Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements

BACKGROUND: Many computational microRNA target prediction tools are focused on several key features, including complementarity to 5'seed of miRNAs and evolutionary conservation. While these features allow for successful target identification, not all miRNA target sites are conserved and adhere to canonical seed complementarity. Several studies have propagated the use of energy features of mRNA:miRNA duplexes as an alternative feature. However, different independent evaluations reported conflicting results on the reliability of energy-based predictions. Here, we reassess the usefulness of energy features for mammalian target prediction, aiming to relax or eliminate the need for perfect seed matches and conservation requirement. METHODOLOGY/PRINCIPAL FINDINGS: We detect significant differences of energy features at experimentally supported human miRNA target sites and at genome-wide sites of AGO protein interaction. This trend is confirmed on datasets that assay the effect of miRNAs on mRNA and protein expression changes, and a simple linear regression model leads to significant correlation of predicted versus observed expression change. Compared to 6-mer seed matches as baseline, application of our energy-based model leads to ∼3-5-fold enrichment on highly down-regulated targets, and allows for prediction of strictly imperfect targets with enrichment above baseline. CONCLUSIONS/SIGNIFICANCE: In conclusion, our results indicate significant promise for energy-based miRNA target prediction that includes a broader range of targets without having to use conservation or impose stringent seed match rules

The System of Nanosecond 280-KeV He+ Pulsed Beam

At Fast Neutron Research Facility, the 150 kV-pulses neutron generator is being upgraded to a 280-kV-pulsed-He beam for time-of-flight Rutherford backscattering spectrometry. It involves replacing the existing beam line elements by a multicusp ion source, a 400-kV accelerating tube, 45{sup o}-double focusing dipole magnet and quadrupole lens. The multicusp ion source is a compact filament-driven of 2.6 cm in diameter and 8 cm in length. The current extracted is 20.4 {micro}A with 13 kV of extraction voltage and 8.8 kV of Einzel lens voltage. The beam emittance has found to vary between 6-12 mm mrad. The beam transport system has to be redesigned based on the new elements. The important part of a good pulsed beam depends on the pulsing system. The two main parts are the chopper and buncher. An optimized geometry for the 280 keV pulsed helium ion beam will be presented and discussed. The PARMELA code has been used to optimize the space charge effect, resulting in pulse width of less than 2 ns at a target. The calculated distance from a buncher to the target is 4.6 m. Effects of energy spread and phase angle between chopper and buncher have been included in the optimization of the bunch length

Investigations of the Supramolecular Structure of Individual Diphenylalanine Nano- and Microtubes by Polarized Raman Microspectroscopy

Polarized Raman microspectroscopy and atomic force microscopy were used to obtain quantitative information regarding the molecular structure of individual diphenylalanine (FF) nano- and microtubes. The frequencies of the Raman spectral bands corresponding to the amide I (1690 cm^–1) and amide III (1249 cm^–1) indicated that the FF-molecules interact by hydrogen bonding at the N–H and not at the CO sites. The calculated mean orientation angles of the principal axes of the Raman tensors (PARTs) obtained from the polarized Raman spectral measurements were 41 ± 4° for the amide I and 59 ± 5° for amide III. On the basis of the orientation of the PART for the amide I mode, it was found that the CO bond is oriented at an angle of 8 ± 4° to the tube axis. These values did not vary significantly with the diameter of the tubes (range 400–1700 nm) and were in agreement with the molecular structure proposed previously for larger crystalline specimens

MicroRNA target site identification by integrating sequence and binding information

High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute protein members can pinpoint microRNA target sites within tens of bases, but leaves the identity of the microRNA unresolved. A flexible computational framework that integrates sequence with cross-linking features reliably identifies the microRNA family involved in each binding event, considerably outperforms sequence-only approaches, and quantifies the prevalence of noncanonical binding modes