Wednesday, July 29, 2015

Whale shark project lets students dive into genetic research


Click here if video does not appear on screen.

By Carol Clark

Biology undergraduates at Emory are studying genetics in a big way: They are the first to take a crack at researching the raw data from the sequence of the genome of the whale shark, the world’s largest fish.

“This project is amazing because we’re actually getting to do scientific work and further research,” says Mansi Maini, a sophomore majoring in neuroscience and behavioral biology.

The project to sequence the whale shark genome is a collaboration between Tim Read, a professor of infectious diseases at Emory School of Medicine, and Alistair Dove, director of research and conservation at the Georgia Aquarium.

Whale sharks can grow up to about 40 feet long. They have huge mouths, and yet they are filter feeders that mainly eat tiny organisms like plankton. Like all sharks, they are ancient animals, among the earliest of jawed vertebrates.

"We have created a unique educational experience in the process of researching the whale shark," says Tim Read, shown at the Georgia Aquarium. Photo by Jack Kearse.

“When we’re looking into the whale shark genome we’re doing a sort of molecular archeological dig,” Read says. “We can see the history of the whale shark in its tissue.”

The researchers are particularly interested in exploring the immune system of the whale shark.

“Better understanding the whale shark genes involved in the adaptive immune system could help us better understand how the immune system works across species, throughout evolution,” explains Megan Cole, Emory's director of undergraduate biology laboratories. “That could help inform how to improve the immune system in humans to work on auto-immune diseases and to improve fighting off infections.”

Cole incorporated research of the whale shark genome into Emory’s undergraduate biology education. The idea is to move away from so-called “cookbook” labs, that simply require students to memorize step-by-step procedures, and get them involved in doing actual science.

The whale shark project offers students the chance, and the challenge, of devising hypotheses and experiments to investigate individual proteins and genes. The students create Wiki pages to post their findings and make newly accumulated knowledge of the whale shark publicly available for others to build on. You can visit the Wiki pages created by Mansi Maini’s student lab group here, here and here.

The work being done by the students is painstaking, but potentially valuable. “Going back to the archeological metaphor, the more people at the dig, the more chance you’ll find that dinosaur bone,” Read says. “So that’s what we’re doing right now, sifting through a vast trove of evidence.”

Related:
The math of shark skin

Tuesday, July 21, 2015

Emory's Ken Ono trumpets U.S. win at International Math Olympiad in Thailand

Elphie selfie: Ono stopped in at an elephant sanctuary and snapped this photo during his visit to Thailand for the International Math Olympiad.

Emory mathematician Ken Ono delivered a special lecture recently at the International Mathematical Olympiad, an annual world championship for high school students from more than 100 countries. The trip to Chiang Mai, Thailand, for the event proved more than worthwhile when the six-member U.S. team took first place.

“This is a super big deal,” Ono says. “It has been 20 years since the USA has won the IMO. We should be super proud of the great work done by these six high schoolers under their coach, Po-Shen Loh.”

In addition to his talk, Ono treated the math Olympians to clips from an upcoming film about Indian math genius Srinavasa Ramanujan. Ono served as the math consultant for the film, titled “The Man Who Knew Infinity.”

Watch a highlight reel of the IMO event below. (Ono is the one wearing the Hawaiian shirt.)


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Tuesday, July 14, 2015

Drone offers stunning aerial views of Georgia's St. Catherines Island

From left: Tony Martin, Alison Hight and Michael Page pose before an alligator pond on St. Catherines with the drone. Photo by Ruth Schowalter.

Southern Spaces recently posted incredible aerial drone footage of St. Catherines, an uninhabited and largely undisturbed barrier island off Georgia’s coast. Below is an excerpt from the summary of the project:

"During a week-long visit to St. Catherines in March 2015, Emory University geographer Michael Page, environmental scientist Anthony (Tony) Martin, and graduate student Alison Hight flew a camera-bearing drone over nearly every type of ecosystem on the island: maritime forests, extensive beaches, back-beach meadows, salt marshes, mud flats, fresh-water ponds, and more. Along with colleagues from Georgia Southern University, Page and Martin have worked together at St. Catherines since 2011, locating, describing, mapping, and writing about alligator dens and gopher-tortoise burrows. The use of a drone enables a new way of studying the island's dynamic ecosystems and scouting locations difficult to reach on foot."

Read more at Southern Spaces.

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Ecology of St. Catherines Island
'Survivor': The marsh episode

Wednesday, July 8, 2015

First images of dolphin brain circuitry hint at how they sense sound



By Carol Clark

Neuroscientists have for the first time mapped the sensory and motor systems in the brains of dolphins. Proceedings of the Royal Society B is publishing the results, showing that at least two areas of the dolphin brain are associated with the auditory system, unlike most mammals that primarily process sound in a single area.

“Dolphins are incredibly intelligent, social animals and yet very little is known about how their brains function, so they have remained relatively mysterious,” says Gregory Berns, a neuroscientist at Emory University and lead author of the study. “We now have the first picture of the entire dolphin brain and all of the white matter connections inside of it.”

The researchers applied a novel technique of diffusion tensor imaging (DTI) on the preserved brains of two dolphins who died after stranding on a beach in North Carolina more than a decade ago. The method for using DTI on a non-living brain was developed relatively recently and had previously only been used for research on deceased humans, primates and rats.

The study focused on the dolphin auditory system, since dolphins – along with several other animals, such as bats – use echolocation to sense their environments. “We found that there are probably multiple areas in the dolphin brain associated with auditory information, and the neural pathways look similar to those of a bat,” Berns says. “This is surprising because dolphins and bats are far apart on the evolutionary tree. They diverged tens of millions of years ago but their brains may have evolved similar mechanisms for using sound not just to hear, but to also create mental images.”

Dolphins emit clicks, squawks, whistles and burst-pulse sounds to communicate, navigate and hunt. Echolocation allows them to perceive objects by bouncing sound off surfaces.

“For decades, we’ve thought of the dolphin brain as having one primary auditory region,” says co-author Lori Marino, a neuroscientist specializing in the brains of dolphins, whales and other cetaceans. “This research shows that the dolphin brain is even more complex than we realized.” 

Formerly on the faculty at Emory, Marino is currently the executive director of the Kimmela Center for Animal Advocacy in Utah. Emory houses a number of preserved cetacean brains collected by Marino, via colleagues at the University of North Carolina, Wilmington, from stranding events. Various environmental agencies respond when dolphins and whales are beached, in an effort to save the animals and return them to the sea. If the animals die, parts of them may be preserved for use in scientific research.

The current study used the brains of a common dolphin and a pantropical dolphin from the Emory collection.

Previous investigations using magnetic resonance imaging (MRI) have revealed the complex anatomy of cetacean brains. But MRI scans only capture images of the brain’s basic structure. DTI focuses on the brain’s white matter, or the fiber pathways that connect neurons and different regions of the brain’s gray matter. DTI can detect the movement of water molecules along these fiber tracks.

The researchers used a special DTI technique for post-mortem brains developed by study co-authors Sean Foxley, Saad Jbabdi and Karla Miller at the University of Oxford. In a living, human brain, a DTI scan takes about 20 minutes. Scanning a post-mortem brain takes much longer, however, since it contains less water.

The dolphin brains posed a particular challenge since they are large – about the size of footballs – and had been preserved for years. They retained only small amounts of the water normally found in healthy tissue.

The researchers hypothesize that dolphins have more than one neural area associated with sound because they are using sound for different purposes.

“The signal was very weak, but it was there,” Berns says. “Each of the specimens required nearly 12 hours of scanning.” The data from the DTI scans allowed the researchers to map out the white matter pathways, essentially the wiring diagram for the dolphin brain, in high detail.

The results show that the dolphin auditory nerve enters the brain stem region and connects both to the temporal lobe (the auditory region of many terrestrial mammals) and to another part of the brain near the apex known as the primary visual region. The researchers hypothesize that dolphins have more than one neural area associated with sound because they are using sound for different purposes.

Dolphins emit clicks, squawks, whistles and burst-pulse sounds to communicate, navigate and hunt. Echolocation allows them to perceive objects by bouncing sound off surfaces.

“Dolphins are the most sophisticated users of biological sonar in the animal kingdom,” Marino says. “They can find fish hidden from sight in sand with ease.”

Experiments have shown that dolphins can echolocate on a hidden, complex 3-D shape and then pick out that shape by sight. “They can rapidly move back and forth between their senses of sight and sound,” Marino says. One dolphin’s echolocation signals and echoes may be picked up by another dolphin, she adds. “They have a complex communication system and a unique ability to emit different types of sounds, like a click and a whistle, simultaneously.”

The researchers hope that their map of dolphin neural circuitry will help unlock secrets of the dolphin mind, including how they communicate and perceive their environment.

“Our study was the first to use this DTI technique on a dolphin brain, and on a specimen that was more than a decade old,” Berns says. “Our success opens up the possibility of using this tool to study the archived brains of all sorts of amazing animals in museum collections around the world.”

Related:
What is your dog thinking? Brain scans unleash canine secrets

Wednesday, July 1, 2015

The math of shark skin



July is shark month at Emory. We’re celebrating the science surrounding our fascination with sharks – creatures that have evolved extraordinary abilities during 450 million years of swimming in the oceans.

By Carol Clark

“Sharks are almost perfectly evolved animals. We can learn a lot from studying them,” says Emory mathematician Alessandro Veneziani.

As an expert in fluid dynamics, Veneziani is particularly interested in the skin of sharks, which is not smooth – as might be expected for such a streamlined, efficient swimmer – but irregular and rough. “It’s counterintuitive,” Veneziani says. “One would expect that smooth skin would make a shark faster in the water but it’s not true, and there is a mathematical reason.”

The ridges, or riblets, on shark skin break up vortexes of water and reduce drag, a phenomena known as the riblet effect. Using differential equations, mathematicians have duplicated this effect so it can be applied to industry. Aircraft, for instance, are painted with special finishes to create a riblet effect.

Veneziani once worked on a project for a European swimwear company. They used the math of shark skin to create swimsuit fabric for competitive swimmers. Tests showed that these swimsuits could significantly reduce drag in the water, to the point that they were banned from the Olympics in 2008.

“In the Olympics, you are not allowed to swim like a shark,” Veneziani says.

The time spent studying the math of shark skin was not wasted effort for Veneziani. He now applies similar principles of fluid dynamics to study how blood flows through human arteries. His lab creates computer simulations to help doctors decide on the best course of action for patients with cardiovascular disease.

“One of the great things about mathematics is that you can gain experience in one specialty, like shark skin, and use it in a completely different area, like blood dynamics,” Veneziani says. “Math is the common language of nature.”

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The math of your heart