Scientia - Winter 2018 by The Triple Helix at UChicago

Scientia

A Journal by The Triple Helix at The University of Chicago

Winter 2018

Cover photo by Naomi Tamar from Unsplash

Scientia 4 8 14 20 27

In Depth

VLA Differences in Patients with Systemic Lupus Erythematosus Across Races Daksh Chauhan

The Role of SK Channels in Purkinje Cells on Motor Coordination Lindsey Jay

Immune Checkpoint Protein Expression in Peripheral Blood Mononuclear Cells Treated with Conditioned Media from Head and Neck and Lung Cancer Cells In Vitro Logan Leak, Lechuang Chen, David Ye, Ge Jin

Low-Cost Gravity Driven Filtration System Designed Using Iron Oxide Nanoparticle-Loaded PU Foam for Arsenic Removal from Polluted Groundwater Sources Arundhati Pillai, Mohammad Amin Faghihi Zarandi, Krishna M. Pillai, Nidal H. Abu-Zahra

Effects of Fragile X Syndrome on the Conductance of Neuronal Mitochondrial Membrane Channels Jorge Salcedo Sifuentes, Sana Sohail, Elizabeth Jonas

Produced by The Triple Helix at the University of Chicago Layout and Design by Elle Rathbun, Production Director Cover Letter written by Clara Sava-Segal, Co-Editor-in-Chief Scientia Board: Clara Sava-Segal, Jeremy Chang, Zainab Aziz, Nikita Mehta, Quang Tran

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In Depth, cont. Biologically Coupled Reduction of Nitrate and Oxidation of Fe(II) Implications for Denitrification in Paddy Soils Kaixin Wang, Ye Chen, Weilin Huang, Dandan Chen

Abstracts Strain-Induced Configurational Twists and Topological Defects in Smectic and Nematic Liquid Crystals Three-Dimensional Architecture and Assembly of TwoDimensional Materials Modifications to the Hall Probes in the MagnetoRotational Instability Machine Computation Analysis and Prediction of Post-Stroke Recovery from Baseline Brain Connectome Metrics Cobalt Super-microparticles Anchored on Nitrogen-doped Graphene for Aniline Oxidation Based on Sulfate Radicals Tracking the Fate of Facial Branchiomotor Pioneer Neurons in the Zebrafish Hindbrain Modeling Early Alzheimer’s Disease Pathology with AAVTau in a Rodent Model of Cognitive Aging Overcoming Catastrophic Forgetting Using Recurrent Neural Networks The Genetic Basis of Alzheimer’s Disease in the Hutterite Population Disruption of the Antiviral RIG-I Pathway by JC Virus Feature-Based Image Alignment Using Affine Transformation HCV Screening and Linkage-To-Care Care Continuum Characterizing the Effect of Alkyl Group Length and Counterion Identity on the Conductivity of Charged Poly2-Vinylpyridine Thin-Film Electrolytes

From Stellar Evolution to Supernovae: Professor Dwarkadas’ Philosophy in Diversifying Research Interests Jarvis Lam

Scientia

About Scientia Dear Reader, The front cover of this issue depicts a jellyfish as an allusion to the assortment of research that we aim to showcase. Back in 2008, Martin Chalfie, Osamu Shimomura, and Roger Y. Tsien won the Nobel Prize in Chemistry for their discovery, isolation and development of the green fluorescent protein (GFP) from the jellyfish Aequorea victoria. Used as a tool for the visualization of changes in live cells, GFP has since been applied to study embryonic development, map out brain cell circuits, visualize the spread of cancer, and for countless other pursuits, truly revolutionizing research. This issue is our most expansive and diverse yet. The primary goal of Scientia is to commend the vital research being conducted by UChicago students. Therefore, we invite you to read our six in-depth articles, featuring unique medical research on the neurobiological mechanisms behind Fragile X Syndrome and spinal cerebellar ataxia, on lupus outcomes across racial and ethnic groups, and on the development of immunotherapy techniques in cancer treatment. In addition, we present two environmental articles on nitrate pollution and the development of a water filtration system. Furthermore, we feature an Inquiry with an astrophysics professor, seven Scientia original abstracts, and some of the best abstracts from the University of Chicago Undergraduate Research Symposium, in collaboration with Phoenix Biology and UCISTEM. Our abstracts highlight research on material fabrication, engineering, stroke analysis, Alzheimerâ&#x20AC;&#x2122;s, neuron tracking, microbiology and energy. As we continue to develop and expand, we will keep exploring new research domains and fields. If you are working on a research project or are interested in a professorâ&#x20AC;&#x2122;s field, consider collaborating with us in the future to see your work in print! We encourage anyone interested to contact any member of our team, listed in the back. For the time being, please enjoy our winter issue of Scientia, by The Triple Helix. Best, Clara Sava-Segal Co-Editor-in-Chief, Scientia

Winter 2018

In Depth VLA Differences in Patients with Systemic Lupus Erythematosus Across Races

Daksh Chauhan, Dr. Jinoos Yazdany, Dr. Patti Katz University of California, San Francisco

Abstract Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that mostly affects women and manifests itself in clinical forms that vary among affected patients. There is a paucity of information regarding the impact of race on the severity of these manifestations. The objective of this study was to investigate the impact of race upon these differences by using the Valued Life Activities Index (VLA), a scale which measures disability. Higher scores indicate that a patient experienced greater difficulty with or was unable to carry out certain everyday tasks. For this study, data was gathered from the California Lupus Epidemiology Study (CLUES). Recruited CLUES patients were called for in-patient visits, while telephone surveys were also conducted to collect clinical and outcome variables. One-way Analysis of Variance (ANOVA) tests were done to look at the VLA score differences. Of the 323 patients interviewed in the CLUES project, the following distribution of race was found: 36% Asian, 30% White, 23% Hispanic, and 11% African American. Through the bivariate analysis of race and VLA, statistically significant differences in VLA means across races (p= 0.0028) were found. Asians and Hispanics tended to have lower VLA scores when compared to Whites and African-Americans. Race lost its statistical significance, however, when other factors such as age (p<0.0001), sex (p=0.0277), SLICC (Systemic Lupus International Collaborating

Clinic) score (p=0.0255), and obesity (p=0.0025), which were found to be of importance by univariate analysis, were included. It was determined that significant variation in VLA means does not exist across races but does for variables such as SLICC score, age and obesity. In essence, race by itself does not impact the clinical severity associated with SLE. Introduction Systemic lupus erythematosus (SLE) can be associated with physical disability among affected patients, but not many measures exist to fully characterize it. This is, in part, related to the variability in manifestations and disease severity that SLE lupus patients could experience throughout the course of their disease. Valued Life Activities Index (VLA), which uses the framework of the disablement model of Verbrugge and Jette [1], is designed to look at a group of 21 activities characterized as obligatory, committed and discretionary [2]. There are 3 novel elements of index. First, it takes into consideration a wide variety of activities. Second, it looks at the personal importance one gives to each activity. And third, it asks respondents in studies to attribute performance difficulties to any health conditions. All these elements make the VLA index a good measure to utilize when understanding SLE lupus. Manifestations and severity of SLE vary

Scientia significantly from patient to patient. While some manifestations such as malar rash and photosensitivity, both being common cutaneous manifestations, may not affect a personâ&#x20AC;&#x2122;s daily life to a great extent, a manifestation such as lupus nephritis, which causes inflammation of the kidneys, can lead to renal failure over time and significantly lower the quality of life. Therefore, it is not feasible to look solely at individual manifestations of SLE to predict the full spectrum of disability. Because VLA looks directly at key, everyday activities, it presents valuable information about disability in patients even if each individual is affected differently. Differences in SLE manifestations and severity have been described to be particularly pronounced across different racial groups. For instance, lupus nephritis, a common manifestation, is particularly more prevalent and severe among non-White patients than it is in White patients [4]. On the other hand, mucocutaneous manifestations are more prevalent in Asians, and both Blacks and Asians tend to have higher hematologic manifestations [4]. Because prevalence of manifestations can vary significantly across races, severity and long-term damage accrual can be different across racial groups as well. The SLICC (Systemic Lupus International Collaborating Clinic) score, which measures organ damage on a scale from 0 to 47, is usually higher for non-White patients than it is in White patients, pointing to higher end-organ damage in non-White patients [3]. Given these differences in manifestations and severity of lupus across racial groups, we decided to evaluate how disability resulting from SLE differs from race to race, as a deeper understanding of these differences can help improve and personalize treatment for this disease. Differences in VLAs across racial groups were analyzed. To look at the differences in VLA, patient data from the California Lupus Epidemiology Study, a large study that recruited lupus patients from San Francisco County, was used. The study included a representation of patients from different race groups. Materials and Methods Sample We studied a sample of 323 patients who came from the California Lupus Epidemiology Study (CLUES), which included African-American, Asian, Hispanic and Caucasian patients. CLUES recruited

patients identified during the California Lupus Surveillance Project, a Centers for Disease Control funded project that aimed to look at prevalence and incidence of lupus in the US. Then, the patients were called for in-patient visits and surveyed over the telephone. In the telephone interview, the patients were asked to rate the difficulty of carrying out certain activities on a four-point scale, a scale which is similar to that of the health assessment questionnaires (0=no difficulty and 3=unable to perform).

VLA Disability VLA disability scale is based on 21 different activities which are classified as obligatory, committed, and discretionary. These three terms are taken from the scale based on definitions of these categories by Verbrugge and Jette [1]. The 21 activities used in the studyâ&#x20AC;&#x2122;s calculations can be found in Table 1. A higher VLA scale corresponds to a greater difficulty in carrying out those activities. Variables In addition to race, other baseline variables of age, gender, poverty, education, disease duration, SLICC score, and obesity were included in the study. SLICC score measures vital organ (such as kidney, heart, etc.) damage in lupus patients and has a range from 0 to 47 points. A SLICC score of 2 or greater is considered high. Looking at just the race and VLA score is misleading due to the underlying influence of baseline variables. Analysis To eliminate the influence of possible confounding variables, bivariate and multivariate analyses were run to look at the influence of all the baseline variables on VLA. Subject Characteristics In the data sample, 88.9% of the patients were women, 22.7% of the patients came from low education backgrounds, and almost a fifth (19%) lived below the poverty line (Table 3). The sample has a high percentage of women because prevalence of SLE in women is greater than it is in men. The average age of the sample was about 45 years, and the average disease duration was about 16 years. The VLA mean for the entire group was about 0.4555, and the average SLICC score was 1.2 (Table 1).

Winter 2018 Analysis When looking at mean VLA score across different races, the average VLA score for Whites (.57) and African-Americans (.62) was higher than that for Asians (.31) and Hispanics (.45). The differences in the VLA scores across racial groups were significant (p=0.0028); thus, a multivariate analysis was completed to eliminate the influence of any confounding variables. The multivariate analysis model, as tabulated in Table 6, shows key baseline variables as well as race. These variables were chosen to eliminate socioeconomic factors and lupus outcome SLICC score as confounding variables. This model calculates how a specific variable affects the VLA mean and can help identify confounding variables that might influence or produce certain results. In the regression analysis model, the parameter estimate is the coefficient of a variable in the larger equation of the VLA mean. The magnitude and sign of the estimate indicates how a variable affects VLA: if the variable has a positive sign, it increases or positively affects the mean VLA score. For example, the parameter estimate for obesity (0.23) indicates that the average VLA score for an obese lupus patient is about 0.23 points higher than that of a non-obese patient (Table 6). For age, which has a parameter estimate of 0.012, a patient will have a VLA score 0.012 points higher than a patient who is one year younger (Table 6). By looking at parameter estimates and p-values from Table 6, it was found that VLA scores do not vary significantly across races when baseline variables such as age, SLICC score, and gender are factored in the multivariate analysis. Variables that were found to significantly affect the VLA score were age (p<0.0001), female gender (p=0.0277), obesity (0.0025), and SLICC score (0.0255). These variables positively impact the VLA score. Table 7 shows bivariate means for VLA scores and multivariate adjusted means. The bivariate VLA means for some groups may seem different from the average VLA score (0.4555), but the multivariate adjusted means are quite close. The multivariate adjusted VLA mean was .41 for both African Americans and Asians, .44 for Hispanics, and .51 for Whites. This shows that, based on this data, there isnâ&#x20AC;&#x2122;t a statistically significant difference in average VLA score across race.

Discussion SLE is a systemic disease that affects the immune system and causes it to attack its own bodyâ&#x20AC;&#x2122;s tissues. Damage can therefore occur anywhere in the body. Since SLE can affect people in myriad ways, looking at disability differences across races is clinically valuable. For instance, studies have shown that patients with severe manifestations such as lupus nephritis were much more likely to have a higher disability or VLA score than someone with a mild manifestation like malar rash. Similarly, severity indices to measure damage accrual also vary as a result of differences in manifestations. Disability is usually common among lupus patients. By analyzing a previous year-long study done at the University of California San FranciscoLupus Outcomes Project, it was found that of the 21 VLA activities, almost half of the studyâ&#x20AC;&#x2122;s patients were unable to do at least one activity, and 91% of the patients reported some difficulty in doing at least one activity [2]. In addition, the study indicates that higher disease severity corresponds to greater disability. However, disability caused by SLE, as indicated by VLA score, does not vary significantly across racial lines as shown by the multivariate regression analysis. Given the previous literature on VLA and differences in manifestations and severity across races, the results from this study were not expected. Since we knew that disease manifestations vary across races and can result in different degrees of disability, we expected to see significant difference in the VLA mean score across races. Initial results seen during the first bivariate analysis of VLA and race were significant because they were not analyzed with the baseline variables. Multivariate analysis of disability and race along with baseline variables must have caught some confounding variables that resulted in the initial bivariate results as seen in Table 4 and Table 5. Our data shows how VLA means for different races would have looked like if adjusted for baseline factors (Table 7). Mean VLA for White (0.51) and African-American (0.41) patients goes down from the original once those factors are accounted for, while the mean VLA for Asian (0.41) patients goes up. The adjusted means are close to the overall sample mean in Table 1. Factors that did affect the VLA mean were age, obesity, gender and SLICC score. SLICC score,

Scientia which measures the disease damage over time, had a positive correlation with VLA or disability. The parameter estimate for SLICC from the multivariate analysis was about 0.05. Higher SLICC therefore corresponded to a higher disability. This is in agreement with the findings of a study done at the University of California at San Francisco [2]. Age, obesity and gender were also factors that positively influenced VLA indices. Patients with the baseline variables of female gender, obesity, or old age were likely to have higher disability. Women possibly had higher VLA scores on average than men because of differences in manifestations between the two genders [6]. Obesity can contribute to higher VLA averages as clinical obesity by itself results in disability to a degree and can exacerbate the VLA disability originating from SLE. Greater age can often correspond to higher disease damage as lupus damage accumulates over time. Though this study sheds more light on SLE lupus and differences in its manifestations across racial lines, it also had its limitations. For instance, the sample in this study only had lupus patients from San Francisco County. This sample might be different from a sample of lupus patients found in another U.S. county. In addition, race was reported by the patients; thus, there may be other genetic-based categories for ancestry that could more accurately indicate how VLA averages were different across races. Another possible factor was the lack of African Americans in the study, something that would have driven up the standard error and affected the accuracy of the intercept for African Americas. Nevertheless, the results from this study open areas of future research to more accurately look at mechanisms behind how factors like age and obesity result in higher disability.

4. Maningding, E. et al. Differences in Clinical Manifestations of SLE across Four Racial/Ethnic Groups: The California Lupus Surveillance Project (CLSP) [abstract]. Arthritis Rheumatol. 68 (suppl 10). (2016) 5. Fries, JF. et al. Measurement of patient outcome in arthritis. Arthritis Rheum. 23:137–145. (1980) 6. Yacoub Wasef, SZ. Gender Differences in Systemic Lupus Erythematosus. Excerpta Medica. 1:12-17. (2004) About the Author Daksh Chauhan is a first-year planning to major in Biological Sciences and minor in Statistics. He is currently working at the Fang Lab at University of Chicago Medicine doing research in atherosclerosis. He hopes to attend medical school and become a physician specialized in cardiology. Acknowledgements I would like to thank my principle investigators on this project– Dr. Jinoos Yazdany and Dr. Patti Katz– for supporting me throughout this project and helping me with the analyses. I also extend my thanks to the Arthritis Foundation for funding my summer internship experience in 2017 at University of California San Francisco and getting me in touch with Dr. Yazdany and Dr. Gabriella Schmajuk, my Principal Investigators on a previous research project.

References 1. Verbrugge, L. et al. The disablement process. Soc Sci Med. 38:1–14. (1994) 2. Katz, P. et al. Disability in Valued Life Activities among individuals with Systemic Lupus Erythematosus. American College of Rheumatology. 59: 465–473. (2008) 3. Sutcliffe, N. et al. The association of socioeconomic status, race, psychosocial factors and outcome in patients with systemic lupus erythematosus. Rheumatology (Oxford). 38: 11301137. (1999)

Winter 2018

The Role of SK Channels in Purkinje Cells on Motor Coordination

Lindsey Jay

Hansel Lab, Department of Neurobiology, The University of Chicago

Abstract Spinocerebellar ataxia (SCA) is characterized by a progressive lack of motor coordination, usually resulting from neurodegeneration of Purkinje cells in the cerebellum. Drugs that have improved motor coordination in patients and mouse models with cerebellar ataxia have been shown to positively modulate small-conductance calcium-activated K+ channels (SK channels). Moreover, mice with a null mutation for the SK2 subunit have a dramatic impairment of motor coordination. However, the role of SK channels in the different parts of cerebellar circuit in controlling motor coordination and contributing to the pathophysiology of cerebellar ataxia remains unclear. Data here are presented supporting a role played by SK2 in Purkinje cells (PC) for the fine control of motor coordination. A new PC-specific knockout mouse model for SK2 (L7-SK2-KO) was used, and these mutant mice were found to have a comparable overall gross motor coordination as assessed by the accelerating Rotarod test. However, a finer analysis of gait performed by DigiGait has revealed longer stride length and time compared to controls. The analysis of PC density in fixed tissue revealed no significant differences caused by the mutation, suggesting that the observed alterations in gait cannot be related to PC loss. Although further experiments will be needed to fully clarify the role of SK2 in motor coordination and memory, these data give an important first indication that, while the lack of SK2 in PC may be functionally compensated without significantly affecting the control of gross motor coordination and memory as assessed by Rotarod, it may play an important role in the finetuning of the gait. Introduction Spinocerebellar ataxia (SCA) is characterized by a progressive loss of motor coordination of voluntary movements and is associated, in most cases, with the neurodegeneration of Purkinje cells (PCs), which generate the only output in the cerebellar cortex. However, some forms of SCA are not associated with PC degeneration, suggesting that impairment of only cerebellar circuit physiology might be sufficient to cause

ataxia. [1] Drugs that can positively modulate small-conductance calcium-activated K+ channels (SK channels) have been shown to improve motor symptoms in patients with cerebellar impairments. [2-4] Positive modulators of SK channels also improved the ataxic phenotypes in mice. [58] Specifically, SK channel activation leads to inhibition of overly excitable, high neuronal activity in ataxic patients by opening K+ channels and inducing hyperpolarization in the cell. In this

Scientia way, normal motor function can be recovered for those with ataxia. Conversely, mice lacking SK2 have a dramatic impairment of motor coordination starting at post-natal days 7-10. [9] These channels regulate Purkinje cells by reducing its excitability depending on intracellular calcium concentration and regulating PC firing patterns. [10, 11] However, it is not exactly clear yet what role SK channels play in the cerebellar circuit for the control of motor coordination nor what the alterations of the circuit physiology underlying ataxic symptoms are. This work will better inform researchers of how to design more effective treatments in the future for SCA by assessing the role of PC-specific SK channels in motor coordination and considering whether targeting PC-specific SK channels for treatment can help treat SCA. A new mouse model has been recently developed to study the role of SK channels with regards to PCs in the cerebellum. Cerebellar PCs play a crucial role in the control of motor functions such as coordination or gait. This mutation was obtained with the CRE-lox system by crossing mice expressing the CRE recombinase under the Purkinje cell-specific promoter L7 (L7-CRE) with mice possessing the sequences recognized by CRE (LoxP sites) flanking the first two codons of the gene encoding for SK2 to have a cell-type specific deletion of those codons resulting in a null mutation. These mice were compared to control littermate mice with the LoxP sites, but lacked CRE expression. Behavioral analysis of PC-specific SK2-KO mice (L7-SK2-KO) was performed to clarify the role of SK2 in PCs for motor learning and coordination. PC density was analyzed to measure cellular effects of SK2 deletions. Golgi staining was also performed to analyze the morphology of PC dendritic arbors. The motor performance of mice was assessed using accelerating Rotarod and DigiGait automated gait analysis. For comparison, the motor performance of two other mouse mutants with dramatic impairments in motor behavior was also analyzed: mice bearing a constitutional null mutation of SK2 (SK2-KO) and a new model for type-6 spinocerebellar ataxia (SCA6), recently developed in Gomez lab (Dept. of Neurology) and currently under investigation (Du et al., in preparation), bearing a null allele and a humanized allele of the gene responsible for SCA6, CACANA1A.

Figure 1. Purkinje cell morphology from Golgi staining procedure. 3-5% of a) Purkinje cells in cerebellar tissue were impregnated with silver chromate to visualize the entire cell structure, with dendritic arbors indicated by red arrows, together with b, c) molecular layer interneurons, microglia, and other cells.

Materials and Methods Immunostaining Mice were anesthetized using ketamine/ xylazine and intracardially perfused with ice-cold 4% paraformaldehyde. Mouse cerebella were post-fixed for at least two hours, then equilibrated with 30% sucrose overnight. Sagittal sections (50 um thick) immunostained for Calbindin (marker for Purkinje cells) and Parvalbumin (marker for GABAergic neurons) and acquired by the University of Chicago microscopy facility (20x magnification; Fig. 2A, 2B) were used. Eight to ten random fields were selected for each animal. The number of PCs and the length of the analyzed traits of PC layer were measured with NIH ImageJ software (count tool and segmented line tool), measuring the length between the first and last PC detected. The density of PC was calculated and averaged per mouse. Differences between L7-SK2-KO and control littermates were tested using a two-tailed unpaired t-test.

Golgi Staining Mice were anesthetized with isofluorane before being sacrificed to obtain freshly dissected mouse cerebella, which were then stained using the FD Rapid GolgiStainâ&#x201E;˘ Kit (FD NeuroTechnologies) to obtain isolated stained PCs. This process resulted in the staining of Purkinje cells (Fig. 1A), as well as molecular cell interneurons, microglia, and other cells (Fig. 2B; cell bodies indicated by red arrows). Images were acquired with a Zeiss AxioCam MRm camera and a 10x IR-Achroplan objective, mounted on a Zeiss Axioscope 2FS microscope (Carl Zeiss MicroImaging). Sholl Analysis To assess the morphological dendritic arborization of the Golgi-stained PCs (arbors

Winter 2018 indicated by red arrows in Fig. 1A), a Sholl analysis will be performed. The molecular cell interneurons, microglia, and other cells besides the Purkinje cells were not further analyzed since our focus was on Purkinje cell morphology. Sholl analysis is a quantitative characterization of the morphology of imaged neurons, consisting of counting the number of dendrite intersections for concentric circles centered at the centroid of the cell body. After determining the critical value (the radius at which there are the most intersections) and the dendrite maximum at that site, the Schoenen Ramification Index can be calculated by dividing the dendrite maximum by the number of primary dendrites at the soma. This will yield a linearized quantification of dendritic arborization.

Rotarod Motor coordination and motor memory were tested with the accelerating Rotarod on a Rotamex 5 (rat spindle, 7.0 cm x 9.5 cm; divided into four lanes), measuring the latency to fall, i.e. how long the mouse was able to run on the rod before falling. An acceleration of 0.1 RPM/0.8 sec was used, starting from 4.0 for up to 3 minutes (40.9 RPM). The latency time to fall was automatically recorded by infrared detectors. A rest time of at least one minute was given between trials. Five trials were run per day for five days. Averages per group per each trial or per day were calculated, and differences between the L7-SK2-KO and control mice were tested with an ANOVA for repeated measures, looking at the effect of genotype, trial, and trial*genotype interaction.

Gait Analysis The gait of the adult mice was recorded with DigiGait (v.14) and repeated at different speeds (20, 25, and 30 cm/s; 15, 20, 25 cm/s for older mice). Mice were placed on a clear treadmill with a camera projecting from beneath to record the bottom of the treadmill. Three to four clips of 3-5 seconds were recorded and analyzed with DigiGait for stride time and stride length. Each parameter at each speed was averaged among clips for each mouse. Differences between mouse groups were tested individually for each parameter at each speed by a two-tailed unpaired t-test. Results The Golgi stains of cerebellar PCs (Fig. 1A) were analyzed to study the morphology of individual PCs. A quantitative analysis of dendritic arborization (Sholl analysis) is currently ongoing to assess PC morphology in L7-SK2-KO and control mice. SK channels are involved in regulating neuronal excitation. Therefore, the possibility that the mutation may affect neuronal viability must still be considered. For this reason, PC density in immunostained cerebellar sections was analyzed which yielded similar results between the two genotypes at 9-10 months of age (L7-SK2-KO: 28.8 +/- 1.8 cells/mm; control: 26.1 +/- 2.6 cells/ mm; t-test p=0.10; Fig. 2C). In order to have an initial assessment of both the overall motor coordination performance and a simple motor learning task, an accelerating

Figure 2. Purkinje cells from a) a L7-SK2-KO mouse and b) a control mouse and c) Purkinje cell densities (control=black, L7-SK2-KO=white). a, b Purkinje cells were stained red for parvalbumin (Pv) and green for calbindin (Cb) and imaged at 20x magnification. c) Cerebellar PC counts were taken manually using the ImageJ counting tool and counting by eye. Length was measured by measuring between the first and last PC counted. Density was taken by dividing PC counts by length and averaged per cerebellum (mean +/- SEM).

Scientia

Figure 3. Latency times for a, b) L7-SK2-KO; c, d) SK2-KO; and e, f) KIKO (white) and their respective control littermates (black) on Rotarod. a, b L7-SK2-KO and control mice latency times per trial (top) and per day (bottom). Mice were 1.4-3.4 months old. c, d SK2 general KO and control mice latency times per trial (top) and per day (bottom). Mice were 8-18 months old. e, f KIKO and controls mice latency times per trial (top) and per day (bottom). Mice were 2.0-3.9 months old.

Rotarod was used. Latency times on Rotarod revealed an increasing latency time along trials and days in both groups, a sign of motor learning, and no significant difference between L7-SK2KO and control mice (Fig. 3A, 3B; ANOVA for repeated measures: trial effect p<0.01; genotype effect p=0.77, trial*genotype interaction

p=0.73). However, the SK2-KO and KIKO mice have severely impaired motor performance that resulted in significantly shorter latency times compared to their respective control groups (Fig. 3C-3F; ANOVA for repeated measures, SK2-KO: trial effect p<0.001, genotype effect p<0.05, trial*genotype interaction p<0.001; KIKO:

Figure 4. Gait analysis of L7-SK2-KO mice (white) and control mice (black). Gait parameters were obtained by DigiGaitâ&#x201E;˘ and averaged per group. a, c Stride times of fore limbs and hind limbs. Mice were 4 months old (left) and 8-12 months old (right). b, d Stride lengths of fore limbs and hind limbs. Mice were 4 months old (left) and 8-12 months old (right). *p<0.05, **p<0.01, two-tailed unpaired t-test.

Winter 2018 trial effect p<0.001, genotype effect p<0.001, trial*genotype interaction p=0.65). To gain a more detailed characterization of motor coordination and its components, the gait of the mice on a treadmill was analyzed at different speeds with the DigiGait system. This analysis revealed differences between the adult L7-SK2-KO and control mice in stride length and stride time at all speeds (Fig. 4A, 4B); L7-SK2KO mice had, on average, longer stride time and stride length compared to control mice. Similarly, the older L7-SK2-KO mice had a trending longer stride length and time compared to control mice; this difference, however, was not statistically significant (Fig. 4B, 4D). Discussion Rotarod Motor Performance Functionally, motor performance on Rotarod (assessing gross motor coordination and learning) was comparable in L7-SK2-KO mice and controls (Fig. 3A, 3B), whereas obvious motor impairment was evident in the KIKO and SK2-KO mice (Fig. 3C-F). This suggests that the expression of SK2 channels in PC do not seem to play a major role for the overall performance in simple motor task.

DigiGait Gait Analysis Upon closer analysis of the gait patterns of the L7-SK2-KO, however, gait analysis revealed longer stride time and length (Fig. 4A, 4C). These gait alterations were evident only through DigiGait analysis. These analyses, therefore, suggest that the L7-SK2-KO mutation is responsible for subtle fine-tuning of gait strategies. The phenotype due to the mutation, then, has a much more subtle effect on motor coordination overall in comparison to KIKO and SK2-KO mice. Furthermore, these subtle gait modifications do not seem to be related to alterations of PC viability, as the loss of SK2 did not affect PC viability even at an age as old as 9-10 months (Fig. 2C). These alterations might be due to increased hyperexcitability in PCs or alterations in PC firing patterns. An electrophysiological characterization of PCs in L7-SK2-KO mice will be needed to identify neurophysiological correlates of the behavioral phenotype. These results provide new insights on the role of SK channels in the different elements of cerebellar circuit.

Conclusions and Future Directions Altogether, these results suggest that the expression of SK2 channels in PCs may play a role in the fine-tuning of gait pattern generation but does not play a major role in gross motor coordination and learning as assessed by DigiGait and Rotarod. Ongoing research will aim to characterize the dendritic arborization of PCs via Sholl analysis. Additionally, electrophysiology experiments in these PCs that are currently ongoing can further elucidate changes in membrane conductance, since SK2 channel activity directly affects the intrinsic excitability of the cell. These next steps, then, will help provide us a molecular understanding of the mutation to correlate with the observed behavioral effects. These results overall may inform us of the role SK2 channels in cerebellar PCs play in spinocerebellar ataxia and what we may be able to target for potential future treatment. References 1. Chopra, R., Shakkottai, V.G. Translating cerebellar Purkinje neuron physiology to progress in dominantly inherited ataxia. Future Neurol 9:187-196. (2014) 2. Romano S., Coarelli G., Marcotulli C., Leonardi L., Piccolo F., Spadaro M., Frontali M., Ferraldeschi M., Vulpiani M.C., Ponzelli F., Salvetti M., Orzi F., Petrucci A., Vanacore N., Casali C., Ristori G. Riluzole in patients with hereditary cerebellar ataxia: a randomised, double-blind, placebo-controlled trial. Lancet Neurol. 14:985991. (2015) 3. Ristori G., Romano S., Visconti A., Cannoni S., Spadaro M., Frontali M., Pontieri F.E., Vanacore N., Salvetti M. Riluzole in cerebellar ataxia: A randomized, double-blind, placebo-controlled pilot trial. Neurology 74:839-845. (2010) 4. Feil K., Claaben J., Bardins S., Teufel J., Krafczyk S, Schenider E, Schniepp R., Jahn K., Kalla R., Strupp M. Effect of chlorzoxazone in patients with downbeat nystagmus: a pilot trial. Neurology. 81(13):1152-8 (2013) 5. Walter J.T., AlviĂąa K., Womack M.D., Chevez C., Khodakhah K. Decreases in the precision of Purkinje cell pacemaking cause cerebellar dysfunction and ataxia. Nat Neurosci. 9:389-397. (2006) 6. AlviĂąa K., Khodakhah K. KCa channels as

Scientia therapeutic targets in episodic ataxia type-2. J Neurosci 30:7249-7257. (2010) 7. Gao Z., van Beugen B.J., De Zeeuw C.I. Distributed synergistic plasticity and cerebellar learning. Nat. Rev. Neurosci. 13:619-635. (2012) 8. Kasumu A.W, Hougaard C, Rode F, Jacobsen TA, Sabatier JM, Eriksen BL, Strøbæk D, Liang X, Belmeguenai A., Hosy E., Bengtsson F., Pedroarena C.M., Piochon C., Teuling E., He Q., Ohtsuki G., De Jeu M.T., Elgersma Y., De Zeeuw C.I., Jörntell H., Hansel C. Intrinsic plasticity complements long-term potentiation in parallel fiber input gain control in cerebellar Purkinje cells. J Neurosci 30:13630-13643. (2010) 9. Bond C.T., Herson P.S., Strassmaier T., Hammond R., Stackman R., Maylie J., Adelman J.P. Small conductance Ca2+-activated K+ channel knock-out mice reveal the identity of calciumdependent afterhyperpolarization currents. J Neurosci 24(23):5301-6. (2004) 10. Hosy E., Piochon C., Teuling E., Rinaldo L., Hansel C. SK2 channel expression and function in cerebellar Purkinje cells. J Physiol 589.14:34333440. (2011) 11. Grasselli G., He Q., Wan V., Adelman J.P., Ohtsuki G., Hansel C. Activity-dependent plasticity of spike pauses in cerebellar Purkinje cells. Cell reports 12(11):2546-2553. (2016) Author Biography Lindsey is a fourth year majoring in biology and neuroscience at the University of Chicago. She hopes to become a pharmaceutical scientist studying neuropharmacology, and she hopes to develop treatments in the future for neurodegenerative diseases such as Parkinson's and Alzheimer's.

Winter 2018

Immune Checkpoint Protein Expression in Peripheral Blood Mononuclear Cells Treated with Conditioned Media from Head and Neck and Lung Cancer Cells In Vitro

Logan Leak1, Lechuang Chen2, David Ye3, Ge Jin2

1The

University of Chicago, 2 Department of Biological Sciences, Case Western University of Dental Medicine, 3Solon High School

Abstract With recent breakthroughs in the field of immunotherapy, elucidating the complex cancer signaling pathways that are used to evade the immune system has become more important than ever before. Cancer cells inhibit an inflammatory response in the immune system, thus preventing T cells from detecting and eliminating the tumor cells. This study examined the immunological profile of peripheral blood mononuclear cells (PBMCs) isolated from the blood of healthy donors. The PBMCs were treated with conditioned media (CM) from four head and neck cancer (HNC) cell lines, with CM from two lung cancer cell lines, or with lipopolysaccharide (LPS), a cell wall component of Gram-negative bacteria that stimulates a control inflammatory immunological response. Control PBMCs received no treatment. CM was collected from cell lines cultured for one week. The PBMCs were given appropriate treatment for 72 hours or no treatment for the control PBMCs. The cells were then removed for total RNA isolation, reverse transcription, and real-time quantitative polymerase chain reaction (PCR) to measure gene expression using specific primers. Expression of inflammatory cytokines Interleukin-1β (IL-1β), IL-4, IL-10, Programmed Cell Death Protein 1 (PD-1), PD-L1, PD-L2, Cytotoxic T-Lymphocyte-Associated Protein 4 (CTLA-4), Lymphocyte-Activation Gene 3 (LAG-3), and T-Cell Immunoglobulin and Mucin-Domain Containing-3 (TIM-3) were assessed. The GAPDH gene served as an endogenous control for gene expression levels. Our data show overexpression of PD-1 and CTLA-4 in HNC CM-treated T cells and LAG-3 and CTLA-4 in lung cancer-treated T cells, implicating these proteins as potential immunotherapeutic targets for these cancers. In future studies, further investigations of cytokine expression in PBMC monocytic cells treated with CM from HNC, lung cancer, and other cancer cells will be conducted to better understand the relationship between tumor cells and the immune system and to develop immunotherapeutic strategies to target cancer. Introduction Cancer is one of the leading causes of morbidity and mortality in the world [1], yet cancer therapies have narrowly focused on using chemical and physical means to eliminate tumors. Recent developments in research on the relationship between cancer and the immune system have

greatly expanded the possibilities for cancer treatment by harnessing the body’s innate ability to eliminate foreign entities. [2]. This approach is known as immunotherapy, and it specifically entails the utilization of the body’s innate and humoral immune responses to distinguish and eliminate cancer cells from the body [3]. Medications to

Scientia treat prostate cancer and melanoma have been successfully developed by targeting cell surface markers Cytotoxic T-Lymphocyte-Associated Protein 4 (CTLA-4) and Programmed Cell Death Protein 1 (PD-1), respectively [4]. By inhibiting these proteins on the surface of cancer cells, the medication permits the immune system to recognize the cancer cells as non-self, allowing them to attack and eliminate the tumor. Such breakthroughs have created optimism about the strategy’s potential ability to treat other forms of cancer. The incidence of cancer is not evenly distributed in the population, with some groups experiencing a disproportionately large number of cases. Acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), is a prevalent illness in today’s society that is related to cancer. Since the HIV virus attacks the immune system by infecting T cells, the body’s immunological response to cancer is greatly diminished, leading to higher incidence of certain AIDS-defining cancers in HIV-infected individuals [5]; however, with the efficacy of antiretroviral therapy in reducing the viral load of HIV-infected individuals, the incidence of these cancers has steadily declined [6]. Certain non-AIDS defining cancers, such as lung cancer, liver cancer, anal cancer, head and neck cancer, and Hogdkin’s lymphoma, which are not directly related to the presence of the virus yet still impact HIV-infected individuals more than those without the virus, have increased in incidence in the HIVinfected population [7]. As a result, the application of immunotherapy to these non-AIDS-defining cancers is more important than ever in the fight to alleviate the additional burden that HIV-infected individuals face due to their increased risk of developing these cancers. This study seeks to better understand the effect of the presence of two non-AIDS defining cancers, namely lung cancer and head and neck cancer (HNC), on the expression of certain immune checkpoint inhibitor proteins in human T cells. Even outside of HIV-infected populations, these two cancers are extremely prevalent, with lung cancer accounting for over 13% of all cancer cases annually [1] and HNC accounting for about 4% of all cancer cases annually [8].

Materials and Methods CM from HNC and lung cancer cell lines was used to treat PBMCs, which were then measured for changes in expression levels of immune checkpoint inhibitor proteins. Expression levels were quantified using real-time polymerase chain reaction (PCR) and flow cytometry compared to treatment with lipopolysaccharide (LPS), a component of bacterial cell walls known to stimulate a control inflammatory response in human macrophage cells [9]. Experimental data suggested selective suppression of specific inflammatory cytokines, and laid the foundation for future targeting of these sites for the purposes of developing immunotherapeutic strategies to combat lung cancer and head and neck cancer. One lung cancer cell line was used: NCI-H1299 (carcinoma) and four head and neck cancer cell lines were used: SCC9 (tongue squamous cell carcinoma), HSC3 (tongue squamous cell carcinoma), TR146 (neck squamous cell carcinoma), and FaDu (hypopharyngeal carcinoma). These cells were plated on 10 cm circular plates and cultured for one week. Fresh media was added to the cancer cell lines, and they were left to grow for one week. During this period, the cells release various signaling proteins secreted by the endoplasmic reticulum into the media, which are intended to stimulate responses in other cells. The fresh media plus the secretory proteins is known as CM [10]. PBMCs were simultaneously isolated from healthy donors and divided into six-well plates for each of the treatment groups. On the same day that the CM was harvested, PBMCs were plated in all six wells of seven six-well plates. PBMCs were isolated from blood samples of healthy donors at Cleveland Clinic Foundation using the Ficoll differential centrifugation technique. Two milliliters of one CM sample were added to every well of one six-well plate, and this was repeated for the remaining four CM samples on four of the other plates. Two plates were given Roswell Park Memorial Institute (RPMI) medium in place of CM. All plates were then placed in the incubator for four days. Then, 20 μL of 20 ng/mL LPS was added to every well of one of the plates that received RPMI. The other plate with RPMI was given no treatment. The plates were left in the incubator for an additional three days. The

Winter 2018 reason for the difference in time for CM and LPS treatment arises from the fact that the response of the cells to LPS occurs over a shorter time frame [9]. Cells were then removed from the plate and isolated either for quantitative real-time PCR or flow cytometry. The Roche High Pure RNA Isolation kit was used to isolate total RNA from the cells that were intended to be analyzed with a real-time PCR. RNA concentrations were measured by a NanoDrop spectrometer. The ThermoFisher High-Capacity cDNA Reverse Transcription Kit was used to conduct 20 μL reactions in a thermal cycler. Following reverse transcription, the SYBER® Green kit was used to run real-time PCR reactions on a 96-well plate (the total liquid volume of each reaction was 20 μL) in the ThermoFisher StepOnePlus Real-Time PCR System. Three trials were run for each experiment, and results were displayed in bar graph format. Glyceraldehyde-3Phosphate Dehydrogenase (GAPDH) was used as an endogenous control for all reactions. Cells intended for flow cytometry were washed with PBS to remove additional media that still remained following removal from the well plate. Each treatment had one control sample of PBMCs cell receiving no antibodies, one control of cells with no antibody to detect nonspecific antibody binding (isotype control), and additional tubes that received treatment with 3 μL of each antibody. The cells were incubated with the stain on ice for 30 minutes and then measured using flow cytometry. Gating for each antibody was set up using the control cells and then applied to the treatments. Relative percentages of cells treated with CM or LPS testing positive for each antibody were then compared to those of the control. Results Head and neck cancer cells (SCC9, HSC3, TR146, and FaDu) were tested for relative expression levels of PD-1, PD-L1, LAG-3, PD-L2, CTLA-4, and TIM-3 using quantitative real-time PCR. The results are expressed in bar graphs (Fig. 1 and Fig. 2) with the heights of the bars representing relative expression levels and the error bars representing the standard error of the three measurements. The head and neck cancer cells were also analyzed using flow cytometry for another

Figure 1. Relative expression levels of PD-1, PD-L1, and LAG-3 in PBMCs treated with SCC9 CM, HSC3 CM, TR146 CM, FaDu CM, and RPMI (control)

Figure 2. Relative expression levels of PD-L2, CTLA-4, and TIM-3 in PBMCs treated with SCC9 CM, HSC3 CM, TR146 CM, FaDu CM, and RPMI (control)

Figure 3. CD3/PD-1 expression levels in PBMCs treated with SCC9 CM, HSC CM, TR146 CM, FaDu CM, or control treatment

measure of expression levels of inflammatory cytokines on the cell surface. Expression of CD3 was also detected to allow for the gating of T cells only. This determined the proportion of cells that tested positive for the cytokines of interest and negative or positive for fluorescein isothiocyanate (FITC). The cytokines of interest are PD-1 (Fig. 3), LAG-3 (Fig. 4), and PD-L1 (Fig. 5). For Fig. 5, PD-L1 expression levels only are shown without comparison against FITC. The proportion of cells

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Figure 4. CD3/LAG-3 expression levels in PBMCs treated with SCC9 CM, HSC CM, TR146 CM, FaDu CM, or control treatment

Figure 7. CD3/TAM expression levels in PBMCs treated with NCI-H1299 CM, LPS, or RPMI (control)

Figure 8. CD3/PD-1 expression levels in PBMCs treated with NCI-H1299 CM, LPS, or RPMI (control) Figure 5. CD3/PD-L1 expression levels in PBMCs treated with SCC9 CM, HSC CM, TR146 CM, FaDu CM, or control treatment

Figure 6. Relative expression levels of IL-4, IL-10, PD-1, PD-L1, LAG-3, CTLA-4 in PBMCs treated with H1299 CM, LPS, and RPMI (control)

Figure 9. CD3/PD-L1 expression levels in PBMCs treated with NCI-H1299 CM, LPS, or RPMI (control)

that test positive for PD-L1 and test positive or negative for FITC is that same as the proportion of cells that test positive for PD-L1, so the FITC measurement is superfluous. PBMCs treated with CM from lung cancer cell line NCI-H1299 were analyzed similarly to the treatments with CM from the HNC cells. Fig. 6

shows quantitative real-time PCR results for expression levels of IL-4, IL-10, PD-1, PD-L1, LAG3, and CTLA-4 in PBMCs treated with H1299 CM, LPS, or RPMI (no treatment, control). The same cells were also analyzed using flow cytometry. The results for expression levels of TAM, PD-1, PD-L1, and LAG-3 are shown in Fig.

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Figure 10. CD3/LAG-3 expression levels in PBMCs treated with NCI-H1299 CM, LPS, or RPMI (control)

Table 1. Summary of relative expression levels of cytokines in PBMCs measured by real-time quantitative PCR for all treatments. (“Up” = upregulated compared to control, “Down” = down-regulated compared to control, “NS” = no significant change, and “-” = no data available)

Table 2. Summary of relative expression levels of cytokines in PBMCs measured by flow cytometry for all treatments. (“Up” = upregulated compared to control, “Down” = down-regulated compared to control, “NS” = no significant change, and “-” = no data available)

7, Fig. 8, Fig. 9, and Fig. 10, respectively. For Fig. 9, PD-L1 expression levels only are shown without comparison against FITC. The proportion of cells that test positive for PD-L1 and test positive or negative for FITC is the same as the proportion of cells that test positive for PD-L1. Therefore, the FITC measurement is unnecessary. Table 1 summarizes all of the results and combinations of the real-time PCR experiments, and Table 2 summarizes the results and combinations of the flow cytometry experiments. Discussion These results indicate variations in expression of inflammatory cytokines in PBMCs that have been treated with CM from HNC cells and lung cancer cells when compared with a control that

has been given no treatment and a control that has been stimulated with LPS. It is important to acknowledge that there are some combinations of cytokines and CM that were not tested due to time and resource constraints. This leaves space for further studies to confirm the trends uncovered by our work and to expand the immunological profile examined for each combination. Potential targets for cancer therapies are cytokines with expression levels that are higher than a control level of expression. For the HNC cell lines (SCC9, HSC3, TR146, Fadu, and H1299), the quantitative real-time PCR results indicate consistent overexpression of PD-1 and CTLA-4. The results of the flow cytometry show that most of the treatment groups resulted in higher expression levels of the cytokines than in the control. Most of the protein expression levels tested using flow cytometry showed higher expression levels than the control. This data can be misleading, however, for it only shows the presence of the proteins and not the activity. As a result, the recommendations in this study are made based upon the differential expression levels seen in the real-time PCR results. For the lung cancer cell line (H1299), the realtime PCR indicates that LAG-3 and CTLA-4 are overexpressed in the PBMCs, suggesting that this protein could be a possible target for lung cancer immunotherapies. Further research would need to be conducted to validate the flow cytometry results and examine the mechanisms by which the constitutive presence of the immune checkpoint proteins on the cell surface is possible without activation. Conclusion The high prevalence of HIV/AIDS, coupled with its intimate relationship with certain malignancies, makes HIV-infected individuals some of the most vulnerable to cancer. Antiretroviral therapies have gone a long way to lower viral loads for those infected, leading to a decrease in certain AIDSdefining cancers. The same, however, cannot be said for other AIDS-defining cancers such as head and neck cancer and lung cancer that have seen an increase in incidence since the dawn of the antiretroviral age. Assessing levels of gene expression allows for suggestions of certain immunotherapeutic targets that can be explored

Scientia for implementation in future treatments for head and neck and lung cancer. Specifically, PD-1 and CTLA-4 are suggested as possible targets for head and neck cancer treatments due to their overexpression when treated with CM from HNC cells compared to expression levels in control PBMCs. The same logic applies to our suggestion of LAG-3 and CTLA-4 as possible targets for therapeutic approaches for combatting lung cancer. Future studies are needed to expand the immunological profile considered and to confirm the trends delineated in this study so that research on potentially life-saving anti-cancer immunotherapies can commence. References 1. Siegel, RL, KD Miller, A Jemal. “Cancer statistics, 2016.” CA Cancer J Clin. 66:7-30. (2016) 2. Sharma, P and JP Allison. “Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential” Cell. 161(2):205-14. (2015) 3. Topalian, SL, GJ Weiner, and DM Pardoll. “Cancer immunotherapy comes of age.” J Clin Oncol. 29(36):4828-36. (2011). 4. Sharma, P, K Wagner, JD Wolchok, and JP Allison. “Novel cancer immunotherapy agents with survival benefit: recent successes and next steps.” Nat Rev Cancer 11(11): 805-812. (2011) 5. Engels, EA, RJ Biggar, HI Hall, H Cross, A Crutchfield, JL Finch, R Grigg, T Hylton, KS Pawlish, TS McNeel, and JJ Geodert. “Cancer risk in people infected with human immunodeficiency virus in the United States.” Int J Cancer 123(1):18794. (2008) 6. Herida, M, M Mary-Krause, R Kaphan, J Cadranel, I Poizot-Martin, C Rabaud, N Plaisance, H Tissot-Dupont, F Boue, J Lang, D Costagliola. “Incidence of non-AIDS-defining cancers ebfore and during the highly active antiretroviral therapy era in a cohort of human immunodeficiency virusinfected patients.” J Clin Oncol. 15;21(18):344753. (2003) 7. Mitsuyasu, RT. “Non-AIDS-defining malignancies in HIV.” Top HIV Med. 16(4):117-21. (2008) 8. Heroiu, A, CE Danciu, and CR Popescu. “Multiple cancers of the head and neck.” Maedica (Buchar) 8(1):80-85. (2013). 9. Ramsey, SA, SL Klemm, DE Zak, KA

Kennedy, V Thorsson, B Li, M Gilchrist, ES Gold, CD Johnson, V Litvak, G Navarro, JC Roach, CM Rosenberger, AG Rust, N yudkovsky, A Aderem, and I Shmulevich. “Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.” PLoS Comput Biol. 4(3): e1000021. (2008). 10. Dowling, P and M Clynes. “Conditioned media from cell lines: a complementary model to clinical specimesn for the discovery of diseasespecific biomarkers.” Proteomics 11(4):794-804. (2011). Author Biography Logan Leak is a second-year student at the University of Chicago majoring in biological sciences with a concentration in cancer biology. He plans on attending graduate school to earn his PhD in bioengineering and conduct cancer research in an industrial setting.

Winter 2018

Low-Cost Gravity Driven Filtration System Designed Using Iron Oxide NanoparticleLoaded PU Foam for Arsenic Removal from Polluted Groundwater Sources

Arundhati Pillai1, Mohammad Amin Faghihi Zarandi1, Krishna M. Pillai1, Nidal H. Abu-Zahra2 1Laboratory

for Flow & Transport Studies in Porous Media, Mechanical Engineering Department, University of Wisconsin-Milwaukee, 2Material Science Department, University of Wisconsin-Milwaukee

Abstract Arsenic contamination of water sources is a problem that affects numerous (especially developing) countries throughout the world. Exposure to exorbitantly high concentrations â&#x2C6;&#x2019; up to 400 parts per billion (ppb) â&#x2C6;&#x2019; of arsenic in water sources leads to numerous health complications, including the development of respiratory, neurological, and cancerous diseases. This study aimed to develop an innovative, low-cost, and gravity driven filtration system using a novel iron oxide nanoparticle-loaded polyurethane (PU) foam with which people in developing countries can have easy access to an effective, affordable and accessible filtration system. The new iron oxide nanoparticle-loaded PU foam was successfully synthesized and its effectiveness was tested with a filtration system consisting of vertical PVC tubing inserted with 10 and 20 cm of PU foam. Samples of arsenic-contaminated water with known concentrations of 100 and 200 ppb were run through each of the systems either once or five times. The system with 20 cm of PU foam and 5 runs successfully filtered around 50-70% of the arsenic from the 100 and 200 ppm samples. The filtration process was quite fast (and hence practical) with each run completed between 5 to 10 minutes. Introduction Arsenic contamination of water is a problem that impacts many parts of the world. Ranging from nations such as the United States and Canada, to developing countries such as Bangladesh, India, and China, arsenic contamination is widespread and has been proven to be extremely injurious to human health. The International Agency for Research on Cancer (IARC) and the U.S. Environmental Protection Agency have both classified inorganic arsenic as a known human carcinogen [1]. This carcinogenic compound contaminates water sources across the world, in contrast to the less harmful organic arsenic compounds that are commonly found in seafood [2]. The bodies of water most affected by arsenic

contamination are groundwater sources. Although the introduction of arsenic in groundwater can occur naturally due to its presence in the surrounding bedrock, especially in areas of West Bengal and China, numerous human activities exacerbate this arsenic contamination. These include industrial activities such as mining, smelting, coal-fired power plants, as well as the environmental effects of various agricultural pesticides used for wood preservation [3]. Numerous options for arsenic filtration are available, including reverse osmosis and anionic exchange systems [5]. However, there is a newer type of filtration material that has potential for usage in filtration systems: polyurethane (PU) foam.

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Figure 1a. After cutting the synthesized IONP-PU foam down to the circumference of the PVC tubing, 20 cm of the foam was inserted into the tubing, as seen in this image. Figure 1b. The system with adhesive used to seal the circumference of the specific end of the PVC tubing with the synthesized IONP-PU foam inserted into it. This decrease in the side flow due to leakage allows for more thorough arsenic removal from water as water particles spend more time within the porous filtration system.

Properties such as permeability, porosity, low costs, recyclability and easy room-temperature fabrication have made this material very attractive as a filter [6]. To date, however, no research has been conducted on the application of this novel synthetic foam for arsenic removal. Iron-oxide is a popular compound for arsenic filtration and is incorporated into many commercial arsenic-filtration products. Prior research has been successful in synthesizing an open cell PU foam that is embedded with iron-oxide nanoparticles (IONPs) [9]. Therefore, these specialized PU foams have great potential to have a significant impact in the future of water filtration. The purpose of this study was first to synthesize a nanocomposite PU foam embedded with iron oxide nanoparticles by incorporating these adsorbent particles within the foam media. After creating such a composite, a low-cost and gravity-driven filtration

system with this iron oxide nanoparticle infused polyurethane foam was developed to not only test the effectiveness of the foam in filtering arsenic present in contaminated water, but also to create an alternative option for filtration that is less expensive, more sustainable, and practical in third-world rural areas with minimal electricity. By developing such a preliminary product, this study hopes to present another option for adsorptive filtration systems that can successfully extract harmful arsenic from water. Methodology Synthesis of Polyurethane Foam with Iron-Oxide In the standard process, the two main components that create the polyurethane foam are 2,4-toluene diisocyanate (TDI) and polypropylene glycol (PPG). Within this study, PPG was used to react with the TDI and allow for the incorporation of the iron oxide nanoparticles into the polyurethane foam synthesis process and ultimately to functionalize the final polyurethane foam product. An experimental setup was established to thoroughly mix and allow for the PPG and TDI chemial molecules to completely react with one another. After the reaction was sustained, the iron oxide nanoparticles in powder form and a few drops of polysiloxane surfactant were added to the PPGTDI mixture. After the mixing process, the glass with the incorporated components was set aside for 24 hours to form the final structure of iron-oxide nanoparticle loaded polyurethane (IONP-PU) foam.

Creating the Gravity-Driven Low-Cost Filtration System For the development of this product, the synthesized IONP-PU foam was compressed into the bottom of polyvinyl chloride (PVC) tubing. For the first initial model, a 10 cm-long block of the synthesized IONP-PU foam was lodged in the PVC tubing. For the second model, 20 cm of synthesized IONP-PU foam was placed in the PVC tubing (Fig. 1a). To avoid lateral flow through the filtration system, a non-toxic polyurethane-based adhesive was used to seal the circumference of the IONPPU foam pieces inserted into the PVC tubing for both models (Fig. 1b). In addition, to allow for the greatest gravitational force to act upon the system, the flexible PVC tubing was zip-tied to a vertical metal ruler (Fig. 2). The final system functioned in a relatively

Winter 2018 Figure 2. The final layout of the proposed gravity-based low-cost arsenic filtration system, attached to a vertical metal ruler to allow for maximum gravitational force to act upon the passing liquid. The water, poured at the top to create a certain column above the sponge, was collected at the bottom after seepage.

straightforward manner. A certain volume of arsenicpolluted water, when poured into the top of the vertical tube, created a water column that used the hydrostatic pressure at its bottom to push water through the pores of IONP-PU foam. The arsenic-laden liquid came in contact with iron-oxide nanoparticles embedded on the walls of the porous medium and thus was adsorbed, filtering the polluted water. It was preferable for the foam to be this porous medium since the circuitous path of water particles through the interconnected pores forced repeated contact between the arsenicladen water and the ironoxide nanoparticles of the pore walls, thus improving the chances of arsenic removal. The high specific area (i.e., total pore-wall area divided by the outer volume of the foam) of the foam made this forced contact (and hence filtration) quite thorough and efficient.

Testing the Filtration of Arsenic-Laden Water by the Proposed System In this study, concentrations of 100 and 200 ppb of arsenic in water samples were tested through the filtration system. This allowed for the analysis of the effectiveness of the synthesized IONP-PU foam and the gravity-driven low-cost systemâ&#x20AC;&#x2122;s ability to filter increasingly dangerous concentrations of arsenic present in many rural Bangladeshi groundwater sources.

Figure 3. Example of a calibration curve. (There are no units for absorbance as it is a ratio.) Samples were created with concentrations of 20, 50, 100, and 300 ppb. These were run through the AAS and were used as the basis to create the calibration curve for each set of data. Based on this curve, the known concentration of the control sample is confirmed and the unknown concentration of the sample run through the filtration system is determined.

Approximately 50 mL of the arsenic water samples were separated before filtration from the testing samples to act as the control. For both the 10 and 20 cm systems (corresponding to the lengths of the synthesized IONP-PU foam plugs lodged in the tube), three separate trials of the samples were run through the system for the following two cases: (a) one batch of three samples filtering through the system only once, and (b) the other batch of three samples filtering through the system five times. After all the samples were run, the collected filtered samples, along with the aforementioned controls, were tested for the percentage change in arsenic concentrations using the Atomic Absorption System (AAS). Three absorbance values were taken from each sample and respective controlâ&#x20AC;&#x2122;s readings, then averaged, and then converted into respective concentration values based on the calibration curve (Fig. 3). Results and Discussions For the 10 cm model of the filtration system, three trials were conducted to analyze the effect of one run on the concentration of arsenic in the water samples. Ultimately, across the three trials conducted, there was an average of a 13-20% decrease in arsenic concentration when running the samples of 100 and 200 ppb arsenic just once through the filtration model containing 10 cm of the IONP-PU foam (Fig. 4(a-c)). Next, the second batch of three trials of arsenic

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Figure 4(a-c): First (a), second (b), and third (c) round of the trails for running the 100 and 200 ppb arsenic water samples through the 10 cm filtration system once. In (a), there was only around an 8-11% decrease in the overall arsenic concentrations. (Note that in 8-11%, the first value of 8% stands for arsenic concentration reduction achieved for the 100 ppb solution while the second value of 11% stands for arsenic concentration reduction achieved for the 200 ppb solution.) In (b), an 18-24% decrease was observed in the overall arsenic concentrations. Finally, in (c), an 11-21% decrease was observed in the overall arsenic concentrations. Note that 1 Âľg/L = 1 ppb.

Figure 5. Results of running the 100 and 200 ppb arsenic water samples through the 10 cm filtration system five times: (a,b) first trial, (c,d) second trial, (e,f) third trial. In (a,b), 8-38% removal was achieved; in (c,d), 10-15% removal was achieved; in (e,f), 8-18% removal of arsenic was achieved.

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Figure 6(a-c). The first, second, and third trials for running the 100 and 200 ppb arsenic water samples through the 20 cm filtration system once. In (a), 47-51% of arsenic was filtered; in (b), 49-50% of the arsenic was filtered; in (c), 50-51% of arsenic was filtered from the samples.

Figure 7. Results of running the 100 and 200 ppb arsenic water samples through the 20 cm filtration system five times: (a,b) first trial, (c,d) second trial, (e,f) third trial. In (a,b), 59-64% of the arsenic was filtered from the 100 ppb and 200 ppb samples of arsenic-tainted water that were run through the system. In (c,d), 64-69% of the arsenic was removed from the water samples. Finally, in (e,f), an impressive 61-73% of the arsenic was filtered from the water samples.

Scientia water samples was run through the 10 cm filtration system. The five runs of filtration, repeated one after another, achieved very similar percentages of arsenic removal as with just one run (Fig. 5(a-i)). With the filtration system containing only 10 cm of the synthesized IONP-PU foam, there were no drastic improvements in the filtering capabilities after five repetitions. Therefore, a filtration system with 20 cm of synthesized IONP-PU foam was tested with the arsenic water samples to determine whether an increased length of the foam plug increases filtration capabilities. For the first three trials conducted using the 20 cm filtration system for just one filtration run, an average of 48-50% of arsenic was filtered from the water samples (Fig. 6(a-c)). We note that by merely doubling the length of the synthesized IONP-PU foam plug, the arsenic removal capabilities for just one round of filtration have increased by three to four folds compared to the 10 cm case. Finally, for the second three trials conducted with the 20 cm filtration system for five runs or cycles of filtration, the highest percentage of arsenic removal within this study was recorded (Fig. 7(a-f)). Comparing the 20 cm and 10 cm systems under five runs, we see a tremendous improvement in performance again. For the 100 ppb samples, the arsenic removal percentages increased by around staggering seven, six and seven folds, while for the 200 ppb samples, the increase is more modest at around one-and-half, five and four folds. Out of the two primary filtration systems created (i.e., 10 cm and 20 cm), the trials conducted with the 20 cm system were most successful. The time required for one sample to be completely filtered (see Table 1) was found to be much lower than in a filtration study that required approximately 9 days for the arsenic to be completely removed from a vertical column [9]. After 20 runs, the filtration time did double, possibly due to swelling or saturation of the foam. Even so, it amounted to less than 10 minutes. This implies a practical utility of the proposed system. Statistical analysis confirmed that the difference in the arsenic concentrations before and after filtration is statistically significant. A paired two-sample T-test (Excel) was conducted

Table 1. Total filtration time for one run of the 20 cm system

and a significance level (Îą) of 0.05 was used to compare the P values calculated (Table 2). All of the differences that resulted in each trial of the filtration system were deemed statistically significant, with the sole exception being the trials conducted with arsenic samples containing 200 ppb run five times through the filtration model with 10 cm of PU foam. This was due to an outlier in the data, and it further confirmed the less significant outcome that resulted from using the model with only 10 cm of PU foam. The filtration model containing 20 cm of PU foam, on the other hand, performed more effectively and produced P values that showed more significant statistical differences in the arsenic concentration of the samples before and after filtration.

Table 2. Paired Two-Sample T-test Statistical Analysis of Efficacy of 10 and 20 cm PU Foam Models Note: The P(T<=t) one-tail results were calculated using the Excel algorithm for the PU foam model containing 10 and 20 cm of the PU foam. (Îą=0.05)

Discussion Many countries suffer from arsenic in their groundwater, which leads to severe health issues if the polluted water is used without filtration. Here we demonstrate that the nanocomposite polyurethane foam, with the embedded ironoxide nanoparticles, could be used to develop a simple, low-cost, gravity-driven filtration device that has potential to effectively remove (or at least significantly reduce) arsenic from polluted water. By testing water samples with 100 and 200 ppb arsenic, it was shown that the 20 cm PU foam plug, compared to the 10 cm plug, was more successful at removing arsenic from water. With only one run, it could effectively remove close to half the arsenic present within the water sample. With just five runs in 28 minutes, up to 70% of the arsenic was filtered. In addition, the models performed better for higher (200 ppb) concentrations of arsenic, thus providing a viable filtration mechanism for nations affected by higher arsenic concentrations. Time taken for one run increased from around 4.7 minutes to around 8.2 minutes at the end of 20 runs. This performance was much better than reported in a previous published study where it took several days to purify similarly

Winter 2018 polluted water [8]. Although there are other arsenic-filtration technologies that are performing with filtration capabilities as high as 95%, electricity is required for said machines [6]. Therefore, the integration of arsenic filtration technologies within third world countries where electricity is not a common resource has been relatively unsuccessful. With the work conducted within this study, a new type of filtration material with significant filtration capabilities is introduced in a system that has potential for smoother integration into many third world countries and their respective societies. If successful, this innovative low-cost technology has the potential to have a significant impact on the well-being of numerous populations in developing countries throughout the globe and will ultimately help those individuals live longer and healthier lives. References 1. Gehle, Kim. "Arsenic Toxicity." Agency for Toxic Substances and Disease Registry, Agency for Toxic Substances and Disease Registry, 15 Jan. 2010 www.atsdr.cdc.gov/csem/csem.asp?csem=1&po=0. Accessed 27 Dec. 2016. 2. "Arsenic." World Health Organization, World Health Organization, June 2016, www.who.int/ mediacentre/factsheets/fs372/en/. Accessed 27 Dec. 2016. 3. Garelick, H. et al. Arsenic pollution sources. Rev Environ Contam Toxico. 197, 17-60. www.ncbi.nlm. nih.gov/pubmed/18982996 (2008) 4. Flanagan, S. V. et al. Arsenic in Tube Well Water in Bangladesh: Health and Economic Impacts and Implications for Arsenic Mitigation. Bull. World Health Organ. 90, 839-846. www.who.int/bulletin/ online_first/11-101253.pdf?ua=1. (2012) 5. Arsenic concentrations (Bangladesh). Chronic Arsenic Poisoning: History, Study and Remediation, u s e r s . p hy s i c s . h a r v a rd .e d u /~w i l s o n /a r s e n i c / countries/bangladesh/bangladesh2-small.jpg. Accessed 28 Dec. 2016. 6. "Drinking Water Program Fact Sheet: Recommendations for Arsenic Removal from Private Drinking Water Wells in Oregon." Oregon Public Health. Oregon Health Authority, public.health. oregon.gov/HealthyEnvironments/DrinkingWater/ SourceWater/ Documents/gw/arsenicremoval.pdf. Accessed 28 Dec. 2016. 7. Cao, X. et al. Polyurethane/Clay Nanocomposites

Foams: Processing, Structure and Properties. Polymer. https://doi.org/10.1016/j.polymer.2004.11.028. 8. Jain, P., and T. Pradeep. "Potential of Silver Nanoparticle-Coated Polyurethane Foam as an Antibacterial Water Filter." Biotechnology and Bioengineering, vol. 90, no. 1, 5 Apr. 2005, pp. 5963. National Center for Biotechnology Information, w w w. n c b i . n l m . n i h . g o v/p u b m e d / 15 7 2 3 3 2 5 . Accessed 28 Dec. 2016. 9. Katsoyiannis, Ioannis A., and Anastasios I. Zouboulis. "Removal of Arsenic from Contaminated Water Sources by Sorption onto Iron-OxideCoated Polymeric Materials." Water Research, vol. 36, no. 20, Dec. 2002, pp. 5141-55. ScienceDirect, w w w. s c i e n c e d i re c t.co m /s c i e n c e /a r ti c l e /p i i / S0043135402002361. Accessed 28 Dec. 2016. 10. Hussein, F. B. "Synthesis and Performance Analysis of Polyurethane Foam Nanocomposite for Arsenic Removal from Drinking Water" (2016). Theses and Dissertations. 1154. http://dc.uwm.edu/ etd/1154 11. Gunashekar, S. "A Study on the Synthesis Structure - Property - Performance Relationship of Bulk Functionalized Polyurethane Foams for Water Filtration Applications" (2015). Theses and Dissertations. 874. http://dc.uwm.edu/etd/874 12. "Dow Polyurethanes - Surfactants Role in Foam Formulations." Dow, The Dow Chemical Company, 3 Dec. 2014, dowac.custhelp.com/app/ answers/detail/a_id/5709/~/dow-polyurethanes--surfactants -role-in-foam-formulations. Accessed 30 Dec. 2016. 13. "Bangladesh: 20 Million Drink ArsenicLaced Water." Human Rights Watch, 6 Apr. 2016, www.hrw.org/news/2016/04/06/ bangladesh-20-million-drink-arsenic-laced-water. Author Biography Arundhati is a first-year student at the University of Chicago majoring in biological chemistry. She hopes to conduct biochemical research in the future.

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Effects of Fragile X Syndrome on the Conductance of Neuronal Mitochondrial Membrane Channels

Jorge Salcedo Sifuentes1,3, Sana Sohail1,3, Elizabeth Jonas2,3 1The

University of Chicago, 2 Jonas Lab, Department of Internal Medicine, Yale University School of Medicine, 3 Jonas Lab, Marine Biological Laboratory

Abstract Fragile X Syndrome (FXS) is the most common cause of inherited intellectual disability. It is characterized by the absence of Fragile X Mental Retardation protein (FMRP), which is known to regulate the expression of neuronal proteins. We hypothesize that some of the pathological phenotypes in neurons of patients with FXS are related to the role of FMRP in regulating the closing of an inner mitochondrial membrane leak channel in neurons and that the absence of FMRP will cause a greater degree of leak channel opening and thus greater membrane conductance. To test this, we have performed patch clamp recordings to compare mitochondrial membrane leakage in FMRP-knockout mice with that of control mice. We also performed an experiment in which we recorded FMRP-knockout mitochondrial membrane conductance, added purified FMRP protein, and then continued recording from the same patch to determine whether or not the protein closed the leak and lowered membrane conductance. We have found that Fragile X mitochondria (FX mitochondria) have greater peak membrane conductance than controls, that FX mitochondria have a greater peak slope conductance than controls, and that addition of exogenous FMRP to FMRP-knockouts lowers membrane conductance. Evaluating the role of this leak channel in FXS will allow for a better understanding of how drugs known to close it can be used to suppress the disorder at an early enough developmental stage to prevent its symptoms from developing.

Funding provided by the University of Chicago Jeff Metcalf Research Fellowship and a grant from the NIH/NINDS.

Introduction Nitrate (NO3 -), an ionic species, is widely found in In FXS, the series of CGG trinucleotide repeats found within the FMR1 gene of all humans is expanded, occurring over 200 times rather than the normal 5-40. This leads to the formation of tenuous, fragile-looking chromosomal segments for which the disorder is named at the location of the gene on the X chromosome. Furthermore, this expansion silences the FMR1 gene, preventing it from producing the protein it normally encodes,

the Fragile X Mental Retardation Protein (FMRP). In people without FXS, FMRP inhibits protein translation in neurons by binding to mRNA. This is essential to the proper development of dendrites, which are the neuronal components responsible for receiving nerve impulses from other neurons. Without FMRP to curb protein translation during development, neurons form pathologically long, thin, and winding dendrites that are thought to be responsible for the cognitive impairments seen in FXS patients. These include diminished synaptic

Winter 2018 plasticity, which describes the positive development of neuronal synapses, or connections, in response to repeated use, and are representative of learning capacity. FMRP’s role in binding to cytoplasmic RNA has been studied extensively. However, works in the process of being published by the Jonas lab, which directed this project, show that besides localizing to dendrites, FMRP also localizes to mitochondria. Located in the inner mitochondrial membrane is F1FO ATP synthase, commonly known as ATP synthase. It consists of two primary components: the FO region, a membrane-embedded portion that contains the c-subunit, a rotating motor ring embedded in the inner membrane, and the F1 region, an arm that protrudes into the mitochondrial matrix and contains the β subunits to which substrate can bind. Preliminary research from the Jonas lab has previously shown that the anti-apoptotic, or celldeath preventing, protein Bcl-xL binds to the β subunit to cause a conformational change in the F1 region to promote ATP synthesis. They have also shown that FMRP also binds to the β subunits. Thus, we hypothesized that FMRP may also have a role in regulating this leak channel, and that the absence of this mechanism in the neuronal mitochondria of FXS patients is also a source of the phenotypic abnormalities seen in their dendrites as well as the intellectual disabilities that go along with them. Investigating the relationship between FMRP and this leak channel is crucial to forming a more holistic picture of the mechanisms responsible for FXS’s phenotypic manifestations as well as gaining insight into the effects of leak channel opening on dendritic formation and metabolic efficiency, specifically. Such findings will facilitate efforts to find new drug targets to combat FXS in its developmental stages. This is also important for understanding the role of FMRP in regulating the leak channel, which is detrimental to synaptic plasticity even in non-FXS patients, is a cause of apoptosis, and could be at the root of other pathologies. It could also have a physiological function that must be considered as the field moves forward in attempts to develop methods that help close it. Materials and Methods Mitochondria were isolated from the brains of FMR1-/- (FMRP-knockout mice, that is, mice

that produce no FMRP and are representative of FXS) and FVB (control/wildtype) mice. These mitochondria were placed in a bath of recording solution mimicking intracellular ion concentrations. A change in the conformation of mitochondrial membrane channels from the closed to the open state is correlated with an increase in the conductance of the membrane, which can be determined by calculating the ratio of current to difference in potential. We can directly measure this membrane conductance using mitochondrial patch clamping. This technique involves lowering a hollow glass micropipette with a wire running through it onto a section of mitochondrial membrane. By applying suction, the micropipette seals onto the patch of membrane. The voltage is then held at potentials from -100 to +100 mV, allowing the current passing through the channels in that patch to be recorded. In the first experiment, mitochondrial patch clamping was performed on n = 7 control mitochondria and on n = 6 FMRP-knockout mitochondria. In the second experiment, patch clamping was again performed on FMRP-knockout mitochondria, but then 10 μL of tagged, purified recombinant human FMRP were added into the mitochondrial bath while recording. Data analysis for both experiments involved measuring and comparing peak conductance values as well as plotting current versus voltage graphs to compare peak slope conductance values. Results The membranes of FX mitochondria were found to have significantly greater conductance than controls. This indicates greater amounts of ion flux across the membrane, which in turn is evidence of the opening or further opening of a mitochondrial membrane channel through which the ions flow. This flux can be extremely detrimental to the metabolic

Figure 1. Representative patch-clamp recording of control and FX mitochondria, both at a hold of +80 mV. The FX membrane reaches a greater peak conductance than the control, measured as the scalar distance from 0 pA.

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Figure 2. Representative current versus voltage graphs of FX and control mitochondria. The slope conductance, as measured by the slope of the line of best fit, was greater for FX mitochondria.

Figure 3. The average peak slope conductance of all FX mitochondria was significantly greater than that of controls.

Figure 4. Patch-clamp recordings at -100 mV demonstrating the effect of adding purified FMRP to FMRP-knockout mitochondria. When the protein was added between the second and third recordings, from left to right, the large conductance channel appeared to close.

Figure 5. Current versus voltage graphs of an FMRP-knockout mitochondrion before and after addition of FMRP. Slope conductance decreased after the addition of FMRP.

processes that occur in the mitochondria and are responsible for producing cellular energy in the form of ATP. Cellular metabolism requires the production of concentration gradients formed by using energy to pump ions into areas of higher concentrations. If these ions are leaking out of the high concentration areas, then energy is being wasted. Therefore, in Fragile X mitochondria, the absence of FMRP is causing opening or further opening of a conductance channel in the mitochondrial membrane, which is causing the metabolic process to become inefficient. Discussion Mitochondrial dysfunction plays a key role in the pathogenesis of Fragile X Syndrome [1]. The goal of the study was to determine if the absence of FMRP, as in people with Fragile X Syndrome, causes the opening of a mitochondrial membrane channel. Results indicate that it does, which paves the way for better understanding the development of FXS symptoms and thus, also for how they may be prevented. By allowing ions to leak through the inner mitochondrial membrane, the channel dissipates the concentration gradient that was created using cellular energy and is crucial to the production of enough energy to fulfill the neuronâ&#x20AC;&#x2122;s needs. This is supported by current work being conducted by the Licznerski lab, a close collaborator of the Jonas lab, which shows that FMRP binds to ATP synthase and increases the amount of ATP produced by cellular respiration. Because the results of this experiment show that the absence of FMRP causes an increase in mitochondrial membrane conductance, they support the notion that the pathogenesis of Fragile X Syndrome is dependent on the role of FMRP in preventing ion channel formation or further openings in the mitochondrial inner membrane. References 1. Valenti, D. Mitochondrial dysfunction as a central actor in intellectual disability-related diseases: an overview of Down syndrome, autism, Fragile X, and Rett syndrome. Neubiorev.2014.01.012. (2014). Author Biography Jorge Salcedo Sifuentes is a second-year student at the University of Chicago majoring in neuroscience. He hopes to attend medical school and become a neurologist as well as a researcher with a focus on neurological pathologies.

Winter 2018

Biologically Coupled Reduction of Nitrate and Oxidation of Fe(II) Implications for Denitrification in Paddy Soils

Kaixin Wang1, Ye Chen2, Weilin Huang3, Dandan Chen3 1The

University of Chicago, 2Rice University, Environmental and Soil Sciences

3 Guangdong

Institute of Eco-

Abstract Nitrate pollution is a severe environmental problem today since it has impacted many rivers, lakes and coastal waters for the past several decades, resulting in serious environmental and human health concerns. The ion-exchange method is one of the most popular present methods for the denitrification of nitrate-polluted waters. By letting the polluted water pass through the strong basic anion-exchange resin, the nitrate ions in water will be exchanged with chloride ions or bicarbonate ions. However, this treatment produces high concentrations of treated saline wastewater, which may cause secondary pollution. A newly discovered lithoautotrophic nitrate-dependent Fe(II)-oxidizing bacteria shows much promise in catalyzing nitrate reduction (denitrification) [1]. In our research, we proposed that Pseudogulbenkiania sp.2002 would couple the reaction between nitrate reduction and Fe (II) oxidation under anaerobic, neutral conditions, and the coupled reactions would transform excess nitrate in surface water into less toxic or harmless gases. We conducted experiments to quantify the rates of NO3- reduction in the presence of Pseudogulbenkiania sp.2002, and the rates of consequent reductions of nitrite via biotic and abiotic processes under anaerobic conditions by using spectrophotometry and chromatography. Our results show that the combined biotic and abiotic reaction dramatically enhanced the removal of nitrate in water as Pseudogulbenkiania sp.2002 enhances the rate of the reaction between Fe(II) and nitrate ions. Finally, based on our research, we proposed a model as an application, which has the potential to solve nitrate pollution in southern China as well as other regions. Introduction Nitrate (NO3 -), an ionic species, is widely found in aquatic systems. The primary sources of nitrate are the decomposition of biomass, discharge of treated and untreated wastewater, and excessive use of fertilizers in agriculture. The continuous accumulation of nitrate in water is one of the causes for surface water eutrophication. Eutrophication has adverse environmental effects including algae booming and hypoxia, which may lead to the deaths

of aquatic animals. The decomposition of dead aquatic animals consumes oxygen and thus reduces the concentration of dissolved oxygen, resulting in anaerobic condition. Eventually, these factors lead to the degradation of water quality; they also account for the offensive odor and taste in source water and threaten safe drinking water. Nitrate has an extremely high solubility and very low affinity for solids. Therefore, it is difficult to separate nitrate from water through physicochemical means. A more

Scientia realistic approach to denitrification of polluted water is biotic reactions that biologically transform nitrate into nitrogen since nitrogen is among the essential nutrients for living organisms such as bacteria. One of the feasible methods to deal with nitrate pollution is to reduce nitrate into nitrous oxides or nitrogen. Previous studies have shown that the redox reaction between nitrates and Fe(II) may occur under specific circumstances. Nitrate, under neutral or alkaline conditions, does not display strong oxidizability. However, under acidic conditions, nitrate does display strong oxidizability, leading to the oxidation of Fe(II) to Fe(III). This phenomenon is caused by the existence of conjugated Ď&#x20AC; bonds in nitrate: The geometric configuration of nitrate tends to be stable, so under acidic conditions (when the concentration of H+ is high), the conjugated Ď&#x20AC; bonds can be broken. This process results in the strong oxidizability of nitrate. For example, as described above, under acidic conditions, the following reaction can occur in the presence of hydrogen ions: This reaction can be generally considered as a transfer of electrons from the ferrous (Fe(II)) ion to the nitrate ion (NO3 -). The ferrous ion is oxidized by nitrate, and nitrate is reduced by the ferrous ion. Hydrogen ions interact with oxygen and at last form water molecules. However, this reaction does not occur spontaneously under neutral conditions. According to the previous research, Pseudogulbenkiania sp.2002 (Pse in abbreviation), a type of lithoautotrophic nitrate-dependent Fe (II)oxidizing bacteria, has the potential to catalyze the reaction above. It is noteworthy that although many pure cultures of Fe (II)-oxidizing bacteria that have the ability to couple nitrate reduction to Fe (II) oxidation have been discovered, among these bacteria only Pse has shown the ability to grow autotrophically (to synthesize its own food from inorganic substances) with Fe(II) oxidation under neutral-pH conditions [1]. Literature also indicates that the Fe(II)-oxidizing microorganisms are able to oxidize different forms of Fe(II) with nitrate as an electron acceptor. [2] While without the bacteria, reduction of nitrate may not occur in neutral pH conditions, with the presence of Pse, nitrate completely reduces in a few weeks. The nitrate-dependent oxidation of aqueous Fe2+ has been described as follows [3]:

In our research, we therefore proposed that under anaerobic condition, Pse would couple the reaction between nitrate reduction and Fe (II) oxidation under neutral conditions. Incidentally, a pH of 7 is also optimal for the growth of Pse. Pse would facilitate the nitrate reduction under neutral pH conditions using Fe(II) as the electron donor, as the ferrous ion is oxidized by nitrate. We further proposed that water denitrification includes not only biotic reactions, but also abiotic reactions that could play a synergetic role in enhancing nitrate removal in water. It is likely that, during abiotic reactions, harmful nitrite, an intermediate product of the biotic transformation of nitrate, can react with a reducing species such as Fe(II) that is present in the water to form nitrous oxide and eventually nitrogen. We hypothesized that it is such coupled biotic and abiotic reactions that transform excess nitrate in surface water into less toxic or harmless gases. To test our hypothesis, a series of experiments were conducted in the laboratory to quantify the rates of NO3- reduction in the presence of Pse, and the rates of consequent reductions of nitrite via biotic and abiotic processes under anaerobic conditions by the use of spectrophotometry and chromatography. Materials and Methods We first cultivated the Pse colony in a sterilized beef extract and tryptone medium. The colony was acquired by centrifuging the complex medium. Once the cultivation of Pse was ready, we began to conduct the biochemical reaction. Five different reaction systems were set up, and each system had three parallel samples (Table 1). We compounded 20ml 0.5M/L NaNO3, 20ml 0.5M/L NaNO2, and 25ml 0.5M/L FeSO 4. Then, Table 1: Experiments Conducted

Winter 2018 we added solutions separately into different control groups in an anaerobic workstation at 37 centigrade. We sampled at 0h, 3h, 9h, 18h, 42h, 90h, and 142h after the reaction began. For Fe(II), we used the ultraviolet-visible (UV-Vis) spectrophotometer to measure the absorbance of the solution when the reaction was complete and then determined the concentration of Fe(II) according to the Beer-Lambert Law. We injected liquid from all samples into ion chromatography to determine the concentration of nitrate and nitrite, and we injected gas in the samplings into gas chromatograph to determine the concentration of nitrous oxide.

Figure 3: Concentration of Nitrate (mol路L-1) in different reaction systems

Results From Figure 1, we see that the concentration of Fe(II) decreased in both the reaction system of killed-cells + NO3 - + Fe(II) and the reaction system of Pse + NO3- + Fe(II). This indicates that the redox reaction between Fe(II) and nitrate ions does exist, and the existence of Pse increases the rate of reaction between Fe(II) and nitrate ions. Figures 1 and 2 show that among the systems Figure 4: Concentration of Nitrite (mol路L-1) in different reaction systems

Figure 1: Concentration of dissolved Fe (II) (mol路L-1) in different reaction systems

Figure 2: Concentration of HCl extracted Fe(II) (mol路L-1) in different reaction systems

in which nitrate ions were present, the reaction system of Pse + Fe (II) + NO3 - was found to react the most rapidly and completely. This result demonstrates that the combined biotic and abiotic reactions dramatically enhances the removal of nitrate in water. Figure 3 indicates that that Fe(II) did not react with nitrate in the system without Pse. This result emphasizes the necessity of Pse in this coupled reaction between nitrate reduction and Fe (II) oxidation, as is expected. Additionally, compared to the rate of nitrate reduction in the reaction system of Pse + NO3 -, that of nitrate reduction in the reaction system of Pse + Fe (II) + NO3 was greater. Such a difference indicates that the presence of Fe(II) increases the denitrification reaction rate. From Figure 4, we see that the reaction of Pse + Fe (II) + NO3 - produced a large amount of nitrite during the first 40 hours of the reaction. However, after 40 hours, the concentration of steadily decreased, indicating that nitrite may have reacted with other chemicals in the reaction system during the experiment. From Figure 5,

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Figure 5: Concentration of nitrous oxides (molÂˇL-1) in different reaction systems

we see that a large amount of nitrous oxide was produced in the reaction system of NO2- + Fe(II). From Figures 4 and 5, we conclude that nitrite is an intermediate product of biotic transformation of nitrate during abiotic reactions, and reacts with a reducing species such as Fe(II) present in water to form nitrous oxide and then nitrogen. Overall, our research provides substantial evidence showing that Pse facilitates the nitrate reduction under neutral pH conditions and during reactions nitrite, the intermediate product of biotic transformation of nitrate, reacts with the Fe(II) present in water to form nitrous oxide. The coupled reaction between the reduction of NO3 and the oxidation of Fe(II) by Pseudogulbenkiania sp.2002 shows the potential of denitrifying water polluted with nitrate. Discussion The results have a significant implication for microbiological removal of nitrate contaminants in the environment. Denitrification of paddy soils in Southern China is critical for the control of nonpoint source (NPS) nitrate pollution in surface water. Rice is grown in large quantities in southern China and nitrogen fertilizers are typically applied in excess, resulting in high concentrations of nitrate in paddy soil, which leads to a significant amount of nitrate contamination in surface water. Denitrification of paddy soil is a promising strategy for the control of eutrophication in China. Due to the high levels of water in paddy soil, the high concentration of iron in southern Chinaâ&#x20AC;&#x2122;s red soil, and the ubiquitous nature of Pse, denitrification of paddy soil via Pse is a highly

suitable avenue to utilize for the control of nitrate levels in this region and other similar regions. As a result, the denitrification of paddy soil can be a powerful process for the control of nitrate concentrations there. Furthermore, iron may be added to paddy soil to optimize the conditions for the denitrification process, hence further helping to reduce eutrophication. This method of denitrification is highly versatile and applicable to many environments with varying types of soil. Moreover, this method can also be utilized for denitrification in domestic wastewater treatment. Based on our research, we may design a model to deal with nitrate pollution as an application. The basic structure of the model is honeycomb iron that is used to provide Fe(II). One of the advantages of honeycomb iron is that it has considerable surface area compared to other geometrical structures, which means that the reaction will be more favorable due to reaction kinetics. On the surface of honeycomb iron, Pse can be cultured. Although the details of this model require further investigation and discussion, we believe that this application shows great promise due to its simplicity and versatility. Implementation of the enhancement of denitrification processes utilizing Pse has the potential to solve nitrate pollution in southern China and in other regions all around the world, and may furthermore be employed in various other processes such as domestic wastewater treatment. Our study indicates that compared to the rate of nitrate reduction in the reaction system of Pse+NO3 -, the rate of nitrate reduction in the reaction system of Pse + Fe(II) + NO3 - is much greater, substantiating that the presence of Fe(II) favorably influences the denitrification reaction kinetics. However, further research should be conducted to investigate the effect of the concentration of Fe(II) on the rate of nitrate reduction, and to find the optimum concentration of Fe(II) for which the nitrate reduction reaches its maximum rate. Acknowledgements This research was supported by the Guangdong Institute of Eco-Environmental and Soil Sciences. We sincerely thank Professor Weilin Huang and Dr. Dandan Chen for their guidance.

Winter 2018 References 1. Weber, K.A., Hedrick, D.B., Peacock, A.D. et al. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl. Microbiol. and Biotechnol. 83, 555-565 (2009) 2. Zhao, L, et al. Biological oxidation of Fe(II) in reduced nontronite coupled with nitrate reduction by Pseudogulbenkiania sp. Strain 2002. Geochim. Cosmochim. Acta 119, 231-247 (2013) 3. Straub, K.L. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. vol. 62 no. 4, 1458-1460 (1996) Author Biography Kaixin Wang is a first-year student at the University of Chicago potentially majoring in mathematics.

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Abstracts

Scientia Original Abstracts Strain-Induced Configurational Twists and Topological Defects in Smectic and Nematic Liquid Crystals Khia Kurtenbach1, Monirosadat Sadati1,2, Luis de Pablo3, Harrison Shapiro3, Samuel Morin3, and Juan J. de Pablo1,2 1Institute

2 Argonne

for Molecular Engineering, The University of Chicago, National Laboratory, 3The University of Chicago Laboratory School

In the De Pablo lab, we study liquid crystal (LC) phases, a state of matter observed between the solid (crystalline) and liquid (isotropic) state. In the LC state, anisotropic molecules flow like liquid, but remain highly ordered over long ranges. There are multiple potential liquid crystal phases, characterized by the degree of order in each material. The nematic LC phase is characterized as having orientational order; molecules tend to point in the same direction (along the director), but do not display positional order. Molecules in the LC smectic state exhibit a degree of translational order not present in nematic phases. Smectic LC molecules maintain orientational order, but also align themselves in layers or planes. LC displays Braggâ&#x20AC;&#x2122;s refraction, refracting light in the visible range; thus, we can study topological defects and LC ordering using a polarized microscope. Our recent work explores the effect of mechanical strain on defect structure and molecular arrangement in nematic and smectic LCs droplets. We induced geometric confinement by dispersing LCs in a polymer (Polydimethylsiloxane (PDMS)) film. In the PDMS film, LCs adopt homeotropic anchoring, such that the rod-like LC molecules line up perpendicular to the substrate with a point defect at the droplet center. PDMS film was stretched uniaxially, forming prolate droplets, and biaxially, forming oblate droplets. Upon uniaxial stretching, nematic LC retains its radial configuration and its defect position remains fixed. However, uniaxial strain on smectic LCs results in a change from a point topological defect, to a line defect, whose length is proportionate to the draw ratio(r/Î&#x201D;r). This reordering can be attributed to misorientation and dilation of smectic layers in the LC droplet. When nematic LC droplets undergo biaxial stretching, the strain-induced topological defect competes with the homeotropic anchoring to result in a configurational director twist. At a critical strain level, dependent on draw ratio and droplet size, the LC molecules in the twisted oblate align normal to their respective stretch axis. For smectic LCs undergoing biaxial strain, the layers transition from radial alignment to parallel alignment, beginning from the droplet center and spreading outwards as strain increases. Future studies involve exploring strain-induced topological defects on additional liquid crystal phases, such as chiral phases. Ultimately, we hope that building a robust understanding of positioning, orientation, and defect assembly in liquid crystal phases may aid in the development of liquid crystal electrooptic devices, biosensors, actuators, and photonics.

Winter 2018

Three-Dimensional Architecture and Assembly of Two-Dimensional Material Maritha A. Wang, Joonki Suh, Fauzia Mujid, and Jiwoong Park

Park Lab, Department of Chemistry and Institute for Molecular Engineering (IME), James Franck Institute (JFI), The University of Chicago Two-dimensional (2D) materials, being only a few atoms thick, can accommodate most imaginable mechanical deformations including crumpling, folding, bending, and collapsing. Simultaneously, they are among semiconductors, metals, and insulators that function as diverse active components in modern electronics. To fully investigate and harness their deformation mechanics, we first fabricate 2D materials with three-dimensional (3D) geometry. We present here a general method to fabricate the corrugated monolayer molybdenum disulfide (MoS2), a representative 2D semiconductor. By employing nanosphere lithography combined with reactive ion etching (RIE), nanoscale corrugations are introduced onto growth substrates with tunable size (50 nm - 1 μm) and non-zero Gaussian curvature. Subsequent metal-organic chemical vapor deposition (MOCVD) growth of MoS2 on these substrates is highly conformal and results in three-dimensionally structured MoS2. This corrugated MoS2 can also be locally patterned by adopting a chromium (Cr) metal hard-mask during RIE processes, allowing for the realization of laterally connected flat-corrugated monolayer MoS2. Furthermore, this patterned and corrugated MoS2 can be vertically assembled with its flat counterparts, leading to a large variety of potential structures. The fabrication strategy presented here therefore opens the door to future studies in deformation mechanics and controllable engineering of 2D materials for innovative applications in areas such as implantable healthcare and sensor technology.

Modifications to the Hall Probes in the Magneto-Rotational Instability Machine

Maria Lysandrou1, Erik Gilson2, Kyle Caspary2, and Hantao Ji2

1The University of Chicago, 2 Princeton Plasma Physics Laboratory, Princeton University

When gas that accretes has high enough angular momentum, it usually forms an accretion disk. Accretion disks are objects that have gas, plasma, and dust. The center of the accretion disk usually is a neutron star or a black hole. In an accretion disk, the ω (speed) decreases radially and the L (angular momentum) increases radially. The angular momentum in the accretion disk is transported outwards and Magneto-Rotational Instability (MRI) is believed to be responsible for the transport. An MRI can be easily explained by thinking of a system that has a central mass (MC) and two different masses, mass inner (MI) and mass outer (MO), connected by a spring. The inner mass has higher speed so it wants to move inside, while the outer mass has higher angular momentum so it wants to move further outside. The spring represents the magnetic field. As the two particles move away from one another, the magnetic field changes (or bends) from the Bz direction to the Br and Bθ vector. At the Princeton Plasma Laboratory, there is an experiment trying to mimic the MRI. The MRI experiment uses galinstan, a mixture of gallium, indium, and tin, in order to try to mimic the instability. The MRI machine has three different rotating parts (inner cylinder, outer cylinder, and a ring between the inner and outer cylinders) moving at three different speeds, in which the metal alloy is located in between the inner and outer cylinder. The machine has hall probes (a device that we use to measure the magnetic field) throughout the inner and outer cylinders of the machine. In the MRI machine, there are hall probes measuring the magnetic field in the Br, but not in the Bθ direction. For my project, I created and tested two hall probes to measure the magnetic field in the Bθ direction. Hall probes consist of an amplifier circuit and sensor chip. The sensor chip was orientated in the azimuthal direction for my project. In order to test how my hall probes would act in the machine, I conducted bench top tests that consisted of moving magnets in front of the sensor chip to see responses when the sensor chip was below, near, or above the MRI threshold. The results indicated that the distance of the magnet is indirectly proportional to the voltage output. It was found that the closer to the MRI threshold, the stronger the magnetic field and the stronger the output from the sensor chip. Given that there was no previous study at the Princeton Plasma Physics lab in the Bθ direction, these findings are imperative to the field.

Scientia

Computation Analysis and Prediction of Post-Stroke Recovery from Baseline Brain Connectome Metrics Kimberly Ho and Dr. Amy Kuceyeski Weill Cornell Medicine Strokes are the fifth leading cause of death in the United States. They result from problems with blood supply to the brain. Many post-stroke patients will find improvement between a month and a year, but it is not well known who will recover and to what extent. This research aims to help medical professionals improve the accuracy of prognoses after strokes, and possibly to choose the most effective treatments. This work uses a neural network, a machine-learning technique, to predict recovery from strokes based on baseline imaging of biomarkers of the anatomical and functional connections in the brain. Neural networks are designed to simulate a biological neural system. The goal of this Artificial Neural Network (ANN) is to predict output variables based on input data. ANNs do so by determining system weights to minimize the least squares. The ANN we use predicts how a patient is expected to recover based on measures extracted from their imaging. The results of this research show promising benefits for ANNs used in clinical settings. A network is used to summarize the structural connectome, which is a map of all grey area regions in the brain. The patient’s baseline imaging and 6-months post-stroke data are entered into the ANN so the network can generate its own predicted 6-months post-stroke datasets. This technique was successful in this experiment which used ANNs to predict how a patient will recover given data history on the stroke. This technology proposes many benefits to the field of neuroscience because it has the ability to decipher patterns between quantitative datasets that represent a patient’s recovery. In addition, explaining the wiring of the connectome, a map of the wirings between grey matter regions of the brain, and its mechanisms continues to be a challenge today. The mathematics and techniques behind neural networks may reveal much about the way the brain functions and the significance of the wirings between the grey regions.

Cobalt Super-microparticles Anchored on Nitrogen-doped Graphene for Aniline Oxidation Based on Sulfate Radicals Xin Qin1, Shuwen Fang2, Lei Zhao1, Penghui Shi1, Jinchen Fan1, Yulin Min1, Qunjie Xu1, and Weifeng Yao1 1Shanghai

Key Laboratory of Materials Protection and Advanced Materials in Electric Power, Shanghai University of Electric Power, 2The University of Chicago Cobalt super-microparticles anchored on nitrogen-doped graphene (Co–NG) and graphene oxide (GO) were prepared using an inexpensive modified Hummer’s method. Graphene Oxide was subsequently tested for heterogeneous oxidation of aniline, the pollutant, with peroxymonosulfate (PMS) in aqueous solutions. Using a variety of techniques such as X-ray diffraction, Raman spectroscopy, dark-field scanning transmission electron microscopy and X-ray photoelectron spectroscopy, the crystal structure, morphology, and textural properties of Co–NG hybrids were characterized, respectively. PMS activation and aniline oxidation were investigated using electron paramagnetic resonance and classical quenching tests. Based on the presence of sulfate radicals (SO4 −•), the results indicated that the catalyst Co–NG was better able to degrade the aniline in water in comparison to other catalysts. 100% decomposition was achieved in 10 minutes. This research offers new insights on heterogeneous catalysis and found Co–NG to be a promising catalyst for water treatment due to its high efficiency, good stability, and reusability. This work has been previously published in Science of Total Environment in 2017

Winter 2018

Tracking the Fate of Facial Branchiomotor Pioneer Neurons in the Zebrafish Hindbrain Sweta Narayan1, Ana Beiriger2, and Victoria E. Prince3 1Summer

Research Fellow, Biological Sciences Collegiate Division, on Development, Regeneration & Stem Cell Biology, 3 Department of Organismal Biology & Anatomy, The University of Chicago 2 Committee

During embryonic development, segmentation of the vertebrate hindbrain leads to the formation of compartments known as rhombomeres along the anteroposterior axis of the neural tube. This segmentation prefigures the development of segmentally organized branchiomotor neurons (BMNs), which contribute to the cranial nerves that innervate muscles in the face, eyes, jaw, and throat. Neural circuits in the vertebrate hindbrain are established in part by embryonic neuronal migration, a process which allows neurons to relocate from their initial birthplace to their final location. In zebrafish, the facial branchiomotor neurons (FBMNs), which contribute to the motor component of the seventh cranial nerve, originate in rhombomere 4 (r4) of the hindbrain and subsequently migrate towards r6/7. This caudal and tangential migration of the FBMNs is well conserved across many vertebrate species, including humans and mice. Thus, studying zebrafish FBMN migration could provide insight into the formation of neural circuitries in the human brain. Recent studies have shown that FBMN migration in zebrafish is led by a set of pioneer neurons, the first neurons to exit r4. Ablation of pioneer neurons blocks successful migration of follower neurons out of r5, suggesting that pioneers are necessary for migration and play a role distinct from that of followers. In the zebrafish olfactory system, which displays a similar pioneer-follower dynamic, pioneers undergo apoptosis after guiding sensory neuron migration. This finding suggests that the pioneers do not play a role in the olfactory system after pioneering a pathway to the olfactory bulb. The goal of this study is to track the cell fates of the zebrafish FBMN pioneers, to determine whether they also undergo apoptosis after leading FBMN migration. Single-cell photoconversions of pioneers and followers (the control) on opposite sides of the hindbrain were conducted in transgenic embryos expressing the photoconvertible protein KAEDE in all cranial BMNs. By imaging photoconverted embryos at 72 and 96 hours post fertilization (hpf), we determined that pioneers do not undergo apoptosis after FBMN migration to r6/7 is complete. Furthermore, we discovered an interesting positional effect in the final localization of follower neurons: followers located closer to the pioneer during migration are more likely to follow it into r7 than more anterior followers. Further studies are required to characterize the mechanisms behind this positional effect.

Scientia

Modeling early Alzheimerâ&#x20AC;&#x2122;s disease pathology with AAV-tau in a rodent model of cognitive aging Melissa Litenski1, Joseph A. McQuail1, Sarah A. Johnson1, Sara N. Burke1,2, and Jennifer L. Bizon1 1McKnight

Brain Institute and Department of Neuroscience, University of Florida, 2Institute on Aging, University of Florida Funding provided by Florida Department of Health grant 7AZ06

The medial temporal lobe (MTL), located at the caudal end of the temporal lobe, consists of a system of anatomically related structures that are essential for the formation of long-term memory. Neuropathologies in this region in the form of beta-amyloid plaques and aberrantly phosphorylated tau tangles, are one of the earliest features of Alzheimerâ&#x20AC;&#x2122;s disease (AD). Although beta-amyloid has received attention as the causative agent of neurodegeneration in AD, specific contributions of tau pathology to AD progression remain less studied. The goal of the current studies was to develop a rodent model that permits analysis of tauopathy in aged animals, with tau expression initiated in brain regions that show earliest pathology in human patients. Tau protein expression was induced in the MTL of young adult (5 months) and aged (24 months) F344 x Brown Norway F1 hybrid rats via AAV-mediated gene transfer. The viral vector containing the human tau gene was stereotactically targeted to the transentorhinal region of the MTL, a region that receives highly processed sensory information of all modalities and provides an important route for transferring information to and from the hippocampus (Area 35 and 36 of perirhinal cortex). Brain tissue was collected eight weeks later and the extent of virus-mediated spread was visualized with immunohistochemical labeling, a technique that uses appropriately labeled antibodies to image discrete components in tissues, of the eGFP reporter tag, total human tau (hTau), AT8, detecting aberrantly phosphorylated tau protein, and Alz50, reflecting early conformational states of neurofibrillary tangles. Although full quantitative analyses are in progress, our preliminary qualitative findings suggest that AAV-mediated expression of human tau accelerates pathology in a manner that mirrors the degree of tau accumulation observed in older adults. Although there is evidence of tauopathy in young adult rats, advanced conformational change in tau protein and tangles were pervasive in aged rats. The absence of tauopathy in both young and aged control rats infused with an empty vector indicates that our model can successfully induce tauopathy in rodents that recapitulates age-related AD neuropathology. Upcoming studies will evaluate the behavioral consequences of AAVmediated tauopathy, quantify the amount and localization of AAV-mediated tau protein over time, test new antibodies that identify different tau tangle conformational states, and analyze pathology after longer incubation periods.

Winter 2018

Selected Abstracts from the 4th Annual UChicago Undergraduate Research Symposium in collaboration with UCISTEM and Phoenix Biology

Overcoming Catastrophic Forgetting Using Recurrent Neural Networks Gregory Grant, Chaihyun (Catherine) Lee, Varun Iyers, Nicolas Masse, and David Freedman David Freedman Lab, Grossman Institute of Neuroscience & Biological Sciences Division, The University of Chicago

Artificial neural networks (ANNs) are artificial intelligence computing systems inspired by the biological pathways between interconnected neurons in the brain. In large part, the goal of the ANN is to imitate human learning via analysis of datasets consisting of well-defined inputs and expected outputs. While training on these datasets, ANNs optimize their internal weighted connections to maximize task performance. Current network models, however, cannot build upon past knowledge, suffering from a phenomenon referred to as â&#x20AC;&#x153;catastrophic forgetting.â&#x20AC;? When a standard ANN trains on a new task, it rapidly forgets any previously learned tasks as its weights adjust to this newest task. To address this problem, we have developed a recurrent neural network (RNN), an ANN composed of high-density, directed, time-sensitive connections, that includes novel implementations of neural circuit aspects. Our RNN implements powerful inhibitory circuits combined with dendritic processing to encourage the network to use non-overlapping information trajectories for different tasks. These circuits, which include selections of neurons that can either increase and decrease synaptic activity, are based on the disinhibition pathways found in the brain. We also have endowed our synaptic connections with a short-term synaptic plasticity model, allowing our RNN to stabilize each taskâ&#x20AC;&#x2122;s most vital connective weights. Preliminary results suggest that weight stabilization leads to a notable improvement in task performance over time, though the RNN is still unable to perfectly retain fully optimized knowledge about previous tasks. In the future, we hope to teach the network using reinforcement learning (RL), a machine learning framework highly analogous to human learning that places ANNs in interactive environments instead of simply showing them datasets. Using RL will allow us to more intuitively develop possible solutions to catastrophic forgetting, as a result of the similarity to human learning. The ability of ANNs to learn, remember tasks, and make decisions with human or super-human performance will provide vast opportunities for learning, growth, and exploration as we continue to explore the boundaries of artificial intelligence and neural modeling. Overcoming catastrophic forgetting through novel synaptic circuitry implementations is integral to developing more advanced ANNs for future use in neuroscience and other fields.

Scientia

The Genetic Basis of Alzheimer’s Disease in the Hutterite Population Anjali Das

Lab of Carole Ober, Department of Human Genetics, The University of Chicago Alzheimer’s disease (AD) is the sixth leading cause of death in the United States and is a progressive neurodegenerative disorder that results in loss of cognitive processes, affecting approximately 5.5 million individuals in the nation. To date, the genetic basis of late-onset AD is not well understood, with the APOE-ε4 allele being the only established genetic risk factor. Although it is the most significant risk factor, only about 40% of individuals with AD have a copy of the APOE-ε4 allele. There are likely other genetic factors that contribute to the disease. Founder populations facilitate mapping of complex phenotypes such as AD because they are relatively isolated groups that descend from few ancestors, and therefore have decreased genetic variation. In this study, we investigate the genetic basis of AD in the Hutterites in 5 cases and 26 age matched controls. Fourteen variants within and close to the MGMT gene in chromosome 10q26.3 region were present in all cases and absent in all controls and thus were significantly associated with AD (p-value = 7.49x10-16). While 10q26.3 has been highlighted in association with AD, none of the significant variants pinpointed in this study have been previously identified. However, the next closest gene is EBF3, which has been implicated in AD in multiple genome-wide association studies. The combination of variants on chromosome 10 and APOE-ε4 were then shown to be associated with olfactory dysfunction (p-value = 0.0164), a known pre-clinical marker of dementia. Lastly, because AD is associated with declining cognition, I also tested associations of both the chromosome 10 variants and APOE-ε4 for association with results from the Raven’s Progressive Matrices Test, a measure of non-verbal intelligence quotient since AD has long been linked to declining intellectual ability. These results suggest that variants in the chr10q26.3 region, possibly in combination with APOE-ε4, contribute to decline in olfactory function and the development of AD in the Hutterites, which also has implications for the development of AD in the general population.

Disruption of the Antiviral RIG-I Pathway by JC Virus Rachel Potter

Lab of Michaela Gack, Department of Microbiology, The University of Chicago JC virus is a polyomavirus, a double-stranded DNA virus without a protein coat, present in over half of the general human population. JC infection in individuals with a well-functioning immune system is usually asymptomatic, but the virus can cause progressive multifocal leukoencephalopathy (PML) in immunocompromised patients, a fatal disease that damages the brain’s white matter. In the vast majority of healthy individuals, the virus is kept in check by the immune system, yet the immune system does not clear the virus, allowing it to establish persistent infection. The first line of antiviral defense is the body’s innate immune response, which acts within hours of the pathogen entering the body. Many viruses have developed mechanisms to evade the innate immune response to establish infection and cause disease. The molecular mechanisms by which JC virus evades innate immunity, however, are not well understood. In order to study the role JC virus proteins play in interfering with the innate immune system, individual proteins of the virus were affinity-purified and binding interactions with host proteins were examined by mass spectrometry analysis. This identified that JC’s Small t Antigen protein binds to the innate immune protein TRIM25, which is an upstream activator of the viral RNA sensor RIG-I that is responsible for the detection of many RNA viruses as well as some DNA viruses. Protein-binding assays demonstrated that binding of the Small t Antigen to human TRIM25 caused disruption downstream in the innate immunity pathway, specifically the inhibition of non-degradative K63-linked ubiquitination of RIG-I, which is important for its downstream signaling ability to trigger an antiviral cytokine response. Our results show a new mechanism that JC virus utilizes to disrupt the RIG-I-mediated innate immune response, and further highlight that viruses from different families have independently developed similar mechanisms to avoid virus detection by RIG-I. Further research is currently being conducted to define the precise mechanism by which Small t Antigen inhibits TRIM25 activity.

Winter 2018

Feature-Based Image Alignment Using Affine Transformation Dmitry Shribak

Brookhaven National Lab, Department of Energy, National Light Source Two, with Xiao-Jing Huang The research project was conducted at Brookhaven National Laboratory in Upton, New York at the x-ray nanoprobe beamline at National Synchrotron Light Source II (NSLS II). The project was centered on creating an interface for tools for users to better process collected data, as well as improving the tools themselves. The project had two parts: creating a graphic user interface (GUI) for the first part and designing a new image alignment algorithm. For the GUI aspect, the project was to implement previously written x-ray imaging python functions into a fully closed program that will allow NSLS users to process experimental data from the beamline for tomographic reconstruction. The GUI was made to be able to input a h5 file and using python’s pyqt and matplotlib packages, display the experimental data as a heat map of pixel values. In addition, the user is able to normalize the image, align images, and find the center of mass of the sample. Using the selected center of mass, the user is then able to perform tomographic reconstruction and display the image array in 3 dimensions. The second part of the project was to create a better method for aligning images. Previously, the images were aligned with cross correlation, which is not considered the most effective method because it leads to errors near the boundaries of the image. Instead, a feature based alignment method was implemented that used the SIFT algorithm to detect and match image features, and correct the linear misalignment as well as the rotational misalignment caused by sample collection.

HCV Screening and Linkage-To-Care Care Continuum Madison Stamos

Lab of Mai Pho, Section of Infectious Diseases, Department of Medicine, The University of Chicago Medical Center While an expanded screening program at the University of Chicago Medicine (UCM) has increased the number of patients tested for Hepatitis C (HCV) according to CDC guidelines, linkage to care (LTC) of HCV infected patients remains challenging. In 2017, the Infectious Diseases Department at UCM adopted an intensive case management LTC practice for HCV infected patients, involving near real-time patient chart reviews, staging of the disease, and referring and scheduling appointments with HCV providers. Our patient sample was categorized into three groups: patients discussed during team rounds at UCM following the LTC practice described above; patients out-of-network who were referred to the Hepatitis C Community Alliance to Test and Treat (HepCCATT); and lastly, patients who were not explicitly followed under either group and who are now being retroactively linked to care. Our primary outcome was linkage, defined as attending an outpatient visit with a provider who can treat HCV. HCV screening and linkage outcomes were summarized over time and stratified by linkage group. From 2014-August 2017, 24,571 patients have been HCV screened at UCM. Of those screened, 1118 (4.6%) were antibody positive, and 642 (2.6%) had a confirmed active infection. 267 (69.2%) of eligible patients were referred to care, and 212 (54.9%) were linked to care. In 2014, the mean number of days between the HCV test date and LTC appointment date was 177.5 (± 235.3). In 2017, the mean number of days was 49.4 (±40.8), a 72.2% decrease from 2014. Stratified by group, the mean number of days was 117.5 (±167.0) for UCM without rounds, 60.1 (±55.6) for UCM with rounds, and 538.0 (±53.7) for HepCCATT. Reasons for eligible patients not being LTC: 104 (59.8%) were in progress, 20 (11.5%) had incorrect contact information, and 43 (24.7%) were lost to follow up. Despite the relatively new intervention of this intensive case management, the mean number of days between HCV test and LTC decreased in patients discussed during rounds compared to those patients who were not. Our next steps are to identify and address barriers that may hinder a patient’s ability to be LTC.

Scientia

Characterizing the Effect of Alkyl Group Length and Counterion Identity on the Conductivity of Charged Poly-2Vinylpyridine Thin-Film Electrolytes Satya Krishnan

Lab of Paul Nealey, Institute of Molecular Engineering, The University of Chicago The advancement of electronics will require improvements in the performance of electrolytes, a critical component of any electrochemical system. Electrolytes possess mobile ions that can move to conduct a current, and ideal electrolytes exhibit high ion conductivity, low electron/hole conductivity, chemical and physical stability, and low toxicity. Recently, block copolymers have received interest as a potential candidate to satisfy these diverse design requirements. The goal of this research project was to study the effect of molecular mobility on the conductivity of a homopolymer electrolyte (poly2-vinylpyridine, or P2VP), a useful model system for future studies into block copolymer electrolytes. P2VP thin film electrolytes were prepared under two mobility conditions. In the first condition, one end of the polymer molecules was anchored to the substrate, and in the second condition, both ends of polymers were mobile within the thin film. Both systems were made conductive via quaternization of the pyridine rings with methyl iodide through a chemical vapor infiltration reaction (CVIR) on prepared thin-film P2VP samples. Measurements were conducted using high surface area interdigitated electrode assemblies and electrochemical impedance spectroscopy (EIS) across a range of temperature and humidity environments. Ion transport mechanisms in polymer electrolyte systems are not yet completely understood, yet a deeper understanding of these mechanisms is necessary for advancements in the designs of next-generation electrolytes. Proposed mechanisms, including waterchannel conduction (in which mobile ions flow continuously through water-mediated pathways) and activation site hopping (in which ions move between energetically degenerate sites) may in fact work in tandem. The dominant mechanism may depend both on properties of the electrolyte system and on the environment. Our results suggest that system conductivity exhibits a biphasic dependence on ambient humidity. This unexpected finding suggests that the dominant ion transport mechanism at higher ambient humidities has a strong dependence on water and that this dependence may require water to be present at a critical threshold value in order to support ion mobility.

Winter 2018

Inquiries From Stellar Evolution to Supernovae: Professor Dwarkadas’ Philosophy in Diversifying Research Interests Jarvis Lam Dr. Vikram Dwarkadas believes in the diversification of research interests. He heads many undergraduate research projects as a Research Associate Professor in the Department of Astronomy and Astrophysics at the University of Chicago, while also participating in civic activities on-campus. Moving to the University of Chicago in October of 2002, Dr. Dwarkadas and his wife have become a fixture of the campus community over the last 15 years. Dr. Dwarkadas received his undergraduate degree from the Indian Institute of Technology in Mumbai, India, an Institute of National Importance [1]. Majoring in Engineering Physics, Dr. Dwarkadas first researched LASER technology in the summer of his third-year. However, his passion has always been astrophysics. “When we did undergraduate school in India, we didn’t have any astronomy or astrophysics courses, but I have always wanted to do it,” recalls Dr. Dwarkadas. With permission from his school, he succeeded in doing his fourth-year research thesis on stellar evolution with professional astronomers at the Tata Institute of Fundamental Research, where he “wrote a FORTRAN code to simulate the evolution of a solar mass star over time.” He went on to receive his Master’s Degree from the University of Virginia, where he worked under Steven Balbus, currently a professor at the University of Oxford. The work involved writing a

hydrodynamic code in FORTRAN, and focused on galactic dynamics. He obtained a PhD at the same university working with Roger Chevalier, focusing on winds, supernovae and their interactions with the surrounding medium [2]. Dr. Dwarkadas explains that there was a lot of interest around a newlyfound supernova, SN 1987A, the “closest detected supernova to us for about the past 330 years,” which inspired his PhD thesis and fuelled much of his later research conducted at the University of Chicago. Before he settled down at the University of Chicago, Dr. Dwarkadas completed post-doctoral fellowships at other institutions. His projects ranged from planetary nebulae at the University of Washington, to particle acceleration in and radio emission from supernovae at the University of Sydney, to windblown nebulae around massive stars at the University of Delaware. “Research topics should be diversified. It’s important to keep your options open, and it is interesting to work on different phenomena that share similar physics principles,” he remarks. At the University of Chicago, Dr. Dwarkadas is involved in a variety of research projects, both with undergraduates and collaborators at the University of Chicago and elsewhere. One recent project was with a University of Chicago undergraduate, Christopher Bochenek, and collaborators at many other institutions. The team detected the first

Scientia X-rays from a Type Ia supernova, SNe 2012ca [3]. A Type Ia supernova is formed when a white dwarf has accreted enough material to exceed the Chandrasekhar mass, becoming unstable and exploding. Up until now, X-rays have only been detected from core-collapse supernovae, created when a massive star starts to collapse under its own gravity [4]. Dr. Dwarkadas explains that “as massive stars lose mass due to winds during their lifetime, a circumstellar medium is formed around the star. When these stars explode as supernovae, they drive a fast-moving shock at tens of thousands of kilometers per second into the surrounding medium. This shock heats up the gas to high temperatures, giving rise to X-ray emission.” The progenitors of Type Ia supernovae do not lose much, if any, material due to winds. Thus, there is not much material around the white dwarf for the shock to interact with, and this results in an absence of X-rays that can be detected. Interestingly, analysis of the X-rays coming from SNe 2012ca suggests that the circumstellar medium around the star is much denser than most core-collapse supernovae. A popular interpretation for this finding is that the Type Ia supernovae is formed as part of a binary-star system, and it is the companion star which provides the medium with which the shock interacts to produce the X-rays. Another suggestion is that the supernova is a result of two white dwarfs merging together, which could also fit with the unusually high density of the circumstellar medium. It is important to understand how a Type Ia is formed, because the study of such objects has given rise to important findings. “In fact, the evidence of an accelerated universe expansion came from Type Ia supernovae,” Dr. Dwarkadas comments. Another of Dr. Dwarkadas’ projects was with the undergraduate Peter Boyajian, and collaborators in the Geophysics Department, as well as at Clemson University. Meteorites that were formed at the time of formation of our solar system show a high abundance of the isotope aluminum-26. Recent investigations by collaborators in the Geophysics Department have shown a low abundance of Iron60. In order to explain this, the team proposed that our solar system originated from a nearby massive star that contains high levels of 26Al [5]. A possible next step is to simulate this process in detail. Within the past few years, Dr. Dwarkadas has worked with various students; several have published their own

research papers as undergraduates in his lab. “I think it’s important to encourage undergraduate students to join and learn astronomy, and try to get them to publish their own research. Some of them have gone on to Caltech, UCLA, and Penn State within the past couple of years,” he notes. In addition, Dr. Dwarkadas conducts other research. Following the philosophy of diversifying his interests, his current research topics includes stellar winds, nebulae around massive stars [6], X-ray and radio emission from supernovae [7], and acceleration and transport of particles in supernovae [8]. “A lot of my projects at the moment involve looking at various types of supernovae at different wavelengths, particularly in X-Rays, radio optical, and gamma-rays,” he comments [8] [9] [10] [11] [12]. He is currently involved in a project with a collaborator at Northwestern University [13] to investigate X-Rays detected from supernova remnants, using a newly developed technique of data analysis. Reflecting on why he has chosen the astrophysics path, Dr. Dwarkadas opines, “astrophysics is one of the fields where you are always waiting for the unexpected. It’s interesting that in astrophysics, apart from the newly detected gravitational waves, most of the data we get comes in the form of light. You can’t touch the object, you can’t feel the object, and sometimes you can’t even see the object in visible light. And yet we have come so far in understanding these entities in terms of where they came from, what they are made of and how they evolve. I guess I just enjoy the challenge.” Having done world class research around the globe, Dr. Dwarkadas is now enjoying his work at the University of Chicago. He lives with his wife near the Logan Center for the Arts, where they enjoy going to art performances and recitals. He is also involved in many activities on campus such as the Sustainability Council, where he had served as a member for many years since 2011, and the Campaign Committee, where he has served as a co-chair from 2010 to 2011. The Sustainability Office honored him with the SAGE Award in 2011. When asked the question of Why UChicago, Dr. Dwarkadas recalls: “I originally came to UChicago in 2002 because it has one of the best Astronomy and Astrophysics Departments in the world. Since then, my wife and I have come to embrace UChicago and Hyde Park as an important part of our lives.”

Winter 2018 References [1] “Institutions of National Importance.” University And Higher Education | Government of India, Ministry of Human Resource Development, Updated 19 Apr. 2016, mhrd.gov.in/ institutions-national-importance. [2] Dwarkadas, Vikram V. "Supernovae and Stellar Wind Interaction with the Ambient Medium." Publications of the Astronomical Society of the Pacific 110, no. 749 (1998): 882. [3] Bochenek, Christopher D., Vikram V. Dwarkadas, Jeffrey M. Silverman, Ori D. Fox, Roger A. Chevalier, Nathan Smith, and Alexei V. Filippenko. "X-ray emission from SN 2012ca: A Type Ia-CSM supernova explosion in a dense surrounding medium." Monthly Notices of the Royal Astronomical Society 473, no. 1 (2017): 336-44. [4] Lerner, Louise. “UChicago scientists detect first X-Rays from mystery supernovas.” UChicago News, University of Chicago News Office, 6 Sept. 2017, n ews.uchic ago.edu /ar ticle/2017/0 8/23/ uchicago-scientists-detect-first-x-rays-mysterySupernovas. [5] Dwarkadas, Vikram, Peter H. Boyajian, M. Bojazi, B. S. Meyer, and N. Dauphas. "Meteoritic Constraints on the Origins of Our Solar System." Chondrules as Astrophysical Objects, May 2017. Accessed November 2017. [6] Dwarkadas, Vikram V.; Rosenberg, Duane. L, “Simulated X-ray spectra from ionized windblown nebulae around massive stars”, High Energy Density Physics, Volume 9, Issue 1, p. 226-230. [7] Dwarkadas, V. V., C. Romero-Cañizales, R. Reddy, and F. E. Bauer. "X-ray and radio emission from the luminous supernova 2005kd." Monthly Notices of the Royal Astronomical Society 462, no. 1 (2016): 1101-110. [8] Dwarkadas, Vikram, Renaud, Matthieu, Marcowith, Alexandre, and Tatischef, Vincent. "Gamma-rays and Neutrinos from Efficient CosmicRay Acceleration in Young SNe." Supernova Remnants: An Odyssey in Space after Stellar Death, Proceedings of the Conference, June 2016. [9] Dwarkadas, Vikram, and Danika Holmes. "Investigating the X-ray Emission from some of the Oldest Known X-ray Supernovae." American Astronomical Society, April 2016. [10] Mathis, Ross and Dwarkadas, Vikram. " SNaX: A Database of Supernova X-Ray Light Curves”. The Astronomical Journal, Volume 153,

Issue 6, article id. 246, 7 pp. (2017). [11] Archambault, S.; Archer, A.; Benbow, W. et al. “Gamma-Ray Observations of Tycho’s Supernova Remnant with VERITAS and Fermi”, The Astrophysical Journal, Volume 836, Issue 1, article id. 23, 8 pp. (2017). [12] Bose, Subhash; Sutaria, Firoza; Kumar, Brijesh, et al. “SN 2013ej: A Type IIL Supernova with Weak Signs of Interaction”, The Astrophysical Journal, Volume 806, Issue 2, article id. 160, 18 pp. (2015). [13] Frank, Kari A., Vikram Dwarkadas, and David N. Burrows. "SPI Analysis of the Supernova Remnant DEM L71." American Astronomical Society, August 2017. About the Author Jarvis Lam is a first-year student at the University of Chicago. He is interested in astrophysics and the study of astronomical objects, and plans to pursue physics and computer science as potential majors.

Scientia

About The Triple Helix

at the University of Chicago

The Triple Helix, Inc. (TTH) is the world’s largest completely studentrun organization dedicated to evaluating the true impact of historical and modern advances in science. Of TTH’s more than 25 chapters worldwide, the University of Chicago chapter is one of the largest and most active. We, TTH at the University of Chicago, are extremely proud of our chapter’s accomplishments, campus presence, and strong connection to other TTH chapters around the world. We continue to work closely with an ever-increasing number of faculty members, and have notably acquired the generous support of the founding Pritzker Director of Chicago’s Institute for Molecular Engineering, Matthew Tirrell, and his department. We have expanded our local organization so that now, we can confidently say that there is a place here for each and every one of our fellow college students. We have consciously and dramatically increased the size of our production, marketing, and events teams, and have watched our group of talented writers and editors grow at unprecedented levels. In fact, we have further expanded the intellectual diversity of our chapter, with TTH members having declared for more than 30 of the University’s different major and minor programs. Finally, we are absolutely thrilled to present the newest issue of our journal of original undergraduate research, Scientia. Over the years, TTH UChicago members have found themselves in research positions around campus, taking advantage of the hundreds of opportunities we are fortunate to have here. We found ourselves wishing, however, that there was an outlet where we could reach out to our peers on campus, to share our projects and project ideas – and to hear or read about their work as well. So we decided to create that outlet ourselves. This was the impetus for our journal, Scientia, which is the culmination of many of our members’ hard work. Since its inception, we have continued to strive for excellence in the diverse world of research by publishing the highest quality of undergraduate research. We hope you enjoy reading our latest issue! Salman Arif President of The Triple Helix at the University of Chicago

Winter 2018

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

David Clark

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

Arthur Lundberg

Senior Assistant Director, Administration and Financial Advising

Tempris Daniels

Student Involvement Advisor

We also thank the following departments and groups: The Institute for Molecular Engineering The Biological Sciences Division The Physical Sciences Division The Social Sciences Division University of Chicago Annual Allocations Student Government Finance Committee (SGFC) Chicago Area Undergraduate Research Symposium UChicago Undergraduate Research Symposium

Finally, we would like to acknowledge all our Faculty Review Board members and the mentors of our abstract authors for their time and effort.

Research Submission Undergraduates who have completed substantial work on a topic are highly encouraged to submit their manuscripts. We welcome both full-length research articles and abstracts. Please email submissions to eic.scientia@gmail.com. Please include a short description of the motivation behind the work, relevance of the results, and where and when you completed your research. If you would like to learn more about Scientia and The Triple Helix, visit thetriplehelixuchicago.strikingly.com or contact us at uchicago.president@thetriplehelix.org

Meet the Staff Scientia

Production

Editors in Chief Jeremy Chang Clara Sava-Segal Managing Editors Zainab Aziz Nikita Mehta Quang Tran Associate Editors Jordan Cooper Josh Everts Katarina Keating Rita Khoury Margaret Lazarovits Hyesan (Sam) Lee Azam Mohsin Harini Shah Maritha Wang Writers: Inquiries Jarvis Lam Dr. Vikram Dwarkadas Daksh Chauhan Writers: In Depth Lindsey Jay Logan Leak Arundhati Pillai Jorge Salcedo Sifuentes Kaixin Wang

Executive President Salman Arif Vice President Nila Ray

Scientia Director Elle Rathbun SISR Director Ariel Goldszmidt

Science in Society Review Editor-in-Chief Aya Nimer Managing Editors Clay Davenport Rachel Gleyzer Sharon Zeng

Web Webmaster William Rosenthal

Events Director Peter Ryffel Coordinators Rachel Gleyzer Franklin Rodriguez

E-Publishing Editor in Chief Isabella Pan Managing Editor Julia Smith