Design and Fabrication of Forged Ti-6Al-4V Blocks with Synthetic Ti-N Inclusions for Estimation of Detectability by Ultrasonic Signal-To-Noise

In the work described subsequently, synthetic “hard alpha” inclusions have been fabricated within Ti-6A1-4V (Ti64) forgings. Several compositions of synthetic hard alpha were made by arc melting Ti sponge and TiN powder. Small solid cylinders of the titanium-nitrogen alloys were made by electro-discharge machining (e. d. m.) the arc-melted ingots to diameters of 0.031, 0.047, 0.062, and 0.078 inches, respectively, with heights equal to the respective diameter. Sets of eight or sixteen each identical cylinders were hot isostatic press (HIP) bonded within forged Ti64 blocks to yield uncracked inclusions with sharp interfaces with the Ti64 matrix. Detectability of the uncracked hard alpha was estimated as a function of flaw size, orientation, and nitrogen content from ultrasonic signal to noise ratios determined from C-Scan images of the blocks. Relationships of detectability to physical properties of hard alpha, and methodologies of signal to noise determinations are discussed

Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro

Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST) databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems, involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually arose because reverse transcriptase can switch templates during transcription^3^. Many newly identified, apparently trans-spliced, RNAs lacked canonical splice sites but were flanked by short regions of homology, leading us to question their authenticity. Here we report that all reported categories of non-canonical splicing could be replicated using an in vitro reverse transcription system with highly purified RNA substrates. We observed the reproducible occurrence of ostensible trans-splicing, exon shuffling and sense-antisense fusions. The latter generate apparent antisense non-coding RNAs, which are also reported to be abundant in humans^4^. Different reverse transcriptases can generate different products of template switching, providing a simple diagnostic. Many reported examples of splicing in the absence of canonical splicing signals may be artefacts of cDNA preparation

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle

Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders

Genome-wide allele- and strand-specific expression profiling

Recent reports have shown that most of the genome is transcribed and that transcription frequently occurs concurrently on both DNA strands. In diploid genomes, the expression level of each allele conditions the degree to which sequence polymorphisms affect the phenotype. It is thus essential to quantify expression in an allele- and strand-specific manner. Using a custom-designed tiling array and a new computational approach, we piloted measuring allele- and strand-specific expression in yeast. Confident quantitative estimates of allele-specific expression were obtained for about half of the coding and non-coding transcripts of a heterozygous yeast strain, of which 371 transcripts (13%) showed significant allelic differential expression greater than 1.5-fold. The data revealed complex allelic differential expression on opposite strands. Furthermore, combining allele-specific expression with linkage mapping enabled identifying allelic variants that act in cis and in trans to regulate allelic expression in the heterozygous strain. Our results provide the first high-resolution analysis of differential expression on all four strands of an eukaryotic genome

MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome

Defects of the translation apparatus in human mitochondria are known to cause disease, yet details of how protein synthesis is regulated in this organelle remain to be unveiled. Ribosome production in all organisms studied thus far entails a complex, multistep pathway involving a number of auxiliary factors. This includes several RNA processing and modification steps required for correct rRNA maturation. Little is known about the maturation of human mitochondrial 16S rRNA and its role in biogenesis of the mitoribosome. Here we investigate two methyltransferases, MRM2 (also known as RRMJ2, encoded by FTSJ2) and MRM3 (also known as RMTL1, encoded by RNMTL1), that are responsible for modification of nucleotides of the 16S rRNA A-loop, an essential component of the peptidyl transferase center. Our studies show that inactivation of MRM2 or MRM3 in human cells by RNA interference results in respiratory incompetence as a consequence of diminished mitochondrial translation. Ineffective translation in MRM2- and MRM3-depleted cells results from aberrant assembly of the large subunit of the mitochondrial ribosome (mt-LSU). Our findings show that MRM2 and MRM3 are human mitochondrial methyltransferases involved in the modification of 16S rRNA and are important factors for the biogenesis and function of the large subunit of the mitochondrial ribosome

The 65th Symposium of the Society for General Physiologists: Energizing research in mitochondrial physiology and medicine

The annual Society of General Physiologists (SGP) symposium has a six-decade legacy as the premier and innovative international meeting for physiologists, cell biologists, and biophysicists. During September 7–11th, 2011, more than 130 scientists participated in the 65th SGP symposium entitled “Mitochondrial Physiology and Medicine” at Woods Hole, MA. In a survey distributed at the end of the conference, participants ranked the overall science and quality of discussions very highly (average of 9.5 out of 10), with multiple respondents noting the highly collegial atmosphere, emphasis on unpublished research, and opportunity for younger scientists to interact with leaders in the field. Recent groundbreaking discoveries demonstrating the pivotal role of mitochondria in human physiology and disease have repositioned mitochondria to the center stage of biomedical research. Mitochondria serve as gatekeepers between cell survival and death, as well as regulate proper cell signaling, energy metabolism, redox balance, and ion homeostasis. Mitochondrial dysfunction is associated with numerous acute and chronic human diseases, including heart failure, ischemia-reperfusion injury, atherosclerosis, cardiomyopathy, stroke, neurodegeneration, diabetes, obesity, cancer, rare diseases, and aging. Clearly, the SGP’s selection of this year’s topic on mitochondrial physiology and disease was timely and fitting

MICU1 Controls Both the Threshold and Cooperative Activation of the Mitochondrial Ca(2+) Uniporter.

Mitochondrial Ca(2+) uptake via the uniporter is central to cell metabolism, signaling, and survival. Recent studies identified MCU as the uniporter\u27s likely pore and MICU1, an EF-hand protein, as its critical regulator. How this complex decodes dynamic cytoplasmic [Ca(2+)] ([Ca(2+)]c) signals, to tune out small [Ca(2+)]c increases yet permit pulse transmission, remains unknown. We report that loss of MICU1 in mouse liver and cultured cells causes mitochondrial Ca(2+) accumulation during small [Ca(2+)]c elevations but an attenuated response to agonist-induced [Ca(2+)]c pulses. The latter reflects loss of positive cooperativity, likely via the EF-hands. MICU1 faces the intermembrane space and responds to [Ca(2+)]c changes. Prolonged MICU1 loss leads to an adaptive increase in matrix Ca(2+) binding, yet cells show impaired oxidative metabolism and sensitization to Ca(2+) overload. Collectively, the data indicate that MICU1 senses the [Ca(2+)]c to establish the uniporter\u27s threshold and gain, thereby allowing mitochondria to properly decode different inputs