Generation of replication-proficient influenza virus NS1 point mutants with interferon-hyperinducer phenotype

The NS1 protein of influenza A viruses is the dedicated viral interferon (IFN)-antagonist. Viruses lacking NS1 protein expression cannot multiply in normal cells but are viable in cells deficient in their ability to produce or respond to IFN. Here we report an unbiased mutagenesis approach to identify positions in the influenza A NS1 protein that modulate the IFN response upon infection. A random library of virus ribonucleoproteins containing circa 40 000 point mutants in NS1 were transferred to infectious virus and amplified in MDCK cells unable to respond to interferon. Viruses that activated the interferon (IFN) response were subsequently selected by their ability to induce expression of green-fluorescent protein (GFP) following infection of A549 cells bearing an IFN promoter-dependent GFP gene. Using this approach we isolated individual mutant viruses that replicate to high titers in IFN-compromised cells but, compared to wild type viruses, induced higher levels of IFN in IFN-competent cells and had a reduced capacity to counteract exogenous IFN. Most of these viruses contained not previously reported NS1 mutations within either the RNA-binding domain, the effector domain or the linker region between them. These results indicate that subtle alterations in NS1 can reduce its effectiveness as an IFN antagonist without affecting the intrinsic capacity of the virus to multiply. The general approach reported here may facilitate the generation of replication-proficient, IFN-inducing virus mutants, that potentially could be developed as attenuated vaccines against a variety of viruses.

An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response

UNLABELLED: Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space.

IMPORTANCE: In natural virus infections, the production of interferons leads to an antiviral state in cells that effectively limits virus replication. The interferon response places considerable selection pressure on viruses, and they have evolved a variety of ways to evade it. Although the influenza virus NS1 protein is a powerful interferon antagonist, the contributions of other viral genes to interferon evasion have not been well characterized. Here, we examined the effects of alleviating the selection pressure exerted by interferon by serially passaging influenza viruses in cells unable to respond to interferon. Viruses that grew to high titers had mutations at many normally conserved positions in nearly all genes and were not restricted to the NS1 gene. Our results demonstrate that influenza viruses have fine-tuned their entire genomes to evade the interferon response, and by removing interferon-mediated constraints, viruses can mutate at genome positions normally restricted by the interferon response.

Interferon-γ stimulates CD14, TLR2 and TLR4 mRNA expression in gingival fibroblasts increasing responsiveness to bacterial challenge

Objective: To investigate the potential effects of IFN-y on the responsiveness of human gingival fibroblasts to bacterial challenge.
Design :mRNA and protein expression of CD14, TLR2 and TLR4 in human gingival fibroblasts was detected by quantitative polymerase chain reaction (Q-PCR) and flow cytometry. The effect of preincubation with IFN-y on subsequent bacterial LPS-induced expression of IL-6 and IL-8 by gingival fibroblasts was determined by ELISA. Bacterial LPS-induced IκBα degradation in human gingival fibroblasts was investigated by western blot.
Results: Human gingival fibroblasts express CD14, TLR2 and TLR4 mRNAs. IFN-y, but not IL-1B, induced mRNA expression of all three receptors and the expression of membrane bound CD14 protein. Pre-incubation of fibroblasts with IFN-y and subsequent stimulation with Escherichia coli LPS or Porphyromonas gingivalis LPS led to increased production of IL-6 and IL-8. LPS-induced pro-inflammatory cytokine production was abrogated by a blocking antibody to CD14. Both E. coli LPS and P. gingivalis LPS induced IκBα degradation in human gingival fibroblasts.
Conclusion: Our data indicate that IFN-y primes human gingival fibroblasts, through the upregulation of CD14 expression, which results in increased responsiveness to bacterial LPS challenge, as determined by pro-inflammatory cytokine production.

Judging Time Intevals using a model of perceptuo-motor control

Estimating a time interval and temporally coordinating movements in space are fundamental skills, but the relationships between these different forms of timing, and the neural processes that they incur, are not well understood. While different theories have been proposed to account for time perception, time estimation, and the temporal patterns of coordination, there are no general mechanisms which unify these various timing skills. This study considers whether a model of perceptuo-motor timing, the tau(GUIDE), can also describe how certain judgements of elapsed time are made. To evaluate this, an equation for determining interval estimates was derived from the tau(GUIDE) model and tested in a task where participants had to throw a ball and estimate when it would hit the floor. The results showed that in accordance with the model, very accurate judgements could be made without vision (mean timing error -19.24 msec), and the model was a good predictor of skilled participants' estimate timing. It was concluded that since the tau(GUIDE) principle provides temporal information in a generic form, it could be a unitary process that links different forms of timing.

Guiding contact by coupling the taus of gaps

Animals control contact with surfaces when locomoting, catching prey, etc. This requires sensorily guiding the rate of closure of gaps between effecters such as the hands, feet or jaws and destinations such as a ball, the ground and a prey. Control is generally rapid, reliable and robust, even with small nervous systems: the sensorimotor processes are therefore probably rather simple. We tested a hypothesis, based on general tau theory, that closing two gaps simultaneously, as required in many actions, might be achieved simply by keeping the taus of the gaps coupled in constant ratio. tau of a changing gap is defined as the time-to-closure of the gap at the current closure-rate. General tau theory shows that tau of a gap could, in principle, be directly sensed without needing to sense either the gap size or its rate of closure. In our experiment, subjects moved an effector (computer cursor) to a destination zone indicated on the computer monitor, to stop in the zone just as a moving target cursor reached it. The results indicated the subjects achieved the task by keeping tau of the gap between effector and target coupled to tau of the gap between the effector and the destination zone. Evidence of tau -coupling has also been found, for example, in bats guiding landing using echolocation. Thus, it appears that a sensorimotor process used by different species for coordinating the closure of two or more gaps between effecters and destinations entails constantly sensing the taus of the gaps and moving so as to keep the taus coupled in constant ratio.

Intercepting beats in predesignated target zones

Moving to a rhythm necessitates precise timing between the movement of the chosen limb and the timing imposed by the beats. However, the temporal information specifying the moment when a beat will sound (the moment onto which one must synchronise one's movement) is not continuously provided by the acoustic array. Because of this informational void, the actors need some form of prospective information that will allow them to act sufficiently ahead of time in order to get their hand in the right place at the right time. In this acoustic interception study, where participants were asked to move between two targets in such a way that they arrived and stopped in the target zone at the same time as a beat sounded, we tested a model derived from tau-coupling theory (Lee DN (1998) Ecol Psychol 10:221-250). This model attempts to explain the form of a potential timing guide that specifies the duration of the inter-beat intervals and also describes how this informational guide can be used in the timing and guidance of movements. The results of our first experiment show that, for inter-beat intervals of less than 3 s, a large proportion of the movement (over 70%) can be explained by the proposed model. However, a second experiment, which augments the time between beats so that it surpasses 3 s, shows a marked decline in the percentage of information/movement coupling. A close analysis of the movement kinematics indicates a lack of control and anticipation in the participants' movements. The implications of these findings, in light of other research studies, are discussed.

High glucose decreases intracellular glutathione concentrations and upregulates inducible nitric oxide synthase gene expression in intestinal epithelial cells

Diabetes is associated with oxidative stress and increased levels of inflammatory cytokines. The aim of the study was to assess the effects of inflammatory cytokines and oxidative stress associated with raised glucose levels on inducible nitric oxide synthase (iNOS) promoter activity in intestinal epithelial cells. High glucose (25 mmol/l) conditions reduced glutathione (GSH) levels in the human intestinal epithelial cell line, DLD-1. Addition of the antioxidant alpha-lipoic acid resulted in the restoration of GSH levels to normal. Upregulation of basal iNOS promoter activity was observed when cells were incubated in high glucose alone. This effect was significantly reduced by the addition of the antioxidant, alpha-lipoic acid and completely blocked with inhibition of NFkappa B activity. Cytokine stimulation [interleukin-1 beta, tumor necrosis factor-alpha, interferon-gamma] induced iNOS promoter activity in all conditions and this was accompanied by an increase in nitric oxide (NO) production. Inhibition of NFkappa-B activity decreased but did not completely inhibit cytokine-induced iNOS promoter activity and subsequent NO production. In conclusion, high glucose-induced iNOS promoter activity is mediated in part through intracellular GSH and NFkappa-B.

Monocyte-derived dendritic cells: a potential target for therapy in multiple sclerosis (MS)

Monocytes can differentiate into dendritic cells (DC), cells with a pivotal role in both protective immunity and tolerance. Defects in the maturation or function of DC may be important in the development of autoimmune disease. We sought to establish if there were differences in the cytokine (granulocyte-macrophage colony-stimulating factor and IL-4)-driven maturation of monocytes to DC in patients with MS and whether drugs used to treat MS affected this process in vitro. We have demonstrated that there is no defect in the ability of magnetic activated cell sorting (MACS)-purified monocytes from patients with MS to differentiate to DC, but equally they show no tendency to acquire a DC phenotype without exogenous cytokines. Interferon-beta1a prevents the acquisition of a full DC phenotype as determined by light and electron microscopy and by flow cytometry. Methylprednisolone not only prevents the development of monocyte-derived DC but totally redirects monocyte differentiation towards a macrophage phenotype. Evidence is evolving for a role for DC in central nervous system immunity, either within the brain or in cervical lymph nodes. The demonstrated effect of both drugs on monocyte differentiation may represent an important site for immune therapy in MS.

An exactly solvable four transition point model

Heavy particle collisions, in particular low-energy ion-atom collisions, are amenable to semiclassical JWKB phase integral analysis in the complex plane of the internuclear separation. Analytic continuation in this plane requires due attention to the Stokes phenomenon which parametrizes the physical mechanisms of curve crossing, non-crossing, the hybrid Nikitin model, rotational coupling and predissociation. Complex transition points represent adiabatic degeneracies. In the case of two or more such points, the Stokes constants may only be completely determined by resort to the so-called comparison- equation method involving, in particular, parabolic cylinder functions or Whittaker functions and their strong-coupling asymptotics. In particular, the Nikitin model is a two transition-point one-double-pole problem in each half-plane corresponding to either ingoing or outgoing waves. When the four transition points are closely clustered, new techniques are required to determine Stokes constants. However, such investigations remain incomplete, A model problem is therefore solved exactly for scattering along a one-dimensional z-axis. The energy eigenvalue is b(2)-a(2) and the potential comprises -z(2)/2 (parabolic) and -a(2) + b(2)/2z(2) (centrifugal/centripetal) components. The square of the wavenumber has in the complex z-plane, four zeros each a transition point at z = +/-a +/- ib and has a double pole at z = 0. In cases (a) and (b), a and b are real and unitarity obtains. In case (a) the reflection and transition coefficients are parametrized by exponentials when a(2) + b(2) > 1/2. In case (b) they are parametrized by trigonometrics when a(2) + b(2) <1/2 and total reflection is achievable. In case (c) a and b are complex and in general unitarity is not achieved due to loss of flux to a continuum (O'Rourke and Crothers, 1992 Proc. R. Sec. 438 1). Nevertheless, case (c) coefficients reduce to (a) or (b) under appropriate limiting conditions. Setting z = ht, with h a real constant, an attempt is made to model a two-state collision problem modelled by a pair of coupled first-order impact parameter equations and an appropriate (T) over tilde-tau relation, where (T) over tilde is the Stueckelberg variable and tau is the reduced or scaled time. The attempt fails because (T) over tilde is an odd function of tau, which is unphysical in a real collision problem. However, it is pointed out that by applying the Kummer exponential model to each half-plane (O'Rourke and Crothers 1994 J. Phys. B: At. Mel. Opt. Phys. 27 2497) the current model is in effect extended to a collision problem with four transition points and a double pole in each half-plane. Moreover, the attempt in itself is not a complete failure since it is shown that the result is a perfect diabatic inelastic collision for a traceless Hamiltonian matrix, or at least when both diagonal elements are odd and the off-diagonal elements equal and even.

Changes in functional behavior of 93 % Pb(Mg1/3Nb2/3)O-3-7 % PbTiO3 thin films induced by ac electric fields

The dielectric properties of Au/[93%Pb(Mg1/3Nb2/3)O-3-7%PbTiO3] (PMN-PT)/(La0.5Sr0.5)CoO3/MgO thin-film capacitor heterostructures, made using pulsed laser deposition, have been investigated, with particular emphasis on the changes in response associated with increasing the magnitude of the ac measuring field. It was found that increasing the ac field caused a change in the frequency spectrum of relaxators, increasing the speed of response of "slow" relaxators, with an associated decrease in the freezing temperature (T-f) of the relaxor system; in addition, other characteristic parameters relating to polar relaxation (activation energy E-a and attempt frequency 1/tau(0)), described by fitting of the dielectric response to a Vogel-Fulcher expression, were found to change continuously as ac field levels were increased.

'Superluminal' tunnelling as a weak measurement effect

We exploit the analogy between the transfer of a pulse across a scattering medium and Aharonov's weak measurements to resolve the long standing paradox between the impossibility to exceed the speed of light and the seemingly "superluminal" behavior of a tunneling particle in the barrier or a photon in a "fast-light" medium. We demonstrate that superluminality occurs when the value of the duration tau spent in the barrier is uncertain, whereas when tau is known accurately, no superluminal behavior is observed. In all cases only subluminal durations contribute to the transmission which precludes faster-than-light information transfer, as observed in a recent experiment.

Information used in detecting upcoming collisions.

In four experiments we examined the nature of the information used in judging whether events would or would not give rise to a collision in the near future. Observers were tested in situations depicting approaches between two objects (lateral approaches) and approaches between an object and the point of observation (head-on approaches), with objects moving according to constant deceleration or sinusoidal deceleration patterns. Judgments were found to be based, to a large extent, on the (in)sufficiency of current deceleration to avoid upcoming collision, as specified optically by tau-dot (tau over dot). However, the information specified, by tau (tau), that is the current (first-order) time remaining until contact, was also found to play a significant role. We deduce that judgment of upcoming collision is based on the detection Of T and its evolution over time, suggesting that observers are sensitive to Deltatau rather than to tau over dot itself.

Observation of Collisionless Shocks in Laser-Plasma Experiments

The propagation in a rarefied plasma (n(e)less than or similar to 10(15) cm(-3)) of collisionless shock waves and ion-acoustic solitons, excited following the interaction of a long (tau(L)similar to 470 ps) and intense (I similar to 10(15) W cm(-2)) laser pulse with solid targets, has been investigated via proton probing techniques. The shocks' structures and related electric field distributions were reconstructed with high spatial and temporal resolution. The experimental results were interpreted within the framework of the nonlinear wave description based on the Korteweg-de Vries-Burgers equation.

Performance projections and design optimization of planar double gate SOI MOSFETs for logic technology applications

In this paper, by investigating the influence of source/drain extension region engineering (also known as gate-source/drain underlap) in nanoscale planar double gate (DG) SOI MOSFETs, we offer new insights into the design of future nanoscale gate-underlap DG devices to achieve ITRS projections for high performance (HP), low standby power (LSTP) and low operating power (LOP) logic technologies. The impact of high-kappa gate dielectric, silicon film thickness, together with parameters associated with the lateral source/drain doping profile, is investigated in detail. The results show that spacer width along with lateral straggle can not only effectively control short-channel effects, thus presenting low off-current in a gate underlap device, but can also be optimized to achieve lower intrinsic delay and higher on-off current ratio (I-on/I-off). Based on the investigation of on-current (I-on), off-current (I-off), I-on/I-off, intrinsic delay (tau), energy delay product and static power dissipation, we present design guidelines to select key device parameters to achieve ITRS projections. Using nominal gate lengths for different technologies, as recommended from ITRS specification, optimally designed gate-underlap DG MOSFETs with a spacer-to-straggle (s/sigma) ratio of 2.3 for HP/LOP and 3.2 for LSTP logic technologies will meet ITRS projection. However, a relatively narrow range of lateral straggle lying between 7 to 8 nm is recommended. A sensitivity analysis of intrinsic delay, on-current and off-current to important parameters allows a comparative analysis of the various design options and shows that gate workfunction appears to be the most crucial parameter in the design of DG devices for all three technologies. The impact of back gate misalignment on I-on, I-off and tau is also investigated for optimized underlap devices.