The chances of detecting life on Mars

AbstractMissions to Mars progressively reveal the past and present habitability of the red planet. The current priority for Mars science is the recognition of definitive biosignatures related to past or present life. Success of life detection missions requires choices of the best mission design, location on Mars and particular sample to be analyzed. It is essential therefore to incorporate as much information as possible into the mission planning stages to maximize the precious opportunities provided by robotic operation on Mars. Bayesian statistics allow us to accommodate the many unknowns associated with a mission that has yet to take place. We have used Bayesian statistics to reveal that although in situ missions are less complex the overall probabilities of a successful mission to detect biosignatures on Mars are higher for sample return. If a mission has been designed with safe landing and operation as a priority, recognizing and avoiding those samples that do not contain the target biosignature is the most important characteristic, while for a mission where the best possible samples have been targeted the probability that the sample contains the target biosignature and that it can be correctly detected is the most dominant issue. Usefully, Bayesian statistics can be used to evaluate the chances of detecting past or present life for missions to different landing sites on Mars. A comparative assessment of Eberswelde Crater and Gale Crater indicates a higher probability of success for the latter and the probabilities of success are consistently higher for the sample return mission variant. Bayesian statistics, therefore, can inform future Mars mission planning steps to help maximize the possibility of success

A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding

High-resolution structures reveal that yeast ribosomal protein L11 and its bacterial/archael homologs called L5 contain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer RNA (tRNA) T-loop. We call this the L11 ‘P-site loop’. Chemical protection of wild-type ribosome shows that that the P-site loop is inherently flexible, i.e. it is extended into the ribosomal P-site when this is unoccupied by tRNA, while it is retracted into the terminal loop of 25S rRNA Helix 84 when the P-site is occupied. To further analyze the function of this structure, a series of mutants within the P-site loop were created and analyzed. A mutant that favors interaction of the P-site loop with the terminal loop of Helix 84 promoted increased affinity for peptidyl-tRNA, while another that favors its extension into the ribosomal P-site had the opposite effect. The two mutants also had opposing effects on binding of aa-tRNA to the ribosomal A-site, and downstream functional effects were observed on translational fidelity, drug resistance/hypersensitivity, virus maintenance and overall cell growth. These analyses suggest that the L11 P-site loop normally helps to optimize ribosome function by monitoring the occupancy status of the ribosomal P-site

A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site

Although the ribosome is mainly comprised of rRNA and many of its critical functions occur through RNA–RNA interactions, distinct domains of ribosomal proteins also participate in switching the ribosome between different conformational/functional states. Prior studies demonstrated that two extended domains of ribosomal protein L3 form an allosteric switch between the pre- and post-translocational states. Missing was an explanation for how the movements of these domains are communicated among the ribosome's functional centers. Here, a third domain of L3 called the basic thumb, that protrudes roughly perpendicular from the W-finger and is nestled in the center of a cagelike structure formed by elements from three separate domains of the large subunit rRNA is investigated. Mutagenesis of basically charged amino acids of the basic thumb to alanines followed by detailed analyses suggests that it acts as a molecular clamp, playing a role in allosterically communicating the ribosome's tRNA occupancy status to the elongation factor binding region and the peptidyltransferase center, facilitating coordination of their functions through the elongation cycle. The observation that these mutations affected translational fidelity, virus propagation and cell growth demonstrates how small structural changes at the atomic scale can propagate outward to broadly impact the biology of cell

High throughput structural analysis of yeast ribosomes using hSHAPE

Global mapping of rRNA structure by traditional methods is prohibitive in terms of time, labor and expense. High throughput selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) bypasses these problems by using fluorescently labeled primers to perform primer extension reactions, the products of which can be separated by capillary electrophoresis, thus enabling long read lengths in a cost effective manner. The data so generated is analyzed in a quantitative fashion using SHAPE Finder. This approach was used to map the flexibility of nearly the entire sequences of the 3 largest rRNAs from intact, empty yeast ribosomes. Mapping of these data onto near-atomic resolution yeast ribosome structures revealed the binding sites of known trans-acting factors, as well as previously unknown highly flexible regions of yeast rRNA. Refinement of this technology will enable nucleotide-specific mapping of changes in rRNA structure depending on the status of tRNA occupancy, the presence or absence of other transacting factors, due to mutations of intrinsic ribosome components or extrinsic factors affecting ribosome biogenesis or in the presence of translational inhibitors

Low Red Blood Cell Vitamin C Concentrations Induce Red Blood Cell Fragility: A Link to Diabetes Via Glucose, Glucose Transporters, and Dehydroascorbic Acid

Strategies to prevent diabetic microvascular angiopathy focus on the vascular endothelium. Because red blood cells (RBCs) are less deformable in diabetes, we explored an original concept linking decreased RBC deformability to RBC ascorbate and hyperglycemia. We characterized ascorbate concentrations from human and mouse RBCs and plasma, and showed an inverse relationship between RBC ascorbate concentrations and deformability, measured by osmotic fragility. RBCs from ascorbate deficient mice were osmotically sensitive, appeared as spherocytes, and had decreased β-spectrin. These aberrancies reversed with ascorbate repletion in vivo. Under physiologic conditions, only ascorbate's oxidation product dehydroascorbic acid (DHA), a substrate for facilitated glucose transporters, was transported into mouse and human RBCs, with immediate intracellular reduction to ascorbate. In vitro, glucose inhibited entry of physiologic concentrations of dehydroascorbic acid into mouse and human RBCs. In vivo, plasma glucose concentrations in normal and diabetic mice and humans were inversely related to respective RBC ascorbate concentrations, as was osmotic fragility. Human RBC β-spectrin declined as diabetes worsened. Taken together, hyperglycemia in diabetes produced lower RBC ascorbate with increased RBC rigidity, a candidate to drive microvascular angiopathy. Because glucose transporter expression, DHA transport, and its inhibition by glucose differed for mouse versus human RBCs, human experimentation is indicated

doi:10.1093/nar/gkm654 Sequence specific detection of DNA using nicking

endonuclease signal amplification (NESA