Upon returning to Yale, the young researchers prepared their specimens for bioactivity screening. They dissected them, culturing minute bits in plates containing growth medium as well as test organisms placed a couple of inches away. The students then waited to see what activity might emerge when the endophytes and their bioactive products proliferated and encountered the test organisms, which included a variety of plant pathogens as well as human-infecting bacteria and fungi. Among them were Candida albicans (a cause of many fungal infections, some now resistant to treatment), Escherichia coli (responsible for many types of infection), and Bacillus subtilis (widely used by researchers as a model organism).

When an endophyte or its products showed visible activity, the students put them through a battery of tests to isolate the source of their bioactivity. DNA samples from several microbes were sent to a Yale laboratory for sequencing. In several cases, the resulting data revealed bacteria and fungi whose genomes differ significantly from any known organism in GenBank, the annotated online collection of all publicly available DNA sequences maintained by the National Institutes of Health. Michelle Schorn, a junior from San Diego, is one of the students who found a novel bacterium. As a result, she says she expects, "to write a paper identifying it and what compounds are in it. Having a publication would be really exciting."

The students probed their microbes further. They grew them in liquid culture and extracted metabolites to look for the biologically active components. The crude extracts were also screened using a variety of biochemical assays. Those steps might include separating out individual molecules using chromatography, studying structure through crystallography, and applying other laboratory techniques to look for interesting and potentially beneficial properties.

As the students dug into their projects, Scott challenged them, "Anything your mind can imagine, go for it. Figure out the taxonomy and what is known. Look beyond that and see what's new. Then you have to decide what you're going for."

Kathleen Fenn may have already discovered something truly new—and potentially medically beneficial—in the rainforest. She collected a stem sample from a Capirona decorticans tree. She hypothesized that it might prove useful after she learned that Amazonian native tribes apply capirona-based concoctions for a variety of medicinal purposes including treating fungal infections, diabetes, and wounds. Back in New Haven, Fenn isolated a strain of pink-colored bacteria from it, which when cultured formed pink crystals on top of the test colonies. A Yale crystallographer identified those crystals as 2,4-diacetylphloroglucinol (DAPG), a broad-scale antibiotic produced by some strains of Pseudomonas fluorescens bacteria. Fenn's preliminary analysis shows that the bacterial strain she isolated produces DAPG on a scale several times greater than any previously reported. She plans to continue her research in hopes of demonstrating that this strain exhibits unprecedented efficiency in antibiotic production—and to learn more about its properties.

Fenn, like several other students in the class, intends to collaborate with various Yale laboratories to see if her molecules have any promising disease-modulating properties. In fact, a Yale School of Medicine scientist has already invited Schorn to screen the extracts she found using his cellular assay for potential Alzheimer's disease treatments. The undergraduates, most of whom expect to continue working on their projects during the current school year, are already thinking like advanced medical investigators, says Strobel.

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