the initial magnetic flux is fragmented along the PIL. The model uses conservation of magnetic helicity and flux, together with equipartition of magnetic helicity, to deduce the twist of the erupting flux rope in terms the geometry of the initial configuration. Interplanetary observations show some flux ropes have a fairly uniform twist, which could be produced when the zipper phase and any pre-existing flux rope possess small or moderate twist (up to one or two turns). Other interplanetary flux ropes have highly twisted cores (up to five turns), which could be produced when there is a pre-existing flux rope and an active zipper phase that creates substantial extra twist.PostprintPublisher PDFPeer reviewe