Tuesday, October 25, 2016

BRAIN grant to fund study of how the mind learns

Biophysicist Ilya Nemenman, left, is developing theories about the brain that can be tested in the lab of biologist Sam Sober, right. (Emory Photo/Video).

By Carol Clark

How does the brain correct mistakes and guide the process of learning a skill? Why do some individuals learn faster than others?

Two Emory researchers – biophysicist Ilya Nemenman and biologist Sam Sober – recently received a $1 million grant from the National Institutes of Health BRAIN Initiative to explore these questions through a theoretical-experimental framework. Their research into how the sensory-motor loop controls and optimizes learning could lead to better protocols to help those dealing with major disruptions to their learned behaviors, such as when recovering from a stroke.

The BRAIN Initiative (Brain Research through Advancing Innovative Neurotechnologies) was launched by President Obama in 2014 as part of a widespread effort to gain fundamental insights for treating a range of brain disorders.

Emory has received other grants from the BRAIN Initiative: In 2015, a $1.7 million award went to neuroscientists Dieter Jaeger (Department of Biology) and Garrett Stanley (Emory-Georgia Tech’s Wallace H. Coulter Department of Biomedical Engineering). They will use the award to explore neural circuits related to sensing and physical action. In 2016, neurosurgeon Robert Gross in the School of Medicine received a $5 million grant to focus on optimizing neurostimulation therapies for epilepsy.

The grant received by Nemenman and Sober is part of a new cohort, opening another phase of the BRAIN Initiative: The development of theoretical, computational and statistical tools.

“Big data by itself is not useful,” Nemenman says. “We also need to come up with methods for understanding such data.”

Nemenman is working on a theory to help explain how the brain learns. “If you are learning something similar to something that you already know, it’s easier than if you are learning something entirely new,” he says. “We see this effect across the animal kingdom, including in humans. And this ability to learn something new changes with age.”

He gives the example that he will always speak English with an accent, since he is a native of Belarus and did not move to an English-speaking country until shortly before he became a student at Princeton. His children, however, will speak English without an accent since they were born in the United States and immersed in English from birth.

Nemenman is collaborating with Sober, who conducts experiments with Bengalese finches. “These songbirds are one of the best model systems available for studying how the brain learns to communicate,” Sober says.

The male songbirds sing to attract a mate, but they are not born with this ability, Sober explains. Instead, the young males learn to sing by memorizing, and then imitating, the singing of their fathers. When a young bird sings the wrong note, it tries to correct its mistake to match the memorized “target” sound.

In experiments, the Sober lab places tiny earphones on a songbird. When the bird sings, the researchers distort some of the notes slightly and play back the sound through the earphones. The bird is tricked into thinking it has sung a note incorrectly and tries to correct it.

Through this method, the lab has found that the birds are able to correct small distortions of sound, but they cannot correct large distortions.

“Many errors are distributed as a bell-shaped curve, but the distribution of singing errors in the birds is not bell-shaped,” Nemenman says. He is developing theories to explain how the difficulty of learning and correcting for large disturbances is related to this peculiar shape of the distribution of errors produced by the brain during learning.

“We can test the theories through experiments and learn more about the process,” he says. “The ultimate goal is to develop predictive models of how individuals learn from their errors that can be extended to other organisms, including humans.”

Nemenman also recently received a grant from the Kavli Foundation, to support workshops, symposiums and journal clubs that foster interdisciplinary theoretical and computational approaches to neuroscience, and bridge researchers at Emory and Georgia Tech.

It is important for physicists to share their expertise and collaborate with other scientists focused on understanding the brain, Nemenman says. As chair of the American Physical Society’s division of biological physics, he strives to establish programs that attract young physicists to neuroscience.

“Physicists are well posed to have a dramatic impact in this area,” he says. “We are trained to do science by combining theory and experiments. We can apply the same techniques to study the brain that we use to study other mysteries of the universe. Many graduate students in physics who came in intending to work on string theory, like I did, are coming out with a PhD focused on theoretical neuroscience.”

How songbirds learn to sing 
Biology may not be so complex after all

Thursday, October 20, 2016

The beauty of math and Pi: Ken Ono chats with Neil deGrasse Tyson on 'StarTalk'

StarTalk formula: What do you get when you add an astrophysicist and a number theorist to a comedian? A fun conversation when those variables are (from left) National Geographic Channel's Neil deGrasse Tyson, Emory mathematician Ken Ono and stand-up comic and writer Eugene Mirman.

“Math is one of the most feared subjects in school,” says astrophysicist Neil deGrasse Tyson, host of the National Geographic Channel’s “StarTalk,” to kick off an upcoming episode with Emory number theorist Ken Ono. “The phrase, ‘I was never good at math’ is probably uttered more than ‘I was never good’ at any other subject. What gives there?”

“Think of it this way,” Ono responds. “If you were an athlete, training for a marathon, you wouldn’t just expect to be fast at it. You’d have to practice. I think the reason people say they’re not good at math is because there’s this belief that if you’re good at math you’re just born with it. And that’s just so untrue.”

You can see a clip from the episode, to air Monday, November 7 at 11 pm, in the video below.

Ono and deGrasse, who are also joined by comedian Eugene Mirman, discuss everything from serial killers to the beauty in hidden patterns and how the Indian mathematician Srinivasa Ramanujan tamed Pi.

The episode, which is devoted to Ramanujan, will also feature actor Jeremy Irons. He will discuss his role as the mathematician G. H. Hardy, Ramanujan's mentor, in the film "The Man Who Knew Infinity." Ono served as an associate producer and the mathematical consultant for the film.

Celebrating math, movies and a miracle

Wednesday, October 19, 2016

Emory biologist nurtures nature in his spare time

Biologist Chris Beck is one of three finalists for the 2016 Cox Conserves Heroes award, for his work with the Clyde Shepherd Nature Preserve. Emory Photo/Video.

By Kimber Williams
Emory Report

As a professor of pedagogy in Emory’s Department of Biology, Chris Beck is engaged in the scientific study of laboratory teaching, with a particular focus on how inquiry-based learning impacts students' science process skills and their understanding of the nature of science.

This month, however, Beck is being recognized for his work involving a very different laboratory.

Beck has been named as one of three finalists for the 2016 Cox Conserves Heroes award for his volunteer work at the Clyde Shepherd Nature Preserve (CSNP), a 28-acre wildlife sanctuary located along the floodplain of South Peachtree Creek in Decatur.

For more than a decade, Beck has volunteered at CSNP, coordinating hundreds of volunteers from both Emory and the wider community, leading fundraising efforts and managing capital improvement projects. Each finalist will be awarded $5,000 to be donated to a local environmental nonprofit of their choice. Beck has selected CSNP as his non-profit.

The final winner will be selected through an online public vote and will receive an additional $5,000 donation to their nonprofit. Voting runs through Oct. 26; final results will be announced mid-November.

Emory Report interviewed Beck to learn more about his efforts with the nature preserve.

Why is the preserve important?

From an ecological perspective, the preserve serves several purposes. It’s located on the floodplain of the south fork of Peachtree Creek, so it has a role in controlling storm water overflow and filtering the water that does flood out.

The preserve is also an important green space to a lot of wildlife, including over 150 to 160 species of birds, as well as amphibians, reptiles and a wide array of plants. It provides a great resource to both the local and broader Atlanta communities, in terms of offering a place to go and see wildlife and walk the trails.

It’s provided educational opportunities as well. Over the years, I’ve brought students from my ecology lab classes there and I know Georgia State University and Oglethorpe University use it, too. Emory has sent hundreds of volunteers there over the years. It’s provided a great way to engage the community.

Read the full interview with Beck in Emory Report.

Tuesday, October 4, 2016

Biology professor holds meetings on the run

Emory biology lecturer Patrick Cafferty (left, blue shorts and shirt) takes one of his weekly office hours on the road for a three-mile run through campus. Emory Photo/Video

By April Hunt
Emory Report

There’s a very good chance Patrick Cafferty runs a different meeting than you do.

The Emory University biology lecturer takes one of his weekly office hours on the road, heading out for a three-mile run through campus with students. It’s part of an overarching goal to truly connect with students in his human physiology class as a teacher and mentor.

“I invite every student to just come in and chat,” says Cafferty, decked out in running shorts and a tank top before one of the weekly runs. “Some are too shy to do it, but they can join a run and just listen, and we get to know each other on a personal level. There is an equalizing aspect of sport.”

Early in the semester, Cafferty is the one doing most of the talking. Part of that is his 10-minute mile pace — slow for a serious triathlete like him but a challenge for some students. But it also lets Cafferty discuss class topics, such as the neurobiology behind cramped muscles or the dilatation of blood vessels serving muscles during exercise, as they are happening to some of the runners.

“This is great for me, because it’s an outlet to exercise, study and develop a relationship with faculty and students all at once,” says Amancio Romero, a junior behavioral biology and neuroscience major who last ran regularly, as a sprinter, in high school.

Call it active learning, something Cafferty has experienced personally. He grew up in Canada, interested first in exploring wildlife and later, studying life from the molecular level. At the same time he grew to understand complex cellular behavior from a biology perspective, he was applying those lessons to his training in Iron Man competitions and cycling. But it was not until graduate school at McGill University in Montreal, when he joined a swim club that welcomed students, staff and faculty, that he realized the value of linking those two worlds.

At McGill, Cafferty ended up in the pool with some professors he never would have otherwise met. He also connected with a professor who ended up being a doctoral mentor.

“There is a reason we have business meetings at lunch or over golf. It’s about being comfortable and being able to have natural conversations,” Cafferty says.

Those realizations prompted Cafferty to launch a run club when he came to Emory as a faculty-in-residence in 2011. Students, faculty and community members participated in that club, which became the model for what he calls his Active Office Hours.

Students who have participated so far include an Emory swimmer who gave up the sport to make time for studying, students who last ran during high school track or cross country, and even one person who had never run before.

One of the students has joined while listening to Cafferty’s lectures on an MP3 device, asking questions as they arise in his headphones.

Another, senior Maiya Smith, came with a screenshot of questions to ask Cafferty during the run through Lullwater Preserve.

“I never heard of a professor doing this before, and I love it,” says Smith, an anthropology and human biology major who ran marathons in high school. “I can see our runs directly connecting to class, and that just makes me want to ask even more questions.”

Like typical desk-bound office hours, the active versions are also a valuable resource for students beyond the classroom.

Cafferty welcomes students outside his class to the runs. He also plans on interval training runs, which will help some runners improve their times while letting everyone regroup to chat.

Conversations vary from campus gossip to current TV shows to classroom lessons, he says. Inevitably, questions come up about fitness or diet trends, issues directly linked to classroom work on nutrition and exercise.

“Running is completely new to me,” says Luke Roberts, a junior biology major who spent a year on Emory’s swim team. “I don’t have any breath left to ask questions, but it’s interesting just to listen and put it all together.”

The benefits spill over to students who don’t want to run, too. More of those students appear to have noticed Cafferty’s passion for biology in general and physiology in particular, and they are showing up more often in his Rollins Research Center office to talk.

“I hope to share something I’m kind of good at and enjoy with them, because I want them to know me,” Cafferty says. “And I think students see if you have a genuine interest in getting to know them.”

Friday, September 30, 2016

Emory's 'Rolosense' rolling to finals of Collegiate Inventors Competition

“I think the advantage we have with our technology is that it's so simple," says Aaron Blanchard, left (a PhD student in Emory's Laney Graduate School and Coulter Department of Biomedical Engineering at Georgia Tech and Emory), shown using the Rolosense with his advisor, Emory chemist Khalid Salaita. 

By Carol Clark

The first rolling DNA motor – the biological equivalent of the invention of the wheel for the field of DNA machines – is headed from its origins in an Emory University chemistry lab to the finals of the 2016 Collegiate Inventors Competition in Washington D.C.

Kevin Yehl and Aaron Blanchard make up one of six teams of graduate students who will be flown to the finals in early November. Yehl and Blanchard developed the DNA motor (dubbed Rolosense), and its application as a chemical sensor, in the laboratory of their advisor – Emory chemist Khalid Salaita.

Blanchard is a PhD student in Emory's Laney Graduate School and the Coulter Department of Biomedical Engineering (BME) at Georgia Tech and Emory, while Yehl recently graduated from Laney and the BME department.

The entries of the elite student teams represent the most promising inventions from U.S. universities. “Their ideas will shape the future,” wrote Michael Oister, CEO of the National Inventors Hall of Fame, in a letter announcing the finalists.

The Collegiate Inventors Competition annually gives out about $100,000 in cash prizes and is considered the foremost program in the country encouraging invention and creativity in undergraduate and graduate students. The competition also promotes entrepreneurship, by rewarding ideas that hold value for society.

The Rolosense is 1,000 times faster than any other synthetic DNA motor. Its speed means a simple iPhone microscope can capture its movement through video, giving it potential for real-world applications, such as disease diagnostics.

Kevin Yehl sets up a smart-phone microscope to get a readout for the particle motion of the rolling DNA-based motor.

"It's exciting," Yehl says. "Previous winners have gone on to start companies with their inventions and become successful scientists. It will be great to get feedback from the judges on the Rolosense."

The judges will include inductees to the National Inventors Hall of Fame, officials from the U.S. Patent and Trademark Office, and scientists from the global healthcare firm AbbVie.

Some of the best discoveries involve serendipity, and that was the case for the Rolosense. Yehl was working last year as a post-doctoral fellow in the Salaita lab, which specializes in visualizing and measuring mechanical forces at the nano-scale. He was conducting experiments using enzymatic nano-particles – micron-sized glass spheres. “We were originally just interested in understanding the properties of enzymes when they’re confined to a surface,” Yehl says.

During the experiments, however, he learned by accident that the nano-particles roll. That gave him the idea of constructing a rolling DNA-based motor using the glass spheres.

The field of synthetic DNA-based motors, also known as nano-walkers, is about 15 years old. Researchers are striving to duplicate the action of nature’s nano-walkers. Myosin, for example, are tiny biological mechanisms that “walk” on filaments to carry nutrients throughout the human body. 

So far, however, mankind’s efforts have fallen far short of nature’s myosin, which speeds effortlessly about its biological errands. Some synthetic nano-walkers move on two legs. They are essentially enzymes made of DNA, powered by the fuel RNA. These nano-walkers tend to be extremely unstable, due to the high levels of Brownian motion at the nano-scale. Other versions with four, and even six, legs have proved more stable, but much slower. In fact, their pace is glacial: A four-legged DNA-based motor would need about 20 years to move one centimeter.

 A cell phone app is in the works.
The Rolosense design mows over these limitations. Hundreds of DNA strands, or “legs,” are allowed to bind to the sphere. These DNA legs are placed on a glass slide coated with the reactant: RNA.

The DNA legs are drawn to the RNA, but as soon as they set foot on it they destroy it through the activity of an enzyme called RNase H. As the legs bind and then release from the substrate, they guide the sphere along, allowing more of the DNA legs to keep binding and pulling.

“The Rolosense can travel one centimeter in seven days, instead of 20 years, making it 1,000 times faster than other synthetic DNA motors,” Salaita says. “In fact, nature’s myosin motors are only 10 times faster than the Rolosense, and it took them billions of years to evolve.”

The researchers next demonstrated the Rolosense could be used to detect a single DNA mutation by measuring particle displacement. Yehl simply glued lenses from two inexpensive laser pointers to the camera of an iPhone to turn the phone’s camera into a microscope and capture videos of the particle motion.

The simple, low-tech method could come in handy for doing diagnostic sensing in the field, or anywhere with limited resources.

Nature Nanotechnology published the work on the rolling DNA motor. The researchers have filed an invention disclosure patent for the concept of using the particle motion of the Rolosense as a sensor for everything from a single DNA mutation in a biological sample to heavy metals in water.

Yehl has since left Emory for a position at MIT, but he continues to work with Salaita and Blanchard on refining the Rolosense.

Blanchard, who has a background in computer coding, is integrating the data analysis of the Rolosense into a smart phone app that will provide a readout of the results.

“I feel really fortunate as a graduate student to be working on this project,” Blanchard says. “As the molecular detection field grows, I think that Rolosense will grow with it.”

For their demonstration during the finals, Yehl and Blanchard plan to hand the judges smart phones and samples of water (including some containing lead), and let the judges use Rolosense to test the samples.

“It can be easy to dazzle with complex technologies like a robot,” Blanchard says, “but I think the advantage that we have with our technology is that it’s so simple. We can let the judges see for themselves how they can use Rolosense to quickly learn something useful, like whether a water source is contaminated with a heavy metal.”

Nano-walkers take speedy leap forward with first rolling DNA motor
Chemists reveal the force within you
Molecular beacons shine light on how cells crawl