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Microarrays: Experimental Design, Data Processing, and Information Generation
Summary: David Walt develops new array technologies and uses them to collect large amounts of data that can be used to understand fundamental aspects of genetics and cell biology. His HHMI project will integrate this experience into undergraduate research, teaching, and outreach efforts and will make scientific research accessible to students who would not normally have the opportunity.
Project Summary
In the first project, undergraduates will engage in intensive multiyear research projects. We generate huge data sets in our research with living cell arrays. Computer science majors will work with graduate student and postdoctoral researchers to develop new methods for analyzing single-cell array data. The goal of this project is to train undergraduates in contemporary methods for analyzing complex biological data and to prepare them for continued studies and work in bioinformatics.
The second project will enlist undergraduates, graduate students, and postdoctoral associates in a collaborative effort to develop outreach materials with a focus on modern chemical biology methods. Our goal is to develop course materials for conducting all aspects of a modern microarray experiment—a type of experiment that typically requires sophisticated and expensive instrumentation. We aim to develop simpler materials that can be used in many different learning environments, including undergraduate courses and K-12 classrooms. Students at all levels—graduate students, undergraduate students, and high school students—will serve as mentors in the project. Undergraduates and K-12 students will learn the excitement of working in a multidisciplinary field and will gain direct knowledge about contemporary research methods as well as the ethical and societal issues surrounding the use of genetic analysis technologies.
The third project will integrate modern experiments in chemical biology into the undergraduate course in organic chemistry. Students will learn how organic chemistry applies to modern drug discovery in a team-learning environment. We aim to give students an appreciation of how modern research is conducted and how science is actually carried out with teams of workers who collaborate on a common goal. In addition, the project will underscore the importance of integrating many scientific and technical fields (chemistry, biology, engineering). Finally, we will develop an undergraduate/graduate course in bioanalytical chemistry that focuses on new methods of analysis.
Research Summary
Our research is in the field of sensors and biosensors, with a particular focus in the area of fiber-optic sensors and arrays. Work in our laboratory has led to new methods for creating high-density sensor arrays, including arrays based on living cells for functional screening, arrays based on principles of the olfactory system, and arrays for studying microbial and mammalian genetics. Our research in the field of optical sensors has led to the elucidation of fundamental principles as well as important applications of sensors and arrays.
A number of studies are being carried out for maximizing the types of information that can be obtained from array experiments. One project is aimed at developing new and efficient ways for identifying and characterizing microorganisms, such as their propensity for pathogenesis and their antibiotic resistance. New approaches to producing phylogenetic trees are being implemented using these array-based methods in conjunction with data analysis. A second project aims to develop new methods for looking at stochastic processes. In this project, we are developing arrays that can isolate individual cells or molecules. These isolated cells and molecules exhibit properties that are very different from their ensemble mean. This work is leading to a better understanding of the behavior of collections of molecules and populations of cells. We are also developing hybrid systems by integrating arrays with microfluidics and by combining optical and electrical transducers to improve the ability to collect greater amounts of data from experiments.
Last updated September 2006
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