Scientia - Winter 2016

Scientia

A Journal by The Triple Helix at The University of Chicago

Winter 2016

Front Cover Photo: Micrograph of ovarian clear cell carcinoma, stained Attribution: Nephron, 2011, Wikimedia Creative Commons License

Scientia Scientia Inquiries:

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The Quantum Life: An Interview with Professor Greg Engel Zeke Gillman

Stressing out Yeast: An Interview with Professor Allan Drummond Andrew Wang

Scientia Abstracts: Physical Sciences Decrypting the Tau Phosphorylation “Code” of Alzheimer’s Disease Through Production of Site-Specifically Phosphorylated Tau Surface Interactions Restrict the Movements of Amyloid- ß Peptides Resulting in Their Rapid Self- Assembly Into ß Sheets; a Molecular Dynamics Study Testing Land Coverage Classification Algorithms for Optimizing Flood Detection in Hyperspectral Image Data Development of Planktonic and Biofilm Bacterial Communities in a Laboratory Scale Model Drinking Water Distribution System Transient Solutions to the Heat Diffusion Equation: Learning with Different

Methods of Solution Measurement of Elastin Expression after in vitro Application of Potassium Channel Openers in RFL6 Cells Freeze-Cast Titanium Oxide Foams in Microgravity pH Dependence of Silk Protein Solution Viscosity Homogeneous Early Metal Complexes for Electrochemical CO2 Reduction Modeling the Energy and Cost Impacts of Excess Static Pressure in Central Forced-Air Heating and Air-Conditioning Systems in Single-Family Residences in the U.S. Red Sequence Measurements of Voronoi-Selected Galaxy Clusters Utilizing Hyperactive MuA Transposase Mutants to Improve Structural Understanding of the Mu Transposition System

Produced by The Triple Helix at the University of Chicago Layout and Design by Irene Zhang, Production Director Cover Letter written by Jake Russell, Co-Editor in Chief Scientia Board: Jake Russell, Luizetta Navrazhnykh, Michael Cervia, Amanuel Kibrom, Erin Fuller

Winter 2016

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Biological Sciences Evolutionary Versatility and Efficiency of Mammalian Masticatory Muscles A TBX5 Driven Network Suppresses Atrial Fibrillation in the Adult Heart Understanding the Role of cAMP-dependent PKA in Regulating Neurotransmitter Release in C. elegans Associations between Religious Practice and HPV Vaccine Knowledge and Utilization among Young Women Age 18-26 Morphometric Study of Bill Variation of Vanga Birds in Madagascar Manipulation of Multiple Motivational Methods and its Effect on Implicit

Learning The Anti-Diabetic Drug Metformin Decreases Autophagy and Increases Apoptosis in Multiple Myeloma Molecular Dynamics and Modeling of Lead (II) Binding to Calmodulin Talk Risky to Me – Risk Perception in Financial Decision Making and Foreign Language Use A Critical Role for Copper in the Regulation of Energy Homeostasis Imputed Single Nucleotide Polymorphism Risk Factors for Bipolar Disorder and Schizophrenia Barcoding for Braincases: Computed Tomography-enabled Landmark Analysis of Pipid Frog Crania Multilingual Exposure Impacts Early Sociolinguistic Judgments Quantum Dot Conjugates Deliver Biomolecules beyond the Blood Brain Barrier “Wait, what do you mean “he?”: Perceptions of Male Victims of Intimate Partner Violence Response of Elaborate Pupils to Changes in Light Intensity The Role of Ubiquitination on Morphine-induced Multidrug Resistance in Human Lung Cancer Identifying the Role of PDLIM5 in Lung Cancer Role of Oxidative Stress and Autophagy Signaling in Osteocyte Response to Spaceflight-like Radiation Phosphorus Phase Associations in the Northern Sargasso Sea Recovering Ancient Plasmodium DNA using Whole Genome In Solution Capture (WISC) Hyperspectral Imaging of Dynamic Camouflage in Juvenile Winter Flounder

Reveals How Color- and Pattern-matching Help Avoid Detection by Shallow- water Predators

In Depth:

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High expression of miR-532-5p, a tumor suppressor, leads to better prognosis in ovarian cancer both in vivo and in vitro Jeremy T. Chang

A Freshman Introduction to Gauge Theory Milo Marsden

Scientia

About Scientia Dear Reader, The front cover of this issue depicts ovarian clear cell carcinoma, a rare malignant form of ovarian cancer. Diseases like this are generally caused by specific faults in the genetic code, with symptoms often appearing too late for treatment to be effective. One of our In Depth articles this quarter discusses novel developments in early diagnosis techniques for ovarian cancer, making use of a new understanding of the role of microRNA in gene regulation, as well as “big data” sets such as the Cancer Genome Atlas (see article “High expression of miR-532-5p...” for more).

As the many spheres of scientific research continue to produce discoveries at a dizzying pace, we at Scientia hope to cut through the haze and bring you a little slice of the brilliant work being done right here at UChicago. In addition to cancer genomics, this quarter’s issue offers a brief introduction to gauge theory, as well as Inquiries with two professors on the bleeding edge of physical and biological chemistry. We also continue our collaboration with other Chicago universities by presenting the very best abstracts from the 2015 Chicago Area Undergraduate Research Symposium as well as selections from the 2015 UChicago Undergraduate Research Symposium.

Scientia is always looking to expand our scope to lesser known areas of research on campus. If you’re finishing up a project and want to see it in print, or if there’s a professor doing some incredible work you think everyone should know about, consider writing for us! We encourage all interested to get in touch with a member of our team, listed in back. In the meantime, please enjoy this issue of Scientia, by The Triple Helix.

Sincerely, Jake Russell Co-Editor-in-Chief, Scientia

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Winter 2016

Scientia Inquiries The Quantum Life: An Interview with Professor Greg Engel Zeke Gillman

Professor Greg Engel’s work doesn’t quite fit into one particular scientific field. Looking at his job titles, one can get an idea of the interdisciplinary nature of his research: professor of the Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and of the College, fellow of the Institute of Molecular Engineering, and co-director of the Biophysical Sciences Graduate Program. Yet to Professor Engel, “these disciplines are man-made concepts, and these sort of bright-line distinctions are very difficult to defend. The ideas and the science transcend the disciplinary boundaries.” Rather, what’s important is that he is doing science and getting answers. “We do what we have to do to answer the scientific questions,” said Engel.

What are those questions that require such a manifold effort? Simply put, he is observing excited state dynamics. This phenomenon occurs when an electron in a molecule absorbs energy, elevating it from its ground state to a higher, or excited state.

“The excited state carries enough energy to do something useful, whether to power a chemical transformation or to create electricity in a solar cell.

Excited states are also fleeting and they are very, very difficult to control. And that sets the stage for everything that we do. We want to understand how to control photochemistry, how to control motion of excited states, and how to use them efficiently,” said Professor Engel.

To better understand these excited states, Professor Engel often turns to biology for inspiration. Within living

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organisms, Engel has found electrons on excited levels moving hundreds of nanometers in a manner that utilizes the laws of quantum mechanics. Once they reach their ultimate destination, these excited electrons can then be transformed into energy that the bacteria or plant may use. By understanding these states, Engel also considers the applications, which include the possible production of synthetic quantum materials.

Professor Engel’s shift into his current line of work came naturally. As a Ph.D student, he built spectrometers to study atmospheric chemistry, “...measuring water vapor in the upper troposphere/lower stratosphere to understand convective transport of water and how water punches up into the stratosphere and into the tropics.”

In other words, increasingly stronger storms due to climate change may transport larger amounts of water to an otherwise very dry part of the atmosphere: the stratosphere. While he enjoyed atmospheric chemistry, Engel’s interests began to shift as he finished his Ph.D. In his time studying the stratosphere, he spoke to colleagues who focused on the ozone layer and began to consider the societal effects of ultraviolet light penetrating the ozone. As a result, Professor Engel, as a postdoctoral researcher, moved to the University of California, Berkeley to pursue these newfound interests. There he worked in the lab of Graham Fleming, acquiring the tools he would later need while managing his own lab. In the Fleming lab, Engel and his peers shot pulses of light at photosynthetic bacteria on the order of a femtosecond (1x10 -15 second),

Scientia a technique otherwise known as ultrafast spectroscopy.

When these short pulses of light hit the photosynthetic complex within the cells of these organisms responsible for photosynthesis, the chlorophyll become excited and energy is then transferred to the reaction center where charge sparation occurs to power the downstream biochemistry of photosynthesis.

It is this energy transfer mechanism in photosynthesis that is among the focal points of the Engel lab today. Within part of the chloroplast, the organelle in plants in which photosynthesis takes place, there are molecules of chlorophyll known as the antenna complex that capture sunlight in discrete packets of light energy.

These light packets are known as photons and they excite electrons within the antenna complex. The difficulty then lies in transferring the energy from these excited electrons to the reaction center. This reaction center is a protein complex that will transform the energy carried by the excitation into a more stable form. To transfer the energy to the reaction center, the excitation must go through a maze-like bridging area in much less than a nanosecond.

On the surface, this seems like an almost impossible feat. Fortunately for the planet’s photosynthetic beings (and for those of us who eat them or use fossil fuels from photosynthesis eons ago), evolution solved this problem. To traverse this maze, the photosynthetic complex employs quantum superposition, an effect of quantum mechanics that allows the excited electrons to simultaneously travel every path within the maze leading to the reaction center.

To study the photosynthetic energy transfer, Engel probes an ancient, anaerobic, photoautotrophic bacteria that survives in low-light conditions at the very bottom of the microbial mat in hot springs deep in the sea. This photosynthetic bacteria known as chlorobium tepidium can be thought of as the Ford Model T of photosynthetic organisms, as opposed to the trees, which Engel compares to the more complicated Ferrari. “ So you start by studying the Model T; you start by studying bacteria[…]If you’re interested in efficient energy transport, you look at the ones that are efficient all the time because they live in a slow, steady, controlled environment under a layer of pond scum,” said Engel.

To observe both how the light harvesting molecules absorb photons and how the quantum effects take place within the bacteria’s FMO complex, Engel and his team employ laser spectroscopic techniques. Thus another part of Engel’s research is focused on finding different techniques to manipulate and measure pulses of light or exploiting its speed to test for quantum effects. All of

Engel’s spectroscopy is concerned with studying light emitted by an organism in response to a light used to excite the same organism. Engel and his colleagues use femtosecond spectroscopy, a technology that produces light at a particular time on the femtosecond (millionths of a billionth of a second) time scale and will then investigate the energy of the light emitted. “It’s like having a fast camera. If you want to look at a bullet going through an apple you need nanosecond resolution because a bullet going through an apple is a fast process,” explained Engel. “Well, we’re a million times faster than that and that sets the stage for how you see something that happens in the millionths of a billionth of a second.

That’s the femtosecond spectroscopy that we do. Now, there are technologies to create very short pulses of light, not coincidentally, on the femtosecond time scale. So what you do is you put in energy at a very specific time, and then a little while later, you probe where that energy is.”

Studying the excited states requires testing new spectroscopic methods. Orders higher than the two dimensional electronic spectroscopy the lab uses have been researched, including a novel 3D nonlinear spectroscopic method that still requires some help from theorists to explain.

Nevertheless, in studying the results of emitted light from biological systems, Engel and his team can see whether or not the system is truly quantum mechanical.

For the green sulfur bacteria, Engel found long-lived quantum beating effects, evidence of superposition of the excited electrons. Basically, Engel and his team found that dephasing (the mechanism that describes the recovery of classical behavior from a quantum system) occurred at a much later time on the femtosecond time scale than expected. In fact, it correlates very well with the time scale of energy transfer.

“So suddenly the system isn’t in some simple classical state at the time the energy transfer happens,” said Engel.

“There are aspects of this quantumness that persist, and that was what got us excited in these early data sets.

We saw something that differed markedly from our theoretical prediction...”

This finding proved the quantum behavior of the bacteria at low temperature (77K). However, much remains unknown in the energy transfer and some members of Engel’s research group continue to look into it.

Professor Engel also looks at other biological complexes that exhibit excited state dynamics. For example, the photo-enzyme known as rhodopsin that lies within the retina of humans and animals is actually a

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Winter 2016 very effective light receptor.

“We look at photo-enzymes like rhodopsin in cow eyes to understand how the isomerization [the process by which one molecule transforms into another molecule with the same atoms, differing only in their configuration] there gives rise to incredibly sensitive detection of light.

Your eyes act almost as a single photon detector. So we want to understand how those processes work so that we can, perhaps not just isomerize a rhodopsin retinal, but to create new energy in chemical bonds,” said Professor Engel.

This research into excited state dynamics is not only influential in biology, chemistry and physics, but also in engineering. Currently, Engel has some lab members working on capturing light through man-made materials, applying the lessons learned from efficient energy transfer in photosynthesis and other biological processes to create new synthetic materials. “...I have some people working on perovskite materials [materials that have a unique crystal structure], trying to understand solar light harvesting in some new man-made materials.”

Engel admits that at times the interdisciplinary work he does can be vexing, especially when it comes to working on such a small time scale. Yet, in the end, the vexation comes with doing great science: “It is incredible and it can be frustrating and maybe because it’s so incredible is why it’s frustrating. The frustration is why it’s a frontier.”

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Stressing out Yeast: An Interview with Professor Allan Drummond Andrew Wang

Fig 1: Tracking aggregation of selected protein reveals that certain soluble proteins progressively become more aggregated under heat shock. In particular, superaggregators (red) aggregate extensively following heat shock.

When you’re a successful human resources manager in charge of all the new recruits at a rapidly expanding tech company, what do you do next? Well, for Professor Allan Drummond, the answer was to quit, go to graduate school, and start his own research lab.

Academic research was the end result of a rather unconventional path for Professor Drummond. He started off as a mechanical engineering and pre-medical student at Princeton, but then decided he didn’t want to do either engineering or medicine. Instead, he joined a start-up software company called Trilogy in 1995. Beginning as a developer, he moved around the company in various positions as it grew, eventually joining human resources as the director for Trilogy University, the training center for new Trilogy employees. While leading the center, however,

he found himself reading textbooks on quantum physics and artificial intelligence after work, realizing that he “[couldn’t] see [himself] in 30 years being a kickass human resources executive.” Thus, after seven years in industry, with no history of research and recommendation letters from the vice-president of human resources, he began to apply to a few top graduate programs that he was willing to quit his job for.

After initially being rejected at the programs to which he applied, Professor Drummond contacted the faculty at CalTech, where he had received an interview.

Originally asking for tips on applying again the following year, one conversation led to another with faculty in the Department of Computation and Neural Systems and his original rejection was changed to an acceptance. Entering

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Winter 2016 the graduate program of CalTech in that same year, his interest in computational neural systems developed into a focus on evolutionary theory. Specifically, he focused on directed evolution, which seeks to shape biological processes using artificial selective pressures. After obtaining his Ph.D., Professor Drummond joined the Harvard Institute for Systems Biology, as an independent Bauer research fellow in 2006. At Harvard, Professor Drummond became more of an experimentalist, studying systems in budding yeast in which proteins were thought to fold into toxic or harmful 3-D configurations in response to external stimuli or genetic mutation – a process known as misfolding.

Now, in the Department of Biochemistry and Molecular Biology here at the University of Chicago, Professor Drummond focuses primarily on studying cellular responses to stress. Specifically, he studies massive assemblies of protein and RNA called heat shock granules (HSGs). These HSGs form in cells in response to higher-than-ideal temperatures which disrupt the careful balance of processes within the cell. Because they form in response to stress, HSGs are thought to be a major component of the injury or recovery pathways for the cell following stress. Malfunctions in stress granule formation and dissociation are associated with the misfolding and aggregation observed in dementia and Alzheimer’s Disease.

Although it is possible to watch how HSGs form and dissolve in response to stimuli under a microscope, it is much harder to characterize their component parts and understand how those parts interact with each other.

In fact, the clearest conclusion from years of previous research has been that these heat shock granules are incredibly complex phenomena with unclear functions, mechanisms, and participants.

Professor Drummond wants to take a different approach to the question of understanding what these stresses are and how they work. “It’s well and good to look at these things inside cells, but we’d like to achieve a molecular understanding of how these things form and dissolve. For a biochemist, this means reconstitution from purified components. If we can do that, we feel like we really have an understanding of how the system behaves.”

To reconstruct the HSG in vitro is no easy task, however.

He needs to first identify the components of these HSGs. Using top-down mass spectrometry he can identify a large number of proteins involved in particular processes.

However, this approach provides no information on location or function of the proteins within the cell.

Professor Drummond also needs to use a bottom-up

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approach integrating expression and purification of HSG proteins with in vitro functional assays to answer questions about what drives these proteins to aggregate and how they function. Altogether, “top-down and bottom-up, it might be a 10 year project to get the things to truly meet in the middle,” but Professor Drummond’s group has recently made some major progress in this direction in a recently published Cell paper.1 This paper characterizes many components of these HSGs and describes the ultimate fate of these components in yeast. While previously 17-18 proteins involved in stress granule formation were known, Professor Drummond’s group identified more than 150 others and found whole new classes of proteins involved in HSG assembly. They also discovered that HSGs form in the nucleus and nucleolus, which is involved in ribosome production, not just in the cytosol of the cell, as previously assumed.

In addition to rapidly expanding the known participants in HSG formation, Professor Drummond’s results also directly contrasted with previous hypotheses about HSG function. HSGs were thought to form a big, insoluble clump of functional and damaged proteins that included misfolded proteins which were dangerous to the cell. These proteins needed to be cleaned up by partially disposing and partially refolding them.

HSGs were considered to be waypoints which stored and protected the cell from toxic proteins prior to degradation. When Professor Drummond’s group studied their newly identified proteins, however, they found something completely different. Every aggregating protein recovered its natural function, without any evidence of destruction. These observations suggest that HSGs may not be comprised of misfolded or damaged proteins, but may actually be deliberately aggregated and disaggregated in response to stressors. Professor

Fig. 2: Fluorescent tagging of cytosolic and nuclear proteins involved in HSG formation and live cell microscopy allows visualization of granule formation following heat shock in yeast

Scientia Drummond argues that the complexity and ubiquity of HSG formationin eukaryotes points to a highly specialized role in lessening the cellular damage done by stressors.

Despite these insights into cellular stress responses, Professor Drummond is clear that the big questions of function and mechanism still stand, with potential for future discovery and investigation.

Seeing as how Professor Drummond’s research has spanned much of biology, going from evolutionary theory to highly experimental work in model organisms, what guided his trajectory in research? It seems like so many scientists attribute their paths to happenstance; how much of his path was planned and how much serendipity?

Professor Drummond says that he feels the serendipity narrative is a little overplayed. “You always have a plan; you have to know where you’re going.

Serendipity lets you find out the best ways to change your plan, but you have to have that plan to start out with.” In his own path, he started out wanting to make quantitative statements about evolution, and from that, began asking focused questions about the theory of molecular evolution. After using the tools of empirical observation and experimentation in his research, Professor Drummond decided to focus on understanding complex biological systems experimentally. In these systems, he has begun to view his approach to research as developing capabilities to study systems of interest in in cells. “The kinds of phenomena we’re working on are so complex, so notably overwhelmingly complicated, that really what we need to do is start playing the game, getting in there, looking at things and seeing what we can see.”

Although he has left the corporate world behind and forged a new path in research, Professor Drummond still applies many skills that he first acquired in business.

He finds that certain aspects of leadership development and management – skills which are emphasized heavily in business – are vitally important when running a lab and mentoring graduate students. As a result, when he talks with graduate students, he focuses on adapting the project his students work on so that they are in line with his students’ skills and goals. In his own graduate school and academic process, Professor Drummond’s familiarity with alternatives in industry gave him personal clarity and drove him to succeed in the often difficult environment of graduate school and academic research.

The choice he made in leaving industry allows him to say with confidence, “I’m so excited to be doing this tough, miserable work right, it’s great!”

References [1]

Wallace EWJ, Kear-Scott JL, Pilipenko EV, Schwartz MH, Laskowski PR, Rojek AE, Katanski CD, Riback JA, Dion MF, Franks AM, Airoldi EM, Pan T, Budnik BA, Drummond DA. Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress. Cell 162 (6) (2015).

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Scientia Abstracts Presented through collaboration with the 2015 Chicago Area Undergraduate Research Symposium and the 2015 UChicago Undergraduate Research Symposum

Physical Sciences Decrypting the Tau Phosphorylation “Code” of Alzheimer’s Disease Through Production of Site-Specifically Phosphorylated Tau Matt Amrofell Northwestern University, Evanston, IL The Tau protein functions as a microtubule stabilizer in neurons. However, when Tau becomes hyper-phosphorylated, neuronal axons degrade due to microtubule destabilization and neurofibrillary tangle formation. These biomarkers are commonly observed and associated with Alzheimer’s disease. However, the mechanistic understanding of the phosphorylation “code” behind this process remains unclear. We hypothesize that combinatorial effects of multiple phosphorylation drive the severity of the disease state. My work seeks to produce site-specific phosphorylated Tau at seven disease-associated sites, singly and combinatorially. I will use a phosphoprotein production platform developed in the Jewett lab that employs three primary innovations: (1) An engineered orthogonal translation system (OTS) capable of incorporating a phosphoserine residue at genetically encoded sites, (2) genomically reengineered E. coli strains that support Amber codon suppression by the engineered translation apparatus, and (3) a cell-free protein synthesis (CFPS) platform for expression of human phosphoproteins. The combination of these technologies expands the genetic code to enable the site-specific incorporation of phosphoserine into proteins. I have generated a human-Tau construct optimized for expression in E. coli, as well as variants with amber codons for phosphoserine incorporation. Phospho-Tau variants will be evaluated in microtubule stability and neurofibrillary plaque formation assays. These experiments will provide a foundation for elucidating how the quantity, density, and distribution of serine phosphorylation contribute to Tau-based pathology.

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Surface Interactions Restrict the Movements of Amyloid- ß Peptides Resulting in Their Rapid Self- Assembly Into ß Sheets; a Molecular Dynamics Study Natnael Doilicho, Dr. Esmael Haddadian, and Dr. Karl Freed The James Frank Institute, Chicago, IL

Structural coloration rises from the interference of light due to the periodic nanostructures found in a material.

In this project we investigated the application of structural colors in pixel display devices. Iron oxide nanoparticle suspensions were utilized as the source of color structuration. By placing a voltage across the pixel, the concentration of nanoparticles can be controlled, controlling the color. At sufficiently high voltages, the pixel devices can begin to demonstrate transparency.

It is desirable for a pixel device to be capable of demonstrating both a strong color response and high transparency. The aim of this project is to investigate the ability of microstructures placed within the pixel device to improve the color response and transparency of unmodified pixels. Line and pillar microstructures in the range of 10-100 um width were synthesized on the inner pixel surface using a photolithography technique.

With the addition of these microstructures, the transparency of the pixel devices greatly improved, while the modified pixel devices are still able to demonstrate a color response. The pillar microstructure pixel devices required a lower voltage to achieve a comparable state of transparency compared to the line microstructure pixel devices.

This technology can be used in a dynamically tintable window, or in outdoor electronic displays. Because structural coloration results from external light diffraction, structural color displays would perform optimally in sunlight.

Testing Land Coverage Classification Algorithms for Optimizing Flood Detection in Hyperspectral Image Data Benjamin Huynh and Dr. Maria T. Patterson University of Chicago, Center for Data Intensive Science, Chicago, IL In remote sensing, hyperspectral imaging instruments provide data with potentially high predictive performance in image classification. However, the limited computational capabilities onboard these sensors do not allow full utilization of the data. For instance, the algorithms onboard NASA’s Earth Observing-1 (EO-1) satellite are limited to using only 12 of 242 spectral bands due to data size. Project Matsu, a cloud-based collaboration with NASA, makes processed hyperspectral data available to the public, within 24 hours of acquisition. This framework facilitates fast access and computational power over the full dataset, allowing us to test machine learning algorithms for land cover classification in hyperspectral data using all 242 bands to improve upon the existing water detection algorithms currently used onboard the satellite. Using a diverse training set of hyperspectral data, we achieve a significant accuracy increase of 5-20%.

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Development of Planktonic and Biofilm Bacterial Communities in a Laboratory Scale Model Drinking Water Distribution System Nicole Minalt Loyola University Chicago, Chicago, IL Drinking water distribution systems (DWDS) contain large numbers of viable microorganisms that exist in structured, surface-attached communities called biofilms. While non-pathogenic bacteria generally dominate these biofilms, the presence of pathogens in DWDS biofilms has been documented. Analysis of drinking water is routinely used as an indicator of pathogen presence within DWDS; however, the relationship between bacterial communities in the bulk water and biofilm communities within DWDS is poorly understood. We used a laboratory-scale pipe loop system inoculated with a bacterial consortium from a municipal DWDS to explore the relationship between attached and planktonic bacterial communities. Next- generation sequencing of bacterial 16S rRNA genes was used to assess taxonomic composition of planktonic and biofilm communities. Robust biofilms developed in the system within several weeks, and these established biofilms resisted colonization by a laboratory strain of Pseudomonas aeruginosa PA01. Sequencing results indicated that planktonic and biofilm communities were initially similar in taxonomic composition, but planktonic and biofilm communities diverged significantly over the six week study, producing distinct communities. Biofilm communities were also more taxonomically diverse and consistently included sequences from the pathogenic genus Legionella, which was rarely detected in the bulk water. These results suggest that monitoring of water may not be adequate to characterize DWDS bacterial communities or to detect the presence of pathogenic organisms within DWDS.

Transient Solutions to the Heat Diffusion Equation: Learning with Different Methods of Solution Guilherme Nogueira Illinois Institute for Technology, Chicago, IL Problems involving the dynamics of heating or cooling physical systems submitted to boundary conditions are of great importance in a wide range of situations. For example, simple situations involving cooling of food to more complex situations such as nuclear reactors all require a good knowledge of the heat dynamics involved in their respective processes. Essentially, the method to solve a steady-state heat diffusion equation, for a series of physical systems, is relatively straightforward. Also, a substantial amount of conclusive research on the topic is widely available.

However, to find the time evolution of temperature for a system is not a simple task and these problems frequently present difficulties which cannot be found using analytical methods. This work provides solutions to the heat diffusion equation in one-dimensional and homogeneous systems when submitted to certain boundary conditions. The solutions are obtained by utilizing the integral transformation method and a series of characteristic functions. For particular sets of boundary conditions, aspects of the solutions are discussed. By comparison of “apparently� different results obtained by using two mathematical methods, some identities are obtained and proved analytically or using computational help. Also we discuss the possibility to analyze more complex systems by using the present results.

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Measurement of Elastin Expression after in vitro Application of Potassium Channel Openers in RFL6 Cells Jaya Paruleka Illinois Institute for Technology, Chicago, IL

The goal of this study is to develop an in vitro assay for elastin expression using RFL6 cells, which were derived from fibroblasts present in rat lung tissue. Vasodilating pharmaceuticals that encourage production of elastin and helper proteins by smooth muscle cells in the arterial wall, particularly potassium channel openers, may increase functional elastic fibers, decrease vessel stiffness, and be a viable treatment option for hypertension. Different dosages of minoxidil and diazoxide, pharmaceuticals within this class, were applied to RFL6 cells, with elastin amounts in response to drug treatments being assessed using a commercial Fastin Elastin assay. From the results obtained, it can be interpreted that diazoxide and minoxidil exhibit changes in elastin content as drug concentration increases, with an especially significant elastin content level at 50 μM concentrations for both drugs. Seeing as these drugs exhibit an effect on increasing elastin content, future work involves transitioning from application of drug to cell line to application of drug to primary cells. Applying minoxidil and diazoxide to arterial cross sections, for example, would be an even more appropriate model for elastin production in blood vessel walls. Overall, this project will shed light on optimal pharmaceutical doses for increasing elastin expression and also provide a relatively high throughput method for testing additional anti-hypertensive drugs that may affect elastin expression, subsequently decreasing arterial stiffness and blood pressure.

Freeze-Cast Titanium Oxide Foams in Microgravity Kristen Scotti Northwestern University, Evanston, IL Freeze-casting, a novel ice-templating technique, involves the solidification of an aqueous suspension to create a porous structure. By introducing a thermal gradient, ice dendrites grow directionally while rejecting particles into interdendritic spaces. Upon sublimation, elongated pores, replicating the ice dendrites are formed. The simplicity of this technique–and the use of water as a solvent–enables scalable and low-cost production of this material. This process was utilized to solidify titanium oxide slurries for fabricating highly-ordered, three-dimensional dye- sensitized solar cell electrodes aboard microgravity flights. This initial research sought to understand how gravity influences microstructures of freeze-cast titanium oxide foams. We posed and sought answers to two basic and fundamental questions: (a) how does gravity affect suspension settling before and during ice solidification, and (b) how does gravity influence convective forces affecting dendritic growth and particle packing behavior within interdendritic space? For optimal electron diffusion, the ideal electrode morphology consists of mesoporous channels aligned in parallel with each other, perpendicularly oriented with respect to the current collector. In comparison to terrestrially solidified foams, materials solidified in microgravity better met this requirement; pore alignment was nearly perpendicular with the freezing surface and average tortuosity was significantly reduced. By masking the forces of Earth’s gravity, we aim to expand the scientific understanding of freeze-cast solidification behavior, ultimately allowing for the improvement of terrestrially-based fabrication methods.

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pH Dependence of Silk Protein Solution Viscosity Clare Singer and Dr. Daniel Blair Georgetown University, Washington, DC Recent interest in silk-based biomaterials for biomedical applications has driven the investigation of the rheological properties of silk fibroin protein solutions and gels. This research took a closer look at the properties of Bombyx mori silk protein solution through a range of pHs as the solution approached a gel state. Common biological buffers at high concentrations relative to the silk but low ionic strengths were used to maintain constant pH while avoiding aggregation independent of pH change. We used viscometry and dynamic light scattering to obtain both a bulk measurement of viscosity and a local measurement of the structural changes occurring at the protein monomer level. We expected to observe an inverse relationship between pH and intrinsic viscosity (a measure of the protein’s contribution to the viscosity). However, our data show non-monotonic behavior, which we are trying to understand in ongoing experiments analyzing the second virial coefficient. This is a correction to the Ideal Gas Law that measures interactions between protein monomers in the system. Furthermore, we unexpectedly observed a direct relationship between pH and the protein’s hydrodynamic radius. We explain this apparent discrepancy by noting that at low pH, medium-sized aggregates dominate the system, but at high pH, erroneous large aggregates may dominate the system and result in an anomalously large average radius. This theory is supported by evidence of a 2.5 times higher laser intensity at lower pHs, indicative of scattering from more objects. By better understanding the process and mechanisms of gelation, we can help researchers create more effective biomaterials.

Homogeneous Early Metal Complexes for Electrochemical CO2 Reduction Mark Sovereign and Jay Bhanot DePaul University, Chicago, IL In an effort to mitigate the environmental impacts of climate change, numerous studies have been conducted on reducing carbon dioxide using a variety of techniques including chemical and electrochemical reduction. Although this is a topic of vigorous study within the field of chemistry, the efficacy of early transition metals at reducing CO2 has yet to be fully explored. Furthermore, utilizing early metals such as Tungsten, Molybdenum, Titanium, and Zirconium has several benefits. These species are abundant and therefore much cheaper than other commonly used but rare metals such as Rhenium. Therefore, the proposed research is to synthesize and study compounds of these early metals that could be utilized as renewable catalysts for CO2 reduction. In particular, the synthesis, characterization, and analysis of Mo(TPP) (TPP = tetra-mesophenyporphyrin) complexes is being attempted as it has not been examined for the efficiency to reduce carbon dioxide to renewable fuels. In addition, metallocene complexes of the form Cp2MCl2 (M = Mo, Zr, Ti) were studied to catalyze electrochemical reduction of CO2 in protic and aprotic environments. Our initial results in these areas will be reported.

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Modeling the Energy and Cost Impacts of Excess Static Pressure in Central Forced-Air Heating and Air-Conditioning Systems in Single-Family Residences in the U.S. Rou Yi Yeap Illinois Institute for Technology, Chicago, IL Many central residential forced-air heating and air-conditioning systems contain high pressure drop elements such as high-efficiency or dust-loaded filters, dirty coils, or constricted or undersized ductwork, which are widely assumed to have substantial energy and economic impacts. However, the overall energy and cost consequences of excess static pressures have not been explored in depth across a wide range of climates, homes, or system characteristics. Therefore, we performed 780 annual building energy simulations using BEopt and EnergyPlus to predict the energy and cost impacts of realistic excess static pressures for typical new and existing single-family homes with both permanent split capacitor (PSC) blowers and electronically commutated motors (ECM) in 15 U.S. climate zones. Results demonstrate that excess static pressures can increase annual energy consumption and costs, but the magnitude varies by blower type and climate zone. Moderate increases in static pressures (i.e., from 50 to 150 Pa) were predicted to yield minimal increases in annual space conditioning energy costs (i.e., less than 3% across all homes, blowers, and climates), while more extreme increases in static pressure (i.e., from 50 to 350 Pa) were predicted to yield average increases in energy costs of ~9% with ECM blowers and ~18% with PSC blowers.

Red Sequence Measurements of VoronoiSelected Galaxy Clusters Brian Welch and Dr. Marcelle Soares-Santos Fermi National Accelerator Laboratory, Batavia, IL Past observations of galaxy clusters have indicated that the member galaxies are clustered in color space as well as physical space. This color clustering defines the cluster red sequence. The red sequence is a tight correlation between galaxy color and magnitude which exists in the red galaxies within the cluster. Because of the observed red sequence, many cluster finders have been developed which identify clusters based on the observation of a red sequence. The goal of our research is to determine whether clusters found using the Voronoi Tessellation (VT) method, which does not rely on the red sequence, exhibit similar characteristics to those found using other red sequence dependent cluster finders. We identify the red sequence in each cluster by fitting a Gaussian Mixture Model to the color distribution attained by subtracting the Dark Energy Survey (DES) r-band magnitude from the g-band magnitude. We then fit two Gaussian curves to this distribution, the higher of which corresponds to the red galaxies and the lower to the blue galaxies. These Gaussian fits allow us to select red sequence galaxies based on whether or not they fall under the red Gaussian curve. Next, we fit a least squares line to the red galaxy data to measure the slope of the red sequence. This information can then be compared to similar analysis done using other cluster finders. We used simulated data to develop the red sequence measurement code and to study the impact of selecting clusters using the VT algorithm on the red sequence. The next phase of the research process will be to run the red sequence characterization on a catalog produced from Dark Energy Survey data by VT. Thus far, the study of the simulated data has yielded results which are consistent with the literature, so we can conclude that the VT cluster finder is functioning properly.

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Winter 2016

Utilizing Hyperactive MuA Transposase Mutants to Improve Structural Understanding of the Mu Transposition System Vishok Srikanth and Dr. Phoebe Rice University of Chicago, Chicago, IL

The DNA transposition system of bacteriophage Mu was the first such system adapted for in vitro use, and remains one of the most thoroughly understood. Its transposase MuA ¬– a member of the “DDE” family of recombinases – shares its catalytic domain with many other DNA transposases and retroviral integrases, making Mu an informative model system for understanding a wide variety of mobile DNA elements. A mutant screen of the MuA gene has identified several hyperactive mutants resulting from single nucleotide substitutions, raising the question of why natural selection has not favored these changes in the wild-type sequence. Since different copies of MuA perform different functions within the active tetramer of the Mu transposition system, the structure of wild type MuA may reflect sequence compromises that negatively affect transposition activity but preserve or promote other crucial interactions and behaviors. My research focused on exploring the structural and kinetic changes underlying the increased activity of these mutant transposases in an attempt to understand what selective pressures may be controlling the evolution of viral integrases besides a drive toward maximal transposition efficiency. Preliminary results show that the reaction kinetics of these mutants can be monitored in vitro and differ from that of wild-type MuA. The kinetic causes of these mutants’ elevated activity levels was further examined using a chimeric MuA construct with modified DNAbinding domains, making it possible to target where wild-type or mutant protomers assemble in the MuA tetramer responsible for transposition. Hyperactivating mutations may also prove useful for attempts to improve upon the current x-ray crystal structure of MuA, as improving the kinetics of the transposition reaction may increase sample homogeneity and thereby favor crystal formation. Although further optimization is required for obtaining crystals suitable for diffraction experiments, I have successfully utilized a hyperactive mutant to crystallize a more complete MuA construct than was used to generate the current crystal structure of the transposase.

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Scientia

Biological Sciences Evolutionary Versatility and Efficiency of Mammalian Masticatory Muscles Lissette Arellano DePaul University, Chicago, IL Rodents are the largest group of mammals and are extremely diverse. Three distinct jaw muscle arrangements have evolved across rodent taxa and remain today. To better understand the function and efficiency of these morphologies, the jaw musculature of ten rodent species that vary in diets and habitats were examined. Measurements of teeth, muscle attachments, mandibles, and jaw muscle lever arms were obtained. The findings indicate that the mouse-rat clade mostly exhibits covariance patterns more similar to those of the squirrel-related taxa than to those of South American caviomorphs. The Northern Luzon giant cloud rat, Phloeomys pallidus, appeared to be an outlier in the mouse-rat clade. Further work was done to find whether a functional, biomechanical difference exists between the muscle systems. Each masticatory apparatus’s mechanical advantage, or ability to amplify force, was obtained for two tasks: chewing and gnawing. By measuring the mechanical advantage for each adductor muscle in mandible positions typical of chewing and gnawing, the relative efficiencies of these masticatory processes were found for each of the ten species. The data collected from these mechanical advantage studies support the initial findings that P. pallidus is an outlier in the mouse-rat clade that uses its masticatory muscles more like a caviomorph than a rodent of the squirrel-related taxa. Overall, the data demonstrate that rodents in the mouse-rat clade exhibit masticatory versatility across morphologies.

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Winter 2016

A TBX5 Driven Network Suppresses Atrial Fibrillation in the Adult Heart Jenna Bekeny University of Chicago, Chicago, IL Atrial fibrillation (AF) is the most common cardiac arrhythmia and is a major cause of morbidity and mortality. Recent genome-wide association studies (GWAS) have implicated a number of genetic loci in AF susceptibility, including the transcription factor TBX5. TBX5 is known for its role in cardiac development, and continues to be expressed in the adult atria. To study the post- developmental role of TBX5, TBX5 was removed with a tamoxifen-inducible Cre recombinase when mice were 6-8 weeks of age. Adult TBX5-deleted mice rapidly developed spontaneous AF, characterized by a surface electrocardiogram showing an irregularly irregular ventricular rate and an absence of p-waves. Mice heterozygous for adult TBX5 deletion showed a similar, though less penetrant, phenotype. To understand the mechanisms of AF onset after TBX5 removal, we evaluated transcript expression of a number of candidate genes linked to AF by qRT-PCR. We found that removal of TBX5 in the adult disrupted expression of a number of ion handling genes including gap junctional proteins (GJA1, GJA5), sodium channels (SCN5a, SCN7a), SR calcium channels (RYR2, SLN, ATP2a2), and potassium channels (KCNJ3, KCNJ5). Mice heterozygous for adult TBX5 deletion also show partial downregulation of these channels. We define a TBX5-dependent network in the atria that maintains atrial conduction.

Disruption of this network manifests as atrial fibrillation. These studies shed insight on the genetics and mechanisms of AF in humans.

Understanding the Role of cAMP-dependent PKA in Regulating Neurotransmitter Release in C. elegans Om Bhetuwal The University of Illinois at Chicago, Chicago, IL The Gαs signaling pathway has been linked to learning and memory in a variety of organisms, including Drosophila melanogaster and mice. Dunce and rutabaga encode key proteins in this pathway in Drosophila, and mutations in these genes are associated with learning defects. When activated, this pathway stimulates adenylyl cyclase (ACY1), which catalyzes cAMP production. cAMP binds to the regulatory subunit of PKA (KIN-2), freeing the catalytic subunit (KIN-1) to phosphorylate its targets. PKA activation has been shown to increase synaptic transmission in both Drosophila and Aplysia, though the specific mechanism underlying this effect is unclear. In order to understand the role of this pathway in regulating synaptic transmission, we investigated two mutant strains in C. elegans that enhance pathway activity, acy-1(ce2) and kin-2(ce179), and one that reduces activity, acy-1(pk1279)Ex87[pmyo-3::acy-1(ce2)].

We examined neurotransmitter release at the neuromuscular junction (NMJ) in these worms using a drug sensitivity assay to the acetylcholinesterase (AChE) inhibitor Dylox. Exposure to Dylox causes acetylcholine (ACh) to accumulate at the NMJ, resulting in paralysis. We predicted that mutant worms with reduced Gαs function release less ACh in the synaptic cleft exhibiting resistance to Dylox. On the contrary, mutant worms with enhanced Gαs activity were predicted to exhibit increased sensitivity to Dylox due to enhanced release and rapid accumulation of ACh. In addition to drug sensitivity, preliminary evidence from electron microscopy and electrophysiological experiments indicate that mutant worms with reduced Gαs function show fewer docked vesicles and lower evoked amplitude than wildtype worms, while mutants with enhanced Gαs function show more docked vesicle and higher evoked amplitude as compared to wild type. These data support our hypothesis that PKA enhances neurotransmitter release at the NMJ.

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Scientia

Associations between Religious Practice and HPV Vaccine Knowledge and Utilization among Young Women Age 18-26 Julia Bodson and Dr. Deanna Kepka Huntsman Cancer Institute, Salt Lake City, UT Though the human papillomavirus (HPV) vaccine has been recommended for nearly a decade, coverage in the US remains below target rates. Beliefs concerning sexual activity may be responsible for such slow uptake; religious groups in particular have opposed the vaccine, claiming that it is unnecessary and may promote illicit sexual behavior.

In Utah, a state featuring a dense religious population, HPV vaccination rates are among the lowest nationwide. This study is the first assessment of the association between religious practice and HPV vaccine knowledge and utilization in Utah. We surveyed 327 insured women aged 18-26 attending the University of Utah Community Clinics about their HPV vaccine knowledge and utilization. Bivariate analysis was used to compare participants who reported practicing an organized religion or not. Odds ratios (ORs) were estimated using logistic regression models to assess the influence of religious practice on HPV vaccine series initiation (≼ 1 dose) and completion (3 doses). General linear models estimated influence of religious practice on number of doses received. A Directed Acyclic Graph was used to identify potential confounders. Among participants who reported religious practice, analogous analysis was performed to compare those who reported that religion guided their daily decisions or not. Religious practice was significantly associated with lower awareness of HPV (p=0.009) and of the HPV vaccine (p=0.020), with not knowing how HPV is spread (p=0.006), with lower importance assigned to the vaccine (p=0.004), and with no provider recommendation for the vaccine (p=0.020). Adjusting for age, education, and marital status, religious practice was associated with lower HPV vaccine initiation (OR=0.502, p=0.007), completion (OR=0.473, p=0.002), and number of doses received (β=-0.434, p=0.005). There were no significant differences between participants reporting that their religion did or did not influence their daily decisions. Results reveal low HPV vaccine knowledge and utilization among religious young women in Utah. These findings suggest that to successfully target religious individuals and their health care providers, it may be necessary to develop sensitive intervention strategies in close collaboration with religious leaders.

Morphometric Study of Bill Variation of Vanga Birds in Madagascar Neno December and Nicole Gracias Loyola University Chicago, Chicago, IL The remarkable level of species diversity and endemism in Madagascar warrants a comprehensive analyses of its fauna to better understand certain aspects of evolution. The Vangidae, an endemic group of birds found only in Madagascar, are exceptionally diverse in terms of morphology and a good model system to test proposed hypotheses of adaptive radiation. Vangas evolved from a single lineage that colonized Madagascar and then radiated into several species that occupy different niches. Our objective is to conduct a wide-ranging morphological examination of bill variation across this family to identify underlying mechanisms of how their variation evolved. We photographed museum specimens from the Field Museum of Natural History and used landmark morphometrics to characterize the shape of bills. We used analytical programs tpsDIG2 and MorphoJ to examine variation of bills across species. Our samples included all related species of vangas from various ecological niches. Our study is the first to quantitatively examine the morphological variation of Madagascan birds and has important implications for better understanding this biodiversity hotspot, as well as understanding the effect of endemism on rate of speciation.

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Winter 2016

Manipulation of Multiple Motivational Methods and its Effect on Implicit Learning

Danbee Chon Northwestern University, Evanston, IL

Previous research has indicated that better implicit learning may occur on a state of regulatory misfit, as regulatory fit seems to induce better learning on conscious tasks. To investigate this idea of regulatory misfit, this study utilized the approach-avoid motivation theory, of which approach motivation seeks to be rewarded, and avoidance motivation seeks to avoid punishment. Implicit learning is a type of memory in which previous experiences assist in the performance of a task without conscious awareness of what is gained from experience. The project’s key question is to examine the effect of cognitive origin of motivation. We hypothesized that the regulatory misfit groups (positive + avoid & negative + approach) will exhibit better implicit learning than the fit groups (positive + approach & negative + avoid). 128 participants were randomly assigned into one of the four conditions before completing an implicit motor sequence learning task, which measures learning on a covertly embedded 12item repeating sequence by comparing participants’ performance on the repeating sequence with unpracticed sequences. A factorial ANOVA revealed that our hypothesis was partially supported, as participants primed with avoid motivation displayed significantly better sequence-specific learning than the approach motivation group.

We relate these findings to the research regarding the motivation theory, which indicates that avoid motivation is generally more powerful than approach motivation and discuss implications for motivation effects on skill learning.

The Anti-Diabetic Drug Metformin Decreases Autophagy and Increases Apoptosis in Multiple Myeloma Julia Tomasson and Dr. Claire M. Edwards University of Oxford, Oxford, United Kingdom Multiple Myeloma (MM) is an incurable plasma cell malignancy with a median survival of 3-4 years with conventional treatment highlighting the need for identification of new therapeutic approaches. The anti-diabetic drug metformin is associated with improved clinical outcomes in diabetic patients with MM, suggesting a potential anti-tumor effect. Epidemiological data suggest therapeutic potential, however, the exact mechanism is yet unknown. In vivo studies from the Edwards lab have shown metformin reduces tumor burden and bone destruction in MM. In vitro, MM cells treated with metformin in glucose-depleted conditions have been shown to induce apoptosis.

Autophagy, a physiological process that deals with the destruction of cells and recycling of cellular constituents, can be induced by nutrient deprivation and high stress conditions, while its deregulation has been associated with many pathological conditions, among them myeloma. We hypothesized that the anti- tumor response to metformin may be due at least in part to dysregulation of autophagy. The aim of my study was to determine the effect of metformin on autophagy in MM cells. Human MM cell lines were treated with increasing concentrations of metformin and effects on autophagy, apoptosis, and viability were assessed using immunoblotting and colorimetric assays.

Immunoblotting showed that metformin treatments inhibited the expression of autophagic regulatory proteins BecN1, LC3i and LC3ii, as well as decreased autophagic flux, as measured by LC3 turnover. Metformin treated MM cells also displayed increased cPARP, a marker for apoptosis. Apoptotic effects were confirmed by decreased cell viability of treated cells. When cells were also treated with bafilomycin, an inhibitor of autophagosome-lysosome fusion and the degradation of LC3ii, autophagic flux was decreased by metformin treatments, suggesting that autophagy was suppressed at an earlier stage. These data suggest that metformin inhibits autophagic activity, which may result in increased apoptosis in MM. Research into the potential therapeutic effects of metformin may both lead to further elucidation of oncological molecular mechanisms, as well as provide a rationale for testing metformin in prospective clinical trials to improve the outcomes of diabetic and non-diabetic patients with MM.

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Scientia

Molecular Dynamics and Modeling of Lead (II) Binding to Calmodulin Amanda Foner Loyola University Chicago, Chicago, IL

Calmodulin (CaM) is a calcium-binding messenger protein found in eukaryotic cells. This protein becomes active when bound with calcium (II) ions. Heavy metals like Pb2+ can displace Ca2+ ions from the protein and permanently deactivate CaM. While the exact mechanism of displacement is unknown, molecular dynamic simulations provide insight into the Pb2+ binding process. Simulations were created to illustrate free Pb2+ ion binding to holo- and apo- conformation CaM to determine if the A) lead (II) would bind to residues found in the intial crystal structure and B) verify effects of protein conformation to lead binding. Calmodulin crystal structures, in the lead (II) bound holo- conformation, were obtained via the RCSB Protein Data Bank (2V01). Then, all bound ions were removed and the resulting holo-conformation protein was placed in a solvent box containing water, Na+ Cl- counter ions, and 40mM Pb2+ (N=100). The same solvent box preparation was used in equilibrating production files for the apoprotein (1CFD). Resulting 60ns simulations, from both the apo- and holo- conformations of CaM, suggest energetic differences between permanent and transient binding of Pb2+ ions. Additionally, multiple residues with lead (II) bound to the protein were identical to that in the initial crystal structure. Future applications of these substrate cloud simulations can include lead drug discovery and determination of active sites in proteins with unknown functions.

Talk Risky to Me – Risk Perception in Financial Decision Making and Foreign Language Use Sophie Holtzmann University of Chicago, Chicago, IL Every day in the international community, individuals of different linguistic backgrounds gather and make decisions that influence the world. This makes especially pertinent the growing body of research suggesting decisions can be affected by language. One realm in which this language effect has been demonstrated is via the framing effect in financial decision making and risk perception. All our decisions are influenced by subtle biases, and one such bias is the framing effect, which shows that persons inaccurately discriminate statistically identical outcomes by whether the outcome is phrased in terms of gains or losses. This is attributed to the emotional reaction induced by cognizing loss, called risk aversion. Keysar (2012) established that foreign-language use combats framing effects by lowering risk aversion. The present study explores whether foreign language generally lowers risk aversion or improves rationality, allowing the user to discern different types of risk more effectively. By offering risky positive and negative expected value decisions to participants in terms of gains and losses, we analyzed how language influences decision outcomes.

We additionally analyzed participant strategy strictness to assess language differences in perceptual differences without the outcome value judgment. Initial analysis suggests that foreign language induces heightened sensitivity to decision outcomes, but not an overall improvement in rationality. These findings have far reaching implications for our quickly growing bilingual world.

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Winter 2016

A Critical Role for Copper in the Regulation of Energy Homeostasis Clara Kao and Dr. Jonathan D. Gitlin Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA Confronted with limited nutrient availability, living organisms demonstrate evolutionarily conserved responses, slowing or arresting metabolic processes to permit adaptation and survival. One such essential nutrient is the metal ion copper, which functions as a cofactor for enzymes involved in many vital cellular processes including energy production, oxygen transport, metabolism, and signal transduction. Tight homeostatic regulation of copper acquisition, distribution, and use is necessary to ensure normal function. Copper enters eukaryotic cells at the plasma membrane via the high-affinity copper transporter Ctr1. In a mouse Ctr1 knockout model, embryo development fails at early stages in utero. To gain a better understanding of how Ctr1 functions in a vertebrate animal we made a zebrafish Ctr1 knockout. Ctr1 mutant embryos lack melanin, a phenotype observed in copper deficient embryos.

However, the most striking phenotype we observe is that development is markedly delayed in Ctr1 mutant larvae compared to siblings. As copper is required for the assembly of cytochrome c oxidase, the regulatory key for energy availability, we hypothesized that this developmental delay is due to decreased mitochondrial energy production. In support of this we observe a decreased amount of the cytochrome c oxidase subunit Cox1 in Ctr1 mutants, leading us to analyze ATP production and markers of mitochondrial abundance and health. Understanding how zebrafish adapt to perturbations in copper regulation may provide new insights into the role of these pathways in vertebrate development and energy homeostasis.

Imputed Single Nucleotide Polymorphism Risk Factors for Bipolar Disorder and Schizophrenia Madeline Klinger and Dr. Elliot Gershon University of Chicago, Chicago, IL The Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) comprises two goals: 1) to identify genetic markers that confer risk for psychoses, and 2) to correlate specific biological traits (intermediate phenotypes) of these disorders with the risk markers. Given that commercially available genotype microarrays present only a fraction of the entire human genome, it is statistically unlikely that any of the biomarkers contained on the microarray will be the true casual risk factor. To solve this problem, imputation software was used in this study. Imputation references the observed data and compares it to given haplotype information on genetic variation from a diverse population reference panel. The Gershon lab division of B-SNIP ran a preliminary genome-wide association study (GWAS) on unimputed data to evaluate genetic differences between control subject and subjects with intermediate phenotypes corresponding to psychoses, such as bipolar disorder and schizophrenia. Preliminary GWAS indicated a significant biomarker on chromosome five at 72,469,919 bp, identified as exm460577. After complete imputation of the study individuals, GWAS was rerun on chromosome five, from 70,000,000-75,000,000 bp. This located two statistically significant biomarkers, at 72,473,899bp and 72,476,096bp, identified as rs6893265 and rs6882901, respectively. These biomarkers are significant risk factors for psychoses.

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Scientia

Barcoding for Braincases: Computed Tomography-enabled Landmark Analysis of Pipid Frog Crania Isaac Krone California Academy of Sciences, San Francisco, CA Despite their unassuming appearance and small size, pipid frogs, including the well-known African Clawed Frog Xenopus, are a diverse and evolutionarily informative group of early-diverging Anura. Though their external morphology is not ostensibly varied, pipid braincases are morphologically diverse. Their small size means that they are often recovered with three-dimensional preservation as fossils. Because molecular evidence is almost never available from fossils, placement of these taxa would normally be based entirely on trait-matrix- based morphological analyses. Our goal was to use 3D imaging and statistical analysis to analyze morphology and affinities of pipids in a less labor-intensive, faster, and more statistically robust way. Using high-energy Computed Tomography (CT) scanning, we modeled and analyzed the braincase morphology of almost two dozen extant and two extinct pipid species: Oumkoutia anae and a recently discovered pipid from the Oligocene of Tanzania. A 20-landmark analysis of the braincases proved highly informative. We also achieved significant and revealing results regarding allometry across pipids and Xenopus, and regarding the disparity of shape diversity in different areas of the braincase across Xenopus.

Using Principal Component Analysis (PCA), we were able to investigate the clustering of species in morphospace across the entirety of sampled taxa and use these data to estimate phylogenetic placement of the two fossil species.

While the affinities of Oumkoutia remain unclear, the fossil pipid from Tanzania can be interpreted with confidence to be a close relative of X. itombwensis.

Multilingual Exposure Impacts Early Sociolinguistic Judgments Danielle Labotka University of Chicago, Chicago, IL

Language is primarily used for communication, but humans can also use information from a person’s speech, such as errors, to make social judgments about them. Exposure to a multilingual environment may afford more experience with communicative patterns, thus making one less likely to judge others’ errors negatively. To test the impact of language exposure on children’s choices in social partners, we tested three different language populations, 3- and 4-year-old monolingual, exposure, and bilingual children, on their understanding of pragmatic errors. Children were provided with two speakers –one who made a pragmatic error (i.e. saying something unrelated to the conversation) and one who did not. Then, we asked children to identify who said something “funny or rude” and who they would rather be friends with. While children across all language groups were accurately able to identify the pragmatically incorrect speaker, bilingual children were less likely than monolingual and exposure children to use this information to influence their friendship preferences. That is, bilingual children, who may encounter errors in communication more often than their monolingual and exposure peers, may reserve judgment on others’ communicative errors while the other two groups do not. Our findings have implications for the social impact of early multilingualism.

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Winter 2016

Quantum Dot Conjugates Deliver Biomolecules beyond the Blood Brain Barrier Connor Lynch and Dr. Glyn Dawson University of Chicago, Chicago, IL Delivery of proteins, enzymes, and other functional biomolecular methods of disease therapy to cells beyond the blood brain barrier remains of paramount importance to addressing neurodegenerative diseases of all types. While certain methods have been devised and tested in vitro, few have shown promise in their ability to deliver functional molecules without disrupting normal cellular activity. To address this problem, we have designed a system capable of traversing the blood brain barrier and plasma membrane of target cells while carrying functional molecules for therapy. We have previously shown that tailored polymer ligands such as DHLA-PEG and compact ligands (CL[14]), self-assembled to CdSe/ZnS core/shell luminescent semiconductor nanocrystals (Quantum Dots [QDs]), may be conjugated to functional biomolecules by a poly-his tag to achieve targeted delivery beyond the blood brain barrier. We now present evidence to demonstrate that QD conjugates penetrate not only beyond the blood brain barrier but also beyond the plasma membrane in target cells. An additional lipo-peptide conjugate, JB577, facilitates endosomal escape of QDs and release to cell cytosol. Using in vitro models of mammalian endothelial and neural cell monolayers as well as intact, 250μm embryonic (E4-E11) chicken and young (P3-P64) mouse brain slice cultures, we have observed that the specific polymer/peptide ligands augment and affect intracellular uptake and colloidal stability of QDs in living tissue following treatments as short as 1 hour. These results remained consistent in an in vivo model: in ovo injections of the QD delivery system into the cerebrospinal column of E4 embryonic chickens revealed minimal to no toxicity, with widespread distribution and intracellular delivery throughout brain tissue.

GFP transfections of slice cultures from both the in ovo and in vitro models and use of NissL stain or DiD/DiOC18 lipophilic tracers on all models were used to visualize individual neurons and glia, confirming intracellular delivery of QDs. Extensive immunohistochemistry and confocal microscopy revealed increased delivery of nanocrystals selfassembled to poly-6-his tagged GFP protein, hTPP1 enzyme, and siRNA, demonstrating the QD’s capability for binding and delivering functional molecules intracellularly. This system could be adapted for many biological molecules and cellular destinations, making QD conjugates a promising method for neurodegenerative disease therapy.

“Wait, what do you mean “he?”: Perceptions of Male Victims of Intimate Partner Violence Jack O’Brien and Yvita Bustos DePaul University, Chicago, IL The purpose of this study is to investigate university students’ perceptions regarding victims of intimate partner violence (IPV). Prior research has suggested that both men and women perceive female perpetrated violence towards men as more acceptable than male perpetrated violence towards women (Arias & Johnson, 1989). In addition, men are less likely to seek help in IPV relationships (Hoff, 2012). In this study, students were asked to watch a video interview of either a male or female victim of IPV. Participants were asked to rate how violent they perceived the abuse to be, the perceived masculinity and femininity of the victim, the perceived reasons the victims stayed in the relationship, and interest in participating in a focus group with victims of IPV (an indirect measure of social distancing). Data collection has been completed. We hypothesized that a male victim would be perceived as less masculine than the average male.

Similarly, we predicted that male participants would be less empathic towards the male victim and would attempt to socially distance themselves. Finally, we hypothesized there will be a significant difference between the number of perceived barriers to leaving an abusive relationship for male and female victims. This investigation is important in understanding how male victims are perceived. It is vital that any victim of IPV is supported.

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Scientia

Response of Elaborate Pupils to Changes in Light Intensity Corey Okinaka and Dr. Lydia Mäthger Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA The eyes of many animals, vertebrates and invertebrates, have pupils that constrict in response to light. Various pupil shapes are known, such as circular, slit-shaped and pinhole pupils, and the optical functions of these relatively simple pupils are well understood. Another group of animal pupils exists that are referred to as “elaborate” pupils because of their complex shapes, frills and protuberances. The underlying reasons for this design have been poorly investigated.

Some elasmobranch fishes, such as the little skate (Leucoraja erinacea), have an elaborate pupil, which consists of a distinctive crescent shaped aperture with multiple dorsally arranged pupillary finger-like protuberances. There has only been circumstantial evidence that the pupil of L. erinacea changes shape in response to changes in light intensity, and the extent of any pupillary transformation was unknown. In an effort to understand the optical functions of the elaborate pupil of L. erinacea, this project set out to test whether the pupil of L. erinacea responds to different light intensities by changing the shape of its aperture. To this end, we measured pupillary area after adapting animals to eight different light intensities, ranging from (~0.0001lx to ~700lx). Eight skates were tested, and we found that all animals decreased their pupil area in response to increasing light intensity. The underlying mechanism of this change is the movement of the dorsal pupil part that bears the finger-like protuberances. The pupil changes shape from a near-circular shape in near total darkness (0.0001lx) to an aperture consisting of multiple triangular pupillary apertures arranged in a crescent in bright light (700lx). The data obtained by this project will aid in elucidating the optical functions of the elaborate pupils in L. erinacea and its possible relationship to retinal physiology. These will be discussed.

The Role of Ubiquitination on Morphineinduced Multidrug Resistance in Human Lung Cancer Kim Pardilla The University of Illinois at Chicago, Chicago, IL Recent research on cancer progression suggests that patients who are administered opioids may become more susceptible to cancer recurrence and metastasis. Previous observations indicated that multidrug resistance (MDR) is increased by morphine (opioid agonist) in lung cancer. The purpose of the study was to elucidate if and how the mu opioid receptor (MOR) regulates MDR against chemotherapy drugs like Paclitaxel. We hypothesized that the MOR regulates morphine-induced MDR in lung cancer through ABCC3 (MDR protein) ubiquitination. A drug treatment test was conducted and involved PYR-41 inhibitor to prevent ABCC3 ubiquitination. Cells were treated for 96 hours with PYR-41, Paclitaxel, and morphine with/without MNTX (MOR antagonist). Rate of inhibition of proliferation was graphed against an increasing amount of Paclitaxel present in the cells. Results displayed an overall decrease in morphineinduced cell viability and proliferation when PYR-41 was added to inhibit ubiquitination in Paclitaxel-treated cells.

Morphine-treated cells with increased MDR towards Paclitaxel displayed increased ABCC3 protein expression. MNTXtreated cells with decreased MDR showed decreased ABCC3 protein expression. Similar to how blocking ABCC3 ubiquitination caused the cell viability and growth to express similar inhibition of proliferation, the ABCC3 protein expression become relatively equal among untreated cells and cells treated with morphine and/or MNTX after the addition of PYR-41. Although the results are preliminary, these findings strongly suggest that MDR in lung cancer cells is controlled by ABCC3 ubiquitination.

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Winter 2016

Identifying the Role of PDLIM5 in Lung Cancer Deborah Park The University of Illinois at Chicago, Chicago, IL Lung cancer is the most common cause of cancer-related death in the United States and has a 5-year survival rate of 15%. Therefore, it is necessary to advance our knowledge on lung cancer progression in order to develop novel therapeutic approaches. PDZ and LIM domain protein 5 (PDLIM5) is member of PDLIM5 protein family that has been implicated in human diseases. The mRNA expression profiles available in the Oncomine Cancer Genomics database show that the levels of PDLIM5 are higher in severe cases of lung cancer, which suggests a potential role of PDLIM5 in lung cancer growth. Transforming growth factor- β1 (TGF-β1) is known to promote lung cancer progression by inducing epithelial-mesenchymal transition (EMT). In order to determine whether TGF-β1 regulates PDLIM5, dosages of TGF-β1 (5 ng/mL, 10 ng/mL) were given to human lung adenocarcinoma cells (A549) for 48 hours. The results indicate that TGF-β1 does not affect PDLIM5 levels, which suggests that the upregulation of PDLIM5 in lung cancer is independent of TGF-β1. Additionally, Western Blot analysis of lung cancer cell lines with wild type PDLIM5 (A549-shCTL) and a derived cell line without PDLIM5 (A549-shPDLIM5) allowed us to measure the level of EMT activity. The data indicates that the presence of PDLIM5 correlates with increased EMT activity. Taken together, we postulate that PDLIM5 may play a key role in lung cancer by promoting EMT.

Role of Oxidative Stress and Autophagy Signaling in Osteocyte Response to Spaceflight-like Radiation Victoria Rael and Dr. Ruth K. Globus NASA Ames Research Center , Moffett Field, CA Spaceflight has deleterious effects on skeletal structure and function, specifically causing a profound loss in bone mass that mimics the aging process. This bone loss is thought to result from increased activity of bone- resorbing osteoclasts and functional changes in osteoblasts, the cells that give rise to mature osteocytes. Our current understanding of the signaling factors and mechanisms that control bone loss is incomplete. However, it is known that oxidative stress, characterized by the excess production of reactive oxygen species or free radicals, is elevated during radiation exposure, one of the risks associated with spaceflight. Here, we examine oxidative stress responses of osteocytes following exposure to spaceflight-like radiation. We hypothesize that (1) oxidative stress as induced by radiation decreases osteocyte survival and increases pro-osteoclastogenic signals and that (2) autophagy is one of the key cellular defenses against oxidative stress. Autophagy is the process in which cellular components including organelles and proteins are broken down and recycled. To test our hypothesis, we exposed the osteocyte-like cell line, MLO-Y4, to 0.5, 1, and 2 Gy of 56Fe radiation (600 MeV/n) and assessed cell numbers and cell cycle distribution as well as markers of autophagy and oxidative stress at various time points post-irradiation. We observed a reduction in cell numbers in the groups exposed to 1 and 2 Gy of 56Fe radiation. In addition, cell cycle analysis by flow cytometry showed that all radiation doses caused a shift in the cell cycle distribution consistent with growth arrest. Compared to sham-treatment, 2 Gy of 56Fe increased FoxO3, SOD1, and RANKL gene expression yet unexpectedly decreased LC3BII protein levels at 4 and 24 hours post-IR. Taken together, these findings suggest that simulated spaceflight radiation invoke antioxidant, pro-osteoclastogenic, and growth arrest responses in osteocytes. The implications of reduced autophagy flux at the time points examined remain to be elucidated.

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Scientia

Phosphorus Phase Associations in the Northern Sargasso Sea

Leonard Shaw and Dr. Maureen Conte Marine Biological Laboratory, Ecosystems Center, Woods Hole, MA

Phosphorus is a crucial micronutrient for marine organisms, used in important biological functions such as metabolism and photosynthesis. In oligotrophic waters, it can be a limiting nutrient for primary productivity. Although most particulate phosphorus is remineralized and recycled in surface waters, a fraction sinks into the deep water column where it is removed from primary producers. The chemical form or “phase” of phosphorus in sinking particles (the particle flux) can determine whether phosphorus in the water column regenerates into dissolved forms that are eventually upwelled to fuel subsequent phytoplankton production or sinks to the seafloor to be buried in ocean sediments. This study is focused on how phosphorus is partitioned among different organic and inorganic phases in the deep ocean flux. We examined deep ocean particles collected by the Oceanic Flux Program (OFP) sediment traps in the Sargasso Sea, an oligotrophic region typical of mid ocean gyres. These particles were collected by the OFP traps at 500m, 1500m, and 3200m depths over a seasonal cycle, from November 2008 (minimum production) through March 2009 (end of spring bloom). Phosphorus in the sample particles was partitioned into seven fractions.

The first fraction was defined as loosely-sorbed phosphorus released from particles into overlying trap cup brine during sample collection. A sequential extraction method (SEDEX) was then used to separate six “operationallydefined” particulate phases: exchangeable phosphorus, iron bound phosphorus, authigenic apatite and carbonate bound phosphorus, detrital apatite, opal bound phosphorus, and residual organic phosphorus. Loosely-sorbed phosphorus released into the brine was found to be the dominant reservoir of particulate phosphorus at 500m (77%) whereas phosphorus quantified by the remaining phases was the largest reservoir at 1500m (64%) and 3200m (76%). Iron bound phosphorus and opal bound phosphorus were the largest carriers of phosphorus in the remaining phases at 1500m (64%) and 3200m (64%). As opal and certain iron oxides have been identified as phosphorus sinks in marine sediments, this research provides new insights into deep ocean phosphorus geochemistry in the particle flux.

Recovering Ancient Plasmodium DNA using Whole Genome In Solution Capture (WISC) Adrian Carcamo and Dr. Carlos D Bustamante Stanford University, Palo Alto, CA Next Generation Sequencing has expanded the field of paleogenomics by allowing for genome-wide sequencing of DNA from ancient organisms. These studies, however, have been confined to samples from cold areas where DNA is preserved from degradation. Tropical samples have no such environmental protection, causing them to be underrepresented in genetic studies. We propose that by using a novel technology – Whole Genome in Solution Capture (WISC), we can enrich for DNA from the malaria-causing parasite, Plasmodium falciparum, in 150-year-old samples from Mauritius, an area historically affected by malaria outbreaks. Before working with the ancient samples, we performed a test experiment by recreating a degraded sample containing 1-1.5% of human DNA and 0.01-0.5% of Plasmodium DNA. We found that WISC was able to enrich the Plasmodium DNA 25-240x. Then, we applied WISC to 6 teeth samples from Mauritius, but were unable to obtain Plasmodium DNA. We conclude that teeth samples, although one of the best sources of ancient human DNA, are not ideal for recovering Plasmodium, indicating the need to test alternative sampling methods. However, we have shown that WISC is a powerful tool that can be applied to enrich targeted DNA, even when there is low endogenous content. By applying WISC to different types of environmental samples to capture ancient Plasmodium DNA, we will be able to gain insight about the evolution of malaria, as well as insights into the evolution of infectious diseases.

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Winter 2016

Hyperspectral Imaging of Dynamic Camouflage in Juvenile Winter Flounder Reveals How Color- and Pattern-matching Help Avoid Detection by Shallow-water Predators Hannah Weller and Dr. Roger Hanlon Marine Biological Laboratory, Marine Resources Center, Woods Hole, MA

Flatfish (order Pleuronectiformes) are well known for their cryptic camouflage abilities; many species can rapidly adjust skin colors and patterns to disguise themselves against a variety of natural substrates. Winter flounder, Pseudopleuronectes americanus, spend much of the first year of life in shallow water, where they exhibit dynamic camouflage to reduce their risk of predation from seabirds and piscivorous fishes. Quantifying the efficacy of winter flounder camouflage in eyes of their potential predators is challenging, since typical imaging systems produce RGB images particular to human vision; most birds are tetrachromatic and different teleost fishes exhibit a wide variety of dichromatic and trichromatic visual systems not directly comparable with human vision. By using a unique hyperspectral imaging (HSI) camera, which records full-spectrum light data spanning 360 nm to 660 nm in 20 nm intervals (16 total channels), we visualized both color and pattern matching through the eyes of a hypothetical predator. Juvenile winter flounder (SL < 6 cm) were tested on local samples of sand and gravel, two visually dissimilar but common shallow-water substrates. Fish were placed in outdoor tanks of either sand or gravel and photographed using the HSI under natural sunlight. The images were assessed for both chromatic and achromatic camouflage. Isoluminance images simulating the color vision of a tetrachromatic avian predator and several di- and trichromatic teleost fish predators reveals excellent color matching in juvenile flounder on both the medium-contrast gravel and the low-contrast sand. Laplacian edge detection of Gaussian-smoothed images, an algorithm thought to closely model vertebrate edge detection methods, indicates that the flounder are also extremely difficult to detect using contrast sensitivity. These findings (i) suggest that the dynamic camouflage exhibited by juvenile winter flounder is highly effective in evading detection from predators, and (ii) indicate that HSI technology has a high potential for providing valuable insights into studies of biological coloration.

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Scientia

In Depth High expression of miR-532-5p, a tumor suppressor, leads to better prognosis in ovarian cancer both in vivo and in vitro Jeremy T. Chang1, Fan Wang2, Chester J. Kao3, and R. Stephanie Huang1

Ovarian cancer is the leading cause of death for gynaecological cancers, ranking fifth overall for cancer-related death among women. The identification of biomarkers and the elucidation of molecular mechanisms for improving treatment options have received extensive efforts in ovarian cancer research. MicroRNAs (miRNAs) have high potential to act as both ovarian cancer biomarkers and as critical regulators of ovarian tumor behavior. We comprehensively analyzed global messenger RNA (mRNA), miRNA expression, and survival data for ovarian cancer from the Cancer Genome Atlas (TCGA) to pinpoint miRNAs that play critical roles in ovarian cancer survival through their effect on mRNA expression. Through a series of informatics filtering of patient samples and experimental validation with ovarian cancer cell lines, we established that overexpression of miR-532-5p in OVCAR-3 cells resulted in a significant decrease in cell viability over a 96-hour time period.

In the TCGA ovarian cancer dataset, we found 67 genes whose expression levels were negatively correlated with miR-532-5p expression and correlated with patient survival, such as WNT9A, CSNK2A2, CHD4, and SH3PXD2A. The potential miR-532-5p-regulated gene targets were found to be enriched in the Wnt pathway. Overexpression of miR-532-5p through miRNA mimic caused downregulation of CSNK2A2, CHD4, and SH3PXD2A in the OVCAR-3 cell line. We have discovered and validated the tumor-suppressing capabilities of miR-532-5p both in vivo through TCGA analysis and in vitro through ovarian cancer cell lines. Our work highlights the potential clinical importance of miR-532-5p expression in ovarian cancer patients.

Introduction Ovarian cancer is the leading cause of death for gynaecological cancers, and ranks fifth overall for cancerrelated death among women.[1] Due to the presence of vague, mild symptoms in many ovarian cancer cases, more than half of patients that are diagnosed with ovarian cancer already have stage 3 or 4 tumors, leading to higher mortality rates.[2] Furthermore, although patients initially respond well to chemotherapy, many ovarian cancer patients relapse with subsequent tumors becoming chemoresistant to traditional therapies.[3,4] Chemoresistance is believed to be a primary contributor

to ovarian cancer death.[4] Overall, the 5-year survival rate for ovarian cancer starting from the time of diagnosis is low at only 45%.[5] In order to improve clinical outcomes in ovarian cancer patients, the elucidation of molecular mechanisms in disease initiation, progression, and prognosis as well as the identification of biomarkers for effective treatment are critical.

MicroRNAs (miRNAs) have attracted great interest in recent years and present a new avenue in cancer research. miRNAs are 20-25 nucleotide RNA segments that regulate gene expression post-transcriptionally by either cleaving messenger RNA (mRNA) with the RNA-induced silencing complex (RISC) or degrading mRNA with the

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Winter 2016 genomic and epigenomic information from large numbers of ovarian cancer patients. The project additionally collected patient survival information, allowing researchers access to prognostic data for ovarian cancer.

[11] We comprehensively analyzed global mRNA, miRNA expression, and survival data for ovarian cancer from TCGA to pinpoint miRNAs that play important roles for ovarian cancer prognosis. For the most promising miRNAs, we identified miRNA-gene pair relationships with TCGA data to predict the functional networks of the selected miRNAs in ovarian cancer. Validation experiments were then performed in vitro with ovarian cancer cell lines to support our TCGA analysis. For this study, we propose and offer confirmation of novel mechanisms between miR532-5p and cancer-related genes previously unknown in ovarian cancer research.

Results Figure 1: Selection pipeline for miRNAs of interest and finding miRNA-gene pairs in TCGA ovarian cancer dataset.

A) Selection pipeline and specific criteria to narrow down the list of possible mature miRNAs to three miRNAs of interest.

B) Selection pipeline and specific criteria to find possible miRNA-gene candidate pairs. Overall survival, gene expression (mRNA), and miRNA expression data (oval shapes) were obtained from TCGA ovarian cancer. Intermediate lists (trapezoid shapes) and findings (diamond shapes and outlined boxes) derived from our analysis of TCGA data sets.

recruitment of GW- proteins.[6] miRNAs have been shown to regulate numerous cell processes such as apoptosis, migration, stress response, and differentiation.[7] Given the important regulatory abilities of miRNAs in cell processes as mentioned above, these non-coding RNA segments play an important role in cancer and are often dysregulated in tumors.[8] Knowledge of key miRNAs that influence ovarian cancer progression can help explicate ovarian cancer tumorigenesis and contribute to the development of improved methods of treating ovarian cancer. For example, one study has found that miR-130a and miR-374a regulate cisplatin-sensitivity, in which the overexpression of these miRNAs in ovarian cancer A2780 cells reduced sensitivity to cisplatin, while the inhibition of the two miRNAs resensitized cisplatin-resistant A2780 cells.[9] With rapid advancement of miRNA technology, including anti-miRs and miR-mimics, the elucidation of miRNA molecular mechanisms may be leveraged to develop new therapies in the future and improve patient outcomes.[10] Comprehensive research into the role of miRNAs in ovarian cancer is needed first in order for nascent clinical applications involving miRNAs to come to fruition.

The Cancer Genome Atlas (TCGA) represents one of the largest efforts for the systematic collection of

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TCGA ovarian cancer analysis to identify miR-532-5p Our first application of TCGA ovarian cancer data was to find clinically relevant miRNAs through independent analysis of survival and miRNA expression data from the RNA-Seq and RNA microarray expression profiles (Fig. 1A). The TCGA assembler (http://health.bsd.uchicago. edu/yji/TCGA-Assembler.htm)[12] was employed when downloading and analyzing TCGA data. Linear regression analysis using TCGA ovarian cancer data sets identified 28 and 150 miRNAs whose expression levels may be correlated with patient survival (p < 0.05) from TCGA RNASeq and microarray data, respectively. The 10 overlapping miRNAs between the two analyses were hsa-miR-150, -505, -877, -199a, -660, -199b, -502-5p, -146a, -532-3p, and -532-5p. After matching for the same consistent direction

Figure 2: Effects of miR-532-5p mimic treatment on cell viability in OVCAR-3 cells.

Treatment with miR-532-5p mimic significantly depressed cell viability over a 96-hour time period when compared to the zero hour population. Control populations experienced increases in cell viability over the same time period. P < 0.0001 is the result of a two-way ANOVA test between the scramble and miR-5325p mimic experiments.

Scientia between miRNA expression and survival in both two analyses, we narrowed the candidate miRNAs to seven (miR-150, -505, -660, -502-5p, -146a, -532-3p, and -532-5p).

Interestingly, all seven of these remaining miRNAs were associated with a protective phenotype in TCGA ovarian cancer, meaning higher miRNA expression correlated with longer patient survival. Subsequently, we selected to perform functional analyses for miR-502-5p, -532-3p, and -532-5p as these miRNAs were relatively understudied in ovarian cancer.

Since miRNAs are known to negatively regulate gene expression to achieve their biological effects and our three selected miRNAs were associated with a protective phenotype, we reasoned that the selected miRNAs would act as tumor-suppressors by downregulating what we termed tumor-inducing genes in ovarian cancer.

To this end, we correlated overall survival with global mRNA profiles. Using the RNA-Seq and microarray data sets, respectively, 1419 and 2568 genes were identified (p <0.05). When limited to only those genes whose expression levels were negatively correlated to survival, the overlap of genes between the two independent analyses produced a list of 250 tumor-inducing genes.

The 2568 survival-related genes from the mRNA microarray profile were then correlated with the microarray expression profiles for miR-502-5p, -532-3p, and -532-5p. 317 genes for miR-502-5p, 293 genes for miR532-3p, and 389 genes for miR-532-5p were identified as genes whose expression correlated with miRNA expression. Finally, these three lists of genes related to miRNA expression were overlapped with the list of 250 tumor-inducing genes. The overlap comparison identified 72 genes for miR-502-5p, 57 genes for miR-532-3p, and 64 genes for miR-532-5p (Fig. 1B). We noticed that there was a heavy overlap of genes among the three lists. For

Figure 3: Effects of miR-532-5p mimic treatment on cell viability in SKOV-3 cells.

Treatment with miR-532-5p mimic depressed cell proliferation over a 96-hour time period. Control populations experienced higher increases in cell viability over the same time period. P < 0.05 is the result of a two-way ANOVA test between the scramble and miR-532-5p experiments.

example, the miR-532-3p-gene list (n=57) and miR-5325p-gene list (n = 64) had 53 overlapping genes. In total, 47 genes were shared among all three miRNA-gene lists, suggesting that miR-502-5p, -532-3p, and -532-5p may be regulating similar gene networks.

Employing the DAVID annotation tool for pathway analysis, we found 26 pathways that were considered enriched in the gene list for miR-532-5p. Among the enriched pathways were skeletal system development (p<0.00062), regulation of cell-substrate adhesion (p=0.01), and angiogenesis (p=0.013). The Wnt pathway (p=0.0098) was also enriched, as miR-532-5p expression correlated with the expression of four genes in the Wnt pathway: WNT9A, CSNK2A2, FZD1, and SFRP4.

A total of four genes were tested in subsequent in vitro validation experiments. Two of these genes (WNT9A and CSNK2A2) are part of the Wnt pathway. One gene, SH3PXD2A, was predicted by three miRNA target prediction tools to be bounded by the sequence of miR532-5p. The miR prediction tools utilized were DIANA (http://diana.imis.athena-innovation.gr/DianaTools/ index.php)[13], TargetScan (http://www.targetscan.org/) [14] , and ComiR (http://www.benoslab.pitt.edu/comir/) [15] . The fourth gene, CHD4, shows a high alteration rate in TCGA ovarian cancer samples (12.2%) according to cBioPortal (http://www.cbioportal.org/) [16,17].

Effect of miR-532-5p overexpression in OVCAR-3 and SKOV-3 cells To validate the tumor-suppressing capabilities of miR-5325p, we transfected cancer cells of the ovarian cancer cell line OVCAR-3 with miR-532-5p mimic with DharmaFECT vectors. The overexpression experiments included three control populations: untreated OVCAR-3 cells (control), DharmaFECT-only treated OVCAR-3 cells (water control), and DharmFECT with negative miRNA control- treated OVCAR-3 cells (scramble control). Priority was given to the scramble control when analyzing the results of miRNA overexpression or siRNA gene knockdown experiments.

We found that miR-532-5p overexpression in OVCAR-3 cells not only led to decreased cell proliferation, but to decreased cell viability overall (Two-way ANOVA test, p <0.05). As shown in Figure 2, OVCAR-3 cell viability decreased significantly over a 96-hour time frame after treatment with miR-532-5p mimic while the cell viability of scramble control cells continuously increased as expected (Studentâ&#x20AC;&#x2122;s t-test, p < 0.05 at all time points measured).

The cell viability in the miR-532-5p mimic treated cells decreased to 45.67%, 26.02%, 18.27%, and 13.12% at 24, 48, 72, and 96 hours, respectively, when compared to the

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Winter 2016 Figure 4: Fold changes in relative CSNK2A2, SH3PXD2A, and CHD4 expression after miR-532-5p mimic treatment on OVCAR-3 cells.

A) miR-532-5p mimic treatment significantly downregulated CSNK2A2 expression at all time points over a 96-hour time period, suggesting that CSNK2A2 is a target gene for miR-532-5p.

B) miR-532-5p mimic treatment significantly downregulated SH3PXD2A expression at 24,72, and 96 hours post-transfection.

C) miR-532-5p mimic treatment significantly downregulated CHD4 expression at all time points over a 96-hour time period, suggesting that CHD4 is involved in the targeted pathways of miR-532-5p. Expression measurements are normalized to B2M. The symbol * signifies a p-value < 0.05 from the Student’s t-test.

a 96-hour time period as shown in Figure 3 (Two-way ANOVA test, p < 0.05). The phenotype produced in SKOV3 cells treated with miR-532-5p mimic was moderate compared to the OVCAR-3 cells, but the SKOV-3 results support the overall tumor-suppressing abilities of miR532-5p in ovarian cancer.

zero hour population. In comparison, the cell viability of the scramble control cells increased to 106.01%, 117.51%, 160.90%, and 197.29% at the same time points.

In another ovarian cancer cell line called SKOV-3, miR-532-5p mimic treatment also produced tumorsuppressing effects by decreasing cell proliferation over

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Effect of miR-532-5p overexpression for CSNK2A2, SH3PXD2A, and CHD4 gene expression We performed quantitative PCR (qPCR) to measure the relative expression of our genes of interest in our miR532-5p overexpression experiments. In OVCAR-3 cells treated with miR-532-5p mimic, CSNK2A2 expression was significantly downregulated compared to controls at all time points over a 96-hour time frame (Student’s t-test, p < 0.05). The qPCR results for CSNK2A2 gene expression are shown in Figure 4A. Compared to scramble controls, miR532-5p caused a 5.523-, 2.345-, 2.928-, and 1.749-fold decrease in CSNK2A2 expression at 24, 48, 72, and 96 hours, respectively.

WNT9A expression levels were below the qPCR detection limit in both OVCAR-3 and SKOV-3 cells.

Therefore, we were unable to conclude the effect of miR532-5p overexpression on WNT9A in either ovarian cancer cell lines.

The overexpression of miR-532-5p significantly downregulated SH3PXD2A gene expression in OVCAR-3 cells (Fig 4B). SH3PXD2A gene expression decreased significantly at 24, 72, and 96 hours by 2.719-, 2.289-, and 1.704-fold compared to scramble treated cells (Student’s t-test, p < 0.05).

When overexpressing miR-532-5p in OVCAR-3 cells, we observed a significant and consistent downregulation

Scientia of CHD4 as well (Fig 4C). Specifically, miR-532-5p overexpression led to 1.445-, 1.368-, 1.374-, and 1.131-fold decreases in CHD4 expression at 24, 48, 72, and 96 hours post-transfection, respectively (Studentâ&#x20AC;&#x2122;s t-test, p < 0.05).

Effect of CSNK2A2 and CHD4 Knockdown in OVCAR-3 cells To confirm that miR-532-5p downregulation of CSNK2A2 and CHD4 indeed produces a phenotypic decrease in cell proliferation, we performed siRNA gene knockdown experiments on CSNK2A2 and CHD4 independently in OVCAR-3 cells. When we knocked down CSNK2A2 in OVCAR-3, there was significant reduction in cell proliferation that led to decreased cell viabilities at 24, 48, and 72 hours. By 96 hours, the OVCAR-3 cells recovered slightly, but the effect of CSNK2A2 knockdown remained significant (Two-way ANOVA test, p < 0.0001, Fig 5).

When we knocked down CHD4 in OVCAR-3 cells through siRNA, we observed that CHD4 also decreased cell proliferation (Two-way ANOVA test, p = 0.0016, Fig 5). The results of qPCRs for both the siRNA CSNK2A2 and CHD4 treated cells confirmed that our siRNA knockdown experiments were successful, and that expression of the targeted genes were significantly downregulated at 24, 48, 72, and 96 hours post-siRNA treatment (Studentâ&#x20AC;&#x2122;s t-test, p< 0.05), even though gene expression almost recovered fully by the 96-hour time point.

Discussion The aim of this study was to identify miRNAs that are clinically relevant to ovarian cancer patient survival and to discover the functional roles these miRNAs possess in tumors. The discovery of important miRNAs can lead to novel insights into ovarian cancer and augment the development of improved prognostics tools or clinical therapies. To these ends, we analyzed in vivo data from TCGA ovarian cancer patients and performed in vitro experiments to validate our proposed miRNA mechanisms.

We selected miR-532-5p as our primary miRNA of interest after filtering miRNAs through a rigorous selection process. In our TCGA analysis, miR-532-5p appeared to confer a protective phenotype to patients in which higher expression of miR-532-5p predicted longer overall survival in patients. After observing this protective phenotype, our next goal was to investigate the mechanisms behind miR-532-5p. When we overexpressed miR-532-5p in the OVCAR-3 cell line, a significant decrease in cell viability was observed, supporting the notion that miR-532-5p is a tumor-suppressor in ovarian cancer cells. By further

Figure 5: Effects of gene knockdown experiments on cell viability in OVCAR-3 cells.

Knockdown of CSNK2A2 significantly reduced cell proliferation over a 96-hour time period, even decreasing cell viability compared to the zero hour population at 24, 48, and 72 hours. P < 0.0001 is the result of a two-way ANOVA test between the scramble and siRNA CSNK2A2 knockdown experiments. Knockdown of CHD4 significantly reduced cell proliferation over a 96-hour time period. P= 0.0016 is the result of a two-way ANOVA test between the scramble and siRNA knockdown experiments.

analyzing TCGA data, we identified a set of genes for which miR-532-5p may regulate in ovarian tumors.

Indeed, we offer confirmation that overexpression of miR532-5p downregulates specific genes such as CSNK2A2, CHD4 and SH3PXD2A. Furthermore, our data support that the downregulation of CSNK2A2 and CHD4 leads to decreased ovarian cancer cell proliferation.

In ovarian cancer, miR-532-5p expression has been found to be downregulated in borderline ovarian neoplasms compared to benign ovarian neoplasms.

[18] However, the function of miR-532-5p appears to be tissue-specific depending on the type of cancer. In an miRNA study of clear cell renal cell carcinoma, miR532-5p was observed to be downregulated in clear cell renal cell carcinoma tissues when compared to adjacent non-tumorous tissues.[19] For retinoblastoma (RB), a primary pediatric intraocular tumor, miR-532-5p-induced expression in retinoblastoma cell lines decreased cell viability, suggesting that miR-532-5p in retinoblastoma possesses tumor-suppressing abilities.[20] In another study, miR-532-5p has been suggested to downregulate the tumor-suppressing gene RUNX3 gene in malignant melanoma, implicating that the miRNA acts as a tumorinducer.[21,22] Additionally, miR-532-5p was observed to be an upregulated miRNA in triple-negative breast cancer tissues.[23] The results from our study indicate that miR-532-5p in ovarian cancer confers a protective phenotype to patients and acts as a tumor-suppressor.

The novelty of our research is that we offer confirmation of the tumor-suppressing functionality of miR-5325p through an analysis of a large collection of ovarian cancer patient samples provided by TCGA and through in vitro experiments with ovarian cancer cell lines. We

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Winter 2016 also propose miR-532-5p regulatory gene networks that have not been elucidated in ovarian cancer previously.

The Wnt pathway is a crucial pathway that regulates cell proliferation, cell fate determination, and cell migration.[24] The canonical Wnt pathway controls intracellular levels of β-catenin, a protein independently involved in cell adhesion and co-transcriptional activity for Wnt signal transduction.[25,26] Dysregulation of the Wnt pathway has been heavily implicated in multiple human diseases, especially in cancers such as colorectal cancer,[27] chronic lymphocyte leukemia,[28] gastric cancer,[29] hepatocellular cancer,[30] prostate cancer,[24, 31] and breast cancer.[24,31] In ovarian cancer, activation of the Wnt pathway plays an important role in ovarian cancer’s chemoresistance to drugs such as cisplatin.

[32] Abnormal activation of the Wnt pathway has also been implicated in epithelial ovarian cancer to promote epithelial-to-mesenchymal transition, which drastically increases tumor aggressiveness.[33] Upregulation of another miRNA, miR-1207, has been shown to suppress SFRP4, a negative regulator of the Wnt pathway. The overexpression of miR-1207 consequently increases tumorigenicity of ovarian cancer cells by the activation of the Wnt pathway.[34] From the DAVID annotation tool in our TCGA analysis, the Wnt pathway was the second strongest associated pathway for the list of genes correlated with miR-532-5p expression. With support from our TCGA analysis and our findings regarding the gene CSNK2A2, a member of the Wnt pathway, we strongly suspect that miR-532-5p is involved in Wnt pathway activation in ovarian tumors.

CSNK2A2, also known as CK2, is considered a master regulatory gene for its role in regulating protein behavior, which is performed mostly through the phosphorylation of target proteins [25]. CSNK2A2 acts as a multisite regulator of the Wnt pathway, and is bestknown for phosphorylating the transcriptional co-factor β-catenin.[25] Increased CSNK2A2 expression has been observed in breast cancer tissue and breast cancer cell lines.[25, 35] Additionally, CSNK2A2 upregulation has been associated with colon cancer progression.[36] Increased expression of CSNK2A2 has also been observed in villous colon adenomas when compared to normal to tubular colon adenomas.[37] In addition to the Wnt pathway, CSNK2A2 is believed to regulate cell behavior through other functions, including NF-κB activation. NF-κB is a transcriptional regulator involved in apoptotic resistance and the promotion of proliferation.[25] In our current study, we found that CSNK2A2 expression was strongly negatively correlated with miR-532-5p expression in

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TCGA ovarian cancer. When we overexpressed miR-532-5p in OVCAR-3 cells, CSNK2A2 expression was dramatically downregulated over the entire 96-hour time period.

This indicates that miR-532-5p negatively regulates a master regulatory gene that controls Wnt pathway activation among other cell functions. In addition, knockdown experiments for CSNK2A2 confirmed that CSNK2A2 is essential for OVCAR-3 cell proliferation, which demonstrates that regulation of CSNK2A2 is a critical functional mechanism for miR-532-5p.

The WNT9A gene encodes for a secreted signaling protein that is involved in the canonical Wnt pathway.

WNT9A has been found to be overexpressed in multiple cancers such as chronic lymphocytic leukemia,[38] colon,[39-41] gastric,[39,40] mammary,[42] and cervical carcinomas.[42] However, WNT9A also has been suggested to suppress cellular proliferation in breast cancer for one study.[43] In ovarian cancer, it has been observed that WNT9A expression was unchanged between biopsies between normal ovarian tissue and malignant tissue.[44] Our TCGA analysis indicated that WNT9A was among the top candidates for miR-532-5p targeting because of its strong correlation in gene expression to miR-532-5p expression.

Additionally, we classified WNT9A as a highly biologicallyrelevant gene to TCGA ovarian cancer due to the high number of gene alterations in patients. Interestingly, we could not reliably measure WNT9A expression with conventional qPCR procedures because the gene’s endogenous expression was extremely low in the cells we tested. Despite our inconclusive results, WNT9A may still interact with miR-532-5p, but the consequences of this regulation remain unclear. Further research is necessary to confirm this regulatory mechanism and to investigate whether the mechanism produces significant phenotypic changes for ovarian cancer.

SH3PXD2A (also known as Tps5) plays an important role in underlying networks of adhesion, signaling, and scaffolding in cell systems.[45] In particular, SH3PXD2A has been discovered as instrumental for the formation of invadopodia, actin-based protrusions of the plasma membrane of metazoan cells. Invadopodia increase the metastatic potential of carcinomas by acting as sites for extracellular degradation, promoting epithelial-tomesenchymal transition.[45-48] Invadopodia is increasingly recognized as one of the major avenues of how cancers metastasize.[49] The prognostic relevance of SH3PXD2A expression has been suggested in gliomas where SH3PXD2A expression was found to be predictive of poorer clinical outcomes in glioma patients, but most clearly for low-grade gliomas.[50] Among the genes we

Scientia checked with miRNA target prediction tools (DIANA, TargetScan, ComiR), SH3PXD2A received the highest scores for compatibility with the sequence of miR532-5p. We found from overexpressing miR-532-5p in OVCAR-3 cells that miR-532-5p indeed downregulates SH3PXD2A expression in most cases. To be noted, we observed that many genes correlated with miR-5325p expression in ovarian cancer were involved in cell adhesion and the extracellular matrix. The confirmation that miR-532-5p regulates SH3PXD2A expression, which plays a critical role in invadopodia and extracellular degradation, supports the argument that miR-532-5p may be an important regulator of cell adhesion and the extracellular matrix in ovarian tumors.

The gene CHD4 acts as a vital component of the nucleosome remodeling and deacetylase (NuRD) complex, an important epigenetic regulatory network.

CHD4 is suspected to play a significant epigenetic role in carcinogenesis by controlling the transcription of genes involved in differentiation.[51-54] In a study involving glioblastoma tumor initiating cells, suppression of CHD4 led to pro-differentiation effects such as inhibition of neurosphere formation, and decreased expression of genes such as SOX2 and EGFR.[51] In serious endometrial tumors, CHD4 was discovered to be frequently possess somatic mutations in CHD4 (17%).[54] Another ovarian cancer study has found that CHD4 inactivation in BCRA2 mutant cancers confers chemoresistance and that reduced CHD4 expression in BCRA2 mutant ovarian cancers correlates with poorer overall survival.[55] CHD4 was found to be strongly negatively correlated with miR532-5p expression in the TCGA ovarian cancer dataset and was observed to have a negative correlation with overall survival in patients. Additionally, CHD4 possessed a high gene alteration rate among TCGA ovarian cancer patients when we queried the tool cBioPortal. We found that CHD4 is consistently downregulated in miR-532-5p overexpressed OVCAR-3 cells. The results of our CHD4 knockdown in OVCAR-3 cells indicate that CHD4 downregulation suppresses ovarian cancer cell proliferation. Taken together, we confirm in this study that miR-532-5p acts through CHD4 and CSNK2A2 to regulate cell proliferation in OVCAR-3 cells, but further research is required to better understand the tumorsuppressing role of miR-532-5p in ovarian cancer.

One of the surprising aspects of our experimentation was the discrepancy of our results between the OVCAR-3 cell line and SKOV-3 cell lines. While we found that miR532-5p overexpression reduced cell viability as a whole in OVCAR-3 cells, we observed only a modest decrease in

cell proliferation in SKOV-3 cells with the same procedure.

We decided to rely on the OVCAR-3 cell line more than the SKOV-3 cell line due to recent research that has cast doubt on the utilization of SKOV-3 as a model system for ovarian serous carcinoma. It is important to note that TCGA collected only serous cystadenocarcinoma samples for ovarian cancer. Two papers have found that the SKOV-3 cell line fares poorly in resembling highgrade ovarian serous carcinomas in terms of molecular biomarkers.[56,57] Another study has observed that SKOV-3 xenografts produce tumors that resemble more the clear cell subtype than serous subtype for ovarian cancer.[58] For these reasons, we believed that the OVCAR-3 cell line was a better model system that was more representative of the clinical population studied in TCGA. In summary, we have discovered that miR-532-5p acts as a significant tumor-suppressor in ovarian cancer and that miR-532-5p expression is connected to ovarian cancer patient survival outcomes. Additionally, we have found that overexpression miR-532-5p downregulates CSNK2A2, SH3PXD2A, and CHD4, possibly regulating the Wnt pathway as well. The validation of the tumor-suppressing capabilities of miR-532-5p confirms that our integrative approach of utilizing in vivo data through TCGA to inform our in vitro experiments can yield important insights for ovarian cancer. With this approach, we propose novel mechanisms between miRNAs and cancer-related genes that had not been elucidated previously. The immediate application of our findings is that miR-532-5p may be used as prognostic tools in ovarian cancer, which has already been proposed for miR-532-5p in colorectal cancer.[59] The better outcome is that our research with miR-532-5p in ovarian cancer will stimulate more extensive research into the molecular mechanism of miR-532-5p in ovarian cancer and be leveraged for the development of clinical therapies for ovarian cancer.

35

Winter 2016 Acknowledgements [25]

I would like to thank my principle investigator Dr. R. Stephanie Huang for supporting this research and giving permission for this project to be presented in University of Chicago’s Scientia. I would like to also thank my collaborators Fan Wang and Chester Kao, and lastly the Biological Sciences Collegiate Division Research Endowments at the University of Chicago.

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Winter 2016

A Freshman Introduction to Gauge Theory Milo Marsden

I want to introduce some of the foundational concepts of gauge theory, the methods of which serve as major analytic tools for theoretical physics. Gauge theory is central in particle physics and condensed matter physics, but even General Relativity can be formulated in terms of gauge theory. As for the explanation of these tools that follows, I aim for accuracy while retaining accessibility. Generally, popularizers of the science of contemporary physics obscure the tools of the science in presentations to the general public. This sacrifices an exposition of the theoretical machinery to obtain conceptual clarity. One would like to expose all the theoretical machinery. Yet, to truly understand how the theory obtains its results requires actually studying the theory. I would like to give a picture of what the theory looks like. I will not necessarily explain all of why the theory appears as it does, and I will use some simplified examples to illustrate what is happening. This will not take away from the overarching idea of what is happening, but rather the practical matters of making it happen.

First, we will need to understand a theoretical tool central to the discussion: Lagrangians. Lagrangians are a valuable tool in both classical physics and Quantum Field Theory. The first problem in physics is predicting how something moves. In a sense this is almost the only problem in physics. Suppose we want to know what the

38

position of the ball is at some arbitrary time t. We say its position at the time t is the vector specifying the position of the ball in our coordinate system at that particular time. Our goal is to find this function .

Through Newton’s laws, we can find it provided we know the forces on the ball, , and the mass of the ball, m. If we know this, Newton’s second law gives us

If we solve this differential equation, then we will know the position of the ball at any time.

This approach takes force to be a fundamental object. We use this fundamental object to make our mathematical models, and we can use it to define other objects that might be useful in calculation. This is not the only way to make such models. We can use other objects as the fundamental starting point of our mathematical models if we take a different approach.

One can, in fact, take energy to be the fundamental object in our mathematical description, and from this one can deduce Newton’s Second Law. This is the better approach from a theoretical standpoint. When we want to make predictions using our theory we will need to solve the same equations regardless. But, if we begin

Scientia with energy as the fundamental concept, we obtain a more natural and succinct language. In this language, it is easier to precisely summarize physical phenomena and develop theories. Moreover, when working in quantum mechanics, the use of forces becomes unwieldy and unnatural. Energy both remains a useful conceptual tool and is easier to use in calculation.

More specifically, we have two concepts we call kinetic and potential energy. We may use these concepts as the starting point in our discussions. Kinetic energy is a function of the particle’s velocity, , and mass, m, given by

and the potential energy is a function of the particle’s position and is determined by configuration of the world.

It will be denoted . We can tell what the particle’s potential energy is at a particular time by simply evaluating V at the particle’s position. Since the particle’s position at the time t is the point ), the particle’s potential energy as a function of time is . Let us look at this in only one dimension for simplicity.

When we began our approach with force, we had to accept two things: a fundamental concept of force and a fundamental law . Now, we begin our approach with energy as the fundamental concept. The corresponding law is called The Principle of Least Action. It states that if we look at what happens to the ball between times t1 and t2, the integral

will be as small as it can possibly be.

The integral is a real number and is called the action. Of all the paths between x(t1) and x(t2), the function x(t) that actually manifests in nature is the one for which the action is the least. The intuition behind this principle is that nature is stingy with energy. There should be as much potential energy and as little kinetic energy as possible. The integrand inside the integral is called the Lagrangian, and it essentially determines how the systems evolves. If one knows how to approach this problem, it is not so hard to show that this minimizing function satisfies the differential equation

whereby

we mean the derivative of the function V(x)

with respect to its variable x evaluated at the point x(t). Since this function depends on x(t) which in turn depends on t, we see that is ultimately a function of t. If we call by the name B(t) we see that we have

which is identical to Newton’s second law. If we had no concept of force, then this B(t) would fill the role force does.

So, we can build our mathematical models with energy as the starting place and obtain the same results as Newton’s laws.

The tools of the Lagrangian approach naturally generalize to quantum field theory (QFT). Here, we have two types of fields: classical and quantum. It may be surprising that the word classical appears at all. Classical physics is immensely important in everyday life. But, in the world of the very small, the laws of classical physics have no predictive power. When we want to predict the behavior of electrons, positrons, and other fundamental particles, we do not look to classical physics. Why, then, do we have something “classical” in our theory?

Each classical field represents a kind of particle. [5] There is the electron field, the photon field, Higgs field, etc. The classical fields take a point in spacetime, and give you a real or complex vector. [4] They are classical in the same sense that gravitation and electromagnetism are classical. When making predictions in electromagnetism, one predicts the behavior of vector fields that are not all that different from these classical fields. In QFT we make predictions using the quantum fields, not the classical ones. We are interested in the classical fields because we get the laws for the quantum fields by looking at the classical fields. [3] To predict the behavior of the classical fields, we again use Lagrangians, but differently than we did before.

In the Lagrangians earlier, we only needed to integrate with respect to time. The Lagrangian needed information about the particle’s position and how this position changed with time. The time variable determined both of these pieces of information. But, position is now an independent variable. Consequently, we want a function of space and time. The Lagrangian looks like:

μ

Where φ=φ(t,x,y,z) is one of these fields. The terms ∂ and ∂μ represent derivatives of the function φ(t,x,y,z) with respect to the variable μ, where μ is one of t,x,y,z. We have a convention that tells us that since this index is repeated, we take the derivatives with respect to each of these variables in turn,

39

Winter 2016 then sum them up. This is the analog of

from the Classical Mechanics case. We do roughly an analogous thing in Classical Mechanics where we say we want the function x(t) that minimizes

While in the QFT case, we say we want the function that minimizes

[4] Through this process of minimizing, we can tell how the classical field changes in time and in space. There’s not a whole lot of predictive power in these classical fields after we know how they evolve. They serve mostly as a stepping stone to get to the quantum fields, which are different in flavor from the classical fields.

Where the output of a classical field is a real or complex vector, the output of a quantum field is a function. More specifically, quantum fields take a point in spacetime and give a function called an operator. An operator is a function that takes in a state of the universe, and gives another state of the universe. So, for a quantum field φ, the value φ(x,y,z,t) is a function. If we have the function φ(x,y,z,t), and feed it a state of the world with 0 particles, it gives us a state of the world with a particle at the point (x,y,z,t) in spacetime. To each of these functions is an associated function that takes a particle away.

These are called the creation and annihilation operators, respectively. We use them to predict how fields interact with each other. If we multiply them together, they represent processes of creation and annihilation. In the case where we have more particles, φ(x,y,z,t) will be some combination of these creation and annihilation operators, creating some particles and removing others. [5] Still, it is not quite clear what the classical fields have to do with the quantum fields. When we are making the transition from classical mechanics to quantum mechanics, we represent states of the world by vectors |ψ called state vectors. We have operators on these vectors which produce other states of the world. We can study exactly which states they give, and from this get information about our physical system. For example, there is the momentum operator, . When we apply it to appropriate states, we get information about a particle’s

›

40

momentum along with our new state. [5] We have such operators corresponding to all classical quantities, and we demand that certain classical relationships hold when written as equations involving operators. These relationships are key to making predictions in QM. We do the same thing when going from classical to quantum fields. For each classical field, we create a quantum version of it, and we demand that the relationships that held for classical fields hold for a quantum field, along with a few other conditions. The process of constructing this quantum theory from a classical one is called Canonical Quantization. [4] Thus, we want to predict the classical fields because the equations that tell us how the classical fields change with time are essential to our ability to make predictions with the quantum fields.

When we have two classical fields multiplied in the Lagrangian, we know that the behavior of one will affect the other. We minimize the integral

by finding a differential equation involving the fields, and if two fields are multiplied in the Lagrangian, the fields will appear together in the differential equations. When we turn this classical equation into a quantum equation, we will have creation and annihilation for each of these fields multiplied together, and this will dictate a physical interaction. That is, the particles represented by these fields will interact. It is possible for two fields themselves to not interact directly, but to interact because they both interact with a third field.

So, the general procedure is to find some equation for the classical fields, and force this relationship to hold with the corresponding quantum fields. [4] It is in predicting the classical fields that gauge theory really comes in.

Recall, when we had the Lagrangian

μ

the terms ∂ and ∂μ represented derivatives of the function φ(t,x,y,z) with respect to the variable μ, where μ is either t, x, y or z. But, there is a problem with our ability to take these derivatives. The set of all possible outcomes from an experiment is not inherently numerical in the same way that the surface of the earth is not inherently numerical.

The outcome of a measurement is obviously a number, but we have to make a way of associating these outcomes to numbers in order to make measurements. This is the same thing as when we want to assign longitude and latitude coordinates to points on the earth. In order to make this association, we must set where the equator is, where the

Scientia prime meridian is, and an orientation of the earth.

This is not such a foreign concept. Consider a circle.

One can do a lot of geometry with a circle without associating points on the circle with numbers. But, in order to do a lot of math with the circle, such as calculus, it becomes necessary to associate the circle with a subset of the real numbers in a way that preserves certain properties. [1] The way we usually do this is pick a point we call 0, a direction we call positive, and associate the each point on the circle with how far 0 is from that point if we are moving along the circle in the positive direction. Now, once we’ve chosen where 0 is and which direction is positive, our answers reflect that choice.

But suppose we want to write down laws that do not depend on that choice, as we do in physics. Or suppose we plan to perhaps change how we identified things in order to make some calculation more convenient.

Then it is important to see how different identifications give different answers. These identifications are called Gauges. [1] In the circle example,we had a single object we associated with numbers. The more complicated and more relevant case is that in which we have many objects we need to associate with numbers. Suppose we have a bunch of circles, each associated with a point on a much larger set. For instance, suppose we have a bunch of circles associated with points on the earth. This could represent, for example, the set of directions one can walk in at some point on the earth. If we choose a point on each of these circles, we’ll have something that looks like a function, and we might think it would be fruitful to take derivatives of it. Or, at least, if we want to write down laws dictating the behavior of some function like this, we will probably phrase it in terms of derivatives. [1] But, not so fast. Each of points we have chosen comes from a different set. Because of this, there is no guarantee they mean the same thing. [1] For instance, suppose you and I are on opposite sides of the world from each other. We both point north, and start walking.

If you visualize this, you will see that when we meet, we’ll be walking in opposite directions. On the other hand, if we both were at the equator, pointed our hands north and then walked toward each other on the equator, we would be pointing our hands in the same direction. So, there is no ready way for us to compare our notions of north, because we get different answers if we compare them in different ways. It is not clear that at different points they mean the same thing. The same things happens when we are trying to look at the set of outcomes from an experiment, there’s no guarantee that

if we are at different points that the things we are talking about mean the same thing.

But, this creates a problem for us. Almost all of our predictive tools involve derivatives. Recall the definition of a derivative in one variable

We take all the differences between the value of the function at x and its value at the nearby point x + h. From this we can construct the derivative. But, we need to have the ability to make such a comparison. This is as true in the multivariable case as in the single variable case. Derivatives represent rates of change. The ability to talk about how a function changes at a point inherently relies on our ability to be at two different points and compare the value of the function at those points. [1] When we are defining a function on an object that is not inherently numerical, we don’t have a good way to compare these values, since we don’t know if they mean the same thing at different points.

There are two ways we can solve this issue and get back to having derivatives. The first is that we can associate all of our not inherently numerical objects with some numerical object. Once we’ve done this, we take the derivative like we normally would. But, there’s a snag. If we do this, the derivative then depends on the way in which we made the identification. That is, it depends on the gauge we choose. Since we are writing down the laws of physics, we want our laws to be independent of such a choice.

Alternatively, we can translate what the value of our function means at one point to what it means at another point very close to it. Look back at the direction example. If you and I are very close, then we can almost compare directions. If we are close, we have a way of translating what your north means at my north, then we can compare them. This is called a connection. [1] In practice, this latter approach allows us to define the derivative in way such that it is independent of what gauge we choose. The details are a little complicated, but what we can do is first choose a gauge,and take derivatives as we normally would. Then, we add in a new field that in some sense compensates for the fact that we need to bring the points to each other in order to be able μ to compare them. [1] So, where before we had ∂ φ and ∂μφ , we now have

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Winter 2016 But, we now find that this changes our Lagrangian, because where we had the term

References [1] [2]

we now get terms like

[3] [4]

[5]

Tao, Terrence “What’s a gauge” What’s New. Wordpress 27 Sept 2008. Web. 19 Jan 2016 Saha, Gopal B. Basics of PET Imaging: Physics, Chemistry, and Regulations.

New York: Springer, 2010. Print.

Peskin, Michael Edward, and Daniel V. Schroeder. An Introduction to Quantum Field Theory. Reading, MA: Addison-Wesley, 1995. Print.

Srednicki, Mark Allen. Quantum Field Theory. Cambridge: Cambridge UP, 2007. Print.

Lancaster, Tom, and Stephen Blundell. Quantum Field Theory for the Gifted Amateur. Oxford: Oxford UP, 2014. Print.

μ

It is clear that we will multiply the fields ∂ , ∂μ, and Aμ. So, they will interact. The compensating field, then, affects the dynamics of our system. So, the compensating field plays a role in the laws of physics.

The exact form of this field depends on gauge we have chosen, but all physically measurable quantities do not. The laws and answers are independent of the gauge we choose. Only our actual calculations depend on the gauge, which is what we expected.

This method essentially gives rise to the quantum theory of electromagnetism. If φ represents the electron field, then φ starts interacting with A. A is called the photon field then, and it represents a photon. φ did not initially interact with itself, but due to its interactions with A it does begin to interact with itself. This is how electrons repel one another. The electrons do not directly interact with one another. Rather, they both interact with the photon field. Specifically, they exchange photons with one another. It is this exchange of photons that gives rise to the force between two electrons.

The same is true if the fields are different. If we have two fields φ and ψ that do not interact directly, but both interact with A, they may affect each other through their interactions with A. This is exactly how protons and electrons interact with one another, by exchanging photons. By understanding how electrons, photons, positrons, and other fundamental particles interact, we can pursue certain technical applications. For instance, consider PET scanning. A patient ingests a chemical that is absorbed into the cells the doctor wants to image.

This chemical emits positrons, and these positrons interact with ambient electrons. This emits two gamma particles, which are high energy photons. They move in approximately opposite directions. By detecting these gamma particles, we can construct an image of what is happening inside the body. [2] This technology is based upon knowing how electrons and positrons interact, how they produce photons, and how these photons then interact with detectors. Knowledge of this sort is central to Gauge Theory.

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Acknowledgements I also want to give special thanks to Christian Ferko.

Almost all the information in this article came with his help, and without him I would not have been able to write any of this.

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

Eleanor Daugherty

Assistant Vice President for Student Life and Associate Dean of the College

Arthur Lundberg

Assistant Director of the Student Activities Center

Brandon Kurzweg

Student Activities 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 uchicago.print@thetriplehelix.org. 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 uchicago@thetriplehelix.org.

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Winter 2016

About The Triple Helix

at The University of Chicago

The Triple Helix, Inc. (TTH) is the world’s largest completely student-run 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, which are perhaps best summed by our title as the William J. Michel Registered Student Organization of the Year in 2012.

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!

Stephen Yu President of The Triple Helix, Inc.

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Meet the Staff Scientia Editors in Chief Jake Russell Luizetta Navrazhnykh Managing Editors Michael Cervia Amanuel Kibrom Erin Fuller Associate Editors Jeremy Chang Clara Sava-Segal Sumer Vaid Andrew Wang Helena Zhang Writers Scientia Inquiries Zeke Gillman Andrew Wang In Depth Jeremy T. Chang Milo Marsden Scientia Inquiry Faculty Dr. Greg Engel Dr. Allan Drummond

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