An Improved Algorithm for RNA Secondary Structure Prediction

Though not as abundant in known biological processes as proteins,RNA molecules serve as more than mere intermediaries betweenDNA and proteins, e.g. as catalytic molecules. Furthermore,RNA secondary structure prediction based on free energyrules for stacking and loop formation remains one of the few majorbreakthroughs in the field of structure prediction. We present anew method to evaluate all possible internal loops of size at mostk in an RNA sequence, s, in time O(k|s|^2); this is an improvementfrom the previously used method that uses time O(k^2|s|^2).For unlimited loop size this improves the overall complexity ofevaluating RNA secondary structures from O(|s|^4) to O(|s|^3) andthe method applies equally well to finding the optimal structureand calculating the equilibrium partition function. We use ourmethod to examine the soundness of setting k = 30, a commonlyused heuristic

Gamow Shell-Model Description of Weakly Bound and Unbound Nuclear States

Recently, the shell model in the complex k-plane (the so-called Gamow Shell Model) has been formulated using a complex Berggren ensemble representing bound single-particle states, single-particle resonances, and non-resonant continuum states. In this framework, we shall discuss binding energies and energy spectra of neutron-rich helium and lithium isotopes. The single-particle basis used is that of the Hartree-Fock potential generated self-consistently by the finite-range residual interaction.Comment: 13 pages, 2 figures, presented by N. Michel at the XXVII Symposium On Nuclear Physics, Taxco, Guerrero, Mexico, January 5-8 200

Spectroscopy with random and displaced random ensembles

Due to the time reversal invariance of the angular momentum operator J^2, the average energies and variances at fixed J for random two-body Hamiltonians exhibit odd-even-J staggering, that may be especially strong for J=0. It is shown that upon ensemble averaging over random runs, this behaviour is reflected in the yrast states. Displaced (attractive) random ensembles lead to rotational spectra with strongly enhanced BE2 transitions for a certain class of model spaces. It is explained how to generalize these results to other forms of collectivity.Comment: 4 pages, 4 figure

miR-CATCH: microRNA capture affinity technology.

Several experimental methods exist to explore the microRNA (miRNA) regulome. These methods almost exclusively focus on multiple targets bound to a single, or perhaps a few miRNAs of interest. Here, we describe a microRNA capture affinity technology (miR-CATCH) which uses an affinity capture oligonucleotide to co-purify a single target messenger RNA (mRNA) together with all its endogenously bound miRNAs. This bench-top method is similar to RNA immunoprecipitation (RIP) and provides an experimental alternative to computational miRNA target prediction

First-forbidden mirror beta-decays in A=17 mass region

The first-forbidden beta-decay of 17Ne into the 'halo' state J=1/2+ of 17F presents one of the largest measured asymmetries for mirror beta-decay feeding bound final states. This asymmetry is studied in the framework of the Shell Model Embedded in the Continuum (SMEC). The spatial extent of single particle orbits is constrained by the proton capture cross-section 16O(p,gamma)17F calculated in SMEC . This allows to estimate the mirror symmetry breaking in 17F/17O and 17Ne/17N nuclei.Comment: 23 pages, 7 figures Misprints correcte

RNA secondary structure formation: a solvable model of heteropolymer folding

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as compared to conventional long handles constructs (approximately 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.Comment: Main paper: 20 pages and 6 figures. Supplementary Material: 25 page

Shell Model Monte Carlo studies of neutron-rich nuclei in the 1s-0d-1p-0f shells

We demonstrate the feasibility of realistic Shell-Model Monte Carlo (SMMC) calculations spanning multiple major shells, using a realistic interaction whose bad saturation and shell properties have been corrected by a newly developed general prescription. Particular attention is paid to the approximate restoration of translational invariance. The model space consists of the full sd-pf shells. We include in the study some well-known T=0 nuclei and several unstable neutron-rich ones around N=20,28. The results indicate that SMMC can reproduce binding energies, B(E2) transitions, and other observables with an interaction that is practically parameter free. Some interesting insight is gained on the nature of deep correlations. The validity of previous studies is confirmed.Comment: 22 pages + 7 postscript figure

Glassy transition in a disordered model for the RNA secondary structure

We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on the exact evaluation of the partition function.Comment: 4 pages, 3 figure

Sorting live stem cells based on Sox2 mRNA expression.

PMCID: PMC3507951This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+)SSEA1(+) cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+) cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(-) cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner