This spring semester, Visiting Assistant Professor Sarah Kingston launched a Computational Genomics course. Students learned both statistical theory and practical applications involved with analysis of genome-scale data.
After the long process of independently analyzing and interpreting omic-scale datasets, students tapped their creative, collaborative talents with a final science communication piece.
Students Rob Barron, Eileen Bates, Steve Cho, and Julia Michels created this fantastic stop-motion video to communicate how genomic research can help conserve fish species.
Bowdoin had a wonderful showing at the Benthic Ecology Meeting/Southeastern Estuarine Research Society meeting hosted in Myrtle Beach, SC over the past week.
Bowdoin Marine Science Semester Alums presented their independent and honors research at the meeting:
Alana Luzzio ’17 spoke on linking genes, environment, and phenotype in Gulf of Maine clam species; Aidan Coyle ’17 talked on physiological and genetic differences between two types of invasive green crabs; and Sam Walkes ’18 presented a poster on adaptive coloration in a species of Gulf of Maine intertidal snail.
Director of Coastal Studies Center Dave Carlon presented work on movement of genes between invasive green crab lineages.
Aidan Coyle won the meeting-wide prize for best undergraduate student talk.
Warm thoughts on a cold day: The Bowdoin Marine Science Semester (BMSS) didn’t slow down upon return from the Kent Island Field Station. Biological Oceanography, taught by Coastal Studies Scholar Bobbie Lyons, was the first module undertaken. Closely on its heels, Marine Benthic Ecology followed, where the classroom shifted to more distant field locations. The first Benthic stop was the Sea of Cortez and Baja California, Sur. BMSS students and faculty spent 10 days in the field learning how to identify tropical fish and invertebrates to collect abundance data on newly installed transects. The data collected renders the first season of a long-term monitoring effort focused on reef communities. After the tropical adventure, the BMSS had a quick turnaround – back in the States only 24 hours – and swapped out shorts for warmer gear to head to Hurricane Island in Maine’s Penobscot Bay. Over the 4-day duration on Hurricane, the BMSS students and faculty conducted transect surveys of the rocky intertidal, took a lab practical focused on rocky intertidal organisms, and started an introduction to molecular ecology.
The Bowdoin Marine Science Semester (BMSS) kicked off the Fall 2016 semester by leaving the country on the first day of class. BMSS students and instructors visited Bowdoin Scientific Station on Kent Island off Grand Manan, New Brunswick, Canada. Off-grid and 5 miles out to sea, students learned about the unique Bay of Fundy ecosystem, collected data for a long-term intertidal monitoring project, and collected Littorine snails for genomic analysis later in the semester.
The Bowdoin Marine Science Semester (BMSS) started off the 2016 Fall semester with a pre-semester “bootcamp” to learn scientific field techniques, species identification, boat handling and safety skills, statistical analysis, and experimental design. BMSS students camped for a week at the Coastal Studies Center. Activities included an oceanographic cruise on the University of Maine’s R/V Ira C, a bio-blitz on Bailey’s Island at the Giant’s Stairs, intertidal monitoring on Wyer’s Island, and seine netting at the CSC.
Alana Luzzio, ’17, is featured on the Bowdoin website for her research on Gulf of Maine bivalves. Luzzio is working in collaboration with both Dr. Sarah Kingston and Dr. David Carlon on her project. (photo, right: S. Kingston)
This spring (2016), the Coastal Studies Center hosted the students of EOS2625: Ocean Acidification as they conducted semester-long acidification experiments examining both larval and adult stages of the local green sea urchin. The course was co-taught by Visiting Assistant Professor Meredith White, a researcher who also served on the Maine Ocean Acidification Commission, and marine sciences Laboratory Instructor Elizabeth Halliday Walker.
Human emissions of carbon dioxide are causing acidification of the ocean at a rate unprecedented in the geologic record, and consequently changing ocean chemistry in ways that may present challenges for many marine organisms. In addition to lowering pH, the changes in carbonate chemistry are making it more difficult for organisms to build calcium carbonate shells or skeletal structures. Because the spines, jaws, and internal skeletal structure of sea urchins are all composed of calcium carbonate, there is some concern about how these organisms will fare in the future.
To investigate the effects of ocean acidification on sea urchin growth and chemical composition, adult urchins were kept in two flow-through seawater tanks at the Coastal Studies Center for two months. In one tank, carbon dioxide was bubbled into the water to maintain a pH approximately 0.5pH units lower than the ambient seawater.
Students measured physiological stress over time by seeing how long it took for urchins to right themselves after being flipped over, and measured weight gain over the course of the experiment. To measure calcification during the experiment, Biology Professor Amy Johnson and Research Associate Olaf Ellers shared a unique method they have used in past research on sea urchins. The students injected the urchins with tetracycline at the beginning of the experiment, and because tetracycline binds to calcium, it gets incorporated into any new skeletal structures that are actively being synthesized. Tetracycline has the additional benefit of fluorescing under certain wavelengths of light, so at the end of the experiment the skeletal structures could be photographed under the epifluorescent microscope to visualize a fluorescent band of growth and measure exactly how much the jaws had grown since the beginning of the experiment.
With help from EOS Professor Emily Peterman, students were also able to assess the chemical composition of the carbonate structures using a brand new scanning electron microscope with energy-dispersive X-ray spectroscopy (EDS). In addition to changes in chemical composition, the electron microscope also revealed the beautiful complexity of the sea urchin skeletal structures, which raised many more questions about calcification!
Finally, sea urchins were spawned to conduct a similar experiment on larvae. In many organisms, larvae are more sensitive to changes in the environment. The spaceship-like sea urchin larvae grow skeletal rods as they develop, which are also calcium carbonate, and students found that larvae reared in high-CO2 conditions had shorter skeletal rods.
The culturing techniques made possible by the facilities at the Coastal Studies Center, and the ability to conduct realistic ocean acidification experiments by manipulating pH with carbon dioxide, were essential to the success of the course and helped reveal the complexities of this growing field of research. Most of all, the interdisciplinary collaboration within the course sparked many new lines of inquiry, and revealed how big problems can be attacked in myriad complementary ways.