A quantitative algorithm was developed and applied to predict target genes of microRNAs encoded by herpesviruses. Although there is almost no conservation among microRNAs of different herpesvirus subfamilies, a common pattern of regulation emerged. The algorithm predicts that herpes simplex virus 1, human cytomegalovirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus all employ microRNAs to suppress expression of their own genes, including their immediate-early genes. In the case of human cytomegalovirus, a virus-coded microRNA, miR-112-1, was predicted to target the viral immediate-early protein 1 mRNA. To test this prediction, mutant viruses were generated that were unable to express the microRNA, or encoded an immediate-early 1 mRNA lacking its target site. Analysis of RNA and protein within infected cells demonstrated that miR-UL112-1 inhibits expression of the major immediate-early protein. We propose that herpesviruses use microRNA-mediated suppression of immediate-early genes as part of their strategy to enter and maintain latency.miRNAs ͉ reactivation ͉ immune evasion M icroRNAs (miRNAs) are 20-23-nucleotide RNA molecules that bind to mRNA targets, generally within their 3Ј untranslated region (3Ј UTR), and interfere with their translation (1, 2). Viruses have co-evolved with cellular miRNAs and many encode their own miRNAs (3). Every herpesvirus genome that has been examined has been found to encode multiple miRNAs, including Epstein-Barr virus (EBV) (4 -6), human cytomegalovirus (HCMV) (4, 7, 8), herpes simplex virus 1 (HSV-1) (9, 10), and Kaposi's sarcoma-associated herpesvirus (KSHV) (4,6,11,12). These miRNAs can potentially function during lytic replication and latency. Lytic replication proceeds in a coordinated three-phase cascade: immediate-early (IE), early and late. IE products prepare the cell for infection and propagate the cascade. Early gene products support replication of viral DNA, and DNA replication is, in turn, a prerequisite for full activation of the late genes that encode the structural proteins of the virus. During latency, the virus is quiescent. A limited subset of the viral genome is expressed, but, importantly, the virus has the potential to reactivate and reenter the lytic cycle. Although the molecular mechanisms of reactivation are not understood, it is widely assumed that the lytic cascade is reinitiated with the expression of IE genes. Ectopic expression of a single IE protein has been shown to reactivate HSV-1 (13, 14), EBV (15), or KSHV (16,17) in cell culture models of latency.Whereas none or only a few protein-coding genes are expressed, multiple miRNAs are transcribed during latency. The HSV-1 miR-LAT lies within one of the latency associated transcripts (LATs), the only viral RNAs known to be expressed in latency. EBV and KSHV miRNAs also are expressed during latent infection. Because they are nonimmunogenic, miRNAs should be optimal agents for suppression of anti-viral responses and to modify behaviors of latently infected cells, and recent reports ...

We present a numerically feasible semiclassical ͑SC͒ method to evaluate quantum fidelity decay ͑Loschmidt echo͒ in a classically chaotic system. It was thought that such evaluation would be intractable, but instead we show that a uniform SC expression not only is tractable but it also gives remarkably accurate numerical results for the standard map in both the Fermi-golden-rule and Lyapunov regimes. Because it allows Monte Carlo evaluation, the uniform expression is accurate at times when there are 10 70 semiclassical contributions. Remarkably, it also explicitly contains the ''building blocks'' of analytical theories of recent literature, and thus permits a direct test of the approximations made by other authors in these regimes, rather than an a posteriori comparison with numerical results. We explain in more detail the extended validity of the classical perturbation approximation and show that within this approximation, the so-called ''diagonal approximation'' is automatic and does not require ensemble averaging. The question of stability of quantum motion, originally formulated by Peres ͓1͔, has recently attracted much interest, due to its relevance to quantum computation and decoherence in complex systems. Peres defined stability in terms of quantum fidelity M (t), the overlap at time t of two states, which were identical at time tϭ0, but afterwards propagated in slightly different dynamical systems, described by Hamiltonians H 0 and H V ϭH 0 ϩV,This quantity is also called Loschmidt echo, because it can be interpreted as an overlap of a state propagated forward for time t with H 0 and then backward for time t with H V , with the initial state. We consider H 0 to be strongly chaotic, although our method is not limited to this case. Even with this restriction, the decay of fidelity has a surprisingly rich behavior: Most surprising recently was the derivation in Ref.͓2͔ that for a certain range of perturbations the decay rate is independent of the perturbation strength.The Loschmidt echo is physically realizable, for example, in NMR spin echo experiments, where back propagation under a slightly different Hamiltonian is feasible ͓3-5͔. There are other examples, which often go unnoticed. An example is neutron scattering, where the scattering kernel can be written as in Eq. ͑1͒, with H V a momentum boosted version of H 0 . Many numerical investigations of fidelity decay ͑FD͒ have been undertaken in various systems ͓6-32͔. Depending on the strength of perturbation, there exist at least four qualitatively different regimes of the decay in chaotic systems ͓6͔: As the perturbation increases, these regimes are perturbative ͑PT͒, Fermi-golden-rule ͑FGR͒, Lyapunov ͑L͒, and the strong semiclassical ͑SC͒ regimes.In the PT regime, in which the characteristic matrix element of the perturbation is smaller than the mean level spacing ⌬, the decay can be described by a combination of perturbation theory and random-matrix theory ͑RMT͒, and is Gaussian ͓6,7͔,For intermediate perturbation strengths, the decay follows the Fermi g...

Considering accessibility of the 3′UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in currently available algorithms, is not an efficient way to rank predictions. Instead, we describe an algorithm which also considers only the accessible binding sites but which ranks predictions according to over-representation. When compared with experimentally validated and refuted targets in the fruit fly and human, our algorithm shows a remarkable improvement in precision while significantly reducing the computational cost in comparison with other free energy based methods. In the human genome, our algorithm has at least twice higher precision than other methods with their default parameters. In the fruit fly, we find five times more validated targets among the top 500 predictions than other methods with their default parameters. Furthermore, using a common statistical framework we demonstrate explicitly the advantages of using the canonical ensemble instead of using the minimum free energy structure alone. We also find that ‘naïve’ global folding sometimes outperforms the local folding approach.

A general quantum-mechanical method for computing kinetic isotope effects is presented. The method is based on the quantum-instanton approximation for the rate constant and on the path-integral Metropolis-Monte Carlo evaluation of the Boltzmann operator matrix elements. It computes the kinetic isotope effect directly, using a thermodynamic integration with respect to the mass of the isotope, thus avoiding the more computationally expensive process of computing the individual rate constants. The method should be more accurate than variational transition-state theories or the semiclassical instanton method since it does not assume a single tunneling path and does not use a semiclassical approximation of the Boltzmann operator. While the general Monte Carlo implementation makes the method accessible to systems with a large number of atoms, we present numerical results for the Eckart barrier and for the collinear and full three-dimensional isotope variants of the hydrogen exchange reaction H + H 2 → H 2 + H. In all seven test cases, for temperatures between 250 and 600 K, the error of the quantum instanton approximation for the kinetic isotope effects is less than ϳ10%.