The Johns Hopkins Gazette: March 31, 2003
March 31, 2003
VOL. 32, NO. 28


Learning to
Dig In

PURA grants introduce 41 undergraduates to the world of research

By Amy Cowles

Johns Hopkins Gazette Online Edition

On his first overseas dig in Umm el-Marra, Syria, last July, aspiring archaeologist Matthew Kroot carefully sifted his way through thousands of years of accumulated earth, helping to uncover an ancient mortuary complex. Researchers hoped to find an untouched royal tomb like the one Kroot's adviser, Glenn Schwartz, had uncovered near the site three years ago.

The good news is they found a tomb from the Early Bronze Age, dating to 2400 B.C. The bad news is someone else had found it first, raiding the space thousands of years ago and leaving behind only a few bones and smashed pieces of pottery.

Matthew Kroot applied for a PURA to join his adviser, Glenn Schwartz, on an archaeological dig in Syria. Although the project didn't go as planned, both consider it a success. Here they're photographed with the JHU Archaeological Collection housed in Gilman Hall.

The looted tomb was the second unexpected turn in Kroot's Provost's Undergraduate Research Award project--he was originally slated to excavate a different building complex before personnel changes required him to switch to the mortuary site. But despite the change in plans and then the empty crypt, both Kroot and Schwartz consider the dig a success. Archaeologists must learn to expect the unexpected--a valuable lesson for Kroot to learn early in his career, Schwartz says.

"This is normal for archaeological expeditions, where you have to be flexible in the field," says Schwartz, Whiting Professor of Archaeology in the Krieger School's Department of Near Eastern Studies. "However, even though the tomb had been robbed, its discovery was very important because it confirmed the existence of a mortuary complex and revealed that the complex was used for at least a century or so, given the date of the pottery."

It's a lesson Kroot wouldn't have been able to afford to learn without a PURA grant.

"Archaeology is always a cash-strapped field," says Kroot, a 22-year-old senior from San Francisco. "To participate in digs, you have to go to field school, where you pay thousands to be somebody's lackey. I wouldn't have been able to participate without the PURA grant."

Since 1993, about 40 students each year have received PURA grants of up to $2,500 to conduct original research, some results of which have been published in professional journals. The awards, funded through a donation from the Hodson Trust, are an important part of the university's commitment to research opportunities for undergraduates.

On Tuesday, April 1, Steven Knapp, university provost and senior vice president for academic affairs, will host the 10th annual Provost's Undergraduate Research Awards ceremony, which will honor the 41 students who conducted their projects in the summer and fall of 2002. The entire Hopkins community is invited to the event, which will take place from 3 to 6 p.m. in the Glass Pavilion at Homewood. It will begin with an informal poster session during which the students will display and talk about their research projects, followed at 4:30 p.m. by the awards ceremony and a reception.

This year, the project topics ranged from robot-assisted surgery to the effects of sleep deprivation on college students. Some PURA researchers arrived at the conclusions they predicted when writing their proposals. Others, like Kroot, found that successful research can be about the journey and not just the destination.

Even though his dig didn't turn out the way he had anticipated, "it was still exciting because there were a lot of specialists from other countries at the site," Kroot says. "I actually only got to dig through the top layers before we had to stop and slow down to make way for the experts who deal with human remains. [But] I got to look over their shoulders and bug them by asking questions about what they were doing." What follows is a sampling of some of the other PURA projects.

When Ashish Patel came to Johns Hopkins, he never thought he'd spend a month in London doing in-the-field humanities research on the question of whether religious stigmatization explained why South Asians of Muslim descent did less well financially than their Hindu counterparts.

"I pictured myself working in a lab," says the sophomore biomedical engineering major from Clarksville, Md. And he is, in fact, doing that. But after taking a Comparative American Cultures class, he got interested in pursuing a humanities project. And a PURA grant allowed him to do it.

Ashish Patel traveled with his tape recorder to London, where he interviewed immigrants of South Asian descent to determine if religious bias kept Muslims from succeeding economically.

Over the course of four weeks last summer, Patel tracked down and did lengthy interviews with 25 immigrants of South Asian descent, including nine Indian Hindus, five Indian Muslims, eight Bangladeshi Muslims and three Pakistani Muslims.

Before he went, his theory was that religious bias kept the Muslim immigrants from doing as well economically in Britain, but his research didn't bear that out. What he found was that the groups that did better had gone from South Asia to establish businesses in East Africa before coming to Britain, and their parents had invested greater resources in educating their children, so that when they did arrive in England, they were better prepared to compete. Also, they had already been exposed to British-style institutions and business practices.

The other immigrants he interviewed had come directly to England from their native countries, and, Patel says, "These parents knew that knowing English and pursuing education were important, but they didn't have the means to support that."

Although Patel's study size is small and not statistically significant, he did probe people for statistically verifiable information, he says. "Indeed, my goal in doing this project was to move away from a general statistical description of immigrant experience in England and describe unique individual stories and the vibrant immigrant culture of the three different ethnic minority communities," he says.

He is now working on a paper that lays out his findings, which he may try to have published.

The research experience itself, he says, was rewarding, although it had a rocky beginning. Before he went to England, he was confident he'd have no trouble locating interview subjects or finding his way around. But once he arrived, he was "pretty nervous" and not sure he could pull it off.

"My first week there, I only had two interviews, so I was off to a slow start," he says. "At first, it was hard for me to go up to people, but by the second week, I had built up my nerve." He tape-recorded all the interviews--each averaged 90 minutes--and then laboriously transcribed them upon his return.

Patel says he really appreciates the opportunity to try something outside his major, and "I would like to do something like this again."
--Glenn Small

Daniell Dokko, a senior majoring in biomedical engineering, used his PURA grant to stay close to home. He spent last summer in Baltimore working with graduate students on a way to give a medical robot a rudimentary sense of "touch" and then send that information instantly to the surgeon who is controlling the machine.

The project is important because minimally invasive operations performed with robotic assistance can speed a patient's recovery by reducing the size of the incision and the need to move other tissue. During such operations, doctors direct a robot from a remote work station, using tiny cameras to guide the machine through delicate work. But generally these surgeons do not know how much force the robot is exerting when they direct it to tie sutures or manipulate the body.

Daniell Dokko, center, worked with sponsor Allison Okamura and doctoral student Masaya Kitagawa on a way to convey a medical robot's sense of 'touch' to the surgeon controlling it.

Johns Hopkins researchers, led by Allison Okamura, assistant professor of mechanical engineering, have been looking for a method of providing such haptic feedback to surgeons, and during his junior year Dokko was permitted to join this team.

Dokko's PURA enabled him to remain at Johns Hopkins last summer to work full-time in Okamura's lab. "First, I worked on adding a tiny sensor called a strain gauge to a robotic surgical tool so that we could measure the forces it exerts when it touches the body and when it ties sutures," says Dokko, who is from La Canada, Calif. "In the second phase we looked at another important issue: Once you have the force information, how do you give it back to the surgeon, who's seated somewhere else in front of a video monitor, guiding the operation?"

For this part of the project, Dokko worked with Masaya Kitagawa, a doctoral student in mechanical engineering from Osaka, Japan. "In traditional surgery, doctors control the amount of force they exert with their hands based on their own experience," Kitagawa says. "We knew that if we could tell the surgeons how much force the robotic 'fingers' were applying, it would be more like their own hands were working inside the patient."

This knowledge can be particularly useful when robotic tools are used to tie a suture. These knots must be firm enough to hold the incision together, but the tool must not apply so much force that it breaks the sutures or injures the tissue. To get the force information to the surgeons, Dokko and Kitagawa tested several ideas. One option was an audio signal that grew louder as the force increased, but some surgeons objected because the operating room already is cluttered with the sounds of spoken commands and medical equipment.

The researchers then focused on a visual system, tucked into a corner of the video screen that a surgeon uses to guide the robot. They devised a bar graph that rises and changes color as the force increases. The surgeon also sees a dotted line that indicates the appropriate level of force for the procedure. Dokko and Masaya added their experimental setup to a da Vinci medical robot being used for training and research at The Johns Hopkins Hospital. Most surgeons who have tested the system have been pleased by it, the researchers say. Dokko and Kitagawa are preparing a paper about their project and hope to present it at a medical technology conference in September.

Dokko, who expects to receive his undergraduate diploma in May, is still weighing graduate school options. But he says the opportunity to work on medical robotics in Okamura's haptics lab has influenced his thinking. "This is definitely something I'm interested in pursuing further," he says. "I've really appreciated the chance to work in a lab here on a project that means something, something where I can see the results of my work. It's much more rewarding than just doing some repetitive task to get practice in a particular subject."
--Phil Sneiderman

Dividing Jerusalem into two cities--one Jewish and one Palestinian--was a key piece of the 2000 Camp David Peace Accords, but so far, that hasn't happened. Jacob Raver, a senior international relations major from Scarsdale, N.Y., wanted a better understanding of why that is the case and also wanted to see for himself whether there is any chance of two Jerusalems peacefully coexisting.

Raver spent time with books and interviewed experts during a visit to Jerusalem this past January. But he also got out into the neighborhoods, both Jewish and Arab.

Jacob Raver wanted a better understanding of why Jerusalem hasn't been divided into Jewish and Palestinian cities, so he traveled there to study and walk the neighborhoods.

"Jacob went to Jerusalem and explored the neighborhoods that would likely form a Palestinian capital," says Steven David, associate dean for academic affairs in the Krieger School of Arts and Sciences, a Middle East expert and Raver's adviser on the project. "By personally walking the walks as to where the borders would be, he was able to gain firsthand insights into this seemingly intractable problem."

While acknowledging the incredible complexity of the situation, Raver says he nonetheless came away believing that two Jerusalems could coexist, functioning perhaps like boroughs do in New York City.

"Facts on the ground," he says, "walls are being built" between Jewish and Arab areas of the city. But, he says, if the city is to be divided peacefully, walls must not be part of the equation. "This is a city that needs to be open," he says. "If you have a wall, a terrorist is going to figure out how to get over that wall. What's more effective than walls is intelligence and cooperation."

Raver, who is studying Hebrew and Arabic and wants to pursue a graduate degree in Middle Eastern studies, acknowledges that a peacefully divided Jerusalem appears unlikely anytime soon. But, he adds, "You don't know what can happen. Things that seem impossible can happen in the Middle East."
--Glenn Small

Senior Erik Lontok switched from premedical study to a focus on virology when he began to get a sense of how amazing and intriguing the basic workings of viruses can be.

"You get me talking about viruses, and my eyes get big," Lontok says with a mischievous grin. "My friends know I'm a real weirdo about it: I love viruses. I just find it amazing that these little parasites can mess with cells so well."

'I love viruses,' says Erik Lontok. Working last summer in the lab of Carolyn Machamer, his sponsor, he conducted original research into infectious bronchitis virus, a suspect in SARS.

This summer Lontok used a PURA grant to conduct research into infectious bronchitis virus, or IBV, a disease that affects chickens and belongs to a broader class of viruses, the coronaviruses, that the Centers for Disease Control recently identified as a leading suspect in a deadly new human disease, sudden acute respiratory syndrome, or SARS.

Lontok's sponsor was Carolyn Machamer, an associate professor of cell biology in the School of Medicine, for whom he's been working for several years. Machamer studies IBV and the cellular organelle known as the Golgi apparatus.

It's far too early to tell if Lontok's basic research will have an impact on clinical efforts to understand and treat SARS. Debate continues among health experts as to whether SARS is caused by a coronavirus, the class of virus that includes IBV and is responsible for about 20 percent of the common cold in humans, or another type of virus altogether. Infectious bronchitis virus has unique genetic features that places it in its own class of cornaviruses, and these features could yield insights into the potential new coronavirus group to which the SARS agent may belong.

Clinical relevance would be icing on the cake for Lontok, who's deeply intrigued by new insights into the basic workings of the virus. For his project, Lontok studied an IBV protein known as the Spike or S protein, probing how IBV creates and incorporates the protein into new virus particles.

"Most viruses infect a cell, get the cell to make copies of itself and its proteins, and when they're ready to leave, they bud out of the outermost cell membrane," Lontok says. "Coronaviruses, though, bud into the Golgi apparatus. There's got to be a reason why they do that, some sort of advantage--viruses are simply elegant, and they don't mess around."

IBV makes an ideal model for study of these kinds of questions, Lontok notes, because it infects only chickens, making it easier for humans to safely study it.

Lontok was able to show that the S protein has an amino acid sequence at its very end that allows cellular machinery to retrieve the protein from the Golgi apparatus to the endoplasmic reticulum, another cellular organelle. The endoplasmic reticulum in turn tends to move proteins toward the Golgi apparatus. This special targeting sequence in the S protein thus keeps it cycling in the cellular compartments where IBV assembles.

At this point it's just a theory, but Lontok wonders if the S protein might not be helping IBV select its assembly site. After receiving his bachelor's degree in biology, the Burbank, Calif., resident plans to continue studying this and other theories about IBV while working toward a master's degree at Johns Hopkins.
--Michael Purdy

A dual major in mathematical sciences and neuroscience, Allison Barker is analyzing numbers derived from digital images of the brain, looking for trends that may help doctors identify patients in the very early stages of Alzheimer's disease. Barker, a 21-year-old senior from Williamsville, N.Y., said her statistical tests indicate that thinning in a part of the brain called the cingulate gyrus is found more often in patients suffering from a type of dementia associated with Alzheimer's.

Allison Barker, here with adviser Carey Priebe, is analyzing numbers derived from digital images of the brain, looking for trends that may help physicians identify early Alzheimer's disease.

Barker is collaborating with faculty members on a paper based on these findings, and the researchers plan to submit the paper soon to a scholarly journal. "These results are very important and exciting," Barker says. "I think it's really amazing that I, as an undergraduate, have been given so much responsibility in an important project like this."

Her research is part of a larger project being conducted at the Center for Imaging Science at Johns Hopkins, which is directed by Michael I. Miller, a professor of biomedical engineering and of electrical and computer engineering. The center is producing three-dimensional computer models of portions of the brain based on magnetic resonance images from patients with Alzheimer's disease and from healthy people. By comparing these images, the researchers hope to identify changes in the brain that occur when the disease is in its earliest stages, an important window of opportunity for medications that might halt or reverse this degenerative ailment.

Barker's involvement began in spring 2002, when her undergraduate adviser, Carey Priebe, asked her to conduct some statistical analyses needed in the project. Priebe, a professor of mathematical sciences who is affiliated with the Center for Imaging Science, urged Barker to find funding to support her efforts. She applied for and received a Provost's Undergraduate Research Award. So last summer, Barker remained in Baltimore, processing numbers representing the thickness of tissue called gray matter in the cingulate gyrus, a section of the brain that is critical to memory and learning functions.

The task was daunting because each brain segment Barker studied was accompanied by up to 400,000 measurements. "The long-term goal is to build a classifier, a way to use these numbers as a predictive tool to find people who may be in the earliest stages of dementia," she says.

Priebe, Barker's faculty sponsor, was available to answer questions and check her results, but he did not try to micro-manage her work, she says. "He was really good about taking a back seat, being there to advise me when I needed it but giving me the project to run with," Barker says. "I can really feel like I produced this from beginning to end."

Barker plans to spend another year on the project as a paid researcher before enrolling in medical school in fall 2004. "I'm very interested in this project and where it's going," she says. "This has been a thrilling experience. That's one of the reasons I came here--because of the way professors are willing to let you get involved in the research. That's really the best way to learn."

Some of her PURA funds will enable Barker to travel to San Francisco in August to discuss her work at a conference of statistics researchers.
--Phil Sneiderman

After three long years of watching his friends pull all-nighters, senior Terry Dean, a neuroscience major from Vineland, N.J., began to wonder if sleep deprivation affected his friends' performance on exams.

So he decided to conduct an experiment: He found four random Johns Hopkins students, deprived them of sleep for more than 24 hours and then stuck them in a small room for Friday night and much of Saturday to see how they would act. By the end of the experiment, he had data on 20 sleep-deprived subjects and 20 controls to compare.

"I did analyses of two different types of data--mood performance and cognitive testing--and they were not significantly correlated with the amount of sleep they had," Dean says.

Dean's sponsor, Richard Allen, a research associate at Bayview Medical Center and an assistant professor of neuroscience at the School of Medicine, said he has not overseen a better project.

"He was very thorough. There are few studies that have looked at the combination of mood and cognitive testing," Allen says. "Other studies look at mood or cognition studies [separately]."

It turned out that sleep deprivation had no clear, consistent impact on student performance but instead was a case-by-case situation.

"I thought I would have something more concrete," Dean says. "But some people don't perform as well, and some people perform as if they got the normal amount of sleep."

Dean says he found it much more difficult to find students willing to be controls and to sleep seven hours per night than to find students eager to endure a long bout of sleeplessness.

Every night for an entire week, control subjects had to be in bed by at least 1:30 a.m. and sleep more than seven hours. And to make sure controls were honest, Dean asked them to wear an activity monitor night and day, whenever they weren't in the shower. "An activity monitor is a wristwatch-shaped device and takes account of the amount of movement for a certain epoch in time," Dean says.

To scrounge up willing controls, Dean had to raise his money offer of $25 to $40. "Nobody wants to have to sleep for seven hours every night right in a row," Dean says.

Dean offered $100 to students willing to go without sleep for his experiment.

Sleep-deprived subjects slept a normal amount the Thursday night before their evaluation; on Friday evening they reported to Dean's Homewood apartment and stayed there until late Saturday afternoon. While they could not sleep, they could take one or two walks if accompanied by one of Dean's assistants.

Altogether, Dean tested 27 sleep-deprived subjects, but he had to throw out the data for the first seven after he decided his original form of testing was inefficient. He had tested both controls and sleep-deprived subjects with cognitive and mood tests to evaluate how much sleep deprivation affects performance. But after testing the first seven sleep-deprived subjects, he realized the word association task he had used failed to provide hard results.

"I gave them a noun, and they gave me [related] verbs," Dean says. "I didn't really have a way to measure these responses, so I changed it to the verbal fluency task, which gives them a letter and counts the numbers of words [beginning with that letter] they generate."

Problems such as his testing flaw taught Dean the intricacies of independent research, and the project gave him the opportunity to research outside a laboratory.

"I want to do research, but finding myself on a bench for hours in a lab doesn't seem interesting to me," he says.

Dean is pursuing a five-year bachelor's/master's degree and will continue research with Allen next year on animal behavior.
--Jessica Valdez

Kristin Olesen, a senior from Racine, Wis., is researching the biochemical changes that occur in birds' brains when sexual rivals enter their turf, triggering defensive outbursts of song.

Working under sponsor Gregory Ball, a professor of psychological and brain sciences, and with support from a PURA, Olesen has been administering doses of the hormone estradiol to canaries. Estradiol is found in estrogen and is a byproduct of testosterone.

Kristin Olesen, working under sponsor Gregory Ball, is researching the biochemical changes that occur in birds' brains when sexual rivals enter their turf, triggering outbursts of song.

"There's some evidence from field studies that when male birds are in a territorial frame of mind during mating season and an invader comes into their territory, they will experience a rapid surge in testosterone production, which is closely followed by increased singing," Olesen explains. "Basically, song is their way of defending their turf, and what we're looking for is how that rapid surge of testosterone relates to the behavior."

After exposing the birds to estradiol, Olesen examines regions of the birds' brains involved in song production and sexual activity for the presence of cyclic AMP response element binding protein, or CREB. When modified through a biological process known as phosphorylation, a phenomenon that occurs more often in the presence of competitors, CREB can act as a transcription factor, promoting the creation of other proteins by binding to DNA. Scientists suspect these other proteins may help trigger brain changes that permit a bird to challenge invaders with a burst of song.

"What I'm looking at right now is just one of multiple, multiple transcription factors that could potentially be activated," Olesen explains. "Once I get done with this protein, I'm hoping to look at tyrosine hydroxylase."

Preliminary evidence from one of the Ball research group's collaborators has shown that tyrosine hydroxylase also gets phosphorylated at an increased rate after a hormone surge.

Olesen plans to attend graduate school at a Wisconsin university, where she hopes to continue to study similar brain mechanisms in rats.
--Michael Purdy

Senior Ali Rabbani, a film and media studies major, set out on a three-week road trip last summer to film what he believed to be the "uncommercialized America," the rural life as yet untouched by corporate media. With funds provided by a Provost's Undergraduate Research Grant, he wanted to capture the simplicity of rural life as a sharp contrast to what he believed to be the commercialization of city and suburban life.

But after driving randomly throughout the United States, he learned that commercial city life is not necessarily inferior to life in rural America; it's only different.

"I wanted to say that people in cities and suburbs are essentially living for the sake of the media and corporations," says Rabbani, who is from Bloomfield Hills, Mich. But what he found, he says, was that people in the country are not too different from people in the city; they only live a different life.

With farmhouses often miles apart and little interaction with neighbors, most rural residents had satellite television and access to commercialized life, he says.

But as one who was born just outside Detroit, Rabbani was struck by the remoteness of much of America. Many of the small towns he visited were "primitive," he says, some only a cluster of houses in the midst of empty farmland.

While he planned to focus on nature shots to contrast with cityscapes, he found that most of his footage featured the stories of the people he met.

"I was really nervous at first because it's intimidating to go up to someone with a camera," Rabbani says. "But most people were friendly and just wanted to talk, especially the older people.

"The film definitely changed," he says. "At the beginning it was supposed to be very abstract, but as I did it, I got into the people aspect, and I decided to make it more like a documentary."

Now, Rabbani has 300 hours of footage for a film he plans to make 30 minutes in length. The first third will show the natural settings of America untouched by human development, the second will feature interviews of people in small towns, and the third will focus on city life.
--Jessica Valdez

The Tenth Annual PURA Ceremony
Check out their results!

To recognize the winners of the 2002 Provost's Undergraduate Research Awards, an event will be held from 3 to 6 p.m. on Tuesday, April 1, in Homewood's Glass Pavilion.

A poster session in which students will have an opportunity to display the results of their research begins at 3 p.m. At the ceremony, scheduled for 4:30 p.m., Steven Knapp, provost and senior vice president for academic affairs, will introduce the honorees, and Theodore Poehler, vice provost for research and chair of the selection committee, will present their certificates. Also on the agenda will be excerpts from "CD Recording of Ernesto Lecuona's Andalucia Suite," Monica Lopez-Gonzalez's summer project. A reception with music by Lopez-Gonzalez follows.

The entire Johns Hopkins community is invited.