Festival of Scholars

Student Abstracts

Determinants of Reincarceration

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The US holds about 5% of the world’s population but 25% of the world’s prison population, and as of 2015 there were 2.4 million people incarcerated in the US. According to a study done by the Bureau of Justice Statistics (BJS) focusing on different demographic groups, some offenders are rearrested at almost a 70% rate, adding to prison overcrowding. In 2010 federal, state, and local governments spent a combined $80 billion on the nation’s corrections systems. The cost of keeping just one inmate imprisoned for one year depending on the state they are located in can cost $80,000. The cost incurred by the huge amount of Americans in prison every year weighs heavily on taxpayers and not enough is done by our justice system to reduce recidivism rates, recidivism is the tendency of an offender to reoffend. This study will evaluate the determinants of reincarceration by analyzing data on Iowa State prison population. With the results of our analysis we will be able to determine what factors have the most influence on an offender’s likelihood to reoffend and subsequently be reincarcerated. The resulting factors can then be used by different types of reentry programs and problem solving courts to determine what demographic groups are most at risk for reincarceration and where to concentrate their efforts towards reducing recidivism and subsequent reincarceration.

Student(s):
Gabriella Alamin

Faculty Mentor:
Dr. Kirk Lesh

Effects of Fatigue Progression on Single Leg Squat Kinematics

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Purpose: Previous research has shown that males and females move differently prior to and after fatigue (Weeks et al., 2015) and that females experience injury 4-6x more than males (Hewett et al., 2005). The purpose of this study was to investigate joint kinematics during the single leg squat in males and females throughout a set of repetitions that evoked fatigue. Methods: Fifteen males and sixteen females, aged 18-25, participated with eight Vicon Vantage V5 cameras (200Hz) capturing twenty-five reflective markers placed on specific anatomical landmarks along with one Kistler force plate (1000 Hz). Subjects performed repetitions until exhaustion. Data was analyzed for the first, middle and last repetitions. SPSS v25 was used to determine significance with p < 0.05. Results: There was a significant difference in the maximum hip flexion with the lead hip flexing more as fatigue increased (84.3±8.6° vs. 88.7±11.1° vs. 94.4±11.6°; p = 0.005) which produced a greater lead hip ROM (p = 0.005). There was no significant difference in the maximum knee flexion angle or the knee flexion ROM due to fatigue. There were differences in the frontal plane knee kinematics associated with fatigue. Differences between male and female subject movements were investigated. Conclusion: Subjects made adjustments in the sagittal plane at the hip and frontal plane at the knee when experiencing fatigue. Understanding how fatigue affects the movement is important to guide safer and more effective movements during the single leg squat. This research was supported by the Aperture Research Fellowship Program.

Student(s):
Jaime Alvarado

Faculty Mentor:
Dr. Michele LeBlanc

Investigating the Role of eIF5A in Entamoeba histolytica Encystation

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Entamoeba histolytica is the single-celled parasite responsible for the intestinal disease amoebiasis. During its life cycle, E. histolytica transitions from an un-infectious form (trophozoite) to an infectious one (cyst) through a process called encystation. The protein eIF5A, or eukaryotic translation initiation factor 5A, is thought to be involved in this transition, but its specific role is unknown. Determining eIF5A’s function in encystation will improve understanding of E. histolytica’s life cycle and advance the development of therapeutics to prevent the spread of amoebiasis. eIF5A is part of eukaryotic cells’ protein synthesis machinery and is specifically involved in the production of proteins with sequences called polyprolines. Such proteins are known to participate in cytoskeleton organization and intracellular communication in other eukaryotes. We hypothesize, therefore, that eIF5A regulates these processes during E. histolytica encystation by increasing production of polyproline-containing proteins. We are using bioinformatics techniques to gain insight into eIF5A’s role in cyst formation by determining 1) which types of E. histolytica proteins contain polyprolines and 2) what roles these proteins might play in encystation. The programs utilized include BLAST, Clustal Omega and STRING. Preliminary results support our hypothesis in that many E. histolytica polyproline-containing proteins are involved in restructuring the cytoskeleton, but protein synthesis patterns throughout E. histolytica’s life cycle suggest that eIF5A’s regulatory role in encystation may be more complex than initially hypothesized.

Student(s):
Emily Armbruster

Faculty Mentor:
Dr. Paloma Vargas

Image Storing Database with built in Image Editor

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With the advent of the “smart phone” nearly everyone carries with them a digital camera. As such, nearly everyone has generated an abundance of digital images, pictures. Keeping those pictures organized has become a daunting task. While many tools exist to do so (e.g. MacOS iPhoto) there is no “one size fits all” solution. Therefore, this project is focused on creating a client/server framework for which a custom image editing, and storage application can be created. The framework will provide for multiple user support each with unique, secure login credentials. The “client side” will provide a graphical user interface (GUI) with which a user can interact via windowing displays and controls. The client will communicate over an Internet port with the “server side”. The server will provide image processing algorithms such as sharpening, blurring, edge detection, etc. as well as access to a database where images are stored. Technologies to be used in creating the system include: Unified Modeling Language (for design and documentation); Java (programming language); JavaFx (graphical user interface framework); MySQL (database management system); OpenCV (open source computer vision/image processing library).

Student(s):
Tristan Arndt

Faculty Mentor:
Dr. Craig Reinhart

The Effects of Pesticides on Genetic Expression in Caenorhabditis elegans

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Pesticides are commonly used throughout the United States and can include fungicides, herbicides, and fumigants. 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 useful model organism to study changes in genetic expression because it has a completely sequenced genome, a simple body plan, and exhibits 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. Methoxychlor and chlorpyrifos structures will be characterized by gas chromatography-mass spectrometry (GC-MS). C. elegans will be exposed to different concentrations of each pesticide for up to 72 hours. Analysis of gene expression variation will be further studied. It is anticipated that tracking changes in genetic expression will require RNA extraction, microarray analysis, linear regression models, and comparisons between produced gene sets and publically available gene sets. Expected results include a delay in development, increased 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.

Student(s):
Vanessa Avalos

Faculty Mentor:
Dr. Grady Hanrahan

Building a Cherenkov Radiation Particle Detector and Counter

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Detectors are the cornerstone of experimental particle physics research. Without them, any research would be theoretical. There were two goals to this project:
1) To build and successfully test a Cherenkov radiation particle detector capable of discerning between muons and particles
2) To expand the scope of our detector to count incoming particles
In order to detect Cherenkov radiation, we used a silicon photomultiplier (SiPM) as the detector, and a sodium iodine crystal as our medium/target. Because our SiPM outputs a very weak signal, we used a buffer to prevent signal loss, and amplified the resultant signal using an operational amplifier (Op Amp). Finally, in order to count the number of incoming particles, we converted the signal from analog to digital using a comparator with hysteresis (Schmidt Trigger). We counted the final digital signals using an 8-bit counter using eight D-type Flip-Flops. Our counter circuit attached to our detector was able to count muons, and particle radiation. Our detector, when attached to an oscilloscope, was sensitive enough to let you discern if the detected particle was a muon or particles. Unfortunately the Schmidt trigger was sending two digital signals instead of one, giving us double the amount of counts per particle.

Student(s):
Javier Berjon de la Parra, Johann Dias

Faculty Mentor:
Dr. Sebastian Carron Montero

Text-to-Image Generation and Colorization with Stacked Attentional Generative Adversarial Networks

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Computer manipulation of natural language has seen rapid advancement in the last few years through the application of generative neural networks. First described by Goodfellow, et al. 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. 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. We 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 collaboration 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 grayscale images given a text description. Our model, which was built with the PyTorch framework, reads in a text description into a neural network that pairs images their descriptions, and then feeds an interpretation of that description into our generative network over multiple stages of generation, first increasing in size, then adding color information.

Student(s):
Tyler Berry, Mayra Plascencia

Faculty Mentor:
Dr. Craig Reinhart

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

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A neurotransmitter, serotonin (5-hydroxytryptamine: 5-HT), has been shown to be involved in the feeding response and hunger state processes of mollusks. Some studies investigated how 5-HT and its antagonists affects the heart by monitoring heart contraction, but few have combined these topics to discuss the relationship between the hunger state, 5-HT, and the heart. 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 were tested. It was expected that the HR of fasting H. trivolvis would increase when exposed to 5-HT and decrease when exposed to mianserin. Fasted and satiated snails were exposed to control artificial pond water and varying concentrations of 5-HT and mianserin. Contractions of the heart were viewed and recorded using a cell phone attached to a dissecting microscope. HR was measured immediately, 30 minutes, and 60 minutes after 5-HT and mianserin solution exposure. 5-HT significantly increased HR in fasting snails up to 60 minutes exposure, while only increasing HR after 30 minutes exposure for satiated snails (P < 0.05). Mianserin significantly lowered the HR after 30 minutes exposure for fasting snails and with satiated snails up to 60 minutes after exposure (P < 0.05). Mianserin also reversed the effects of 5-HT for satiated snails up to 60 minutes exposure, but for fasting snails after 30 minutes exposure (P < 0.05). This research assists in uncovering systems that govern the heartbeat and how they are influenced by factors like metabolism.

Student(s):
Sara Beylik

Faculty Mentor:
Dr. Kenneth Long

Optimizing Protein Solubility for Crystal Formation

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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 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 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. Future research directions include testing whether a combination of additives, glycerol, and substrates succeeds in maintaining the solubility of FslA. Different pH levels of buffer will also be tested as a variable for solubility.

Student(s):
Deana Bitar

Faculty Mentor:
Dr. Katherine Hoffmann

A Cross Comparison of Olfactory and Stress Behaviors Between Two Species of Canines

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Olfaction is one of the primal instincts of canines and is often used for surivival. In captive species, this instinct may be altered and higher frequencies of stress may be present. The present study compares olfactory and stress behaviors between two canine species. Specifically, our species were Canis hallstromi (New Guinea Singing Dog)and Canis latrans (coyote). The data for this observational study was collected via ad Libitum and instantaneous focal sampling. An ethogram was constructed to track olfactory and stress behaviors in both species. Intra- and inter-group statistical analyses were used to compare frequency and type of behavior. The New Guinea Singing Dogs were found to have a significantly higher frequency (p= 0.0040) of the nose to the ground behavior. Hazel the coyote was found to have a significantly higher (all p < 0.05) frequency of multiple stress behaviors (ears back, growling, and pacing). In understanding stress and olfaction, trainers can use these data to develop more enriching training techniques, especially those that take advantage of the canine’s natural olfactory instincts.

Student(s):
Christian Bustillos

Faculty Mentor:
Dr. Lorenzo Ramirez

The Role of Type II Secretion of Legionella pneumophila in Growth at 25, 35, and 42 Degree Celsius

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Legionella pnuemophila (Lpn) is a gram negative bacteria that occurs naturally in freshwater and human-made water systems. Lpn thrives in water systems found in water towers, air conditioning systems, and misters. Lpn is an opportunistic pathogen known as the causative agent for Legionnaires Disease in immunocompromised patients, with symptoms presenting as pneumonia. Bacteria have up to six secretion systems used for survival in environments. Type II Secretion System 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 Lpn survival in the environment. The goal of our study is to determine the role of Type II Secretion System in Lpn survival at 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 nttA, nttB, and wild type (130b) at 25, 35, and 42 degrees Celsius. We collected samples and measured optical density at 0, 24, 48, and 72 hours. We determined that there is a significant difference (p<.01) between bacterial growth of nttA and nttB at 24 and 42 degrees Celsius when compared to 130b wild type. Future studies will involve testing these strains at additional biological or environmentally relevant temperatures, conditions, and hosts.

Student(s):
Kayla Cross

Faculty Mentor:
Dr. Paloma Vargas

The Role of Type 2 Secretion System’s Protein LegP on Legionella pneumophilia

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Legionella pneumophilia (Lpn) is a gram-negative bacterium that is found in fresh water or in man-made water systems. Lpn targets immunocompromised people, and is the causative agent of Legionnaire’s Disease or severe pneumonia. Within the human host, legionella has been shown to invade alveolar macrophages and is able to colonize freshwater amoeba. Previous studies (Cianciotto, 2008, Tyson et al. 2013) implicated the type two-secretion system of Lpn is infection of both, amoeba and human hosts. Subsequent studies identified that there are 25 effector proteins secreted by the type two-secretion system, including LegP, that aid in the survival of Legionella pneumophila. In this study, LegP was tested to assess the effect of temperature in Lpn growth at 24 degree Celsius and 37 degree Celsius using spectrophotometry. At 24 degree Celsius, LegP does not appear to play a role in Lpn growth, therefore the role of LegP at additional temperatures will be assessed.

Student(s):
Patricia Del Rio

Faculty Mentor:
Dr. Paloma Vargas

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

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Urine Washing, or 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; its function remains unknown. The purpose of my study was to examine patterns of urine washing in wild squirrel monkeys and test four functional hypotheses. 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, occurrence of stressful situations, and distance to observer. In addition, all UW instances were recorded with note of the same variables. The ambient 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, UW most likely does not serve as sexual communication in squirrel monkeys. However, in 29% of juvenile urine washes, the individual was looking at the observer. Furthermore, in 7% of juvenile occurrences, the juvenile urine washed after a stressful situation in the group. Preliminary results support UW as a mechanism of anxiety displacement.

Student(s):
Nathan Delacth

Faculty Mentor:
Dr. Anita Stone

Java-based Chatroom Application Using Encryption for Sending Messages

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The primary focus of this project is simply to create a chatroom application using message encryption to send messages over a local SQL server between every client logged into the server. The goal of this project is to successfully integrate a server that can potentially manage an online chatroom over the web. The methodology will consist of constructing simple versions of the final program in order to research the libraries/external software I’ll be using. Once I have gained an understanding of the tools at my disposal, I can take those simple programs and add more depth to them so that I can use them for my project. This process of “research, then development” will be repeated until the project is complete. I expect to have a fully-operational chatroom program that can run on two computers using the school’s local connection.

Student(s):
Cole Elpel

Faculty Mentor:
Dr. Craig Reinhart

Using Natural Language Processing to Communicate Ideas More Clearly in Writing

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Word-processing software such as Microsoft Word and Google Docs have become the standard when it comes to expressing ideas digitally. However, more often than not, most of what is written in a rough draft for any sort public document includes a plethora of “fluff”: filler words, run-on sentences, and nonsensical phrases. This is a problem that goes beyond the spell and grammar check capabilities of a text processor. As a result, writers of any kind, such as students and journalists, often have to go back to eliminate or modify redundant sentences in their works. To reduce the time that writers spend eliminating redundant sentences and paragraphs, this study explores and investigates algorithms that will parse a corpus to remove filler content without changing the meaning of the original work and quantifies their effectiveness by counting the amount of filler content removed per each pass of the program. This process is implemented using the Natural Language Tool Kit, a collection of Natural Language Processing (NLP) libraries written in the Python programming language.

Student(s):
Giovanni Flores

Faculty Mentor:
Dr. Craig Reinhart

Metagenomic Analysis of the Thomas Fire Burn Site

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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. Understanding the effects the microenvironment has on the macro environment will aid in a deeper understanding of the effects and requirements of environmental reconstitution. The purpose of this research was to gain a deeper understanding of the metagenomic composition of the different soil environments. 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. QIIME 2 was used to conduct analyses on the soil fasta data gathered from the Illumina MiSeq. Prior to analysis of the diversity of data, low quality data points were eliminated by assigning a depth value of 1109. Then the following QIIME 2 protocols were run: Faith Phylogenetic Diversity (measuring soil microbiota richness), differences in communities (fire samples in first and second month), and beta diversity within those communities.

Student(s):
Giselle Gallardo

Faculty Mentor:
Dr. Theresa Rogers

Tournament Bracket Application

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As computer science is in constant demand in modern society, it is of great importance to create applications that make tasks easier to complete. This mobile application will allow users to create tournament brackets for various sports and activities such as tennis and baseball on the go. As a result, the primary goal of this project is to make it easier to create tournament brackets. In addition, a secondary goal is for tennis players to be able to have statistics taken for them during their matches to give an idea of what needs to be worked on in their game. In order to achieve the goals of the project, the project will undergo a mixture of waterfall and agile methodology. This means as portions of the coding are completed, they will be tested. Alongside this, the overall scope of the project will be done sequentially. Once all aspects of the project are completed, they will be combined to create the final application, a tournament bracket maker.

Student(s):
Yahn Gawrit

Faculty Mentor:
Dr. Craig Reinhart

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.

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We are conducting a large scale screen for novel sources of cryptic genetic variation (CGV) in natural populations of Drosophila melanogaster. The screen is based on a model for the production of head defects by the extra eye mutation (ee), which is incompletely penetrant, variably expressed, and conditionally dominant. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a key molecule in the JAK-STAT signaling cascade implicated in embryonic eye field establishment. In ee strains, a P transposable element insertion maps near a gene (Su(var)2-10), and is the putative target of RNAi-induced heterochromatization. The proposed epigenetic model predicts that new mutant phenotypes may be uncovered in crosses between ee lines and flies from natural populations that harbor P-elements at various genomic locations. Such novel mutants are predicted to be incompletely penetrant and variably expressed, caused by epigenetic silencing via RNAi-induced heterochromatization of genes residing at genomic positions near P-elements. In an initial study described here, we conducted a screen for such mutations by scoring progeny of crosses of 16 separate wild-derived lines to ee. In one such cross, a new mutation, crybaby (cby), was recovered. Cby exhibits the properties expected of an epigenetically-triggered mutation. Our results to date suggest that variation in natural populations may include cryptic, epigenetic sources linked to transposable elements, which are revealed under particular genetic contingencies. Screens of multiple wild strains for additional examples of cryptic phenotypes are ongoing (with one possible, additional variant discovered to date), as are genetic and molecular characterization of the cby and eephenotypes.

Student(s):
Dagem Getahun, Lauren McAllister, Makena Wolfram

Faculty Mentor:
Dr. David Marcey

A Biomechanical Analysis of Long Snapping With and Without a Block

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The aim of this study was to understand how reaction forces (RFs) are generated during the American Football long snap and to determine the effect of a secondary blocking action on the primary long snapping action. Because the goal of the primary long snapping task remains constant, we hypothesized the introduction of a secondary blocking action would not have an impact on RFs or linear impulses generated during the long snap. Highly skilled subjects (n = 11, 6 college, 5 high school, 18.9 ± 1.2 years old) volunteered to participate. Subjects completed 6 snaps of the no block (NB), block left (LB) and block right (RB) condition toward a customized net in a pseudo-random order with each foot supported by a force platform (Kistler, 1200Hz). Three-dimensional RF data was normalized by body weight. Linear impulse was calculated and normalized by body mass. Comparison of RFs and linear impulse revealed that players in this study increased peak posterior RF (p = 0.001) while maintaining peak resultant RF with a secondary blocking action (p = 0.181). A larger posterior linear impulse with a blocking action (p = 0.003) was determined to be force-based due to the lack of change in push phase duration across conditions (p = 0.327). Ultimately, players seemed to maintain their resultant force while regulating the direction of reaction force in the posterior and vertical directions. This regulation may help prepare players for the secondary blocking action.

Student(s):
Jonathan Goldstein

Faculty Mentor:
Dr. Travis Peterson

Determining the Kinetics of Desferroxiamine Dusing Isothermal Titration Calorimetry

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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.

Student(s):
Eliana Goncuian

Faculty Mentor:
Dr. Katherine Hoffmann

Subtrate and pH Structural Studies of FslA

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Francisella tularensis (FslA) is a bacterium which creates siderophores. Siderophores are metal chelators, and play a key role acquiring critical iron for bacteria survival. 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 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 makes them ideal 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 Staphyloccocus aureus (MRSA). 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. We propose to determine FslA structure through x-ray crystallography in its apo form, as well as its bound to substrate forms. Currently, we have found a problem maintaining the solubility of FslA. We 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, and pursuing additives to enhance solubility of FslA.

Student(s):
Genova Hernandez, Deana Bitar

Faculty Mentor:
Dr. Katherine Hoffmann

Taste Aversion & Effect of Epicatechin on Memory Formation in Lymnaea stagnalis.

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The freshwater snail, Lymnaea stagnalis, is a valuable model species in the research of learning and memory. In this study, we investigated the effect of varying the duration of epicatechin-exposure on memory formation in L. stagnalis. Epicatechin, a flavonoid found in abundance in dark chocolate and green tea, has been shown to enhance memory formation in L. stagnalis in operant conditioning experiments. We used a taste aversion conditioning protocol to train and assess the memory formation of snails by pairing electric shock with sucrose (a strong stimulant of feeding). We performed a pre-conditioning test on unconditioned snails to assess the response to sucrose (100mM agar pellets) as bites per minute. The shocks (8V, 55msec, 25 shocks per conditioning-session) were delivered by a pair of needle electrodes via a built-in 10-volt stimulator of Biopac® MP36 data acquisition unit. Three conditions were tested: a control group (no epicatecin exposure), short-term exposure (epicatechin exposure immediately after conditioning for 40min) and long-term exposure (snails raised in epicatechin-infused pond-water). Memory was formed if there was a decrease in response towards sucrose (bites per min) in the 24h post-conditioning test compared to the pre-conditioning test. We found that both the short-term exposure (p= .0000546) and long-term exposure (p= .015) had significant decreases in response. Our results also showed that memory-facilitation was dependent on high calcium concentration in pond-water (80mg/L Ca2+). We are currently comparing the strength of the memory formed between short- and long-term exposure to epicatechin by performing 48h and 72h post-conditioning tests.

Student(s):
Helen Hong

Faculty Mentor:
Dr. Kenneth Long

Synthesis of Metal-organic Frameworks as Efficient Drug Delivery Systems

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Metal-organic frameworks (MOFs) are versatile hybrid materials that are highly crystalline and porous, presenting high surface area. 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. 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. All of the results are going to be characterized by NMR, GCMS, and PXRD. In conclusion, we expect that the MOF is crystallizable and can be used as an efficient drug delivery system.

Student(s):
Gregory Hovhanessian

Faculty Mentor:
Dr. Jesus Cordova Guerrero

Synthesis and purification of N-Hydroxy-N-(5-aminopentyl)succinamic acid (HSC)

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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. 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. 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. Purification by HPLC has not yielded successful separation; however, C-18 column has shown promising results with model and real system. The purified compound can be used to study the kinetics and structure of DesD to broaden more understanding on NIS synthetases.

Student(s):
Yoojin Jang

Faculty Mentor:
Dr. Jason Kingsbury

The Effect of Temperature on the Rate of Anaerobic Metabolism in Mytilus galloprovincialis

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The anaerobic waste product succinate is produced by mussel Mytilus galloprovincialis during periods of low tide. What is not known is if anaerobic metabolism is suppressed or elevated during thermal stress. This preliminary experiment assessed the effects of temperature on succinate production in mussels. Mytilus galloprovincialis were collected and acclimated for five hours in three environments including anaerobic hot, anaerobic cold, and aerobic cold. Following acclimation, each mussel was dissected and its gill tissue was tested for succinate levels using a colorimetric assay. Results revealed a slight and non-significant elevation of succinate in the anaerobic hot condition. Mussels are important foundation organisms and studying them allows valuable insight into the health of the intertidal zone. Experiments with larger sample sizes are needed to finely elucidate how mussels adjust their anaerobic metabolic pathways under varying temperature.

Student(s):
Emily Johnson

Faculty Mentor:
Dr. Kwasi Connor

Tiling 2-Deficient Rectangles with L-Pentominoes

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The L-pentomino is a shape made of five unit squares connected at their edges to form an L shape with one leg shorter than the other. We study using the L-pentomino to tile a region, that is, to cover a region completely with copies of this shape without overlap, which is an interesting mathematical puzzle to explore. The region that we tile is a 2-deficient rectangle, which is an m × n rectangle partitioned into unit squares that is missing two unit squares. The goal is to find locations for the two removed squares that produce a tileable rectangle when m ≡ 1, n ≡ 2 (mod 5) and when m ≡ 3, n ≡ 4 (mod 5). We obtain results by starting with small 2-deficient rectangles that are tileable and building onto them in a generalized way. We also use previous results on tiling non-deficient and 1-deficient rectangles in order to prove statements about 2-deficiency.

Student(s):
Monica Kane

Faculty Mentor:
Dr. Michael Gagliardo

Milk Derived Extracellular Vesicles (EVs) Effect on Human Immune Cell Response in Vitro

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The biology of organisms is influenced by the molecular communication between cells. Cells release extracellular vesicles (EVs) as a mode of inter-cellular contact carrying cargo between cells. This study focused on milk-derived EVs and their effect on human immune cell responses in vitro. Milk samples were collected from cows at RVC. Two assays were performed to determine whether 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 of untreated and LPS treated conditions. LPS mediates ROS and stimulates macrophages to release cytokines. The ELISA assay was done to measure the effect of milk-derived EVs on the secretion of TNF-α from THP-1. The ROS assay results showed cows in the early lactation period elicited an inflammatory response, treated or untreated. 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. 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.

Student(s):
Charnpreet Kaur

Faculty Mentor:
Dr. Charlotte Lawson

Development of a New Carboxylic Acid Protecting Group

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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. In this work, we proposed the synthesis of a new carboxylic acid protecting group that is easily installed. Five substrates were tested: mesitylaldehyde, 4-isopropylbenzaldehyde, 4-bromobenzaldehyde, paradimethylaminobenzaldehyde, and 3-methoxybenzaldehyde. These substrates were used to form hydrazones and esters. 4-bromobenzaldehyde and 4-isopropylbenzaldehyde were found to be very unstable in solution, as analyzed by 1H NMR. Mesitylaldehyde, para-dimethylaminobenzaldehyde, and 3-methoxybenzaldehyde successfully produced hydrazone. Stability tests were conducted on the 3-methoxybenzaldehyde and mesitylaldehyde esters in various acidic and basic conditions. Results are yet to be confirmed by GCMS. Future work includes stability tests in NaOH and DIBAL-H.

Student(s):
Harleen Kaur

Faculty Mentor:
Dr. Jesus Cordova Guerrero

High Granularity Calorimeter Detector

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The purpose of the study was to increase the precision performancecharacterization studies of the High Granularity Calorimeter detector moduleprototypes for the Compact Muon Solenoid in the Large Hadron Collider.Methods: to participate in the Beam-time experiment that aims to collect datausing version 3 of the High Granularity Calorimeter detector, as well as to be ableto read the data from the beam-time and the previous experiments in order to study.the relationship between the performance of the detector and environmentalconditions such as humidity and temperature. The Beam-time took place in theCompact Muon Solenoid lab in the Large Hadron Collider at CERN, Geneva,Switzerland. The programs used to collect and read the data are custom Python,C++ and ROOT – based. Looking through the data that was collected at UCSB and CERN, westudied specifically at noisy pixels in our detectors. We will present the result ofour study of the correlations between such electronic noise and the energyresolution of the detector.

Student(s):
Hend Kordy

Faculty Mentor:
Dr. Sebastian Carron Montero

Digital 3D Image Reconstruction via Sonar Rangefinding

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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. Much of the work in image reconstruction focuses on the techniques and algorithms that infer depth from images. Specifically, many methods attempt to utilize visual cues, such as stereo parallax. However, a different approach is rangefinding, which utilizes active time-of-flight sensors for distance measurements. Rather than inferring depth information from images, depth data can be directly measured using time-of-flight sensors such as a sonar or laser range finder. 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 camera, and a sonar sensor. The camera and sonar sensor were mounted to the robotic arm and calibrated to enable accurate measurement of scene data. Image and depth data were registered in a single coordinate system and visually rendered into a 3D representation of the scene using the software ImageJ. Experiments were conducted to find the optimal parameters for image and depth data collection. Results show that the system can create 3D models of primitive shapes, such as rectangular prisms. The sonar sensor is limited due to surface reflectance variability and noise and, thus, exploring other sensors, such as LiDAR, may be worthwhile.

Student(s):
Kevin Lee

Faculty Mentor:
Dr. Craig Reinhart

Real-Time Object Detection via YOLO

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Object detection is the task of finding specific objects in an image or video. Applications of object detection range from smart surveillance, self-driving cars, to medical diagnostics. Traditional approaches use feature descriptors, such as SIFT or HOG, and learning classifiers, such as a support vector machine. However, more popular approaches for object detection utilize recent advances in deep learning and make significant improvements over traditional approaches. Typically, these methods use deep convolutional neural networks (CNNs) to detect objects in images. Creating fast and accurate object detection systems remains an active area of research in computer vision. Deep learning approaches such as R-CNN (Region-Based Convolutional Neural Network) provide high accuracy but lack the computational speed necessary for real-time detection speeds. YOLO (You Only Look Once) solves the problem using a radically different approach: YOLO reframes object detection as a regression problem and applies a single CNN to the entire image. YOLO is able to offer real-time processing speeds, ranging from 45 FPS (frames per second) to 155 FPS. The goal of this project is to reimplement YOLO and reproduce results comparable with the original implementation. The project will use the Python programming language, the PyTorch deep learning framework, and OpenCV computer vision library. A pre-trained network, such as AlexNet or VGG-16, will be repurposed via transfer learning for the project task. Amazon Web Services cloud GPUs will be used for training the YOLO model.

Student(s):
Kevin Lee

Faculty Mentor:
Dr. Craig Reinhart

Characterization of nahM and nahOM Protein Complex

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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.) have determined the structure of dmpFG along with identifying the unique water filled intramolecular channel. However, we still do not know how the individual subunits communicate, and that is the goal of the present research. To understand inter-subunit communication, we want to determine the structure of nahM protein on its own and as part of the nahOM protein complex. We believe, that comparing the structure of nahM protein when it is alone and when it is bound to another protein will provide insights into the formation of the nahOM protein 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. The gene product was transformed into the competent E. coli BL21 cells. The cell cultures were grown Luria Broth in the presence of 0.2% dextrose and 100 mg/ml ampicillin. The cultures were lysed using digital sonifier and 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 protocols to drive the protein from the insoluble fraction into the soluble fraction.

Student(s):
Nodirkhon Mamatov

Faculty Mentor:
Dr. Robert Richards

Kinematical Properties of the Cartwheel Galaxy to Infer Formation of Ring Galaxies

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The Cartwheel Galaxy is a ring galaxy, a type of peculiar galaxy. When looking at the formation and evolution of a galaxy, scientists look at the mass distribution within the galaxy. By observing spectral measurements of the Cartwheel Galaxy, the redshift of the spectral lines gives us the apparent distance between Earth and the Cartwheel Galaxy, giving us enough information to calculate the acceleration and the ages for each part of the outer ring, the inner ring, and the spokes of the galaxy. Furthermore, looking at the luminosity of the three respective areas gives more information on the ages of the stellar populations. The velocities are measured by the Doppler Shift in the spectral lines and used to calculate an acceleration and age. By calculating the ages of each part of the galaxy, I conclude if the galaxy is formed by two galaxies that collided or if they naturally form this way.

Student(s):
Kaualani Maneafaiga

Faculty Mentor:
Dr. John Deisz

Plastic Microfiber Ingestion by Mytilus Californianus in the Channel Islands Harbor, California

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Microfibers are an emerging threat to terrestrial and aquatic habitats worldwide. Their prevalence in the environment raises toxicity concerns due to their ability to concentrate high levels of persistent organic pollutants (POPs) and their potential to bioaccumulate within food webs. They are equivalent in size to planktonic organisms, making them available to a range of marine invertebrates. In past studies, the bivalve mollusc Mytilus californianus has been shown to accumulate and retain these plastics through ingestion, digestion, and adherence. Through previous student research, an abundance of microfibers has been identified in the Channel Islands Harbor in Oxnard, California. The number of microplastics in the surrounding bivalves have yet to be examined. I aim to determine the frequency and characteristics of microfiber pollution in wild M. californianus communities in this location. Due to a high prevalence of wastewater, runoff, and water reuse in residential areas, I expect the samples collected further inland will have a higher uptake percentage of microfibers than the samples collected near the channel delta. The mussels will be collected randomly from both sites and dissected. Hydrogen peroxide will be used to digest the organic matter and a saline solution will be added to separate the microfibers from the dissolved liquid via flotation. The mixture will be filtered by vacuum filtration over a cellulose nitrate membrane filter. Microfibers will be examined, counted, and characterized under a compound light microscope and images will be taken using an iPhone 5s camera. All experimental procedures are designed to minimize potential contaminants.

Student(s):
Chloe Mankin

Faculty Mentor:
Dr. Andrea Huvard

Investigating the Antagonistic Effects of Microbial Isolates TER-MGF-1 and KB20

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Antimicrobial-resistant and multi-drug resistant organisms are plaguing the clinical sector, creating a global crisis. This crisis is perpetuated by the insufficient effort by pharmaceutical companies to discover novel antibiotics to contend with the increased rate of antibiotic-resistant infections. ESKAPE pathogens are of particular concern as they are regarded the problematic pathogens possessing multi-drug resistance, likewise constituting the majority of nosocomial infections in the United States. Programs like Tiny Earth aim to involve undergraduate students in the discovery of new antibiotics from soil microorganisms. My project aims to contribute to the reservoir of research on antibiotic discovery by investigating two of these soil microbes, TER-MGF-1 and KB20, that antagonize ESKAPE pathogens. A collection of transposon mutants will be formed by random transposon insertion into the genomes of TER-MGF-1 and KB20 in order to disrupt antibiotic production and ultimately identify genes involved in antibiotic production. Transposon delivery requires electroporation to transform cells with a plasmid vector. For successful electroporation, it must be determined at which points TER-MGF-1 and KB20 grow best (log phase). As such, I have been conducting growth curves of each isolate. Once optimal growing conditions are elucidated, we will move forth with transposon mutagenesis and characterization of antibiotic production genes.

Student(s):
Julianna Martinez

Faculty Mentor:
Dr. Theresa Rogers

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.

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Students are conducting a large scale screen for novel sources of cryptic genetic variation (CGV) in natural populations of Drosophila melanogaster. CGV may be an underappreciated component in the spectrum of natural variation upon which natural selection can act. The screen is based on a model for the production of head defects by the extra eye mutation (ee), which is incompletely penetrant, variably expressed, and conditionally dominant. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a key molecule in the JAK-STAT signaling cascade implicated in embryonic eye field establishment. In ee strains, a P transposable element insertion maps near a gene (Su(var)2-10), and is the putative target of RNAi-induced heterochromatization. The proposed model predicts that new mutant phenotypes may be uncovered in crosses between ee lines and flies from natural populations known to contain P-elements. Such novel mutants are predicted to express epigenetic signatures via RNAi-induced heterochromatization of genes near P-elements. An initial screen was conducted for such mutations by scoring progeny of crosses of 16 separate wild-derived lines to ee. In one such cross, a new mutation, crybaby (cby), was recovered. Cby exhibits the properties expected of an epigenetically-triggered mutation. Our results suggest that variation in natural populations may include cryptic, epigenetic sources linked to transposable elements, which are revealed under particular genetic contingencies. Screens of wild strains for additional examples of cryptic phenotypes are ongoing, as are genetic and molecular characterization of the cby and ee phenotypes.

Student(s):
Lauren McAllister, Makena Wolfram, Dagem Getahun

Faculty Mentor:
Dr. David Marcey

Maximizing Solubility of FslA for Future Kinetic Work

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The effectiveness of antibiotics is decreasing at an alarming rate in what is called the antibiotic crisis. Recognizing the strong correlation NIS siderophores have with virulence in bacteria, targeting NIS synthetases in antibiotic design appears to be 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 Tularemia. 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. A higher melting temperature translates to a greater overall stability. The DSC experiment also revealed if FslA is unstable at the working temperature of FslA, 23 °C. The melting point range for FslA was found to be 70-90°C, well above my working temperature, 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.

Student(s):
Drew Miles

Faculty Mentor:
Dr. Katherine Hoffmann

MyChess: A Chess Companion App

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To a chess player, their rating is the sum of hours of work, study, and risk undertaken for the pursuit of advancement of knowledge and ability. The purpose of this app is to fill the void of a user-friendly interface for accurately representing professional chess players’ accomplishments and tournament performance. I will be doing this by creating an iOS mobile app utilizing my backend and software design experience to reach my fellow chess players. This app will use the JSoup API to scrape player ratings from uschess.org, an outdated and clunky website, which is currently the only reliable way to access rating data. It will then integrate the data with a smooth, user friendly UI on a massive scale. My hope is this app will further strengthen and supplement the sense of pride a chess player receives as they work their way up the rating ladder.

Student(s):
Nathan Mittenzwey

Faculty Mentor:
Dr. Craig Reinhart

Structure Determination of NRPS Independent Siderophore Synthetase DesD Complex Using X-ray Crystallography

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Iron is essential for bacteria to survive. When iron concentration is low, bacteria secrete siderophores. Siderophores can be assembled via two pathways. They 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. In our lab, we focus on non-ribosomal peptide synthase independent siderphore (NIS), 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 is model enzyme. In this research, we will find the structure of DesD binding to different substrates to figure the enzyme specificity and flexibility of loop capping the binding site. X-ray crystallography technique will be used to solve the atomic level structures of apo, substrate, and product-boned complexes. The atomic level structure of DesD bound to large substrate dfoB and ATP will be solved utilizing computer programs CCP42i, COOT, Refmac5, and Mosflm software. Future work will include structure-based inhibitor design to prevent DesD from binding to substrate and thus prevent synthesis of a virulent factor in pathogenic bacteria.

Student(s):
Yasi Mojab

Faculty Mentor:
Dr. Katherine Hoffmann

Identification of factors which bind long non-coding RNA to chromatin in Drosophila

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Dosage compensation is an epigenetic mechanism which equalizes the gene expression of an uneven number of chromosomes. Many organisms have developed various mechanisms to correct this imbalance. In Drosophila melanogaster, there is an upregulation of the single X-chromosome in the males to compensate for its monosomy. Upregulation of this male X-chromosome is performed by the dosage compensation complex (DCC). The DCC contains long non-coding RNAs Rox1/2 which organize the chromatin of the X chromosome in Drosophila males so that transcription can occur at a rate two times higher to match that of females. But how this critical non-coding RNA binds to the chromatin remains unknown. My project focused on identifying which factors participate in targeting non-coding RNA to chromatin. The UAS/Gal4 RNAi activation system was used in Drosophila to knock down candidate genes that affect different steps in RNA processing. Following knock down, RT-qPCR was conducted on male salivary glands to determine efficiency of knock down. If a successful knockdown was determined, then FISH (fluorescence in situ hybridization) against the non-coding RNA roX1 was conducted in salivary gland cells. Knock down of Hrb98DE showed no delocalization of roX1 by RNA FISH while Knockdown of Rrp6 and Dis3 (exosome component) showed partial delocalization of roX1. Knockdown of Saf-B and SF1 (spliceosome components) showed presence of extra nuclear soluble roX1. Together, the results of this project will shed light on which factors are required to bring a noncoding RNA to chromatin and will lead to a better understanding of dosage compensation.

Student(s):
Javier Montelongo, Javier Montelongo, Jennifer Aleman

Faculty Mentor:
Dr. Maya Capelson

Lumin: Android Lightmeter for Photography

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In professional photography, primarily when shooting using film, it is important to obtain correct exposure settings. In order to obtain correct exposure, most professional photographers rely on a handheld light meter that is constructed specifically to meter either incident light (light being cast upon subject) or reflective light (light being reflected from subject.) For the purpose and cost of this project, I will be creating a mobile light meter app for Android OS using Android Studio IDE with the Android SDK and the Android emulator. My goal is to create an Android App that allows users to meter light by taking an image through his/her android phone, and then extracting the metadata from that image to calculate the ideal exposure settings based on the ISO, f-stop, and shutter speed that the image was taken. It is important to notice that some film emulsions can react differently to natural light than compared to digital sensors so to test this, I plan to run initial tests by metering for a few different cameras: the first round of tests will be using a Pentax K-10d with a Sears 50mm lens; if those tests are successful, I will run the next round of tests to meter for a Minolta X-700 35mm camera, with both an MD 50mm lens and an adjustable zoom 28 - 85mm MD lens, with Kodak Ektar100 film.

Student(s):
Andrew Nelson

Faculty Mentor:
Dr. Craig Reinhart

THE Effect of Fire on Soil Microbial Community Diversity

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Soil microorganisms decompose active soil organic matter, a necessity for nutrient recycling and ecosystem function. Environmental changes such as temperature, pH, or moisture can affect the microbial decomposition of active soil organic matter. Catastrophic events, such as wildfires, can lead to a decrease in available nutrients by removing organic matter, deteriorating soil structure, volatilization, and erosion. In this study, microbial communities were monitored over time in wildfire burned and unburned regions of the Ventura Botanical Gardens that were effected by the Thomas Fire in 2017. Soil samples were collected 1, 2, 4, and 6 months after the fire. Microbial community DNA was extracted from soil samples, the V4 region of 16S rRNA gene amplified by PCR then sequenced using Illumina ® MiSeq. The sequences will be analyzed using Quantitative Insights into Microbial Ecology 2 (QIIME ™ 2). In the early months after the fire we expect lower soil microbial diversity in burned regions relative to unburned regions. Over time the burned region may reach similar levels of microbial diversity. Understanding microbial community changes as soil recovers from wildfires will aid in the design of ecosystem recovery techniques.

Student(s):
Kyrra Nielson

Faculty Mentor:
Dr. Theresa Rogers

The Effects of Ocean Microplastic on the Digestive System of the Mussel Mytilus galloprovincialis

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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 to have negative implications for the health of many marine organisms once ingested. The intertidal mussel, Mytilus galloprovincialis is a widely distributed filter-feeding organism that is exposed to fluctuations in the intertidal-zone as well as microplastics in its environment. We assessed whether microplastics affect the function of its digestive gland by measuring amylase digestive enzyme activity in mussels exposed to microplastic particles under laboratory conditions. The experimental design consisted of 8 separate glass beakers filled with 1,000mL of sea-water (17°C): 4 beakers were low-food conditions and 4 beakers were high-food conditions (3 mussels per beaker). This experimental design was completed twice to investigate alternative microplastic scenarios. The first experimental beakers received 10um microplastics diluted in water to maintain a microplastic concentration of 110 particles/mL daily (below real-world conditions). The second experimental beakers received the same microplastic-type diluted in water to a concentration of 220 particles/mL daily (above real-world conditions). Our results indicated that enzyme activity of amylase in all microplastic-treatments did not differ from those in control treatments in either low or high-food concentrations. Hence, M. galloprovincialis did not modulate digestive enzyme activity once subjected to microplastics although it is likely that they ingested them. This could be due to reduced feeding rate or compensation for any negative effects the plastics may have posed.

Student(s):
Cj O'Brien

Faculty Mentor:
Dr. Kwasi Connor

Compact Muon Solenoid upgrade for the High Granularity Calorimeter and Particle Identification

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We will present the results of our summer efforts to develop testing capabilities forsilicon based pixel detector prototypes, which constitutes the essential component of the High Granularity Calorimeter (HGCAL) upgrade of the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in Switzerland. The HGCAL upgrade is a collaborative effort involving California Lutheran University, UCSB, CERN and other institutions to increase the discrimination resolution for hadronic and electromagnetic particle showers, as well as provide an improved determination of the energy scale for hadronic quark-gluon particle showers. This past summer, the silicon based pixel detector prototypes went under a beam test at CERN. We are presenting data analysis results of our characterization of the detector particle identification efficiency, in particular for electrons, muons, and pions particle beams.

Student(s):
William Parquette, Hend Kordy and Johann Dias

Faculty Mentor:
Dr. Sebastian Carron Montero

Compact Muon Solenoid upgrade for the High Granularity Calorimeter and Particle Identification

View abstract

We will present the results of our summer efforts to develop testing capabilities forsilicon based pixel detector prototypes, which constitutes the essential component of the High Granularity Calorimeter (HGCAL) upgrade of the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in Switzerland. The HGCAL upgrade is a collaborative effort involving California Lutheran University, UCSB, CERN and other institutions to increase the discrimination resolution for hadronic and electromagnetic particle showers, as well as provide an improved determination of the energy scale for hadronic quark-gluon particle showers. This past summer, the silicon based pixel detector prototypes went under a beam test at CERN. We present data analysis results of our characterization of the detector particle identificationefficiency, in particular for electrons, muons, and pions particle beams.

Student(s):
William Parquette, Hend Kordy and Johann Dias

Faculty Mentor:
Dr. Carron Montero

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

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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.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.

Student(s):
Melissa Pepper

Faculty Mentor:
Dr. Kwasi Connor

Applications of Error-Correcting Codes

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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, error correcting codes have gone beyond their tradition 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 viewed through set theory which gives another perspective on how these ECC work. This research examines the Hamming Code where various ways to explain the methodology behind the detection and correction process are discussed. This research also investigates further applications of the Hamming Code in a team competition and magic tricks through a set theoretic approach and find reasonings as to how these applications are guaranteed to work given properties of the Hamming Code. Moreover, I aim to expand on the applications of the Hamming Code to show its true significance as a perfect ECC.

Student(s):
Luis Perez

Faculty Mentor:
Dr. John Villalpando

The negative effects of traumatic brain injuries on cerebral blood flow and cerebrovascular flow attributes

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Background: Traumatic brain injuries (TBI) in sports has has increased considerably during the last decade with research focusing on the immediate impact of the injury on the athlete and more focused in the neuropsychological aspect of the injury. However, their is a lack of research on the long-term physiological impact that TBIs have on the brain. Aim: The aim of the present study is to investigate the negative effects that TBIs have on cerebral blood flow and cerebrovascular flow attributes (n=18). Methods: Participants anthropometric measurements and blood pressure were measured. Participants underwent an ultrasound scanning of their common and internal carotid artery on the right side of the neck and cerebrovascular flow attributes were recorded. Correlation analysis was performed at a statistical significance level of p ≤ 0.05. Results: Significant relationships were found when relating TBIs to cerebral blood flow and cerebrovascular flow attributes. Conclusion: Athletes that undergo multiple TBIs in their athletic careers may have disrupted cerebral blood flow and cerebrovascular flow attributes.

Student(s):
Jarrett Rodriguez

Faculty Mentor:
Louise A Kelly

Sentence Generator Using Markov Chain Monte Carlo

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Markov Chain Monte Carlo is a method for running simulations multiple times to produce data to generate samples. This method has applications in physics, biology, and other fields. This method has been used to try to solve the traveling salesperson problem and is used in the Metropolis-Hasting algorithm. For this project, Markov Chain Monte Carlo will be used to generate words based off of a text file. This method will then be used to generate sentences based off of the same text file.

Student(s):
Armando Santana

Faculty Mentor:
Craig Reinhart

Cryptography using RSA and Elliptic Curve Cryptography

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Cryptography is a subject that relates to both Mathematics and Computer Science. Some applications of cryptography involve securing messages, credit card information, and personal information such as social security number. This project investigates the mathematics behind two methods of encryption: RSA and Elliptic Curve Cryptography. RSA is an encryption method that involves modular arithmetic and large prime numbers, while Elliptic Curve Cryptography involves elliptic curves over a finite field, the discrete logarithm problem and modular arithmetic. This project also looks at how one cryptosystem differs from the other and what are the benefits and drawbacks of each cryptosystem.

Student(s):
Armando Santana

Faculty Mentor:
Karrolyne Fogel

Synthesis of Spirocyclic Compounds via Claisen Rearrangement

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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. 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 is 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 a grignard reagent, 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 further research, 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. 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.

Student(s):
Jessica Shin

Faculty Mentor:
Dr. Jesus Cordova Guerrero

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

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What is the microscopic nature of the superconductivity in Strontium Ruthenate, (Sr2RuO4)? Sr2RuO4 is a metal that becomes a superconductor at low temperatures around 1.5 Kelvin. Sr2RuO4 is an unconventional superconductor with 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 sheets, largely ignoring the third dimension. My hypothesis is that three-dimensional effects of electron interactions within Sr2RuO4 can resolve current discrepancies in the understanding of this material. To accomplish this, I used C++ computer programming language to build a computer simulation that models the interaction of the electrons using the laws of quantum mechanics. When the parameter allowing third-dimensional interaction 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 three-dimensional analysis of this material. Our code could help explain properties of the superconductivity of Sr2RuO4. This could transfer to other metals and give a better understanding of known superconductors and their properties, and help to discover new superconducting materials. Many superconductors are similar 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 two-dimensional interactions. Our code can be generalized and used to create three-dimensional models for other metals as well.

Student(s):
Jamie Shultz

Faculty Mentor:
Dr. John Deisz

Exploring Maternal Care, Learning Mechanisms, and Social Behavior in Ring-tailed Lemurs.

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The purpose of this research is to compare humans and lemurs in three aspects: maternal care, social behavior, and learning mechanisms. This study focuses on three Ring-tailed lemurs, a mother/daughter pair and a male, at America’s Teaching Zoo at Moorpark College. For maternal care, we explored the behavioral interactions between the mother/daughter pair and time spent together during observation. We explored the introduction of a new male lemur to the mother/daughter pair’s enclosure. Finally, we investigated learning mechanisms involved with Positive Reinforcement Training with lemurs. Ring-tailed Lemurs are the most common animal in zoos, so it is important to understand their social behavior and learning mechanisms to minimize issues with animal interactions, and increase their well being. For the male lemur’s tunnel data, there was no correlation between time he spent in the tunnel and how far he traveled. The behaviors that were significantly associated with success during training was holding the fence, looking around environment, and climbing down. When comparing humans to lemurs, both process information in a serial order, babies have a great attachment to their mother, but differed in how they interacted with new primates. We share more than 90% of our DNA with lemurs, and this study emphasizes similarities in maternal care and learning mechanisms; some scientists go as far as saying that maternal care and hierarchy in primates are the precursor to human morality. For future directions, it is crucial to explore introduction processes between lemurs at zoos to minimize conflict.

Student(s):
Lorena Silva

Faculty Mentor:
Dr. Lorenzo Ramirez

Cloning and Expression of Entamoeba histolytica eIF5A in Escherichia coli

View abstract

Entamoeba histolytica (Eh) is a parasitic eukaryote that causes amoebiasis in humans. Eh has a two-stage life cycle comprised of the non-infectious trophozoite 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 and organ abscesses. A goal of the Entamoeba community is to understand the life cycle of Eh, specifically the molecular mechanisms that leads Eh to transition from the trophozoite to the cyst. Previous studies (Ehrenkaufer, 2007) have focused on identifying Eh proteins involved in the trophozoite-cyst transition. One protein identified 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 Eh genome encodes for three eIF5A isomers. In this study, in order to determine the role of eIF5A in the E. histolytica life cycle, we will clone one eIF5A isoform in an expression vector for 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 Eh eIF5A (151540) DNA. The results of PCR were confirmed via agarose gel electrophoresis. Ligation of pET 14 and 44 vector DNA with Eh DNA was similarly confirmed after E. coli transformation. Future work will include primer design editing as well as ligation and transformation experiments.

Student(s):
Kayla Sircy

Faculty Mentor:
Dr. Paloma Vargas

Base Catalyzed Synthesis of Functionalized Indoles

View abstract

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 which 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 this 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.

Student(s):
Alexandra Stewart

Faculty Mentor:
Dr. Jesus Cordova Guerrero

Multi-Core Joins

View abstract

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 organizations rely heavily on data integration to pull information from multiple sources in order to make data driven decisions. 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 computers which have multiple cores, allowing them to perform multiple tasks simultaneously. Ideally the more cores that a computer has the 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.

Student(s):
Daniel Suarez

Faculty Mentor:
Dr. Graham Matthews

Metabolic Pathway Elucidation of Stable Oxidative Phenolic Compounds

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This study tested the link between chlorinated phenolic compounds as well as the formation and electrophoretic separation of stable metabolites found in urine. Establishing direct pathways and developing sensitive/selective analytical tools to measure and characterize xenobiotics provides a defined link between potential hazards and suspected health effects. Methodologically, 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 separation of the chlorinated phenols and their oxidative metabolites were demonstrated through capillary electrophoresis (CE) under the following conditions: 75 mM sodium tetraborate buffer (pH = 8.5) with 5 % methanol and 50 mM SDS, +10.0 kV running voltage, injection time = 5.0 s, effective capillary length = 55 cm, and run temperature = 20 °C. Although the compounds were not fully characterized, CE allowed for a secondary method of peak and baseline confirmation. 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. Further studies will be concentrated on human sampling, likely both blood and urine, to allow for near in-situ, real-time, monitoring of chlorinated phenols for expanded toxicological studies. Finally, we will provide guidance for the application of metaheuristic computational tools to aid in future studies involving parallel chemical separation and screening. This approach will prove valuable for future investigators involved in studying complex biological samples.

Student(s):
Leslie Tran

Faculty Mentor:
Dr. Grady Hanrahan

Climate Change Effects of Temperature and pH on Coral Bleaching as modeled in Aiptasia Pallida

View abstract

Coral reefs are vulnerable to increases in ocean surface temperature and ocean acidification, which can lead to a reaction called coral bleaching. Aiptasia pallida, a tropical species of anemone, was used as the model species to understand these phenomena of temperature and pH changes predicted by the Intergovernmental Panel on Climate Change (IPCC) by the year 2100. Cell counts were taken to quantify the number (in cells per mL) of expelled zooxanthellae, or bleaching, that occurred. Temperature tests were observed from 24 to 27 degrees Celsius and pH tests were done from 7.6 to 8.1. Simultaneous experiments of both parameters were then conducted using the same measurements for comparison to understand the impact of pH and temperature concurrently, as we see in our oceans today. Results to come.

Student(s):
Hannah Travers

Faculty Mentor:
Dr. Andrea Huvard

The Prevalence and Succession of the Pacific Oysters in Oxnard, California

View abstract

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, scientists questioned the adaptability of the oyster as it could have the potential to cause ecological succession by outcompeting the keystone species. Within Channel Islands Harbor in Oxnard, California, sightings of the Pacific Oyster have recently been reported in the area. In order to track if these Pacific Oysters have the potential to cause an ecological disturbance, growth rates and experimental coverage were collected at two separate locations for the Pacific Oysters, as well as the keystone species, Mytilus. Surveillance of the area was done to find that the oysters preferred living among rocks, where one could be spotted about every 5 feet. Two locations were chosen where environmental parameters (temperature, salinity, dissolved oxygen) were measured to see if there was any correlation with growth rates. Ceramic plates were placed under water at each location in the harbor and were observed for the growth of the two species. The Mytilus and Crassostrea gigaswere identified, and the longitudinal axis was measured of each individual weekly. The data was then used to find the average increase in growth from initial settlement to its apex size dividing that by the number of weeks. Growth rates and coverage of both species were then used to compare and make a conclusion whether the Pacific Oyster is causing an ecological disturbance.

Student(s):
Austin Truong, Amy Elise Wilkerson

Faculty Mentor:
Dr. Andrea Huvard

Parking Space Finder

View abstract

As more people rely on their vehicles to get from point A to point B, finding a parking space can be a challenge at times, leaving one driving around aimlessly through the aisles. Instead of spending time searching, wouldn’t it be easier to know exactly where the available parking spaces are located? By simulating a parking system with toy cars and sensors along with an accompanying mobile application, finding an available spot is made easier. The Ultrasonic and Infrared sensors placed at the front end of each parking space, one through ultrasonic waves and the other through infrared light are able to detect if a toy car is occupying a space. As the spaces are updated, the mobile application notifies the user of the number of spaces and the location of the parking spaces. In the end, reducing the amount of time it takes to find a parking spot.

Student(s):
Anahi Villanueva

Faculty Mentor:
Dr. Craig Reinhart

Prophylactic Mastectomy at Ventura County Medical Center

View abstract

Many breast cancer patients elect to remove the contralateral breast that is not affected by breast cancer, commonly referred to as a contralateral prophylactic mastectomy, or CPM. CPM has been extensively studied and does not improve survival in patients who do not have a deleterious genetic mutation (Kruper et al.). A genetic mutation of either gene BRCA 1 or BRCA 2 increases the likelihood of cell division and the risk of developing breast cancer. CPM in patients who are genetically predisposed via a BRCA mutation are ethically justified and often, Physician encouraged. Nonetheless, CPM rates in the United States have increased over the past 20 years, with most patients having no strong genetic, familial, or personal risk factors. In non-genetically high-risk patients, our cancer program recommends following national standards and we encourage patients with poor health or those with only an average risk of CBC, not to choose CPM, since this specific patient population is the majority of women opting for CPM in the US (Tuttle et al.). We are concerned, however, that we may be providing CPM to patients outside of these criteria. We would like to analyze the decision making process, current methods of counseling, and our rates of CPM in our institution. We hope to identify areas to improve in our education and counseling for these patients and their surrounding communities to ensure sure we are providing sufficient emotional, scientific, and medical support in a way to minimize the patient’s potential need for emotional and physical recovery.

Student(s):
Andrew White

Faculty Mentor:
Dr. Shawn Steen

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.

View abstract

We are conducting a large scale screen for novel sources of cryptic genetic variation(CGV) in natural populations of Drosophila melanogaster. The screen is based on a model for the production of head defects by the extra-eye mutation(ee), which is incompletely penetrant, variably expressed, and conditionally dominant. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a key molecule in the JAK-STAT signaling cascade implicated in embryonic eye field establishment. In ee strains, a P transposable element insertion maps near a gene (Su(var)2-10), and is the putative target of RNAi-induced heterochromatization. The proposed epigenetic model predicts that new mutant phenotypes may be uncovered in crosses between ee lines and flies from natural populations that harbor P-elements at various genomic locations. Such novel mutants are predicted to be incompletely penetrant and variably expressed, caused by epigenetic silencing via RNAi-induced heterochromatization of genes residing at genomic positions near P-elements. In an initial study described here, we conducted a screen for such mutations by scoring progeny of crosses of 16 separate wild-derived lines to ee. In one such cross, a new mutation, crybaby(cby), was recovered. Cby exhibits the properties expected of an epigenetically-triggered mutation. Our results to date suggest that variation in natural populations may include cryptic, epigenetic sources linked to transposable elements, which are revealed under particular genetic contingencies. Screens of multiple wild strains for additional examples of cryptic phenotypes are ongoing (with one possible, additional variant discovered to date), as are genetic and molecular characterization of the cby and ee phenotypes.

Student(s):
Makena Wolfrom, Lauren McAllister, Makena Wolfrom Dagem Getahun

Faculty Mentor:
Dr. David Marcey

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Schedule of Events

Science Showcase: Poster Session

Student Abstracts

Determinants of Reincarceration

Effects of Fatigue Progression on Single Leg Squat Kinematics

Investigating the Role of eIF5A in Entamoeba histolytica Encystation

Image Storing Database with built in Image Editor

The Effects of Pesticides on Genetic Expression in Caenorhabditis elegans

Building a Cherenkov Radiation Particle Detector and Counter

Text-to-Image Generation and Colorization with Stacked Attentional Generative Adversarial Networks

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

Optimizing Protein Solubility for Crystal Formation

A Cross Comparison of Olfactory and Stress Behaviors Between Two Species of Canines

The Role of Type II Secretion of Legionella pneumophila in Growth at 25, 35, and 42 Degree Celsius

The Role of Type 2 Secretion System’s Protein LegP on Legionella pneumophilia

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

Java-based Chatroom Application Using Encryption for Sending Messages

Using Natural Language Processing to Communicate Ideas More Clearly in Writing

Metagenomic Analysis of the Thomas Fire Burn Site

Tournament Bracket Application

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.

A Biomechanical Analysis of Long Snapping With and Without a Block

Determining the Kinetics of Desferroxiamine Dusing Isothermal Titration Calorimetry

Subtrate and pH Structural Studies of FslA

Taste Aversion & Effect of Epicatechin on Memory Formation in Lymnaea stagnalis.

Synthesis of Metal-organic Frameworks as Efficient Drug Delivery Systems

Synthesis and purification of N-Hydroxy-N-(5-aminopentyl)succinamic acid (HSC)

The Effect of Temperature on the Rate of Anaerobic Metabolism in Mytilus galloprovincialis

Tiling 2-Deficient Rectangles with L-Pentominoes

Milk Derived Extracellular Vesicles (EVs) Effect on Human Immune Cell Response in Vitro

Development of a New Carboxylic Acid Protecting Group

High Granularity Calorimeter Detector

Digital 3D Image Reconstruction via Sonar Rangefinding

Real-Time Object Detection via YOLO

Characterization of nahM and nahOM Protein Complex

Kinematical Properties of the Cartwheel Galaxy to Infer Formation of Ring Galaxies

Plastic Microfiber Ingestion by Mytilus Californianus in the Channel Islands Harbor, California

Investigating the Antagonistic Effects of Microbial Isolates TER-MGF-1 and KB20

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.

Maximizing Solubility of FslA for Future Kinetic Work

MyChess: A Chess Companion App

Structure Determination of NRPS Independent Siderophore Synthetase DesD Complex Using X-ray Crystallography

Identification of factors which bind long non-coding RNA to chromatin in Drosophila

Lumin: Android Lightmeter for Photography

THE Effect of Fire on Soil Microbial Community Diversity

The Effects of Ocean Microplastic on the Digestive System of the Mussel Mytilus galloprovincialis

Compact Muon Solenoid upgrade for the High Granularity Calorimeter and Particle Identification

Compact Muon Solenoid upgrade for the High Granularity Calorimeter and Particle Identification

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

Applications of Error-Correcting Codes

The negative effects of traumatic brain injuries on cerebral blood flow and cerebrovascular flow attributes

Sentence Generator Using Markov Chain Monte Carlo

Cryptography using RSA and Elliptic Curve Cryptography

Synthesis of Spirocyclic Compounds via Claisen Rearrangement

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

Exploring Maternal Care, Learning Mechanisms, and Social Behavior in Ring-tailed Lemurs.

Cloning and Expression of Entamoeba histolytica eIF5A in Escherichia coli

Base Catalyzed Synthesis of Functionalized Indoles

Multi-Core Joins

Metabolic Pathway Elucidation of Stable Oxidative Phenolic Compounds

Climate Change Effects of Temperature and pH on Coral Bleaching as modeled in Aiptasia Pallida

The Prevalence and Succession of the Pacific Oysters in Oxnard, California

Parking Space Finder

Prophylactic Mastectomy at Ventura County Medical Center

A Genetic Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster.