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.

Betzig2Friday 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:

schistosomasmallOne 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.

Rossner1croppedIn 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.)

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.