Two PABPC1-binding sites in GW182 proteins promote miRNA-mediated gene silencing

Previous studies have suggested that the mechanism of miRNA-mediated silencing may differ between human and Drosophila cells. Here, a direct comparison demonstrates that the mechanism is conserved and the GW182–PABP interaction is required for silencing in vivo

Using a Crowdsourcing Knowledge Base to Support the Sustainability and Social Compromise Skill in Computer Science Engineering Studies

The Skill "Sustainability and Social Commitment" is commonly accepted as essential in today's world. However it proves tricky to introduce into the curriculum, mainly because of lack of knowledgeable teachers. To address this issue we present a knowledge base that brings together scientific articles, books, videos, compilations of data, experiences, etc., related to sustainability and knowledge areas associated with computer science engineering. This is a valuable tool that should provide to the teacher accurate and useful information in the research task of finding links between her course and the "Sustainability and Social Commitment" skill

Sub-harmonic resonant excitation of confined acoustic modes at GHz frequencies with a high-repetition-rate femtosecond laser

We propose sub-harmonic resonant optical excitation with femtosecond lasers as a new method for the characterization of phononic and nanomechanical systems in the gigahertz to terahertz frequency range. This method is applied for the investigation of confined acoustic modes in a free-standing semiconductor membrane. By tuning the repetition rate of a femtosecond laser through a sub-harmonic of a mechanical resonance we amplify the mechanical amplitude, directly measure the linewidth with megahertz resolution, infer the lifetime of the coherently excited vibrational states, accurately determine the system's quality factor, and determine the amplitude of the mechanical motion with femtometer resolution

A review on the clinical implementation of respiratory-gated radiation therapy

Respiratory-gated treatment techniques have been introduced into the radiation oncology practice to manage target or organ motions. This paper will review the implementation of this type of gated treatment technique where the respiratory cycle is determined using an external marker. The external marker device is placed on the abdominal region between the xyphoid process and the umbilicus of the patient. An infrared camera tracks the motion of the marker to generate a surrogate for the respiratory cycle. The relationship, if any, between the respiratory cycle and the movement of the target can be complex. The four-dimensional computed tomography (4DCT) scanner is used to identify this motion for those patients that meet three requirements for the successful implementation of respiratory-gated treatment technique for radiation therapy. These requirements are (a) the respiratory cycle must be periodic and maintained during treatment, (b) the movement of the target must be related to the respiratory cycle, and (c) the gating window can be set sufficiently large to minimise the overall treatment time or increase the duty cycle and yet small enough to be within the gate. If the respiratory-gated treatment technique is employed, the end-expiration image set is typically used for treatment planning purposes because this image set represents the phase of the respiratory cycle where the anatomical movement is often the least for the longest time. Contouring should account for tumour residual motion, setup uncertainty, and also allow for deviation from the expected respiratory cycle during treatment. Respiratory-gated intensity-modulated radiation therapy (IMRT) treatment plans must also be validated prior to treatment. Quality assurance should be performed to check for positional changes and the output in association with the motion-gated technique. To avoid potential treatment errors, radiation therapist (radiographer) should be regularly in-serviced and made aware of the need to invoke the gating feature when prescribed for selected patients

Electron-phonon interaction effects in semiconductor quantum dots: a non-perturbative approach

Multiphonon processes in a model quantum dot (QD) containing two electronic states and several optical phonon modes are considered by taking into account both intra- and nterlevel terms. The Hamiltonian is exactly diagonalized, including a finite number of multiphonon processes large enough to guarantee that the result can be considered exact in the physically important energy region. The physical properties are studied by calculating the electronic Green’s function and the QD dielectric function. When both the intra- and interlevel interactions are included, the calculated spectra allow several previously published experimental results obtained for spherical and self-assembled QD’s, such as enhanced two-LO-phonon replica in absorption spectra and up-converted photoluminescence to be explained. An explicit calculation of the spectral line shape due to intralevel interaction with a continuum of acoustic phonons is presented, where the multiphonon processes also are shown to be important. It is pointed out that such an interaction, under certain conditions, can lead to relaxation in the otherwise stationary polaron system.Fundação para a Ciência e a Tecnologia (FCT

MicroRNA159 Can Act as a Switch or Tuning MicroRNA Independently of Its Abundance in Arabidopsis

The efficacy of gene silencing by plant microRNAs (miRNAs) is generally assumed to be predominantly determined by their abundance. In Arabidopsis the highly abundant miRNA, miR159, acts as a molecular “switch” in vegetative tissues completely silencing the expression of two GAMYB-like genes, MYB33 and MYB65. Here, we show that miR159 has a diminished silencing efficacy in the seed. Using reporter gene constructs, we determined that MIR159 and MYB33 are co-transcribed in the aleurone and embryo of germinating seeds. However in contrast to vegetative tissues, MYB33 is not completely silenced. Instead, miR159 appears to shape the spatio-temporal expression pattern of MYB33 during seed germination. Transcript profiling in a time course during seed germination in wild-type and a mir159 mutant in which miR159 is almost absent, revealed that transcript levels of the GAMYB-like genes were similar between these two genotypes during germination, but much higher in the mir159 mutant once germination had completed. This attenuation in the silencing of the GAMYB-like genes was not explained by a decrease in mature miR159 levels, which remained constant at all time points during seed germination. We propose that miR159 acts as a tuner of GAMYB-like levels in Arabidopsis germinating seeds and that the activity of this miRNA is attenuated in the seed compared to vegetative tissues. This implies that the efficacy of miRNA-mediated silencing is not solely determined by miRNA abundance and target transcript levels, but is being determined through additional mechanisms

A novel class of microRNA-recognition elements that function only within open reading frames.

MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level. Multiple reports have also indicated the ability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function through similar mechanisms regardless of the locations of their sites of action. Here, we report a class of miRNA-recognition elements (MREs) that function exclusively in CDS regions. Through functional and mechanistic characterization of these 'unusual' MREs, we demonstrate that CDS-targeted miRNAs require extensive base-pairing at the 3' side rather than the 5' seed; cause gene silencing in an Argonaute-dependent but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences of miRNAs that target CDS versus the 3' UTR and suggest that CDS-targeted miRNAs may use a translational quality-control-related mechanism to regulate translation in mammalian cells

miR-122 activates hepatitis C virus translation by a specialized mechanism requiring particular RNA components

In animals, microRNAs (miRNAs) generally repress gene expression by binding to sites in the 3′-untranslated region (UTR) of target mRNAs. miRNAs have also been reported to repress or activate gene expression by binding to 5′-UTR sites, but the extent of such regulation and the factors that govern these different responses are unknown. Liver-specific miR-122 binds to sites in the 5′-UTR of hepatitis C virus (HCV) RNA and positively regulates the viral life cycle, in part by stimulating HCV translation. Here, we characterize the features that allow miR-122 to activate translation via the HCV 5′-UTR. We find that this regulation is a highly specialized process that requires uncapped RNA, the HCV internal ribosome entry site (IRES) and the 3′ region of miR-122. Translation activation does not involve a previously proposed structural transition in the HCV IRES and is mediated by Argonaute proteins. This study provides an important insight into the requirements for the miR-122–HCV interaction, and the broader consequences of miRNAs binding to 5′-UTR sites

Transiting exoplanets from the CoRoT space mission VIII. CoRoT-7b: the first Super-Earth with measured radius

We report the discovery of very shallow (DF/F = 3.4 10-4), periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which we interpret as due to the presence of a transiting companion. We describe the 3-colour CoRoT data and complementary ground-based observations that support the planetary nature of the companion. Methods. We use CoRoT color information, good angular resolution ground-based photometric observations in- and out- of transit, adaptive optics imaging, near-infrared spectroscopy and preliminary results from Radial Velocity measurements, to test the diluted eclipsing binary scenarios. The parameters of the host star are derived from optical spectra, which were then combined with the CoRoT light curve to derive parameters of the companion. We examine carefully all conceivable cases of false positives, and all tests performed support the planetary hypothesis. Blends with separation larger than 0.40 arcsec or triple systems are almost excluded with a 8 10-4 risk left. We conclude that, as far as we have been exhaustive, we have discovered a planetary companion, named CoRoT-7b, for which we derive a period of 0.853 59 +/- 3 10-5 day and a radius of Rp = 1.68 +/- 0.09 REarth. Analysis of preliminary radial velocity data yields an upper limit of 21 MEarth for the companion mass, supporting the finding. CoRoT-7b is very likely the first Super-Earth with a measured radius.Comment: Accepted in Astronomy and Astrophysics; typos and language corrections; version sent to the printer w few upgrade