From GPS to GFPu: Calit2 Summer Scholars Conduct Research in the Health Sciences
NOTE: This report is Part Two in a two-part series on the research being conducted by this year's Calit2 Summer Undergraduate Research Scholars (Part One focused on students working on projects in the arts and humanities).
San Diego, Calif., Sept. 13, 2012 — In the famously beautiful climate of San Diego, advocates of the great outdoors are not difficult to come by. UC San Diego junior Michael Lam, however, is quick to note that spending time outside is not only enjoyable, but an imperative for good health.
“Simply being outside really has a lot of health benefits,” says Lam. “You get vitamin D, and there’s also an increase in physical activities, you’re less likely to be depressed and you have reduced stress.”
Along with 29 other UC San Diego students, Lam is a participant in Calit2’s 2012 Summer Undergraduate Research Scholars Program, a 10-week program that provides undergraduates with the opportunity to conduct full-time research under faculty supervision. In addition to granting students $3,000 each in scholarship money, the program includes twice-weekly seminar sessions that advise the scholarship winners on applying to graduate school, creating research posters for poster sessions, writing resumes and other related subjects. On Wednesday, Sept. 19, during UC San Diego’s Welcome Week, the program participants will present their research in a poster session in Calit2’s Atkinson Hall from 2 to 5 p.m.
Because the Summer Scholars come from a variety of academic fields, their research projects have taken place in labs spread across the UC San Diego campus. Lam’s work, however, is based at Calit2 itself: under the supervision of Prof. Jacqueline Kerr, he spent his 10 weeks in the Summer Scholars Program working with the Center for Wireless and Population Health Systems (CWPHS) in Atkinson Hall. As part of an ongoing effort to combine wireless technologies with preventive health care, Lam uses GPS technology to accurately track the time people spend outdoors and to extract information about their environment and physical activity levels.
Lam, who is majoring in General Biology, states that previous studies have shown the benefits of outdoor activity, yet observes that many researchers struggle to obtain accurate time measurements from subjects who spend time outdoors. Typically, he says, they choose to base their research on self-reported information, which leaves room for error.
“If I asked you right now how much time you spent outside yesterday, you’re not going to give me the precise, down-to-the-minute level,” he says. “But if you use GPS, you can.”
To this end, CWPHS conducted a study in which 40 participants were given a small GPS unit and a Microsoft-manufactured SenseCam (a camera that automatically takes pictures at roughly 20-second intervals, to be worn by a neck strap). They were also given an accelerometer, which senses changes in the speed and direction of motion. By wearing the SenseCam and the GPS for three to five days, the study participants provided the CWPHS researchers with nearly 2,000 hours of GPS signal data and over 230,000 SenseCam photos as material for comparison.
“By looking at the pictures that were captured and also the signal that was recorded,” explains Lam, “we can calculate the best cutoff to determine when people are inside and when they’re outside.”
The GPS calculations were performed by plugging the data into a Calit2-developed web-based program called the Personal Activity Location Measurement System (PALMS), which calculates information about physical activity and geographical location based on GPS input. “That program pretty much just merges the accelerometer and GPS data and tells us what the participants were doing, where they were doing it, how much physical activity they were doing and how much time they were doing it,” says Lam.
Lam notes that planned future studies will phase out the SenseCam and simply process the participants’ GPS data in PALMS to determine whether they are indoors are outdoors at a given moment. The SenseCam is taxing not only for researchers – it took a year for CWPHS to code the 230,000 pictures obtained from their study – but also for the participant.
“It’s a burden for the participant to wear a device that they have to put on their chest; it stands out,” he says. “So the ultimate goal is to remove that, use those pictures as a ground truth and just use the GPS.”
The ease and accuracy of GPS measurements from PALMS have substantial implications for preventive health and policy-making.
“The biological aspect of this is your genome,” says Lam, “and your environment really triggers the genes that you have.” He quotes a saying in biology: if genes are the bullet, environment is the gun.
“The big picture is then for policymakers to support and preserve a safe outdoor environment,” he says. “Your environment – your town and your neighborhood’s structure – can encourage you to go outside or to stay indoors. So that’s the really big picture of it, is to really have an impact on public health – to support regulations for a safe outdoor environment.”
Neuron Firing Patterns in the Basal Forebrain
Just as Lam’s GPS calculations track outdoor and indoor physical activity, sophomore Aditi Gupta’s research measures activity levels of a different kind: she has been working in Prof. Douglas Nitz’s cognitive science lab, studying how neurons in the basal forebrain fire as rats learn a task.
“The basal forebrain is unique in the sense that it’s the only subregion of the brain that has projections to go to different parts of the brain,” including the motor and prefrontal cortexes, explains Gupta, a bioengineering major. Because of these chemical connections between neurons, the basal forebrain “can kind of coordinate attention.”
Moreover, she observes, “it’s been implicated in diseases like Alzheimer’s disease, dementia, senility and the aging process. What it seems like right now is that damage in the basal forebrain causes one to not be able to pay attention as well, so that’s why damage in the basal forebrain causes some of these diseases – or studies show that it seems to.”
To investigate the basal forebrain’s connections to learning and attention, Gupta examines the rats’ basal forebrain neurons as they learn to perform a “reach task” over the course of 15 days. Each rat is placed in a small box with a window that connects to a platform. When a sugar pellet is placed on the platform, the rat must learn to reach its paw through the window to obtain it. Touching the sugar pellet disturbs a piezoelectric sensor on the platform, which releases an electrical charge and allows Gupta to pinpoint the precise moment of contact; electrodes implanted in the rat’s brain permit her to track the level of activity in its neurons during the five seconds before and after touching the pellet.
“What we’ve seen is that a lot of neurons have a huge spike in activity at the moment the rat touches the pellet, or right afterwards,” says Gupta. Interestingly, however, this result holds true only for what she calls success trials, in which “the rat is able to correctly grasp the pellet and bring it all the way back to its mouth.” In failure trials, the results are strikingly different: neuron activity actually decreases when the rat makes contact with the pellet but doesn’t succeed in capturing it. It is this discrepancy between the success and failure trials, she suggests, that may hold the most clues.
“The fact there is a decrease during failures kind of points to the idea that maybe the basal forebrain is sending a learning signal,” she says. “One of the projections of the basal forebrain goes to the motor cortex, and we know for a fact that the motor cortex changes as you learn a new activity. So the spike in activity might be a learning signal telling the motor cortex that that was the correct way to do the task, and the decrease might be a signal saying that was the wrong way to do it.”
Although Gupta’s research potentially has extensive applications to dementia and to related diseases, she remains focused on the task at hand – learning more about how the basal forebrain functions. The applications will follow later.
“I think it would be really interesting to be able to learn exactly how the basal forebrain works and how it controls attention. And I think the more you learn about a thing – the more information you have about it – the more you can apply it to a bunch of different things,” she says. “(There are) tons of different applications that we couldn’t even think of right now.”
Tracking Protein Degradation in Neurons Using Green Fluorescent Protein
Like Gupta, April Guan’s summer research topic has links to the possible causes of Alzheimer’s. In Prof. Gentry N. Patrick’s neurobiology lab, Guan, a junior majoring in biochemistry, has been studying the human ubiquitin proteasome system (UPS) pathway, engineering green fluorescent protein to target neurons’ dendritic spines.
Guan, who began working with Prof. Patrick the winter of her freshman year, states that the medical applications of the lab’s research first drew her interest. The UPS pathway, which breaks down damaged proteins in cells, has connections to “a lot of neurodegenerative diseases, like Alzheimer’s and Parkinson’s,” she says. “This pathway regulates the level of protein in the cell, and studies found out a lot of these diseases have aggregate damaged protein,” indicating that the pathway failed to degrade the protein as it normally should.
In keeping with these potential links to neurodegenerative diseases, Guan’s research examines the UPS pathway specifically in neurons, using a type of green fluorescent protein called GFPu as a “reporter” that reveals the pathway’s activity. Before the reporter is broken down by the UPS pathway, its color is bright; as the UPS pathway degrades it, its brightness decreases, indicating greater activity in the neuron.
As Guan explains, however, GFPu has drawbacks: “The problem is that it spreads throughout the neuron, and we just want to look at a specific part, because that’s where most of the major activity is.” This area consists of the neuron’s dendritic spines, which jut out from the dendrites. It is here that Guan’s project begins: her goal is to modify GFPu so that it targets the dendritic spines.
In order to target this region, Guan inserts a new gene, PDZ2, into the green fluorescent protein reporter. After cloning the modified reporter, GFPu-PDZ2, “a lot of troubleshooting” is necessary to ensure its efficacy. This troubleshooting involves running Western blots with the new material, which entail arranging samples in a gel container according to the length of time they have been left to degrade in neurons. In a process called gel electrophoresis, she then runs an electrical charge through the gel, causing the sample fragments to separate into different bands depending on their size. Later, she can detect the contents of the bands and determine whether the new material is working correctly.
“The longer the protein is in the cell, the more it’ll get degraded,” Guan says. “That’s what we expect from the reporter. So at zero time-point, we should see a lot of protein expressed because it doesn’t degrade as much.”
Because Guan’s project contributes to ongoing research on the UPS pathway in Prof. Patrick’s lab, she expects to continue working on it during the coming academic year. She credits the Calit2 Summer Scholars Program with helping her deepen her knowledge of the lab’s work.
“I really learned a lot of stuff in these 10 weeks, especially because I didn’t have classes,” she says. “We really have a lot of research going on, and I’m very glad that I can be part of it.”
Story by Micah Siegel
Tiffany Fox, (858) 246-0353, email@example.com