Summary: My research interests include algorithmic processes in nature.  I am investigating the mechanism and capabilities of a natural molecular computing environment present in the single cell organisms, called ciliates. Ciliates have two types of nuclei per cell. One type is somatic and the other is germ line. The germ line nucleus is an encrypted version of the somatic nucleus. Following conjugation a copy of the new germ line nucleus is decrypted to form the new somatic nucleus. This decryption process can be manipulated to reliably yield predictable products, and the progress of the decryption process can be monitored under laboratory conditions.

Minimum Classes: N/A

Projects: One of the Summer 2015 projects focuses on investigating the computational capabilities of the ciliate decryption technology. Fellows working on this project will learn about a model for how the ciliate cellular machinery can process information to solve computational problems, and use this information to explore specific computational applications of the ciliate decryption capabilities. A second project for this summer involves analyzing DNA from the ciliate Oxytricha trifallax (Sterkiella histriomuscorum). The micronuclear genome sequencing project has produced large volumes of data. Preliminary analysis of this data has yielded a number of unexpected encryption patterns that at first glance seem incompatible with a current decryption model. A deeper analysis of the data is required to confirm whether there indeed is a discrepancy with the current model, and to then substantiate adapting the model. This project will require computer work. A third project for this summer involves studying specific DNA taken from various time points during the micronuclear decryption process of the ciliate Stylonychia lemnae. The objective is to read, in as much as it is possible, from the sampled time points, algorithmic steps taken by the ciliate decryption machinery towards decryption of micronuclear DNA and correlate the data with the results predicted by a model for the process. Students working on this project will learn how to determine from the model of the process what products ought to result during intermediate steps taken during decryption, how to design primers to search for these products in the available DNA, and how to align these intermediate products with the micronuclear and macronuclear template DNA. All these projects are a continuation of work conducted in summers 2011, 2012, 2013 and 2014 by undergraduate mathematics REU teams and an INBRE fellow (summer 2012) at Boise State University. Students do not need an advanced background in any of these areas to work on these projects. The main attributes needed are committed interest in the project(s), intelligent thinking and good work habits. Students working on these projects will orally present their work at a weekly research report meeting, at an undergraduate research symposium, and at the Idaho Conference on Undergraduate Research (in late July) at Boise State University.

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