Transfer RNA genes experience exceptionally elevated mutation rates.

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at , and , respectively

Laser Light Sheet Flow Visualization of the Space Launch System Booster Separation Test

Planar flow visualizations were obtained in a wind tunnel test in the NASA Langley Research Centers Unitary Plan Wind Tunnel using the laser-light-sheet method. This method uses a laser to illuminate fine particles generated in the wind tunnel to visualize flow structures. The test article was designed to simulate the separation of the two solid rocket boosters (SRBs) from the core stage of the NASA Space Launch System (SLS) at Mach 4 using a scale model. The test was run on of the SLS Block 1B Cargo (27005) configuration and the SLS Block 1B Crew (28005) configuration. Planar flow visualization was obtained only on the crew configuration. Air at pressures up to 1500 psi was used to simulate plumes from the booster separation motors (BSMs) located at the nose, and aft skirt of the two boosters. The facility free stream was seeded with water vapor, which condensed and froze into small ice crystals in the tunnel nozzle expansion. A continuous wave green (532 nm) laser sheet was used to illuminate the ice crystals, and the resulting Mie-scattered light was collected with a camera. The resulting images clearly identify shock waves and other flow features including BSM plume shapes. Measurements were acquired for different BSM pressures and booster separation locations

The UCSC Archaeal Genome Browser

As more archaeal genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at , currently with 26 archaeal genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community

Space Launch System Booster Separation Supersonic Powered Testing with Surface and Off-Body Measurements

A wind tunnel test was run in the NASA Langley Unitary Plan Wind Tunnel simulating the separation of the two solid rocket boosters (SRB) from the core stage of the NASA Space Launch System (SLS). The test was run on a 0.9% scale model of the SLS Block 1B Cargo (27005) configuration and the SLS Block 1B Crew (28005) configuration at a Mach of 4.0. High pressure air was used to simulate plumes from the booster separation motors located at the nose and aft skirt of the two boosters. Force and moment data were taken on both SRBs and on the core stage. Schlieren still photos and video were recorded throughout testing. A set of points were acquired using Cross-correlation Doppler Global Velocimetry (CCDGV) readings to get 3 component velocity measurements between the core and the left-hand SRB. The CCDGV laser was utilized to record flow visualization in the same location, between the core and the left-hand SRB. Pressure Sensitive Paint data were taken on a separate set of runs. Computational Fluid Dynamics (CFD) runs were computed on a subset of the wind tunnel data points for comparison. A combination of the force/moment, CCDGV and Pressure Sensitive Paint (PSP) data (as well as schlieren images) at the CFD-specified test conditions will be used te the CFD simulations that will be used to build an SLS booster separation database flight conditions

Particle Image Velocimetry Applications Using Fluorescent Dye-Doped Particles

Polystyrene latex sphere particles are widely used to seed flows for velocimetry techniques such as Particle Image Velocimetry (PIV) and Laser Doppler Velocimetry (LDV). These particles may be doped with fluorescent dyes such that signals spectrally shifted from the incident laser wavelength may be detected via Laser Induced Fluorescence (LIF). An attractive application of the LIF signal is achieving velocimetry in the presence of strong interference from laser scatter, opening up new research possibilities very near solid surfaces or at liquid/gas interfaces. Additionally, LIF signals can be used to tag different fluid streams to study mixing. While fluorescence-based PIV has been performed by many researchers for particles dispersed in water flows, the current work is among the first in applying the technique to micron-scale particles dispersed in a gas. A key requirement for such an application is addressing potential health hazards from fluorescent dyes; successful doping of Kiton Red 620 (KR620) has enabled the use of this relatively safe dye for fluorescence PIV for the first time. In this paper, basic applications proving the concept of PIV using the LIF signal from KR620-doped particles are exhibited for a free jet and a twophase flow apparatus. Results indicate that while the fluorescence PIV techniques are roughly 2 orders of magnitude weaker than Mie scattering, they provide a viable method for obtaining data in flow regions previously inaccessible via standard PIV. These techniques have the potential to also complement Mie scattering signals, for example in multi-stream and/or multi-phase experiments

Characterization of Fluorescent Polystyrene Microspheres for Advanced Flow Diagnostics

Fluorescent dye-doped polystyrene latex microspheres (PSLs) are being developed for velocimetry and scalar measurements in variable property flows. Two organic dyes, Rhodamine B (RhB) and dichlorofluorescence (DCF), are examined to assess laser-induced fluorescence (LIF) properties for flow imaging applications and single-shot temperature measurements. A major interest in the current research is the application of safe dyes, thus DCF is of particular interest, while RhB is used as a benchmark. Success is demonstrated for single-point laser Doppler velocimetry (LDV) and also imaging fluorescence, excited via a continuous wave 2 W laser beam, for exposures down to 10 ms. In contrast, when exciting with a pulsed Nd:YAG laser at 200 mJ/pulse, no fluorescence was detected, even when integrating tens of pulses. We show that this is due to saturation of the LIF signal at relatively low excitation intensities, 4-5 orders of magnitude lower than the pulsed laser intensity. A two-band LIF technique is applied in a heated jet, indicating that the technique effectively removes interfering inputs such as particle diameter variation. Temperature measurement uncertainties are estimated based upon the variance measured for the two-band LIF intensity ratio and the achievable dye temperature sensitivity, indicating that particles developed to date may provide about +/-12.5 C precision, while future improvements in dye temperature sensitivity and signal quality may enable single-shot temperature measurements with sub-degree precision

Climate, wildfire, and erosion ensemble foretells more sediment in western USA watersheds

The area burned annually by wildfires is expected to increase worldwide due to climate change. Burned areas increase soil erosion rates within watersheds, which can increase sedimentation in downstream rivers and reservoirs. However, which watersheds will be impacted by future wildfires is largely unknown. Using an ensemble of climate, fire, and erosion models, we show that postfire sedimentation is projected to increase for nearly nine tenths of watersheds by \u3e10% and for more than one third of watersheds by \u3e100% by the 2041 to 2050 decade in the western USA. The projected increases are statistically significant for more than eight tenths of the watersheds. In the western USA, many human communities rely on water from rivers and reservoirs that originates in watersheds where sedimentation is projected to increase. Increased sedimentation could negatively impact water supply and quality for some communities, in addition to affecting stream channel stability and aquatic ecosystems

tRNA methylation resolves codon usage bias at the limit of cell viability.

Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3'-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival

Last months of life of people with intellectual disabilities: A UK population-based study of death and dying in intellectual disability community services.

BACKGROUND: Population-based data are presented on the nature of dying in intellectual disability services. METHODS: A retrospective survey was conducted over 18 months with a sample of UK-based intellectual disability service providers that supported over 12,000. Core data were obtained for 222 deaths within this population. For 158 (71%) deaths, respondents returned a supplemented and modified version of VOICES-SF. RESULTS: The observed death was 12.2 deaths per 1,000 people supported per year, but just over a third deaths had been deaths anticipated by care staff. Mortality patterns, place of usual care and availability of external support exerted considerable influence over outcomes at the end of life. CONCLUSION: Death is not a common event in intellectual disability services. A major disadvantage experienced by people with intellectual disabilities was that their deaths were relatively unanticipated. People with intellectual disabilities living in supported living settings, even when their dying was anticipated, experienced poorer outcomes