Student Research Symposium

Saturday, October 20, 2018, 9am-12pm

Archives

Saturday, October 20, 2018
9:00am - 10:30am
Oral Presentations

Location: Lundring Events Center

Multi-Core Joins

Program: Swenson Science Summer Research Fellowships
Faculty: Graham Matthews, Ph.D., Computer Science
Student: Danny Suarez

Data Integration is the process of combining together multiple tables of data from different data sources to create one uniform view of the data. This is an important topic as many groups and organizations rely heavily on data integration to pull information from multiple sources in order to make data-driven decisions. Many of these decisions cannot be made through one source alone, so it becomes essential to find efficient techniques to perform data integration. The primary operation of data integration is called a join. A join operation combines two tables of data according to some criterion. Typically when integrating data there are multiple join operations to be done between multiple sources, so it is important to perform these operations as quickly as possible. Our research consists of implementing and analyzing methods to efficiently execute chains of joins. The methods that we investigate are geared towards modern day computers which have multiple cores, allowing them to perform multiple tasks simultaneously. Ideally, the more cores that a computer has, the faster and more efficient our methods will be. The first method we implemented is the phased approach in which we read in data followed by processing it. Secondly, we have a method called the multi-phased approach which has multiple read-process phases. Our testing showed that in both approaches more cores did increase the speed but not to the extent that we expected. We also looked at the differences in performance between the phased and multi-phased approaches. Our hypothesis was that the multi-phased approach would be more efficient than the phased approach, however our results showed no significant difference between the two. We were able to make significant improvements along the way to each approach, but our results show that there is still room to improve on our methods.

When Beauty Harms: Revitalization and Environmental Justice along the Los Angeles River

Program: Pearson Scholars Summer Program for Leadership and Engagement in a Global Society
Faculty: Michael Brint, Ph.D. , Political Science
Student: Nakeissa Abbassi

The lack of policy mechanisms for recognition and resolution of environmental justice issues within environmental planning and improvement programs creates negative impacts on communities. Following key environmentalist action, such as ecological restoration and beautification, revitalized communities become appealing to new tenants willing to pay for amenities, thus displacing and gentrifying original communities with higher costs of living. Under current legislation such as the California Environmental Quality Act (CEQA), the Los Angeles River Revitalization Master Plan (LARRMP) has witnessed demographic displacement within the same communities it aims to improve. The purpose of this study is to determine how communities along the LA River are being impacted by the disjunction between revitalization plans and environmental justice issues. This research was conducted through policy and plan analysis, census data analysis, site visits, and interviews with individuals in the government sector, advocacy groups, and community. It was found that stakeholders can knowingly or unknowingly exploit legal loopholes present in the CEQA to bypass addressing environmental justice issues. While the LARRMP acknowledges underrepresented communities, it is not required to address potential displacement or gentrification. Subsequently, as long as communities are slated to be revitalized, displacement and gentrification persists in environmental justice communities along the River, demonstrated through demographic shifts and disproportionate increases in property values. Mitigation strategies, as seen in the 2018 Resilient Los Angeles plan, are still in early planning phases with medium to long-term timeframe goals that will not be addressed for five years or more, allowing for the continuation of negative impacts. The current environmental legislation does not adequately address environmental justice issues within environmental reform. Through policy recommendations and new legal definitions, this research can inform future legislation to better address environmental justice issues.

The Effects of Pesticides on Genetic Expression in Caenorhabditis Elegans

Program: Undergraduate Research
Faculty: Grady Hanrahan, Ph.D., Biology
Student: Vanessa Avaloas

Pesticides are commonly used throughout the United States and can include fungicides, herbicides, and fumigants. Different populations exposed to these chemicals involve those working (or going to school) in areas treated with pesticides and living in areas near exposure. To study the dangers of these pesticides at a genetic level, a robust research model is needed. Caenorhabditis elegans (C. elegans) is a very useful model organism to study changes in genetic expression because it has a completely sequenced genome, a simple body plan, and shows similarity to mammals in genomics and biochemistry. The goal of this study is to determine the effects of methoxychlor and chlorpyrifos on genetic expression in C. elegans. The chemical structures of the methoxychlor and chlorpyrifos will be characterized by gas chromatography-mass spectrometry (GC-MS). C. elegans will be cultured in T-75 tissue flasks and exposed to different concentrations for up to 72 hours. Observations, including any noticeable alteration in development or phenotypic expression, will be made at different periods. Changes in gene expression will be analyzed through RNA extraction, processing of the genome (possibly from an outside source), microarray analysis, linear regression models, ANOVA tests, and comparisons between the produced gene sets and publicly available gene sets. Expected results are that the pesticides will induce a delay in development, alter metabolism, increase the incidence of cell repair, and alter innate immunity functions. It is also expected that there will be disruption of mitochondrial function and calcium homeostasis, as well as inhibition of acetylcholinesterase (AChE), which will contribute to neuronal degeneration. Overall, the findings of this study will contribute to a better understanding of how harmful pesticide exposure can be to humans and the permanent effects these substances may have.

Applications of Error-Correcting Codes

Program: Undergraduate Research
Faculty: John Villapando, Ph.D., Mathematics and Computer Science
Student: Luis Perez

Error correcting codes (ECC) are used every day for data transmission, which many people are not aware of. ECC, found in information theory, use methods to handle possible errors that may arise from electronic noise, to the scratch of a CD. Recently, ECC have gone beyond their traditional use. ECC can be used in applications from performing magic tricks to detecting and repairing mutations in DNA sequencing. In addition, ECC including Hamming Codes and Reed-Muller Codes, can be viewed through set theory, which give alternate perspectives on how these ECC work. In this research, various perspectives are examined in explaining the Hamming Code methodology behind error detection and correction. In addition, the Hamming Code’s properties as a perfect ECC are described through set theory and graph theory. Interestingly, the same conclusions can be found through the explanation of these methods which ultimately supports that ECC can be viewed more universally. This research also investigates further applications of the Hamming Code in a team competition and magic tricks through a set-theoretic approach. Reasonings as to how these applications are guaranteed to work given properties of the Hamming Code are also investigated. Moreover, applications of the Hamming Code are expanded to show its true significance as a perfect ECC. An investigation is done on the Hat Problem (a team competition) where all the conditions and outcomes of the game are explained through properties found in Hamming Codes. There is also an investigation on the Parity Card Trick, which is justified by elementary ECC concepts. An alternative perspective, similar to the syndrome method, is used to explain the Parity Card Trick where its properties are also validated through the Hamming Code. Finally, a more advanced version of the trick is created, and conditions of the trick are established through the Hamming Code. 

Regulation of Reaction Forces during a Long Snap with and without a Block

Program: HSI STEM ALLIES
Faculty: Travis Peterson, Ph.D., Exercise Science
Student: Johnathan Goldstein

To date, there has been no previous research analyzing the movement pattern of an American Football Long Snap. The regulation of lower extremity reaction forces (RFs) during a well-practiced goal-oriented task (GOT) has the ability to affect the upper extremities throughout the movement pattern. The aim of this study was to understand how ground reaction forces (GRF) are generated during the GOT of Long Snapping (LS). Eleven highly skilled male athletes aged 18-22 with at least two years of LS experience participated in this study. Subjects completed a total of 18 Long Snaps standing on two portable force plates (Kistler, 1200 Hz) covered with synthetic turf. Six long snaps were completed for each condition - No Block (N), Block Right (R), and Block Left (L). Snaps were performed at a distance of 14.5 yards while aimed at a target (Wizard Kicking® Solo-Snap) that simulated the average sized punter. The scoring system was based on the amount of adjustment needed by the punter prior to the kick (5/4=R/L hip, 3/2=R/L shoulder, 0=miss). Peak RF and net linear impulse (LI) were calculated in the mediolateral (ML), anteroposterior (AP), and vertical (V) directions during the initiation of the Snap. The initiation of a long snap was identified on a RF-time chart and defined in terms of AP values. Preliminary results show the relationship the lower extremities have with the athletes LS performance. Uneven push between the L and R legs in all three directions have a direct correlation to the direction of the snap; relating to the amount of compensation needed by the snapper. Much work is still to be completed before any statistically significant data can be published. With reproducible methods and materials and the initiation of the Long Snap defined (Push-Phase), future efforts will be focused on creating an index for analyzing the performance of a Long Snapper which would include the athlete’s RF’s in addition to the snap’s speed and accuracy.

Bioacoustics & Temporal Variation of Understory Bird Species in Premontane Cloud Forest

Program: Undergraduate Research
Faculty: Edgardo Arevalo, Ph.D., School for Field Studies , Biology
Student: Amir Mejia

A premontane tropical forest comprises a diversity of habitats and microhabitats that support a variety of species. Due to this habitat structure, it has been considered as a possible factor in the evolution of bioacoustics in bird species. It also is suggested that most forest birds have adapted to sing lower pitched songs that could potentially be effective in dense habitats rather than open habitats. This subject is relevant because it indicates how some bird species could have adapted to their physical environment in the most optimal vocalization pitch. Therefore, the objective of this research is to test the signal emission and assess the bioacoustics presence of the two focal species in two different habitats. In this study, the focal species were the Henicorhina leucophrys (Gray-breasted Wood-Wren) and Catharus fuscater (Slaty-backed Nightingale-Thrush). The data was collected by putting a song meter in a mature forest trail and another in a secondary growth forest. The song duration was then measured in Raven Pro 1.4, organized in Microsoft Excel 2011, and analyzed using PAST 3.14. The findings concluded that there is not enough structural difference to induce changes in the singing time of the species. However, the time distribution in the temporal variation has been affected. For future implications, more factors can be tested for and comparing the data to the same species found in different forest environments since these species are unique to cloud forests. Another study can be done focusing on the oddity of the temporal variation.

10:30am - 12:00pm
Poster Session

Location: Soiland Gym

When Beauty Harms: Revitalization and Environmental Justice along the Los Angeles River

Program: Pearson Scholars Summer Program for Leadership and Engagement in a Global Society
Faculty: Michael Brint, Ph.D. , Political Science
Student: Nakeissa Abbassi

The lack of policy mechanisms for recognition and resolution of environmental justice issues within environmental planning and improvement programs creates negative impacts on communities. Following key environmentalist action, such as ecological restoration and beautification, revitalized communities become appealing to new tenants willing to pay for amenities, thus displacing and gentrifying original communities with higher costs of living. Under current legislation such as the California Environmental Quality Act (CEQA), the Los Angeles River Revitalization Master Plan (LARRMP) has witnessed demographic displacement within the same communities it aims to improve. The purpose of this study is to determine how communities along the LA River are being impacted by the disjunction between revitalization plans and environmental justice issues. This research was conducted through policy and plan analysis, census data analysis, site visits, and interviews with individuals in the government sector, advocacy groups, and community. It was found that stakeholders can knowingly or unknowingly exploit legal loopholes present in the CEQA to bypass addressing environmental justice issues. While the LARRMP acknowledges underrepresented communities, it is not required to address potential displacement or gentrification. Subsequently, as long as communities are slated to be revitalized, displacement and gentrification persists in environmental justice communities along the River, demonstrated through demographic shifts and disproportionate increases in property values. Mitigation strategies, as seen in the 2018 Resilient Los Angeles plan, are still in early planning phases with medium to long-term timeframe goals that will not be addressed for five years or more, allowing for the continuation of negative impacts. The current environmental legislation does not adequately address environmental justice issues within environmental reform. Through policy recommendations and new legal definitions, this research can inform future legislation to better address environmental justice issues.

Applying Computational Statistics to Support Reproducibility in an Introductory Statistics Course

Program: HSI STEM ALLIES
Faculty: Christopher Brown, Ph.D., Mathematics
Student: Stephanie Allen

For many students in the sciences, an introductory statistics course may be the only formal statistics training they receive. Introductory statistics courses are currently stagnant. The curriculum was written when computations were performed by hand, a data set with 80 records and 3-4 variables was considered large, and accepted practices did not require disclosure of computational methods or software used. There are few attempts to incorporate reproducibility into an introductory statistics course, even though many research journals now incorporate such requirements into their editorial processes.The goal of this study is to explore the feasibility of incorporating programming in RStudio and the topic of reproducibility into an Introductory Statistics course. As well, as a subproject, a goal is to produce a reproducible study on the 2015 United States Mortality data set provided by the CDC. We first created 15 examples of how to use RStudio to gain an understanding of data using introductory statistics topics. For this, we used the Iris Data Set and ran RStudio through the free online server Cocalc. These introductory statistics tools were also employed to analyze the mortality data set. Creating examples using the Cocalc server was successful. However, we found that Cocalc did not support our dataset from the CDC. Thus, students will need to have computer equipment that can support a full version of RStudio in order to work with larger datasets. When using the above methods on the mortality data set, we discovered a significant difference in age at the time of death when comparing married and single individuals using an unpaired t-test (p-value < 2.2e-16). We hope to use this research to encourage introductory students to ask more questions about why these results might be significant and dive deeper into the numbers by investigating other confounders. Based on these results, we now believe that it is feasible to incorporate RStudio programming, and the topic of reproducibility, into an introductory statistics course.

Effects of Sex, Fatigue and Lead Leg Preference on Single Leg Squat Kinematics and Kinetics

Program: Undergraduate Research
Faculty: Michele LeBlanc, Ph.D., Exercise Science
Student: Jamie Alvarado, Tyler Lindholm

There are several factors that contribute to knee injuries, including muscle imbalances, hormones, lower extremity body asymmetries and movement patterns. Single leg squats are a movement often used to determine knee health, rehabilitate an injured knee or strengthen the knee and hip musculature. Purpose: The purpose of this study was to determine how fatigue and lead leg affect lower extremity joint kinematics and kinetics during the single leg squat.  Additionally, a comparison of these values between males and females was made. Methods: Thirty healthy subjects (15 males, 15 females) with no prior experience in the single leg squat between the ages of 18-25 participated in the IRB-approved study. Twenty-five reflective markers were placed on specific anatomical landmarks. After a warmup and practice trials, 3-dimensional marker data was collected using an 8-camera Vicon motion capture system (200Hz) and ground reaction force data were obtained with a Kistler force plate (1000 Hz). Subjects performed repetitions until exhaustion for each leg with rest between legs.  Lead leg order was randomized.  To ensure movement consistency, a low point band was used to identify when the lead leg knee was flexed approximately 90 degrees. A support leg stand was utilized to standardize the non-support leg position. Data were analyzed for the first, last and middle repetitions to determine the progression of fatigue.  Three factors (sex, lead leg, and repetition) were considered during the statistical analysis with p < 0.05 denoting significance. Results:  Males and females did not differ in age or activity level. However, male subjects had a higher BMI.  Males fatigued in fewer repetitions than females for both legs. Males had the greatest difference between lead leg repetitions (p<0.05). More males preferred to have their right leg lead while females had no difference in lead leg preference. Understanding how gender affects the movement is important as it may help inform athletes, coaches, trainers, and therapist to differences that exist due to gender.

eIF5A: A Potential Key to Preventing Amoebic Dysentery

Program: Swenson Science Summer Research Fellowships
Faculty: Paloma Vargas, Ph.D., Biology
Student: Emily Armbruster

Entamoeba histolytica is a single-celled parasite responsible for the intestinal disease amoebiasis or amoebic dysentery. During its life cycle, E. histolytica (Eh) transitions from an un-infectious form (the trophozoite) to an infectious one (the cyst) in a process known as encystation. Little is known about encystation at the molecular level, but a protein known as eIF5A, or eukaryotic translation initiation factor 5A, is thought to be involved in the process. Determining the function of eIF5A in E. histolytica encystation will contribute to our overall understanding of how the parasite’s life cycle proceeds. If we can understand eIF5A’s role in E. histolytica’s life cycle, this will improve our overall understanding of the requirements for and processes of encystation. Adding to our knowledge of this key step in the parasite’s life cycle will advance investigations into the development of novel therapeutics to prevent disease transmission. Before the function of eIF5A can be determined, eIF5A itself must be produced and purified for use. PCR and restriction enzyme digest were used to prepare the E. histolytica gene EHI_186480, an isoform of eIF5A, and plasmid pET44a for ligation. The PCR primers were specifically designed so that cloned eIF5A proteins would carry a 6x His Tag for easy purification.  The recombinant plasmid was then transformed into competent E. coli cells, and agarose gel electrophoresis was used to confirm whether ligation had been successful. Agarose gel electrophoresis revealed that digestion of the recombinant plasmid produced several DNA bands.These results indicate that ligation had not been successful.  In future, the primers designed for eIF5A gene PCR will be re-examined, and the previously described procedures will be re-attempted with the new primers in hopes of producing properly ligated recombinant plasmids.

Development of a New Carboxylic Acid Protecting Group

Program: Undergraduate Research
Faculty: Jesus Cordova Guerrero, Ph.D., Chemistry
Student: Alicia Asmundson

In organic chemistry, multiple functional group sites can be problematic if the chemical transformation must be performed chemoselectively. Protecting groups can alleviate this problem by isolating the functional group involved in the reaction while maintaining the rest of the structure. In this work, we propose the development of a new and efficient carboxylic acid protecting group, via a two-step process, namely the synthesis of the protected carboxylic acids followed by stability tests under various reaction conditions. The synthesis of this protected carboxylic acid is a two-step process. Starting with various benzaldehyde substrates, hydrazones were synthesized using hydrazine and ethanol under Nitrogen at room temperature to serve as a protecting group precursor. Following the purification of the hydrazones, an esterification step was performed to protect the carboxylic acid using 4-methoxybenzoic acid, dichloromethane, manganese oxide, and potassium phosphate at room temperature, resulting in a protected carboxylic acid, the final product of the synthesis. Out of several starting substrates, the m-tolualdehyde and the 3,4-dimethoxybenzaldehyde were the most stable and easily purified. The meta-tolualdehyde substrate yielded 28%, and the 3,4-dimethoxybenzaldehyde substrate yielded 74%. Both products were confirmed via NMR. Once the esters were synthesized, the protecting groups were tested under hydrolysis and monitored via GCMS and TLC at 5 minutes, 15 minutes, 1 hour, 3 hours, and 24 hours. Both esters were shown to be stable for 24 hours at room temperature under hydrolysis conditions. In the future, we will analyze the protecting groups’ stability under different conditions such as reduction, acid, base, and hydrogenation. Following the completion of the stability tests, we hope to have developed a new synthesis for a carboxylic acid protecting group that is stable under various conditions and can be applied to academic, pharmaceutical, and food research.

The Effects of Pesticides on Genetic Expression in Caenorhabditis Elegans

Program: Undergraduate Research
Faculty: Grady Hanrahan, Ph.D., Biology
Student: Vanessa Avaloas

Pesticides are commonly used throughout the United States and can include fungicides, herbicides, and fumigants. Different populations exposed to these chemicals involve those working (or going to school) in areas treated with pesticides and living in areas near exposure. To study the dangers of these pesticides at a genetic level, a robust research model is needed. Caenorhabditis elegans (C. elegans) is a very useful model organism to study changes in genetic expression because it has a completely sequenced genome, a simple body plan, and shows similarity to mammals in genomics and biochemistry. The goal of this study is to determine the effects of methoxychlor and chlorpyrifos on genetic expression in C. elegans. The chemical structures of the methoxychlor and chlorpyrifos will be characterized by gas chromatography-mass spectrometry (GC-MS). C. elegans will be cultured in T-75 tissue flasks and exposed to different concentrations for up to 72 hours. Observations, including any noticeable alteration in development or phenotypic expression, will be made at different periods. Changes in gene expression will be analyzed through RNA extraction, processing of the genome (possibly from an outside source), microarray analysis, linear regression models, ANOVA tests, and comparisons between the produced gene sets and publicly available gene sets. Expected results are that the pesticides will induce a delay in development, alter metabolism, increase the incidence of cell repair, and alter innate immunity functions. It is also expected that there will be disruption of mitochondrial function and calcium homeostasis, as well as inhibition of acetylcholinesterase (AChE), which will contribute to neuronal degeneration. Overall, the findings of this study will contribute to a better understanding of how harmful pesticide exposure can be to humans and the permanent effects these substances may have.

Effect of Environment on Limb Morphology Tradeoff in Sceloporus occidentalis and its Effect on Sprint Speed and Bite Force.

Program: Swenson Science Summer Research Fellowships
Faculty: Kristopher Karsten, Ph.D., Biology
Student: Shant Balci

Limb lengths of lizards inhabiting broader areas are often longer than lizards that live on uneven or narrow substrate. These longer limbs often correlate to faster sprint speed. Our study aims to determine if urban lizards, living on broad, human-made surfaces have longer limbs & faster sprint speeds than their non-urban counterparts. In addition, we wanted to determine if body size and bite force (a trait important for territory dominance) were different between urban and non-urban populations. We hypothesized lizards from urban environments (CLU campus) will have longer limbs, sprint faster, & stronger bite forces compared to those from more natural areas (Mt Clef and Cheeseboro Canyon). We captured lizards May-July usually between 0900-1200 h. Once captured, we recorded their location via GPS and environmental data such as habitat type, time of day, and substrate width. Once in the lab, we placed lizards in an incubator at 35C; the temperature found to be optimal for testing sprint speed. We measured sprints speeds by sprinting each lizard, individually, down a 2m track with IR sensors placed 25 cm apart. Each lizard sprinted three times with 1 hr rest between each trial. We measured bite force for three trials per lizard using a calibrated force transducer. Before release, we marked all lizards (to identify individuals) using a unique combination of toe-clipping and small paint dots. The mean body size (SVL) of urban lizards was 69.8 ± 1.53 mm (CLU campus; N = 19) whereas non-urban lizards were 66.9 ± 3.45 (N = 2; Mt. Clef) & 72.1 ± 1.80 mm (N = 14; Cheeseboro). The mean bite forces were 4.55 ± 0.21 N (CLU), 4.08 ± 0.64 N (Mt. Clef), & 4.80 ±0.24 N (Cheeseboro). The mean maximum sprint speeds were 2.08 ± 0.17 m/s (CLU), 2.94 ± 0.84 m/s (Mt. Clef), & 2.37 ± 0.17 m/s (Cheeseboro). Limb length measurements are in progress using digital photographs and ImageJ software. The project’s scope is to determine if there are differences in these important traits among lizard populations with different selection pressures.

Generative Adversarial Networks for Image Generation from Natural Language

Program: Undergraduate Research
Faculty: Craig Reinhart, Ph.D., Computer Science
Student: Tyler Berry

Computer generation of content from natural language has seen rapid advancement in the last few years through the application of generative neural networks. First described by Goodfellow, et al. (2014) was a generative adversarial network, that pit two competing neural networks against one another – one, a generator that attempts to create an output that could plausibly be a member of a given dataset, and another, a discriminator that ascertains the validity of generated outputs against that same dataset. These two networks are trained against each other, and therefore improve one another. Xu et al. (2017/2018) later proposed several key innovations for the generation of images from given text inputs, including stacking multiple networks in succession to create high-resolution outputs, and the use of attentional methods to associate words with areas of images to encourage the development of fine-grained detail. Our team sought to expand upon this work by generating luminosity and color information separately in our images, rather than generating them concurrently. We hoped that this elaboration would yield a text-to-image generation method that would achieve fine-grained detail more rapidly than previous models, and also potentially provide a method to colorize greyscale images given a text description. Our model reads in a text description into a neural network that has been trained on a dataset that pairs images and text descriptions, and then feeds an interpretation of that text into our network at multiple stages of generation, first increasing in size, then adding color information. We built our model with the Python programming language and the PyTorch framework and trained our model on a cloud-based computer. We have been able to effectively replicate the results that Xu et al. achieved for greyscale images, but have had less robust success with consistently generating appropriate color information for our images. We hope to continue to adjust parameters in our model in order to generate quality color images in the future.

The Effects of Serotonin and Mianserin on the Heart Rate of the Pond Snail Helisoma trivolvis in Satiated and Fasting States

Program: Swenson Science Summer Research Fellowships
Faculty: Kenneth Long, Ph.D., Biochemistry and Molecular Biology
Student: Sara Beylik

Serotonin (5-hydroxytryptamine: 5-HT) is a neurotransmitter that has been shown to be involved in the feeding response and hunger state processes of mollusks. Some studies have investigated how 5-HT and its antagonists may affect the heart by monitoring heart contraction, but few have combined these topics to discuss the relationship between the hunger state (fasting), 5-HT, and the heart. The purpose of this study was to test the effects of 5-HT and the 5-HT receptor antagonist mianserin on the heart rate (HR) of the pond snail Helisoma trivolvis when satiated and fasting. My hypothesis was that the HR of fasting H. trivolvis would increase when exposed to 5-HT and decrease when exposed to mianserin. Fasted and satiated pond snails were exposed to control artificial pond water and varying concentrations of 5-HT and mianserin. The heartbeat responses to the solutions were measured in beats per minute. Contractions of the heart were viewed using a dissecting microscope and were recorded using a cell phone. The heart rate was measured immediately, 30 minutes, and 60 minutes after 5-HT and mianserin solution exposure. The HR of fasting snails significantly decreased for most snail size ranges (P < 0.05). 5-HT significantly increased HR in fasted and satiated snails after immediate exposure and up to 60 minutes after exposure, while mianserin significantly lowered the HR in fasting and satiated snails after 30 minutes exposure (P < 0.05). Mianserin reversed the effects of 5-HT for satiated snails during immediate exposure and for fasting snails after 30 minutes exposure (P < 0.05). These results indicate that the effect of 5-HT is mediated by either the 5-HT2 or 5-HT7 receptors and not the 5-HT1 and 5-HT4 receptors. This research should assist in uncovering the systems that govern the heartbeat and how they may be influenced by outside factors such as metabolism.

Optimizing Protein Solubility for Crystal Formation

Program: HSI STEM ALLIES
Faculty: Katherine Hoffmann, Ph.D., Biochemistry and Molecular Biology
Student: Deana Bitar

Antibiotics have been used for several years to treat bacteria-related illnesses and diseases. However, with antibiotic resistance on the rise, many bacteria, such as Methicillin-resistant Staphylococcus aureus (MRSA), have become resistant to every current class of antibiotics. The overall goal of the Hoffmann lab is to create a new class of antibiotics that will be developed using structure-based drug design. The target protein for this project comes from Francisella tularensis, which is highly virulent. Its protein, FslA, synthesizes a virulence factor for the bacteria. FslA is very insoluble over time and tends to prematurely precipitate out of solution. It is a very understudied protein, and its structure is still unknown. The goal of our work this summer was to optimize the solubility of FslA using different pH levels of the buffer as well as small molecule additives, which are also known as sugar. Overexpression and purification of the protein were the first two steps necessary in order to optimize FslA’s solubility and set up crystals. Due to technical difficulties, significant time was spent troubleshooting instrumentation (including broken purification columns and burned out fuse boxes in the incu-shaker). Once these complications were resolved, we were able to confirm FslA overexpression and purification via SDS PAGE gels. We also determined that sugars such as sucrose, glucose, and trehalose were all insufficient at 100mM concentrations to successfully stabilize FslA’s solubility for over thirty minutes. Future research directions include testing whether a combination of additives, glycerol, and substrates are more successful in maintaining the solubility of FslA. Different pH levels of buffer will also be tested as a variable for solubility. Once protein solubility is optimized, we will follow with crystal set ups.

The Role of Type II Secretion of Legionella pneumophila in Growth at 25 and 35 Degree Celsius

Program: Swenson Science Summer Research Fellowships
Faculty: Paloma Vargas, Ph.D., Biology
Student: Kayla Cross

Legionella pnuemophila (Lpn) is a gram-negative bacteria that occurs naturally in freshwater and human-made water systems. Legionella pneumophila thrives in water systems found in large buildings such as water towers, air conditioning systems, and misters. In 1971, the first recorded outbreak of this disease was at the Legion Convention in Philadelphia. Legionella pneumophila is an opportunistic pathogen known as the causative agent for Legionnaires Disease in immunocompromised and elderly patients, with symptoms presenting as pneumonia. Bacteria can have up to six secretion systems used for survival in environments. Type II Secretion System, one of the systems utilized, has shown to play a role in the survival of Lpn through the secretion of twenty-five different proteins. While some work has been completed to characterize the role of these secreted effectors in host infection, we do not yet know the role of the Type II Secretion System on Legionella pneumophila survival in the environment. The goal of our study is to determine the role of the Type II Secretion System in Lpn survival at 17, 25, 35, and 42 Celsius. We used spectrophotometry to measure growth of Lpn Type II Secretion system mutant strains, which are missing individual effectors to test growth at various temperatures. Our study focused on the strains ProA, PlaC, LspF, nttA, nttB, and wild-type (130b) at 25℃ and 35℃. We collected samples and measure optical density at 0, 24, 48, and 72 hours. Data analysis is still in progress to determine the effect that each strain plays in the survival of Legionella pneumophila at 25℃ and 35℃. Future studies will involve testing these strains at additional, biological, or environmentally relevant temperatures, conditions, and hosts.

Patterns of Urine Washing Among Adult and Juvenile Squirrel Monkeys in Amazonian Brazil

Program: Swenson Science Summer Research Fellowships
Faculty: Anita Stone, Ph.D., Biology
Student: Nathan Delacth

Urine Washing, also known as UW, is a behavior common among neotropical primates. This behavior consists of an individual urinating onto its palms and subsequently rubbing the urine onto its feet. The function of this behavior remains unknown. The purpose of my study was to examine patterns of urine washing in wild squirrel monkeys and test four functional hypotheses for its occurrence. Previous work had shown that juveniles urine wash more than adults do in my study population. The study took place in the Eastern Amazonia, approximately 150km east of Belém, Brazil. I collected behavioral data on two groups of wild squirrel monkeys (adults and juveniles) for six weeks through two sampling methods (N=85 contact hours). In focal samples, I recorded the individual’s age, sex, activity, nearest neighbor, the occurrence of stressful situations, and distance to the observer. In addition, all UW instances were recorded with a note of the same variables, with the addition of ambient temperature and humidity. The temperature and humidity  also were recorded every 30 minutes while contact remained with the group. Initial analyses showed that the average rate of UW was 1.76 instances/hour (N=147 observations). UW frequencies among age-sex classes were as follows: one-year-old juveniles accounted for 41% of observations, followed by second-year juveniles (31%), adult females (16%), and adult males (12%). Because UW was most frequent among juveniles, particularly young juveniles, UW most likely does not serve as a sexual communication mechanism in squirrel monkeys. However, in 29% of juvenile urine washes, the individual was looking at the observer. Furthermore, in 7% of juveniles UW occurrences, the juvenile urine washed after a stressful situation in the group. The preliminary results mostly support UW as a mechanism of anxiety displacement, but further analysis will provide a better understanding of the function of UW.

Can News Story Comparisons be Used to Identify Fake News?

Program: Swenson Science Summer Research Fellowships
Faculty: Chang-Shyh Peng, Ph.D., Computer Science
Student: Cole Elpel

With the rise of independent news sources, the concept of “fake news” has always been an active threat. The goal of this project is to make an attempt at understanding how fake news works by directly checking a news story for misinformation.

 

The hypothesis is that if multiple news stories on a central topic are accurate, they should share the same (or similar) information. Through a comparison of these news stories with one another, we can determine if a story is fake or not. The process of doing so will require some sort of program that can run a comparison system that can provide a percentage of similarities between one news story and a series of news stories. To accomplish this, the program will use the programming language Python. Using a library called “Newspaper3k,” the program can extract any news story given its URL. With each story, the program then uses a library called “nltk” to acquire the article’s text and keywords. It then filters out the “facts” of each article using this information to be used in comparisons. These newly-filtered stories are then compared against one another using a method called “cos-similarity” which allows us to get percentages based on every single story compared against every other story we collected with the program. These percentages are then interpreted as follows: 50% and above = related, 30 - 40% = related, but on a different aspect of the story, 30% and below = unrelated.

 

Experiments and tests run using this project have shown preliminary success in meeting the 50% threshold. These results, with the proper confirmation, could provide us with a new understanding of how fake news is identified. Seeing as how a method for doing this has been hotly debated, this project could provide a significant step in fighting this issue that has become/will be more apparent in the past and years to come.

Analysis of Bacterial Colonies in Burned and Unburned Soil Environments as Conducted using DNA Shearing and Metagenomics

Program: Swenson Science Summer Research Fellowships
Faculty: Theresa Rogers, Ph.D., Biology
Student: Giselle Gallardo

The use of metagenomics as a means of understanding the microenvironment has displayed uses in both the furthering of a comprehensive understanding of the environment and the means by which one can find new ways to go about it. It is known that there has been an increase in wildfires to affect the environment and understanding the effects the microenvironment has on the macro environment will aid in a deeper understanding of the effects and requirements of environmental reconstitution. With a better understanding of the physiological interactions of the soil microenvironment, a better understanding can be gained of how the devastation of a wildfire can affect life on both the macro and micro level.  The purpose of this research was to gain a deeper understanding of the metagenomic composition of the different soil environments. It was expected that that there would be key differences seen in the physiological interactions of bacteria in healthy soil environments and post-burn soil environments. There would be a possibility of genetic differences that could account for proliferation of certain bacterial colonies in post-burn colonies over others. In order to study the differences in environments, samples were collected from the Thomas Fire site (Ventura Botanical Gardens) over a 6-month period. DNA extraction, shearing, and bioinformatics protocols were then conducted in order to illustrate the composition of the bacterial environments. In the beginning stages of the research it has become apparent that there is a difference in the amount of dsDNA within 1st and 6th month samples and future work will explore the differences in phylogeny of the bacterial environments. The phases of reconstitution are easily observable when analyzing the macroenvironment, however the phases of reconstitution for bacterial colonies is not as well understood and furthering of that knowledge will provide a comprehensive understanding of the wildfire phenomenon that is so prevalent within the California state.  

Responses to YouTube Apologies: Expressions of Sincerity and Forgiveness in YouTube Comments by Age

Program: Culver Fellowship
Faculty: Jean Kelso Sandlin, Ph.D. and Monica Gracyalny, Ph.D., Marketing Communications
Student: Alyssa Gee, Claire Thompson

As social media are increasingly used to host the video apologies of public figures, public relations professionals have adjusted their strategies to fit platforms that incorporate elements of both mass communication and interpersonal communication. However, some research suggests that the verbal content and nonverbal delivery of an apology video posted on social media may have little impact on the audience’s opinion of the figure, at least as reflected in the audience posted comments. One possible explanation for this is that the public figure’s prior reputation may have a greater impact on audiences than either the apology itself or the commenters’ demographics. The purpose of this study was to investigate how public figure reputation, apology delivery, and audience characteristics influence audience perceptions. Each participant was randomly assigned to read a negative or positive biography of a fictitious CEO who committed a transgression, and randomly assigned a deviant or normative video apology (based on nonverbal cues) or a text-only apology. The verbal apology content was consistent across all three conditions. Comments were analyzed from 600 survey participants who were asked to leave a “YouTube comment” after watching the apology. Two trained independent coders coded 594 comments. Consistent with past research, the majority of the comments coded reflected a negative opinion of the public figure, although the deviant apology was more likely to be deemed insincere than the normative or text-only apology. In addition, female participants were more likely than males to leave strong negative comments, whereas males were more likely to leave strong positive comments. Finally, older participants were more likely to rate an apology as sincere or neutral and leave more positive comments.

Regulation of Reaction Forces during a Long Snap with and without a Block

Program: HSI STEM ALLIES
Faculty: Travis Peterson, Ph.D., Exercise Sceince
Student: Johnathan Goldstein

To date, there has been no previous research analyzing the movement pattern of an American Football Long Snap. The regulation of lower extremity reaction forces (RFs) during a well-practiced goal-oriented task (GOT) has the ability to affect the upper extremities throughout the movement pattern. The aim of this study was to understand how ground reaction forces (GRF) are generated during the GOT of Long Snapping (LS). Eleven highly skilled male athletes aged 18-22 with at least two years of LS experience participated in this study. Subjects completed a total of 18 Long Snaps standing on two portable force plates (Kistler, 1200 Hz) covered with synthetic turf. Six long snaps were completed for each condition - No Block (N), Block Right (R), and Block Left (L). Snaps were performed at a distance of 14.5 yards while aimed at a target (Wizard Kicking® Solo-Snap) that simulated the average sized punter. The scoring system was based on the amount of adjustment needed by the punter prior to the kick (5/4=R/L hip, 3/2=R/L shoulder, 0=miss). Peak RF and net linear impulse (LI) were calculated in the mediolateral (ML), anteroposterior (AP), and vertical (V) directions during the initiation of the Snap. The initiation of a long snap was identified on a RF-time chart and defined in terms of AP values. Preliminary results show the relationship the lower extremities have with the athletes LS performance. Uneven push between the L and R legs in all three directions have a direct correlation to the direction of the snap; relating to the amount of compensation needed by the snapper. Much work is still to be completed before any statistically significant data can be published. With reproducible methods and materials and the initiation of the Long Snap defined (Push-Phase), future efforts will be focused on creating an index for analyzing the performance of a Long Snapper which would include the athlete’s RF’s in addition to the snap’s speed and accuracy.

Determining the Kinetics of Desferroxiamine D from Streptomyces coelicolor using Isothermal Titration Calorimetry

Program: Undergraduate Research
Faculty: Katherine Hoffmann, Ph.D., Biology
Student: Eliana Goncuian

The long-term objective for this research is to create a new class of antibiotics that targets the non-ribosomal peptide synthetase independent siderophore (NIS) pathway in bacteria. The focus of my current research is to quantify the kinetic constants and obtain the kinetics curve of Desferroxiamine D (DesD), from Streptomyces coelicolor, reacting with its large substrate, desferroxiamine G (dfoG). To do this we used Isothermal Titration Calorimetry (ITC) to collect data, and GraphPad Prism software to fit the kinetics curves, as well as, calculate the kinetics constants. We successfully gathered and analyzed ITC data for both the catalytic and non-catalytic forms of DesD. However, almost identical curves for both the catalytic and non-catalytic (negative control) reactions was observed. We hypothesized that the data reflected hydrolysis and dilution of the cofactor (adenosine triphosphate, ATP) and substrate (dfoG) which masked the data from the catalytic reaction. We rearranged our experimental set up to minimize concentration changes for cofactor and substrate and successfully recollected data. Future directions include repeating the experiment with variable magnesium chloride to explore the concentration needed for maximal function. This data will be the foundation for future drug tests (inhibition of kinetic function) to determine the efficacy of the drugs against DesD.

Determining the Structure of NIS Synthetase FslA via Solubility Studies

Program: HSI STEM ALLIES
Faculty: Katherine Hoffmann, Ph.D., Biochemistry and Molecular Biology
Student: Gevona Hernandez

Francisella tularensis (FslA) is a bacterium which creates siderophores. Siderophores are metal chelators and play a key role in acquiring critical iron for bacteria survival. When a bacteria’s iron levels are too low, siderophores are released to retrieve iron from the environment. In a human host, this causes an iron deficiency and allows the virulent bacteria to thrive. Siderophores are assembled in two main pathways, one of which is not well studied and is called the Nonribosomal Peptide Synthetase - Independent Siderophore pathway (NIS).

 

NIS synthetases are a family of proteins which assemble siderophores in NIS pathways. The unique structure, chemistry, and role in virulence make them good drug targets for structure-based drug design. In the bacteria F. tularensis, the siderophore produced is called rhizoferrin, and the NIS synthetase protein is FslA. Rhizoferrin strongly resembles the siderophore from Methicillin-Resistant Staphylococcus aureus (MRSA) a worldwide health issue. Currently, the NIS synthetase family of proteins, particularly FslA, lacks basic research. A drug designed against FslA would potentially be effective against MRSA. 

 

The Hoffmann lab is pursuing structure-based drug design by inhibiting the synthesis of the siderophores in the NIS synthetase step. In order to design an inhibitor, the structure of the FslA protein must be determined. We propose to determine its structure through x-ray crystallography in its apo form, as well as its bound to small and large substrate forms. Currently, the Hoffmann lab has found a problem maintaining the solubility of FslA. We had hypothesized that the solubility of FslA would be enhanced by the binding of substrates before crystal trials. We used substrates Citrate and Diaminobutane, as well as ATP--as a cofactor for energy. We found several crystal hits, one of which created a diffraction-quality crystal. Future directions include reproducing this crystal, collecting data on it, and pursuing additives to enhance the solubility of FslA.

Taste Aversion and the Effect of Epicatechin on Memory Formation in Lymnaea stagnalis

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Kenneth Long, Ph.D., Biology
Student: Helen Hong

Memory helps define who we are, and stress is known to affect memory formation. Epicatechin, a phytochemical found in dark chocolate and green tea, has been shown to enhance memory formation in rodents and gastropods. The purpose of this study was to test the effects of epicatechin on memory formation in the pond snail, Lymnaea stagnalis. We hypothesized that epicatechin will enhance memory formation. We tested whether snails would associate electric shocks with sucrose, a food that stimulates feeding behavior in this species (taste aversion conditioning). A pair of needle electrodes separated by 21.5 mm delivered shocks to the water on each side of the snails. We performed a stimulus strength-duration experiment to determine the optimal stimulus parameters for the conditioning. Our criterion for a behavioral response was a full-body withdrawal that lasted for 10-14 seconds.  We found the threshold stimulus strength of 4 volts and chose 8 volts as the stimulus strength with a duration of 55 msec (the “behavioral chronaxie”). A pre-conditioning feeding response test (bites per minute, bpm) was performed to observe response toward sucrose (100 mM in an agar pellet) prior to conditioning. We then applied shocks that caused withdrawal and termination of feeding. Snails were tested 24h post-conditioning and their response to sucrose was measured. If a memory was formed, bpm should be significantly lower than for the pre-conditioning test. Two groups of snails (n=10 per group) were tested under the same conditions: a control group and a group exposed to 15mg/L epicatechin 40 minutes immediately after conditioning. Two-tailed paired t-tests were performed. We found no effect of epicatechin on memory in these trials (p > 0.05). We then tested the effects of increased calcium concentration (80mg/L) in the testing water. There was a significant reduction in bpm in the 24h-memory test compared to the pre-conditioning test (p = 0.0000546). In conclusion, the results showed that epicatechin enhanced memory formation in the presence of high calcium.

Audience Perception of Women’s Communication Style in a Political Crisis

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Monica Gracyalny, Ph.D., Marketing Communications
Student: Heather Wilson-Hooker

As our nation’s political climate continues to change, crisis communication is becoming an increasingly important factor in public opinion. With over 300 million people involved during a political crisis, communicators must present information as clear and concise while maintaining a calm and collective demeanor. Previous research suggests that female communicators in particular face difficulties persuading an audience compared to male communicators. The purpose of this study was to investigate how a woman’s communication style, either masculine or feminine, influenced the persuasiveness of a political crisis message, as well as audience perceptions of likeability and credibility. The experiment manipulated gendered communication styles (masculine or feminine) in a mock political crisis. 398 participants completed an online survey where they were randomly assigned to view one of two videos of a female actor presenting a press release during a hypothetical political crisis, demonstrating either a feminine communication style or masculine communication style. The verbal content and nonverbal cues were manipulated in each video. The survey asked questions about the extent to which participants were persuaded by the message, as well as participants’ perceptions of the Press Secretary’s credibility and likeability. Results showed that female participants were less likely to be persuaded by the feminine communication style than the masculine style. However, there was no difference in persuasive effects for male participants. This is consistent with past research on persuasion that found that males and females respond differently to female communicators. There were also no differences between the two communication styles and audience perceptions of credibility and likeability for either males or females. The results from this study add to the literature addressing the challenges that female communicators face in a male traditional role, especially in the political arena.

Synthesis of Metal-Organic Frameworks as Efficient Drug Delivery Systems

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Jesus Cordova Guerrero, Ph.D., Biochemistry and Molecular Biology
Student: Gregory Hovhanessian

Metal-organic frameworks (MOFs) are versatile hybrid materials that are highly crystalline and porous, presenting high surface are. They are comprised of organic linking units (usually carboxylic acids) and metal clusters that allow for extensive customization of pore size and composition. The versatility of these materials makes them excellent candidates for biomedical applications, such as efficient drug storage and controlled delivery. Chemotherapeutic agents present a wide variety of chemical architectures, mostly small molecules that in many cases do not present biospecificity, leading to high and frequent dosage, limited pharmacokinetics and unfortunate side effects. Considering the structural properties and low toxicity of MOFs, it has been recently investigated to possibly use these materials for a controlled drug release with a high drug storage capacity. This project will allow for the development of an efficient anticancer therapy via the synthesis of a MOF as a model system comprised of an organic linker bearing a pseudo-drug that upon exposure to a specific wavelength of light, the pseudo-drug portion can be released. This work aims to develop efficient anticancer therapies via the application of metal-organic frameworks as vehicles for the controlled drug delivery in three steps. First, the synthesis of the Organic Linker via a five-step synthesis bearing a substituted coumarin system as the pseudo-drug. Second, the Crystallization of MOFs expected the synthesis of Zr- and Fe-based MOFs by mixing the organic linker in the presence of a suitable metal cluster under thermal conditions. Third, photocleavage of pseudo drug which includes the release of the pseudo-drug, via irradiating the MOF with light, to obtain the free pseudo-drug as well as an oxidized MOF. So far, we have completed half of the synthesis of the organic linker, namely the nitration of 2,5-dibromobenzaldehyde and the reduction of the aldehyde group to an alcohol. In conclusion, we expect that the MOF is crystallizable and can be used as an efficient drug delivery system.

Synthesis and Purification of N-Hydroxy-N-(5-aminopentyl) Succinamic Acid (HSC)

Program: Undergraduate Research
Faculty: Katherine Hoffmann, Ph.D. and Jason Kingsbury, Ph.D., Biochemistry and Molecular Biology
Student: Yoojin Jang

The Non-ribosomal peptide siderophore Independent Synthesis enzyes (NIS synthetases) in prokaryotes allow harvesting of iron with chelators called siderophores. These NIS synthetases have been under-studied, for structural and biochemical description on sub-types and iterative proteins are not known. Purpose: The broader aspect of this project is to understand how NIS synthetases work. The purpose of this particular project was to synthesize and purify N-Hydroxy-N-(5-aminopentyl)succinamic acid (HSC) in order to study structure and kinetics of DesD, a NIS enzyme.Method: The synthesis portion had N-(Benzuloxy)-N-[5- (benzyloxycarnonylamino)pentyl]succinamic acid was dissolved in tert-butanol. 0.1N HCl (mixture of concentrated HCl and 1,4-dioxane) and 10% Pd-C were also added. The reaction mixture was placed under H2(g) for three hours, stirring. The reaction mixture was filtered through celite and the solvent was removed under vacuum. The purification part of this project was executed with model system. N-(5-amino-pentyl)-succinamic acid. The crude material of real system and model system were purified by both HPLC and C-18 column chromatography. Results: Synthesis has yielded solid-like residue along the walls as well as some crystals on the bottom of the reaction vial. The identification of the product has not been validated by H NMR. Purification by HPLC has not yielded successful separation; however, C-18 column has shown promising results with model and real system. Conclusion: The synthesis of N-Hydroxy-N-(5-aminopentyl)succinamic acid should be scaled to grams-quantity when every aspect of this project is adjusted and perfected. The purified compound can be used to study the kinetics and structure of DesD to broaden more understanding on NIS synthetases.

Cloning and Characterization of ClpV1, an ATPase from the Bacteria, Pseudomonas putida

Program: HSI STEM ALLIES
Faculty: Robert Richards, Ph.D., Biology
Student: Jason Krastein

The type VI secretion system (T6SS) was initially discovered by Pukatzki in 2006 while screening numerous isolates of Vibrio cholerae for novel virulence factors and is present in approximately one-quarter of all Gram-negative bacteria.  This system is able to deliver virulent proteins from the bacterial cytosol to target cells using a unique injection-like mechanism.  Energy sources to transport these toxins comes from two ATPases, TssM and ClpV. The system works as a channel that allows proteins or protein -DNA complexes to enter or leave the cell. The movement is driven by ATPases found in the cytoplasm by giving energy to large a translocation complex through large conformational changes. The T6SS family is the most versatile of secretion system due to its large variety of functions; some are used to translocate virulence factors, while others facilitate horizontal gene transfer. A subunit of the T6SS is the ClpV. This subunit is important in order to contract the sheath of the TssC subunits. However, it is inferred that ClpV has other roles such as interacting with other compounds or proteins.

 

The focus of this research was to test protein-protein interaction studies under different conditions to identify novel adaptor or regulatory proteins associated with ClpV ATPase. The methods continued as follows: Grow P. Putida and obtain DNA, PCR the ClpV gene (Add attachments for specific vectors), insert it into a vector (pet 44+b or aLICator), transform BL21 E. Coli competent cells, express ClpV with his-tag, isolate and conduct basic enzymatic assays to determine activity.  Additionally, we plan on preparing two truncated constructs of the ClpV gene. One construct will possess only one ATPase domain and the other will have both (wild type). To date, the ClpV gene has been amplified via PCR and we have amplified two truncated versions. These truncated constructs will be tested to see if both ATPase domains are necessary for the activity of ClpV.

Digital 3D Image Reconstruction via Sonar Rangefinding

Program: Swenson Science Summer Research Fellowships
Faculty: Craig Reinhart, Ph.D., Computer Science
Student: Kevin Hwa Lee

3D image reconstruction is the process by which a 3D model is generated using a set of 2D images. One of the main challenges of image reconstruction is depth determination; projecting a 3D scene onto a 2D image results in loss of depth, an essential visual component of 3D objects. Much of work in image reconstruction focuses on the techniques and algorithms that infer depth from images. Specifically, many methods attempt to model the human visual system and utilize visual cues, such as stereo parallax, occlusion, and focus. However, a different approach for depth determination is rangefinding, which utilize time-of-flight sensors for distance measurements. Rather than inferring depth information strictly from images, depth data can be directly measured using time-of-flight sensors. The focus of this project was to create a 3D image reconstruction system that measures depth in real-time using a sonar rangefinder.

 

The reconstruction system used the following tools: a robotic arm, a digital camera, a sonar sensor. The camera and sonar sensor were mounted to the robotic arm and calibrated to enable accurate measurement of scene data. Thereafter, the camera and sonar sensor were used to collect image and depth data from the scene. The robotic arm was used to allow both sensors to make precise movements through space. After data collection, image and depth data were registered in a single coordinate system and visually rendered into a 3D representation of the scene using the image processing software “ImageJ.” Multiple experiments were conducted to find the optimal parameters for image and depth data collection. The implementation of the image reconstruction system was successful. Results show that the system can create 3D models of primitive shapes, such as rectangular prisms. Future work will be done to measure its performance on more complex shapes. The sonar sensor is limited due to surface reflectance variability and noise and, thus, exploring other sensors, such as LiDAR, may be worthwhile.

What’s Culture Got to do With It? Rwanda’s Road to Cooperation and Integration from Ethnic Conflict

Program: Pearson Scholars Summer Program for Leadership and Engagement in a Global Society
Faculty: Gregory Freeland, Ph.D, Global Studies, Political Science, and Psychology
Student: Anna Lundsten

This project deals with the question, can culture generate a sense of cooperation and integration after ethnic conflict? We hypothesized that Rwanda’s seemingly recovery is directly linked to the promotion of traditional dance and culture; not only linked, but directly proportional, to Rwanda’s success is the government's support of traditional practices. To answer this question, research was conducted through literature research, site visits, cultural events, and informal interviews. To date, the results have shown that a governmental push of preserving culture, specifically a unified Rwandan culture, has had immense, lasting impact on Rwanda’s recovery. Governmental offices, specifically tailored to cultural preservation are focused on creating one central Rwandan identity. Rwanda strives to institute a Rwandan nationalism throughout their country by accurately teaching pre-colonial Rwanda history and culture. Specifically, the government focuses history on the colonial creation of the Hutu and Tutsi groups, that previously had never been ethnic groups. This research not only tells the story of a thriving Rwanda, but it strives to ensure that readers understand the misconceptions that are often learned about Rwanda.  It serves as an educational tool not only for those who study the Rwandan genocide but for those who wish to understand the incredible history of a country in its fight to succeed. Research on such topics not only impacts the readers but impacts the writers themselves. It forces the question, is what you are taught in your life really the truth, and if not how will you react? Will you strive to find the truth, or will you be content to live in a world where what you were taught must be correct?

Protein Characterization of nahO and nahM

Program: HSI STEM ALLIES
Faculty: Robert Richards, Ph.D., Biochemistry and Molecular Biology
Student: Nodirkhon (Nodir) Mamatov

Phenol has been identified as one of the primary environmental pollutants (Mahiudddin et al., 2011,). Degradation of phenol via meta-cleavage pathway (A. Platt et al., 1995) is the terminal reaction sequence in the catabolism by Pseudomonas strains of a wide range of aromatic compounds including phenols. The nahOM genes encode enzymes catalyzing the two terminal reactions of the meta pathway, namely 4-hydroxy-2-oxovalerate aldolase (HOA) and acetaldehyde dehydrogenase (acylating) ADA, respectively (A, Platt, et al., 1995). In this project, we plan to analyze the nahOM complex to gain a better understanding of the meta-cleavage pathway.It has been hypothesized that the crystal structure of 4-hydroxy-2-oxovalerate aldolase transcribed from nahOM will be similar to its homologue – dmpFG. Previous research (Nathalie et al.) has determined the structure of dmpFG along with identifying the unique water-filled intermolecular channel. However, we still do not know how the individual subunits communicate. To understand intersubunit communication, we want to determine the structure of nahM protein on its own, and of the nahOM complex. To determine the structure of nahOM, the PCR product of nahOM gene was obtained. No further work has been done on the structure of nahOM due to the unavailability of vectors required for ligation and transformation. Regarding nahM, the synthesized gene product in vector with his-tags was obtained. Next, the gene product was transformed into competent E.coli BL21 cells. The cell cultures were grown in Luria Broth in the presence of 0.2% dextrose and 100ug/ml ampicillin. The cultures were lysed using digital sonifier, and the proteins were purified using Ni-NTA beads. We have found that nahM is predominantly in the insoluble fraction. Because a protein can be structurally characterized in its soluble form, currently we are developing experiment to drive the protein from insoluble fraction into the soluble fraction.

Maximizing Solubility of FslA for Future Kinetic Work

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Katherine Hoffmann, Ph.D., Biochemistry and Molecular Biology
Student: Drew Miles

It is our common misfortune that the effectiveness of antibiotics is decreasing at an alarming rate. Indeed, many are no longer viable as a means of treatment. Recognizing the strong correlation NIS siderophores have with virulence in bacteria, targeting NIS synthetases in antibiotic design appears a promising solution to the antibiotic crisis. NIS synthetases, such as FslA, have novel fold and chemistry which makes them an interesting subject for research as well as an excellent target for antibiotics. FslA catalyzes the creation of the siderophore rhizoferrin via two bonds: a molecule of citric acid is added to each amine in putrescene in an iterative manner. NIS synthetases are a necessary step in the biosynthetic pathway to produce NIS siderophores, virulence factors in such illnesses as MRSA and Tuleremia. Using Differential Scanning Calorimetry, thermal assays were run in varying buffer conditions to determine the optimal buffer conditions for FslA to maximize solubility for the protein. DSC data included a melting point for FslA in each buffer solution. The DSC experiment will also reveal if FslA is unstable at the working temperature of FslA, 23 °C. The buffer solution in which FslA melts at the highest temperature translates to greater overall stability. We found that the melting point range for FslA (70-90°C) is well above my working temperature with it (35-37°C), allowing me to conclude that stability is not a factor in the insolubility of FslA. Overcoming the relative insolubility of FslA will allow kinetics research to be done which will establish a baseline for future inhibitor testing and represent the preliminary binding studies and pilot kinetic work for FslA. This future research promises the first characterization of FslA and one of the first for NIS synthetases.

Structural Studies of the Iterative Enzyme DesD: Cooperativity, Substrate Variability and Conformational Changes

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Katherine Hoffmann, Ph.D., Biology
Student: Yasi Mojab

Iron is essential for bacteria to survive. When iron concentration is low, bacteria secrete siderophores. This mechanism enable bacteria to use iron in the environment. Siderophores may be assembled by non-ribosomal peptide synthetase (NRPS)- dependent pathway, which uses large complexes and poly-ketide reaction, or NRPS-independent siderophores known as NIS-pathway. Our lab is focus on NIS independent siderphores, because they are associated with virulence in pathogenic bacteria. Streptomices coelicolor produces NIS siderophores Desferrioxamines B, and Desferrioxamines E. Utilizing the same pathway containing four enzymes: DesA, DesB, DesC, and DesD. NIS synthetase unique structure and chemistry, DesD was the model enzyme used in our lab. To prevent enzyme from reacting with the substrate, mutant form of the enzyme was used. The goal of this research was to figure the enzyme specificity and flexibility of loop capping the binding site by solving the atomic level structure of DesD.

 

In this research, structure of DesD bound to ATP and dfoB was solved. X-ray crystallography technique, CCP4i2 computer software, COOT and REFMAC5 within CCP4i2 was used to solve the atomic level structures of product-boned complex. Data were validated through PDB-REDO. The Rwork and Rfree for the solved structure were 25% and 30% respectively. These R values were relatively higher than the apo structure which had the Rwork and Rfree of 17% and 20% respectively. This may be due to the fact that the apo structure is symmetrical and no substrate is involved. In contrast, the solved structure has substrate only on one side due to its negative cooperativity.

 

The statistical analysis along with the electron density suggests that the substrate is present, which further evidence the broad substrate specificity of DesD. Future work will include structure- based inhibitor design to prevent DesD from binding to substrate and thus prevent synthesis of its siderophore, which can be a new class of antibiotic.

Global Climate Compacts and Emission Reduction

Program: Overton Summer Research Program in Economics
Faculty: Matthew Fienup, Ph.D., Economics
Student: Kathryn Monohan

Changing environmental conditions and the consequences affect every living thing to some degree. Therefore, climate change is an impending issue consistently receiving global attention; resulting in international policies regulating carbon dioxide (CO2) emissions, in an attempt to lessen human impact on the atmosphere. This research will evaluate whether or not the participation in global climate compacts, specifically the Kyoto Protocol (1997), reduce global emission levels. Game Theory was the baseline for the null hypothesis stating global climate compacts do not effectively reduce emissions. If there is found to be no change or an increase in global CO2 emissions after the creation and implementation of these two compacts, then monetary resources are exhausted ineffectually. The regression used is a difference in difference approach. Data was gathered from the European Commission Joint Research Centre on levels of carbon emissions in the years 1995 and 2010 for all countries included in the research. This models directly investigates the change in emissions between the two years, while controlling for other economic and environmental variables, to see if the Kyoto Protocol had any effect on emission levels. This research’s initial results find Kyoto to reduce carbon emissions minorly. Two other primary findings are countries with more Net National Income per Capita, and population density are more likely to be high emitters, but countries participating in multiple climate compacts tend to be “greener” and effectively reduce emissions. While this research found some reduction of emissions based on Kyoto, there should be a cultural shift to eliminate all green-washing and necessitate binding target emissions for any ratified country. Climate change is impending and threatens the lifestyles of many cultures and people; so knowing one international policy is effective in reducing emissions should incentivize more wide-spread implementation and funding.

The Effects of Ocean Microplastics on the Digestive System of the Globally Distributed Mussel Mytilus Galloprovincialis

Program: Swenson Science Summer Research Fellowships
Faculty: Kwasi Connor, Ph.D., Biology
Student: CJ O'Brien

Plastic pollution that enters the marine environment never fully breaks down and becomes fragmented into smaller pieces. While this plastic may be small in size, it is known by the scientific community to have negative implications for the health of many marine organisms once ingested. The intertidal mussel, Mytilus galloprovincialis is a widely distributed keystone species that is exposed to fluctuations in the intertidal-zone as well as microplastic in its environment. We assessed whether microplastics effects amylase digestive enzyme activity in M. galloprovincialis under laboratory conditions using the Somoygi-Nelson method, as described by German and Bittong (2009). The experimental design consisted of 8 separate glass beakers, filled with 1000ml of Instant Ocean water. Each beaker contained an air stone and three mussels which were randomly selected from the maintenance tank. A total of 24 mussels were used for this experiment.To simulate varying intertidal conditions in a laboratory, two food regimes were implemented: four beakers received high food concentration (0.0898/mL) of food and four beakers received the low food concentration (0.018/mL). All 8 beakers received the same concentration (1.09 μl) of 10um microplastic diluted in water in order to satisfy 110 particles/mL daily (Van Cauwenberghe et al. 2018). Our laboratory results indicated that enzyme activity of amylase in microplastic treatments did not differ (>0.05) from those in control treatments in either low or high food concentrations. Results from our laboratory experiments indicated that M. galloprovincialis did not modulate digestive enzyme activity once subjected to microplastics at low ambient concentrations. This could be due to reduced feeding or compensatory strategies.  Future experiments will subject mussels to higher ambient microplastics concentrations. 

Photo Sender

Program: HSI STEM ALLIES
Faculty: Chang-Shyh Peng, Ph.D., Computer Science
Student: Alberto Ortiz

Technology has changed over the years, mainly due to humanity’s need to simplify the world around them and unravel all its mysteries. However, technology has yet to unravel its full potential to the world. The potential that it holds is the ability to completely create a fluid experience for the user. Through the tailoring of our needs, humanity has pushed computerization to its brink to create this new technological modern era. Thus, there is no need to be repeating tasks that can be easily automated using programming languages. This research attempts to focus on this concept of creating a seamless world by creating an application that automates the laborious task of printing pictures to specific orders. Instead of needing human interaction to print each specific order, the application will streamline the process by efficiently reading the order from the customers and communicating back to the printer. This will allow photo studios to spend their resources more efficiently. The development of the application has begun, and the user interface for both photo studio and client has been tested and still undergoing further testing. Further development of file sharing and communication between the printer and the application is still in development. The concrete results will produce an application that can reduce human labor within a photo studio. Through the process of making the application, the potential results will lead to a greater understanding on how to make different pieces of technology work with each other while still ending up with the needed result. The implications of the research will give more attention to the need of automation within our daily lives. This is the step towards continuing the conversation of further melding automation and technology together. Technology is at our fingertips, and it can be manipulated to do everything we need and want within our own imagination. Therefore, we must no longer spend any of resources on time-consuming tasks when resources can be spent much more efficiently.

Thermal Response in the mussel, Mytilus galloprovincialis, under Anaerobic Conditions

Program: Undergraduate Research
Faculty: Kwasi Connor, Ph.D., Biology
Student: Melissa Pepper

Life in the intertidal zone must adapt to changes in their environment due to daily tidal changes. The mussel, Mytilus galloprovincialis, is a stationary bivalve found in tidally-regulated bays along the California coast. Mytilus galloprovincialis is ecologically important because they filter the water column, are model organisms of extreme environments, and bio-indicators of global climate change. During low tide, mussels are exposed to air and thermally stressed leading to valve closure and onset anaerobic metabolism. This study evaluated the effect of high temperature during low tide on gene-expression of heat-shock protein, HSP-70. For our first experiment, we placed mussels (N=3) in three beakers that simulated three different physiological conditions (aerobic cold, anaerobic cold, and anaerobic hot) for 6 hours. After 6 hours, we dissected all mussels and analyzed the gill tissue. Our second experiment tracked gene-expression temporally through a low-tide heating event. We immediately dissected four mussels at time 0 from the tank and left 12 more mussels out on a lab bench. Four mussels were dissected every 3 hours for a 6-hour period; after 6 hours, we reintroduced the last four mussels to the tank and dissected an hour later. The gene-expression assay included RNA extraction, cDNA synthesis, and quantitative PCR. There was a robust elevation in the amount of HSP-70 mRNA expressed in the anaerobic hot mussels when compared to the aerobic and anaerobic control mussels (p <0.01). In addition, results from the temporal experiment showed that the level of HSP-70 mRNA was highest when the mussels were out of the water and fell once the mussels were reintroduced to the tank. These results suggest mussels are well adapted to the extreme environment of the intertidal zone. The effect of global climate change on these organisms is unknown, but continues to be investigated.

Applications of Error-Correcting Codes

Program: Undergraduate Research
Faculty: John Villapando, Ph.D., Mathematics
Student: Luis Perez

Error correcting codes (ECC) are used every day for data transmission, which many people are not aware of. ECC, found in information theory, use methods to handle possible errors that may arise from electronic noise, to the scratch of a CD. Recently, ECC have gone beyond their traditional use. ECC can be used in applications from performing magic tricks to detecting and repairing mutations in DNA sequencing. In addition, ECC including Hamming Codes and Reed-Muller Codes, can be viewed through set theory, which give alternate perspectives on how these ECC work. In this research, various perspectives are examined in explaining the Hamming Code methodology behind error detection and correction. In addition, the Hamming Code’s properties as a perfect ECC are described through set theory and graph theory. Interestingly, the same conclusions can be found through the explanation of these methods which ultimately supports that ECC can be viewed more universally. This research also investigates further applications of the Hamming Code in a team competition and magic tricks through a set-theoretic approach. Reasonings as to how these applications are guaranteed to work given properties of the Hamming Code are also investigated. Moreover, applications of the Hamming Code are expanded to show its true significance as a perfect ECC. An investigation is done on the Hat Problem (a team competition) where all the conditions and outcomes of the game are explained through properties found in Hamming Codes. There is also an investigation on the Parity Card Trick, which is justified by elementary ECC concepts. An alternative perspective, similar to the syndrome method, is used to explain the Parity Card Trick where its properties are also validated through the Hamming Code. Finally, a more advanced version of the trick is created, and conditions of the trick are established through the Hamming Code. 

An Examination of the Educational Barriers and Experiences and Coping Strategies of First-Generation Latina College Students

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Akiko Yasuike, Ph.D., Sociology
Student: Maria Rodriguez

Previous research has identified several factors that have affected the experiences of first-generation Latina college students. These factors include family expectations outside of school, psychological episodes, and limited resources on campus. Building on these research findings, this study examines the educational barriers that first-generation Latina college students in Ventura County face and their coping strategies while pursuing higher education. I conducted five in-depth interviews and used a snowball sampling method to identify the participants. The interviews were recorded, transcribed, and coded to identify common themes among the participants. I used a pseudonym to ensure confidentiality. I identified six common themes: Conflict between family expectations and academic demand, the difficulty that comes with parents’ undocumented status, psychological episodes due to the stress of taking multiple roles, resources and support provided by academic programs, peer and mentor support, and identity development through participation in Mexican/Latino club organizations. The study shows that through university programs, student clubs and individuals on campus provide informational resources and emotional support, they do not necessarily address issues that arise due to the difference between middle-class mainstream college expectations and Latino/Mexican cultural expectations at home effectively. In addition, the study also shows the importance of culturally sensitive mental health care. My study does not give the overall picture of all the barriers and coping strategies that this population faces due to the limited time and participants that I interviewed. Therefore, future studies need to recruit a larger sample of participants from institutions of different sizes to understand their experiences fully. However, the study findings give the institutions an insight into the challenges and coping strategies of this population to better assist the first-generation Latina college students in their academic success.

Gendered Perceptions of Numbers

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Andrea Sell, Ph.D., Pychology
Student: Emma Rumpf-Snavely

Gender is a highly discussed topic in political, cultural and psychological platforms. With changing attitudes towards the definition of gender, it is important to conduct research that is reflective of the way people think about gender in its current context. This experiment explores the possible differences in how humans perceive gender across different mediums. We hypothesized that participants would perceive masculinity and femininity differently across auditory and visual platforms. This hypothesis was explored by asking participants to look at pictures of numbers and listen to numbers read aloud. Participants were recruited through Amazon’s MTurk (N=293). They varied in terms of gender (f=124, m=167), age (M=35.57, SD=11.29), and education level.  All participants were located in the United States. In this within-subject study, participants listened to numbers read aloud as well as looked at pictures of numbers. After they saw or heard a number, they rated each on a bipolar scale of masculine to feminine. The results showed that five out of the ten pairs of numbers had significant differences in the way gender was perceived across auditory and visual conditions. For example, the number one was rated as masculine in the visual condition (M=4.34) and feminine in the auditory condition (M=6.05, p<.000). Additionally, on average all numbers were rated as more feminine than neutral across both platforms (all p’s <.001) except the number one, which was scored as neutral (p=0.087). In addition, we found that participants older than 47 were more likely to score numbers differently than younger participants.  For example, younger participants rated the number one as visual (M=4.13) and auditory as (M=6.23) while older participants rated one visually as (M=3.90) and auditory as (M=6.84). This research shows that gender’s influence on perception can be seen in the way people see stimuli, even neutral subjects such as numbers. In a world that is readily talking about gender, it is important to recognize the potential impact it has on our understanding of information.

Synthesis of Spirocyclic Compounds via Claisen Rearrangement

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Jesus Cordova Guerrero, Ph.D., Chemistry
Student: Jessica Shin

Because of their rigid structure and three-dimensional stereochemistry, spiro compounds have proven to be effective frameworks in the work to produce various reagents for anti-cancer medicine production. Although research of spirocyclic compounds have already started to amass a corroboration of preliminary data, the synthesis of producing such compounds has proven to be challenging.1 In view of these facts, we decided to present a representative synthesis scheme and test how efficient the synthesis of the spiro compounds are. What our research wants to answer is, “Is there a better way to produce this compound in a more efficient and cost-effective way?”. We have proposed a new scheme to gain access to these spiro compounds from commercially available reagents in order to optimize production and lower costs of manufacture. The method used was a seven-step synthesis with the final two steps utilizing McMurry coupling and Claisen rearrangement respectively. Currently, with the substrate, 2-cyclohexen-1-one protected using (4-((tert-butyldimethylsilyl)oxy)butyl)magnesium bromide, the oxidation, and acetylation, we have confirmed that the acetylation successful, affording an 82% yield. The identity of the acetylated substrate was characterized by proton NMR. With this progress, we will proceed with the successive steps of the synthesis to test its efficiency.  Because such compounds are difficult to produce, our project is one that will possibly create a more efficient synthesis practice. We will apply it towards different types of spiro compounds, contribute to anti-cancer research and those affected by this disease. Later on, we hope to diversify our scope by introducing different variations and later contribute to the investigation of the different modes of interaction with the cancer cell lines.2 While further studies will be needed to understand the mechanism, our studies along with others will contribute to the oncology field with the suggestion spiro structures have the potential to inhibit cancer cell growth considerably.

Mathematical Models for the Island Fox, Feral Pig, Golden Eagle System Incorporating a

Program: Swenson Science Summer Research Fellowships
Faculty: Christopher Brown, Ph.D., Mathematics
Student: Caroline Sinclair

In a robust mathematical model of the interaction of golden eagle, feral pig, and island fox populations, determine the potential behaviors of the model system and whether or not they are realistic. Method: Create mathematical models for the golden eagle, feral pig, and island fox three species system incorporating a strong demographic Allee effect in the island fox population. These models will be continuous-time dynamical systems (first-order differential equations). Two different Holling functional responses will be investigated to determine appropriateness for predation terms in the models. Analyze long-term qualitative behavior of the proposed models, to include nondimensionalization, local linear analysis near coexistence equilibria, and symbolic bifurcation analysis for single parameters as possible. Numerically analyze bifurcations for bifurcations arising from interactions of pairs of parameters by simulating system behavior numerically and search a parameter space for bifurcations. Review numerical software operation as needed. Produce a comparison of simulated results and results observed in data. Results to date: Under certain restricting conditions, the different models produced equilibrium points, where both species coexist without either going extinct. The parameter space that produced these coexistence equilibria contain potential boundaries for how many coexistence points there are and their stabilities.The comparison between the restoration of the island fox and the predicted behavior from the model will better inform conservationists of the impacts that different predator and prey species have on the species in question, specifically with regards to the island fox conservation efforts.

Cloning and Expression of Entamoeba Histolytica eIF5A in Escherichia Coli

Program: Swenson Science Summer Research Fellowships
Faculty: Paloma Vargas, Ph.D., Biology
Student: Kayla Sircy

Entamoeba histolytica (Eh) is a parasitic eukaryote that is the causative agent of amoebiasis in humans.  E. histolytica has a two-stage life cycle comprised of the non-infectious trophozoite, or eating state, which causes the majority of disease symptoms and the dormant, infectious cyst stage which is transmitted via the fecal-oral route in contaminated food or water.  Although a majority of those infected are asymptomatic, symptoms can include severe dysentery, bloody stools, and organ abscesses. A goal of the Entamoeba community is to understand the life cycle of E. histolytica, specifically the interest focuses on the molecular mechanisms that leads Eh to transition from the trophozoite stage to the cyst stage.  Previous studies (Ehrenkaufer, 2007) have focused on identifying E. histolytica proteins involved in the trophozoite-cyst transition. One protein identified in this study as a possible contributor to life stage transition is eIF5A, which has been shown to be involved in translation initiation and elongation, mRNA regulation, and cell reproduction in other organisms. The Entamoeba histolytica genome encodes for three isomers of eIF5A. In this study, in order to determine the role of eIF5A in the E. histolytica life cycle, we will clone one of three eIF5A isoforms in an expression vector for later use in expression in E. coli.   Primers specific to the E. histolytica gene 151540 were created with 6X HIS tags and two restriction enzyme sites. Polymerase Chain Reaction (PCR) was then used to amplify E. histolytica eIF5A (151540) DNA.  The results of the PCR were confirmed via agarose gel electrophoresis.  Ligation of pET 14 and 44 vector DNA with E. histolytica DNA was similarly confirmed in an agarose gel after E. coli transformation. Future work will include primer design editing as well as additional PCR, ligation, and transformation experiments.

Dramaturgy for Shakespeare’s The Two Noble Kinsmen and Othello

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Michael Arndt, PhD., Sociology
Student: Ruth Smitherman

As a dramaturg the goal is to ask and answer the question, why this play and why now? Especially when we talk about Shakespeare. Why do we keep doing these plays? How do we keep audiences connected? If these questions are asked our audiences are more present and engaged and bring those conversations into their own lives and are able to connect with others with more empathy. For these productions I started by reading the unedited script and the edited script. I went deeper into background research, asked the directors questions about their vision for the piece, and if they need specific research done. I then put together the information on the website for actors and designers. I was available at every rehearsal to answer questions and talk to the director as needed. For The Two Noble Kinsmen I focused on the same-sex relationships which had varying levels of intimacy and the complex nature of love and it’s many forms. The intersections of Medieval and Greek literature in the play was important in this production. For Othello my work was focused on race and gender to supplement my director’s research. He chose not to use it, but I created the summary for the production and made his edited script closer to the Arden correcting word usages, spelling, punctuation, and capitalization. The Two Noble Kinsmen is important because we see people of different sexualities being represented in a story that is approachable for anyone. At pre-show talk backs people couldn’t believe that the characters were truly engaged in homoerotic discourses. People leave being able to empathize with queer characters and the knowledge that they’ve always existed. Othello is a difficult play, we all struggled with the treatment of people of color and women in the text. It’s important to do this play so we have these discussions, especially when they are extremely difficult and personal. The community left these productions with more empathy, more curiosity, and a deeper connection to the productions because of my work.

Base-catalyzed Synthesis of Indoles

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Jesus Cordova Guerrero, Ph.D., Biochemistry and Molecular Biology
Student: Alexandra Stewart

Indoles are heterocyclic compounds that are commonly found in nature and play a significant biological role when isolated and combined with other compounds or organic materials. There are many variations of indoles, and each variation has a different function within an organism. This allows for diverse applications in drug synthesis, medicine, and pharmacology. The ability of indoles to inhibit tumor growth and block biological receptors by replicating the structure of an organism’s proteins makes them an ideal compound for the treatment of certain cancers and infectious diseases. Previous research has shown that there are a variety of ways to synthesize indoles. One example is the Fischer reaction which uses the sigmatropic rearrangement mechanism to form carbon-carbon bonds. The goal of our research is to determine an efficient synthesis of indoles in two steps using commercially available starting materials via Suzuki coupling followed by a base-catalyzed Michael Addition-oxidation reaction. This process will represent an effective method for the synthesis of indoles and potentially reduce the cost of production for medications containing this functional group. The optimal base, catalyst, and solvent combination for the reaction between 2-nitrophenylboronic acid and 2-bromo-2-cyclohexanone was determined and afforded 15% yield of nitro-2-substituted α, β -unsaturated cyclohexenone. This compound was reduced via hydrogenation using palladium on carbon to yield an amino-2-substituted α, β -unsaturated cyclohexenone which then cyclized in situ to give a tetrahydrocarbazole derivative. The identity of this indole derivative was characterized by gas chromatography-mass spectrometry which confirmed that the product had a molecular weight of 171 grams/mol.

Multi-Core Joins

Program: Swenson Science Summer Research Fellowships
Faculty: Graham Matthews, Ph.D., Computer Science
Student: Danny Suarez

Data Integration is the process of combining together multiple tables of data from different data sources to create one uniform view of the data. This is an important topic as many groups and organizations rely heavily on data integration to pull information from multiple sources in order to make data-driven decisions. Many of these decisions cannot be made through one source alone, so it becomes essential to find efficient techniques to perform data integration. The primary operation of data integration is called a join. A join operation combines two tables of data according to some criterion. Typically when integrating data there are multiple join operations to be done between multiple sources, so it is important to perform these operations as quickly as possible. Our research consists of implementing and analyzing methods to efficiently execute chains of joins. The methods that we investigate are geared towards modern day computers which have multiple cores, allowing them to perform multiple tasks simultaneously. Ideally, the more cores that a computer has, the faster and more efficient our methods will be. The first method we implemented is the phased approach in which we read in data followed by processing it. Secondly, we have a method called the multi-phased approach which has multiple read-process phases. Our testing showed that in both approaches more cores did increase the speed but not to the extent that we expected. We also looked at the differences in performance between the phased and multi-phased approaches. Our hypothesis was that the multi-phased approach would be more efficient than the phased approach, however our results showed no significant difference between the two. We were able to make significant improvements along the way to each approach, but our results show that there is still room to improve on our methods.

The Marine Succession of the Pacific Oysters in Channel Islands Harbor, Oxnard, CA

Program: Swenson Science Summer Research Fellowships
Faculty: Andrea Huvard, Ph.D., Biology
Student: Austin Truong

The native Japanese Pacific Oyster, also known as the Crassostrea gigas, is one of the most translocated marine species in the world, causing economic and ecological damage. Identified as a marine invasive species, which are organisms that are non-native to an ecosystem causing harm, scientists questioned how these species are able to survive in different environments and outcompete other native species. Within Channel Islands Harbor in Oxnard, California, sightings of the Pacific Oyster have recently been reported attached to docks, rocks, and some boats in the area. In order to track if these Pacific Oysters will have any ecological damage to the area, succession rates were collected for the Pacific Oysters, as well as the keystone species, Mytilus californianus. Surveillance of the area was done to find that the oysters preferred living among docks, where one could be spotted about every 5 feet. Two locations were chosen where environmental parameters (temperature, salinity, dissolved oxygen, water nutrient analysis) were measured to see if there were any correlation between growth rates. Sediment plates were placed under water at each location in the harbor and were observed closely for the stages of succession. The Mytilus californianus and Crassostrea gigas were then identified by numbers or letters, which then the longitudinal axis was measured weekly. The data will then be used to find the average increase in growth from initial settlement to its apex size dividing that by the number of weeks. Results so far showed that within 3 weeks of putting the plates out, there were no signs of growth on the plate. As weeks 4-7 came along, stage 1 of succession was recorded with signs of algae and Bugula present, increasing in coverage over time. At week 8, stage 2 of succession was observed with signs of bryozoans, tunicates, and sponges attached to the plate. Stage 3 of succession has yet to occur as there have been no signs of juvenile bivalves at this moment. Data collection is still ongoing and will continue until May 2019 in which a conclusion could be made.

Bioacoustics & Temporal Variation of Understory Bird Species in Premontane Cloud Forest

Program: Undergraduate Research
Faculty: Edgardo Arevalo Ph.D., School for Field Studies, Biology
Student: Amir Mejia

A premontane tropical forest comprises a diversity of habitats and microhabitats that support a variety of species. Due to this habitat structure, it has been considered as a possible factor in the evolution of bioacoustics in bird species. It also is suggested that most forest birds have adapted to sing lower pitched songs that could potentially be effective in dense habitats rather than open habitats. This subject is relevant because it indicates how some bird species could have adapted to their physical environment in the most optimal vocalization pitch. Therefore, the objective of this research is to test the signal emission and assess the bioacoustics presence of the two focal species in two different habitats. In this study, the focal species were the Henicorhina leucophrys (Gray-breasted Wood-Wren) and Catharus fuscater (Slaty-backed Nightingale-Thrush). The data was collected by putting a song meter in a mature forest trail and another in a secondary growth forest. The song duration was then measured in Raven Pro 1.4, organized in Microsoft Excel 2011, and analyzed using PAST 3.14. The findings concluded that there is not enough structural difference to induce changes in the singing time of the species. However, the time distribution in the temporal variation has been affected. For future implications, more factors can be tested for and comparing the data to the same species found in different forest environments since these species are unique to cloud forests. Another study can be done focusing on the oddity of the temporal variation.

Effect of forest structure in song activity of Gray-breasted Wood-Wren

Program: Undergraduate Research
Faculty: Edgardo Arevalo, Ph.D., School for Field Studies , Biology
Student: Angelika Pasion

Avian species widely use acoustic communication for species recognition, mate attraction, and territorial defense. Habitat has greatly influenced the evolution of bird songs. To further understand the effects of habitat, this study aims to understand how forest structure affect vocal communication. Two different forest types were examined to determine its effect on the song activity of the Gray-breasted Wood-Wren (Henicorhina leucophrys) at the lower Montane Rain Forest life zone in Monserrat de Coronado, Costa Rica from July 25- July 27. Three conditions were compared: the total frequency of focal species present, number of calls produced per minute, and number of calls produced in different weather conditions. Acoustic sounds were collected using a Wildlife Acoustic SM2+ Song Meter which recorded sounds from 4-6am. The recordings were uploaded into Raven Pro 1.5 to analyze the number of calls produced each hour. The number of calls within the frequency range of 1-5 kHz at 2-minute intervals was recorded into Excel and then analyzed using t-tests (p<0.05), and chi-square (p<0.05) in Past 3.14. It’s expected that in a mature forest, there would be more Gray-breasted Wood-wren present because of the heavy understory and food abundance within the forest. Meanwhile, there would be a higher number of calls in the secondary forest because of the demand to modify amplitude to prevent acoustic masking from geophonic sounds. Lower numbers of call are expected during rainy days due of the effect of rain on animal activity. As a result, a higher number of Gray-breasted Wood-Wren were present in the secondary forest (χ2=11.16, DF=1, p=0.0008). Also, the average number of calls was significantly higher in the secondary forest (t-test=7.0469, DF=119, p=1.960E-11), and significantly higher number of calls produced in the absence of rain (χ2=113.07, DF=1, p=2.08E-26). This study is essential in providing information about the bird activity of a common bird species in the rainforest and could serve as baseline information for further research on the effects of different habitats.

The Three-Dimensional Effects on the Superconducting State of Strontium Ruthenate

Program: Swenson Science Summer Research Fellowships
Faculty: John Deisz, Ph.D., n/a
Student: Jamie Shultz

Research Question: What is the microscopic nature of the superconductivity in Strontium Ruthenate, (Sr2RuO4)? Strontium Ruthenate is a metal that can become a superconductor at low temperatures around 1.5 to 3 Kelvin. Strontium Ruthenate is an unconventional superconductor with abnormal properties that have baffled scientists since its discovery in 1994. Attempting to explain the discrepancies in the results of recent experiments, current research has looked at the interaction of electrons in the metal along two-dimensional graphite-like sheets but has largely ignored the third dimension. Hypothesis: My hypothesis is that the three-dimensional effects of electron interactions within Sr2RuO4 can resolve current discrepancies in the understanding of this material. Methods: To accomplish this, I used C++ computer programming language to build a computer simulation that models the interaction of the electrons in three dimensions using the laws of quantum mechanics. Results: We have built the code modeling the electrons in three dimensions. When the parameter allowing interaction in the third dimension is turned off, the results from this code match the results of our two-dimensional code suggesting that our model is accurate in an important limiting case, setting us up for fully three-dimensional analysis of this material. Importance: Our code could help explain the properties of the superconductivity of Sr2RuO4, a long-standing problem. This could transfer and relate to other metals and give us a better understanding of known superconductors and their properties, which in turn will help us to discover new superconducting materials. There are many superconductors with similar structures to Sr2RuO4 where the atoms in a plane are spaced closer together than atoms in different planes. For this reason, many models look only at the interactions in two dimensions. Our code can be generalized and used to create three-dimensional models for these other metals as well.

Metabolic Pathway Elucidation Towards Time – and Dose-Dependent Electrophoretic Screening of Stable Oxidative Phenolic Compounds

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Grady Hanrahan, Ph.D., Chemistry
Student: Leslie Tran

This study tested the link between phenolic compounds as well as the formation and electrophoretic separation of stable metabolites found in urine. Sterically encumbered carbonyl groups were examined, and gas chromatography-mass spectrometry (GC-MS) was used to confirm the presence and stability of oxidative metabolites of model chlorinated phenols. Then, baseline resolved the separation of the chlorinated phenols and its oxidative metabolites were demonstrated through capillary electrophoresis (CE). These results provide key metabolic inferences from chlorinated phenols as well as the improvements in the ability to separate and detect changes in urinary metabolites in response to exposure to phenolic compounds.  

Milk-Derived EVs Effect on Human Immune Cell Response in Vitro

Program: Undergraduate Research
Faculty: Charlotte Lawson, Ph.D., Chemistry
Student: Charnpreet Kaur

The biology of organisms is strongly influenced by the molecular communication between cells. Cells release extracellular vesicles (EVs) as a mode of inter-cellular contact carrying molecular cargo between cells. As emerging biomarkers of disease and a novel, non-invasive method of research, EVs have become an important area of study. This study focused on milk-derived EVs and their effect on human immune cell responses in vitro. Milk samples were collected from cows in the dairy herd of Royal Veterinary College (London, UK). Two different assays were carried out to determine whether milk-derived EVs from cows at different stages of lactation modulate inflammatory responses of human THP-1 monocytes in vitro; a fluorescent based assay to measure reactive oxygen species (ROS) production and an ELISA to measure tumor necrosis factor TNF-α, in the presence or absence of lipopolysaccharide (LPS). The ROS assay was done on 6 samples per set in both untreated and LPS treated conditions. LPS mediates ROS and stimulates macrophages to release cytokines. The ELISA assay was done to test milk-derived EVs and their effect on the secretion of tumor necrosis factor TNF-α, from THP-1. TNF-α is a cytokine, and THP-1 is a human monocytic cell line derived from leukemia patients. The ROS assay results showed that cows in the early lactation period elicited an inflammatory response, whether cells were untreated or treated. Late lactation periods did not show a significant response, however the ELISA assay showed higher TNF-α levels when exposed to milk-EVs over 125 days. This was only seen in the LPS treated cells, whereas the untreated samples did not express TNF-α. The mechanisms driving the effects of EVs on the immune system is unclear, however we speculate that it might be related to the constituents of the cargo. Further studies are needed to pinpoint the precise cause of the similarities and differences in lactation periods and their effect on the human immune system.

Development of a New Carboxylic Acid Protecting Group

Program: HSI STEM ALLIES
Faculty: Jesus Cordova Guerrero, Ph.D., Biochemistry and Molecular Biology
Student: Harleen Kaur

In the field of organic synthesis, the presence of several reactive functional groups can present a challenging problem when a chemical transformation needs to be performed in a selective manner. A suitable protecting group must preserve the chemistry of the original molecule, be easily installable and removable, be chemoselective, and afford the product in good yield. One of the most efficient ways to protect carboxylic acids is via the formation of methyl esters, via the reaction of carboxylic acids in the presence of thermally unstable diazoalkanes. In this work, we proposed the synthesis of a new carboxylic acid protecting group that is easily installed, without the need of handling such hazardous materials. Five substrates were tested: mesitylaldehyde, 4-isopropylbenzaldehyde, 4-bromobenzaldehyde, paradimethylaminobenzaldehyde, and 3-methoxybenzaldehyde. These substrates were reacted with hydrazine and ethanol, under nitrogen atmosphere, to form their respective hydrazones. 4-bromobenzaldehyde and 4-isopropylbenzaldehyde are very unstable in solution, as analyzed by 1H NMR. Mesitylaldehyde, para-dimethylaminobenzaldehyde, and 3-methoxybenzaldehyde were successful in producing hydrazone. The purified hydrazone products were used to perform esterification in conjunction with 4-methoxybenzoic acid at 0 ℃ in the presence of KH2PO4, MnO2, and CH2Cl2. Percent yields of hydrazones ranged from 53%-95%. Percent yields of esters ranged from 23%-95%. All products were purified via flash chromatography. All product formation was confirmed via 1H NMR and 13C NMR. Stability tests were conducted on the 3-methoxy ester and the mesityl ester in HCl/H2O/THF, NaBH4/H2O/dioxane, CH3COOH/CH2Cl2, TFA/CH2Cl2, and H2/ Pd/C, and were monitored at intervals of 5 min., 15 min., 1 h, 3 h, and 24 h. Results are yet to be confirmed by GCMS. Future work includes stability tests in NaOH and DIBAL-H, and finding conditions for deprotection of the carboxylic acid.

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