A Journal by The Triple Helix at the University of Chicago
Front and Back Cover Photos: Penguins. Booth Island, Antarctica. 2013 Photos by Sarah Larson
Scientia 4 11 14 16 18
In Depth Feasibility of Wood Chip Permeable Reactive Barriers for Large Scale In-Stream Denitrification Jonathan Pekarek
Works in Progress Stable Thermophoretic Trapping of Genetic Particles at Low Pressures Frankie Fung
Molecular Epidemiology of Recurrent MethicillinResistant Staphylococcus aureus Infections Tuyaa Montgomery
Barriers to Long-Acting Reversible Contraception Preethi Raju
Photos: Nature and Laboratory
Produced by The Triple Helix at the University of Chicago Layout and Design by Helena Zhang, Production Director Cover Letter written by Clara Sava-Segal, Co-Editor-in-Chief Scientia Board: Clara Sava-Segal, Jeremy Chang, Nilanjana Ray, Abhinav Ranjan, Quang Tran
Abstracts A Piezoelectric Biosensor for Biomechanical Cellular Measurements Guiding Cancer Therapy through Non-Invasive Quantitative Molecular Imaging of Cancers: Testing EGFR Status vs. Erbitux Therapy Impact of Abstinence-Only Sex Education on Teen Birth Rates at the State Level IR-SEC Studies of Group 6 and 7 Metal Carbonyl Catalysts for CO2 Reduction The Effect of Parental Support and Involvement on Sense of Belonging in School in African American Male Adolescents
24 26 28 30 2
Inquiries Mathematical Methods Meet Macromolecules: An Interview with Dr. Loretta Au Christian Porras
From Plant Biologist to Master of Biology Mimansa Dogra
"It's a Long Story" An Inquiry with Professor Diane Lauderdale Katie Zellner
A Theoretician and Experimentalist Walk into a Lab Meetingâ€Ś A Conversation with Drs. David and Elizabeth Kovar Samara Singh
About Scientia Dear Reader, The front cover of this issue presents an Antarctic scene of a penguin. One of many photos from our photography section, a new segment we have integrated in an effort to expose the many aspects of science. In addition to exploring student photography, we have included Works in Progress articles on flourishing projects currently being conducted on campus. By pairing these new sections with our traditional abstracts, iniepth articles and inquiries with professors, we intend to create a more substantial image of scientific exploration. This issue covers groundbreaking research in a variety of fields. It includes coverage on nitrate removal rates, levitation work, research on MRSA and potential in sex education. I encourage you to read our four Inquiries and notice not only the multidisciplinary approaches and projects that our faculty undertakes, but also the unique and vast career trajectories they have taken. You can learn about the use of computational models in biology or about the transition from a Bachelors of Arts in religion to doing epidemiological research. We have also continued our collaboration with other Chicago universities by incorporating several abstracts from the Chicago Area Undergraduate Research Symposium. Science is multifaceted and we hope to capture the diversity within the field through our exploration of new research domains and article types. Therefore, we encourage all who are working on a research project, interested in the work of a professor, or are photographers and would like to see your work in print to work with us. We encourage all interested to contact any member of our team, listed in the back. For the time being, please enjoy our spring issue of Scientia, by The Triple Helix. Best,â€¨Clara Sava-Segal Co-Editor-in-Chief, Scientia
In Depth Feasibility of Wood Chip Permeable Reactive Barriers for Large Scale In-Stream Denitrification Jonathan Pekarek, Dr. Kenneth Foreman Marine Biological Laboratory, Woods Hole, MA Abstract Since the Industrial Era, humans have been steadily loading nitrate into streams and groundwater, a practice that leads to problems like eutrophication and toxic algal blooms. Diverting water through underground wood chip beds that promote growth of denitrifying bacteria has seen increasing use as a way to reduce nitrate in water before the water reaches the estuary. These wood chip permeable reactive barriers have been used to remove nitrate from groundwater with wide levels of success, but the use of these systems in stream water has drawn less attention due to the larger temperature variations and faster flow rate of stream water. The nitrate removal rate response of these barriers to different temperatures, residence times of water, and wood chip sizes were tested in microcosms fed with nitrate-spiked stream water. Higher rates of nitrate removal were found with higher temperatures, longer residence times, and larger wood chip sizes. A robust equation was created that can predict nitrate removal rates based on these three independent variables. Significant responses of the microcosms to the three varied conditions were found, indicating that finding optimal conditions of these variables is very important for efficient nitrate removal in these barriers. Optimal residence time depends on temperature and wood chip size, but nitrate removal rate only increases with higher temperatures up to the experiment’s warmest sampling point of 20˚C. In addition, wood chips larger than 0.5” in diameter were found to be nearly three times as effective at nitrate removal in comparison to wood chips smaller than a 0.25” in diameter. These findings show that these barriers can be effective in summer stream conditions, and provide insight as to how they can be designed for efficient nitrate removal. Introduction In soil, there exist three forms of inorganic nitrogen: ammonium (NH4+), nitrite (NO2-), and nitrate (NO3 -). In a natural environment, ammonium enters the soil through either fixation of nitrogen gas (N2) by microbes in the soil or through decomposition of organic nitrogen. Nitrifying bacteria then turn the ammonium first into nitrite, and then into nitrate. Nitrate has high solubility in water and does not
adhere to soil due to its negative charge, so it is easily transported from the soil by water, such as when it rains. This nitrate travels through water until it eventually reaches an estuary, where an ocean meets the freshwater from land. Estuarine systems are habitats composed of algae and phytoplankton species that require nitrogen in the water in order to grow. However, estuaries are typically nitrogenlimited, meaning that among carbon, nitrogen, and
Scientia phosphorous, the three key elements needed to produce biomass, nitrogen is the least abundant relative to the amount needed to produce biomass. Nitrate transported into estuarine systems by rivers and streams can provide the algae and phytoplankton in the system with the nitrogen needed to grow and reproduce, which will then get transported up the food chain. Many anthropogenic processes disturb the amount of nitrate that enters these estuarine systems. Spreading nitrogen onto fields in fertilizers, pumping nitrogen into the ground as wastewater, and increasing the amount of nitrogen that is deposited from the atmosphere due to pollution lead to abnormally high levels of nitrogen in estuarine systems.  When this happens, the rates of algae and phytoplankton growth and reproduction increase due to the higher amount of available nitrogen. If too much nitrate enters the estuary system, then an overgrowth of algae called an algal bloom can occur. These algal blooms cover the water in a layer of algae, and when they die and are decomposed by bacteria, the oxygen in the water can be depleted due to respiration. This can create massive fish die-offs and can also be toxic to humans.  These impacts have led to continual research into solutions for reducing the amount of nitrate entering estuaries due to human activity. Many methods have been proposed to reduce the amount of nitrogen entering estuaries, one of which is diverting water through permeable reactive barriers filled with wood chips to remove the nitrates through denitrification by microbes.  These microbes use the wood chip organic matter as a carbon source in the denitrification chemical reaction: This N2 escapes as gas, resulting in the removal of nitrogen from water (Figure 1). To find which factors control the denitrification efficiency of these barriers, three steps were followed. First, ambient temperature, wood chip size, and residence time of water in six different wood chip cores were varied. Relationships between these independent variables and nitrate removal rate were then established. Second, the conditions that would create optimal denitrification efficiency were examined. From the previously elucidated relationships, a model that determines nitrate
removal rate of permeable reactive barriers given residence time, temperature, and wood chip size was then established. From this model, the combination of these conditions that would lead to the greatest nitrate removal efficiency was found. Optimal barrier design was then modeled. This model was used to optimize a plan to build one of these barriers in the Coonamessett River in Falmouth, Massachusetts for most efficient nitrate removal.
Figure 1: Graphic showing basic mechanism of the functioning of wood chip permeable reactive barriers. Water high in nitrate enters through one end of the barrier where the microbes use the nitrate in the water and the organic matter (OM) in the wood chips in denitrification to produce energy. The water is denitrified as it flows through the barrier and eventually exits through the other end along with nitrogen gas and carbon dioxide.
Methods The experiment consists of a laboratory component and a field component. In the laboratory component, permeable reactive barrier microcosms from six cylindrical PVC containers were made by filling three of them with wood chips below 0.25” diameter and the other three with wood chips above 0.5” diameter, and connecting them to a pump attached to a water reservoir spiked with nitrate. By varying pump speed, nitrate removal performance was tested at water residence times of 8, 5.5, 3, and 1.5 hours. In addition, the effect of microcosm temperatures on nitrate removal was tested. The experiment varying pump speed was run at temperatures of 20°C, 12°C, and 5°C. Residence
Figure 2: Graphic showing my planned sampling procedure. For both of the two wood chip sizes I varied the temperature three times, and for each of the three temperatures I planned to vary the residence time four times and have three replicates for each of these combinations of conditions.
Spring 2017 times of 3 and 1.5 hours were not tested for 5°C and an extra 22 hour residence time for 20°C was added in order to get useful data. The concentrations of dissolved nitrate, ammonium, inorganic carbon, and oxygen in the water flowing out of each microcosm were measured at each combination of wood chip size, residence time, and temperature (Figure 2). For the field experiment, two larger versions of the laboratory microcosms were set up in a stream in North Falmouth and nitrate-spiked stream water stream water spiked with nitrate was pumped into the two PVC containers. The residence time was altered by adjusting the pump speed, and temperature was determined by the temperature of the stream the containers were in. Measurements were taken in December, with stream water temperatures below the lowest temperature tested in the laboratory experiment. Samples were collected from the outflow at the end of the container, but also through four additional ports on the side of the container that allowed additional residence times to be observed. Results In the laboratory experiment, the initial residence times chosen for this experiment were too short to see significant removal of nitrate in the wood chip cores – the highest percent nitrate removal in any of the systems was 30%, found at the longest initial residence time and highest temperature. The data for the nitrate removal with respect to time at 20°C (Figure 3) predicts full nitrate removal at a residence time of 22 hours. Experimentally, roughly complete nitrate removal for large wood chips at 22 hours was found. Additionally, nitrate removal rates at
Figure 3: Graph showing nitrate removed vs. residence time for wood chips above a half an inch in diameter. There is a linear trend line for each of the sets of residence times for each of the temperatures. 20°C has an extra residence time point added after the initial experimental plan and 5°C does not have the shortest two residence times.
12°C and 5°C were much lower than at 20°C. At the 8 hour residence time, nitrate removal at 12°C was 13.5% of nitrate removal at 20°C. Nitrate removal increases linearly with residence time at both 20°C and 12°C, although the relationship for 12°C is less certain because there is less removal. The difference in nitrate removal between large and small wood chips is significant. For the 20°C set of conditions, the rate of nitrate removal with respect to residence time for small wood chips (≤0.25” diameter) was about 0.35 times the rate for large wood chips (≥0.5”) (Figure 4). Significant changes in the other variables measured were found. Dissolved oxygen removal was larger at higher temperatures and longer residence times: At 20°C and a residence time of 8 hours the average percent dissolved oxygen removal was 87%, while at the same residence time and a temperature of 12°C it was 69%. At 20°C and a residence time of 1.5 hours it was 35% (Figure 5). As dissolved oxygen is removed by the wood chips, the amount of dissolved inorganic carbon increases in a
Figure 4: Graph showing nitrate removed vs. residence time for wood chips under a quarter of an inch in diameter. The gray trend line is the trend line from the 20°C set of residence times for the large wood chips as a comparison.
Figure 5: Graph of percent of dissolved oxygen removed compared to the inflow water vs. residence time. A logarithmic fit was applied to the 20°C and 12°C temperature sets of points.
Figure 6: Graph of μM of dissolved oxygen removed compared to the inflow vs. the μM increase in DIC compared to the inflow. An increase in DIC sees a corresponding decrease in DO until about 200 μM of DO is removed, at which point DO removed stays constant and DIC added continues to increase.
Figure 7: μM of ammonium removed compared to the inflow vs. residence time for the three temperatures tested.
linear relationship that breaks down once dissolved oxygen is drawn down about 200 uM (Figure 6). To ensure that dissimilatory nitrate reduction to ammonium (DNRA), a microbial process that converts nitrate to ammonium, was not occurring in the microcosms in place of denitrification, the ammonium concentrations of the inflow and outflow of the microcosms were measured, which found low concentrations of ammonium in the inflow, which were then removed by the microcosms. Higher amounts of ammonium removal occurred in warmer conditions with longer residence times, with 20°C conditions removing, on average, 1.48 times the amount of nitrate removed in 12°C conditions (Figure 7). On average, 467 milliliters of water out
of 628 milliliters of total volume were drained from the microcosms, implying that the microcosms had an average of 73% void space. The field experiment was performed in late autumn, and water temperatures were low. At the time of the last sampling, the water temperature was 4.5°C. The residence times for the field experiment were also short compared to the residence times in the lab experiment that saw any removal – the longest field residence time was 3.5 hours. Even at 20°C, where the highest nitrate removal rate is expected, only 6.5% nitrate removal was seen at the 3 hour residence time in the lab experiment. Due to the cold temperatures, the field experiment saw no measurable response of nitrate removal to residence time (Figure 8). Discussion
Figure 8: Percent nitrate removal vs. residence time results for a series of field experiment samples with large wood chips and at a water temperature of 4.5°C.
Because water has to be anoxic for denitrification to take place , denitrification is not expected to occur in most of the sampled conditions due to the presence of significant amounts of oxygen (Figure 5). In previous studies, influent concentrations of dissolved oxygen even lower than the ones in this experiment led to low rates of nitrate removal, indicating that nitrate removal depends heavily on oxygen concentration.  There is a linear trend between dissolved oxygen removed and dissolved inorganic carbon increase up to about 200 µM dissolved oxygen removal (Figure 6). After that, dissolved inorganic carbon increases without
Spring 2017 a corresponding decrease in dissolved oxygen. Microbial aerobic respiration is occurring during the linear portion of the graph, but the subsequent increase in dissolved inorganic carbon with no drawdown of oxygen indicates that there is some process producing carbon dioxide without using oxygen – if these barriers are functioning as intended, this process should be denitrification. There is some nitrate removal in the microcosms even when residence times are short enough to not see much oxygen removal (Figure 3). This could be due to high rates of nitrogen immobilization by microbes or the presence of anoxic pockets in the interiors of the wood chips that allow denitrification to occur even when the rest of the water flowing through the microcosms is still toxic. This second hypothesis also explains the lower nitrate removal seen in small wood chips compared to the large wood chips. The small wood chips have less volume per unit, so oxygen can penetrate deeper into them thus leaving less anoxic interior space. The small wood chips saw, on average, less than half the nitrate removal compared to large wood chips for each residence time of the 20°C temperature (Figure 4). This is contrary to the initial hypothesis that the small wood chips would have a slightly higher amount of nitrate removal due to the larger total surface area, which is in contact with the water. Data from various literature sources suggest little difference in nitrate removal rate between small and large wood chips in groundwater permeable reactive barrier systems.  Additionally, the drastic nitrate removal response to temperature was also unexpected. While biological processes do tend to be slower as temperature decreases, they are not typically slowed to such an extent. When fitting the impact of temperature on nitrate removal rate to a Q10 function, an equation that is used to quantify the response of biological processes to temperature, a Q10 coefficient of 11.6 is calculated. This is an unusual result because this coefficient is typically in the range of 2 to 3. This coefficient indicates that the nitrate removal rate will be multiplied by 11.6 with every 10°C increase in temperature.  Other experiments have found Q10 values lower than 2 for permeable reactive barriers like the ones used in this study, with one source posting a coefficient of 1.6.  This discrepancy in the data could be a result of the short time period in which this experiment was done. The microbes only had 1.5 days to adjust to the temperature change, but if the adjustment period had been longer, then perhaps the wood chips would have been better able
Figure 9: Residuals graph with modeled values on the y axis and observed values on the x axis. The 1:1 line is plotted.
to denitrify the water under colder conditions. Other experiments have shown that significant levels of nitrate removal can occur in temperatures below the 5°C minimum tested in this experiment.  The Q10 function, along with an equation for nitrate removal responses to residence time and wood chip size, were used in a multiple nonlinear regression equation to create a model for nitrate removal based on the three conditions:
R is equal to residence time, S is a binary variable that is 1 when wood chips are below a quarter inch in diameter and 0 when wood chips are above a halfinch in diameter, and T is equal to temperature. The residuals plot showing the agreement between the modeled and observed data has an R2 value of 0.89 for the 1:1 line fit. This indicates good agreement between the model and the observed data (Figure 9). Additionally, the data points all seem to be mostly randomly distributed around the
Figure 10: Residuals plot showing the distribution of points around the 1:1 line. Amount of difference between the modeled and observed values is on the y axis and the observed rate of nitrate removal is on the x axis.
Scientia 1:1 line, indicating that the model accounts for all relationships in the data (Figure 10). The lack of a significant nitrate removal trend in the field experiment supports the findings of the lab experiment and the model, at least in the sense that insignificant removal was expected at the low temperatures and residence times of the field experiment (Figure 8). To validate the model for conditions that are expected to see nitrate removal, the field experiment should be undertaken again in the summer, when it is warmer, and at longer residence times.
Figure 11: Modeled total nitrate removal vs. residence time for three temperatures: 20°C, 16°C, and 12°C. The points show a slight upward curvature.
Using the model, total nitrate removal vs. residence time was derived for three different temperatures: 20°C, 16°C, and 12°C (Figure 11) by multiplying the nitrate removal rate by the residence time for each point to find how much nitrate in total would be removed after a certain residence time, given a certain nitrate removal rate. Figure 11 shows that temperature has a substantial effect on nitrate removal rate. The residence time needed to get to 100% nitrate removal more than doubles with an increase of 4°C. There is an increase in nitrate removal rate in each step increase of residence time as seen by the upward curvature of the graph, indicating that 100% nitrate removal is ideal for the highest nitrate removal rate. Thus, in order to maximize the nitrate removal efficiency of these barriers, one should design them such that they are as close to this 100% nitrate removal threshold as possible. If the residence time is too short, the nitrate removal rate will be suboptimal due to the slow nitrate removal rates during the first few hours in which the water is in the barriers. If the residence time is too long, the nitrate removal rate will be suboptimal because clean water
will be needlessly flowing through the barrier once all of the nitrate has already been removed. This model was used to optimize a possible implementation of these barriers on the Coonamessett River in Falmouth, Massachusetts. For this implementation, large wood chips were used. To begin, the ratio of the dry weight of the wood chips in the microcosms to the water volume in the microcosms was found. The average dry weight of the wood chips in the microcosms was 78 grams, and the average water volume in the microcosms was 465 milliliters, so this ratio is 167.7 grams per liter. This is the mass of wood chips needed to build a barrier that can hold a liter of water. Then, the following equation was used:
where R is equal to the desired residence time for the barrier in hours, F is equal to the flow rate of the inflow in liters per hour, and M is the mass in grams of wood chips needed for a barrier that can have that residence time given that flow rate. This equation can be outlined in this way: if a residence time of 20 hours is desired, then the amount of wood chips that should be used is the amount needed for a barrier that can hold twenty times the flow rate the water in liters per hour. The Coonamessett River has a flow rate of 1,110,000 liters/hour.  In order to minimize the impact of the barrier on the flow of the river, only twenty percent of this flow from the river will be diverted in this scenario. With a hypothetical desired residence time of 20 hours, the mass of wood chips needed was calculated:
To find the amount of land needed to build such a barrier, the ratio of the average total volume of the microcosms to the mass of wood chips in the microcosms was used. The average total volume of the microcosms is 28 mL, and since:
This implies that:
Spring 2017 If the depth of the barrier is two meters, then 0.74 acres of land is needed for a barrier with a residence time of 20 hours and a flow rate of 1,110,000 liters/ hour, which is roughly half of a football field. This calculation is made on the assumption that percent nitrate removal rate has the same relationship with residence time and temperature no matter what the nitrate concentration of the inflow water is. This assumption was made because the number of denitrifying microbes should increase with the concentration of nitrate in the inflow water, due to denitrification being a more favorable process as the concentration of nitrate in the water increases. However, this increase in microbes may not be enough to completely compensate for the increased concentration of nitrate. Because the relationship between nitrate removal and nitrate concentration in the microcosms was not tested, this relationship is a possible topic of further study and a possible addition to the model.
Conclusions Residence time, temperature, and wood chip size all greatly affect nitrate removal rates, and temperature and wood chip size in particular affect the rate of nitrate removal more than expected. The Q10 coefficient for temperature was over five times what is expected for biological processes, and small wood chips remove nitrate about 0.35 times as effectively as large wood chips despite their larger surface area and tighter packing into the pipes. Long residence times, high temperatures, and large wood chip sizes are the most beneficial conditions for nitrate removal, to a point. As demonstrated in the modeled relationship between total nitrate removal and residence time, there is an optimal residence time for nitrate removal for each temperature – a residence time any longer or shorter would decrease efficiency. An optimal residence time for nitrate removal for each temperature has been demonstrated, and there are likely optimums for temperature and wood chip size as well, even though they were not found in this project. Further work is needed to investigate these likely optimums.
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from watersheds to estuaries: verification of the Waquoit Bay nitrogen loading model. Biogeochemistry 49, 277-293 (2000)  Ryther, John H., Dunstan, William M. Nitrogen,
Environment. Science 171(3975), 1008-13 (1971)  Schipper, Louis A., Robertson, Will D., Gold, Arthur J., Jaynes, Dan B., Cameron, Stewart C. Denitrifying bioreactors— An approach for reducing nitrate loads to receiving waters. Ecological Engineering 36(11), 1532–1543 (2010)  Payne, W.J. Reduction of Nitrogenous Oxides by Microorganisms. Bacteriological Reviews 37.4, 409–452. (1973)  Healy, M.G. et al. Denitrification of a nitrate-rich synthetic
materials. J. Environ. Sci. Health Part A https://dx.doi. org/10.1080/10934520600614371 (2006)  Reyes, B. A. et al. Mammalian Peripheral Circadian Oscillators Are Temperature Compensated. Journal of Biological Rhythms 23.1, 95-98. (2008)  Cameron, S.C. et al. Nitrate removal and hydraulic performance of carbon substrates for potential use in denitrification
ecoleng.2010.03.010 (2010)  Robertson, W.D., and Merkley, L.C. In-Stream Bioreactor for Agricultural Nitrate Treatment. Journal of Environmental  Howes B. et al. Linked Watershed-Embayment Model to Determine Critical Nitrogen Loading Thresholds for Great/Perch Pond, Green Pond, and Bournes Pond, Falmouth, Massachusetts. Massachusetts Estuaries Project, Massachusetts Department of Environmental Protection, Boston, MA, USA. (2005)
Acknowledgments Thanks to my adviser, Dr. Kenneth Foreman, for his assistance and enduring dedication to research and implementation of permeable reactive barriers. In addition, thanks to Steve Leighton, who provided much assistance especially with the field portion of this project. Thanks to Edward Rastetter for his assistance with the modeling in this project. Thanks to Rich McHorney and the Semester in Environmental Science Teaching Assistants – Madeline Gorchels, Helena McMonagle, and Leena Vilonen – for their help with lab setup and analyses. Finally, thanks to the Town of Falmouth, Massachusetts and the Falmouth Water Quality Management Committee for their support of this project and their funding of the field portion of this project. About the Author Jonathan Pekarek is a third-year majoring in Environmental Science with a minor in Statistics. He hopes to pursue a PhD in a field related to water sciences and to participate in field research.
Works in Progress Stable Thermophoretic Trapping of Genetic Particles at Low Pressures Frankie Fung, Laboratory of Dr. Cheng Chin Introduction Particle levitation provides an ideal platform for the study of particle interactions in an isolated environment. Current methods for levitation include using radiation pressure , electromagnetic forces on charged particles, and high-intensity sound waves . A recent scheme is capable of levitating centimeter-sized dust aggregates above a hot surface by ~100 Îźm using the Knudsen compressor effect, which involves temperature-induced gas flow . Particle levitation in a vacuum has applications in space and atmospheric research. For example, levitation of dust particles by a temperature gradient may be related to the formation of protoplanetary disks, the early accretion of material that leads to planet formation . Our team reports on an experimental setup that achieves stable levitation of various particles at pressures P = 1~10 Torr. The apparatus does not require any electromagnetic forces or the Knudsen compressor effect. Instead, it only requires a strong temperature gradient that gives rise to the thermophoretic force. We observe stable levitation of polyethylene spheres, ceramic spheres, hollow glass bubbles, ice particles and even lint strands. In particular, we take advantage of the levitation stability to measure the levitated height of polyethylene spheres while varying the temperature distribution. For the scope of this paper, we intend to verify experimental data with theory for this
setup. Using numerical simulations, we obtain reasonable agreement between our experimental data and theoretical calculations over the range of temperatures where levitation remains stable. Methodology The large temperature gradient created within our apparatus, shown above, gives rise to what is known as thermophoretic force. Air molecules coming from the warmer bottom plate carry more momentum compared to those from the colder top plate. Therefore, there is a transfer of momentum in the upwards direction due to collisions between air and polyethylene particles. This change in momentum is the thermophoretic force that balances gravity and leads to levitation. Levitation achieved with this setup is also radially stable. Because the bottom plate is larger than the top plate, the temperature gradient has a radial component pointing towards the vertical axis, in addition to a vertical component. This leads to a radial confining force which prevents the particles from drifting outside the gap between the two plates. Quantitatively, the thermophoretic force is given by:
where is the thermal conductivity of the medium (rarefied air in our case), is the most
Figure 1: Experimental apparatus. The copper plate and liquid nitrogen bucket establish a temperature gradient. The pressure is regulated by a vacuum pump and a needle valve that opens to atmosphere. Temperature of the copper plate is measured with a thermistor and regulated with a Peltier cooler. An imaging setup using a blue LED light records the dynamics of the levitating particles.
probable speed of the air molecules, m is the molecular mass, kB is the Boltzmann constant, and f T is a dimensionless thermophoretic parameter that depends on the Knudsen number Kn = /a, the ratio between the molecular mean free path , and the particle radius a, where is the dynamic viscosity of the medium. The levitation height is theoretically given by: where kg/m is the density of polyethylene spheres, g = 9.8 m/s is gravitational acceleration, and is particle volume determined from the particle radius. There have been multiple theoretical attempts at modelling the dependence of f T on Kn. The experimental setup is illustrated in Fig. 1. A stainless steel bucket is situated 10 mm above a copper plate (with diameter of 33.7 mm) at the center of the vacuum chamber. The bottom of the bucket acts as a cold plate (with diameter of 25.4 mm). By filling the steel bucket with liquid nitrogen, cooling it down to 77 K, while keeping the copper plate at room temperature, we create a strong temperature gradient between the two plates, giving rise to the thermophoretic force that levitates the particles. To monitor the temperatures of the plates, we embed a thermistor in the bottom plate and insert a K-type thermocouple into the steel bucket. Furthermore,
a Peltier cooler is situated underneath the bottom plate for temperature control. For every experiment, we first deposit a batch of polyethylene particles on the bottom plate. After sealing the chamber, we pump the chamber down to the desired pressure and then add liquid nitrogen to the top plate to cool it down. By vibrating the chamber externally, we give the particles some small initial momentum, which allows the thermophoretic force to take over and levitate them. We can control the number of levitating particles by varying the strength of vibration. Two cameras are installed to monitor the levitating particles. An LED provides illumination within the chamber. One camera faces the chamber perpendicularly to the beam, while the other faces the LED and provides a close-up view of the particles. The first camera provides information of the location of the particles, while the second gives information about their sizes and shapes. To determine our experimental value of f T, we only levitate one polyethylene sphere and vary the temperature of the top plate while monitoring the position of the particle. We allow the liquid nitrogen in the steel bucket to evaporate, causing the temperature gradient to decrease; consequently, the particle gradually descends. By conducting a numerical simulation of the temperature distribution within the chamber (given boundary conditions of the temperatures of the two plates and the chamber), we can obtain all the information required to equate equations 1 and 2 and extract the value for f T for different values of Kn. Results We set out to verify our experimental data with existing theory. Our results are plotted in Fig. 2, which depicts the theoretical predictions compared to our experimental measurements of versus Kn. Our measurements are consistent with the theories of Takata et al.  and Yamamoto et al. , but not with Talbot et al. . We attribute the discrepancies between the measurements on the three particles to systematic uncertainties, such as those caused by possible misalignment of the two plates, the limited resolution of the imaging system and non-uniform temperature distribution within each of the two plates. Looking into the future, we hope to explore the interesting dynamics between multiple levitating particles and the possibility of levitating new objects.
Figure 2: Comparison between from experimental measurements and theoretical models. Thermophoretic parameter is compared with theoretical calculation by Takata et al.  (solid line), Talbot et al.  (dotted line), and Yamamoto et al.  (dashed line to the upper left) . The different colors of experimental data points correspond to the three particles examined at different pressures.
About the Author Frankie Fung is a third-year student at the University of Chicago majoring in physics. References
 Ashkin, A. Optical Levitation by Radiation Pressure. Appl.
Phys. Let., 19(8),283. (1971) 
Suthar, K. Levitating water droplets formed by mist
particles in an acoustic field. International Ultrasonics Symposium Proceedings, 467. (2014)  Kelling T. Ice particles trapped by temperature gradients at mbar pressure. Rev. Sci. Instrum., 82,11. (2011)  Wurm G. Light induced disassembly of dusty bodies in inner protoplanetary discs: implications for the formation of planets. Mon.Not Roy.Astron.Soc., 380:683-690. (2007)  Takata S. Thermophoresis of a Sphere with a Uniform Temperature: Numerical Analysis of the Boltzmann Equation for Hard-Sphere Molecules. Prog. Astronaut. Aeronaut., 159,626. (1994)  Yamamoto K. Thermophoresis of a spherical particle in a rareďŹ ed gas of a transition regime. Phys. Fluids, 31(12),3618. (1988) 
Talbot L. Thermophoresis of particles in a heated
boundary layer. Journal of Fluid Mechanics, 101(4),737. (1980)
Molecular Epidemiology of Recurrent Methicillin-Resistant Staphylococcus aureus Infections Tuyaa Montgomery, Laboratory of Michael Z. David Staphylococcus aureus (S. aureus) is a Grampositive bacterium that is one of the most common causes of skin and soft-tissue infections (SSTI) throughout the world. This pathogen also causes sepsis, pneumonia, and bloodstream infections (1). The prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) has greatly increased in the thirty years since its discovery in 1961 (2). Recurrent infections in patients with SSTI caused by MRSA are quite prevalent. In a recent study that followed children and adults after treatment of an S. aureus-caused SSTI's in Los Angeles and Chicago, among 330 index subjects, 182 were infected with the USA300 MRSA strain, and 39% of those individuals had a recurrent infection by month 3 (3). Recurrent MRSA infections present a large healthcare problem, since microbial resistance limits the available antimicrobial treatments that are normally used to treat infections. While some risk factors that contribute to recurrent MRSA SSTI are known, the molecular epidemiology of these infections—specifically the contribution of genetic factors—remains more nebulous. My experiment will attempt to discover the specific strain of MRSA responsible for the recurrent infection by genotyping, and I will compare the results in order to determine if an initial infection with a specific strain of MRSA makes an individual more susceptible to a recurrent infection. In order to investigate this, samples of MRSA
must be obtained from the University of Chicago MRSA Center. Through a partnership with the Center for Disease Control, MRSA samples from patients at the University of Chicago Bernard A. Mitchell Hospital have been collected and stored in the MRSA Center. The initial infection strains of these patients have been frozen down in skim milk and stored at subzero temperatures; the freezing of bacterial cultures in skim milk prevents bacteria from cell death, following cycles of freezing and thawing. These initial infection isolates have also already been genotyped using Multilocus sequence typing (MLST)—a technique that utilizes the DNA sequences of the internal fragments of multiple housekeeping genes to characterize bacterial isolates. Individuals who pass through the screening process are then contacted in order to obtain consent in the study; these are individuals whose infection is their first MRSA infection. Once consent is obtained, we are allowed to monitor them for two years and observe whether any recurrent infections occur. Within the two-year period, if there is a recurrent infection in their record, the original recurrent infection isolate can then be located in storage, where it has been frozen down in skim milk and cataloged. In order to reawaken the bacteria, the isolates are thawed at room temperature, and then cultured on blood agar TSA plates in an incubator. Currently in the United States, USA300 is
Scientia the most common strain that results in communityassociated MRSA (CA-MRSA). PCR assays can first be performed in order to determine if the isolate is USA300. A positive Panton-Valentine Leukocidin (PVL) and mecA PCR assay is 98% sensitive for USA300 CA-MRSA (4). Panton-Valentine Leukocidin is a cytotoxin, whose presence is a virulence factor in MRSA strains (5), while mecA is a gene that confers resistance to bacteria against β-lactam antibiotics (methicillin, penicillin, etc.). If the PCR assays do not reveal the presence of PVL and mecA, then further genotyping must be performed. Multilocus sequence typing (MLST) can determine the isolate’s specific sequence type. MLST involves the sequencing of the DNA fragments of seven housekeeping genes: arcC, aroE, glpF, gmk, pta, tpi, and yqiL. The sequences of these genes can then be compared to known alleles at each locus via the MLST database (6). In this database, every isolate has been assigned a seven-digit allelic profile that defines its sequence type (ST) (7). Once the sequence type is defined, it can be compared to the sequence type of the initial infection. Since USA300 is the most common strain in the United States, it would not be surprising to see that a good portion of these isolates is USA300. After assigning a type to each one-year postinfection isolate, these types will be compared to the initial infection isolate, i.e., whether it is the same strain that has caused another infection or a different strain. Another important question that could be answered by this study is if certain strains of MRSA infections are more likely than others to cause another infection. There are several potential applications of these results: with more knowledge surrounding the molecular epidemiology of recurrent infections, doctors will be able to follow new risk stratification protocols and determine which patients are at a higher risk for recurrence, and thus prevent these patients from becoming ill again.
(1) David MZ, Daum RS. Community-associated methicillin-
resistant Staphylococcus aureus: epidemiology and clinical consequences of an emerging epidemic. Clin Microbiol Rev.2010;23:616–687. (2) Baddour, Manal M. The Case for MRSA and Treatment of Methicillin Resistant Staphylococcus Aureus. Methicillinresistant Staphylococcus Aureus (MRSA): Etiology, At-Risk Populations and Treatment. 2 (2010). (3) Miller, L. G., S. J. Eells, M. Z. David, N. Ortiz, A. R. Taylor, N. Kumar, D. Cruz, S. Boyle-Vavra, and R. S. Daum. "Staphylococcus aureus Skin Infection Recurrences Among Household Members: An Examination of Host, Behavioral, and Pathogen-Level Predictors." Clinical Infectious Diseases 60, no. 5 (November 26, 2014): 753-63. doi:10.1093/cid/ciu943. (4) Chadwick, S. G., Prasad, A., Smith, W. L., Mordechai, E., Adelson, M. E., Scott E. Gygax, S. E., “Detection of Epidemic USA300 Community-Associated Methicillin-Resistant Staphylococcus aureus Strains by Use of a Single Allele-Specific PCR Assay Targeting a Novel Polymorphism of Staphylococcus aureus.” Journal of Clinical Microbiology 51, no. 8 (August 2013): 2541–2550. doi: 10.1128/JCM.00417-13. (5) Melles, Damian C. "Panton-Valentine Leukocidin Genes in Staphylococcus aureus." Centers for Disease Control and Prevention. December 16, 2011. https://wwwnc.cdc.gov/eid/ article/12/7/05-0865_article (6)
seqdef&page=profiles&scheme_id=1 (7) Robinson, D.A., Enright, M.C., “Multilocus sequence typing and the evolution of methicillin-resistant Staphylococcus aureus.” Clinical Microbiology and Infection 10, no. 2 (February 2004): 9297. doi: http://dx.doi.org/10.1111/j.1469-0691.2004.00768.x.
About the Author Tuyaa Montgomery is a third-year student at the University of Chicago majoring in biological sciences, with a specialization in global health, and minoring in Slavic languages. She hopes to attend graduate school and enter the world of biomedical research. Tuyaa works at the MRSA Research Center. Her PI is Dr. Michael Z David.
Barriers to Long-Acting Reversible Contraception Preethi Raju Teen pregnancy rates are seven times higher in the United States than in other developed countries . Long-acting reversible contraception (LARC) methods are highly effective at preventing pregnancy that could contend against extremely high rates of unplanned pregnancies, especially among teens. However, LARC use remains disproportionally low in the U.S. compared to less effective methods of contraception; only 11.6% of women (ages 15-44)
used LARC according to the 2010 National Survey of Family Growth. Fewer teens overall used LARC . A possible explanation is that LARC is not as wellknown as other forms of contraception. Although several studies confirm this, it seems that low LARC use actually stemms from underestimating LARC effectiveness and safety as compared to other more well recognized forms of contraception. A post-hoc analysis of 221 women has demonstrated this same
Scientia effective methods. Moreover, in terms of surveying doctors it is not clear how many doctors will recommend the contraceptive to women who are younger and/or nulliparous (a woman who has never given birth), since previous studies have shown that doctors are less likely to recommend LARC under those circumstances . If possible, doctors at the University of Chicago Medical Center will be surveyed to gauge their thoughts on recommending LARC and their perceptions of how many women, when recommended LARC methods, are actually willing to use it. About the Author Preethi is a third-year biology and economics major in the College. References
1. Daniels K. et. al. National Health Statistics Reports No.
trend . I hypothesized that we can increase LARC use by increasing LARC education and access. I plan to conduct another literature review of LARC education and barriers to learning about LARC in terms of access, costs, and safety. In addition, I plan to review broad sexual health curriculum criteria in the general Illinois area and the Chicago Public School system. I will also survey 8th graders in specific schools (i.e. Kozminsky Community Academy) to see how disproportionate the awareness of LARC is compared to less effective contraceptive methods. Finally, I plan to survey the Peer Health Exchange (PHE) about its LARC knowledge and its success with teaching LARC, and, if possible, University of Chicago doctors on how likely they are to recommend LARC and why. If possible, I would like to survey family planning clinic patients on how much they learned about LARC from their provider and how likely they are to use it in the future. From an initial analysis of Illinois sexual health curriculum, it is apparent that there is no mention of LARC, its use, nor the concept of dual protection. On the other hand, the PHE has a specialized curriculum that includes guidelines on all LARC methods. It will have to be seen whether students effectively learn about LARC and whether they are willing to use it after post-PHE class surveys are analyzed. Students may still be reluctant to use LARC because of its higher costs and lower accessibility, and because they are less familiar with it than traditional, less
55 (2015). 2. Mosher W. et. al. National Health Statistics Reports No. 55 (2012). 3. Gilliam M. et al. Development and testing of an iOS waiting room “app” for contraceptive counseling in a Title X family planning clinic. Amer. J. Obstetrics and Gynecology 5, 481.e1–481.e8 (2014). 4. Teal S.B. et al. Awareness of long-acting reversible contraception among teens and young adults. J. Adolesc. Health. 52 (4 Suppl):S35-9. doi:10.1016/j.jadohealth.2013.01.013 (2013).
Photos: Nature and Laboratory 1
1. Sarah Larson. Natural Arch. Booth Island, Antarctica. 2013 2. Sarah Larson. Cacti. Joshua Tree, California. 2013 3. Laura Yuan. Sea Urchin, University of Chicago. Spring 2016 4. Laura Yuan. Drosophila melanogaster, University of Chicago. Winter 2016 5. Katie Zellner. Two Clytia Hemisphaerica, Malamy Lab, University of Chicago. Fall 2016 6. Sarah Larson. Fire. Murmansk, Russia. 2015 7. Laura Yuan. Embryonic Zebrafish, University of Chicago. Spring 2016 8. Sarah Larson. Reindeer. HonningsvĂĽg, North Cape, Norway. 2015 9. Laura Yuan. Developing Embryonic Zebrafish, University of Chicago. Spring 2016 10. Sarah Larson. Koi, Shanghai, China. 2013 11. Laura Yuan. Drosophila melanogaster, University of Chicago. Winter 2016
Abstracts in collaboration with the Chicago Area Undergraduate Research Symposium (CAURS)
A Piezoelectric Biosensor for Biomechanical Cellular Measurements Tiffany Simmons1, Zacharia Tharakan1, Rajesh Prabhu Balaraman2, Punit Kohli2, and *Farhan Chowdhury1 Southern Illinois University Carbondale Department of Mechanical Engineering and Energy Processes, Southern Illinois University Carbondale Department of Chemistry and Biochemistry, Southern Illinois University Carbondale email: email@example.com, *correspondence: firstname.lastname@example.org 1 2
Physical forces have significant roles in many cellular functions such as contraction, relaxation, spreading, crawling, division, migration, invasion etc. for maintaining normal tissue homeostasis and disease progression. However, there are very few biosensors available that can easily visualize and quantify all of these functions with a direct readout in real-time. Herein, we devised a piezoelectric (PZT) zinc oxide nanowire biosensor that can serve as a universal biosensor. We selected zinc oxide for the nanowires because of their strong piezoelectric charge contact and crystalline structure. The device was fabricated by sputtering indium tin oxide (ITO) slides with gold, which acts as a catalyst for the nanowires. The slides were placed in a solution phase chemistry of Zn(NO3)2. 6H2O (Zinc Oxide), hexamethylenetetramine (HMTA), and NH4OH (Ammonia) to grow the zinc oxide nanowires. To optimize this device, we varied conditions such as the length of time the slides were in the solution, the temperature of the solution, and the annealing temperature of the sputtering. The nanowires were characterized by scanning electron microscopy. As the cell attaches to the nanowires, cellular contractile forces bend the nanowires which in turn generate electrical charges. After calibration, we can detect physical forces involved in critical cellular functions. In the future, we aim to use the device to characterize a tumorigenic cancer subpopulation and examine their force generation during cell invasion. Our versatile biosensor can be utilized in many applications in addition to biomechanical characterization of cells.
Guiding Cancer Therapy through Non-Invasive Quantitative Molecular Imaging of Cancers: Testing EGFR Status vs. Erbitux Therapy Kristin E. Wills1 , Negar Sadeghipour1, Scott C. Davis2, Kenneth M. Tichauer1 Illinois Institute of Technology Department of Biomedical Engineering, Illinois Institute of Technology Thayer School of Engineering, Dartmouth College
Molecular targeted therapies are a form of cancer treatment that target specific biological molecules within the body. One frequently targeted cell-surface protein is the epidermal growth factor receptor (EGFR), a receptor frequently over-expressed in many cancers. The drug Erbitux is an antibody-based molecular targeted therapeutic used to target EGFR; however, there is currently no method of monitoring this treatment in vivo. The “paired imaging agent” model (co-injecting control (“untargeted”) and targeted imaging agents) has been demonstrated to be able to quantify cellsurface protein concentrations in tumors. This technique can be used to determine the relationship between drug-target concentrations and the drug response. The preliminary protocol for the research was to inject the mice’s flanks with 6 different cancer cell lines (both pancreatic cancer and head and neck cell lines). Three mice were used and a different cell line was injected into each flank. The mice were injected with the fluorescent dye IR800-ABY- 029 and IRDye700 carboxylate in the tail vein and the signals from both agents were preliminarily measured in blood and muscle to evaluate the “background kinetics” of the two imaging agents (blood kinetics and kinetics in the non-binding muscle tissue). Initial results established that there were large differences between the background kinetics of the agents, indicating that conventional kinetic models will not adequately determine the concentration of EGFR. As the differences in the kinetics of the agents is primarily due to a difference in blood kinetics, these variances can be corrected using a deconvolution technique the lab has developed. As this project continues to show promising results, it is believed that this will aid in the personalization of cancer treatment plans as well as help eliminate ineffective drugs in the field of cancer treatment.
Impact of Abstinence-Only Sex Education on Teen Birth Rates at the State Level Sarah Permut Northwestern University, Department of Sociology email: email@example.com
The US continues to experience disproportionately high teen birth, pregnancy, and STD rates compared to other developed nations and the appropriate type of sex education for American adolescents’ has been a constant source of debate. Over the last 13 years, the US federal government has invested over $1.5 billion in abstinence-only education in attempt to improve adolescent health outcomes. While there have been studies on how abstinence-only education programs impact their students, there has been little investigation into how abstinence-only education funding and programs influence health outcomes at the state level. Furthermore, there has been little research conducted on the impact of the Community-Based Abstinence Education (CBAE) funding program, a particularly restrictive form of abstinence-only education. Using teen birth rate data from the last 13 years, this study seeks to investigate whether abstinence-only education funding and programs impact teen birth rate at the state level. I analyze an original panel dataset using multivariate analysis and lagged dependent variable models to find that increases in funding levels for total abstinence-only and CBAE education, as well as the existence of CBAE programs, are associated with increases in teen birth rate. Evidence from lagged dependent variable models suggests that a causal interpretation of this association may be warranted. These findings indicate that abstinence-only education programs do not improve adolescents’ health outcomes, and provides potential evidence that abstinence-only education is harmful to young women’s health.
IR-SEC Studies of Group 6 and 7 Metal Carbonyl Catalysts for CO2 Reduction Cesar Saucedo and Kyle A. Grice DePaul University, Department of Chemistry The electrochemical responses of Mo, W, Cr, Mn, and Re metal carbonyl compounds were studied in organic solvents for use in the reduction of carbon dioxide. The group 6 metal catalysts showed significant responses under CO2, indicating CO2 reduction, whereas the group 7 compounds did not. In order to better understand the reaction mechanisms, infrared spectroelectrochemistry (IR-SEC) was used. The compounds were reduced electrochemically and the infrared spectra were taken as the reductions occurred. Additionally, the reduced compounds were studied in the presence of carbon dioxide to determine how they reacted with CO2. The group 6 species are rare examples of complexes that are electrocatalysts for CO2 reduction without the need of electroactive ligands.
The Effect of Parental Support and Involvement on Sense of Belonging in School in African American Male Adolescents Catherine L. Montgomery and Noni K. Gaylord-Harden Loyola University Chicago, Department of Psychology McNair Scholars Program, Loyola University Chicago email: firstname.lastname@example.org Sense of belonging in school for African American youth is an important predictor of academic and behavioral outcomes. Sense of belonging is defined as the connection between the individualâ€™s perception of his or her role with respect to other people, groups, objects, organizations, environments, or spiritual dimensions . The purpose of the current study was to examine the effect of family structure (two-parent versus single parent) as a moderator of the relationship between parental support and involvement and sense of belonging in the school setting in African American male adolescents. Participants included 234 African American male adolescents (mean age = 15.21, SD = 1.08). Participants completed measures assessing school belongingness, parental support, parental involvement, and a demographic form. It was hypothesized that (1) Higher levels of parental support will predict higher levels of sense of belongingness in school for African American male adolescents; (2) Higher levels of parental involvement will predict higher levels of sense of belongingness in school for African American male adolescents; (3) The association of parental support and parental involvement to sense of belongingness in school will be stronger in two-parent families versus single-parent families. Hierarchical regression analyses were conducted to test the relationship between parental support and involvement and sense of belonging in school, as well as to test for moderation effects of family structure (single-parent, mother-headed household versus two-parent household). Consistent with predictions, higher levels of perceived parental support and parental involvement predicted higher levels of perceived school belongingness in participants. Inconsistent with predictions, family structure did not moderate the associations between parenting and school belongingness. Findings from the current study could lead to an enhancement or creation of programs for the support of students as well as their families to produce a greater sense of belonging in school. References  Hagerty, B. M., Lynch-Sauer, J., Patusky, K. L., Bouwsema, M., & Collier, P. (1992). Sense of belonging: A vital mental health concept. Archives of psychiatric nursing, 6(3), 172-177.
Inquiries Mathematical Methods Meet Macromolecules: An Interview with Dr. Loretta Au Christian Porras Dr. Loretta Au, a William H. Kruskal Instructor in the Department of Statistics, melds together her passions for mathematics and biology in her work. Originally interested in becoming a medical doctor, Dr. Au instead decided to pursue research in computational biology—a field that allows her to use both math and statistics to better understand how biology works. Dr. Au graduated with a B.A. in Mathematics from New York University in May of 2008, and was on track to apply for medical school during her senior year. While she admits that she “didn’t really know how to get started with research as an undergrad,” Dr. Au decided to find a research position that would enable her to apply her coursework background in mathematics. Her hospital project coordinator recommended a biostatistics lab at the hospital where she was already a volunteer. During her time there, she began cultivating her research interests, and Dr. Au was able to find another position later with the public health department at a nearby laboratory in New York City, where she focused on microbiology. From working in both wet and dry lab settings, she noticed that her true interests were at the intersection of biology and statistical analysis: “I thought, ‘this is really interesting; I’d rather pursue this over med school.’” She decided her senior year to pursue a Ph.D. at Stony Brook University in New York, delving further into computational biology and bioinformatics. As a graduate student, Dr. Au began her work on understanding the boundaries of protein fitness using computational methods. Stony Brook University is known for its research in computational molecular modeling, which influenced her research focus: “When everyone around you is really good at this particular thing, it made sense to start working with them on it.” The dead-end elimination (DEE) algorithm is
a computational search method commonly used in protein design, and her thesis was developing a “systematic way to simulate single mutations in proteins using DEE.” It works by finding and avoiding “dead ends,” or combinations of variables that do not contribute to minimizing the energy of a given system. In this setting, the system of concern is the entire protein macromolecule. As systems with lower energy values tend to be more stable, the most favorable structures for mutated protein sequences can be determined by searching for the sequences with the lowest system energy, and then finding the corresponding three-dimensional coordinates to represent the protein. Dr. Au’s research relied on measurements of the modeled structural stability and binding interactions of the proteins as metrics for defining their fitness. Protein sequences with the greatest fitness were those with the most stability that maintained binding interactions. Essentially, Dr. Au worked to answer the question “If I systematically change each position to all of the other 20 amino acids, what’s going to happen to the fitness?” Her strategies were capable of predicting amino acids that were fundamental for stabilization as well as protein– protein interactions in a G-protein heterotrimer, and helped provide insight into the relationship between sequences and tertiary structure. Dr. Au continued to develop her career as both a researcher and an educator when she joined the faculty at the University of Chicago as a William H. Kruskal Instructor in the Department of Statistics in September of 2014. “I really enjoy teaching and being able to do research here,” she comments on her decision to work at the University of Chicago. A statistics instructor for the past three years, Dr. Au values the connections she makes with her undergraduate students, with
Scientia interests in mathematics and biology through her work in bioinformatics and protein design serves as an example for students to follow their passions. Motivated to continue learning more about proteins and the influence of their structure on their function, Dr. Au expresses curiosity and enthusiasm for her work. The overarching question, “how do you start with 20 amino acids and end up with so much diversity in biology?” inspires her to strive for an answer.
Model system of 1GP2 Gα1β1γ 2 G-protein heterotrimer (top left) with β-propeller subunit and γ subunit (top right), α subunit (bottom left), and G beta-gamma complex (Gβγ) side view (bottom right)
the added ability to view her field through both the broader scope of the STAT 220 course, and the focused perspective of her computational biology research. After arriving at the University of Chicago, her research focus shifted towards repeat proteins, a class of proteins that are composed of characteristic repeating regions and can entertain a wide variety of functions. Dr. Au works with β-propeller repeat proteins and G-protein heterotrimers, whose β-subunit is a repeat protein, and she continues to examine protein sequences under the lens of evolution, working with sequence alignment algorithms such as MUSCLE (Multiple Sequence Comparison by Log-Expectation), and using R for statistical analysis. Dr. Au’s other project, with Biochemistry and Molecular Biology Professor Allan Drummond, is focused on detecting coevolutionary signals in intrinsically disordered proteins. Intrinsically disordered proteins (IDPs) have an unusual variability in tertiary structure, but are still able to function. By analyzing the consequences of change to the sequences of these proteins, Dr. Au hopes to better understand how amino-acid sequences affect function, when structural information is unavailable. Her research can potentially lead to new ideas for protein design, as she works towards understanding what evolution is capable of. “If you start to understand the rules of protein evolution, you can start to think of other methods to engineer proteins,” she says. Referring to the importance of sharing research developments with and learning from her peers, Dr. Au advises, “Find other people who don’t necessarily do the same thing you do, but even when their work is related it can help you think about your project. It’s good to have an outside perspective.” Dr. Loretta Au’s ability to combine her academic
About the Author Christian Porras is a first-year student at The University of Chicago double majoring in Molecular Engineering and Biological Sciences. He hopes to attend graduate school and study Bioinformatics and Proteomics.
From Plant Biologist to Master of Biology Mimansa Dogra Dr. Jocelyn Malamy, Master of the Biological Sciences Collegiate Division at the University of Chicago, expertly juggles all of her responsibilities. Besides maintaining the BSCD, she is the Principal Investigator of two research projects and teaches undergraduate biology courses. Her true passion, however, is plant biology. As an undergraduate student at Tufts University, she took classes under George Elmore, who taught the only plant biology courses available there at the time. In the summers, she studied Chlamydomonas, single-celled algae. This algae has an asymmetric photoreceptor on its body that allows it to notice the presence of light. The lab Dr. Malamy was working in was interested in learning how the algae swim and orient with respect to light. She helped write a program that tracked the movement and position of the cells. She worked for two years — after getting her bachelor’s degree — at Harvard’s teaching labs, where she joined a team primarily responsible for running the undergraduate laboratories, much like the BSCD at the University of Chicago. She worked as a technician and teaching assistant for the summer school. When there were breaks between school sessions, she volunteered in different labs to gain more research experience. One of the labs she volunteered in was run by Lawrence Bogorad, president of the American Physiology Plant Society at the time. Dr. Malamy’s work in this lab further cemented her desire to enter the field of plant biology. Following her stint at the Harvard teaching labs, Dr. Malamy applied to the molecular biology and agricultural plant physiology graduate programs at Rutgers. Since she wasn’t sure which direction she wanted to go in, she was pleased to be accepted into their interdisciplinary program. “In most programs, you are accepted into one department or one graduate program, and then you do your rotations and pick the lab in which you want to do your research… This was a weird experimental program where they were going
to take a small number of people who could move fluidly through any programs that they wanted,” Dr. Malamy said. After experimenting with horticulture, plant physiology, and molecular plant research, she ended up joining a molecular plant biology lab run by Dan Klessig. She completed her graduate study in six years, followed by a post-doctoral fellowship at New York University for another six years. At the conclusion of her fellowship, Dr. Malamy joined the University of Chicago as a faculty member. During its initial years, Dr. Malamy’s lab primarily focused on plant biology, and recently received funding to examine the signaling molecules and hormones in the plant vascular system. The lab focuses on identifying these long-distance molecules, and is currently trying to determine other proteins that move between the leaves and roots of the plants. This project is particularly exciting because it may provide some insight into plant evolution and communication. “Plants have vascular systems that move the sugars all around the plant, much like our own vascular system. And once you have a river moving around the entire body, it’s very tempting, from an evolutionary point of view, to throw other things in it, like hormones and proteins,” said Dr. Malamy. “In agriculture, if you want to improve plant growth in harsher environments, with limited nutrients and warmer temperatures, you have to know how plants work. There is communication within the plant, and this is a fundamental property about plants that we do not know. When a leaf gets infected with a virus, how does it tell the rest of the plant that there is a problem?” This question has piqued her interest for decades, having researched long distance signaling in response to viral infections while she was in graduate school. Besides her research in plant biology, Dr. Malamy is conducting another research project – the study of how jellyfish heal wounds. Since her lab is interested in the plasticity of plant regeneration, a quality that also exists in jellyfish, this project will apply previous work to novel research questions. “The big question is, what makes some animals able to regenerate, while others cannot?” This question has fascinating implications for human biology and medicinal treatment. This transition was also motivated by factors out of Dr.
Malamy’s control. “Plant biology funding is absolutely horrible these days, so it’s good to diversify a little bit. There’s a lot of things in the scientific world that are really exciting, and sometimes we have to get excited about things that are fundable.” She isn’t displeased about this change in focus, though – “For me, it is very stimulating to switch scientific directions. It rejuvenates you and pushes you a bit.” Currently, her lab is focusing on the capacity for jellyfish to heal epithelial wounds. The epithelial cells – cells than make up the skin and outer linings of organs – in jellyfish and humans are similar, although jellyfish have the unique ability to close wounds to these cells in under an hour. “You can watch the cells, in real time, walk across the wound and stitch themselves back together again,” says Dr. Malamy. Regarding the jellyfish system, Dr. Malamy notes that it is important to learn about how an organism discovers, responds to, and fixes a wound. “There are a lot of people who study epithelial wound healing, but do so in tissue cultures. For the jellyfish, it is just jelly, with a single layer of epithelial cells sitting on top. So, you can see everything happening in an intact animal.” She notes that both of her research projects cover areas that haven’t been traversed yet. “Both of the questions [we are studying] are fundamental questions.” How do plants communicate? What causes some organisms to heal faster than others? Dr. Malamy is eager to find the answers to these questions. Besides her research, Dr. Malamy has also taken on the role of Master of the BSCD. She attempts to split her time evenly between her research and the Mastership. The job of the Master is to ensure that the undergraduate biology program is successful. At the bare minimum, the Master must guarantee that the courses have faculty and the labs are both fully and
adequately staffed. The Master is also responsible for determining the budget of the division. Besides these duties, Dr. Malamy has more ambitions for the BSCD. “You get to think about what would add new, exciting opportunities for the undergraduates,” she says. “We have to keep up with the current climate in science. Science education can get stagnant very quickly if you don’t stay on top of things because science itself changes quickly.” For example, previous Masters have added more quantitative subjects such as math and programming to the biology program, as a greater number of researchers are expected to utilize these skills. Dr. Malamy’s vision for the program is to have one major initiative for each of the three years she will hold the Master position. During the first year, she hopes to create more undergraduate opportunities at the Marine Biological Laboratory in Woods Hole, Massachusetts. The BSCD recently introduced three new courses for undergraduates, which are scheduled to begin right before the upcoming fall quarter. These courses are three-week intensive courses and include Invertebrate Zoology, Microbiomes Across Environments, and Observing Proteins in Action. During her second year, Dr. Malamy is hoping to streamline the undergraduate search process for research positions. In her third year, Dr. Malamy’s goal is to adjust and improve the catalog of biology courses available to non-biology majors. Dr. Malamy acknowledges that being both a researcher and administrator is taxing work, as both of these positions are full-time jobs. Her increased responsibilities mean that she isn’t able to teach as much as she would like to. She is currently the professor of an introductory genetics section, although this may be her last year teaching the course. In past years, she taught Genetics in Model Organisms, focusing on epigenetics in plant biology, and a graduate ethics course. “What faculty do is split time between research and service, and since I’ve taken up the Mastership, I’ve had to give up my other contributions.” However, Dr. Malamy says that the students she mentors make the work worth it. “It is really great to be working with students who are engaged, curious, and bright – I wouldn’t have this experience anywhere else.” About the Author Mimansa Dogra is a first year student at the University of Chicago. She is interested in infectious diseases and genetics, and plans to study biology and statistics.
"It's a Long Story" An Inquiry with Professor Diane Lauderdale Katie Zellner Epidemiology, the study of patterns, causes, and effects of disease in various populations, requires an understanding of mathematics, biology, public health, and geography. Given its interdisciplinary nature, a varied academic background is necessary. However, Professor Diane Lauderdale, chair of University of Chicago’s Department of Public Health sciences, has an even more diverse background than you would expect. How did a scholar of medieval history, religious studies, and library science end up in public health? “It’s a long story,” she said laughing. “I actually started out in college—intending to study math.” Lauderdale’s mother was a statistician, a rare occupation for a woman in her generation. Thanks to this influence, Lauderdale grew up aware that women could excel in STEM. “She did really interesting work through World War II, actually, including bombing patterns for the Princeton math department and continued to work as a statistician… She stopped in the 50s when she had children because she desperately wanted to have a normal life, but I grew up knowing what statistics was and had an extremely positive view of the field [even though] most people had no idea what it was back then.” However, despite this positive upbringing in mathematics, Lauderdale’s studies in the math department did not last long. “This was the 1970s,” she said, “and I found the math department in college to be fairly sexist. I decided to find a field to study where there were also women faculty members.” This proved to be more difficult than it should have been since, at the time, there were fewer than a dozen women faculty members in Harvard’s Faculty of Arts and Sciences. She finally decided to study medieval history, focusing on historical times when people of different cultures and religions came together—a subject quite similar to epidemiology. Like many college seniors, she did not really know what she wanted to do after graduation.
Following in the steps of those before her (and after), she decided to go to graduate school in the same field and figure it out there. She attended the University of Chicago to continue studying the history of religions at the Divinity School. For a few years she studied history and religion in India, which she enjoyed, but not enough to justify learning the numerous languages needed to pursue what was typically a ten-year long doctoral degree at the Divinity School. “What happened then, well… I had met a man,” she said. She and that man have now been married for thirty-eight years. While she was beginning her program at the Divinity School he was finishing up medical school. To stay with her, he had ranked all the Chicago options highest for his residency program. So when she decided to leave the Divinity School with a master’s degree, she knew she had to stay in Chicago. Although she had acquired a unique skillset including competency in various languages such as Arabic and Sanskrit, Lauderdale was unsure what to do. The University of Chicago still had their Library School graduate program, and she thought this would be a useful application of her skillset. After Lauderdale finished school, she worked as an editor before becoming a reference librarian, switching to part-time once she had kids. After her second child, she knew it was time to reconsider her career. She enjoyed being a reference librarian, but if she advanced in library science, she would eventually stop doing the parts she relished the most. She decided to search a new path. “This one little fact,” she said, “changed my life.” The fact: her husband had his medical journals sent home rather than to his office. As Lauderdale was working part-time and taking care of her children, she read all of the articles she could understand. “What I was following at that point was the beginning of the AIDS epidemic and it seemed like the most important thing I could possibly be doing—working in epidemiology.”
Scientia In order to try out epidemiology before committing to a program, she took an introductory course at the University of Illinois School of Public Health. About two weeks into the course she realized that this was a perfect fit for her and soon joined the UIC doctoral program in Epidemiology, studying chronic disease epidemiology. “And this is where we get back to my background in history,” said Lauderdale. “I was particularly attracted to immigration studies—a classic natural experiment in epidemiology.” She would look at times when people immigrated to find out whether geographic variations in diseases had more to do with environmental or genetic factors. She did her dissertation estimating national hip fracture incidence rates for different ethnic groups of Asian Americans, deducing the year of immigration by using year of issuance information inferred from Social Security numbers. “One of the faculty members in the department called my research more numerology than epidemiology.” Lauderdale quickly found an opportunity after finishing her doctorate. “By an extraordinary piece of good luck,” the University of Chicago had opened a department in epidemiology, biostatistics, and health services research exactly as she had finished her doctorate at UIC, and she was hired. It was not a typical first job for a new PhD because there was not an established cohort to build research on, but this led to more creativity and innovation. Lauderdale’s main research area now is in sleep, performing population-based studies on sleep behavior and how it relates to health. She also looks at the role of social factors in sleep and how people’s perceptions of sleep relate to more objective measures. “What I found is that how people feel about their health and their social circumstances influence their perceptions of sleep. It’s a fascinating area because people really care about sleep, but it is not clear what much of the published research based on self-reported sleep really means.” In addition, Lauderdale continues to do studies on US immigration and has also explored infectious diseases. Working with the Argonne National Lab, she built a model of the Chicago population to try to understand the history of community-based Methicillin-resistant Staphylococcus aureus, a bacterium responsible for several difficult-to-treat
infections in humans. Although it took some time, Lauderdale was able to find her passion in epidemiology. “I’m glad things went the way they did. It turns out it was really useful that I had children when I did. I started here when I was forty and they were already in school...” It often feels that young scientists have to figure out their career paths and interests right away, but Professor Lauderdale’s story suggests that is not always the case. “If there’s a lesson in this it’s that you really don’t know where things will take you and there is a lot more flexibility in the system than you think.” Dr. Diane Lauderdale is a professor and Chair of the Department of Public Health Sciences at the University of Chicago. She received a BA in Religion from Harvard, MA degrees in Divinity and Library Science from the University of Chicago and a PhD in Epidemiology from the University of Illinois School of Public Health. She started at the University of Chicago as an Assistant Professor in 1996. She teaches Introduction to Epidemiology and Population Health during Fall Quarter. About the Author Katie Zellner is a fourth year student studying biology and creative writing, interested in public health and science communication. After graduation, she will be working as a consultant for Cerner where she will be helping hospitals implement electronic medical record systems.
A Theoretician and Experimentalist Walk into a Lab Meeting… A Conversation with Drs. David and Elizabeth Kovar Samara Singh While David Kovar was playing soccer at Wesleyan College in Ohio, Elizabeth Kovar was up north at the University of Connecticut running track. As undergraduates, they each developed their passions—his for biology and hers for math and chemistry. Of all the things to bring them together, their paths finally converged in graduate school while beginning their separate research projects on the actin cytoskeleton. However, before they could teach together at the University of Chicago, they each pursued independent careers in science. Dr. David Kovar began his undergraduate experience earning a chemistry degree, like his father. This plan briefly changed to a journalism degree before he ultimately decided to study biology instead. His love for biology began his junior year and solidified the following year when one of his professors got him involved in independent research. He pursued his burgeoning passion for biology by performing graduate research at Purdue University, where he studied the plant cytoskeleton using corn pollen as his experimental model. While there, Dr. David Kovar’s interest for biochemistry and the actin cytoskeleton flourished—though at the expense of developing a serious corn pollen allergy. Unable to continue studying the plant models he worked with in graduate school, he transitioned to fission yeast during his postdoctoral research on the cytoskeleton at Yale University, which proved to be a much simpler system to study. While there, the adoption of Total Internal Reflective Fluorescence (TIRF) microscopy revolutionized his research, allowing him to observe actin assembly and better understand the behavior of individual filaments in the yeast. TIRF microscopy allowed Dr. Kovar to “visualize actin filament assembly in real time, which had never been done before.” The technique
permitted the behavior of each specific filament to be observed individually, as opposed to the general assembly of filaments throughout the entire cell. As a postdoctoral fellow, Dr. David Kovar utilized TIRF to understand the role of the protein formin in actin assembly. His research confirmed that this protein increases the elongation rate in actin filament assembly, while protecting the filament by binding to the elongating end. Dr. David Kovar joined the University of Chicago staff in 2005 with the purpose of “studying how actin is organized in the right time and place to facilitate different fundamental processes using fission yeast as model organisms.” He joined the research faculty at the University of Chicago initially as an assistant professor and gained full professorship in 2016. At his lab, Dr. David Kovar’s research involves tracing proteins using fluorescent tags to determine their location within actin networks and creating model networks of how these proteins interact inside cells. The second portion of his research involves the purification of these observed proteins and investigating the isolated samples in vitro to study how they specifically contribute to actin assembly. On the other hand, Dr. Elizabeth Kovar initially planned to be a mathematician as an undergraduate at the University of Connecticut; she surprised herself when she double majored and eventually received Bachelor of Science degrees in both mathematics and chemistry. She had added chemistry to her undergraduate curriculum when she discovered how much she loved the challenge the subject presented for her. For Dr. Elizabeth Kovar, chemistry didn’t come as naturally to her as math, but this only fueled her interest. Continuing her graduate studies at Indiana University, Dr. Elizabeth Kovar studied the statistical mechanics of the cytoskeleton, allowing her to fuse
Scientia her interests in math and chemistry. While studying there, she inadvertently met Dr. David Kovar, who himself was a graduate student at the neighboring institution of Purdue University. The two graduate students met when Dr. David Kovar’s lab requested the assistance of Dr. Elizabeth Kovar’s lab with the statistical analysis of data obtained from a corn pollen cytoskeleton experiment. As their two labs collaborated on plant cytoskeleton research, David and Elizabeth began dating, finding a common ground in their interests in biology and chemistry. When Dr. David Kovar began to perform his postdoctoral research at Yale University, Dr. Elizabeth Kovar started her postdoctoral research at Harvard University in statistical mechanics. Dr. Elizabeth Kovar reminisced that once David received a position at the University of Chicago as an assistant Professor, she joined him in the city of Chicago and continued her research at Northwestern University as a postdoctoral fellow, jokingly citing “the things one does for love” as the reason for her move back to the Midwest. Once in Chicago too, she started her research in biology, with both Kovars finally in the same city. Soon after, Dr. Elizabeth Kovar joined the teaching faculty at the University of Chicago as well. Though the two Dr. Kovars have established themselves as integral members of the Biological Sciences Department, they take very different approaches and positions within their work. Dr. Elizabeth Kovar focuses her time on the computational and educational research of the biology curriculum, teaching a variety of courses related to quantitative biology. Similarly, as part of the Biology Department, Dr. David Kovar is also a member of the research faculty, teaching fewer courses with a heavier focus and spending more time on his research. Drs. David and Elizabeth Kovar collaborate on the courses they teach at UChicago; she runs the computational lab component for the cellular biology course he teaches, and she frequently contributes to courses he teaches, when he believes her chemistry expertise will enhance the lectures. She uses a quantitative approach to the biology curriculum by integrating computational experimentation and math modelling into biology courses. Dr. Elizabeth Kovar stopped her full-time research about ten years ago when she had kids, but she continues her computational research on
a smaller scale, with her time prioritized towards teaching undergraduate courses. In terms of teaching, Dr. David Kovar’s favorite course as an instructor during his time at the University of Chicago has been an undergraduate course on the cytoskeleton that he taught with fellow professor, Dr. Mo Gupta. They taught this course for five years until Dr. Gupta left last year, and Dr. David Kovar currently teaches a variety of courses as a contributing professor and teaches courses on cellular biology for both graduate and undergraduate courses. He’s always been very interested in teaching courses and one day may consider moving to a university where teaching will be his primary focus. He also believes that he gets just as much, if not more, out of teaching the undergraduates and graduate students in his own research lab. This more personalized instruction makes him feel like “their coach, helping them develop their skills over time.” Smiling, Dr. David Kovar ends by stating, “By the time they leave they’re better than I am, moving on to bigger and better things.” About the Author Samara Singh is a second-year student majoring in biochemistry, and she is currently conducting research under Dr. Alexander Chervonsky at the University of Chicago.
About The Triple Helix
at the University of Chicago
The Triple Helix, Inc. (TTH) is the world’s largest completely studentrun organization dedicated to evaluating the true impact of historical and modern advances in science. Of TTH’s more than 25 chapters worldwide, the University of Chicago chapter is one of the largest and most active. We, TTH at the University of Chicago, are extremely proud of our chapter’s accomplishments, campus presence, and strong connection to other TTH chapters around the world. We continue to work closely with an ever-increasing number of faculty members, and have notably acquired the generous support of the founding Pritzker Director of Chicago’s Institute for Molecular Engineering, Matthew Tirrell, and his department. We have expanded our local organization so that now, we can confidently say that there is a place here for each and every one of our fellow college students. We have consciously and dramatically increased the size of our production, marketing, and events teams, and have watched our group of talented writers and editors grow at unprecedented levels. In fact, we have further expanded the intellectual diversity of our chapter, with TTH members having declared for more than 30 of the University’s different major and minor programs. Finally, we are absolutely thrilled to present the newest issue of our journal of original undergraduate research, Scientia. Over the years, TTH UChicago members have found themselves in research positions around campus, taking advantage of the hundreds of opportunities we are fortunate to have here. We found ourselves wishing, however, that there was an outlet where we could reach out to our peers on campus, to share our projects and project ideas – and to hear or read about their work as well. So we decided to create that outlet ourselves. This was the impetus for our journal, Scientia, which is the culmination of many of our members’ hard work. Since its inception, we have continued to strive for excellence in the diverse world of research by publishing the highest quality of undergraduate research. We hope you enjoy reading our latest issue! Salman Arif Co-President of The Triple Helix at the University of Chicago
Acknowledgements The Triple Helix at the University of Chicago would like to thank the following individuals for their generous and continued support: Dr. Matthew Tirrell
Founding Pritzker Director of the Institute for Molecular Engineering
Assistant Vice President for Student Life and Associate Dean of the College
Senior Assistant Director, Administration and Financial Advising
Student Involvement Advisor
We also thank the following departments and groups: The Institute for Molecular Engineering The Biological Sciences Division The Physical Sciences Division The Social Sciences Division University of Chicago Annual Allocations Student Government Finance Committee (SGFC) Chicago Area Undergraduate Research Symposium UChicago Undergraduate Research Symposium
Finally, we would like to acknowledge all our Faculty Review Board members and the mentors of our abstract authors for their time and effort.
Research Submission Undergraduates who have completed substantial work on a topic are highly encouraged to submit their manuscripts. We welcome both full-length research articles and abstracts. Please email submissions to email@example.com. Please include a short description of the motivation behind the work, relevance of the results, and where and when you completed your research. If you would like to learn more about Scientia and The Triple Helix, visit http://thetriplehelix.uchicago.edu or contact us at firstname.lastname@example.org.
Meet the Staff Scientia
Editors in Chief Jeremy Chang Clara Sava-Segal Managing Editors Nilanjana Ray Abhinav Ranjan Quang Tran Associate Editors Derrick Tang Hyesan Lee Zainab Aziz Nikita Mehta Maritha Wang Margaret Lazarovits Writers: Inquiries Christian Porras Loretta Au Samara Singh Drs. David & Elizabeth Kovar Katie Zellner Dr. Diane Lauderdale Mimansa Dogra Dr. Jocelyn Malamy Works in Progress Frankie Fung Preethi Raju Tuyaa Montgomery In Depth Jonathan Pekarek
Science in Society Review
Scientia Director Elle Rathbun SISR Director Ariel Goldszmidt
Marketing Director Nilanjana Ray
Web Webmasters Jeremy Chang Tima Karginov
Events Director Peter Ryffel Coordinators Jonathan Chuang Franklin Rodriguez
E-Publishing Editor in Chief Aliya Moreira Managing Editor Bella Pan
Editor-in-Chief Annie Albright Managing Editor Aya Nimer
Executive Co-Presidents Stephen Yu Salman Arif
Contact Us Email: email@example.com Website: http://thetriplehelix.uchicago.edu
The Scientia division is rolling out the Spring issue! This time. we're thrilled to introduce two new sections to our journal: Works in Prog...