Category: Students Page 39 of 42

Hands-On Lab Experience Helps Student Set Goals

On July 23, 2012

Story and Photos by Gabriel Aikens, NCCU Summer intern

The bubbling of reactions and the sight of stern-looking, goggle-wearing scientists with lab coats on the verge of discovering the next big cure is what goes on in Duke’s biology labs, right? No, not at all.

Besides seeing lab coats and a variety of beakers, one might be surprised to also find people in hoodies or khaki shorts and sneakers listening to their favorite songs and joking with each other.

Morgan Morrison has been working with the plant Arabidopsis thaliana in the lab of Xinnian Dong in Duke Biology.

Don’t be fooled by the relaxed environment however. These graduate and undergraduate students are hard at work, including intern Morgan Morrison, a North Carolina Central University senior from Charlotte interning at Duke’s Institute of Genome Sciences & Policy (IGSP) Summer Fellowship Program. Morrison and her colleagues spend their days transferring samples into geno-grinders (machines that grind plant tissue), carefully extracting chemicals with pipettes, and handling subzero nitrogen which sizzles and hisses loudly as samples are lowered into it..

Morrison was accepted into other summer internships but chose Duke’s because of her interest in genomics and her attraction to the university.

This internship is offered to a select few students from around the nation to take on various projects. Morrison is undergoing two projects, observing plant-microbe interactions and cloning plants to study their transcription of genes.

“I’m observing the microbes (microscopic organisms) to find useful plant-derived compounds for combatting infections,” says Morrison. “I’m cloning plants to see how resistant they are to a given disease.”

Morrison is doing molecular cloning, which is different from making genetically identical copies like cloning in the movies. Molecular cloning is the engineering of transgenic plants, which are plants containing genes transferred from another species. The plant she works with is Arabidopsis, a small flowering plant that’s a member of the mustard family.

To perform molecular cloning, she first identifies a protein of interest (POI) that might confer resistance to the Arabidopsis and then through a series of steps inserts the DNA coding sequence of that POI into the DNA of Arabidopsis. Then she conducts experiments test whether the new protein conferred resistance.

Morrison developed a fascination with scientific research after an AP Biology II course where she worked with Drosophila (fruit flies).

Learning lab skills will help Morgan decide on a career path.

“At the time, I didn’t know which field of science would be best for me, but I especially wanted to be involved in chemistry.”

She’s pursuing a B.S. in Pharmaceutical Science at NC Central University with a concentration in Chemistry, followed by going into a Ph.D program. “Right now, my purpose here at this Duke internship is to determine if I want to do research, and if so, what I’d like to research,” she says.

So far, she finds the internship beneficial and plans to combine her new knowledge with her future plans, which includes going to pharmacy school or becoming a patent lawyer. “As a scientist, I feel that it is good to be well-rounded in every aspect of science, via biology, chemistry, or desk work because basic skills and information are always relevant wherever you go,” she says.

Congo native Musoki Mwimba is mentoring Morrison during the internship. He’s an N.C Central University alumnus and graduate student in Duke’s Department of Biology. His interest is pharmaceutical science and part of his training and pursuit of a doctorate is mentoring newcomers. He says this requirement helps “improve his communication skills with others.”

“Though I like working by myself, working with the mentees is great because I’m learning from them,” Mwimba says. “As I see what their aspirations are, I try to help them reach them.”

As she works alongside Mwimba, Morrison wants to absorb as much as she can from this experience. “I hope to gain better understanding of what people do in this lab and master the projects I’m working on,” she says. “I’m happy I chose to come here.”

Trinity Junior in Phoenix for Summer, Doing Real Research

By sa160@duke.edu

On July 23, 2012

In Biology, Genetics/Genomics, Medicine, Students

By: Nonie Arora

Sonya Jooma, Trinity '14, provided by Steve Yozwiak

Rising Trinity Junior Sonya Jooma is in Phoenix, Arizona this summer working at the Translational Genomics Research Institute (TGen) as an intern in the TGen-Duke Biomedical Futures Program. This is the first year TGen and Duke have partnered to offer a funded biomedical research internship exclusively for Duke students. Jooma and a second Duke undergrad, Geoff Houtz, are the first two students to participate in this pilot program.

The TGen-Duke Biomedical Futures Program joins the growing list of Duke programs for students excited about genomics, such as the Genome FOCUS program and the Institute for Genome Sciences & Policy Summer Fellowship. In fact, the Genome FOCUS spurred Jooma’s enthusiasm for genomics research. Last year, she worked in the John Willis lab researching plant genetics as part of the Howard Hughes Research Fellows Program.

Her project at TGen, in the lab of Dr. Lisa Baumbach-Reardon, centers on the genetic basis of Infantile Spinal Muscular Atrophy. This disease causes muscle weakness and abnormality at birth. Afflicted children often die before their second birthday. According to Jooma, there are cases of this disease for which the genetic basis is unknown. As part of her lab’s exome sequencing project, they hope to identify mutations involved in the disease.

Jooma says her TGen experience has been great so far. She finds it similar to working in a research lab at Duke because of the similar lab hierarchy. However, she appreciates that TGen has overarching specific goals that focus on translating discoveries to clinical diagnostics and therapies. Jooma also looks forward to attending professional development workshops and presenting her work at TGen’s annual intern research symposium in July.

Ultimately, Jooma’s experience at TGen will be one of many exciting research projects: she hopes to pursue a career in biology research.

Sleuths Take Over Science This Summer

By Karl Bates

On July 17, 2012

In Animals, Biology, Science Communication & Education, Students

Story and Photos by Gabriel Aikens, NCCU Summer Intern

Science Sleuths Lance Cook, Alex St. Bernard, and staff member Emily Milligan work together on dissecting a cow's ankle, called the fetlock.

While many teens spend their summer days playing Xbox and watching cartoons, some eighth and ninth graders are constructing catapults and dissecting cow knuckles as part of Summer Science Sleuths at Duke, a two-week program that exposes kids from across the country to science in fun and creative ways.

On a recent Thursday morning inside the Biological Sciences Building, the kids dissected cow fetlocks, which are similar to the upper knuckle joints in a human hand. There were looks of amazement, curiosity, and disgust as Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure with the fetlock.

“Feel free to take one home to barbeque,” Aguiar joked. Some of the kids weakly smiled, but overcame their queasy feelings the more they operated on the fetlock with their scalpels.

“It was cool,” said ninth grader Samantha Goetz from Cream Ridge, New Jersey. “The activity is similar to what I want to do when I get older, like surgery and such.”

Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure on the fetlock to sleuth Natalia LeMay.

The point of the dissection was to have a better understanding of joint movement, as well as identify bone cartilage, ligaments, and synovial fluid, which is a lubricating liquid inside the joint that provides nutrients to joint tissues.

On other days during the two-week camp, the Sleuths created solar ovens, built rafts, and visited the Videri Chocolate Factory in Raleigh to learn how chocolate is made. The kids were housed in dorms at Duke and had picnics and cookouts on campus, as well as dinner at the Durham Bulls Athletic Park.

To be considered for selection to participate in Summer Science Sleuths at Duke, campers completed a survey on attitudes toward science, had a parent submit an application and had a teacher complete the recommendation form.

“This is the second year of the Summer Science Sleuths at Duke program,” said Chris Adamcyzk, executive director of the Duke Center for Science Education and creator of the program. “We want to make science fun for the kids,” she says. “ We carefully design the curriculum so that they can be introduced to a breadth of science, while making connections to their real world. Although they do experiments in the lab, they also interview scientists and take field trips to connect interesting science with everyday life.”

Fetlocks are similar to human knuckles, but a whole lot larger.

Making science fun for the kids is also the goal of Frederick Dombrose, President of The Hartwell Foundation, which funds the program.

“This wasn’t designed for kids who were at the top of their science class,” he said. “We created this for bright kids who have an interest in science so we can inspire them. This is an opportunity that most of them would’ve never been exposed to, so we want them to enjoy themselves and take advantage of this.”

'Chicken' Logic Secures Planes, Trains and Ports

By Ashley Yeager

On July 13, 2012

In Business/Economics, Computers/Technology, Lecture, Mathematics, Science Communication & Education, Students

By Ashley Yeager

U.S. goalkeeper Hope Solo deflects a penalty kick. Credit: AP

Soccer penalty kicks, ‘Chicken’ and other games may thwart terrorist attacks, drug smugglers and even freeloaders trying to board trains without tickets.

It’s not so much the intensity and adrenaline of the games that lead to better security, but the logic the players use, says Vincent Conitzer, a professor of computer science and economics at Duke.

This logic is called game theory and now scientists are using it to compute solutions for security issues, Conitzer explained at a July 11 talk with undergraduates completing summer research projects on campus.

During the talk, Conitzer gave a brief overview of game theory using real-world examples, such as penalty kicks in soccer and a set of drivers playing chicken. In the soccer example, he described a “zero-sum game” between the goalie and the kicker, where no matter the outcome, one player wins and the other loses.

But in the case of chicken, in which two cars drive straight at each other until one of the drivers “chickens out” and diverts course, the stakes of each choice are a bit higher. If both drivers stay straight, they crash. It’s no longer a zero-sum game.

When it comes to preventing security problems, there are more angles of attack, smuggler entry points and ways to board a train than the simple left, right or straight of these game examples.

Cars and buses wait to clear a security checkpoint at LAX. Credit: cardatabase.net

To make predictions about what the bad guys will do in the security scenarios, Conitzer is working with Milind Tambe and his group at USC. The team has designed game theory algorithms to set the schedule of security checkpoints and canine rounds at LAX airport, smuggler-scouting in Boston Harbor and even methods for preventing terrorist attacks in Mumbai.

Tambe “treats the problem of Mumbai personally” since that is his home city, Conitzer said, adding that he is only directly involved in this project with the USC group.

While the talk focused mainly on security applications, Conitzer also thinks that some “surprising new applications have yet to emerge” from the work. The new uses won’t necessarily help win a game of chicken or score a penalty kick.

But they could help scientists understand how to better use incentives to designgames with only good outcomes, such as encouraging smart energy use.

Citation: “Computing Game-Theoretic Solutions and Applications to Security.” Conitzer, V. In Proceedings of the 26th National Conference on Artificial Intelligence (AAAI-12), Toronto, ON, Canada, 2011.

A Desensitized Fool Can Be a Little Monster

By sa160@duke.edu

On June 13, 2012

In Behavior/Psychology, Business/Economics, Students

By Nonie Arora

Lady Gaga Caution Tape Outfit, Credit: New York Magazine

Look at the Lady Gaga photo, how shocking do you find it?

Many people find Lady Gaga’s outfits shocking. But they don’t always think so the fifth time they see the same outfit. According to a recent study, extra exposure to photographs of Lady Gaga changes how subjects predict others will react to seeing the image for the first time.

Troy Campbell, a marketing PhD student in Fuqua, conducted a study to determine whether people who are desensitized by repeated exposure to a shocking picture will be able to accurately predict how someone else will react. He conducted the research with Ed O’Brien at the University of Michigan and other social scientists at Duke University, the University of Michigan, and the University of Colorado. Their overall finding is that desensitized subjects don’t do as well at predicting others’ reactions.

A simple example of desensitization would be hearing the same joke five times. It gets less funny. Generally people believe that experience leads to predictive knowledge, so it’s interesting that that test subjects got worse at predicting how others would respond to the Lady Gaga photographs.

In follow-up studies, Campbell and colleagues found that more exposure to the same jokes made people worse at selecting a joke that unexposed audiences would find the funniest. According to Campbell, people generally understand that they and others desensitize at times, but they frequently fail to notice and correct for it in themselves and others, and that can lead to poor decisions.

Troy Campbell

“Desensitization can not only turn us into ‘fools’ who tell the wrong jokes but also ‘monsters’” Campbell says. In one study, the researchers exposed two groups of human subjects to a painful noise for 5 or 40 seconds and then asked how painful the last few seconds of the noise was. The people who heard the sound for longer found the last few seconds to be less painful. The subjects were also asked to predict how painful 5 seconds of the noise would be for a person who had never heard the sound. People who had heard the sound for longer said the next five seconds would be less painful. Now what is fascinating is that people exposed to the sound for 40 seconds reported that they would feel less guilty when exposing the noise to someone else. Presumably, this is because the group of people exposed to the noise for 40 seconds perceived less pain in the last few seconds because they became desensitized.

Campbell says it can be dangerous when people project their sensibilities on to other people.

Campbell and O’Brien are looking to continue this line of work by investigating whether people are forgetting their original response of how they felt when they first saw the Lady Gaga image. This is one way to consider the bigger question: “Are memories we’re not thinking about truly gone or can they be accessed completely or in a flawed way?” How about you, do you remember distinctly finding the Lady Gaga photograph less shocking a minute ago? Campbell and his colleagues want to know; leave a comment below and help them with their future research.

Before coming to Duke, Campbell studied psychology at UC Irvine where he was mentored by Elizabeth Loftus and Peter Ditto. He began his undergraduate studies focused on creative writing, but became more interested in psychology. He thinks that social science is exciting because it can test competing theories of conventional wisdom. Good ideas can come from day to day conversations, according to Campbell. Campbell also worked for a summer as a Disney Imagineer, which gave him the opportunity to improve visitors’ Disney experience. Now, Campbell is collaborating with Peter Ubel and Dan Ariely as he pursues his doctoral degree in marketing from Fuqua.

Student Profile: Jack Matteucci

By sa160@duke.edu

On June 13, 2012

In Computers/Technology, Physics, Students

By Nonie Arora

It may be summer, but student scientists are still on the job. Rising Trinity junior Jack Matteucci is heading to CERN in a few weeks to join the many scientists working with data from the Large Hadron Collider.

A Simulated Collision Producing a Higgs Boson Particle, Wikimedia Commons

Scientists working with data from the Large Hadron Collider are trying to determine whether the Higgs Boson, the so-called “God particle” exists. While the Higgs Boson has been called the “God particle” by some because it is currently the last predicted particle in the Standard Model to be observed, physicists are less fond of the name. “There is no doubt that it’s a huge missing piece to the puzzle, accounting for the observed phenomenon know as invariant mass, but it by no means explains everything about particle physics,” Matteucci says.

Einstein’s famous E= mc^2 showed a relationship between mass and energy. According to Matteucci, the Higgs Boson and its associated field would account for certain observed nonsymmetrical weak interactions, which would explain why certain particles have an inherent mass apart from the energy from their motion.

When collisions happen in Large Hadron Collider, thousands of protons collide and sophisticated computer programs must separate these interactions. After these interactions have been separated, data analysts like Matteucci enter the picture. He will be using ATLAS computing to analyze decay processes of elementary particles and confirm particle interactions.

Jack Matteucci

“During these interactions a plethora of particles are created and destroyed within tiny fractions of milliseconds which decay and lead to secondary products,” Matteucci explained. “Then, scientists try to backtrack to information about primary particles.”

While the collective effort is huge, the data is still analyzed one person at a time and interactions have to be confirmed thousands of times, according to Matteucci.

At Duke, Matteucci works under the guidance of Al Goshaw, the James B. Duke professor of physics. He’s also collaborating with Meg Shea and Yu Sheng Huang to build a cosmic ray detector. Cosmic rays are high-energy particles from the sun. Particles are produced from the interaction of the sun’s radiation and the Earth’s atmosphere. The team in Goshaw’s lab believes this detector will be very reliable and will be used to test more precise, future detectors.

A Tour of an All-White Garden

By Karl Bates

On May 29, 2012

In Biology, Field Research, Students

Photos and story by Gabriel Aikens, NCCU summer intern

The Sarah P. Duke Gardens have added a new collection behind the Doris Duke Center that is anything but colorful. The redesigned Page-Rollins White Garden, dedicated on May 3^rd, features plants that have white blooms. As Duke President Richard H. Brodhead said at the dedication of the new collection, it’s “white, white, white, but each so different. Look at these foxgloves, and look beyond them at the roses; each so different.” Indeed, this garden has much variety that is explored in the following pictures.

Shortly after the garden was dedicated, the gardens offered a tour titled “Plants of Distinction: Alba-White Foliage and Flowers.” Guests learned of the different plant species in this all-white garden as well as how to take care of the different flowers and plants.

Bobby Mottern, tour guide and Director of Horticulture, explaining one of the plants. Mottern says the gardens are “a good place to work” and he “really enjoys the staff.”

Deer love to eat flowers, but plant these and they will stay away. These are foxgloves and they’re poisonous, yet beneficial; they contain digitalis, a potent heart medicine.

Garden heliotropes, which typically bloom in pink, are believed to have been brought from Europe by early settlers.

These white azaleas are spring bloomers, native to East Asia.

There are a few plants in the collection with non-white features. This Solomon's Seal is native to China and is used as an herb for medicinal purposes.

Maji Moto: Dispatches from a Drought

By sa160@duke.edu

On May 29, 2012

In Animals, Biology, Field Research, Students

By: Nonie Arora

Photogram of Drought in Amboseli Basin, Courtesy of Courtney Fitzpatrick and Horse & Buggy Press

All of the wildebeest died. The cattle died. The zebra died.

The people starved.

“Someone once told me that as we live, we either become broken or we soften,” says Courtney Fitzpatrick, a graduate student in evolutionary biology who conducted fieldwork in Kenya’s Amboseli basin during 2009, the worst drought in living memory. “In hindsight I see that making Maji Moto was a panicked attempt not to break.”

Maji Moto, Swahili for “hot water,” is the name of the watering hole Fitzpatrick encountered every morning going from camp to the baboon study range. Her work of creative nonfiction, Maji Moto: Dispatches from a Drought, is composed of lyrical essays and photographs that detail the protracted suffering of the ecosystem imposed by the drought. Fitzpatrick says the experience truly tested her ability to protect her empathy.

Fitzpatrick was there to study sexual selection, mate choice, and reproduction. While humans have “concealed ovulation,” many old world monkeys like chimps and baboons have an exaggerated signal of fertility called an estrous swelling. It has been hard to fully understand the evolution or function of this trait in the past, according to Fitzpatrick. Her hypothesis was that estrous swellings evolved like a peacock’s tail – as a consequence of sexual selection pressure. She set out to answer the question of whether males prefer females with larger swellings.

Fitzpatrick is a field biologist at heart. To study organisms in their natural environment, she spent about eighteen months obtaining measures of swellings in Kenya’s Amboseli basin through the Amboseli Baboon Research Project. The project is ongoing from the 1960s and has rich longitudinal data. For Fitzpatrick, measuring thousands of swellings was tedious and required careful attention to detail. But in the end, she says now that “it’s just fun having all that data.” Along with measuring estrous swellings, she observed mating behaviors such as how close males stayed to females and how they groomed each other.

Broadside from Maji Moto, Courtesy of Courtney Fitzpatrick and Horse & Buggy Press

Maji Moto originated organically as Fitzpatrick compiled essay blog posts and photographs she had shared with friends and family during her time in Kenya. She was “seeing incredible sights I couldn’t not photograph.” As the drought became more serious, so did her writing. By the end, her creative nonfiction was as serious as the science. Fitzpatrick said she couldn’t analyze the data free from distress until after Maji Moto was finished.

Fitzpatrick brings a unique background to her scientific endeavors: she studied studio art as an undergraduate student and taught photography for a New York social service organization before pursuing graduate school. She grew up in naturalist family, and so was always interested in evolution and behavior. When she started missing the sense of intellectual engagement from an academic environment, she decided to pursue graduate school at Duke.

Her studio art background had practical implications – comfort with the camera made it easier to collect her data, which involved taking pictures and making careful measurements. But even more so, thinking about the world from an artist’s perspective informs the way she thinks about and does science. Fitzpatrick says the process of generating hypotheses often requires relaxed creativity, like a painter conceiving an image on a canvas. Moreover, many scientists are loyal to particular methods, like artists, as they “arrive closer and closer to an unknown truth.”

The book and photographic prints from Maji Moto are on display in the Foyer Gallery (401B Foster Street) every Friday from 11am to 2 pm. The hand-printed, limited edition art book is also available for purchase from Horse and Buggy Press. Now that Maji Moto has been published, Fitzpatrick’s next steps are finishing her dissertation and beginning a postdoctoral fellowship at the National Evolutionary Synthesis Center in Durham, studying theoretical models of sexual selection.

Rethinking science on pandemic-potential viruses

By Ashley Yeager

On May 18, 2012

In Animals, Biology, Genetics/Genomics, Global Health, Medicine, Students

By Ashley Yeager

Debates over experiments subjecting ferrets to modified bird-flu strains had scientists and politicians seriously questioning how to approach and publish studies on pandemic-potential viruses. Credit: J. Smalley/NaturePL.com

Making mutant forms of bird flu and publishing the results caused a major squawk in the public and in the political and scientific communities over the last year.

The issue was whether the new mutants could ward off a major pandemic of bird flu or start one, explained Stephanie Holmer, a graduate student in Duke’s Department of Cell Biology.

She raised the issue during the May 18 meeting of the Science and Society Journal Club.

The row began when researchers at the University of Wisconsin-Madison and the Erasmus Medical Center in the Netherlands independently tweaked strains of the H5N1 virus, commonly named the bird flu. The strains, the teams report, are more easily transmitted between ferrets, the lab-double for humans.

“The fear was that if the mutant forms of the virus got out of the lab, bioterrorists could use them to make a super-virus and start a pandemic. But there was not any guarantee that what the scientists had was a weapon. The mutant strains weren’t even that efficient at killing a ferret,” Holmer said.

During the forum, about a dozen students and faculty from departments across campus debated whether this kind of research should have been done, if journal editors should publish the full results and what can be done to prevent future squawks about similar types of research.

Electron micrograph of influenza A virus. (Centers for Disease Control, Erskine Palmer)

Scientists want to study H5N1 to find out how fast the virus mutates and how virulent those strains are in mammals, including humans. So far, outbreaks of the non-mutant form of the bird flu in humans have been limited. The cases, about 100 to 200 from 2003-2012, have occurred most often in Indonesia, Egypt and Vietnam, according to statistics from the World Health Organization.

In two separate papers, the teams from Madison and the Netherlands reported the strains of H5N1 that seemed to be more virulent in ferrets. The Madison team submitted its paper to Nature; the Netherlands’ team submitted to Science. Both papers came under government scrutiny before they were published because the methods in each could potentially be misused to make a bioweapon.

But the researchers had already presented their data at conferences, and they had institutional approval to initiate the experiments, facts that led Subhashini Chandrasekharan, co-coordinator of the journal club, to wonder aloud why it took until the point of publication to prompt a government and scientific scuffle over the experiments and the results.

“I’m not a virologist, but I don’t find any reason that the study should not be done or that the results should not be published. The jump of this virus from birds to humans is going to happen. It’s only a matter of time. If we already understand the mutations, then we’ll be faster at finding treatments and vaccines,” Chandrasekharan said.

She added that if a bioterrorist is going to make a weapon from a virus, it didn’t seem likely that they’d need the papers, which were finally approved for publication on April 20, to make the mutations. They’d do it anyway, she said, explaining that preventing publication was probably not going to be “the wall” to stop a terrorist from plotting an attack.

That issue, of course, raises another whole set of squawks.

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

Category: Students Page 39 of 42

Hands-On Lab Experience Helps Student Set Goals

Trinity Junior in Phoenix for Summer, Doing Real Research

Sleuths Take Over Science This Summer

'Chicken' Logic Secures Planes, Trains and Ports

A Desensitized Fool Can Be a Little Monster

Student Profile: Jack Matteucci

A Tour of an All-White Garden

Maji Moto: Dispatches from a Drought

Rethinking science on pandemic-potential viruses

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