Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism

Polycistronic transcripts are considered rare in the human genome. Initiation of translation of internal ORFs of eukaryotic genes has been shown to use either leaky scanning or highly structured IRES regions to access initiation codons. Studies on mammalian viruses identified a mechanism of coupled translation termination-reinitiation that allows translation of an additional ORF. Here, the ribosome terminating translation of ORF-1 translocates upstream to reinitiate translation of ORF-2. We have devised an algorithm to identify mRNAs in the human transcriptome in which the major ORF-1 overlaps a second ORF capable of encoding a product of at least 50 aa in length. This identified 4368 transcripts representing 2214 genes. We investigated 24 transcripts, 22 of which were shown to express a protein from ORF-2 highlighting that 3' UTRs contain protein-coding potential more frequently than previously suspected. Five transcripts accessed ORF-2 using a process of coupled translation termination-reinitiation. Analysis of one transcript, encoding the CASQ2 protein, showed that the mechanism by which the coupling process of the cellular mRNAs was achieved was novel. This process was not directed by the mRNA sequence but required an aspartate-rich repeat region at the carboxyl terminus of the terminating ORF-1 protein. Introduction of wobble mutations for the aspartate codon had no effect, whereas replacing aspartate for glutamate repeats eliminated translational coupling. This is the first description of a coordinated expression of two proteins from cellular mRNAs using a coupled translation termination-reinitiation process and is the first example of such a process being determined at the amino acid level

Inferring the location of neurons within an artificial network from their activity

Inferring the connectivity of biological neural networks from neural activation data is an open problem. We propose that the analogous problem in artificial neural networks is more amenable to study and may illuminate the biological case. Here, we study the specific problem of assigning artificial neurons to locations in a network of known architecture, specifically the LeNet image classifier. We evaluate a supervised learning approach based on features derived from the eigenvectors of the activation correlation matrix. Experiments highlighted that for an image dataset to be effective for accurate localisation, it should fully activate the network and contain minimal confounding correlations. No single image dataset was found that resulted in perfect assignment, however perfect assignment was achieved using a concatenation of features from multiple image datasets

Ablation debris control by means of closed thick film filtered water immersion

The performance of laser ablation generated debris control by means of open immersion techniques have been shown to be limited by flow surface ripple effects on the beam and the action of ablation plume pressure loss by splashing of the immersion fluid. To eradicate these issues a closed technique has been developed which ensured a controlled geometry for both the optical interfaces of the flowing liquid film. This had the action of preventing splashing, ensuring repeatable machining conditions and allowed for control of liquid flow velocity. To investigate the performance benefits of this closed immersion technique bisphenol A polycarbonate samples have been machined using filtered water at a number of flow velocities. The results demonstrate the efficacy of the closed immersion technique: a 93% decrease in debris is produced when machining under closed filtered water immersion; the average debris particle size becomes larger, with an equal proportion of small and medium sized debris being produced when laser machining under closed flowing filtered water immersion; large debris is shown to be displaced further by a given flow velocity than smaller debris, showing that the action of flow turbulence in the duct has more impact on smaller debris. Low flow velocities were found to be less effective at controlling the positional trend of deposition of laser ablation generated debris than high flow velocities; but, use of excessive flow velocities resulted in turbulence motivated deposition. This work is of interest to the laser micromachining community and may aide in the manufacture of 2.5D laser etched patterns covering large area wafers and could be applied to a range of wavelengths and laser types

Seasonal flight activity of the ambrosia beetle, Trypodendron lineatum (Oliv.), for 1959, near Parksville, B.C.

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Seasonal flight activity of the ambrosia beetle, Trypodendron lineatum (Oliv.), for 1959, near Parksville, B.C.

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X-Ray Synchrotron Emitting Fe-Rich Ejecta in SNR RCW 86

Supernova remnants may exhibit both thermal and nonthermal X-ray emission. We present Chandra observations of RCW 86. Striking differences in the morphology of X-rays below 1 keV and above 2 keV point to a different physical origin. Hard X-ray emission is correlated fairly well with the edges of regions of radio emission, suggesting that these are the locations of shock waves at which both short-lived X-ray emitting electrons, and longer-lived radio-emitting electrons, are accelerated. Soft X-rays are spatially well-correlated with optical emission from nonradiative shocks, which are almost certainly portions of the outer blast wave. These soft X-rays are well fit with simple thermal plane-shock models. Harder X-rays show Fe K alpha emission and are well described with a similar soft thermal component, but a much stronger synchrotron continuum dominating above 2 keV, and a strong Fe K alpha line. Quantitative analysis of this line and the surrounding continuum shows that it cannot be produced by thermal emission from a cosmic-abundance plasma; the ionization time is too short, as shown both by the low centroid energy (6.4 keV) and the absence of oxygen lines below 1 keV. Instead, a model of a plane shock into Fe-rich ejecta, with a synchrotron continuum, provides a natural explanation. This requires that reverse shocks into ejecta be accelerating electrons to energies of order 50 TeV. We show that maximum energies of this order can be produced by radiation-limited diffusive shock acceleration at the reverse shocks.Comment: ApJ, accepted; full resolution images in http://spider.ipac.caltech.edu/staff/rho/rcw86chandra.p