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Although the ribosome is a very general catalyst, it cannot synthesize all protein sequences equally well. Certain proteins are capable of stalling the ribosome during their own synthesis. Stalling events are used by both prokaryotic and eukaryotic cells to regulate gene expression. Characterization of natural stalling peptides shows that only a few strategically placed amino acids are needed to inactivate the ribosome. These motifs share little sequence similarity suggesting that there are more stalling motifs yet to be discovered. Here we use two genetic selections in E. coli to discover novel stalling peptides and detail their subsequent characterization. Kinetic studies show that some of these nascent peptides dramatically inhibit rates of peptide release by release factors. We find that residues upstream of the minimal stalling motif can either enhance or suppress this effect. In other stalling motifs, such as polyproline sequences, peptidyl transfer to a subset of aminoacyl-tRNAs is inhibited. Translation factor EF-P alleviates pausing of the polyproline motifs, but has little or no effect on other stalling sequences. The EF-P ortholog eIF5A also alleviates pausing of polyproline sequences in yeast. Our studies show that short peptides sequences are capable of stalling the ribosome during elongation and termination through different mechanisms. These sequences are underrepresented in bacterial proteomes and show evidence of stalling on endogenous E. coli proteins.

Research has been conducted in recent years to determine the dynamic behavior of aircraft in unusual flight attitudes, particularly at very high angle-of-attack or post-stall conditions. The possibility that future advanced fighter aircraft will have the ability to perform controlled maneuvers at such attitudes is indicated by the current military aircraft flying qualities specification, MIL-STD-1797. As it becomes more important to understand the dynamics of aircraft at such flight conditions, the need for a meaningful and useful assessment of aircraft departure resistance in varying attitudes will increase proportionally. This thesis surveys some of the measures of departure susceptibility currently in use and examines a candidate for a new departure resistance criterion which offers distinct advantages over the traditional metrics. The new departure resistance criterion, called DP_SSV is essentially a measure of how much uncertainty the nominally stable plant can tolerate before being driven unstable. DP_SSV is calculated using structured singular values. In this thesis, DP_SSV is calculated over various flight conditions for a typical high-performance fighter aircraft which is represented by a full six degree of freedom, nonlinear simulation. The results are compared with those obtained by using a traditional departure susceptibility metric and by examining the eigenvalues of linearized forms of the aircraft model. The new criterion DP_SSV is shown to provide more information about the departure susceptibility of an aircraft than C_{ηβ_DYN} traditional metric, and to produce results in good agreement with the eigenvalue analysis of the stability of the aircraft for the conditions studied. The interpretation of DP_SSV is discussed, and suggestions for future investigation are also presented. / Master of Science

In this thesis, the Leishman-Beddoes method of determining airloads for an airfoil undergoing dynamic stall is studied over a range of Mach numbers. To validate the method for conditions where little experimental data is available, a computational fluid dynamics solver is utilized to provide airload predictions for comparison to the Leishman-Beddoes results. It is found that even for high Mach numbers the Leishman-Beddoes method provides reliable predictions for lift coefficient. However, at the higher Mach numbers pitching moment is sometimes overpredicted at high angle of attack. This is seemingly due to an inability to accurately determine the center of pressure in the high speed unsteady flow environment.

No description available.

Thesis (M.S.)--West Virginia University, 2005. / Title from document title page. Document formatted into pages; contains xiv, 86 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 73-76).

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Ribosomes stall on defective messenger RNA transcripts in eubacteria. Without a mechanism to release stalled ribosomes, these cells would die. Transfer-messenger RNA (tmRNA) and small protein B (SmpB) reactivate stalled ribosomes in a process known as trans-translation. Together, tmRNA and SmpB mimic alanyl-tRNA, entering the A site of stalled ribosomes and accepting transfer of the stalled polypeptide. A portion of tmRNA is then positioned as a template for the ribosome to resume translating. The tmRNA open reading frame encodes a proteolysis tag to mark the aberrant polypeptide for degradation and a stop codon to release the ribosome. How are tmRNA and SmpB allowed into stalled ribosomes? In normal translation, decoding mechanisms carefully monitor the anticodon of tRNAs entering the A site and select only those that are complementary to the mRNA codon. How do tmRNA and SmpB get around the decoding machinery? It appears that interactions between the SmpB C-terminal tail and the decoding center are responsible. Using an in vivo tagging assay and an in vitro peptidyl-transfer assay, we monitored the effect of mutations in the SmpB tail on trans-translation. We found that mutations in SmpB that prevent helix formation are unable to support peptidyl transfer. We also found that while mutation of key nucleotides in the ribosomal decoding center severely inhibit peptidyl transfer to normal tRNAs, these mutations do not inhibit peptidyl transfer to tmRNA. We conclude that the SmpB tail stimulates peptidyl transfer by forming a helix that interacts with the ribosome to signal decoding in a novel manner. How is the tmRNA open reading frame positioned for the ribosome to resume translating? Mutation of the tmRNA nucleotide A86 alters reading frame selection. Using a genetic selection, we identified SmpB mutants that restore normal frame selection to A86C tmRNA without altering frame selection on wild-type tmRNA. Through rational mutation of the SmpB tail we identified an SmpB mutant that supports peptidyl transfer but prevents translation of the tmRNA open reading frame. We conclude that SmpB plays a functional role in selecting the tmRNA open reading frame.

A one-dimensional, stage-by-stage axial compression system mathematical model has been constructed which can describe system behavior during post-stall events such as surge and rotating stall. The model uses a numerical technique to solve the nonlinear conservation equations of mass, momentum, and energy. Inputs for blade forces and shaft work are provided by a set of quasi-steady stage characteristics modified by a first order lagging equation to simulate dynamic stage characteristics. The model was validated with experimental results for a three-stage, low-speed compressor and a nine-stage, high-pressure compressor. Using these models, a parametric study was conducted to determine the effect of inlet resistance, combustor performance, heat transfer, and stage characteristic changes due to hardware modification on post—stall system behavior. / Ph. D. / incomplete_metadata

The ability of twelve distortion indices to predict stalling behavior in aircraft gas turbine engines was investigated using J85-GE-13 turbojet engine data, TF30-P-3 turbofan engine data, and modified T64-GE-6B compressor test-rig data. The indices were tested for correlation capability with constant speed loss in stall pressure ratio, constant mass loss in stall pressure ratio, and engine speed where appropriate. Predictive indices/models were compared directly with experimental data. In addition, the concept of including the effects of compressor dynamic response by modifying the inlet total pressure profile rather than the index was investigated. This was done by evaluating the accuracy of parallel compressor theory and two simple AP/P indices first using measured inlet total pressure data and then using modified or "effective" inlet total pressure profiles. A procedure was developed for deriving the effective inlet total pressure distribution from the measured distribution. / Master of Science