Science Communication with Computational Genomics

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.

Other creative projects included describing the role of long non-coding RNAs in cancer, microbial metagenomics and type II diabetes, gene expression-related health impacts of performance enhancing drugs, and microevolution in rapidly changing environments.

The final presentation even ended with interactive art (directed by students Nora Cullen, Pilar Giffenig, Sofi Lopez, Alana Luzzio, and Casey Silvernale).

Marine Science Semester Alums attend the 46th Benthic Ecology Meeting in Myrtle Beach, SC

Sam Walkes ’18, Aidan Coyle ’17, Dave, and Alana Luzzio “17 celebrate the success of the meeting.

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.

Aidan Coyle ’17and Sam Walkes ’18 meet acclaimed coral reef biologist Dr. Howard Lasker.

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.

Aidan Coyle ’17 wins best undergrad student presentation.

BMSS 2016 Independent Project Symposium 12/16/16

Welcome and Introduction (2:15pm)
Session 1: The Intertidal (2:30pm)

Testing desiccation stresses and visual predation as mechanisms for maintaining a potential color polymorphism cline (Sam Walkes ’18)

Is the European Periwinkle invasion really from Europe? (Caroline Carter ’19)

Saving the snails: how feeding preferences of Carcinus maenas on Littorina littorea may determine the survival of Ilyanassa obsoleta (Meret Beutler ’19)

Predation of the softshell clam Mya arenaria by the nemertean worm Cerebratulus lacteus (Elizabeth Givens ’17)

Session 2: Aquaculture and Fisheries (3:45pm)

Does Mytilus edulis ingest and process the microplastics in Harpswell Sound?                 (Anna Blaustein ’19)

Finding an Easy and Efficient Method of Growing Microalgage for Biofuel: The Effect of Difference in Light and Nitrogen on Phaeodactylum tricornutum Lipid Production         (Maya Morduch-Toubman ’18)

Multiple Species Interactions in Harpswell Sound Lobster Traps (Isaac Schuchat ’19)

Session 3: Ocean Acidification and Environmental Change (4:45pm) 

Fundulus heteroclitus lateralization efficacy in response to rising sea temperatures and ocean acidification (Jonathan Harrison ’19)

The Effects of Climate Change Stressors on the Sea Star, Asterias forbesi, Regeneration (Amber Rock ’19)

The Effects of Ocean Acidification on Shell Resource and Assessment Behavior of Hermit Crab Pagarus longicarpus (Jackie Ricca ’19)

The Effects of Eutrophication and Oxygen Depletion on Bioluminescence in the Tropical Dinoflagellate Pyrocystis lunula (Ripley Mayfield ’19)

Bowdoin Marine Science Semester Concluding Remarks (5:45-6:00pm)

Holiday Reception to Follow (6:00-9:00pm)

From Baja to Hurricane Island

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.

 

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#BMSS2016 observing Whale Sharks feeding in La Paz Bay #bowdoincollege

A post shared by Sarah Kingston (@scarletscience) on

 

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BMSS 2016 visits Bowdoin Scientific Station on Kent Island

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.

arriving on Kent Island
arriving on Kent Island

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Sheep Island
Sheep Island
whale stranding remains
whale stranding remains

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Jonah crabs hanging in the intertidal on Kent Island #BMSS2016 #bowdoincollege

A video posted by Sarah Kingston (@scarletscience) on


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setting up intertidal temperature data loggers
setting up intertidal temperature data loggers

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Kent Island intertidal transects
Kent Island intertidal transects

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dessert!
some post-dinner core work
some post-dinner core work
Littorina saxatilis on Kent Island
Littorina saxatilis on Kent Island

Green crab collection during #BMSS2016 field trip to Kent Island #bowdoincollege

A video posted by Sarah Kingston (@scarletscience) on

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Bowdoin Marine Science Semester off and running

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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.

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Bongo nets! #bowdoincollege #BMSS2016 #CoastalStudiesCenter on the UMaine RV Ira C

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Students learn new techniques out on the Ira C

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Plankton party! #BMSS2016 #bowdoincollege #CoastalStudiesCenter

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#BMSS2016 Bootcamp boat safety training #bowdoincollege

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Bio Blitz at Giant’s Stairs

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Snorkeling at Ash Point in Harpswell

#BMSS2016 students snorkeling at Ash Point #bowdoincollege

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Finding the bottom at Ash Point #BMSS2016 #bowdoincollege

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Seine net skills
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Intertidal transects on Wyer’s Island

 

Ocean acidification presents challenges for marine organisms

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.

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Experimental setup at the Coastal Studies Center.

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.

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After the adult urchin experiment was completed, students spawned urchins to study larval development

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.

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Nine-day-old sea urchin larvae

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.

Story written by Lab Instructor Elizabeth Walker