JViz.Rna--a Java tool for RNA secondary structure visualization.

Many tools have been developed for visualization of RNA secondary structures using a variety of techniques and output formats. However, each tool is typically limited to one or two of the visualization models discussed in this paper, supports only a single file format, and is tied to a specific platform. In order for structure prediction researchers to better understand the results of their algorithms and to enable life science researchers to interpret RNA structure easily, it is helpful to provide them with a flexible and powerful tool.jViz.Rna is a multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file formats. The same structure can be viewed using any of the models supported, including linked graph, circle graph, dot plot, and classical structure. Also, the output is dynamic and can easily be further manipulated by the user. In addition, any of the drawings produced can be saved in either the EPS or PNG file formats enabling easy usage in publications and presentations.

A permutation-based genetic algorithm for the RNA folding problem: a critical look at selection strategies, crossover operators, and representation issues.

This paper presents a Genetic Algorithm (GA) to predict the secondary structure of RNA molecules, where the secondary structure is encoded as a permutation. More specifically, the proposed algorithm predicts which specific canonical base pairs will form hydrogen bonds and build helices, also known as stems. Since RNA is involved in both transcription and translation and also has catalytic and structural roles in the cell, determining the structure of RNA is of fundamental importance in helping to determine RNA function. We introduce a GA where a permutation is used to encode the secondary structure of RNA molecules. We discuss results on RNA sequences of lengths 76, 210, 681, and 785 nucleotides and present several improvements to our algorithm. We show that the Keep-Best Reproduction operator has similar benefits as in the traveling salesman problem domain. In addition, a comparison of several crossover operators is provided. We also compare the results of the permutation-based GA with a binary GA, demonstrating the benefits of the newly proposed representation.

The design and synthesis of selective prostaglandin analogs as bone anabolic agents for the potential treatment of osteoporosis.

A series of prostaglandins selective for the human FP receptor have been synthesized and evaluated as potential therapeutics for the treatment of osteoporosis. The compounds proved to be potent (nanomolar binding affinity) and selective (> 100x) ligands for the human FP receptor in vitro, and increased bone volume in the ovariectomized rat in vivo.

Effect of the Normal Microflora on Survival of Salmonella typhimurium Inoculated into a Hydroponic Nutrient Solution.

Salmonella typhimurium (ATCC 14028) was inoculated into nutrient solution collected from a hydroponic lettuce farm. The objective was to determine the effect of the presence or absence of the normal microflora of the nutrient solution on growth and persistence of Salmonella . In the unsterilized nutrient solution, Salmonella did not exceed 104 CFU ml-1, even when introduced at that concentration in the presence of a starting total aerobic count of 103 CFU ml-1 for the normal flora. Growth of Salmonella appeared to be suppressed, while that of the normal flora was unaffected and reached the usual level of 105 - 106 CFU ml-1 by 24 h. The normal microflora apparently restricted growth of Salmonella , and by 48 h after its introduction, Salmonella counts were decreasing. Salmonella inoculated into filter-sterilized nutrient solution grew rapidly to as high as 108 CFU ml-1, demonstrating that the nutrient solution contained the elements necessary to promote exponential growth of the bacterium. However, the fact that these levels were not achieved in the presence of other organisms, strongly suggests that Salmonella could not compete favorably with the normal flora of the hydroponic system.