Duke Research Blog

Following the people and events that make up the research community at Duke.

Author: Ashley Yeager (Page 1 of 11)

Spherical Cows Help Turn Proteins to Crystals

By Ashley Yeager

"Physicists want to do what to me?" (Courtesy SXC.HU)

The spherical cow is a long-standing physics joke, funny to us, but maybe not to her.  (Courtesy Marijn van Braak)

It may be impossible to tip a spherical cow. But by searing one on the computer, scientists may have found the best recipe yet for transforming proteins into crystals.

Crystallizing a protein is not as simple as throwing it in the freezer and letting it chill, the way liquid water turns to ice. “We would like to know what is going on at that fundamental level when we crystallize a protein. But we don’t,” said Patrick Charbonneau, an assistant professor of chemistry, physics and computational biology at Duke.

But by looking at each protein as if it were a spherical cow with sticky patches, Charbonneau said scientists could learn more about the standard set of interactions that transform proteins from a liquid solution into crystals.

The idea of a spherical cow is not new. It comes from an old physics joke where a farmer calls the local university for advice on getting his cows to produce more milk. The university sends a physicist who looks at the barn, the cows and their production and says, “First, assume the cows are spherical and in a vacuum . . . ”

“Physicists idealize everything to the extreme, which could be why their most recent attempts to explain protein crystallization don’t quite work,” Charbonneau said.

Scientists want to know the fundamentals of protein crystallization because proteins are essential for living creatures to survive. Proteins come in many different shapes and have a variety of functions, and their structures explain how they interact with other molecules in the human body — information that often leads to more targeted medications.

To study protein shape, scientists precipitate them from liquid solutions into crystals, which is how DNA’s double helix structure was revealed. Physicists have also tried to model protein shape through computer simulations. In Charbonneau’s new model, he combines physicists’ past simulations based on the spherical cow model with the best protein-crystal-making insights from structural biology.

The new hybrid is what Charbonneau calls the patchy cow model. To develop it, he and his students digitally recreated the structure of the protein rubredoxin as a spherical cow, making it resemble a basic blob-like molecule. The team then applied patchy areas, which acted like the atomic interactions shaping the structure of a protein.

“We found the model actually works, giving us a patchy picture that does predict some of the crystal structure of proteins,” Charbonneau said. It is the first time a simulated model of protein crystallization has matched well with the temperature, salinity and other crystal-forming conditions structural biologists observe in the lab. And “it’s the first time that we can draw clear physical insights from how the model compares with experiments,” he added.

A single protein crystal of lysozyme (Courtesy Wikimedia)

A single protein crystal of lysozyme (Courtesy Wikimedia)

Charbonneau first began working on the protein crystallization problem as a post-doc at Amolf in the Netherlands. When he came to Duke in 2008, he met David and Jane Richardson — leaders in the field of protein crystallization and structural biology. From them, Charbonneau began to realize that physicists and structural biologists don’t know each other’s work. “We don’t cite each other, and we don’t trust each others’ descriptions of protein crystallization,” he said. The goal of his work, he explained, is to convince the disciplines to begin talking to each other.

The biggest problem for both camps is that they know the atomic and molecular interactions that should be involved in crystallizing a protein, but they “cannot make sense of what is going on. It’s figuring out the mechanism, the physical process, that is frustrating,” Charbonneau said. His new model tries to paint the physicists’ spherical cows from the perspective of the observations the Richardsons and others have already made in the crystallography community.

Charbonneau anticipates that the patchy spherical cow model might help structural biologists predict what conditions they need to crystallize any protein of their choice. But first, he said, the team needs to put their model to another test, simulating crystallization in more complex proteins, such as physicists’ favorite, lysozyme.

Citation: “Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study,” Diana Fusco, Jeffrey Headd, Alfonso De Simone, Jun Wang, and Patrick Charbonneau. Soft Matter, November 8, 2013. 10.1039/C3SM52175C.

New App May Help Protect Wild Dolphins

By Ashley Yeager

A screenshot from a new app, the Nai'a Guide, which provide info about eco-friendly dolphin-watching tours in Hawai'i. Credit: Demi Fox, Lenfest.

A screenshot from a new app, the Nai’a Guide, which provide info about eco-friendly dolphin-watching tours in Hawai’i. Credit: Demi Fox, Lenfest.

Traveling to Hawai’i sometime soon?

If so, you’re probably excited to experience spinner dolphins in the wild. If not, you can still dream about it. And now, there’s an app for that.

Scientists at Duke’s Marine Lab in Beaufort, N.C. have released the Nai’a Guide — a new iPad app that teaches users about wild Hawai’i spinner dolphins and how to see the animals without harming them. Tourists can use the app to plan an eco-friendly tour to experience the dolphins.

“If we can harness the power presented by mobile technology for conservation and responsible tourism, we have the chance to reach a wide audience and really make a difference for these animals,” says Demi Fox, a postgraduate researcher at the Lenfest Ocean Program who developed the app, along with Duke marine biologist Dave Johnston.

Nai’a is the Hawaiian word for dolphin. The Nai’a Guide explores the biology and ecology of spinner dolphins with photos, videos and sound clips. It also describes sustainable dolphin-based tourism practices outlined NOAA’s Dolphin SMART program.

With the Nai'a Guide, users can learn about spinner dolphins and their habits. Credit: Demi Fox, Lenfest.

With the Nai’a Guide, users can learn about spinner dolphins and their habits. Credit: Demi Fox, Lenfest.

Designed by Fox and developed by an online company called Kleverbeast, the Nai’a Guide also connects tourists with sustainable tour operators so everyone can make more responsible decisions when going to see spinners.

“The principles advocated within the Naia Guide could also be useful for dolphin-based tourism in other places, and with other species. Many of these best practices are generalizable,” Johnston says.

He and other scientists are concerned about human interaction with wild dolphins and other species worldwide. In Hawai’i, the main concern is that spinner dolphins rest during the day in the same shallow bays that people use for snorkeling, kayaking and swimming. Many tourists misinterpret the dolphins’ close proximity and curiosity for playfulness and try to swim with and even ride the animals while they are sleeping.

Intense and consistent human interactions could affect the dolphins’ health over time, Johnston says. The negative effects may also threaten the animals, a resource the state uses to draw tourists to the islands. As a result, he and colleagues at Murdoch University’s Cetacean Research Unit have been tracking spinner populations and monitoring their interaction with people in the Hawai’i island bays.

Researchers study dolphins in boats and high on the cliffs of Hawai'i Island, which is covered in the new app. Credit: Demi Fox, Lenfest.

Researchers study dolphins in boats and high on the cliffs of Hawai’i Island, which is covered in the new app. Credit: Demi Fox, Lenfest.

Scientists “can do all the science in the world, but until we share our findings broadly and in an accessible way, we will not effect serious change,” Fox says. She included the team’s research in the app so users can better understand researchers’ concerns about human-dolphin interactions and can make more informed decisions when choosing a dolphin tour.

“My hope is that the app will serve as an ecological conscience,” she says.

The app, available in Apple’s iTunes Store, can also be found on Twitter @NaiaGuide and on its website, http://www.naiaguide.org.

Early Primate Leaping Set Stage for Human Airtime

By Ashley Yeager

From primate ancestors that leaped like a dwarf lemur is where we got our ability to jump, a new study suggests. Photo courtesy of Mireya Mayor.

Primate ancestors that leaped like a dwarf lemur may be where we got our ability to jump, a new study suggests. (Photo courtesy of Mireya Mayor and Shaquille O’Neal).

Over a puddle, up to the basket, off the high dive — we all take leaps from time to time.

Now, new research suggests that this acrobatic lifestyle began far back in our evolution, when the earliest primates were first emerging on Earth.

“What this study suggests to us is that a very unusual and impressively acrobatic lifestyle jumping through the trees set us on the road to evolving many of features we recognize today in primates, including humans,” says Duke evolutionary anthropologist Doug Boyer.

Boyer and colleagues measured the ankle bones of 73 living and 38 extinct species of primates and found that throughout primate evolution, even our earliest ancestors were developing the bone structure to support long jumps. The results appear July 3 in PLoS ONE.

From the data, the scientists concluded that the ankle mechanics for better leaping in primates began to evolve around 55-60 million years ago. Boyer says natural selection seemed to favor a lifestyle of increasingly acrobatic locomotion in trees, including leaping long distances rapidly between branches.

Scientists had previously noticed that exceptional leapers had unusually elongated ankles. Boyer’s study, however, is the first to simultaneously test for effects of both body mass and behavior on ankle-bone elongation.

The team found a trade-off between body mass and ankle elongation. At larger body masses, ankles were proportionally shorter regardless of behavior. Yet, among animals of similar body size, the leapers had proportionally longer ankles, Boyer says. This was true among even fairly large primates, a contradiction to scientists’ earlier view that there was no behavioral benefit of ankle elongation for bigger animals.

The study is also the first to look at incremental evolutionary changes leading from our earliest primate ancestors to all the modern living forms. Whether leaping was an important behavior for the earliest primates has been controversial.

From their fossil data, Boyer and colleagues could see that early primates were not specialized leapers. “For the most part many of them were generalists, clamoring around on trees, jumping around now and then, but possibly preferring to scamper rather than make huge leaps,” he says.

The ankle bone serves a fulcrum to launch leapers' into the air. The longer the lever, the better the jump, in most cases. Credit: Doug Boyer, Duke.

The ankle bone serves a fulcrum to launch leapers’ into the air. The longer the lever, the better the jump, in most cases. Credit: Doug Boyer, Duke.

This particular conclusion was not new. But the researchers’ approach — looking at incremental evolution — allowed them to see more of a change. “The earliest primates were already better leapers than their ancestors, and the data show their descendents became even better yet,” he explains.

The measurements also suggest that initial elongation of the bones for specialized leaping evolved two independent times in primates – once in lemur ancestors and once in the ancestor of tarsiers, monkeys, apes and other anthropoids like us.

The study didn’t directly address human leaping, and it doesn’t mean humans with longer ankles are better leapers. But, Boyer notes, it’s not out of the range of possibility.

Citation: “Evolution and allometry of calcaneal elongation in living and extinct primates.” Boyer, D. et al. July 3, 2013. PLoS ONE. doi: 10.1371/journal.pone.0067792

Grey Seal’s Travels Hint at Animal’s Unknown Habits

By Ashley Yeager

This juvenile male grey seal swam up onto a North Carolina beach recently, surprising locals. Image courtesy of: StarNews Online.

This juvenile male grey seal swam up onto a North Carolina beach recently, surprising locals. Image courtesy of: StarNews Online.

On May 23, visitors to Carolina Beach met an unexpected guest — a male grey seal.

The 300-plus-pound juvenile was somewhat of a surprise to North Carolinians, since his typical habitat ranges from the coastal waters of Canada and extend south to about New Jersey. It is the first time a grey seal has been seen as far south as the Carolinas.

But the seal’s southern swim wasn’t too surprising to Duke marine biologist Dave Johnston.

“Things have been weird with seals for the last ten years or so. We’ve been seeing more harp, hooded and grey seals much farther south, usually the males,” he says.

To track seals’ travel patterns, Johnston and his colleagues have started attaching cell-phone enabled GPS tags to the animals in the Cape Cod region. They tagged their first grey seal, Bronx, last summer and from his transmissions alone have learned where the creatures like to hang out, how deep they can dive and just how far they can swim.

Bronx has covered the equivalent of the land area of Massachusetts and Connecticut combined during his swims. He’s explored below the ocean depths nearly 900 feet — a little more than a tenth of a mile, and he’s even made an international trip, crossing into Canadian waters.

But Bronx swims mostly in the waters near Cape Cod and Nantucket Islands, Johnston says.

Grey seals like Bronx have had a rough history in the region. In the 1800s, humans hunted and killed the entire population living in the Gulf of Maine. For a long time, there were few or no sightings of the animals. But since 1972, grey seals have been protected under the Marine Mammal Protection Act and are now returning in larger numbers to the shores of what was once their native habitat.

This map shows where a GPS tagged seal, Bronx, has swum since last summer. Image courtesy of Dave Johnston, Duke.

This map shows where a GPS tagged seal, Bronx, has swum since last summer. Image courtesy of Dave Johnston, Duke.

Some Cape Cod locals aren’t too happy about that. The seals come ashore in large groups, disrupting beach access in certain areas, and they leave behind their waste. They get caught up with fishermen’s gear and try to steal their catch, and the seals aren’t the friendliest marine mammals.

“People like dolphins. They tend not to like seals as much,” Johnston says, explaining that grey seals are smart, excellent predators and can be aggressive towards humans. “They can be loud and obnoxious, and they will bite,” he says.

That’s a challenge for both the seals and residents of the Cape Cod.

Part of the tagging effort is to increase people’s understanding of how grey seals interact with the ocean environment surrounding Cape Cod, and it could possibly explain why some of the animals are swimming as far south as the Carolinas.

The team is heading to the Cape Cod in early June to attach tags to seven more grey seals. The goal is ultimately to use the tracking data to improve the relationship between humans and seals there, Johnston says.

‘Street Cred’ Key to Leadership, Coach K says

By Ashley Yeager

Former politician Ron Paul speaks at the 2013 Feagin Leadership Forum. Credit: Ashley Yeager, Duke.

Former presidential candidate Ron Paul, an MD from Duke Medical School,  speaks at the 2013 Feagin Leadership Forum. Credit: Ashley Yeager, Duke.

Credibility is key for becoming a leader, both basketball coach Mike Krzyzewski and former politician Ron Paul told a group of Duke medical school students on May 18.

The two spoke as part of the Duke Sports Medicine Feagin Leadership Forum, a weekend meeting focused on ethical leadership.

“Ethical leadership takes courage, integrity and character,” Krzyzewski said. “You can see ethics and talk about ethics. But to do it, you’ve got to feel it.”

He, along with Paul and the other speakers and panelists, told the audience anecdotes where they had to choose to be ethical despite the decision not being the easiest or the most favorable among their peers.

Joanne Kurtzberg, a specialist working with children’s blood disorders, explained her difficult decision to send a patient to Europe for treatment using umbilical cord blood. The procedure was life-saving but had not yet been approved by the FDA in the U.S.

The decision and Kurtzberg’s pioneering effort in umbilical cord banking and treatments earned her what Krzyzewski called “street cred.” He said those looking to lead should be in constant search of credibility from their peers because it is one of the most important ways to show a person is willing to what is hard and difficult but the right thing to do.

While the audience was a mix of military, business and medical leaders, Krzyzewski tailored his speech mainly to the 2013 Feagin Medical Scholars, 16 medical school students who receive additional training in moral and ethical leadership, public speaking and other skills to make them well-rounded doctors.

Krzyzewski said the program is unique because it combines “two of the best jobs in the world,” being a doctor and being a leader. “Getting into medicine is huge,” he said, and becoming a leader “makes you part of something bigger.”

This program, he added, can take ethical leadership in medicine to a level no one has reached before, making it the gold standard, not only in the U.S., but also worldwide.

Success now lies in the scholars developing their “street cred.”

Hope for Understanding Ourselves Goes to the Dogs

By Ashley Yeager

Brian Hare and Evan MacLean, co-directors of Duke's Canine Cognition Center, play with Lilu, a labradoodle. Credit: Ashley Yeager, Duke.

Brian Hare and Evan MacLean, co-directors of Duke’s Canine Cognition Center, play with Lilu, a labradoodle. Credit: Ashley Yeager, Duke.

Lilu, a beautiful brown poodle-labradoodle mix, couldn’t sit still. Scents of pizza and peanut butter dog treats and the sights of new people easily distracted her.

The ADD behavior could be one trait that made her fail out of service-dog training.

“Six out of every ten dogs wash out of service training. But it’s hard right now for scientists to understand why,” said Duke evolutionary anthropologist Evan MacLean, co-director of the university’s Canine Cognition Center.

He, along with biological anthropologist Brian Hare and geneticist Misha Angrist spoke about ‘Genes, Brains and Games’ in man’s best friend as part of the Science and Society Journal Club on April 26.

MacLean and Hare explained that dogs have taken on many jobs in human society, acting as everything from pets, to our eyes and ears to being like coal-mine canaries searching for hidden bombs and missing people.

“Dog vocations require different sets of cognitive skills,” MacLean said. He studies military dogs, looking for traits that make them more suited for service tasks than pets like Lilu.

MacLean would ultimately like to identify the genetic components that underlie the characteristics suited for each type of job that a dog might do.

Scientists are interested in correlating dogs’ cognitive traits to their associated genes because the animals are “the most exquisite example of artificial selection,” Angrist said.

In Portuguese water dogs, for example, just six substitutions in individual DNA bases of the dogs explain variations in body size. In humans, nearly every gene could factor into height. It’s the same challenge that makes understanding human cognition and intelligence difficult at the genetic level.

Of course, defining cognition and intelligence at the conceptual level isn’t so clear cut either. “It’s so hard for people, journalists and the general public, to understand multiple intelligences,” Hare said.

He explained that at a basic level, cognition is the ability to make inferences, and that when we think of intelligence we think of IQ and standardized tests. These tests, however, measure only one type of intelligence. They don’t measure the ability to empathize, to verbalize a new idea or to put two completely separate ideas together to form a new one, which are other, important facets of intelligence, or really multiple intelligences.

At the Canine Cognition Center, and through the citizen science website Dognition, Hare and MacLean use standardized tests to study the variation in dogs’ intelligence. The tests, unlike the SAT or ACT, “cast a wide net across skills sets dogs could use for different vocations,” Hare said.

Dogs like Lilu, he added, are “really the hope of the world” for understanding cognition.

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