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%.

During hematopoiesis, lineage-and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor KAP1 in this process. Hematopoietic-restricted deletion of Kap1 in the mouse resulted in severe hypoproliferative anemia. Kap1-deleted erythroblasts failed to induce mitophagy-associated genes and retained mitochondria. This was due to persistent expression of microRNAs targeting mitophagy transcripts, itself secondary to a lack of repression by stage-specific KRAB-ZFPs. The KRAB/ KAP1-miRNA regulatory cascade is evolutionary conserved, as it also controls mitophagy during human erythropoiesis. Thus, a multilayered transcription regulatory system is present, where protein-and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an important differentiation event.Through the process of erythropoiesis, about one hundred billion new red cells are generated every day in the human adult bone marrow. This process is initiated by the differentiation of hematopoietic stem cells (HSC) into the earliest erythroid progenitor, which was identified ex vivo as a slowly growing burst-forming unit-erythroid (BFU-E). This erythroid progenitor morphs into the rapidly dividing CFU-E (colony-forming unit-erythroid), the proliferation of which is stimulated by the hypoxia-induced hormone erythropoietin. Further differentiation occurs through a highly sophisticated program orchestrated by lineage-and stage-specific combinations of protein-and RNA-based transcription regulators (1-3). It culminates in the elimination of intracellular organelles including mitochondria and the nucleus to yield the fully mature erythrocyte, containing on the order of 250 million molecules of hemoglobin as almost sole cargo. Much is still to be learned about the molecular mechanisms of these events, not only to understand the cause of red cell disorders, but also to aid the in vitro manufacturing of the large supplies of oxygen-carrying cells for transfusion.Higher vertebrate genomes encode hundreds of KRAB-ZFPs that can bind DNA in a sequence-specific fashion through a C-terminal array of C2H2 zinc fingers and recruit the ‡ Corresponding author. didier.trono@epfl.ch.

Articles you may be interested inVibrationally resolved spectra provide a stringent test of the accuracy of theoretical calculations. We combine the thawed Gaussian approximation (TGA) with an on-the-fly ab initio (OTF-AI) scheme to calculate the vibrationally resolved emission spectra of oligothiophenes with up to five rings. The efficiency of the OTF-AI-TGA permits treating all vibrational degrees of freedom on an equal footing even in pentathiophene with 105 vibrational degrees of freedom, thus obviating the need for the global harmonic approximation, popular for large systems. Besides reproducing almost perfectly the experimental emission spectra, in order to provide a deeper insight into the associated physical and chemical processes, we also develop a novel systematic approach to assess the importance and coupling between individual vibrational degrees of freedom during the dynamics. This allows us to explain how the vibrational line shapes of the oligothiophenes change with increasing number of rings. Furthermore, we observe the dynamical interplay between the quinoid and aromatic characters of individual rings in the oligothiophene chain during the dynamics and confirm that the quinoid character prevails in the center of the chain. © 2014 AIP Publishing LLC.

Reactivation of human cytomegalovirus (HCMV) is a significant cause of disease and death in immunocompromised patients, underscoring the need to understand how latency is controlled. Here we demonstrate that HCMV has evolved to utilize cellular microRNAs (miRNAs) in cells that promote latency to regulate expression of a viral protein critical for viral reactivation. Our data reveal that hsa-miR-200 miRNA family members target the UL122 (immediate early protein 2) 3= untranslated region, resulting in repression of this viral protein. Utilizing recombinant viruses that mutate the miRNA-binding site compared to the sequence of the wild-type virus results in lytic rather than latent infections in ex vivo infections of primary CD34 ؉ cells. Cells permissive for lytic replication demonstrate low levels of these miRNAs. We propose that cellular miRNA regulation of HCMV is critical for maintenance of viral latency. IMPORTANCEHuman cytomegalovirus (HCMV) is a herpesvirus that infects a majority of the population. Once acquired, individuals harbor the virus for life, where the virus remains, for the most part, in a quiet or latent state. Under weakened immune conditions, the virus can reactivate, which can cause severe disease and often death. We have found that members of a family of small RNAs, termed microRNAs, encoded by human myeloid progenitor cells are capable of repressing a key viral protein, thus enabling the virus to ensure a quiet/latent state. As these progenitor cells mature further down the myeloid lineage toward cells that support active viral replication, the levels of these microRNAs decrease. Together, our data suggest that host cell microRNA regulation of HCMV is important for the quiet/latent state of this pathogen.

A general semiclassical expression for quantum fidelity ͑Loschmidt echo͒ of arbitrary pure and mixed states is derived. It expresses fidelity as an interference sum of dephasing trajectories weighed by the Wigner function of the initial state, and does not require that the initial state be localized in position or momentum. This general dephasing representation is special in that, counterintuitively, all of fidelity decay is due to dephasing and none is due to the decay of classical overlaps. Surprising accuracy of the approximation is justified by invoking the shadowing theorem: twice-both for physical perturbations and for numerical errors. Beyond justifying the approximation, the shadowing theorem makes the dephasing representation practical: without shadowing it would be impossible to find numerically the precise trajectories needed in a semiclassical approximation. It is shown how the general expression reduces to the previously known special forms for localized states. The superiority of the general over the specialized forms is explained and supported by numerical tests for wave packets, nonlocal pure states, and for simple and random mixed states. The tests are done in nonuniversal regimes in mixed phase space where detailed features of fidelity are important. Although semiclassically motivated, the present approach is valid for abstract systems with a finite Hilbert basis provided that the discrete Wigner transform is used. This makes the method applicable, via a phase-space approach, to problems of quantum computation.