PubMed · 8346427
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J I Brauman. 1993-08-13. Computing in science.. https://doi.org/10.1126/science.8346427
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In the past few years two fascinating and new scientific fields, the science of DNA-structure and topology and the theory of molecular computers have been growing independently. The main goal of this paper is to establish an interesting connection between them and to propose a novel paradigm for the future construction of DNA-computing devices based on supercoil energetics. The basic principle of the proposed model can also be applied to describe the communication between topologically closed segments in real genomes, which is believed to take part in the complex process of gene regulation. An implementation of the recent model is proposed by which polynomials of one real variable can be evaluated in a simple in vitro recombination assay.
The growth of yeast cells to high densities at low, but constant, oxygen concentrations is difficult because the cells themselves respire oxygen; hence, as cell mass increases, so does oxygen consumption. To circumvent this problem, we have designed a system consisting of a computer-controlled gas flow train that adjusts oxygen concentration in the gas flow to match cellular demand. It does this by using a proportional-integral-differential algorithm in conjunction with a three-way valve to mix two gases, adjusting their proportions to maintain the desired oxygen concentration. By modeling yeast cell yields at intermediate to low oxygen concentrations, we have found that cellular respiration declines with oxygen concentration, most likely because of a decrease in the expression of genes for respiratory proteins. These lowered rates of oxygen consumption, together with the gas flow system described here, allow the growth of yeast cells to high densities at low oxygen concentrations. This system can also be used to grow cells at any desired oxygen concentration and for regulated shifts between oxygen concentrations.
The complexity of genome data limits the usefulness of traditional database management systems. The highly interconnected structure of genome data can be captured in a data representation language based on the mathematical formalism of graphs. We have tailored graphs for describing genome data and have developed a database management system, called the Data Note System, for developing small databases to capture data from genome laboratories. To simplify the use of the Data Note System, a series of tools with graphical user interfaces has been developed. The system is designed to be easy to install and use by novice database developers with a minimal amount of computer expertise. We describe the tools and present examples of their use. The system consists of a storage facility, a schema editing tool to simplify the design of small databases, and three tools for data entry and querying.