With our 2006 HHMI professor grant, we established the Rainforest Expedition and Laboratory (REAL), a three-part program that introduces undergraduates to research by giving them an opportunity to discover novel microorganisms and potentially beneficial bioactive products. The central premise of REAL is that biological and chemical diversity is an engaging way for novice scientists to make original and useful observations about the natural world.
Our focus is on endophytes, microorganisms that live on healthy plants. Estimates suggest there are more than one million endophytic fungi, only a small fraction of which have been characterized. So students have an opportunity to identify not only new a species but perhaps a new genus.
REAL begins with a spring semester course that prepares students for the expedition and subsequent laboratory research. Topics include the botany, ecology, microbiology, plant and microbe taxonomy, chemical characterization of natural products, molecular and structural analysis, and commercial product development. Students come up with a plant-related research question based on their scientific interests and develop a research plan to address that question. They are required to find a Yale professor who can suggest assays to screen for compounds related to their research. The students spend spring break on a two-week expedition to the Amazonian rain forest in South America, where they collect plant samples.
Back on campus, the students use the samples to culture new microorganisms in a summer laboratory course. They become the experts on the new organisms they culture, isolate, characterize, and name. They screen these microbes for molecules that could have beneficial applications for human health or sustaining healthy ecosystems. One student in the program sought to identify compounds for treating Alzheimer’s disease. Another explored the ability of endophytes to degrade plastic. Since 2006, almost 70 students from three institutions—Yale, the Catholic University in Ecuador and Montana State University—participated in the program. We collected more than 1,200 plant samples and isolated about 1,500 endophytes. Many of these are new species and several are from a new genus. In the process of doing field and lab work, the students learned about biodiversity, the process of scientific inquiry, and the open-ended possibilities still available for scientific investigation.
Because it is unlikely that their research can be completed during the summer, students have the option of continuing their work over subsequent semesters in Yale laboratories. Of the 43 students who could continue their research projects after the summer course, 40 elected to do so. Research from the REAL program has resulted in eight papers in journals, including PLoS ONE, Microbial Ecology, and Nature Chemical Biology. Additionally, data collected by REAL students provided preliminary data for six grant applications involving their faculty collaborators. More than 50 percent of the students who participated in REAL pursued Ph.D. or M.D./Ph.D. degrees, a rate that is five times higher than the typical rate of Ph.D. pursuit among graduating Yale science students. These results indicate that the REAL model for undergraduate student research can impact student outcomes.
With our new HHMI funding, we will continue REAL expeditions and endophyte research with a total of 64 Yale undergraduates over the next four years. We will continue our focus on sophomore students and will work to maintain diversity in our program, including approximately 20% from groups underrepresented in the sciences and 50% women, which exceeds the current representation in the Yale student population. Students will be encouraged to publish at least one paper and present their work at a local or national meeting. Our goals are for all REAL students to graduate with a science degree, and the majority of graduates to pursue scientific research through doctoral, medical, or M.D./Ph.D. programs.
We will also disseminate the principles of the program to other institutions. Even the most novice scientist can collect plant samples and culture microbes. That, coupled with the diversity of endophytes and abundance of those remaining to be characterized, makes REAL a program that can be adapted to many learning environments. To test the dissemination process, we have established partnerships with the University of Texas at Austin, Miami University of Ohio, Catholic University of Ecuador, and The Johns Hopkins University School of Medicine. We hope to identify other partners in subsequent years. We plan to produce a program manual and related materials as resources for institutions wanting to implement a program like REAL.
HHMI Project-Related Publications
Strobel, S.A., and G. A. Strobel. "Plant Endophytes as a Platform for Discovery-based Undergraduate Science Education." Nature Chem. Biol. 3 (2007): 356-359.
Smith, S. A., et al. Bioactive Eendophytes Warrant Intensified Exploration and Conservation." PLoS ONE 3 (2008): e3052.
Bascom-Slack, C.A., et al. "Multiple, Novel Biologically Active Endophytic Actinomycetes Isolated from Upper Amazonian Rainforests." Microbial Ecology 58 (2009): 374-383.
Our laboratory investigates the structure and function of RNAs including ribozymes, the ribosome and riboswitches. We are interested in how RNA, which is composed of building blocks best suited for a role in storing genetic information, can catalyze biologically essential chemical reactions and bind selectively to small molecules. To explore this question, we use chemical, biochemical, and biophysical methods ranging from organic synthesis to x-ray crystallography. We have demonstrated that RNA uses catalytic strategies that are strikingly similar to those of proteins, including catalysis promoted by active-site metal ions and the use of catalytic cofactors. Using biological diversity discovered through the undergraduate REAL program, we are also exploring the enzymes responsible for biofuel production from cellulosic biomass.