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

Students exploring the Innovation Co-Lab

Category: Students Page 41 of 42

Max Leung, Caped Crusader Against DNA Damage

By Becca Bayham

His lab colleagues call him Batman, the Toxic Knight.

To the rest of the world, he is Maxwell Leung, a PhD candidate in Duke’s environmental toxicology program. For the past five years, Leung has worked in the lab of Joel Meyer (AKA “Super-enviro-man”) fighting for environmental justice with pipettes and PCR machines.

Leung spoke about his research Jan. 27 as part of the Nicholas School’s continuing series on toxicology. Leung studies how exposure to certain environmental chemicals can affect organisms’ later-life development by damaging their DNA.

Cells contain two types of DNA: nuclear DNA (found in the nucleus) and mitochondrial DNA (found in mitochondria, which generate most of a cell’s energy).

“When people talk about DNA damage, they are usually referring to DNA damage and revision occurring in nuclear DNA,” Leung said.

A ligase enzyme repairs damage to nuclear DNA (National Institute of General Medical Science)

For the most part, special packaging and multiple repair mechanisms protect nuclear DNA from harm. However, mitochondrial DNA lack certain repair mechanisms, and little is known about their packaging. In the lab, Leung evaluated damage to both types of DNA by exposing worm larvae to short bursts of UV radiation. He found that, while nuclear DNA damage was partially repaired during the 24 hours between exposures, mitochondrial DNA damage continued to accumulate.

Further study of the exposed worms suggested that mitochondrial DNA damage at an early life stage can cause adverse effects such as reduced energy production, DNA transcription and oxygen consumption in adults. Given this connection, Leung sought to identify environmental chemicals that are capable of damaging mitochondrial DNA. Of the six chemicals he tested, one targeted mitochondrial DNA over nuclear DNA, and caused visible neurological effects: paraquat, a widely-used herbicide.

Which raises the question: if one out of six tested chemicals had this effect, then how many other environmental chemicals could cause that type of damage?

Unfortunately, mitochondrial DNA damage disproportionately affects neurological tissues; neurons require a great deal of energy and thus contain large amounts of energy-producing mitochondria. Studies have found strong associations between genes in mitochondrial DNA and neurodegenerative disorders such as Parkinson’s disease.

After the lecture, I spoke to Leung about why he decided to study science, and how he came to Duke.

“When I was in junior high, there was a TV show called ‘Success Stories’ in Hong Kong, featuring a number of famous Chinese scientists pursuing scientific careers in U.S. They went on to become National Academy members, win Nobel Prizes, and make important contributions to science and our world. That left an impression on me.”

Now, Leung hopes to write his own success story. He received his undergraduate degree in Food and Nutritional Science from the University of Hong Kong, and a master’s degree in Food Toxicology from the University of Guelph in Canada.

Leung came to Duke in 2007, following a visit to Joel Meyer’s newly-established environmental toxicology lab. At the time, the lab was “literally empty,” with just four PCR machines and a lab technician from Canada. Fifteen researchers work in the lab now, and each has been christened with their own superhero nickname including such characters as “Terror Byte,” the “Nano Ninja,” and “Wonder Worm Woman”.

“I enjoy the people I come across in science more than the science itself,” Leung said. “I enjoy doing experiments, giving talks and writing papers, but it is always the interesting people that I get to know through these activities that keep me going everyday.”

100 Days to State-Wide Science Festival!

kid looking at science

Duke students, faculty and staff wowed an all-ages crowd at the USA Science and Engineering Festival in Washington in Oct. 2010. (Photo: Chris Adamczyk)

Organizers of the second North Carolina Science Festival did a bit of counting and decided there are only 100 days left to the statewide celebration of all things science, research and just plain cool.

You can check out the sprawling calendar of more than 260 events scheduled for the April 13-29 festival here: www.ncsciencefestival.org

Duke will be bringing some hands-on displays to the 24-hour opening of the new Nature Research Center in downtown Raleigh on April 20 and 21. Some of our chemistry students also will be taking their show on the road for school appearances during the 16-day festival, and we’re working on getting some Duke faculty into school classrooms.

Festival events are aimed at showcasing science, technology, engineering and mathematics (STEM) for all ages and just sort of celebrating how cool it is that all this activity is going on around us in North Carolina.

Please scan the calendar and see if you and your family might be able to catch some of the hands-on activities, science talks, lab tours, nature experiences, exhibits, performances and other events.

The organizers expect more than 150,000 North Carolinians to participate.

(PS – Everyone’s welcome to participate too: Organizations interested in hosting events during the 2012 Festival can submit their events at the Festival’s website.)

NC Science Festival logo

 

Solving problems with iPad (or Android) apps

eCLIP iPad applicationBy Becca Bayham

When a patient comes into the E.R. with a lung problem, doctors usually put them on a ventilator. Unfortunately, this procedure helps some patients, but hurts others. Doctors have difficulty predicting which will be the case, due to a lack of data on risk factors. A predictive model was recently developed to solve this problem, but the calculations require more time and information than E.R. doctors usually have.

Enter Raquel Bartz, an emergency room doctor at Duke Hospital. She envisioned an iPad application where doctors and family members could input the necessary medical information, and the app would spit out the treatment protocol for a particular patient. Bartz turned to Richard Lucic and Robert Duvall’s Software for Mobile Devices class (COMPSCI 196) to make her idea a reality.

The result? An application called eCLIP, developed by students last Fall and available now in iTunes’ App Store. (See photos at left)

eCLIP is one of five applications created by students during the two semesters COMPSCI 196 has been offered. Lucic and Duvall described the course — and its various student-produced applications — at last week’s Visualization Friday Forum, sponsored by the Visualization Studies Initiative (http://visualstudies.duke.edu/) and Duke’s computer science department.

“We’re trying to teach students about the mobile app world,” Lucic said. “In addition, we’re trying to teach students about the software development process, from conception of an idea to delivering a product to a client.”

Lucic emphasized the importance of teamwork, as well as the value of visual design skills for increasing a product’s appeal. Furthermore, user testing is a critical step for identifying problems.

This semester, nine clients pitched their application ideas. Students voted for their favorite projects, and three were ultimately chosen:

  • Ajay Patel, IT Manager in the Duke Cancer Center, wanted a way to track medical samples during processing and reduce human error
  • Allison Besch, educational curator for the North Carolina Maritime Museum, wanted a fun, educational tool for teaching marine resource conservation to 4th graders
  • Rachel Cook, Duke alumna and former futures trader, wanted an app to encourage microlending and bridge the gap between lenders and borrowers

Each client worked with a team of 3-4 students, and met with them every other week to discuss the team’s progress.

“A lot of students are learning how to code mobile apps for the first time, so there’s only 6-7 weeks of actual coding time,” Duvall said.

Despite the time crunch, students try to present a finished product to their clients by the end of the semester. But who keeps the app going after the course’s conclusion?

“What we’re trying to do is have the students provide enough documentation and write their code well enough that the app can be maintained by the client’s organization,” Lucic said. “Clients have been thrilled with the experience. I think we’ve done a superb job of meeting their needs, as much as you can in a one-semester course.”

Particles of light overcome their lack of attraction

By Ashley Yeager

This waveguide shows an electric field moving from right to left. Credit: Setreset, Wikimedia Commons.

Electrons typically repulse each other. But sometimes they can actually attract each other and pair up, which is why superconductors exist. The particles that make up light, on the other hand, have no charge and rarely appeal to or repel one other.

Now, Duke theoretical physicist Harold Baranger and his collaborators think it’s possible to get these particles, called photons, to pair up, and stay that way, as they travel through space.

The new idea could help with the development of quantum communications, and possibly quantum computing in the future, Baranger says.

Particles of light do not have electric charge so they’ve got no attraction to the particles around them. That lack of attraction gives photons the ability to travel long distances without losing information, a good trait for building quantum networks.

But, the photons’ reserve has a drawback. It makes it more difficult for scientists to control each particle and retrieve the information it carries. To rein in the seemingly aloof photons, physicists have designed cavities that trap them and boost their contact with individual atoms.

In these cavities, the particles pass one by one through an atom in a phenomenon called a photon blockade. But, the cavities trap the photons for a really long time, so they pass through the cavities really slowly, which isn’t good for networking — especially in this age of instant information.

Using pencil and paper, Baranger, his student Huaixiu Zheng and colleague Daniel Gauthier, figured out that they could avoid the problems with the cavities if the photons instead went into a one-dimensional structure, called a waveguide, which also channels the photons past an atom one by one.

In the waveguide, a control atom acts as an intermediary between the incoming particles. The first photon passes through the atom and changes its state.

This diagram shows a photon blockade in a waveguide. Multiple photons (left, yellow) pass by the control atom in a one-by-one manner, ending with a train of single-photon pulses and empty pulses (gray). Courtesy of Harold Baranger, Duke.

The atom then interacts differently with the next photons, which ultimately causes the two particles of light to interact. What’s surprising, Baranger says, is that the photons are still bound to each other for a long time, even as they move away from the atom that paired them.

These bound states also end up producing a photon blockade much like in a cavity, but through a completely different mechanism, and the photons move a lot faster, he says.

The work, which appears online in Physical Review Letters, “paves the way” for experimentalists who want to try to build quantum networks without using cavities, Baranger says. He says experiments in this area may be done at Duke in the next few years.

Right now, he plans to work out what happens to the photons if more than one atom sits in the waveguide. The photons will be interacting in a lot of different places, and “one can imagine that there could even be a quantum phase transition, giving rise to some new quantum state,” he says. “But, that’s just a hope at this point.”

CITATION: Cavity-Free Photon Blockade Induced by Many-Body Bound States. Zheng, H., Gauthier, D., and Baranger, H. Phys. Rev. Lett. 107, 223601 (2011).

DOI: 10.1103/PhysRevLett.107.223601

The Paul Farmer Way of Life

By Prachiti Dalvi

One of Duke’s most distinguished alumni and one of global health’s biggest names, Paul Farmer, MD, PhD, discussed his latest book “Haiti After the Earthquake at Duke on Saturday afternoon.

(See Complete Video of his Talk)

So, what should Duke students take from this individual who just like us lived in Wannamaker, wrote for the Chronicle, and once roamed this Gothic wonderland? “Start as early as you can.”

Upon graduating from Duke in 1982 with a BA in medical anthropology, Farmer spent a year in Haiti: a decision that would help him become the kind of physician he always imagined himself as and would help him uncover his lifelong passion. Farmer then returned to Harvard University (which he humorously referred to as “the Duke of the North”) to obtain his MD and PhD in medical anthropology.

Now, Dr. Farmer is Chair of the Department of Global Health and Social Medicine at Harvard Medical School and the Kolokotrones University Professor, one of the highest honors that can be granted to a faculty member. He has been awarded the Conrad N. Hilton Humanitarian Prize and the MacArthur Foundation Genius Award for his work.

“We must counter failures of imagination.”

Just five years after leaving Duke, Farmer co-founded Partners in Health (PIH), an international health organization committed to improving health care in developing countries. This nonprofit organization focuses on building sustainable health care systems rather than simply treating patients. However, Farmer believes that their biggest challenge lies in breaking the cycle of poverty and disease. And, in essence, helping the Haitian community imagine a world where these hurdles can be overcome.

PIH aids developing countries establish sustainable health systems by recruiting community members to be involved in all aspects of designing and implementing a health system. The hospitals that PIH helps establish in Haiti are operated by Haitian doctors, nurses, and medical students.

This nonprofit organization is grounded in the belief that health and education are vital for development. Partners in Health works with partner organizations and national ministries of health to operate projects in twelve different countries all over the globe.

“You might lose the battle, but you won’t lose the war.”

When a magnitude 7 earthquake struck near Port-au-Prince, Haiti’s capital, on January 10, 2010, the effects were everlasting. The toll the earthquake took on Haiti was augmented by the lack of resources and the unexpectedness of the disaster. In fact, the earthquake depleted resources to the extent that it was difficult for Haitian firms to meet minimal process requirements. Resources had to be brought in from outside sources.

One of the most striking issues was facing the largest epidemic of cholera Haiti had ever witnessed. Academic institutions such as Duke and Harvard played a huge role in providing medical relief and “we can be proud of the role academic medicine played” during this critical time period. Farmer claims “Universities have a role to play” in helping bring healthcare equality to developing countries.

Although the earthquake brought with it a great deal of destruction, it also brought with it the opportunity to invest resources in building a sturdier foundation for the health care system. For example, rather than accentuating either treatment or prevention we can now integrate treatment and prevention.

“It’s wonderful to be around, hopeful, optimistic, young people like you.”

Dr. Farmer emphasized the role teaching plays in innovation. According to Farmer, innovation comes from change. Change comes from critical feedback loops. And, critical feedback loops come from discussion. Education is critical in generating conversation and new ideas. As one ages, pessimism begins to sink through and we need fresh minds to bring light to the optimistic aspects of life.

Yet Farmer’s work in Haiti remains fresh and optimistic. “Although Haiti does not have a teaching hospital, doesn’t it deserve a good teaching hospital?” asks Farmer. Currently, PIH is constructing Mirebalais Teaching Hospital. When completed, the hospital will house 320 beds, serve approximately 500 patients daily and will train the next generation of Haiti’s doctors, nurses, and medical professionals.

 

Your brain on memories

By Ashley Yeager

Students map the molecules associated with memory and how they flow through a brain cell. Courtesy of Craig Roberts, Duke.

9/11. JFK’s assassination. A man on the moon.

These words probably evoke a memory of where you were and how you reacted, if you were alive when the events occurred.

The exact molecules and brain processes that form memories and make some memories stronger than others haven’t been worked out yet. But by “walking” through our brain cells, a team of Duke students is taking a more vivid look at how we remember the past.

With Duke computer science faculty, neuroscientist Craig Roberts and his students have created and tested a virtual representation of our brain cells. In this world, students move around a virtual neuron, rearranging and organizing molecules to express their understanding of our memories.

In this 3-D environment of a neuron, students can mock how molecules flow through the brain to make memories. Courtesy of Craig Roberts, Duke.

Working in a shared digital space from individual computers, the students collaborate in both real life and cyberspace to model the flow of molecules from brain cell to brain cell. Computer scientists Julian Lombardi and Mark McCahill designed the neuronal landscape on Open Cobalt, a community-based, open-source web page for developing virtual, 3-D workspaces.

Roberts, the assistant director of education of the Duke Institute for Brain Sciences, says he trying to harness the “eventuality of the Internet,” where we’ll explore ideas and solve scientific problems on media-rich, multi-dimensional websites.

Roberts says he wanted to teach students about learning and memory. But he also wanted to experiment with whether 2-D or 3-D environments affected how different types of learners participated in class and retained what they were supposed to be studying.

He and undergrad student Daniel Wilson assessed the learning types of the students in the neurobiology class and then gauged their reactions to the 3-D environment compared to the 2-D work done in a collaborative Google document.

A 2-D Google doc mapping molecule movements for making memories. Courtesy of Craig Roberts, Duke.

“We’re finding that active learners perceive greater benefit from the 2-D environment than reflective learners. Visual learners perceive greater benefit than verbal learners from the 3-D environment,” Robert says. He presented the 3-D neuronal environment, his research results and other learning media he has been experimenting with at the 2011 Society for Neuroscience meeting in Washington D.C. on Sat. Nov. 12

By developing different environments in which students can learn, teachers may be able to engage all their students, independent of learning style, Roberts says.

He also said he “sees it as icing on the cake” that in a neurobiology course on learning and memory, students are working in a “learner-centric,” non-lecturing environment to expand their understanding of how they remember and recall the past.

Greening a classroom, student-style

By Becca Bayham

When students sit down in a classroom, their minds are (usually) on the course material. However, in the case of classroom A158 in the LSRC, the paint on the walls might be just as interesting as the writing on the blackboard.

The Duke Environmental Leadership Program (DEL) provides environmental education for business and community leaders. When the program decided to renovate one of its classrooms, it took a somewhat different approach.

Rather than opting for Duke’s usual vendors, the program sought recommendations from a team of students taking professor Deb Gallagher’s Sustainable Business Strategy class, offered jointly by the Nicholas School and the Fuqua School of Business.

“[DEL’s] vision was two-fold – to provide a green classroom that reflects the spirit of the Nicholas School, as well as to provide an executive atmosphere,” team member Debbie Breisblatt says.

The student team — composed of Breisblatt, Kealy Devoy, Stephen Hiser and Jennifer Weiss — researched sustainable options on DEL’s behalf, with each group member tackling one of four categories: technology, furniture, lighting and miscellaneous (storage solutions and floor/wall coverings). The team produced a final recommendation with three levels: green, greener and greenest.

The lowest level (green) included low-hanging fruit such as low- or no-VOC paint and furniture that fulfilled some environmental criteria. Higher levels were more expensive, largely because they incorporated more technology (such as a telepresence system that would reduce the need for travel). Presented with these options, DEL administrators were able to choose a mix that worked best for their sustainability goals and their budget.

“I think it’s great that [DEL] realized how important it is for it to walk the walk and incorporate sustainability into its operations as well as it is able. A lot of companies are in that position right now… they realize that they should do X, for environmental and ethical reasons, but they don’t know how to get there,” Devoy says.

The team finalized its recommendations last spring, and the classroom renovation took place over the summer. DEL incorporated a number of the team’s suggestions, such as zero-VOC paint and furniture made with recycled material. The cost was not substantially higher than a regular classroom remodel, Devoy says.

“One of the other objectives for this renovation was to showcase what a green classroom could look like at Duke and hopefully to inspire other departments to take environmental factors into consideration when they renovate,” Breisblatt says.

Devoy says she wishes that more on-campus departments and organizations would take advantage of grad students’ abilities.

“I think the value of student labor is a lot higher than people think it is. We have skills. There are tons of grad programs with students that could do things we currently hire consultants for,” she says.

The 'Pre-research' Path

By Pranali Dalvi

Senior Arun Sharma may be studying biology, chemistry, and genome sciences and policy at Duke, but don’t expect to see him trading in his lab coat for a white coat anytime soon. Sharma says he is ‘pre-research’ rather than ‘pre-med’.

His interest in research was piqued by his father, a physicist. Growing up in that lab-coat environment showed Sharma that he could one day make his own discoveries. After coming to Duke, Sharma realized he could start on this path early and immersed himself into research as a first-semester freshman.

“I thought it was cool that as just an undergraduate, an eighteen year-old, I was able to make new discoveries and participate in long-term research projects,” Sharma says.

Through the Howard Hughes Research Fellows Program, Sharma was matched up with his current mentor, Dr. Gerard Blobe in the Department of Pharmacology and Cancer Biology, where he has been investigating the molecular mechanisms behind angiogenesis, or blood vessel formation, in tumors. The concept behind his research is simple: if you can cut off the blood supply to the tumor, you can essentially kill the tumor.

Specifically, Sharma’s work revolves around the endoglin protein, a cell surface receptor in endothelial cells, which line the interior of blood vessels. Endoglin has a unique interaction with two other proteins (SMAD2 and BMP), which had not been previously characterized. When a specific member of the Bone Morphogenetic Protein (BMP) family binds to endoglin, SMAD2 is involved in a signaling cascade: SMAD2 is driven to the nucleus, where it prevents cell proliferation, or cell growth, and thus prevents angiogenesis. The long-term application of Sharma’s research would be drug discovery to initiate this signaling cascade and prevent angiogenesis, subsequently killing the tumor by cutting off blood supply.

Sharma wanted to share his passion for research with other undergraduates so he co-founded the Duke Undergraduate Research Society (DURS) along with classmates Peter Dong, Nick Schwartz, and Vivek Subramanian to show students that research is a realistic goal and that it is highly accessible to undergraduates.

“People think that in research you have to have a lot of training, a lot of background to get anything done productively,” Sharma says.

To encourage students to experiment with research (no pun intended!), DURS hosts renowned faculty speakers such as Dean Nancy Andrews from the School of Medicine and Steve Nowicki at lunch and dinner events. DURS– along with the Undergraduate Research Support Office – has also established Visible Thinking, an undergraduate research symposium – the largest of its kind – that gives students the opportunity to discuss their research with peers and faculty members during a poster session.

“I like to think that [this organization] is going to be my legacy at Duke after I graduate,” says Sharma.

After graduation, Sharma plans to attend graduate school to explore cardiovascular disease development and to eventually become a principal investigator (PI), leading his own lab.

“One thing I’m definitely going to do as a PI is something my own PI, Dr. Blobe, did: provide undergraduates with the opportunity to work in a lab,” he says.

Do we judge ourselves by our covers?

By Becca Bayham

After giving a lecture at a major women’s magazine, Dan Ariely was faced with a dilemma — in the shape of a huge Prada duffel bag.

As the behavioral economist walked down the street with the bag (a gift from the magazine), he wondered whether he should display the large Prada logo to passersby or hide it against his side.

He decided to hide the logo, but “I was surprised that I still felt like I was walking around with a Prada bag,” Ariely said. “What if I had Ferrari underwear… would I walk a little faster?”

How do the things we wear affect how we think about ourselves? Ariely explored this question (among others) at a Chautauqua lecture on Oct. 18.

In one of Ariely’s experiments, subjects wore shirts emblazoned with the word “stingy” or “generous.” After wearing the shirts around for awhile, participants completed tasks that evaluated their generosity. Strangely enough, “generous” t-shirt wearers gave more during these tasks than those with the “stingy” shirt on.

The word on a participant’s shirt “kind of penetrated their personality,” Ariely said. Notably, the effect was just as strong when participants wore shirts with the writing on the inside.

“Telling ourselves who we are seems to be a crucial element,” Ariely said.

It’s like giving money to a beggar. Giving money doesn’t instantly make you a better person, but it points out certain qualities in yourself. We learn about ourselves the same way that we learn about other people — by observing our actions.

In another study, women were given designer purses, but some were told that their purses were fake. Then participants played a game where cheating was advantageous.

Everyone started fairly enough, but eventually began to cheat. And once they’d cheated a little bit, they just cheated the rest of the time.

“We call this the ‘what the hell’ effect. Everyone who’s been dieting knows this feeling… I’m not good, so I might as well enjoy,” Ariely said.

Interestingly, women wearing counterfeit goods started cheating a lot earlier. Did having fake bags “penetrate their personality,” just as in the t-shirt experiment?

“What if fashion’s not just about telling other people who we are, but also about telling ourselves who we are?” Ariely said.

Do Higher Public Sector Wages Increase Corruption?

Graph showing Corruption in different countries of the world. Source : Transparency International

By Vansh Muttreja

I have always wondered about the reasons for corruption and its harmful effects on a country. It is a huge problem and a major cause for growth inhibition and stagnation in the third world countries. Corruption has plagued the economic and social foundations of these countries for a long time, but it is only recently that public awareness about this issue has risen.

The Corruption Perception Index Rankings released by Transparency International rank some of the fastest growing economies of the world — like India, Indonesia, Russia and China — as some of the most corrupt. A major reason why illiteracy and poverty continue to tarnish these countries despite government policies is because of corruption at every level of the supply chain. That is why corruption has become such an important topic to study today. And that is precisely my area of study for my Economics Honors Thesis. Specifically, I am focusing on the effects of wages of government officials on corruption in developing countries.

A majority of illegal money exchange happens in the public sector. In most developing economies around the world, public sector salaries tend to be lower than private sector salaries. These wage differentials between civil servants in the public and the private sector represent an important variable in the quantification of corruption levels within a country. Understanding these effects over time will help us know the relationship between the wages of civil servants and corruption. One study has shown that the amount that public sector employees from Albania earn through corruption is around 257% of their actual salaries. That is a shocking result, especially given the fact that if you look at how this affects the entire country — corruption accounts for more than 16% of Albania’s GDP!

The goal of this economics research is to look at how the changes in public sector wages over time have affected corruption. I also aim to understand these results in terms of what it means for the anti-corruption policy development in the country. For example, if an increase in public sector wages actually increases corruption, then anti-corruption policy should not concentrate on increasing wages, but instead look at providing incentive based government work schemes and enforcing tighter regulations.

(Previously, I have also done some research on mobile computing and gesture-based interfaces at the SyNRG lab at Duke. You can check out details about the research here.)

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