Archive for July, 2015

Today is the last day to apply for a travel award to get to this neuroscience celebration! Details here.

It’s reunion time for the MBL SPINES course, with a day-long symposium planned for this fall in Chicago. Held a day before the annual Society for Neuroscience meeting, the symposium will be a chance to catch up with friends, network, attend presentations, and celebrate the community the SPINES course has created.

The Summer Program in Neuroscience, Ethics, & Survival (SPINES) is an intense, month-long program held each summer at the MBL since 1995. It integrates training in lab techniques, grant writing, ethics, and public speaking, among other skills essential for early-career scientists. The course is also a networking opportunity and a way to build community for underrepresented groups in science, the target audience for the course. This symposium will celebrate the achievements of alumni students and faculty and expand the SPINES network across years and career stages to promote networking and collaboration.

The symposium will be held on October 16th, 2015 at the University of Chicago, and there is still time to apply for a travel award to help get there. More information can be found here, and details on the travel grant can be found here. Please contact Chinonye Nnakwe, Ph.D., at spinessymposium(@)gmail.com with questions.

SPINES students hard at work in the lab. Photo credit: Tim Kleindinst

SPINES students hard at work in the lab. Photo credit: Tim Kleindinst

Call this the Age of the Microbiome. Just a few short years ago, in 2012, the first “map” of the microbial species that live on and in the human body was published. Today, the data just keep coming that reveal the myriad connections between a person’s health—or an organism’s behavior—and the status of his, her or its microbiome, with correlations found in traits ranging from obesity to autism to ulcerative colitis.

One of the researchers at the forefront of microbiome research is Jack Gilbert, group leader for Microbial Ecology at Argonne National Laboratory and Associate Professor at the University of Chicago, as well as a faculty member at MBL. Catch up with Gilbert and the latest frontiers in microbiome research here, in a detailed profile in this month’s issue of The University of Chicago Magazine.

Bacteria-forming-a-mixed-biofilm-on-colon-cancer-tissue.-Credit-Jessica-Mark-Welch,-Blair-Rossetti,-and-Christine-Dejea, MBL

Bacteria forming a mixed biofilm on colon cancer tissue. Credit Jessica Mark Welch, Blair Rossetti, and Christine-Dejea, MBL

By Kelsey Calhoun

Vision has been studied inside and out for more than a century, resulting in some textbooks presenting the visual system as essentially understood. But María Gomez and Enrico Nasi, adjunct scientists at the Marine Biological Laboratory (MBL), don’t agree. They have spent the last several years investigating non-visual photoreceptors, cells whose function remains elusive in eyes filled with rods and cones. They reveal an important clue to how these cells work—how calcium triggers the electrical light response— in a recent paper published in Proceedings of the National Academy of Sciences.

Enrico Nasi and Maria del Pilar Gomez

Enrico Nasi and Maria del Pilar Gomez

Studies of vision traditionally divided light-sensitive cells into two distinct classes: those of vertebrates and those of invertebrates. The two classes were so different from each other that they were thought to represent two separate lines of evolution. But a few phenomena presented problems with this view. The most dramatic is the fact that blind people, who lack functioning rods and cones—the only photoreceptive cells previously thought to exist in vertebrates—can recover from jet lag, somehow sensing the light that resets their circadian rhythms. “A new type of photosensitive cell was later discovered in the mammalian eye that is responsible for these functions,” says Nasi. “Another dogma bites the dust.”

It is these non-visual photoreceptors, sometimes called circadian photoreceptors, that Nasi and Gomez, both professors at the Universidad Nacional de Colombia, were interested in studying. “What are these sensors? The idea that they might be just like photoreceptors of invertebrates—this is beyond blasphemy,” says Nasi. If true, “this leads to rewriting the evolutionary history of vision.” But studying these cells presented a few practical challenges. In vertebrates, the cells are few and far between, and have no unique shapes or markers to make them easy to find.

Amphioxus can grow as long as 2.5 inches, and it is very difficult to tell their head from their tail. Other than that, they are a very useful animal model. Photo by Hans Hillewaert.

Amphioxus can grow as long as 2.5 inches, and it can be difficult to tell the head from the tail. Photo by Hans Hillewaert

So Gomez and Nasi turned to an unassuming, fish-like invertebrate called a lancelet or amphioxus. This creature holds a unique place on the evolutionary tree of life, at the branching point between vertebrates and invertebrates. It has other advantages: the photoreceptors that interest Gomez and Nasi are easy to find in the organism, and manipulate. The evidence they found in the simple amphioxus suggests that vertebrates’ non-visual photoreceptors may mimic those found in amphioxus—that the visual systems of vertebrates and invertebrates are not as different as previously thought.

Their paper tackles the final step of the pathway that lets these photoreceptors translate incoming light into signals to the organism. Most of the pathway was already known, but solid evidence for the last step was elusive: How was light converted to an electrical cell signal that could be communicated to other cells?

Gomez and Nasi investigated the flood of calcium that is released when the circadian photoreceptors were exposed to light. They showed that calcium provoked the electrical cell signal, very similar to what happens with normal light stimulation. “It reproduces the native response,” says Gomez. This flood of calcium is the link that lets these photoreceptors communicate with the rest of the organism.

“We’re rather happy to see something that fully reproduces the light response for the first time,” Nasi says. But, he adds, “We don’t want to make claims that this is going to be general to all species.” Whether this discovery proves to be common in other species or not, it’s clear the field of vision and light-sensing cells still has much to reveal.

Citation:
Peinado G, Orsano T, Gomez M, and Nasi E (2015). Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors in amphioxus. PNAS, DOI: 10.1073/pnas.1420265112

By Rachel Buhler

Two journalists who received fellowships from the MBL Logan Science Journalism Program are spending the next week with scientists pursuing environmental field research at Toolik Field Station in Arctic Alaska, including studies of global climate change.

SJPtoolik2015resized

Michael Werner and Meera Subramanian at the Arctic Circle, 150 miles north of Fairbanks.

The two fellows, freelance journalist Meera Subramanian and freelance journalist/ filmmaker Michael Werner, both attended the program’s hands-on course at the MBL in June, undertaking field and laboratory research to “step into the shows of the scientists they cover.”  Last Tuesday, they flew into Fairbanks, Alaska, as the starting point for their journey to Toolik, which entails a minimum eight-hour drive and a passage across the Arctic Circle.

Subramanian has been blogging  — with striking photos and videos of the Arctic tundra and its scientist inhabitants — on the program’s blog, “A Toolik Field Journal.”

Over the years, the Logan Science Journalism Program has granted fellowships to hundreds of journalists from prominent news organizations, including The New York Times, The Wall Street Journal, Science, National Public Radio, The Washington Post, USA Today, CNN, and Scientific American. Journalists from Africa, Brazil, Sweden, India, Japan, the United Kingdom and other countries have also received fellowships.

One of the largely unexplored habitats on Earth lies under the ocean: the sediments, rocks, and fluids layered under the pressure of a gigantic basin of water. What lives down there, and how deep does life go? What strategies do microbes have for surviving in this environment? MBL Associate Scientist Julie Huber is among the people asking these questions, and this week she contributes a commentary in the journal Science on a team’s discovery of the deepest subseafloor life yet.

Julie Huber. Credit: Diana Kenney

Julie Huber. Credit: Diana Kenney

Using a drilling system aboard a research vessel off the Shimokita Peninsula of Japan, the international team “drilled the deepest scientific borehole to date to examine the abundance, taxonomic composition, and biosignatures of subseafloor microbial communities in sediments from 400 to almost 2,500 meters (about 1.5 miles) beneath the seafloor,” Huber writes. They detected microbial life at all depths, including methane-producing archaea in deeply buried coal-bed deposits.

As expected from prior studies, the concentration of microbes decreased steadily with depth in the shallow subseafloor layers. However, microbes were scarce–barely detectable—below about 1,500 meters. This was surprising, given that temperatures in the deep samples didn’t exceed ~60 degrees C, “well within the growth range of most microbes,” and “both carbon and hydrogen are plentiful energy sources, particularly in the coal bed layers,” Huber writes.

“Why so little life, then?” Huber writes. “It is difficulties with biomolecule repair, as the authors suggest, or something else like porosity or pressure? Uncovering what limits the biomass in this unusual environment will certainly be a focus of future studies.”

Huber is associate director of the MBL’s Josephine Bay Paul Center, as well as associate director of the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI).

###

Huber JA (2015) Making methane down deep. Science 349: 376-377.

Inagaki F et al (2015) Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349: 420-424.

Article in The Washington Post quoting Huber on Inagaki et al.

Ever wonder what it takes to keep MBL scientists working away? Here’s a clue, in the form of a time-lapse video of the daily upkeep required for the many zebrafish being studied at the MBL this summer. University of Chicago undergraduates Melissa Li and Clara Kao pressed “go” on a video camera and then went about their daily routine of feeding, cleaning, and generally caring for all the fish in the Zebrafish Facility. “We basically make sure everyone is happy and healthy,” Kao says. The 24-second video went up on a blog they’re keeping on their summer of research at the MBL: Summer People, Some Are Not (tagline: Some Are Zebrafish).

http://summerpeoplesomearenot.tumblr.com/post/123742373728/the-daily-grind

These two rising juniors are working in Jonathan Gitlin’s lab this summer, a change from the labs they work in back in Chicago. “When you switch labs for the summer, you get a different sort of snippet of the scientific world,” Li says. Both are interested in coming back to the MBL after the summer is over- Kao is in fact here for her second summer, and is interested in coming back for the Physiology course. With any luck, the blog and video collection will get a chance to expand.

By Kelsey Calhoun

The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka” but “That’s funny…”
—Isaac Asimov (1920–1992)

The process of science is rarely predictable: there are some 180s, some hard left turns, and quite a few long and winding roads. Graduate student Drew Friedmann can attest to this fact: a year and a half ago he was pursuing a completely different research topic and getting nowhere. But it was at the end of some long and frustrating months that he uttered some of the most exciting words you can hear from a scientist: “That’s funny,” or more specifically in this case, “Zebrafish don’t see with their tails.”

Primary motor neurons fluorescing in the young zebrafish, home to the unexpected VALopA Photo cred: D. Friedmann & Isacoff Lab

Primary motor neurons fluorescing in the young zebrafish, home to the unexpected VALopA. Photo credit: D. Friedmann & Isacoff Lab

Friedmann, a 2015 Grass Fellow at the MBL, had originally set out to study what controls the movement of zebrafish. These two-inch-long fish are widely studied, partly because they are transparent when young, making it easy to track their development. Ehud Isacoff’s lab at University of California-Berkeley, where Friedmann is a graduate student, has mapped the flow of calcium—a proxy for neuronal activity—in the nerve cells of developing zebrafish as they move.

Taking this further, Friedmann hoped to focus on how these young fish manage to move by looking at their gap junctions, the direct connections between cells which help them talk to one other. But there are over 30 different types of building blocks, called connexins, that make up these gap junctions, and few clues as to which ones help control movement as the zebrafish develop. Friedmann spent a long, frustrating year tackling this question with different tools and methods, without getting many interesting results.

DSC_0356

One day, he tried genetics. Analyzing only the neurons controlling movement in zebrafish tails—the most motile part of the fish—yielded a long list of active genes. One gene on the list, VALopA, caught Friedmann’s eye, because it codes for an opsin, a light-sensitive protein usually only found in eyes. “I went, what is that doing here?” Friedmann remembered. “There are no eyes in the sample!”

The “that’s funny” moment seemed odd enough to merit a little digging. “I’ll just flash some lights and see what happens,” Friedmann thought. The Isacoff lab uses a plethora of microscopes to track the flow of calcium around zebrafish, including a bright green laser. “I was expecting to flash the laser and see a calcium event,” Friedmann explained. But no such luck—light was not stimulating the neurons, embedded with light-sensitive proteins, to fire. Frustrated, Friedmann tried for a while longer, and finally noticed something else odd. If these neurons really didn’t respond to light at all, there should have been a random calcium spike or two right after a light flash, but there wasn’t. There was never a spike after a light flash; instead, the light was actually inhibiting the neurons from firing.

Motor neurons innervating the zebrafish tail Photo credit: D. Friedmann & Isacoff Lab

Motor neurons innervating the zebrafish tail
Photo credit: D. Friedmann & Isacoff Lab

This presents a whole new unexpected puzzle: Why are light-sensitive, movement-controlling neurons inhibited by light? “This opens up two, maybe three big questions,” Friedmann says. “One is how, one is why, and one is how common is this?” Zebrafish always lay their eggs at sunrise, so their development may be affected by light and movement, making it evolutionarily advantageous for the two to be linked. Friedmann’s goal this summer at MBL is to figure out what other cells and systems these light-sensitive neurons are connected to, and trace the full circuit involved in light response. He’s supported at the MBL by a Grass Foundation fellowship, which are given to early-career scientists to carry out independent, investigator-designed projects. The Grass Lab at MBL provides space, cutting-edge equipment, supplies, and housing, so young scientists can spend a summer dedicated to experimentation.

The ability to detect light evolved before eyes, Friedmann explains, and when eyes did evolve, there was no reason to get rid of the old way of sensing light, especially for transparent creatures like zebrafish. These light-sensitive neurons may be heavily involved in healthy zebrafish development and behavior, paving Friedmann’s winding road with all sorts of interesting questions.

The family, friends, and colleagues of Catherine N. Norton (1941-2014), former director of the MBLWHOI Library, gathered in Lillie Auditorium on June 19 to honor her memory. As befitting Norton, who was ever-positive and energetic, the event was inspiring, enlightening, and celebratory of her life, family, and pioneering professional accomplishments.

Family, friends and colleagues of Cathy Norton gathered in Lillie Auditorium to celebrate her life. Credit: Tom Kleindinst

Cathy Norton’s family, friends, and colleagues gathered in Lillie Auditorium to share stories of her life and great contributions to library science. Credit: Tom Kleindinst

Speakers at the celebration honored Norton’s vision and vibrancy, and her major legacy to the library sciences worldwide through her prescient leadership in establishing digital collections, databases, and informatics tools at the MBLWHOI Library. Excerpts from the speakers’ remarks are below.

Diane Rielinger, co-director of the MBLWHOI Library, announced the Catherine N. Norton Endowed Fellowship, which has received donations from more than 110 family members, friends, and colleagues. This endowed fund will support projects by students or early-career fellows that use the MBLWHOI Library or Archives and uphold the principles Norton championed by being “openly accessible, collaborative, innovative, connective, and laying the foundation for new scientific knowledge.”

****

Cathy always made sure we thought big. She encouraged us to see only opportunities—there were never problems. She didn’t just embrace technology; she pushed it forward with innovative programs that increased access and discovery, such as the Biodiversity Heritage Library. Cathy made sure our library was the first one out of the gate to digitize our collection with the project’s funding, and we developed procedures and policies that others adopted when they started scanning their collections. We learned an incredible amount so fast. — Diane Rielinger, Co-director, MBLWHOI Library

Cathy was one of the most amazingly effective and fun people I have ever worked with. She was a larger-than-life-sized person. Cathy was held in very high repute in library circles: She put MBL in the world league of libraries. And the most important thing to her was family.
— Donald Lindberg, Director Emeritus, National Library of Medicine

Cathy was far ahead of the curve in the Woods Hole community with respect to electronic journals and databases and “informatics.” The community owes a great debt of gratitude to Cathy for her vision, leadership, and hard work that kept the MBLWHOI Library at the forefront of library science and services, and well poised for the future. I assume that by now Cathy has assumed leadership of the Celestial Library and Archives. If so, they are in for an exciting time in the Celestial Realm! — John Farrington, Dean Emeritus, Woods Hole Oceanographic Institution

Cathy exemplified the “sanguine” temperament: open, caring, creative, bubbly, open to human beings but concerned about subject matter. Years ago, I asked her whether a journal should be published in print or digital formats. She said, “Do it both ways: for the present and for the future.” — Gerald Weissmann, Editor-in-Chief, The FASEB Journal and MBL Trustee Emeritus

My work with Cathy was a wonderful ride. We managed to be in the right place and time when new Internet technology came along and she found the money to wire the MBL. She enabled and supported me in the ability to discover and learn by doing, and she also gave me critical life lessons in how to lead a team. And Cathy always managed to have a lot of fun along the way. — David Remsen, director of MBL Marine Resources, who worked with Norton on MBL information systems (including the development of uBio) from 1991-2006

Cathy was a force of nature. The lessons she taught to all of us graduate students on the digital History of the MBL Project were a result of her indomitable spirit, pushing through every roadblock, and her joie de vivre. We carry these qualities forward in the project.
— Kate MacCord, project manager, MBL History Project

Cathy was exceedingly easy to love. She was an audacious friend. — John Monahan, family friend

I never met Cathy, but this is what I have heard about her: “inspirational but funny,” “very determined but kind,” “incredibly focused but managed to be positive.” These are the attributes we want to continue at MBL. — Hunt Willard, MBL President and Director

Audience members also shared their memories, many humorous, touching, or revealing of Norton’s “can-do” spirit. The memorial concluded with music performed by the Falmouth a capella group Notescape.

 

If you check the MBL’s Twitter feed during the summer months, you’ll be treated to quick, highly enthusiastic, and often visually beautiful dispatches from the MBL’s Summer Courses. The students and faculty are pursuing up-to-the-minute questions in life sciences research using a wide array of high-end imaging equipment, and some of the images they produce are eye-popping. Here are just a few recent Twitter posts from MBL students and faculty:

Vincent Boudreau (@viboud), a graduate student in the Physiology Course from University of North Carolina, Chapel Hill, Tweeted out this video, which he and several students made during the course’s biochemistry bootcamp under the supervision of Sabine Petry of Princeton University and Robert Fischer of the National Institutes of Health. “This bootcamp experiment taught us students how to do the biochemical legwork involved to get these microtubules to give us such stunning images,” Boudreau says. Microtubules (red) can be seen branching off of one another, marked by the green EB1 protein at their outwardly growing extremity. Video made with a Nikon TIRF microscope.

The MBL Embryology Course, tweeting under the hashtag #embryo2015, has shared one striking image after another. This is a tardigrade (a bizarre-looking, microscopic, water-dwelling animal) imaged with light-sheet microscopy by two students in the course: Christina Zakas, a post-doc at New York University who tweets @CZakDerv, and Nick Shikuma, a post-doc at Caltech.

tardigrade-C-Zakas-Embryology-2015

Tardigrade stained with DAPI to highlight nuclei and imaged on the Zeiss lighsheet Z1. Credit: C. Zakas and N. Shikuma, MBL Embryology course

Speaking of Embryology, several students in the course are blogging about their MBL experiences at the Node, an online community resource run by The Company of Biologists.  Check out their impressions of the course — its sheer intensity, its “exquisite coordination,” and the fun that balances all the hard work.

Embryology Course Co-director Alejandro Sánchez Alvarado, an expert Tweeter, once in a while reminds the students to step back from the bench, take a deep breath, and enjoy the beauty of Woods Hole. He called this scene “the rewards of Eel Pond after a rich day of learning and experimentation.”

Eel Pond, Woods Hole. Credit: Alejandro Sánchez Alvarado of the Stowers Institute/HHMI

Eel Pond, Woods Hole. Credit: Alejandro Sánchez Alvarado of the Stowers Institute/HHMI

 

By Rachel Foley

Every July, the Woods Hole community anticipates an event that is unique on Cape Cod, and possibly in the whole country. The annual Fourth of July parade, organized by the MBL Club, is a festive celebration of all things Woods Hole, from the MBL itself to sea life, science, and all things quirky. The parade, which takes over Water Street, draws a large audience to this tiny village, from locals to summer people to unsuspecting tourists just looking for a cup of coffee. Leading the parade was this year’s grand marshal, Jack Gilbert, an associate professor from the University of Chicago. As a band played enthusiastically behind him, Gilbert lead the passionate crew down the road.

Several memorable participants from the MBL included Grass Fellows and faculty, wearing grass hula skirts and hats and carrying humorous signs. The crew from the Marine Resources Department were preceded by manager Dave Remsen, riding his handmade horseshoe crab creation. Another clever use of cardboard came in the form of a model of the Gemma, the MBL’s collecting boat, carried by members of the Biology of Parasitism summer course. Other 2015 MBL courses were represented, including Embryology and Neural Systems and Behavior, bearing costumes and props to act out various scientific processes. The Biology of Parasitism course also dressed as a few of their research organisms, while the Summer Program in Neuroscience, Ethics, and Survival (SPINES) course dressed as pirates. Spectators could clearly see how much fun those walking in the parade had, though it was not always clear to the onlookers what some participants represented.

More notable characters included “Lobster Claus” (envision a Santa Claus-lobster hybrid), the Woods Hole folk dancers showcasing their moves, several dogs sporting patriotic bandannas, and jelly fish represented by girls holding decorated umbrellas.

Spectators and participants enjoyed refreshing watermelon slices outside the MBL Club to wrap up the festivities. The MBL Club’s annual Fourth of July Parade is a one-of-a-kind event that showcases what a special place Woods Hole is, year after year.