Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages.

Genome-wide investigations of host-pathogen interactions are often limited by analyses of mixed populations of infected and uninfected cells, which lower sensitivity and accuracy. To overcome these obstacles and identify key mechanisms by which Zika virus (ZIKV) manipulates host responses, we developed a system that enables simultaneous characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring uninfected primary human macrophages. We demonstrate that transcriptional responses in ZIKV-infected macrophages differed radically from those in uninfected neighbors and that studying the cell population as a whole produces misleading results. Notably, the uninfected population of macrophages exhibits the most rapid and extensive changes in gene expression, related to type I IFN signaling. In contrast, infected macrophages exhibit a delayed and attenuated transcriptional response distinguished by preferential expression of IFNB1 at late time points. Biochemical and genomic studies of infected macrophages indicate that ZIKV infection causes both a targeted defect in the type I IFN response due to degradation of STAT2 and reduces RNA polymerase II protein levels and DNA occupancy, particularly at genes required for macrophage identity. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected macrophages thereby reveals the coincident evolution of dominant proviral or antiviral mechanisms, respectively, that determine the outcome of ZIKV exposure

Quantum recoil effects in finite-time disentanglement of two distinguishable atoms

Starting from the requirement of distinguishability of two atoms by their positions, it is shown that photon recoil has a strong influence on finite-time disentanglement and in some cases prevents its appearance. At near-field inter atomic distances well localized atoms, with maximally one atom being initially excited, may suffer disentanglement at a single finite time or even at a series of equidistant finite times, depending on their mean inter atomic distance and their initial electronic preparation.Comment: 13 pages, 1 figure, submitted to Physical Review on august 2

Suppression of decoherence by bath ordering

The dynamics of two coupled spins-1/2 coupled to a spin-bath is studied as an extended model of the Tessieri-Wilkie Hamiltonian \cite{TWmodel}. The pair of spins served as an open subsystem were prepared in one of the Bell states and the bath consisted of some spins-1/2 is in a thermal equilibrium state from the very beginning. It is found that with the increasing the coupling strength of the bath spins, the bath forms a resonant antiferromagnetic order. The polarization correlation between the two spins of the subsystem and the concurrence are recovered in some extent to the isolated subsystem. This suppression of the subsystem decoherence may be used to control the quantum devices in practical applications.Comment: 32 pages, Chinese Physics (accepted

Moving Atom-Field Interaction: Correction to Casimir-Polder Effect from Coherent Back-action

The Casimir-Polder force is an attractive force between a polarizable atom and a conducting or dielectric boundary. Its original computation was in terms of the Lamb shift of the atomic ground state in an electromagnetic field (EMF) modified by boundary conditions along the wall and assuming a stationary atom. We calculate the corrections to this force due to a moving atom, demanding maximal preservation of entanglement generated by the moving atom-conducting wall system. We do this by using non-perturbative path integral techniques which allow for coherent back-action and thus can treat non-Markovian processes. We recompute the atom-wall force for a conducting boundary by allowing the bare atom-EMF ground state to evolve (or self-dress) into the interacting ground state. We find a clear distinction between the cases of stationary and adiabatic motions. Our result for the retardation correction for adiabatic motion is up to twice as much as that computed for stationary atoms. We give physical interpretations of both the stationary and adiabatic atom-wall forces in terms of alteration of the virtual photon cloud surrounding the atom by the wall and the Doppler effect.Comment: 16 pages, 2 figures, clarified discussions; to appear in Phys. Rev.

Blocking Zika virus vertical transmission.

The outbreak of the Zika virus (ZIKV) has been associated with increased incidence of congenital malformations. Although recent efforts have focused on vaccine development, treatments for infected individuals are needed urgently. Sofosbuvir (SOF), an FDA-approved nucleotide analog inhibitor of the Hepatitis C (HCV) RNA-dependent RNA polymerase (RdRp) was recently shown to be protective against ZIKV both in vitro and in vivo. Here, we show that SOF protected human neural progenitor cells (NPC) and 3D neurospheres from ZIKV infection-mediated cell death and importantly restored the antiviral immune response in NPCs. In vivo, SOF treatment post-infection (p.i.) decreased viral burden in an immunodeficient mouse model. Finally, we show for the first time that acute SOF treatment of pregnant dams p.i. was well-tolerated and prevented vertical transmission of the virus to the fetus. Taken together, our data confirmed SOF-mediated sparing of human neural cell types from ZIKV-mediated cell death in vitro and reduced viral burden in vivo in animal models of chronic infection and vertical transmission, strengthening the growing body of evidence for SOF anti-ZIKV activity

The Rotating-Wave Approximation: Consistency and Applicability from an Open Quantum System Analysis

We provide an in-depth and thorough treatment of the validity of the rotating-wave approximation (RWA) in an open quantum system. We find that when it is introduced after tracing out the environment, all timescales of the open system are correctly reproduced, but the details of the quantum state may not be. The RWA made before the trace is more problematic: it results in incorrect values for environmentally-induced shifts to system frequencies, and the resulting theory has no Markovian limit. We point out that great care must be taken when coupling two open systems together under the RWA. Though the RWA can yield a master equation of Lindblad form similar to what one might get in the Markovian limit with white noise, the master equation for the two coupled systems is not a simple combination of the master equation for each system, as is possible in the Markovian limit. Such a naive combination yields inaccurate dynamics. To obtain the correct master equation for the composite system a proper consideration of the non-Markovian dynamics is required.Comment: 17 pages, 0 figures

Moving Atom-Field Interactions: Quantum Motional Decoherence and Relaxation

The reduced dynamics of an atomic qubit coupled both to its own quantized center of mass motion through the spatial mode functions of the electromagnetic field, as well as the vacuum modes, is calculated in the influence functional formalism. The formalism chosen can describe the entangled non-Markovian evolution of the system with a full account of the coherent back-action of the environment on the qubit. We find a slight increase in the decoherence due to the quantized center of mass motion and give a condition on the mass and qubit resonant frequency for which the effect is important. In optically resonant alkali-metal atom systems, we find the effect to be negligibly small. The framework presented here can nevertheless be used for general considerations of the coherent evolution of qubits in moving atoms in an electromagnetic field.Comment: 9 pages, 1 figure, minor change

Entanglement, recoherence and information flow in an accelerated detector - quantum field system: Implications for black hole information issue

We study an exactly solvable model where an uniformly accelerated detector is linearly coupled to a massless scalar field initially in the Minkowski vacuum. Using the exact correlation functions we show that as soon as the coupling is switched on one can see information flowing from the detector to the field and propagating with the radiation into null infinity. By expressing the reduced density matrix of the detector in terms of the two-point functions, we calculate the purity function in the detector and study the evolution of quantum entanglement between the detector and the field. Only in the ultraweak coupling regime could some degree of recoherence in the detector appear at late times, but never in full restoration. We explicitly show that under the most general conditions the detector never recovers its quantum coherence and the entanglement between the detector and the field remains large at late times. To the extent this model can be used as an analog to the system of a black hole interacting with a quantum field, our result seems to suggest in the prevalent non-Markovian regime, assuming unitarity for the combined system, that black hole information is not lost but transferred to the quantum field degrees of freedom. Our combined system will evolve into a highly entangled state between a remnant of large area (in Bekenstein's black hole atom analog) without any information of its initial state, and the quantum field, now imbued with complex information content not-so-easily retrievable by a local observer.Comment: 16 pages, 12 figures; minor change