Category: Students Page 33 of 42

A Summer In The Lab, Wounding Flies

On July 15, 2014

By Ashley Mooney

Senior biology major and chemistry minor Rachel Shenker is working as a Dean’s Summer Research Fellow, trying to figure out how certain proteins affect wound-healing in flies.

Rachel Shenker is in Durham this summer, not Sydney.

In particular, she’s working with a protein called integrin, a cell surface signaling protein found in every animal from sponges to humans. Shenker, who is from Rockville Centre, New York, is studying how the protein is involved in fruit fly embryo development and wound healing.

Using fluorescent dyes and a microscope, Shenker is able to see where the protein of interest is in the fly embryos as they develop. She also records images of the embryos for later comparisons.

“What I find really interesting about it is to see how the smallest protein can really change an entire organism,” Shenker said. “Every organism has it in different combinations, so that’s why it’s really relevant to humans and other animals.”

This is the alpha subunit of an integrin receptor. Fruitfly receptors have 5 of these; mammals have 18. (Credit: European Bioinformatics Institute)

Shenker is still trying to understand how integrins function in normal fly embryos, and has not yet started experiments that involve wounding the embryos and observing their reactions. She said once she has a better idea of how the proteins work, she will begin wound-healing experiments.

Shenker conducted similar research in high school and decided to get involved in Biology Professor Daniel Kiehart’s lab after seeing his name in several published papers. She began working in his lab during orientation week of her freshman year, and has been doing research and independent studies ever since. Shenker will use her current research to complete a senior thesis this year.

Beyond her involvement with research, Shenker volunteers at the Duke Cancer Center, is involved with the Jewish Student Union and participates in Greek life. She is also on the executive board of Duke Global Medical Brigades, and has gone on a few trips to Honduras with the program.

“We went to some of the rural areas of Honduras and volunteered in a clinic that we set up to help provide basic healthcare to citizens who really needed it,” she said. “It was a great experience that really put me out of my comfort zone.”

Shenker is currently applying to medical school.

Math and Comp Sci Junior Studies Fruit Flies

By Karl Bates

On July 9, 2014

In Animals, Biology, Computers/Technology, Mathematics, Students

By Ashley Mooney

Dorsal closure is a stage in fruitfly embryonic development that is used to study wound-healing.

Roger Zou, a computer science and math major from Solon, Ohio, is working on creating more efficient ways to study wound-healing in fruit flies. It turns out that the way fruit flies heal actually has implications for how mammals heal too.

The junior is developing computational methods that can more accurately quantify cellular properties of fruit flies. As fruit fly embryos develop, he tracks cells through space and time to learn more about a process called dorsal closure. It’s a developmental stage that is similar to wound healing, where a gap in the embryo’s epithelium—which is like its skin—is closed by the coordinated effort of different types of cells. (see movie below)

Roger Zou is a junior spending the summer in Dan Kiehart’s lab.

“It’s fun to study the morphological forces because it’s not entirely understood how organisms develop,” Zou said.

In his analysis, Zou uses a laser under a microscope to make cuts on areas of the fly embryos. After making cuts, Zou uses computational methods to measure the wound healing.

Beyond collecting such data, Zou is developing a computer program that analyzes images from the microscope more accurately.

Zou has worked in Biology Professor Daniel Kiehart’s lab since his freshman year. His project was originally a component of a graduate student’s dissertation, but after she graduated, he continued some aspects of her research.

His project has been funded by the Dean’s Summer Research Fellowship for two consecutive summers. He also has done several independent study projects. Although Zou is planning on publishing his research this summer, he will likely use the data eventually to do a senior thesis.

Several of Zou’s math and computer science classes have given him a background in the techniques needed to use a computer to analyze large sets of image data, he said.

“My favorite thing about my research is the ability to learn new things independently,” Zou said. “[Kiehart] is very good at leading me in the right direction but allowing me to be very independent and I think because of that I’ve been able to learn a lot more and learn from my mistakes.”

Outside of his research, Zou is a teaching assistant for the computer science class Data Structures and Algorithms. He also tutors Duke students in organic chemistry and middle school children in math through the America Reads*America Counts program. And he also does web development for The Chronicle, Duke University’s independent student newspaper.

After graduating, Zou said he hopes to pursue a PhD in either computational biology or computer science or maybe go for a combined MD-PhD program. No matter which program he chooses, Zou said he wants to continue doing research.

[youtube http://www.youtube.com/watch?v=Yk-O_W1Wqbc?rel=0]

Student's Summer is a Deep Dive into Deep Math

By Karl Bates

On July 2, 2014

In Mathematics, Students

By Ashley Mooney

Math and computer science student Will Victor is spending his summer immersed in Albert Einstein’s theory of general relativity and learning to conduct mathematics research.

Will Victor is a rising senior at Duke who’s spending the summer studying math — for fun!

Victor, from Aiken, South Carolina, is working with math and physics Professor Hubert Bray to explore how geometry relates to general relativity. General relativity explains how gravity affects space and time — pulling on them to create curvature we can both predict and measure. Think of how a world map must have curved latitude and longitude lines so that the representation of distances between spots on the curved surface of the globe are correct.

Victor is studying a class of objects called manifolds. It’s a field of math that describes the surface of complicated structures — anything from landmasses to a misshapen wad of clay — and it has practical applications in areas of mathematical physics such as black holes, dark matter and dark energy, the phenomena that Victor’s mentor studies.

“There’s a lot to be said about how fun it is to really know what the boundaries of the field are and to think about how we might attack answering the questions of what we don’t know,” Victor said.

This summer, he’s reading mathematical research and doing practice problems to learn the material. “I work problems every day to prepare my mind for research,” Victor said. He also works with Bray’s graduate students to see how they are tackling their own research questions.

The rising senior is part of the PRUV Fellowship program, a 6-week research mentorship sponsored by the Department of Mathematics. After the summer, he will participate in independent studies and eventually write a senior thesis on his research or pursue graduation with distinction.

Victor said his math classes have been essential to preparing him for research by helping him solve math problems, learn theorems, improve proof techniques and get exposure to different types of problems.

“Having a depth and breadth of mathematical knowledge is essential to being able to conduct research in the field,” Victor said. “Learning mathematics consists of acquiring both a formal language and a toolbox of argumentative frameworks which allow a student to speak precisely about theoretical problems.”

Victor noted that the classes he has taken in algebraic structures and classical analysis have provided the framework for talking about any type of modern mathematical question.

Beyond his research, Victor is involved with the selective living group Round Table and a member of the juggling club. He also works with the Community Empowerment Fund, an organization that works with and fosters relationships with the working poor in Durham and Chapel Hill.

“Our goal is to empower people to eventually obtain stable housing and stable employment,” Victor said. “We provide an accountability source for them, so we meet and talk weekly.”

After graduation, Victor says he hopes to go to graduate school in math and continue doing math research. “I enjoy the field I’m in, but I haven’t seen enough math to necessarily know this is what I’m most interested in,” Victor said. “I want to get exposed to more before deciding what I will specialize in.”

Interfaith Groups Build Bridges Praying Together

By Karl Bates

On June 26, 2014

In Behavior/Psychology, Guest Post, Students

By Eric Ferreri, News & Communications

Organizations are turning to prayer to help bridge differences among employees, according to a new study involving a Duke University graduate student.

The study finds that interfaith group prayer serves as a “bridging cultural practice” within multi-faith groups studied by three researchers including Brad Fulton, a PhD student in Duke’s sociology department.

Interfaith prayer builds bridges if diversity is acknowledged and accepted. (iStock photo)

The study, published this month in the American Sociological Review, consists of data from a national study of multi-faith community organizing groups.

Interfaith group prayers took place in about 75 percent of the diverse gatherings analyzed over two years. Those prayers are considered a “bridging cultural practice,” a way to help people of disparate backgrounds find common ground.

Fulton acknowledged that prayer doesn’t work for all groups or organizations. But bridging practices aren’t just religious in nature. Some could involve food, sports or other activities. And he believes organizations that focus on the similarities of their people but ignore differences aren’t realizing the full benefits of diversity.

“It is risky to simply assume that people from diverse backgrounds will automatically work well together,” he said. “More diversity tends to correspond with more challenges. But organizations tend to be more effective when they engage, rather than avoid, the varied backgrounds represented in their workforce.”

Fulton is one of three co-authors of the paper along with Ruth Braunstein of the University of Connecticut and Richard L. Wood from the University of New Mexico.

Primary funding for the national study was provided by Interfaith Funders, along with secondary grants from the Hearst Foundation, Society for the Scientific Study of Religion, Religious Research Association, the Louisville Institute, and Duke University.

Duke Undergrads Sink Their Teeth into Evolution Research

By Erin Weeks

On June 16, 2014

In Animals, Biology, Faculty, Genetics/Genomics, Science Communication & Education, Students

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

By Erin Weeks

The evolution of thick tooth enamel helped turn our species into hard food-chomping omnivores, and two undergraduates are taking a bite out of research to unravel how that happened. Amalia Cong and Ben Schwartz are building on the work of a recent paper that identified precisely where in the human genome natural selection worked to give our species thick tooth enamel. The original study looked only at the potential role of four genes with a known role in tooth development — so now the team is broadening their scope.

“They’re really excited to expand out and push the envelope on new genes,” said Christine Wall, associate research professor of evolutionary anthropology and one of the authors of the paper, along with professor of biology Greg Wray.

Cong and Schwartz arrived in the Wall and Wray labs last summer through a special research session at Duke, the Howard Hughes Vertical Integration Partners (VIP) Program. For ten weeks, they received a crash course in primate evolutionary genomics.

“They had very little time, and the progress they made was astounding,” Wall said. “The success that they had is really a testament to how hard they worked. This has developed into their own research.”

“We’ve begun to expand our tooth enamel gene analysis to include proteins in conjunction with the RNA in order to gain a more holistic understanding of the evolutionary differences that exist between chimpanzees and humans,” Schwartz said. He will continue to work in the lab through this summer, turning the work into a senior thesis.

“One of our goals was to look at the relative expression of these few genes,” Schwartz said, which they’ve done by comparing tooth development in primates of different ages. “Our results correlated very heavily with known functions of these genes in other animals, such as rats.”

The experience has given both students a taste for research, which they hope to continue doing after graduating from Duke. Cong, who hails from a small city outside of Toronto, will be attending dental school in the fall, while Baltimore native Schwartz is interested in pursuing a joint MD/PhD.

Visibly Thinking about Undergrad Research

By Karl Bates

On April 23, 2014

In Science Communication & Education, Students, Visualization

By Karl Leif Bates

Undergraduate research is kind of a big deal at Duke.

The grand finale of nearly 200 of this year’s undergrad projects was a giant poster session called “Visible Thinking,” hosted by the Office of Undergraduate Research Support on April 22.

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

This annual showcase just keeps getting bigger, louder and more crowded, which is a great testament to the involvement of undergrads in all areas of Duke’s research enterprise.

The posters and proud students wearing their interview suits filled all the common areas of the first and second levels of the French Family Science Center on Tuesday and spilled into a few out-of-the-way corners as well.

“For many of the students this is the culmination of their four years, in which they’ve made that transition from student to scholar,” said Ron Grunwald, director of the URS office. “They’re no longer simply learning what other people have discovered, they’re discovering things on their own.”

Indeed, Rebecca Leylek wasn’t the least bit discouraged by having to check her experiment every six hours around the clock for days on end to see how the mice’s wounds were healing. The second phase of her project was a protocol she developed and got approval for and it didn’t have the six-hour part. She’s off to grad school at Stanford in immunology.

Ani Saraswathula, who co-chaired the Duke Undergraduate Research Society, apparently missed the deadline for getting his poster into the printed program, but his science on brain tumors was pretty awesome. He’s sticking around after graduation for an MD/PhD at Duke.

The new Bass Connections research teams brought nearly two dozen posters, showing off projects about energy, environmental health, art history, online education, cognitive development, and decision-making.

And then, there was just an amazing assortment of stinky lemurs and pathogenic yeast and budding investigators talking curious faculty and students through amazing posters like this: Understanding the role of BNP signaling in pak-3 mediated suppression of synaptic bouton defects in spastin null Drosophila.

So, in addition to quizzing the young scientists about their findings, we thought we’d ask a few of them to recite their impressive poster titles from memory:

[youtube http://www.youtube.com/watch?v=HWJWEs427WM?rel=0]

Rhyne King: Unearthing an Ancient Religion

By Olivia Zhu

On March 27, 2014

In Field Research, Students

By Olivia Zhu

Rhyne King, a senior from Greensboro, North Carolina, plunges into the depths of history to retrieve remnants of long-past civilizations. Rhyne is currently writing his senior thesis on the religion of the Achaemenid Empire of Persia, which existed in modern day Iran until 330 B.C.E., when Alexander the Great’s army conquered it. Specifically, Rhyne is focusing on what the Achaemenid religion was and how the Achaemenids treated foreign religions. Rhyne says that it is rather difficult to directly compare the Achaemenid religion to any modern religion, but that some imagine it to be similar to Zoroastrianism.

Rhyne’s skill set and dedication to his research are extraordinary in and of themselves. After spending the summer studying with Professor Jacques Bromberg, Rhyne added the skill of reading Old Persian to his repertoire of languages, which includes Latin, Greek, and Persian. He uses Old Persian, the language of the Achaemenid kings, to read inscriptions about their religion. Rhyne has also traveled to the British Museum in London to inspect Achaemenid inscriptions and art.

An inscription Rhyne studied at the British Museum

Rhyne pioneers investigation into the Achaemenid empire by balancing Greek accounts, which currently form a majority of the body of knowledge about the civilization, with Persian sources. He says that up to this point, historians have not reconciled the two sources systematically. Rhyne is particularly fascinated by the Achaemenid empire’s tolerance of religion. He emphasizes, however, that their tolerance, immortalized in the Cyrus inscription from Babylon, was not an ancient declaration of human rights; rather, it was the system that proved most convenient for them.

Throughout his four years at Duke, Rhyne has also served as president of the Round Table selective living group and the Latin Club, and he has played for the marching band. Rhyne plans to continue researching the Achaemenid Empire in graduate school, and to someday become a professor.

Grad Student Solves 30-Year-Old Physics Problem

By Erin Weeks

On March 27, 2014

In Faculty, Mathematics, Physics, Students

By Erin Weeks

Sometimes an age-old question just needs a fresh set of eyes.

That was the case in Duke’s physics department, where a graduate student and professor recently resolved a calculating dilemma that has vexed computational physicists for decades.

Emilie Huffman, second year PhD student in physics

Emilie Huffman is a second-year PhD student from Charlotte, North Carolina. Last spring she began working with Shailesh Chandrasekharan, an associate professor and the director of graduate studies in physics, on what’s known as a sign problem.

Chandrasekharan is a theoretical nuclear and particle physicist who specializes in solving sign problems, which arise when one uses certain computational algorithms to calculate the behavior of large numbers of particles called fermions.

“Almost all the matter we know of are made with fermions,” Chandrasekharan said. “As building blocks of matter, it’s very important to be able to do calculations with them.”

But calculations of such complexity get tricky, and sign problems make it easy for wrong results to surface.

“It’s a very broad problem that affects almost all fields of physics involving quantum mechanics with strong correlations, where Monte Carlo methods are essential to perform calculations,” Chandrasekharan said.

Some in the field have simply moved on since the 1980s, leaving interesting questions plagued by sign problems unexplored. Other scientists have found workarounds and approximations. Very few, including Chandrasekharan, have tried to figure out solutions through the years. Huffman began work to expand on one of her advisor’s solutions, involving a grouping concept called fermion bags, and apply them to a new class of problems.

“She finally figured out a nice formula,” Chandrasekharan said. “Although the formula is quite simple and elegant, I couldn’t guess it.”

“In physics, often there’s a truth, and if you’re hitting on the right truth, everything starts falling into place.” Chandrasekharan says that’s what happened when he began applying Huffman’s formula to a class of problems.

Their paper appeared recently in the journal Physical Review B’s Rapid Communications.

“Now that I have a solution, I can begin to apply it,” Huffman said. Starting with condensed matter physics, Huffman plans to apply her solution to various questions that have been stymied by sign problems. “I can use this solution to study properties of graphene,” she said, referring to the single-layer carbon that has been touted as the strongest material in the world. Many puzzles remain in the field, especially involving multi-layer graphene sheets.

Wherever she turns her attention next, it’s clear Huffman has a promising career ahead.

Citation: “Solution to sign problems in half-filled spin-polarized electronic systems,” Emilie Huffman and Shailesh Chandrasekharan. Physical Review B Rapid Communications, March 12, 2014. DOI: 10.1103/PhysRevB.89.111101.

Some Animals Move Through The Treetops With Help From A Stiff Back

By Karl Bates

On March 26, 2014

In Animals, Biomedical Engineering, Lemurs, Students

Guest post from Robin A. Smith, Duke Lemur Center

Some tree-dwelling animals move through the forest with the help of an unlikely tool — a stiff back. A more rigid spine seems to help stabilize their trunks as they reach across gaps in the canopy, according to Duke researchers.

The slender loris (Loris tardigradus) is able to exploit tender tips of tree branches by moving slowly and keeping a stiff back rather than leaping from branch to branch. (Credit: David Haring, Duke Lemur Center)

The findings appear in the March 2014 issue of the Journal of Morphology.

Animals that live in the treetops need to be good at crossing gaps between trees in order to move and forage in the canopy without constantly climbing up and down. Some animals leap, hop or bound from branch to branch, flying through the forest in a feat of aerial acrobatics. But others move more slowly and deliberately, reaching out and grabbing onto the tips of the nearest tree to form a bridge and pulling themselves across.

The latter strategy helps some animals venture onto slender branch tips where young leaves and fruits are often found –- perches that are too thin and delicate to leap off without buckling, said lead author Michael Granatosky, a grad student in Evolutionary Anthropology.

To investigate the anatomical traits that help some animals bridge rather than bound between branches, Granatosky and colleagues pored over skeletons in museums and took measurements of the spines and ribs of 22 species — including lemurs, treeshrews, anteaters, opossums and squirrels. Some of the species move slowly and cautiously through the treetops, while others leap and jump.

The researchers also analyzed the bridging behavior of two pairs of closely-related species — the bare-tailed woolly opossum versus the gray short-tailed opossum, and the fat-tailed dwarf lemur versus the slender loris — while the animals negotiated custom-made jungle gyms.

The opossum study was part of a previous experiment by co-authors Daniel Schmitt and Pierre Lemelin at Duke, and the primate study was conducted at the Duke Lemur Center.

The researchers found that the species that bridged more often, or for longer periods of time, had narrower spaces between adjacent ribs and vertebrae.

[youtube http://www.youtube.com/watch?v=VA8diXNvffY?rel=0]

Their more tightly-woven spines limit their ability to bend side-to-side, but enable them to hold their body out straight to span openings in the canopy without relying on brute muscle strength alone, Granatosky said.

The study was funded by the Force and Motion Foundation and by a National Science Foundation Graduate Research Fellowship to Michael Granatosky.

CITATION: “Functional and evolutionary aspects of axial stability in Euarchontans and other mammals,” Granatosky, M., et al. Journal of Morphology, March 2014. DOI: 10.1002/jmor.20216. http://onlinelibrary.wiley.com/doi/10.1002/jmor.20216/abstract

Managing a Lab: The Parts You Won't Learn in Class

By Erin Weeks

On March 14, 2014

In Faculty, Lecture, Science Communication & Education, Students

Panelists (L-R) Sally Kornbluth, Jessica Monserrate, Mohamed Noor and Susan Smith (Photo: David Steinbrenner)

By Erin Weeks

For many researchers in training, making it as a scientist involves the dream of one day running their own lab. But becoming the head of a laboratory takes far more than research chops — you’ve got to have serious people skills, too.

A March 13 panel called “Managing a Lab: Insights from Academia and Industry” advised an auditorium of Duke postdocs and PhD students on how to meet the management challenges they may face one day as principal investigators (PI). “Effective lab management can be as crucial to career success as the research itself,” the description for the session read.

Sally Kornbluth, Vice Dean for Basic Sciences at Duke Medicine and Duke’s provost-elect, drew from her own experience as a PI as she walked the audience through the nitty-gritty of building a lab from the ground up.

“The lab takes on the style of the PI,” she said. The job of the lab head is to set its scientific direction, obtain grant money and hire the right people.

PIs have to make decisions about what kind of leader they want to be — how accessible do they want to be? How will they motivate their lab members? How will they deal with difficult personnel situations? Some of these questions will be determined by the lead scientist’s personality, Kornbluth said, but others may require trial and error to figure out.

The panel, put on by the Office of Postdoctoral Services, included three other lab managers representing both academia and industry: Mohamed Noor, professor and chair of the biology department; Jessica Monserrate, a scientist at Bayer CropScience and former Duke postdoc; and Susan Smith, a scientific investigator at Stiefel and also former Duke and Duke Med postdoc.

The speakers fielded questions reflecting anxieties about the work climate many students and postdocs will soon enter, in which grant budgets are shrinking and PI positions are highly competitive. But the audience also asked evergreen questions about careers in science, like how to keep up lab morale and balance research with family life.

“Choose your spouse very wisely,” Kornbluth said, drawing laughs.

Sally Kornbluth, Duke's soon-to-be Provost, talks about managing a lab. The talk will be available online soon.

Sally Kornbluth, Duke’s soon-to-be provost, talks about managing a lab (Photo: David Steinbrenner). The talk will be available online soon.