Archive for July, 2010

Duncan Mitchison-Field by Susana Montenegro Gouveia

Susana Montenegro Gouveia, a student in the Physiology course, is the winner of @MBL’s “Photo of the Week” contest. Susana won a free ticket to the MBL Gala concert, featuring the Tokyo String Quartet, this Sunday at 8 PM in Lillie Auditorium. Congratulations, Susana!

Gouveia’s photo shows Duncan Mitchison-Field, son of MBL visiting investigators Tim Mitchison and Christine Field of Harvard Medical School, engrossed in his own intellectual pursuits while his parents help guide Physiology students through their lab work.

“Sometimes (Chris Field) brings the kids with her to the lab,” says Gouveia. “They adapt so nicely to the lab environment, as though they were at home. Duncan was just seated in a corner of the lab, very focused on reading his own book. He was there for hours, so concentrated that he didn’t notice me taking his picture…It really seems that love for reading and acquiring new knowledge is part of his family. Duncan is very young but already shows lots of curiosity, and I wouldn’t be surprised if he were a great scientist in the future.”

@MBL welcomes submissions of photos to be considered for posting as “Photo of the Week.” Please send your photo, along with a caption that identifies any people in the photo (names correctly spelled) to: mblnews@mbl.edu.

Betzig2By Diana Kenney and Sarah Stanley

Friday was the last day MBL Physiology and Neurobiology students had Eric Betzig’s latest invention to explore. Two weeks ago, Betzig (left) brought his new contribution to high-resolution microscopy to the MBL from his lab at HHMI’s Janelia Farm campus and installed it in the central microscopy facility on the ground floor of Loeb.

“It’s really at the very bleeding edge,” Betzig says of his microscope, “but it’s a really good time to bring it (to the MBL), where all sorts of world-class cell biologists throw everything they can think of at it. We can learn through trial by fire what works and what doesn’t.”

The microscope combines two concepts—plane illumination microscopy and Bessel beams—to allow for high-resolution imaging within live cells. Cell components are labeled with fluorescent markers, and excitation of these markers by specific wavelengths of light allows them to be visualized by the microscope. (See video below to hear Betzig explain how his Bessel beam plane illumination microscope works).

The microscope is the just latest invention that Betzig has test-run at the MBL. In 2007, Betzig loaded his cutting-edge PALM (photoactivated localization microscopy) equipment into the back of an SUV and drove it up to the Physiology course, upon the invitation of Physiology faculty member and NIH senior investigator Jennifer Lippincott-Schwartz. PALM allows scientists to discriminate molecules only two to 25 nanometers apart, a vast improvement on the previous 200-nanometer limitation. At the MBL, Betzig, Lippincott-Schwartz, Jim and Cathy Galbraith of the NIH, Hari Shroff, a former Physiology student, and students then in the course worked feverishly around the clock with PALM. “By the end of two weeks, we had gotten PALM to work with live cells for the first time!” says Lippincott-Swartz. Not only that, but they got PALM to work with two colors of fluorescent probes rather than one, and demonstrated that it could be used to track single molecules in live cells. “It was a spectacular session, and it led to several publications,” Lippincott-Swartz says.

What’s next for Betzig? “I don’t know how many times we’ll invent a new microscope,” Betzig says, “but when we do, the MBL is a good place to be for that kind of intense trial to try to find out what works.”

Janelia Farms/HHMI scientists Thomas Planchon, Research Specialist; Eric Betzig, Group Leader; and Liang Gao, Postdoctoral Scientist, have been testing a new microscope with the help of MBL students and faculty.

Janelia Farm/HHMI scientists Thomas Planchon, Research Specialist; Eric Betzig, Group Leader; and Liang Gao, Postdoctoral Scientist, have been testing a new microscope with the help of MBL students and faculty.

Eric Betzig works on the new microscope.

Eric Betzig works on the new microscope.

Betzig discusses the new Bessel beam plane illumination microscope:

In this clip, Betzel’s microscope allows for visualization of histones – proteins associated with DNA – inside a pig kidney cell:

Here, the microscope reveals a network of mitochondria – cellular components that synthesize ATP, the “fuel” of the cell – inside a human cancer cell:

schistosomasmallBy Sarah Stanley

One morning this month, students in the MBL’s Biology of Parasitism (BoP) course learned all about the parasitic worm Schistosoma mansoni (left, courtesy of eol.org) and its effects on the body. Lecturer Andrew S. MacDonald of University of Edinburgh led the class through a detailed overview of the freshwater-borne worm, which can directly enter the skin upon contact. Over 200 million people worldwide are currently infected with Schistosoma, making it an important focus of research.

While the invading strategies of parasites understandably attract a lot of attention, the BoP course is also focusing heavily on interactions between parasites and the immune system. “Without looking at the immune system, you’re only looking at half the story of the parasite,” MacDonald emphasized during his talk. Indeed, according to course faculty member Yasmine Belkaid of the National Institute of Allergy and Infectious Diseases, one major theme of this year’s BoP course is how microbes naturally found in the intestines affect the body’s immune response to intruders.

Later that day, BoP students explored this theme in their lab work, looking at the immune responses of mice exposed to Schistosoma. By the end of their seven weeks here, students will have drawn on several areas of biology to explore a variety of topics in parasitism, including details of malaria infection and drug design for patients infected with parasites.

“I love parasitology because it’s not an isolated field,” Belkaid says. “There are lots of fields to touch on: immunology, molecular biology, evolution, and ecology, for example.”

This summer marks the 30th anniversary of the BoP course.

BoP students Anna Protasio and Sumaira Hasnain prepare cells for sorting by a method known as fluorescence-activated cell sorting (FACS). The cells are from mice infected with the parasitic worm Schistosoma mansoni, and will be sorted based on the immune molecules they have produced in response to the infection.

BoP students Anna Protasio and Sumaira Hasnain prepare cells for sorting by a method known as fluorescence-activated cell sorting (FACS). The cells are from mice infected with the parasitic worm Schistosoma mansoni, and will be sorted based on the immune molecules they have produced in response to the infection.

Rossner1croppedBy Sarah Stanley

In January 2006, two high-profile papers by South Korean researcher Woo Suk Hwang were retracted after they were found to be based on fabricated data. Hwang and his lab members claimed to have successfully cloned human stem cells for the first time. But their results were discarded after it was found that, in addition to engaging in other types of data fraud, they had misleadingly altered images of stem cells.

The incident, which made headlines worldwide, is a perfect example of scientists succumbing to “the temptation of image manipulation,” according to Mike Rossner (above), executive director of the Rockefeller University Press and former managing editor of the peer-reviewed research publication Journal of Cell Biology (JCB).

Altering digital images is easy for anyone with access to Adobe Photoshop or similar digital image editing software. Many nonprofessionals regularly touch up their personal digital photos. It seems natural that scientists, who typically present their data in the form of images, would find it helpful to edit photos to clarify their results. But researchers who modify figures risk misleading their readers, whether or not they intend to deceive.

Rossner, who gave the MBL Special Lecture in Bioethics last week, heads up a powerful effort to detect image manipulation before papers are published in JCB. In many cases, detecting image manipulation is as simple as altering contrast (see image below) or examining mirror images in Photoshop. These techniques can reveal problems like deletion or addition of part of an image, duplication of an image, and misleading contrast adjustments. JCB examines every image used in papers submitted for publication, ensuring any image manipulation does not violate its thorough guidelines.

JCB guidelines divide manipulation misconduct into two categories. Inappropriate manipulation violates the journal’s guidelines but does not lead to misinterpretation of data. Fraudulent image manipulation does result in data misinterpretation. Rossner reports that more than 25 percent of all manuscripts submitted to JCB have at least one inappropriately altered image that needs to be remade, while one percent contain fraudulent images, keeping such papers from being published.

Rossner shared some of the responses JCB receives from investigators when they are informed of inappropriate or fraudulent image manipulation in their manuscripts. Some are indignant. “Everyone does it,” read one author’s e-mail. Others insist that the manipulation is OK because it is more representative of their overall data set. But, Rossner says, “We do get mostly appropriate responses from authors.” Indeed, many authors are grateful to be notified of image issues before publication, since the repercussions of publishing a paper with fraudulent data can ruin careers.

After presenting tips on how to avoid inappropriate image manipulation, Rossner shared a new tool that allows readers to view the original, raw images that the authors obtained from their lab equipment. Called JCB DataViewer, it is currently only used for images in JCB articles but, according to Rossner, “we hope this may become a model for a standard for publication of image data in the publishing industry.” JCB developed the DataViewer in collaboration with Glencoe Software, which utilizes an open-source microscopy environment (OMERO) co-developed by Jason Swedlow, co-director of the MBL’s Analytical and Quantitative Light Microscopy course.

Rossner finished his talk by emphasizing that science does not equal art. “You are looking for the most accurate representation of your data, not the prettiest representation of your data.”

The top panel of this figure appears to display adjacent cells in a microscope image. But adjusting the contrast of the image reveals that some of the cells were copied into the figure from another photo. (from Rossner, M., and Yamada, K. M. (2004) J. Cell Biol.166:11-15.)

The top panel of this figure appears to display adjacent cells in a microscope image. But adjusting the contrast of the image reveals that some of the cells were copied into the figure from another photo. (from Rossner, M., and Yamada, K. M. (2004) J. Cell Biol. 166:11-15.)

By David Gallagher

The 4th of July parade is one of the must-see events of a Woods Hole summer. If you missed this year’s parade, here are a few photos by MBL Club coordinator Daisy Glazebrook.

Students in the Research Experiences for Undergraduates (REU) program at the MBL show their colors. The NSF-sponsored program is directed by Alan Mensinger of University of Minnesota, Duluth and Paul Malchow of University of Illinois, Chicago.

Students in the Research Experiences for Undergraduates (REU) program at the MBL show their colors. The NSF-sponsored program is directed by Alan Mensinger of University of Minnesota, Duluth and Paul Malchow of University of Illinois, Chicago.

Course assistants from the Children’s School of Science and their walking volcano.

Course assistants from the Children’s School of Science and their walking volcano.

"Uncle Sam" (MBL Director and CEO Gary Borisy) leads the parade.

"Uncle Sam" (MBL Director and CEO Gary Borisy) leads the parade.

SPINES (Summer Program in Neuroscience, Ethics and Survival) participants on the march.

SPINES (Summer Program in Neuroscience, Ethics and Survival) participants on the march.

MBL Communications interns Daisy Glazebrook and Elizabeth Kelly refreshed parade-goers with watermelon slices.

MBL Communications interns Daisy Glazebrook and Elizabeth Kelly refreshed parade-goers with watermelon slices.

Denise LoydA grad student, a post-doc, and a visiting scientist walk into a lab. What happens? Well, better science! Better, that is, than for a group composed of all post-docs, or all grad students, or all scientists from the same institution, according to Denise Loyd (left), an assistant professor at MIT’s Sloan School of Management.

Loyd, who studies the effects of diversity in groups, presented her research last week in a talk sponsored by the Woods Hole Diversity Initiative.  Loyd provided evidence that the presence of diversity in a group strengthens discussions in which final group decisions are made. Groups in which a majority of members fall into one category (based on race, background, institution affiliation, etc.), while a minority fall into another, put more time and thought into their conclusions.

We might assume the benefits of diversity in groups are solely attributable to the unique perspectives of the minority members. However, Loyd’s research shows that the simple existence of diversity can alter group dynamics in such a way that brings out different, positive behaviors in majority members, such as showing greater openness to others’ ideas.

Loyd also emphasized the importance of seeking out the unique strengths of members who may have lower perceived status in a group, such as undergraduates working in a lab with graduate students and post-docs. Her talk will no doubt prove useful to Woods Hole scientists and other community members seeking to strengthen group efforts. It also might help explain why the peer-to-peer dynamic in the MBL’s courses—where students problem-solve real-world research problems alongside some of the world’s top scientists—is often so energizing and productive.

Loyd’s talk was part of a Woods Hole Diversity Initiative event series called  “Synergy and the Group; the Hidden Power of Diversity.” For more information on upcoming events, visit http://www.woodsholediversity.org/.

It was 10 PM on a Friday, and students in the MBL’s Neural Systems and Behavior Course (NS&B) were hard at work in their Loeb lab. Some hovered over contraptions used for monitoring fly flight behavior. Some peered through a microscope at a portion of the crab nervous system. Michael Dickinson of CalTech, a former co-director of NS&B, took a break from teaching as he strolled between lab machinery while strumming “The Girl from Ipanema” on a ukulele.

When cautioned not to stay up too late (they had a 9 AM lecture to attend the next day), course assistant Gaby Maimon replied, “Oh, we’re just getting started!”

NS&B students are in for eight weeks of rigorous labs and lectures, learning about the neural basis of behavior. According to course director Paul Katz of Georgia State University, whose research involves the strange movements of the colorful Spanish shawl sea slug, the students were using Friday night to finish up the second of four course cycles. In this cycle, students learned about fly flight behavior, the sensory systems of electric fish, and the stomatogastric nervous system of crabs, which controls movement of the crustacean’s stomach.

Friday morning, NS&B students had been treated to the second of two lectures by Dickinson, who has contributed greatly to the study of animal physiology and behavior. His fascinating talk covered several aspects of fly flight aerodynamics and behavior, including how fly flight might have evolved. Dickinson used high-speed photography and videos to illuminate the details of fly flight, and discussed recent advances in the study of animal behavior.

This week, NS&B students start cycle three of their course, studying the behaviors of the nematode worm C. elegans, the mouse, and the zebrafish.

Michael Dickinson explains the proper way to prepare and use tools for attaching electrodes to fly neurons.

Michael Dickinson explains the proper way to prepare and use tools for attaching electrodes to fly neurons. Photo by Sarah Stanley.

Gaby Maimon and student Margarita Agrochao attach an electrode to a fly neuron. The monitor on the left allows them to visualize the neuron and the electrode, while the right monitor displays the whole fly.

Course assistant Gaby Maimon and student Margarita Agrochao attach an electrode to a fly neuron. The monitor on the left allows them to visualize the neuron and the electrode, while the right monitor displays the whole fly. Photo by Sarah Stanley.

Part of what makes the MBL unique is that its biologists are able to learn so much from the marine animals found just offshore. Fundamental biological processes in these creatures are often similar or identical to those in other species, including humans. For example, MBL scientists use sea urchins to study embryo development, sharks to study the neural basis of behavior, and squid to study nerve cells.

Last week, members and guests of the MBL Board of Trustees and Board of Overseers enjoyed a tour  aboard the MBL’s collecting boat, the R/V Gemma. Below is a photo tour of their excursion, as sea urchins, starfish, and other model organisms destined to help MBL scientists in their studies were netted. Animals collected on the R/V Gemma are brought back to the MBL’s Marine Resources Center, where they are maintained until they’re used for research.

R/V Gemma crew members prepare to haul in a net used for catching plankton.

R/V Gemma crew members prepare to haul in a net used for catching plankton. The boat leaves from Eel Pond in Woods Hole and heads two miles offshore into Vineyard Sound for sample collection.

____________ explains the importance of plankton as copepods, small crustaceans, swim around in his sample jar.

Ed Enos, superintendent of the MBL's Aquatic Resources Department, explains the importance of plankton in the food chain as copepods (small crustaceans) swim around in his sample jar. Looking on is William (Bill) Zammer, a member of the MBL Board of Overseers.

Crew members bring in a net after dragging it along the seafloor to catch crabs, sea urchins, starfish, and other creatures.

Crew members bring up a scallop dredge after dragging it along the seafloor to catch crabs, sea urchins, starfish, and other creatures.

A crab tries to escape across the deck, away from the sea urchins and shells piled up behind it.

A crab wanders away from the sea urchins and shells piled up behind it. Crew members will sift through the pile, keeping some animals for MBL research and returning the rest to the ocean.

One catch of the day is this slimy set of translucent squid egg cases.

One catch of the day is this slimy set of translucent squid egg cases.

This sea star is regenerating a lost leg, a process that has been studied at the MBL.

This sea star is regenerating a lost leg, a cellular process that is studied at the MBL.
Back in Eel Pond, the Gemma is docked near the Marine Resources Center. Ebert Hall is in the background.

Back at Eel Pond, the R/V Gemma is docked near the Marine Resources Center. Ebert Hall is in the background.

For more information on the R/V Gemma, visit http://www.mbl.edu/mrc/outreach/gemma.html.

Nine science journalists and editors are rubbing elbows with polar researchers at the lab bench and in the field as part of the MBL’s Science Journalism Program at Toolik Field Station in Arctic Alaska. The Polar Fellows were awarded the unique opportunity to learn about Arctic climate change from the experts while participating in data collection and analysis. Before returning home on July 2, the Fellows will have visited the Arctic National Wildlife Refuge, the Brooks Range, the Arctic coastal plain, and the Prudhoe Bay oil field.

In true journalistic fashion, the writers have been keeping a blog of their Arctic experience. Check it out here: http://toolikblog.wordpress.com/.

The 2010 MBL Polar Fellows are:

Victoria Barber, News Editor, The Arctic Sounder
Michael Barnes, Freelance Science Documentary Producer/Director
Julia Gross, Freelance Print Journalist, Germany
Louisa Jonas, Louisa Jonas Media
Julia Kumari Drapkin, Global Post, Argentina Correspondent
Susan Moran, Freelance Print Journalist
Ben Shaw, Producer/Editor, National Geographic Weekend
Chelsea Wald, Freelance Science Journalist
Gretchen Weber, Associate Producer, Climate Watch, KQED

Polar Fellow Gretchen Weber, associate producer for KQED’s Climate Watch, snapped this stunning shot in Alaska’s Brooks Range.

Polar Fellow Gretchen Weber, associate producer for KQED’s Climate Watch, snapped this stunning shot in Alaska’s Brooks Range.