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A combination of algorithms to search RNA sequence for the potential for secondary structure formation, and search large numbers of sequences for structural similarity, were used to search the 5'UTRs of annotated genes in the Escherichia coli genome for regulatory RNA structures. Using this approach, similar RNA structures that regulate genes in the thiamin metabolic pathway were identified. In addition, several putative regulatory structures were discovered upstream of genes involved in other metabolic pathways including glycerol metabolism and ethanol fermentation. The results demonstrate that this computational approach is a powerful tool for discovery of important RNA structures within prokaryotic organisms.

In this work, we describe a strategy for the detection and characterization of microorganisms associated with a potential biological warfare attack or a natural outbreak of an emerging infectious disease. This approach, termed TIGER (Triangulation Identification for the Genetic Evaluation of Risks), relies on mass spectrometry-derived base composition signatures obtained from PCR amplification of broadly conserved regions of the microbial genome(s) in a sample. The sample can be derived from air filtration devices, clinical samples, or other sources. Core to this approach are “intelligent PCR primers” that target broadly conserved regions of microbial genomes that flank variable regions. This approach requires that high-performance mass measurements be made on PCR products in the 80–140 bp size range in a high-throughput, robust modality. As will be demonstrated, the concept is equally applicable to bacteria and viruses and could be further applied to fungi and protozoa. In addition to describing the fundamental strategy of this approach, several specific examples of TIGER are presented that illustrate the impact this approach could have on the way biological weapons attacks are detected and the way that the etiologies of infectious diseases are determined. The first example illustrates how any bacterial species might be identified, using Bacillus anthracis as the test agent. The second example demonstrates how DNA-genome viruses are identified using five members of Poxviridae family, whose members includes Variola virus, the agent responsible for smallpox. The third example demonstrates how RNA-genome viruses are identified using the Alphaviruses (VEE, WEE, and EEE) as representative examples. These examples illustrate how the TIGER technology can be applied to create a universal identification strategy for all pathogens, including those that infect humans, livestock, and plants.

Quantitative measurements of second harmonic and first harmonic Doppler were carried out using two ultrasound contrast agents, Albunex ® and FS069. The RMS amplitudes of the Doppler shift spectra were measured as a function of the concentration of the agents, frequency and transmitted acoustic pressure. The results showed that, for a given lot of contrast agent investigated, FS069 was able to produce higher levels of first and, especially, second harmonic signals compared to Albunex. Under the same experimental conditions, the RMS Doppler amplitude (RDA) of FS069 was 3.8 ± 0.8 dB higher than Albunex at first harmonic and 12.6 ± 0.8 dB higher at second harmonic. The ratio of the second harmonic to first harmonic RDA, which we called R2R1, decreases at a rate of 7 dB/MHz for both agents with increasing frequency. The difference in the value of R2R1 between FS069 and Albunex at any frequency was approximately 4.5 dB. R2R1 was found to increase linearly as a function of the transmitted acoustic pressure for both agents. Simulations using the Rayleigh-Plesset equation show a decrease of R2R1 at a rate of 5 dB/MHz. Comparison of experimental results with theory indicates that the shell elasticity parameter may be an increasing function of the mean diameter of the bubbles.

We report the first measurement of rotationally and vibrationally product-state-resolved absolute cross sections for H+H 2 and H+D 2 collisions. There is generally good agreement between these experimentally determined partial reaction cross sections and those that result from quasiclassical trajectory calculations.