Archive for the ‘At MBL’ Category

At MBL: Taxonomy Toy Not Just For Bioinformaticists

Sep07

Taxatoy Graphic

The number of descriptions (y-axis) are shown for every year between 1750 and 2000 (x-axis). Significant historical events that coincide with noticeable changes in year-to-year trends are noted with arrows. (Credit: I.N. Sarkar, R. Schenk and C.N. Norton/BioMed Central)

The final installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts. The following story originally appeared on the MBL Website.

Cathy Norton may be on to something: Bioinformatics toys for scientists. Sure, they won’t be as popular as Super Soakers or Frisbees, but hers is a niche audience. Currently on the market is Taxatoy, a computer interface that lets users create customizable graphs to depict the number and variety of species discovered since 1750, when the Latin classification system began. (For instance, using the program I learned that out of the nearly 2.3 million listed species, 31 are lobsters). The tool was developed by the MBLWHOI Library in 2007 and is now freely accessible online.

According to Norton, who directs the MBLWHOI Library, the idea for Taxatoy came out a steering committee meeting for the Encyclopedia of Life. Chair James Hanken, a Harvard professor and herpetologist, wanted to know how many books on snakes were out there. “Everyone kind of stared and said. ‘We’re not sure how to do that,'” Norton recalls.

After thinking about the problem, she asked Indra Neil Sarkar, Informatics Manager at the MBLWHOI Library, to figure out how many new species were described before 1923, the year at which copyright restrictions begin in the United States. He began with uBio, a catalog of names of all known organisms discovered pre- and post 1923.  Sarkar imported each listed species’ name, who first assigned it, and what year. He and Ryan Schenk, who assisted with the project, then used this information to design Taxatoy out of an Excel workbook.

In a paper published online at BioMed Central in May 2008, Sarkar, Schenk, and Norton explored historical trends first visible through Taxatoy. A plot of all species described between 1750 and 2000 revealed spikes of discovery in 1754, 1758, and 1775. These dates can be correlated with the respective publication dates of Species Plantarum, Systema Naturae, and Systema Entomologica, the three major works of Carl Linnaeus, the father of modern taxonomy. The graph also showed that while the number of new species described overall declined during the World Wars, which might warrant further investigations into relationships between conflicts and their impact on taxonomic science. “When you start looking at it, suddenly you see new and different patterns,” Norton says. “That’s the excitement of building any bioinformatics tool.”

Although Taxatoy began as a librarian’s way to answer a specific question, it turned into a tool to actually ask questions and get many answers. “It’s interesting for environmental conservation reasons as well,” Sarkar says. “One may want to know if a particular taxonomic group is well described or under-described – Should I bother looking for more of these?”

He also sees educational applications. “I can imagine a fifth-grade quiz question: Why do you think bacteria are only available after 1910?” Sarkar adds. “Well, the logical answer is that’s the year the modern microscope became popular.”

However people are using Taxatoy, it’s a hit at BioMed Central. The paper describing historical trends quickly became one of the site’s top-accessed articles of 2008. Try it out at http://taxatoy.ubio.org.

Posted by Joseph, under At MBL  |  Date: September 7, 2008
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At MBL: Plastics Suspect in Lobster Illness

Aug16

Shell Disease Lobster

This drooping lobster is missing limbs and painted with dark spots, the tell-tale signs of shell disease. (Credit: Joseph Caputo/MBL)

The 4th installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts. The following story originally appeared, along with more photos, on the MBL Website.

The search for what causes a debilitating shell disease affecting lobsters from Long Island Sound to Maine has led one Marine Biological Laboratory (MBL) visiting scientist to suspect environmental alkylphenols, formed primarily by the breakdown of hard transparent plastics.

Preliminary evidence from the lab of Hans Laufer suggests that certain concentrations of alkylphenols may be interfering with the ability of lobsters to develop tough shells. Instead, the shells are weakened, leaving affected lobsters susceptible to the microbial invasions characteristic of the illness.

“Lobsters ‘know’ when their shell is damaged, and that’s probably the reason when they have shell disease, why they molt more quickly,” says Laufer, a visiting investigator at the MBL for over 20 years and professor emeritus of molecular and cell biology at the University of Connecticut. “But ultimately, they still come down with the disease. And we think the presence of alkylphenols contributes to that.”

Like any crustacean, lobsters shed their shells multiple times in one lifetime. After molting, the outer skin of the soft and exposed lobster will begin to harden. It is here that Laufer thinks the alkylphenols are doing their damage. At this point, a derivative of the amino acid tyrosine, whose function is to harden the developing shell, is incorporated. It is known that alkylphenols and tyrosine are similarly shaped and Laufer suspects that the toxin may be blocking tyrosine from its normal functions. He is at MBL this summer to measure the amount of competition between the two molecules. Alkyphenols are also known to act as endocrine disruptors.

Laufer discovered the presence of alkylphenols in lobsters serendipitously while investigating a tremendous lobster die off at Long Island Sound in 1999, when shell disease, first observed in the mid-1990s, was noted to be on the rise. Although an unusually hot summer, it was also the first time New York City sprayed mosquito populations to prevent the spread of West Nile virus. Laufer, who began his career as an insect endocrinologist, suspected the toxins from the sprayings may have contributed to the lobster die off. In 2001, while searching for the mosquito toxins in lobsters, he instead found alkylphenols.

“It’s a real problem,” Laufer says. “Plastics last a long time, but breakdown products last even longer. Perhaps shell disease is only the tip of the iceberg of a more basic problem of endocrine disrupting chemicals in marine environments.”

Posted by Joseph, under At MBL  |  Date: August 16, 2008
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At MBL: When Fish Talk, Scientists Listen

Jul17

Midshipman

Late stage midshipman larvae (about 30 days old and 20 mm length) attached to a rocky substrate. Credit: Margaret Marchaterre, Department of Neurobiology and Behavior, Cornell University

The 3rd installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts. The following story originally appeared, along with more audio and video clips, on the Marine Biological Laboratory Website.

A male midshipman, a close relative of the toadfish, doesn’t need good looks to attract a mate – just a nice voice. After building a nest for his potential partner, he calls to nearby females by contracting his swim bladder, the air-filled sac fish use to maintain buoyancy. The sound he makes is not a song or a whistle, but a hum; more reminiscent of a long-winded foghorn than a ballad. Female midshipman find it very alluring, and they only approach a male’s nest if he makes this call.

In a paper published this week in Science, three Marine Biological Laboratory (MBL) visiting investigators show that the sophisticated neural circuitry that midshipman use to vocalize develops in a similar region of the central nervous system as the circuitry that allows a human to laugh or a frog to croak, evidence that the ability to make and respond to sound is an ancient part of the vertebrate success story. The research is presented by Andrew Bass of Cornell University, Edwin Gilland of Howard University College of Medicine, and Robert Baker of New York University Medical Center.

“Fish have all the same parts of the brain that you do,” says Bass, the paper’s lead author. The way our brains work is also similar. Just as we have neurons that coordinate when our larynx and tongue change shape to produce words, toadfish and midshipman orchestrate the movement of muscles attached to their swim bladder to produce grunts and hums.

Using larval toadfish and midshipman, the group traced the development of the connection from the animal’s vocal muscles to a cluster of neurons located in a compartment between the back of its brain and the front of its spinal cord. The same part of the brain in more complex vertebrates, such as humans, has a similar function, indicating that it was highly selected for during the course of evolution.

Scientists have known for decades that these fish make sounds, but they are not the only species whose hums, growls, and grunts have meaning. “There’s reason to suggest that the use of sound in social communication is widespread among fishes,” Bass says.

This research is an example of the growing field of evolutionary neurobiology, which aims to understand the evolution of behavior through neurobiology. According to Bass, fish are an incredibly successful group, making up nearly half of the living species of vertebrates, and vocal communication may be partly responsible. “The kind of work we’re doing contributes to answering questions as to why these animals are so successful,” Bass says. “We’re only touching the tip of the iceberg here.”

The majority of this research was completed at the MBL over the past five years, although the question of how fish communicate through sound first came to Bass as a graduate student studying the neurobiology of fish at the University of Michigan. In the summer of 1986, Bass, then a summer instructor at the MBL, met Robert Baker, who was also researching the neurobiology of fish calling. For years they discussed fish social behavior with the roots of the hypothesis tested in the Science paper first published in 1997 and the research to test that hypothesis beginning in 2003. “The whole project began at the MBL,” Bass says. “It’s where collaborations happen.”

Posted by Joseph, under At MBL  |  Date: July 17, 2008
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At MBL: Do You Hear What Squid Hear?

Jun24

T. Aran Mooney monitors the squid before beginning the brainwave experiment.

T. Aran Mooney monitors the squid as it is sedated by Magnesium Chloride before beginning the brainwave experiment. Credit: Joseph Caputo/MBL

The 2nd installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts.

The ocean is a noisy place. Although we don’t hear much when we stick our heads underwater, the right instruments can reveal a symphony of sound. The noisemakers range from the low frequency bass tones of a fish mating ritual to the roar of a motorboat. The study of how underwater animals hear is a growing topic in marine science, especially with regards to naval sonar and whales. This summer at the MBL, zoologist T. Aran Mooney will be the first scientist to look at cephalopod hearing, using the squid, Loligo pealeii, as a model. To learn how sensitive the translucent animals are to noise, he is monitoring squid brainwaves as they respond to various sounds, specifically the echolocation clicks of its main predators, the sperm whale, beaked whale and dolphin.

“Sound is one of the most important cues for marine animals. Light doesn’t travel well through the ocean. Sound does much better,” says Mooney, who is a Grass Fellow at the MBL and beginning postdoctoral research at the Woods Hole Oceanographic Institution this fall. He predicts that squid probably hear very low frequency sounds, which means they pick up on fish tones and boat traffic. A better understanding of what these animals hear could reveal how human-induced noise affect cephalopods and how their auditory system evolved separately from that of fish.

Reading a squid’s brainwaves will take days of preparation. Mooney has been testing his experimental protocol for the past few weeks. He begins his experiments with a trip to the Marine Resources Center, where dozens of squid swirl around in a tank the size of a small above-ground pool. They travel as a school, so catching one doesn’t look like much trouble. But squid with their big yellow eyes are visual animals, and can see a net coming as soon as it hits the water. He catches one that suits his experiment, transports it to a bounce-proof wagon and covers it with a black plastic bag so not to stress the squid out during its trip to the lab.

In the corner of of one of the wet labs in the MBL’s Loeb Laboratory is a sound proof booth designed with a squid in mind. Mooney places his catch, now sedated, on a netted hammock within a plastic basin filled with water. As carefully as a doctor tends to his patient, he hooks the squid up to an IV with the sedative, Magnesium Chloride, so it remains calm during the experiment. As soon as the squid stops jetting, pushing its body forward with a splash of water, he inserts two pin-sized electrodes near the squid’s brain.

The squid is submersed in a soundproof booth while Mooney measures its brainwaves. Credit: Joseph Caputo/MBL

The squid is submersed in a soundproof booth while Mooney measures its brainwaves. Credit: Joseph Caputo/MBL

With the squid in place, Mooney turns to his computer and watches the brainwaves. Another scientist, MIT/WHOI fellow Wu-Jung, keeps an eye on the squid. “Give it a squeeze,” Mooney says to her, “make sure it’s ok.”

“Yeah, he’s breathing,” Wu-Jung replies, referring to the squid.

While the squid is relaxed, Mooney transmits a sound chosen from a computer program he helped design while a Ph.D. student at the University of Hawai’i. The sound is just a tone, nothing the squid would recognized in nature. By playing a number of these tones across a frequency, Mooney can tell which the squid recognizes according to its brainwave activity, measured by the electrodes.

Mooney has many more weeks to go before he knows what squids can hear. If they happen to respond to one of the predator echolocation clicks, it would mean the two species might have an evolutionary relationship. His experiment teaches us that science doesn’t yet have all the answers, and finding them requires getting a little wet.

Posted by Joseph, under At MBL  |  Date: June 24, 2008
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At MBL: The Gemma of Eel Pond

Jun13

North Atlantic Squid swimming in a research tank at the Loeb Laboratory at the Marine Biological Laboratory. These squid have some of the largest nerve fibers in the animal kingdom. Scientists at the MBL dissect the squid to better understand how the brain works.

The 1st installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts.

Dr. Joseph DeGiorgis came to Woods Hole at 21 as a diver. For an entire summer he spent his mornings underwater, searching for research specimens to be used by scientists at the Marine Biological Laboratory (MBL). Now a post-doc at the National Instiitutes of Health, DeGiorgis has and will continue to come to the MBL each summer. He and a number of people on the campus have described a magic about this place, where thousands of scientists pass through the laboratories each year and several chapters in the history of biology have been written.

After hearing Dr. DeGiorgis tell his story, and describe some new research about kinesins, a family of motor proteins he specializes in, we walked over to his lab to dissect a squid. This wasn’t a special request by me of course, he wanted to show the squid giant axon to a group of science journalists taking part in a week-long course in biomedicine. The axon, a nerve fiber that connects with multiple nerve cells to control the squid’s jet propulsion system, is one of the largest in the animal kingdom.

After entering Dr. DeGiorgis’s lab, passing tanks with the squid, he chose one of the backwards swimming creatures, cut off its head with a pair of scissors and began the dissection. He needed to remove the squid’s ink sac and multiple hearts before getting to the axon, which was an easy to spot ridge along the animal’s side.

Later that afternoon, the journalists and I prepared for an exclusive sea voyage aboard the RV Gemma, the MBL’s collecting boat since the 1980s. (Its named after the Amethyst gem clam, a small mollusk). The boat is equipped with large trawling nets, which scrape along the bottom of the sea as well as nets that pick up life in the water column. We waited as the boat sailed under the Water Street bridge and past Martha’s Vineyard to our trawling destination. Diamond, the ship’s seadog, circled the boat, occasionally poking her head over the water.

When the nets came back, all kinds of sea creatures were scattered over the boat’s floor. Many different species of whelks, sea stars, yellow sponges, crabs, and sea urchins were quickly sorted into buckets by the ship’s crew. Any organisms that wouldn’t be used for research were thrown back. The journalists and I passed the animals around. We felt the odd tickle of a sea star extending its legs to grab hold of your arm, the pinch of a small shore crab in an unfamiliar environment and the prickle of a purple sea urchin.

For the crew, some who have been aboard the Gemma for decades, others just weeks, this is just another day at work.

Posted by Joseph, under At MBL  |  Date: June 13, 2008
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