Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental condition

Comparison among Various Expressions of Complex Admittance for Quantum System in Contact with Heat Reservoir

Relation among various expressions of the complex admittance for quantum systems in contact with heat reservoir is studied. Exact expressions of the complex admittance are derived in various types of formulations of equations of motion under contact with heat reservoir. Namely, the complex admittance is studied in the relaxation method and the external-field method. In the former method, the admittance is calculated using the Kubo formula for quantum systems in contact with heat reservoir in no external driving fields, while in the latter method the admittance is directly calculated from equations of motion with external driving terms. In each method, two types of equation of motions are considered, i.e., the time-convolution (TC) equation and time-convolutionless (TCL) equation. That is, the full of the four cases are studied. It is turned out that the expression of the complex admittance obtained by using the relaxation method with the TC equation exactly coincides with that obtained by using the external-field method with the TC equation, while other two methods give different forms. It is also explicitly demonstrated that all the expressions of the complex admittance coincide with each other in the lowest Born approximation for the systemreservoir interaction. The formulae necessary for the higher order expansions in powers of the system-reservoir interaction are derived, and also the expressions of the admittance in the n-th order approximation are given. To characterize the TC and TCL methods, we study the expressions of the admittances of two exactly solvable models. Each exact form of admittance is compared with the results of the two methods in the lowest Born approximation. It is found that depending on the model, either of TC and TCL would be the better method.Comment: 34pages, no figur

Star Formation in the Most Distant Molecular Cloud in the Extreme Outer Galaxy: A Laboratory of Star Formation in an Early Epoch of the Galaxy's Formation

We report the discovery of active star formation in Digel's Cloud 2, which is one of the most distant giant molecular clouds known in the extreme outer Galaxy (EOG). At the probable Galactic radius of ~20 kpc, Cloud 2 has a quite different environment from that in the solar neighborhood, including lower metallicity, much lower gas density, and small or no perturbation from spiral arms. With new wide-field near-infrared (NIR) imaging that covers the entire Cloud 2, we discovered two young embedded star clusters located in the two dense cores of the cloud. Using our NIR and 12CO data as well as HI, radio continuum, and IRAS data in the archives, we discuss the detailed star formation processes in this unique environment. We show clear evidences of a sequential star formation triggered by the nearby huge supernova remnant, GSH 138-01-94. The two embedded clusters show a distinct morphology difference: the one in the northern molecular cloud core is a loose association with isolated-mode star formation, while the other in the southern molecular cloud core is a dense cluster with cluster-mode star formation. We propose that high compression by the combination of the SNR shell and an adjacent shell caused the dense cluster formation in the southern core. Along with the low metallicity range of the EOG, we suggest that EOG could be an excellent laboratory for the study of star formation processes, such as those triggered by supernovae, that occured during an early epoch of the Galaxy's formation. In particular, the study of the EOG may shed light on the origin and role of the thick disk, whose metallicity range matches with that of the EOG well.Comment: Accepted by The Astrophysical Journal (18 pages, 9 figures; a version w/full-resolution color figures is available at http://www.ioa.s.u-tokyo.ac.jp/~naoto/papers/apj.cl2_quirc/ms2p_final.pdf

Tables of Hyperonic Matter Equation of State for Core-Collapse Supernovae

We present sets of equation of state (EOS) of nuclear matter including hyperons using an SU_f(3) extended relativistic mean field (RMF) model with a wide coverage of density, temperature, and charge fraction for numerical simulations of core collapse supernovae. Coupling constants of Sigma and Xi hyperons with the sigma meson are determined to fit the hyperon potential depths in nuclear matter, U_Sigma(rho_0) ~ +30 MeV and U_Xi(rho_0) ~ -15 MeV, which are suggested from recent analyses of hyperon production reactions. At low densities, the EOS of uniform matter is connected with the EOS by Shen et al., in which formation of finite nuclei is included in the Thomas-Fermi approximation. In the present EOS, the maximum mass of neutron stars decreases from 2.17 M_sun (Ne mu) to 1.63 M_sun (NYe mu) when hyperons are included. In a spherical, adiabatic collapse of a 15$M_\odot$ star by the hydrodynamics without neutrino transfer, hyperon effects are found to be small, since the temperature and density do not reach the region of hyperon mixture, where the hyperon fraction is above 1 % (T > 40 MeV or rho_B > 0.4 fm^{-3}).Comment: 23 pages, 6 figures (Fig.3 and related comments on pion potential are corrected in v3.

TGF-β type II receptor expression in thymic epithelial cells inhibits the development of Hassall's corpuscles in mice

TGF-βRII signaling prevents the development of Hassall's corpuscle