Biological researchers wield some powerful new tools these days, capable of measuring minute quantities of DNA, protein and small molecules in living systems. Mapping the networks of the ebb and flow of these basic units of biomachinery is fundamental to the data-intensive disciplines of genomics, proteomics and metabolomics, which are helping revolutionize both biology and medicine.
But despite the wave of new insight that these techniques bring to bear on modern biological questions, Herrick Brown, the assistant curator of the College of Arts and Science's A.C. Moore Herbarium, knows that there are other, just-as-invaluable repositories of data stored in research institutions throughout the world.
And he's doing his part to make USC's vault of data accessible to the international research community.
The Herbarium houses more than 120,000 plant specimens, collected from the early 1800s to the present day. Since 2008, Brown, who earned both a bachelor's and master's degree at USC, has overseen the ongoing transfer of data associated with each specimen—scientific name, date of collection, geographic location and so forth—into an online portal, the Flora Caroliniana. It's a natural extension for a long-time naturalist. Growing up, Brown collected a menagerie of frogs, toads, turtles, snakes and guinea pigs, setting up racks of aquariums and vivariums in his parents' garage.
A modern shotgun sequencer can churn out a massive database of information, but it can never provide the snapshot in time that resources like the Herbarium preserve. "It's a physical record of a particular point in time," said Brown. "It proves that something was there at that time—and that, for example, it flowered in a certain location in a given month."
This kind of information is particularly relevant as climate and habitats change over time. "Plant behavior is tied very closely to climatological fluctuations and if you get a large enough dataset, you can address some very important questions," he said. "And within the herbaria throughout the U.S. we have a huge dataset."
Herbaria tend to largely represent local flora. Taken together, the holdings of the constellation of herbaria can be used to address much larger questions of biogeography. But access remains a problem.
"Traditionally, the researcher's work has involved this painstaking task of going to each individual herbarium, pulling the groups of specimens they're interested in, and poring over them individually one by one," said Brown. "But now with all the digitization efforts that have put so much information on the web, you can often get exactly what you want, very quickly."
USC's effort to move data online recently moved into overdrive. In the past year, the Herbarium team put more than 11,000 new entries into the Flora Carolinana, bringing the total number of records online to more than 80,000.
One source of the increased rate of progress was technical—better data entry systems are a constant quest for Brown as data manager. But just as important was the long-term contribution of undergraduate workers in the Herbarium.
Keith Mearns and Kendall Ackerman walked the commencement walk in May knowing that they had contributed to this internationally utilized resource on USC's campus.
For two years Mearns, an anthropology major with a minor in environmental studies, and Ackerman, who earned a Bachelor of Science in public health with a minor in hearing and speech disorders, entered data and worked to streamline the transfer of hand-written records of physical specimens into the Flora Caroliniana.
"Because they became so familiar with the programs, they discovered ways of more quickly making multiple entries that I wasn't aware of," said Brown.
And spending two years doing the work helped both Mearns and Ackerman understand the kinds of quirks that would sometimes arise and help refine the means of addressing them. "Some of our international specimens were collected in countries that don't even exist anymore, like Czechoslovakia," said Ackerman. "So we had to learn how to work through problems like that."
"The Herbarium has been very active over the past year," said curator John Nelson, "and Keith and Kendall deserve a lot of credit for that."
The Herbarium has also set up an online collaboration with Clemson University, whose plant collection in the state is second in size only to USC's. Together, the two universities offer a Flora Caroliniana that has been accessed from multiple countries on every continent except Antarctica.
For Brown, who worked for several years at the Smithsonian Institution before returning to USC, that kind of access is essential for being able to efficiently address essential scientific questions. He also works as an assistant botanist for the S.C. Department of Natural Resources, charged with finding, managing and monitoring populations of rare, threatened and endangered species. USC's Herbarium contains a detailed record of a number of plant species that have moved onto that list over the course of time—and even gone missing in the state.
"With 120,000 specimens, the Herbarium wasn't built in a day," said Brown. "All of the folks who did that hard work—went out and fed a bunch of mosquitoes and ticks while collecting the samples—they've made it possible to answer some very important questions today about species endangerment."
Explore further: A synthesis of the 36451 specimens from the UNEX Herbarium in a new data paper