Collaborative marine science took a leap of global proportions on June 21, 2014. At carefully orchestrated times on that day, hundreds of scientists around the world collected ocean samples, using standardized protocols, as part of the first international Ocean Sampling Day (OSD). They were united by the goal of identifying the microbial communities in all the samples–no small task given that one drop of seawater contains about 20 million microbes.

This movie features MBL Associate Scientist Linda Amaral-Zettler, who took a lead role in OSD as a scientific adviser to the project’s European sponsor, MicroB3, and who actively sampled and helped coordinate sampling in the Azorean Islands. Building a knowledge base of marine microbes is critical for understanding the impact of global challenges to ocean health, such as a warming climate.

“Sampling is expensive,” Amaral-Zettler says. “The more we can leverage individual regional efforts and resources, the better we will be in protecting the ocean.”

As soon as they were collected, the samples were frozen and shipped to Max Planck Institute for Marine Microbiology in Bremen, Germany. The next step is to identify “who” are in the samples through DNA extraction and analysis.

OSD will take place again in 2015 and hopefully into the future, Amaral Zettler says, which would provide a long-term perspective on how marine microbial diversity changes over time. “We need to understand how things are changing in order to protect them.”

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By Wallace Marshall
Co-director, MBL Physiology Course

Last month, I had a problem. I was teaching in the MBL Physiology course, using the giant, single-celled organism Stentor as a model system for students to learn quantitative approaches in cell biology. Stentor, which live in ponds, eat by creating a vortex of water that drags food into the cell’s mouth. The flow is created by thousands of cilia—tiny, hair-like cell parts that swing back and forth pushing fluid around. (Cilia are also critical for making the mucus in your airway flow away from your lungs, and patients with defects in these cilia can be really sick. So the question of how cilia make fluid flow is very important from a medical perspective. )

Stentor is a genus of large, trumpet-shaped ciliates, commonly found in freshwater ponds. Credit: EOL / micro*scope

Stentor is a genus of large, trumpet-shaped ciliates, commonly found in freshwater ponds. Credit: EOL / micro*scope

One of the students in our class, Shashank Shekhar from the CNRS Institute, France, had become interested in how the cell generates this pattern of fluid flow. Shashank started tracking the flow by putting small plastic beads into the water around the Stentor and then taking video images of the beads moving. This is a pretty standard approach in fluid dynamics called particle image velocimetry (PIV). But it’s not that commonly used in biology, and we didn’t entirely know what we were doing. The software we had been trying to use to track these particles didn’t give really nice flow lines. So this was the problem: How to use the flow of these tiny beads to figure out the pattern of flow around the cell as it feeds.

Frustrated by this problem, I decided to go get some coffee from Woods Hole Market. On the way back, I ran into my colleague Magdalena Bezanilla, an MBL Whitman Investigator from University of Massachusetts, Amherst, who works on cell biology. She thinks a lot about things moving inside cells so I figured I could get her input into our PIV challenge.

We ended up chatting about the problem in the MBL’s Waterfront Park, and while we were talking, a couple of guys emerged from the harbor in full scuba gear, carrying a huge metal bracket upon which was mounted a video camera and a laser. (This would be quite weird back home but it’s business as usual in Woods Hole.) I asked the guys what they were up to and they said they were using PIV to study the flow of fluid around ctenophores! Ctenophores or comb jellies are jellyfish-like animals that swim using cilia. So at the exact moment that we were pondering how to use PIV to track cilia-generated fluid flow in our single-celled organisms in the Physiology course, a guy walks out of the water and announces that he is doing the exact same thing, for comb jellies! (Those people who say that Woods Hole is a magical place are telling the truth.)

The guys with the scuba gear and lasers were Jack Costello of Providence College and Sean Colin of Roger Williams University, Whitman Investigators working for the summer at the MBL. Jack offered to give us advice about how to analyze our data, so I sent Shashank over to Jack’s lab in the Rowe building. With Jack’s help and expertise, Shashank was able to get beautiful flow lines from his data (see photo), which clearly reveal the pattern of cilia-generated flow around the Stentor cell while it feeds. Our big problem was solved in a single day due to a fortuitous combination of people, courses, coffee breaks, cells, beaches, marine organisms, and advanced technology. And that’s what summer at the MBL is all about.

Fluid flow around Stentor visualized through particle image velocimetry. Courtesy of Wallace Marshall.

Fluid flow around Stentor as it feeds, visualized by particle image velocimetry. Courtesy of Wallace Marshall.

Thank you to Wallace Marshall of the University of California, San Francisco, for contributing this post. All MBL scientists, students, community members, and visitors are invited to submit items for the MBL’s blog. Please contact Diana Kenney: dkenney@mbl.edu.

Akash Srivastava, a student in the Brown-MBL Graduate Program in Biological and Environmental Sciences, successfully defended his Ph.D. dissertation entitled “Transdifferentiation of Liver to Pancreas” on August 18 at Brown University. Srivastava, a student in the Molecular Biology, Cell Biology and Biochemistry Department (MCB) at Brown, conducted his research at the MBL’s Eugene Bell Center for Regenerative Biology and Tissue Engineering under the advisement of MBL Associate Scientist Marko Horb. His doctoral committee members also included Rich Freiman, Kristi Wharton, and Eric Morrow from the MCB Department.

Srivastava’s doctoral research helped to elucidate the molecular mechanisms involved in transdifferentiation of liver to pancreas in the frog Xenopus laevis. He identified a previously unknown role of a highly conserved beta-catenin inhibitor protein (Chibby) in transdifferentiation of liver to pancreas and in normal pancreas development. His research also provided a better understanding of the function of Wnt/beta catenin signaling in pancreas development. Funding for his research came from the Horb lab at with grant support from the National Institutes of Health.

After completing his final manuscripts, Srivastava plans to work as a validation consultant in the pharmaceutical industry.

Akash Srivastava defends his thesis at Brown University for his Ph.D. in the Brown-MBL Graduate Program.

Akash Srivastava defends his thesis at Brown University for his Ph.D. in the Brown-MBL Graduate Program.

UChicago Center in Delhi

MBL Marine Resources Manager Dave Remsen and University of Chicago Center in Delhi Executive Director Bharath Visweswariah

Marine Resources Manager Dave Remsen recently visited the University of Chicago Center in Delhi, India while traveling there on other business. UChicago opened the new Center last spring, billing it as an “intellectual destination” offering 17,000 square feet of lecture halls, seminar rooms and offices designed to invite and expand global collaboration across institutions and disciplines. The Center is interested in fostering collaborations within three broad areas of study: Business, Economics, Law, and Policy; Culture, Society, Religion, and the Arts; and Science, Energy, Medicine, and Public Health.

While at the Center, Remsen met with Executive Director Bharath Visweswariah to discuss the new MBL-UChicago affiliation and potential collaborative opportunities between the Delhi Center and the MBL. Stay tuned for more information.

View photos of University of Chicago Center in Delhi here.

Take a look at the eye-popping, deep-sea exploration footage in this video about the Center for Dark Energy Biosphere Investigations (C-DEBI). Julie Huber, associate director of the MBL’s Bay Paul Center, is also associate director of C-DEBI, a National Science Foundation Science and Technology Center at the University of Southern California.

The researchers involved with this collaborative national center, Huber says, are asking the “big questions” about life in the deep ocean and below the seafloor. “We are at the exponential exploratory phase,” says Huber, who is on the pioneering edge of discovering subterranean microbial life.

This video was produced by Mira Zimet at USC Dornsife College of Letters, Arts and Sciences.

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