Student Research Symposium

October 19-31, 2020

Schedule

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Monday, October 19, 2020
8:00am
2020 Virtual Student Research Symposium

Location: Virtual


A Generalization of the Hardy Distribution for Golf Hole Scores

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Christopher Brown, Mathematics
Student: Ryan Kyaw

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In golf, the likelihood of success for each shot is primarily dependent on the result of the previous shot. Hence, Markov Chains may be used to model the progress that a player makes each hole. Modelling and predictions in sports have grown rapidly in recent years, and athletes and teams use predictive models to improve. In “The Hardy Distribution for Golf Hole Scores” by A.H.G.S. Van der Ven, the author uses categorical descriptors to model a golfer’s progress as a random walk. To improve the detail and accuracy of Van der Ven’s model, our proposed models will include the general states that may occur throughout the golf course. Primarily, we will be focusing on the distance to the hole that a player has on any given shot. We will be using the Beautiful Soup package of the Python programming language to web scrape the PGA Tour data needed to estimate state transition probabilities. Several models will be created and compared to PGA data to analyze golf hole scoring. Ultimately, we will see that our models produce fairly accurate score distributions. 

A Markov Chain Analysis of the XFL Overtime Rules

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Christopher Brown, Mathematics
Student: Jazmine Toledo

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In 2018, a new alternative competitive league referred to as the XFL introduced unique football overtime rules. In an attempt to make the football overtime rules fairer, the XFL implemented rules which differ significantly from the NFL rules. The purpose of this project was to investigate how fair the NFL overtime system is compared to the XFL overtime model using the NFL overtime model proposed by Jones, The New Rules for NFL Overtime. Jones claims that the NFL overtime system neatly balances out the coss toss advantage without significantly extending the expected length of the game. Although the system may seem mathematically appealing there is still some skewness favoring the team that wins the coin toss. To identify which overtime system is fairer, we created a discrete-time Markov chain model of the XFL overtime rules and compared the model outcomes for the two rule sets.  We also provide some discussion about the concept of fairness in the context of overtime scenarios. The XFL claims these rules are fairer.  Thatis, if given equally skilled competitors who enter overtime, they will have the same chance to win. We also explored a second XFL claim: that their rules lead to shorter overtimes.  To accomplish this, we equated steps in the Markov chain model with times and evaluated the claim that the XFL overtimes lead to shorter over time than the current NFL overtime rules. We discovered that the XFL overtime rules are fairer than the current NFL overtime rules and it can also be demonstrated that the XFL overtimes are shorter than the current NFL overtime rules.

A review on modern methods for the synthesis of spirocyclic & Organic Chemistry textbook: Practice problems and applications

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Cordova, Chemistry
Student: Jessica J Nasr

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The goal of this research project was to develop a literature review on spirocyclic compounds and practice textbook for Organic chemistry. The first step for the literature review was to conduct literature searches to find the most current reports in the synthesis spirocycles. This was followed by the analysis and discussion of the reports by the type of transformation. This was then used to write a coherent review article for subsequent publication. For the textbook the first step was to find articles that include chemical reactions that will be included in the textbook which will then be organized into chapters for different chemical reactions. The spirocyclic review will be submitted for publication by the end of this year. The spirocyclic review is important because it encompasses recent reports for the synthesis of spirocyclic which will provide further knowledge of this unique characteristic structure in the scientific community.The organic chemistry textbook is important because it will help enhance the knowledge for organic chemistry college students by providing them with a useful tool to strengthen their knowledge in this field.

A Screen For Inducible Epigenetic Variation in Natural Populations of Drosophila melanogaster

Program: Aperture Summer Research Fellowship
Faculty: Dr. David Marcey, Biology
Student: Gabriella Moreno

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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.  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 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, 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. This project consists of  additional screens of multiple wild strains for examples of cryptic phenotypes.

 

Am I Latino?: Erased Indigenous Identities in Southern California

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Dr. Cynthia Duarte, Sociology
Student: Xochitl Lopez

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Oftentimes in our everyday life, we use terms like “Latino,” “Latinx,” or “Hispanic” to categorize people from Mexico, Central, or South America. These terms are used to complete official paperwork or government documents, in academia, and life in general. However, using these colonizing terms erase indigenous identities. Indigenous communities continue to flourish and thrive in Mexico, despite Spanish colonization over 500 years ago. This is most represented in southern Mexican states in indigenous communities through languages, customs, and traditions as seen in various indigenous groups of Mexico such as the Mixtecos, Zapotecos, and Triquis.

Most literature regarding indigenous populations of Mexico revolves around adult migrants, their demographics, and settlement/labor experiences. Of the literature that discusses second generation children of Mexican immigrant, there is very little scholarship on the narratives of the indigenous youth from Mexico and their identity development. This research highlights the narratives of young, female, indigenous college students and what being indigenous in Southern California means to them. Based on 14 qualitative in depth interviews of indigenous college bound youth, I was able to find common themes within school experiences, dealing with stereotypes and microaggressions, as well as how they navigate their indigenous identity while living in Southern California, where the idea of “Latinidad” dominates Mexican narratives.

Analysis of Microfibers in Sardina pilchardus and Rastrelliger kanagurta

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Bryan Swig, Biology
Student: Steven Ortez Hernandez

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A study on microfibers was done to determine the quantity of microfibers within Sardina pilchardus and Rastrelliger kanagurta. Fish were dissected and the gills and gut were extracted. The extracted organs were measured and ground into a paste; which was suspended in a brine solution. The solutions were then filtered through a vacuum pump, and the results were analyzed using light microscopy. When Sardina pilchardus (Sardine) was compared to Rastrelliger kanagurta (Indian Mackerel) we found that there were significantly more microfibers in Rastrelliger kanagurta than they were in Sardina pilchardus ( t=0.004, df=68 p≤0.05). When small  Sardina pilchardus were compared to large size to determine which size contain the greater number of microfibers, we found that there was no significant difference between both fish sizes (t=0.53, df= 43,p≥0.05), when small Rastrelliger kanagurta were compared to large, we found that there was no significant difference between both sizes as well.( t=0.37, df=19, p≥0.05). 

Analysis of Microfibers in Sardina pilchardus and Rastrelliger kanagurta

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Bryan Swig, Biology
Student: Keury Ortez Hernandez

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A study on microfibers was done to determine the quantity of microfibers within Sardina pilchardus and Rastrelliger kanagurta. Fish were dissected and the gills and gut were extracted. The extracted organs were measured and ground into a paste; which was suspended in a brine solution. The solutions were then filtered through a vacuum pump, and the results were analyzed using light microscopy. When Sardina pilchardus (Sardine) was compared to Rastrelliger kanagurta (Indian Mackerel) we found that there were significantly more microfibers in Rastrelliger kanagurta than they were in Sardina pilchardus ( t=0.004, df=68 p≤0.05). When small  Sardina pilchardus were compared to large size to determine which size contain the greater number of microfibers, we found that there was no significant difference between both fish sizes (t=0.53, df= 43,p≥0.05), when small Rastrelliger kanagurta were compared to large, we found that there was no significant difference between both sizes as well.( t=0.37, df=19, p≥0.05). 

Are Robots Responsible? Extended and Shared Moral Responsibility

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Lacey Davidson, Philosophy
Student: Rishabh Sarin

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Holding others and ourselves responsible for actions and the consequences of actions is a major and accustomed part of our moral practices and our social relationships. Philosophers have thought a lot about the conditions under which individuals are morally responsible for their behavior. Artificial Intelligence (AI) has challenged and changed our conceptions about moral responsibility. This is because most theories of moral responsibility are focused on individual human agents. Now we must ask: how can moral responsibility be distributed appropriately?

Can moral responsibility be extended from a human agent to their creation or shared between a human and their creation? For example, if a human agent develops a self-driving car and this self-driving car kills someone, who is responsible and why? This research will help us identify the conditions under which responsibility can be said to extend from an agent to their creation or be shared between an agent and their creation. The primary method in this paper is to use AI case studies to develop a theory of moral responsibility that can account for emerging technologies.

Although we cannot give a final solution to a problem that expands by the day as our digital society grows, developing a set of conditions for extended and shared moral responsibility can help us determine what to do in future cases. Automatic cars and robots are not a fantasy anymore. Questions that we have never asked ourselves arise about safety, dependability, and moral responsibility. We find it silly to think about putting cars in jail or blaming a robot for stepping on our toes, but ordinary questions of moral responsibility will soon arise for non-human non-agents and non-human quasi-agents (robots with higher-order intentional systems) that will not be easy to answer. Thinking through responsibility in these cases (before we must apply them) is essential within an increasingly technological world. This research will not only help AI interface companies, but also philosophers, students, and anyone who owns wears, or uses emerging technology.

Artificial Neural Network Platform Development for Chemical Toxicity Model Assessment

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Grady Hanrahan, Chemistry
Student: Kieudiem Nguyen

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Artificial Neural Networks (ANN) is a mathematical computing system that imitates neurons in the human nervous system, in which ANN collects and classifies information according to a specific structure. They can be trained to recognized patterns in a complex data set, and in particular, their self-learning capabilities enable them to be optimized for better prediction with sufficient accuracy as more relevant data become available. In this project, the ANN platform was created in a MATLAB format for designing the network, assessing network functionality, and optimizing the model factors. The dataset was divided into three models with various divisions of data. Each network model was trained and compared to experimental results under a supervised learning model using a two-layer feed-forward network with one hidden layer, from three up to fifteen hidden neurons. Subsequently, the performance of all models was observed under the correlation coefficient as well as the model error and discrepancies between predictive and experimental results. The model had ten hidden neurons with 70% data for training, 30% data for validating, and testing had the most remarkable performance as it had a high correlation as well as a small discrepancy in predictive result with a total of seven iterations for validation and four iterations for error validation. Therefore, an optimized ANN model will prove its accuracy and robustness when deploying them to assess the toxicity of phenolic-related compounds via chemical structure and function. Furthermore, they will predict toxicity values for human health assessment and industrial worker exposure.

 

 

Keywords: artificial neural networks; prediction, chemical toxicity; human health.

Black Reparations: An Argument for the Necessity and Practicality of Righting Past and Continued Racial Injustice

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Dr. Brian Collins, Philosophy
Student: Lindy Ortiz

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Black Americans have faced racial injustices for hundreds of years. From slavery to Jim Crow to discrimination to police brutality. These injustices not only affect the social status of Black Americans but also their economic status. The purpose of this research is to argue that the United States is an unjust society because it has failed to adequately correct for the injustices against Black people. The aim is also to provide a reasonable solution to righting years of wrongs through reparations. The questions that will be explored are: Are Black Americans owed or entitled to reparations, and if so, what form of reparations would be most effective in achieving justice? I will answer these questions by providing a presentation of John Rawls’s theory of justice and demonstrate how, in his view, the United States should be considered an unjust society. I also consider the debate between Tommie Shelby and Charles Mills on the use of Rawls to argue for racial justice. Then I claim that Black Americans are entitled to reparations in order for them to have justice for slavery, Jim Crow laws, Discrimination, etc. I do this by describing the injustices of the past and how they relate to the present. I also explore possible critiques or objections to reparations and refute those objections with an explanation of how Black Americans are affected by past and present injustices and how reparations would help us create a better, more just future. Lastly, I will offer multiple suggestions or options for reparations that I believe will be most effective in achieving justice. To summarize, this research finds that Black  Americans are indeed owed reparations for the past and continued wrongdoings and that the best forms of reparations are government programs that focus on improving economic equality for Black Americans.

Can a high dietary nitrate intake attenuate the detrimental effects of chronic alcohol consumption on the vasculature?

Program: Aperture Summer Research Fellowship
Faculty: Dr. Allan Knox, Exercise Science
Student: Michael Diaz

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Introduction: Alcohol-related deaths are the 3rd leading preventable cause of death in the United States. Moreover, excessive alcohol consumption can lead to various chronic health risks to include high blood pressure, stroke, liver disease, digestive problems, and heart disease. Various studies have shown fruit & vegetables (F&V) to improve vascular function, as well as reducing the risk for cardiovascular disease and overall mortality. A meta-analysis of over 833K participants across 16 cohort studies reported an all-cause mortality decrease by 5% for each serving of F&V. However, what remains to be understood are the simultaneous effects of alcohol & F&V consumption on the vasculature. The aim of this investigation was to determine if a diet high in nitrates, which is commonly found in some F&Vs, can mitigate the detrimental effects of alcohol consumption. Methods: A literature review was conducted utilizing PubMed and Google Scholar to identify potential studies that examined the prevalence between alcohol and F&V consumption. Key search terms and phrases included alcohol consumption, fruits and/or vegetable consumption, dietary nitrates, cardiovascular disease, and all-cause mortality. After reviewing the literature, all trends and significant findings were identified and reported. Results: Several key findings were discovered during this research, though with some restrictions. Numerous studies have reported cardioprotective benefits with “moderate” consumption of alcohol, mostly due to specific ingredients obtained from natural sources (e.g., flavonoids, polyphenols). In addition,  there were significant gaps discovered in our research. The reliability of self-assessment surveys, dose-specific inaccuracies, and lifestyle changes across longitudinal analyses were called into question. Conclusion: Although there is sufficient evidence to suggest the cardioprotective benefits of F&Vs, as well as moderate alcohol consumption, there is little-to-no research looking at the effects of both high F&V and high alcohol consumption on the vasculature.

Catalysis Mechanism Proposal for DesD

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Hoffmann, Chemistry
Student: Nathan March

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Our labs previous studies have shown Arg306 is critical for catalysis and structure models have shown His443 and Glu467 are spatially oriented to participate in substrate binding and catalysis of the substrate similar to Arg306.

Purpose: The intent of this study was to propose a reaction mechanism for the adenylation step as no previous studies have investigated the adenylation step of the NIS Synthetases.


Hypothesis: We hypothesized that Arg306, His443, and Glu467 are catalytic and necessary for binding of substrate to DesD.


Methods: To determine the possible reaction mechanism we reviewed literature of the NIS synthetase family. AcsD, a NIS Synthetase, had prior research into the second step of the mechanism. A review of the mechanism of ATPase was conducted as DesD catalyzes the ester bond between ATP and substrate. Additionally, we will use a well-established protein overexpression in E. coli, and affinity purification on an AKTA Start FPLC will be used to produce the DesD variant, His443Ala, for crystallization.


Conclusion: The adenylation step of the mechanism proposed requires His443 to stabilize the carboxylic group of the substate. The substrate then initiates a nucleophilic attack on alpha phosphate of adenosine ejecting pyrophosphate as a leaving group. Arg306 stabilizes the charged intermediate and the pyrophosphate which deprotonates Glu467 as it leaves the active site.    DesD performs a unique and understudied chemistry. The mechanism through which this unique chemistry occurs is valuable as a model for the NIS Synthetase family of enzymes. This project is part of a larger, long term goal of the lab, which is to map critical interactions in the binding site for structure-based inhibitor design. The design of an inhibitor for this target would represent a potential new class of antibiotics to combat pathogenic bacteria that synthesize NIS siderophores.

Chronotype, Ostracism, and Coping in Young Adults

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Amanda ElBassiouny, Psychology Department
Student: Rachel Ayala

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There are known biological, sociological, and psychological differences between chronotypes which may indicate the important role this trait has in one’s daily life, such as dealing with stress. Therefore, the purpose of this study is to examine the possible differences in mental health measures between morning and evening chronotypes focusing on the impact self-compassion (SC) may have on how effective positive reframing (PR) is when coping with ostracism in young adults. 

Data is being collected in the 18-25 age range through MTurk. Participants complete a scale labeling them as a morning or evening type, then asked to recall an experience of ostracism. Each participant is randomly placed in one of five conditions differing in coping order or strategy: SC/PR, PR/SC, PR, SC, or control. They then respond to mental health scales including stress, mood, and anxiety. It is expected that participants who used SC and PR to cope will report less psychological distress than those in the conditions who did not engage in both strategies. Anticipated implications suggest that considering chronotype may aid in increasing the effectiveness of future health behavior change interventions by focusing on the individual at the young adult age.

Classifying Infrared Emission Line Stars Using Optical Spectroscopy

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Mary Oksala, physics
Student: Van Haslett

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Massive stars are not expected to have solar-like magnetic fields due to their difference in internal structure. However, there is a rare subset of these stars that do have large, stable magnetic fields, denoted as Bp stars for their peculiar spectra, which can include emission features. These emission lines, created by material trapped in the magnetic field, have a similar appearance as another group of B-type stars, Be stars, although the physical cause is quite different, as these stars are not magnetic. The purpose of this study is to distinguish the Bp stars from the Be stars by comparing the star’s rotation velocity to the velocity of the material orbiting these stars to determine if the emission is caused by the presence or lack of a magnetic field. 

After cleaning and normalising our data, measurements of our sample of eight stars’ rotational velocities, using optical spectroscopy by the CFHT and Macator telescopes, were made applying the best fit synthetic model for an appropriate set of stellar parameters to measure the rotationally broadening or vsini of the helium line at 4388 Å. The velocities of the orbiting material were previously measured from the peak of infrared emission lines from hydrogen in a previous study. 

With our measured vsini, we compared the rotational velocity of the star to the velocity of the material orbiting them. Our fits have suggested that two of our targets are Bp stars, while three are clearly Be stars. Another interesting result from this study is the visual inspection of the spectrum of SS 453, which clearly shows that this system is a binary star system, with two unique spectral profiles superimposed within the spectrum. Although our results need further testing using spectropolarimetry to find out if these stars have a magnetic field, our study points to the possible addition of two new Bp stars, increasing the small number of previously known Bp stars.

 

Comparison of Female and Male Golf Swing Kinetics and Force Production

Program: Swenson Science Summer Research Fellowships
Faculty: Travis Peterson, Exercise Science
Student: Michele Birkner

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Golf is a popular sport that is enjoyed by both men and women. It is beneficial to understand if men and women perform the golf swing differently, to properly match training techniques and enhance performance. Previous research found that men used higher joint moments in the downswing phase than women which resulted in stronger force production (Kang et al. 2018).This study aimed to determine if men and women generate force similarly during a golf swing. Nine highly skilled collegiate golf players (5 females, 4 male) participated in accordance with the local IRB. Players performed 10 golf shots toward a target downrange with a 6-iron with each foot fully supported by a force plate (1200 Hz, Kistler). Reaction forces (RFs) were calculated in the mediolateral (ML) and anteroposterior (AP) directions and normalized by body weight. Linear impulse was calculated as the area under the force-time curves. The period of interest was defined as the time when the player’s target leg RF became posterior until ball contact. Statistical differences between groups were determined using independent t-tests (α = 0.05). Females and males generated similar ML (p = 0.408) and AP (p = 0.229) net linear impulse. The average target leg ML RF was directed away from the target for females (0.066 ± 0.026 BW) and for males (0.064 ± 0.021 BW, p = 0.843). Average rear leg ML RF was directed towards the target for females (-0.090 ± 0.038 BW) and (-0.059 ± 0.032 BW, p = 0.241) for males. The average target leg AP RF was directed posteriorly for females (-0.098 ± 0.026 BW) and for males (-0.137 ± 0.032 BW, p = 0.088. Average rear leg AP RF pointed anteriorly for females (0.054 ± 0.019 BW) and males (0.065 ± 0.028 BW, p = 0.511). Females generated linear impulse over a longer duration of time (0.371 ± 0.032s) than males (0.304 ± 0.051 s, p = 0.046). Females may use the extra time as a mechanism to generate the required linear impulse or they could be utilizing different swing strategies to achieve the same outcome. Future research with larger samples will further understand these sex differences.

Critical Catalytic Residues of NIS Synthetase, Desferroxiamine D

Program: National Science Foundation Summer Research Fellowship in Chemistry
Faculty: Dr. Katherine M Hoffmann, Chemistry
Student: Eliana Goncuian

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Introduction: 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 crystallize and solve the structure of Glu467Ala (mutant) Desferrioxamine D (DesD) bound to its large substrate, desferroxiamine G (dfoG), and cofactor, adenosine triphosphate (ATP). This mutation was chosen because I have piloted a new assay to determine the kinetic profile of wild type (Wt) DesD. This assay has allowed our lab to confirm one of three hypothesized catalytic residues (Arg306). Residue Glu467 is believed to be another critical catalytic residue.

Methods: To obtain crystals, the protein had to be transformed, overexpressed, and purified. After pure protein was obtained and confirmed, the hanging drop vapor diffusion method was used to set up mutant DesD in various conditions.

Results: Crystals were grown and data was gathered by Dr. Katherine M. Hoffmann. X-ray diffraction data was collected and used to solve the structure with CCP4i2 along with REFMAC5 and Coot software. The crystals diffracted to 1.88Å. Backbone errors have been corrected in all four chains, A, B, C, and D. R-factor is 24.9% and free R-factor is 26.9%. We are confident that ATP and Mg2+ are present in the binding site, and predict that the adenylate intermediate of the substrate is present too. Once the structure has been solved, it will be published on the Protein Data Bank (PDB). This data will be the foundation for future drug tests to determine the efficacy of the drugs against DesD.

Development of dopaminergic neurons in Lymnaea stagnalis

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Kenneth Long, Biology
Student: Miguel Angel Gomez

Background. Both cognitive and behavioral deficits often develop with age, particularly in age-related conditions such as Parkinson’s disease. Parkinson’s disease is usually not directly life-threatening, but affects quality of life. Neural deficits, specifically the loss of dopaminergic neurons, can be present in Parkinson’s patients. Previous studies have been conducted using Lymnaea stagnalis, as a model for the human nervous system. Dopaminergic neurons in Lymnaea are large and easy to visualize.  Damage to dopaminergic neurons in Lymnaea produces Parkinson’s-like changes in their nervous system.

Goal. The purpose of this study was to visualize dopaminergic neurons in developing and juvenile snails using immunohistochemistry.

Research Plan. Due to the closure of campus because of Covid-19, I was not able to perform the planned experiments.  I developed a research plan that will be used once campus is reopened. Dopaminergic neurons will be visualized by using antibodies to tyrosine hydroxylase (TH), the enzyme that regulates dopamine synthesis. Ganglia from the young Lymnaea will be isolated and homogenized for protein analysis using SDS-PAGE.  Western blots will determine whether non-commercial antibodies to TH bind to snail TH.  Once confirmed, we will then perform immunocytochemistry. Ganglia will be fixed in buffered formaldehyde, embedded in agarose, and sectioned using a vibratome. Secondary antibodies with either HRP or fluorescent probes will be used to detect anti-TH. Dopaminergic cells will be visualized using brightfield and fluorescence microscopy. Of interest is the large dopaminergic RPeD1 neuron that is involved in memory and respiration in Lymnaea.

Significance. Our results may help our understanding of Parkinson’s disease. Rotenone is a pesticide that produces Parkinson’s-like effects in rodents and Lymnaea. We may extend this study to determine the effects of rotenone in developing Lymnaea. Studying rotenone and similar chemicals would increase our understanding of Parkinson’s and possibly help with its prevention.

Dramaturgical Research on Macbeth

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Michael Arndt, Theatre Arts
Student: William Pena

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Dramaturgical Research on Macbeth

Will Peña

Michael Arndt

 

William Shakespeare’s Macbeth is a standout play in his oeuvre due to its dreadful nature and occult themes. This makes it a particular challenge to direct, design, and perform even beyond the usual obstacles that accompany producing Shakespeare for a modern audience. However, through careful study of the text and previous performances, one can bring the bard’s world onstage in a compelling and engaging way. This study is known as dramaturgy, and the goal of this research project was to assist Brett Elliot’s work as director for Macbeth by Kingsmen Shakespeare Company. The Arden Shakespeare is one of the foremost collections of Shakespearean research and is a vital tool to understanding the early modern English used in Shakespeare’s plays. While it may seem simple at first glance, a comprehensive understanding of the work is critical to elevate a production from simply reciting words as rote. Cambridge’s Shakespeare in Production: Macbeth is also essential to understanding the successes and failures of previous interpretations of Macbeth by providing critical analysis of their acting, costumes, and staging. These sources and others were compiled into an accessible website for use by the entire cast, crew, and creative team for the Kingsmen Shakespeare Company to use in their upcoming production. A summary of the play was also created to assist audience comprehension of the show as they watch it. Finally, a dramaturgical statement was written to emphasize the importance of creating Shakespeare for a modern audience. Both of these works will be published in the show’s program and given to the audience. Dramaturgy is distinguished from traditional literary analysis due to the fact that it is done to assist in the creation of a piece of art. This research will be used to keep the tradition of Shakespeare not only alive but thriving. The poetry of Shakespeare’s work demands thoughtful effort on the part of the entire company and the dramaturg facilitates that effort.

Exploring Differences in the Impressions of the Insanity Plea Based on a Defendant’s Religious Affiliation and Criminal Motive.

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Amanda ElBassiouny, Psychology
Student: Kayla Sircy

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This study investigated differences in mock juror’s perceptions of Not Guilty By Reason of Insanity (NGRI) case based on a defendant’s religious affiliation and motive. 

Participants evaluated the NGRI case of a defendant (Christian/Muslim/Agnostic/unstated) after having committed murder by a certain motive (voice of: God/devil/unidentified) and evaluated the NGRI’s believability.

There was a significant religious affiliation by motive  interaction on NGRI believability, F(6, 632)= 2.75, p=.012, ηp2=.025. When the motive was the Devil’s voice, mock jurors felt a Christian (M=5.02, SD=1.40) and religion unstated (M=5.21, SD=1.56) defendant were significantly more believable than an Agnostic (M=4.28, SD=1.86). When the motive was an unidentified voice, the Agnostic (M=5.02, SD=1.53) was more believable than the Christian (M=4.26, SD=1.97) or Muslim (M=4.32, SD=1.83). A Christian was more believable when they heard the devil (M=5.02, SD=1.40) vs. an unidentified (M=4.26, SD=1.97) voice.  An Agnostic defendant was more believable when they heard an unidentified (M=5.02, SD=1.53) voice vs. the devil(M=4.28, SD=1.86). This has implications for future NGRI definitions and cases.

 

Expression of the Cytochrome P450 Oxido-Reductase Gene (Cpr) in extra eye and wild-type Drosophila melanogaster.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. David Marcey, Biology
Student: Zachary Katz

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The variably expressed extra eye (ee) mutation in Drosophila melanogaster (the common house fly) produces head deformities such as duplicated and/or missing bristles and head cuticle, and in severe conditions, an extra number of eyes and antennae. In addition to variable expression, the mutation possesses several other interesting features such as: ee is both conditionally dominant as well as incompletely penetrant. The ee mutation is most likely caused by a transposable P-element insertion into a 5’ exon of the Cytochrome p450 reductase (Cpr) gene. Sequencing of this P-element and using a flanking process on the genomic DNA shows a reverse orientation of the P-element with respect to the transcriptional polarity of Cpr, which results in the presence of anti-sense P-element RNA within the Cpr transcript.

My research mentor, Dr. David Marcey, has developed a P-element induced, RNAi-based, epigenetic model to explain the exotic genetic behavior of ee that proposes a down regulation of a negative regulator of the JAK-STAT signaling pathway. Su(var)2-10 is the Drosophila ortholog of mammalian Protein Inhibitor of Activated STAT (PIAS).  Su(var)2-10 inhibits JAK-activated STAT92E in early eye development; the Su(var)/STAT92E ratio is important in determining correct eye size (Betz, et al., 2001).  The ee mutation is posited to down regulate Su(var)2-10 expression by the P-element insertion into Cpr and subsequent RNAi-induced heterochromatization of the Su(var)2-10 genomic region due to a nearby P-element insertion. 

I will use a biochemical assay (colorimetric) to examine the levels of the Cpr oxido-reductase in ee and control lines. Protein extractions will be performed and protein levels normalized prior to the use of a colorimetric assay and measurement of absorbance levels. Standard curves will be generated in order to quantitate Cpr enzymatic levels in experimental and control extracts. We predict that expression of the Cpr gene will be reduced in extra eye flies due to the insertion of the P-element

Fasting and Its Correlation to Cerebral Hemodynamics

Program: Undergraduate Research
Faculty: Allan Knox, Exercise Science
Student: Luke Rodarte

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Introduction: Prolonged periods of nutrient abstention (fasting) has been reported to induce beneficial physiological and cognitive implications. Early research has shown that refraining from caloric intake can potentially promote beneficial cardiometabolic responses-as well as improved overall cognitive function. However, data is lacking combining the physiological implications of improved cognitive function in fasted individuals. The enhanced neurovascular coupling may be a potential mechanism as the reported improvements in vascular function may be translated to augmented cognition. The aim of this investigation was to perform a systematic review of the existing literature concerning fasting and cerebral blood flow. 

Methods: Literature searches were completed in Google Scholar, PubMed, Web of Science, Public Library of Science, and The New England Journal of Medicine using the following keywords; fasting, fasting trials, effects of fasting, fasting, and vascularity, fasting, and endothelial function.

 

Results: Four studies were identified, On average, systolic blood pressure decreased by 6 mm/Hg, and diastolic blood pressure decreased by 5 mm/Hg. Total blood triglycerides and LDL cholesterol on average both decreased by 0.5 mmol/L. Blood glucose levels decreased on average by 0.56 mmol/L and insulin fell by 0.813 mmol/L. There was no meaningful impact on HDL cholesterol.

Conclusion: As a result of the evidence, fasting shows a trending decrease in cardiometabolic responses which is linked to enhanced cardiovascular function, endothelial function, neurovascular coupling, and cognitive function. No studies have examined the effects of fasting on cerebral blood flow.

Golf Shaft Stiffness Affects Reaction Force Generation

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Travis Peterson, Exercise Science
Student: Luke Vankeersbilck

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Introduction: To complete a golf swing, players need to regulate reaction forces to stay balanced (Egret et al. 2003). It has been determined that players did not respond predictably to changes in shaft mass (Haeufle et al., 2012) and could often not tell the difference between shafts of differing stiffness (Milne & Davis, 1992). Most previous studies have focused on the ball or club kinematics with mixed results. This study aims to determine if golf club shaft properties influence player kinetics during a golf swing.

Methods: Highly skilled NCAA Division III men’s and women’s golf players (3 male, 4 female) volunteered to participate in accordance with the local IRB. Players performed 10 golf shots toward a target downrange with drivers of different shaft overall stiffness (S vs XS). Players stood with each foot supported on a force plate (1200 Hz, Kistler) covered in a thin layer of synthetic turf which allowed players to wear their own spiked golf shoes. The period of interest was defined as the time when the player’s target leg reaction force becomes posterior until ball contact. This period coincides with the down swing. Linear impulse was calculated as the area under the force–time curves during the interval of interest and was normalized by body mass. Differences between conditions were determined by a dependent t-test (α = .05).

Results: Target leg mediolateral (ML) linear impulse was amplified away from the target with the extra stiff shaft (.357 ± .096 N*s/kg) compared to the stiff shaft (.340 ± .083 N*s/kg, p = .041). Conversely, rear leg ML linear impulse was amplified toward the target with the extra stiff shaft (.436 ± .142 N*s/kg) compared to the stiff shaft (.405 ± .132 N*s/kg, p = .070). Net ML linear impulse did not change between shaft conditions (p = 0.46).

Conclusions: These results may indicate that players unintentionally adjusted force generation strategies to compensate for a shaft of greater stiffness which required coordination of both legs. It is important for the player to understand how their golf shot outcomes are affected by club characteristics since players have so many options to tailor their equipment. It is equally important to balance their equipment with the force generation demands placed on the player. This can help players effectively individualize their set of golf clubs.

Hand Gesture Control

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Craig Reinhart, Computer Science
Student: Maramawit Bereda

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The virtual interaction between humans and machines has evolved overtime, altering the way we perform various activities. Specifically, there has been a growth in the use of modern technology to virtually control various types of robots for different fields such as medicine and production industries. Hand gesture controlling has become one of the major developments in artificial intelligence. The purpose of this research is to examine the Leap Motion Controller and use its features to enable hand gesture control of a robot. The research primarily focuses on the extent to which we can use the motion controller to effectively replicate hand gestures such as swiping and grasping onto the robot. The method I am using for this research is to first thoroughly examine the Leap Motion Controller’s hand gesture recognition capabilities, which is the main tool I am using to command the robot arm. I will write code to read and interpret gesture data from the motion controller. Next, I will examine the abilities of the industrial robot and how we can effectively control it using hand gestures. My final and most important task will be to develop software that utilizes the data coming from the Leap Motion Controller and transforms it to motion commands for the industrial robot arm. The result from my research so far show the Leap Motion Controller’s abilities to sense hand gestures from different angles and distances. I was able to examine the limitation of the motion controller and to what extent it can show data of my hand gestures. I was also able to examine the code for the motion sensor and the data it prints for my hand gestures. In conclusion, this research is focused on utilizing the Leap Motion Sensor to get data of hand gestures and replicate those same movements onto the robot. The results from this research will be helpful in offering alternative means of physical movement for those who are severely sick or disabled. On top of that, the findings of this research can also be used in fields of medicine, mass production industries and others to enhance the performance of physical activities.  

 

How Many Sprint Trials is Enough? Avoiding Bias When Estimating Maximum Sprint Performance in Western Fence Lizards

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Kristopher Karsten, Department of Biology
Student: Robin Bedard

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The objective of my research was to contribute to the understanding of whole-organism performance in the Western Fence Lizard, Sceloporus occidentalis. Whole-organism performance traits include any quantitative measures of how an organism performs at an ecologically relevant task. I have specifically focused on the locomotor performance of sprinting in S. occidentalis because it is a key measure of whole-organism performance in this species. Sprint performance in S. occidentalis is positively correlated with fitness with respect to both natural selection and sexual selection. Knowing when an individual uses their maximal performance provides insight into what selective pressures are acting on that specific trait because an organism is expected only to use their maximal performance capacity for survival or reproductive success. Thus, maximal sprint performance is often studied in S. occidentalis and many other species. However, laboratory sprint measurements have been found to be consistent underestimations of an organism’s true maximal speed. This is because of the lack of consideration of intra-individual variation. To contribute further to these findings, I conducted maximal sprint trials on a population of 27 S. occidentalis. Each lizard was sprinted between 1-11 trials and the fastest speed was recorded as the individual’s maximum. Lizards were incubated for 1 hour at their optimal temperature prior to each sprint and ran 2-3 trials per day to provide adequate rest time. The maximal speeds range between 0.551 m/s and 3.846 m/s. I hypothesized that individuals with a greater number of sprint trials will have an average maximal speed that is faster than those with fewer trials. My results supported my hypothesis, showing the average sprint speed of the population increased as the number of trials increased with an average of 1.96 m/s for one trial and 2.66 m/s for 8+ trials. Variance started at +/-0.56 for 1 trial and decreased until 3 trials, staying relatively constant at +/-0.31 thereafter, meaning the measurements of accuracy for average m/s are precise.

Improved Optimization and Chemical Characterization for Urinary Metabolite Screening via pH Manipulation.

Program: Aperture Summer Research Fellowship
Faculty: Dr.Grady Hanrahan, Department of Chemistry
Student: Sara Ortiz Ramirez

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This study examined the chemical characterization of environmental and health-related phenolic compounds via the combination of computational modeling and solution pH manipulation. We hypothesized that this study would allow for greater insight into identifying and characterizing urinary metabolites that are crucial to environmental risk assessment. Prior work has shown that theoretical biotransformation pathways allowed for greater understanding of chemical structure and the identification of reactive species. Next, we will focus our efforts on developing and optimizing neural network computational platforms and particle swarm optimization algorithms to aid in future instrumental studies. Matlab software will be utilized in all computational technique development. The theoretical examination of GC-MS will be covered, followed by practical studies on the instruments using reference phenolic compounds. Next, relevant statistical methods will be employed to assess the R values of the input and output data sets. As a result of this, we will assess theoretical pathways and chemical toxicity of potential reactive metabolites. We anticipate success in utilizing novel computational techniques, pH manipulation, and pharmaceuticals to optimize our chemical separation technology (GC-MS). This is expected to allow us to both separate completely and characterize complex chemical compounds associated with deleterious human health effects. Therefore, this study will allow for greater insight into identifying and characterizing metabolites that are crucial to environmental risk assessment. Ultimately, it will lead to an enhanced understanding of underlying disease mechanisms and related toxicity exposure important for industrial workers and the general public.

Indigenous Voices of Santa Susana Field Laboratory: Environmental Storytelling and Remediation

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Bryan Rasmussen, English and Environmental Studies
Student: Colin Virgines

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The Santa Susana Field Laboratory (SSFL) in the Simi Hills has a complex and conflicting environmental history. Serving as the home to many sacred sites for the Indignous Chumash people, the landscape also holds the potential to connect the Santa Monica Mountains and the Los Padres National Forest, in aid of ecologically critical habitat linkage for the region’s imperiled mountain lion population. Established as an engine-testing facility for Rocketdyne in the 1940’s, its partial nuclear meltdown in 1959 has poisoned the environment and has caused a cleanup controversy, yet to be resolved. As a result of these overlapping, contradictory, and ongoing histories of the human relationship to land, SSFL offers a unique opportunity to apply environmental storytelling techniques with Indigenous histories to promote remediation of land. While the focus of the project was split into three parts; the Indigenous perspective, the environmental perspective, and the community perspective; the goal is to record the stories of SSFL, with special emphasis on Indigenous history and people. Most conversations surrounding environmentalism typically focus on the ecological and community impact, but rarely include the Indigenous perspective. The inclusion of Indigenous voices to the conversation regarding the SSFL cleanup represents an important step towards raising community awareness of environmental justice. By conducting interviews with individuals closely related to each perspective, a story map of the history of SSFL was created. Each perspective was imperative to the development of the conversation behind the history of SSFL, as the centralization of each topic came to highlight the ways in which they intersected with one another. Our understanding of modern environmentalism relies on our ability to understand the history of the land and to see how each perspective overlaps with each other. Environmental storytelling presents a unique relationship between environmentalism and culture, and can act as a guide for humanity as we come to integrate changes to the holocene.

Involvement in AP Classes and Burnout in College

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Jodie Kocur, Psychology
Student: Kiah Vastine

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Burnout is a phenomenon whose influence has recently been studied in many different contexts.  Burnout is defined by three major dimensions: exhaustion, cynicism about the value of one’s work, and a feeling of inadequacy. Though the term was restricted to those working in the health services domain at its inception, it has since gained more common usage in other contexts as well. For example, recent work has begun to investigate burnout experienced by students. Results of qualitative research, such as interviews and focus groups, have found that high-stakes tests like Advanced Placement (AP) tests can be a major source of stress for high school students. Moreover, other studies have also found inverse correlations between burnout and measures of cognitive function and GPA. This study seeks to determine whether this experience of burnout extends into students’ college academic experiences. The hypotheses of this study are that: 1) students who took AP classes will have higher burnout scores in college than non-AP students, 2) the level of burnout in college will increase with the number of AP classes and 3) level of burnout will correlate negatively with college GPA. Participating high school graduates from the United States between ages 18 and 26 (n = 276) completed an online survey on Qualtrics. Participants reported the number of AP classes that they had taken and their college GPA, and completed the self-report School Burnout Index (Salmela-Aro, 2009). Students that took AP classes in high school were found to have significantly higher levels of burnout in college than those that did not, t(274) = 1.83, p < 0.05, however, the number of AP courses did not relate to the level of burnout (F =(4, 271) = 0.591, p = .670). Burnout scores were also found to be significantly negatively correlated with college GPA, r(274) = -.275, p < .01. The results of this research will be used to assess the support needs of students in AP classes.  Future research should aim to determine preventative measures for burnout in students. 

Ketogenic Diet’s Vascular Risk Factors: A Systematic Review and Meta-Analysis

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Allan Knox, Exercise Science
Student: Madalyne Nolte

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Introduction: It is known that the leading cause of death in the United States is due to cardiovascular disease.  Previous research has shown that there is a strong relationship between high fat consumption and raised cholesterol levels which can lead to atherosclerosis.  Thus, it is often believed high fat diets will eventually cause heart disease, though this outcome has not been observed from the Ketogenic diet.  Previous research of the Ketogenic diet has been directed towards individuals who are at risk of cardiovascular disease, diabetes, and can be used in aid of epilepsy.  The Ketogenic diet is a high fat, low carbohydrate diet with the purpose of lowering blood sugar and insulin levels.  This study aimed to provide evidence towards whether the cholesterol levels and arterial hemodynamics differed amongst healthy or obese populations when prescribed this diet; bringing awareness of diets that improve overall health and body composition.  Methods: This study was performed by conducting a systematic review along with a metanalysis.  Searches of PubMed and Google Scholar were conducted to find relevant literature that compared healthy and obese individuals who were either prescribed the Ketogenic diet or an alternative diet such as the Plant-based, Mediterranean, or Calorie Deficit.  Results: This study found that there were no significant differences between the HDL or LDL particles in individuals on the diets.  There were also no significant differences found for systolic or diastolic blood pressure.  Conclusion: Although there were no significant differences of cholesterol levels or blood pressure found amongst the diets studied, there was implication of different populations having different responses to the Ketogenic diet.  This implication suggests that “fad” diets are not always correct for every individual.  Future studies are warranted to provide more information on how the specific populations respond to the Ketogenic diet.

 

Labeling and the AP Program: How Labeling Students as AP or Non-AP Affect Their Academic Success, Academic Self-Efficacy, and the School's Academic Culture

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Dr. Heidi Coronado, Sociology
Student: Yolanda Arciniega

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Schools are valued as a place that offers students fundamental academic, social and cultural skills. While schools can offer students opportunities, they can also place limitations. The process of academic tracking, while intended to better the learning environment for students, has affected the opportunities accessible to students of varying tracks. While there is a pre-consisting belief that students learn better or more in groups of similar abilities, grouping students based on academic abilities often fosters labeling and stigmatization of students. The labeling theory proposes that individuals subconsciously perceive how others see them which overtime forms the basis of their identity. In some cases, negative social labels or stigmas, alter one’s behavior toward others as well as the person’s self-concept and social identity. The aim of this study is to examine the educational experiences of students who graduated from public high schools in the United States, particularly of students who were in Advanced Placement (AP) and/or in non-AP classes, using the labeling theory framework. There will be about eight participants who are 18 years old or older and that have graduated from or worked at a U.S. public high school. Participants will be interviewed, complete a questionnaire, and will be invited to an optional focus group where they will be debriefed on common themes found. Data is currently being collected but previous research suggests there are distinctions in resources dispersed to AP and non-AP tracks. In addition, existing literature suggests that labels along with their attached characteristics may affect students in each respective track. Gaining more information regarding the varying experiences students encounter in AP or non-AP classes will provide more information on the implications of academic tracking on a student's academic success, academic self-efficacy and a school's academic culture. These potential findings may help to create solutions that will be able to lessen the educational achievement gap. 

Measuring Justice: Evaluation Design for the Ventura County Family Justice Center

Program: Culver Behavioral Science Research Fellowship
Faculty: Dr. Molly George, Criminology & Criminal Justice
Student: Bailey Hendrix & Sofia Debroy

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The Ventura County Family Justice Center (VCFC) opened in January of 2020; its primary goal is to provide services for victims of domestic abuse, sexual assault, and human trafficking. The VCFJC is based on the larger family justice center movement, which has revolutionized how family violence and victimization are addressed in the US. Family Justice Centers flip a system that was initially designed for the professionals who serve survivors, by instead prioritizing survivors who need to work with professionals. The purpose of our research study is to better understand evaluation research, as well as the history, background, and scholarly research on the family justice center in order to design the most effective way to conduct an evaluation of the Ventura County Family Justice Center. We first began by reading extensively about evaluation research and family justice centers, then we created an annotated bibliography of the existing literature and used this to create a literature review. Based on our background knowledge acquired from our research, we were able to begin identifying and developing a research design strategy for the VCFJC. With our research, we were able to acquire a more in-depth understanding of evaluation research and family justice centers. Additionally, we were able to lay the framework for a future evaluation of the VCFJC. This evaluation will eventually allow the VCFJC to help its community members and vulnerable populations, as well as allow the university to have a direct community impact. Our hope is that insights drawn from this longer-term study will be useful for the program staff and key stakeholders to direct on-going programming, as well as launching future initiatives.

Microfibers Found Within Mytilus californianus and M. edulis from Newport Harbor and a Coastal Ventura Jetty

Program: Swenson Science Summer Research Fellowships
Faculty: Andrea Huvard, Biology
Student: Quinn Moultrie-Margolin

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As the number of plastic debris exposed to marine environments increases, irrevocable damage to the environment is inevitable. These microfibers are so small yet make up over 90% of all plastic debris. Due to their planktonic nature, they are being ingested by individuals of all phyla, especially filter feeders. This study aims to determine if there is a statistically significant difference in the mean number of microfibers within Mytilus californianus and Mytilus eduliscollected from Newport Harbor, and a Coastal Ventura Jetty. These mussels where measured, then had their contents dissected, mashed, and suspended in a saline solution. This mixture was filtered via suction filtration and examined under a Swift Instruments International series 80 light microscope. After conducting a quantitative analysis of the microfibers, it was found that across all size variants, mussels collected from Newport Harbor (n=48) contained significantly more microfibers than mussels collected from the Ventura Jetty (n=48) p<0.05. The findings of this study suggest that not only do large mussels contain significantly more microfibers than other size variants, but the magnitude of imminent microfiber sources drastically increases the number of microfibers found in mussels.

Microfibers of the Gut and Gills of Sardine, Sardina pilchardus

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Andrea Huvard, Biology
Student: Ashley Rauda

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A microfiber is a microscopic strand of plastic measuring under 5μm long. Our clothes are the main source of microfibers, strands primarily fall off when we wash our clothes. These fibers end up in the ocean and are ingested by living organisms, like fish. The aim of the present study is to investigate and quantify the number of microfibers found in the digestive tract and gills of the Sardine fish, Sardina pilchardus. In comparing the number of microfibers from the digestive tract and gills, it was expected that there would be more microfibers in the digestive system. This would be due to the fish ingesting more microfibers than would pass through their gills. The fish were dissected and the gills and digestive tract of each was removed to be mashed up in a mortar and pestle. Mashed digestive system and gills were placed into a saltwater and allowed to sit for a total of 24 hours. Leaving the samples in the saltwater allowed the microfibers to float to the top of the beakers, making the filtering process much quicker. The contents of each beaker were filtered using a vacuum pump and examined under a microscope. The microfibers were counted and sorted by color. Results determined that in terms of quantity, more microfibers were found in the digestive tract compared to the gills. However, after conducting a t-test it was determined that the results were not significant since the p-value was 0.13 (p > 0.05). In conclusion, there was no statistical difference between the quantity of microfibers in the digestive tract compared to the gills of the Sardina pilchardus. Although there was no statistical difference found between the organs sampled, it is important to note that of the forty-nine fish that were sampled, all contained microfibers. The quantity of microfibers found in each fish shows the extreme pollution of the ocean these microfibers have caused which may be damaging to the fish as well as their ecosystem.

Modeling effects of interventions on COVID-19 spread

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Christopher Brown, Mathematics
Student: Gianna Alamillo

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Modeling effects of interventions on COVID-19 spread

Gianna Alamillo

Dr. Christopher Brown 


Purpose: The effects of interventions in different counties within the United States, was analyzed to assess the growth rate of the coronavirus disease COVID-19. 


Methods: Data was collected between the time period of January 22, 2020 through July 13, 2020 from 8 counties (Los Angeles County, CA; Ventura County, CA; Miami-Dade County, FL; Orange County, FL; Monroe County, NY; New York County, NY; Dallas county, TX; Harris County, TX) and outcomes of the interventions for COVID-19. SIR compartmental modeling was then used as a way to organize data and analyze the rates of change between each stage of the virus. 


Results: The rate of spread while interventions were applied, slowed down the rate of spread during that specific time period (when intervention(s) were applied). The rate of spread when interventions were removed caused a large increase in the rate of spread. The PCapita rates were very high in counties with large populations.


Conclusions: It was found that the region that had a higher population had the virus spread more rapidly and infected far more people in comparison to the region with the smaller population. Interventions applied overall decreased the growth rate of COVID-19 significantly more than if no interventions were implemented at all.  

Molecular Mapping of P-Transposable Element Insertions in the Genomes of Drosophila melanogaster Strains

Program: Swenson Science Summer Research Fellowships
Faculty: David Marcey, Biology
Student: McKenzie Kelly

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The variably expressed extra eye (ee) mutation in Drosophila melanogaster produces head deformities that can include missing and/or duplicated bristles and head cuticle, as well as supernumerary compound eyes and antennae. In addition to variable expression, ee is both incompletely penetrant and conditionally dominant. The ee mutation is likely caused by a transposable P-element insertion into a 5’ exon of the Cytochrome p450 reductase (Cpr) gene. It is posited that this P-element induces the interference RNA pathway that ultimately leads to the heterochromatization of other P-elements and the genes flanking them. DNA sequences, obtained by next generation sequencing, of multiple genomic regions that flank P-element insertions in the genomes of several ee lines and other lines with newly derived mutations that are putatively caused by the same mechanism as ee were used in this research. The methods used to map the precise genomic loci of these P-element insertions include several functions of the bioinformatic software Galaxy. Trimming shortened the sequences as it removed the splinkerette primer, the P element end and short length sequences. Bowtie aligned and filtered the sequences based on alignment and mapping score. Pileup quantified the multiple reads that align to the reference genome in one location. The range of P-element flanking regions in different parts of the genome produced the location of P-element insertions. JBrowse and Integrated Genome Browser software were used to catalog the possibly heterochromatized genes flanking P-elements. The amount and location of P-element insertions has been identified in all ee lines. The genes in the thirty-seven P-element flanking region of one ee strain, JG1, are currently being investigated. The molecular mechanisms by which transposable genetic elements can serve as potent regulators of eukaryotic gene expression are only beginning to be worked out. My work is relevant to this emerging field, and may hold significance for both Genetics and Evolutionary Biology.

NIS synthetases Structure Review of IucA and IucC

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Katherine Hoffmann, Chemistry
Student: Pablo Paredes

Purpose: Iron is vital for living organisms since it plays a role to allow protein’s biological activity in metabolic processes such as aerobic and anaerobic ATP biosynthesis. NIS synthetases are important because one of the members of the family is present in many of the pathogenic bacteria so it can be used for one model for all instead of a specific model for a specific bacterium.

Methods: A literature review of the four NIS synthetases family member was done with a focus on Iron uptake chelate type C and A. Structures were obtain from IucC Bailey et al and IucA Bailey et al that was uploaded in the Protein Data Bank. IucA and IucC were pulled from the Protein Data Bank and overlay with one another in the PyMol program. DesD structure was obtained and overlay with IucA and IuC separately. Each thumb helixes were label in the structures that had it present and compare. Missing sequence loops and helixes that were present in IucC were overlaid with DesD.

Results: The overlay of the structure demonstrates a lack of modeling in IucC with its alpha thumb helix being short both its chain A and B, missing loops of IucC, DesD continues them without breaking. A complete model of IucA overlay with DesD demonstrated that its alpha thumb helix was short and completely off the helix of DesD. DesD helix continues in its second helix going into its dimerization interface which IucC and IucA can’t continue.

Conclusion: NIS synthetases family members have similar structure model once overlay with each other. The slight change in the structure can make them an outliner such as IucA and IucC which also leads to a change in its oligomerization. Five of the eight family members have the same structure format. DesD has a well-made model to be used with what each member of its family lacks it contains. DesD can be used for the main mapping of antibiotic design against pathogenetic bacteria siderophores.

Physical Activity Levels of California Lutheran University Students during the COVID-19 Pandemic

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Allan Knox and Dr. Amanda ElBassiouny, Exercise Science
Student: Narre Erhart

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Introduction: The COVID-19 pandemic enforced lockdown measures that limited an individual’s ability to perform normal day-to-day activities which may have included habitual exercise. Lockdown measures were experienced within the California Lutheran University (CLU) community which may have impacted physical activity levels within the student population. Therefore, the aim of this projects was to determine the physical activity levels of students enrolled at California Lutheran University. 

Methods: The World Health Organization (WHO) STEPS questionnaire was used to measure physical activity levels of students enrolled at CLU. 

Results: Reponses showed that 51% of students met the vigorous activity recommendations of 75min.wk-1and 42% of students met the moderate activity per recommendations of 150min.wk-1

Conclusions: The COVID-19 pandemic may have negatively impacted CLU student activity levels as more than half of the studied population did not meet current exercise guidelines of 150min.wk-1. These data suggest that although current measure to combat the spread of COVID-19 may place individuals as risk of developing non-communicable disease associated with physical inactivity.

Publication of a Newsletter and Literature Review

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Jesus Cordova Guerrero, Department of Chemistry
Student: Crystal Cendejas

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Two projects were developed, a newsletter titled “STEM Research at CLU” and a literature review titled “A review of modern methods for the synthesis of alkenes.” The newsletter aims to highlight the research achievements of faculty and students over the past year at California Lutheran University in order to provide valuable information to students interested in research. The newsletter is expected to include as many research faculties as possible and to focus on the specifics of each project to be shared with the CLU community. In addition, this newsletter will be published on the CLU website. In the second project, the review will be based on modern methods of alkene synthesis. The construction of alkenes in organic synthesis plays a key role in constructing molecular frameworks and universal materials. The aim of this article is therefore to provide useful applications for the synthesis of alkenes and to write a review of the unique types of alkenes in order to better understand how they are formed and behave under different reaction conditions. This review collaborates with the PI and two students from the Chemistry Department at the University of Tampa. Literature searches were conducted to find the most up-to-date reports published in the last six years using SciFinder Scholar. Subsequently, reports were reviewed and discussed by weekly meetings and presentations of the literature while using ChemDraw to draw chemical structures and reaction mechanisms. The reports were then organized into four groups according to the type of transformation, including carbonyl, transition-metal catalyzed olefination, elimination reactions, and miscellaneous. The publication is planned to be submitted to the European Journal of Organic Chemistry and is expected to include recent reports on the synthesis of alkenes as a strategy to advance knowledge in the scientific community.

Quantification of microfiber pollution in Loligo Opalescens

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Andrea Huvard and Dr. Brian Swig, Biology (Marine Biology)
Student: Edward Martinez

Abstract

In the past decade, there has been a growing interest in aquatic microfiber research. As a result, the knowledge of how microfiber pollution has impacted many species of fish has grown substantially, especially for filter feeders such as mussels. However, the same cannot be stated for squids as microfiber studies were scarce or non-existent at the time of this study. The purpose of this study was to perform a quantification of synthetic microfibers (microfibers) present in the digestive tract of Loligo opalescens (California market squid). This was accomplished via the dissection of the digestive tract from the squid samples, which were mashed into a paste with a mortar and pestle. The paste was washed five times with 100mL of a distilled salt water solution in order to suspend the microfibers on the surface to be pipetted onto a filter paper for Buchner vacuum filtration. After being allowed to dry, the filter papers were then quantified under a light microscope for synthetic microfibers. It was observed that the California market squid had been affected by microfiber pollution with the 22 samples analyzed containing a minimum of 9 microfibers and a maximum of 65 microfibers. The average was calculated to be 28 microfibers, which, for context, is slightly less than half of the average found in Argonauta nuoryi, another cephalopode and tertiary consumer, that had an average length that is about four times longer than that of the squid samples analyzed (Del et. al.). The results stress the need of further microfiber research of key stone species, such as the California market squid, that are vital for the wellbeing and survival of their respective aquatic ecosystems in order to raise awareness of how widespread the effects of microfiber pollution have become. This heightened awareness will hopefully induce legal action to establish measures to minimize the amount of microfiber pollution that finds its way into global waters and their inhabitants.

Keywords: microfiber, California market squid, digestive tract, pollution

Quantification of microfiber pollution in Loligo Opalescens

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Andrea Huvard and Dr. Brian Swig, Biology (Marine Biology)
Student: Edward Martinez

Abstract

In the past decade, there has been a growing interest in aquatic microfiber research. As a result, the knowledge of how microfiber pollution has impacted many species of marine organisms has grown substantially, especially for filter feeders such as mussels. However, there is still a lack of information on squids in this sector. The purpose of this study was to perform a quantification of synthetic microfibers (microfibers) present in the digestive tract of Loligo opalescens (California market squid). This was accomplished via the dissection of the digestive tract from the squid samples, which was mashed into a paste with a mortar and pestle. The paste was washed five times with 100mL of brine solution and vacuum filtered. After being allowed to dry, the microfibers were quantified under a light microscope. 22 samples were analyzed and contained a minimum of 9 microfibers and a maximum of 65 microfibers, with an average of 28 microfibers, which, for context, is slightly less than half of the average found in Argonauta nuoryi, another cephalopode and tertiary consumer, that had an average length that is about four times longer than that of the squid samples analyzed (Del et. al.). The results stress the need of further microfiber research of key stone species, such as the California market squid, that are vital for the wellbeing of their respective aquatic ecosystems in order to raise awareness of how widespread the effects of microfiber pollution have become to induce legal action to establish measures to minimize the amount of microfiber pollution in the future.

Keywords: microfiber, California market squid, digestive tract, pollution

Quantification of Microfibers in the Gastrointestinal Tract of Loligo opalescens

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Andrea Huvard, Biology
Student: Alexandria De Leon

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The presence of anthropogenic waste is ever increasing. Focus has been drawn to plastic waste in our oceans for items on a larger scale such as water bottles and plastic containers in previous years, but only recently has attention been paid to plastics on the micro level. Research has been conducted on the prevalance of microplastics in water and sediment, as well as filter feeding organisms and some species of fish. However, our focus should also be drawn to other organisms on higher trophic levels as well. This study was aimed to identify whether microfibers were present in the gastrointestinal tract of Loligo opalescens. Microfibers, a form of microplastic that originate from synthetic clothing, are often found in our food and water. California market squid were dissected and microfiber content was quantified under a microscope following filtration. Results showed an average of twenty-eight microfibers per squid, supporting our hypothesis that microfibers have reached these organisms on the tertiary trophic level.

Quantification of Sediment Microfibers from the Sycamore Canyon Beach

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Huvard, Earth and Environmental Science
Student: Talya Cohen

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Microfibers are a fast-growing concern in environmental issues; they are a pollutant that are quickly accumulating in and affecting ocean ecosystems, and are present in most of the Earth’s watersheds, especially the U.S.. Microfibers are a form of microplastics shed by synthetic materials such as fleece when washed. Watersheds, particularly Ventura watershed, is an area flooded with microfibers. Ventura county, like most watersheds surrounding urban areas, leads off into the ocean through different rivers. Although microfiber research has begun to pick up speed over the past decade, little to nothing has been done in Ventura county. We have decided to take various sediment samples across the Ventura watershed and it’s various zones, as well as comparing them to similar areas in the Los Angeles County watershed zones. Sediment is then placed into 500 mL beakers and mixed with seawater. Once settled, the seawater is then poured into a Buchner Funnel filtration system with a filter paper. Each sample was mixed and filtered 3 times, in the hopes to clear the sample of microfibers. Finally, the filter paper will then be analyzed underneath a microscope to count the amount of microfibers present on the filter paper. In each of the areas chosen to be analyzed, it is expected that microfibers will be at every location sampled. From this data, we hope to conclude that there is a significant difference among the various watershed zones, so that variables that contribute to microplastic pollution can be further analyzed.

Quantifying Microfibers in Southern California Coastal Sediments

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Andrea Huvard, Earth and Environmental Sciences
Student: Elijah Hill

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Is there a significant difference in the distribution of microfibers between the two very different environments such as an open shoreline and an enclosed harbor? It is hypothesized that the sample site Lido Isle will have a higher concentration of microfibers when compared to the sample site Ventura State Beach. This hypothesis is derived from the fact that Lido Isle is located in the largest small craft harbor on the West Coast and experiences high amounts of commercial traffic and inundation of people on the isle almost year-round. My methodology consists of taking sample sediments from both sites and then further dividing them into 100 mL samples which will then be run through the filtration process. This process consists of placing a 100mL sample and 200mL of artificial seawater into a 600mL beaker. The contents of the beaker are stirred until the material is suspended and then it was left to settle until it was deemed stratified enough. The artificial seawater and any suspended materials were then poured into a Buchner funnel filtration system in a manner that ensured no sediment entered the system. This entire process is called a wash and each sample was washed five times. Once done filtering the filter paper used in the system is removed after each wash in order to be analyzed. Each filter paper will be analyzed underneath a microscope to count the number of microfibers per wash and sample; color and estimated size will also be recorded. Results show that while there was a difference noted between Lido Isle and Ventura State Beach this difference was not statistically significant. Also shown in the results is a difference between not only the sample sites but also between the north and south sides of these locations. This could be the result of currents or of the location of microfiber sources such as wastewater discharge points. My hypothesis was proven correct even if the difference was not statistically significant, there was still an observed difference in the totals found with Lido Isle having an elevated amount when compared to Ventura State Beach. In conclusion, Southern California is being impacted by microfiber pollution and if they are being found in sediments they are also able to infiltrate many other aspects of the environment which is cause for alarm as their carcinogenic nature can be extremely detrimental.

Quantifying the Amount of Microfibers Found in Southern California Coastal Sediments.

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Mia LeClerc, Earth and Environmental Science
Student: Mia Leclerc

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How does the distribution and abundance of microfibers vary along coastal regions and what are the consequences of having Microfiber settling into coastal sediments? It is expected that there will be higher amounts of microfibers found in Newport harbor compared to Ventura State Beach. It’s hypothesized that the number of microfibers present will be elevated in regions with increased industrial or commercial traffic and water discharge. My procedure consisted of analyzing sediment samples collected from Ventura State Beach and from Newport Harbor. Following the collection of samples, sediment was dried out in order to find the actual mass per container to ensure accurate results with minimal room for error. Sediment samples are placed into 600 mL beakers (200 mL of instant salt water with 100 mL of sand) and mixed so that microfibers are suspended in water, this saltwater with the sand mixture is then poured into a Buchner Funnel filtration system that is attached to a pump to filter out the saltwater. Each sample will be analyzed underneath a microscope to count the number of microfibers; color and size will be recorded from each sample and then the data will be analyzed in Microsoft Excel. My results showed that the sediments at Newport Beach Harbor contained more microfibers compared to Ventura State Beach. This could be due to the little movement in the water area and the microfibers coming from our laundry machines are dumping the microfibers here causing the microfibers to settle in sediments. My hypothesis was correct, more microfibers were found in sediments that are closer to residential areas where our washing machines are polluting the runoff water. In conclusion, microfibers are polluting the sediments along the Southern California coast and this is negatively affecting marine organisms and even humans because the microfibers leach out toxins.

Racial Difference in Exercise Response: A Systematic Review

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Allan Knox, Exercise Science
Student: Sophia Armienta Ojeda

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Introduction: Cardiovascular disease (CVD) is the leading cause of death in the United States. A comparison of mortality rates show that African American and Latinx populations are 

disproportionately affecting mortality rates. The top leading risk factors for developing CVD are obesity, sedentary lifestyle , diet, and diabetes. Methods: To understand this link, a systematic review of over 35 scholarly peer-reviewed articles was conducted.  Once the data needed was collected, it was synthesized, by using tabulation of characteristics, quality and effects. Results: In the systematic review, it was found that despite engaging in higher amounts of reported physical activity than their white counterparts, Latinx have the least amount of overall fitness (“Physical Activity in US Youth: Impact of Race/Ethnicity, Age, Gender, and Weight Status” 2010).  The American Diabetes Association recognizes that 12.5% of Hispanics and 11.7% of non-Hispanic blacks are diagnosed with diabetes, and only 7.5% of non-Hispanic whites have the same diagnosis (National Diabetes Statistics Report 2020). Similarly, non-Hispanic blacks had the highest prevalence of self-reported obesity (39.1%), followed by Hispanics (33.3%) and non-Hispanic whites (29.3%) (CDC Adult Obesity Mapping). These results are unexpected, as an increase in physical activity is a typical treatment prescribed to those who want to improve their overall and cardiovascular health. Limitations in the study included a lack of studies specifically looking at the Latinx community. Conclusion: Disproportionally high Latinx CVD mortality rates and physiological differences between races leads us to believe that there is a difference in exercise response. Further studies need to be conducted comparing the mortality rates and physiological differences between races to test for a difference in exercise response. From these studies, health professionals can assess if a change in workout recommendations for the Hispanic community is an effective treatment for poor CVD.

Review of Spirocycles and an Organic Chemistry Textbook

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jesus Cordova Guerrero, Chemistry
Student: Kayla Klussman

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The function of many complex molecules found in natural products and pharmaceutical industries rely on the unique bicyclic structure of spirocyclic compounds. Of particular interest to researchers is how to efficiently synthesize such spirocyclic compounds through cascade processes. Literature searches were conducted to collect experimental data on reactions that have been published. Then, individual articles were written to summarize the experiments done in those published articles and the data they included was sorted into categories, such as the type of reactions and reaction conditions used to synthesize the specific spirocyclic products. Afterwards, the summaries were combined into a review on the synthesis of spirocyclic compounds involving cascade processes. Currently, the review is in the final stages of editing and will then be submitted to the European Journal of Chemistry for publication. 

The other project completed this past summer focused on enhancing students’ experience in organic chemistry by creating a textbook of practice problems about the reactions learned during their semester course. A similar process was taken to create this textbook as compared to writing the review on spirocycles: reactions were searched for in the scientific database SciFinder, the reaction conditions provided in appropriate journal articles were summarized, then this data was organized by reaction type and placed into their respective chapters. This way students may look up a particular reaction, practice writing the mechanism of getting from reactants to products, and see novel methods in which the reactions they are studying have been utilized in research. Thus far, practice problems for the majority of the material covered in the first semester of organic chemistry has been written and is being refined for publication.

Overall, the aforementioned review will further knowledge in the scientific community on the subject of spirocyclic compounds and the textbook will enable students to better understand material within the scope of organic chemistry.

 

Solving the Structure of NIS Synthetase DesD Variant R306Q

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Katherine Hoffmann, Departments of Chemistry and Biology
Student: Raquel Barnard

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Desferrioxamine D (DesD), from Streptomyces coelicolor, is a member of the NIS Synthetase family. DesD synthesizes siderophores which help microorganisms survive by effectively scavenging ferric iron from the environment. The DesD variant R306Q has had Arginine (R) replaced with Glutamine (Q) at amino acid residue 306.

Purpose: The purpose of this research was to solve the structure of NIS Synthetase DesD variant R306Q in order to analyze the structure with substrates, ATP and DfoG, bound.

Methods: Previously collected x-ray diffraction data of DesD variant R306Q was imported into the program CCP4i2. In CCP4i2, each unique chain was checked for gross errors between the electron density map and the known amino acid sequence. Next, various molecules were generated, un-modelled density blobs were modeled, and the structure was refined. After solving the structure in CCP4i2, the data was imported into PyMol where the solved structure was translated into alpha helices, beta strands, and floppy loops exposing interfaces, channels, and other features of the protein’s structure. Additionally, the dimerization of DesD variant R306Q was compared with the dimerization of other members of the NIS Synthetase family from published articles.

Results: The protein was crystallized with ATP and DfoG, however none were ordered in this solved structure. Overall completeness was 98.3%, R Factor was reduced from 0.30 to 0.26, and RFree was reduced from 0.34 to 0.30. Over 1300 water molecules, a few glycerol molecules, and multiple magnesium and chlorine ions were added. It was found that the presence or absence of thumb alpha helix 1 drives dimerization.

Importance: With this structure solved, it can be uploaded to the NCBI Protein Data Bank to be accessed by the public. By continuing to solve variant structures, analyses of structure, mechanism and kinetics can be discovered and published. DesD is a possible drug target due to being an essential enzyme in certain virulent bacteria.

STEM Research

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jesus Cordova-Guerrero, Chemistry
Student: Morgen Lakpour

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Introduction: Undergraduate students are typically unsure about which field of research they would like to go in to, especially when information on faculty’s past projects is not readily available to them. However, once students do participate in directed research at Cal Lutheran, they inquire about a graduate school fit for them, which often requires an extensive amount of time to read up on. Purpose: Publication of a newsletter that highlights a variety of Cal Lutheran’s faculty research will strike the interest of potential student researchers to conduct STEM research at CLU. Students who are interested in furthering their studies can use the database to find a California graduate school best suited for them. Methods: A STEM faculty list was generated by researching all the faculty members that participated in the three previous research symposiums. Each student was assigned approximately eight to twelve faculty members to contact via email with a word document to fill out about their research accomplishments and a photo/video release form to sign. Once the documents were completed, a zoom interview was conducted to further discuss the formatting of his/her article. In terms of the database, a Google spreadsheet was created of all the California graduate programs that conduct STEM research at the Ph.D. or M.A. level. The spreadsheet was divided by institution, location, sector, department, field, faculty members’ biographies and a link to his/her research website. Results: A total of 18 faculty members contributed their research accomplishments for publication in the newsletter. Across 15 different California counties, a total of 124 institutions were involved in STEM research at the Ph.D. or M.A. level. However, of the fifteen counties, five did not participate in biological or chemical research. Conclusion: Research is very important for students because it enhances their knowledge, helps them learn how to work individually and collaboratively, and it jumpstarts one’s career path.

STEM Research at CLU Newsletter and Organic Chemistry Textbook: Practice Problems and Applications

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Jesus Cordova Guerrero, Chemistry
Student: Noah Shepard

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Newsletter: An equitable opportunity for undergraduate research is elusive to many students because these highly sought-after positions are limited and not widely promoted.  Our goal was to increase awareness of these opportunities through the creation of the STEM Research at CLU newsletter.  The first edition of this newsletter will contain articles celebrating the work that research driven CLU faculty have completed, which is intended to give students a starting point for their research aspirations. With the increase of awareness research positions will become more competitive allowing for a stronger pool of research candidates.

Textbook:  Organic chemistry is notoriously difficult subject for some students to adequately comprehend.  To assist these students, a  supplemental textbook is being developed.  This textbook will contain practice problems and show practical applications of common organic chemistry reactions. Our goal is to add context to these reactions by including specific information about how the synthesized products are useful. By including interesting facts about each reaction we hope to reinforce the knowledge and comprehension.

 

Study of NFC Technology, and (Serious) Security Loophole

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Tianle Xi, Computer Science
Student: Tianle Xi

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NFC (Near field communication) is a wireless data transfer method, which enables two electronic devices to communicate by a short distance. Since it is widely supported on mobile phones, it brings a lot of convenience to users. However, NFC chips are passive data stores, and can therefore be read without notice. Any NFC reader can read from NFC-compatible credit cards or access keycards, save the information, and even write the information to a blank chip to make a copy of the original chip. 

Twenty NFC chips are tested with different shapes and protocols, using ACR-122U and integrated NFC reader on the android device. Next, through the research of the  security level of a NFC door lock key card, the encryption level of the protocol, the potential of duplicating the key, and the attempt of brute force attack are analyzed. 

The read distance of NFC chips depends on the size of both the reader and the chip. For NFC cards, it is about 7cm from ACR-122U, 6cm from the available android device. For NFC tags which have smaller chips, it is about 4cm and 3cm, respectively. With a larger size reader, the read distance can be increased to 20cm. On the other hand, the key for the NFC door lock is still using MIFARE Classic®. The lock only reads and memorizes NFC tag’s 8-bit hexadecimal Unique Identification Number (UID) as keys, which does not feature any encryptions. Lastly, the read speed test for potential brute force attack on the UID results in 1 second per read. 

The read distance is long enough to allow the reader to access other’s tags without notice, which leads to serious security concerns. The encryption algorithm of the NFC lock’s chip was reverse engineered in 2008. More surprisingly, modern NFC locks still only use UID as the key, which can be easily decoded without the use of any classical encryption algorithm. Brute force would not be feasible since it can take up to 168 seconds (~136 years).  However, replication of UID can be implemented by reading the tag, then either writing it onto a rewritable UID card or emulating it with an android device.

Study of QCD Background of VBF Higgs at CMS in CERN

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Sebastian Carron-Montero, Physics
Student: Connor Hinthorn

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In 2012, using a large particle collider at CERN in Switzerland, physicists found a particle that had never yet been discovered, the Higgs Boson. A reason this particle is important is because the Higgs Boson is linked to the Higgs Field which affects the mass of most particles. There are 4 main processes to the first order of perturbation theory that can produce the Higgs through a proton collision, and the only one that has not been experimentally observed yet is known as Vector Boson Fusion (VBF). This process is not only important because it describes a new decay and production channel for a fundamental particle, but it is expected to play a role in the search for SuperSymmetric (SUSY) particles. The search for SUSY particles is one of the central quests of particle physics, given that it is a central component of most Grand Unification Theories which seek to unify all four known forces of nature into one theory. The main focus in our research, in collaboration with fellow student-researcher Julian Van Geest, is  produce a machine learning algorithm that can clean our data, recognizing VBF Higgs more reliably. We seek to optimize our selection criteria to try and precisely pick out the collisions we want to analyze from all of the other background collisions that are recorded. The primary focus of my colleague is the study of the simulated VBF Higgs signal process, and my primary objective is to study a source of background noise known as the quark jet QCD hadronic diffraction. The combination of both of our studies seek to improve the filtering of our data through the use of a trained neural network algorithm. We will present our initial efforts in developing our data analysis software, including the filtering of our data and our first stabs at establishing a neural network framework. We will also present our successful initial studies of a process that is very similar to the VBF Higgs, the Drell Yan Z boson production and decay. We used Drell Yan simulated and Data events from the CMS at CERN to validate our data analysis particle reconstruction algorithms.

Su(var)2-10 Gene Expression in Mutant and Wild-type Drosophila melanogaster using Quantitative PCR

Program: Swenson Science Summer Research Fellowships
Faculty: David Marcey, Biology
Student: Emily Jabourian

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Purpose: The objective of the study is to test the validity of the extra eye (ee) model proposed by Dr. David Marcey by examining the level of Su(var)2-10 expression in mutant versus wild-type genotypes via quantitative PCR (qPCR). This project is based on a model for the production of head defects by the ee, which is incompletely penetrant, variably expressed, and conditionally dominant. The model posits P-transposable element, 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 that is implicated in embryonic eye field establishment. In ee strains, a P transposable element insertion maps near the Su(var)2-10 gene, and is the putative target of RNAi-induced heterochromatization. Goals: It is expected that the experiments will yield Su(var) mRNA levels that are significantly lower in the ee versus the wildtype genotype due to the suppression of this gene explained by the proposed mechanism. ResearchDesign: The proposed epigenetic model will be tested by utilizing qPCR to quantify mRNA levels in experimental and control genotypes. Methods: I will isolate mRNA from flies of these genotypes, make complementary DNA (cDNA), and then use primers specific to the Su(var)2-10 exon 1-exon2 junction to determine levels of expression. Primers for a control gene (elongation factor) will be used to normalize expression profiles. Significance:My investigations are expected to be relevant to understanding the mechanisms by which tissues are partitioned into distinct developmental fields, an important feature of multicellular organisms’ ontogeny.

Sudan in America: Racial and Religious Identities of Sudanese Americans

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Rose Aslan, Religion
Student: Maddie Atkins

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Some scholars have written about the binary identities of people from Sudan and South Sudan. It is said that people from Sudan are Arab and Muslim, and those from the South are Black African, Christian. This causes segregation and dehumanization of others and promotes racism, not only in Sudan, but also for those who immigrate to the United States. In 2011 South Sudan became the newest nation because of this binary divide, along with other political reasons. This split created an even further divide and denied the African and Black identity to many Sudanese people. This relates to Sudanese immigrants in the United States because of the complex identities that are here. People from Sudan have many different influences on their identity, including race and religion and the goal of this research is to prove that identities for Sudanese American are much more complex than what is seen on the outside. This research was done through, reading scholarly peer reviewed journals, virtual and traditional ethnography. Social media and blogs were used as personal accounts along with direct interviews.  As more Sudanese Americans are being interviewed and more blogs and journals are being found it is becoming more apparent how race, ethnicity and religion impact Sudanese American’s identities. The scholars who have written about the binary complex are incorrect in labeling Sudan as Arab and Muslim. The engagement in African American culture, self-identifying as Black, the participation in Black Lives Matter along with speaking Arabic, and being a practicing Muslim point to a more complex identity and not just Arab and Muslim.

The Analysis and Characterization of Phenolic Compounds via Cytochrome P450 Enzymatic Processes

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Grady Hanrahan, Chemistry
Student: Somanea Tranin

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Currently there are limitations in our ability to chemically separate and analyze phenolic-related compounds that affect human health. As a result, this study examined the use of a novel, two-pronged approach to analysis and characterization using theoretical bio transformation pathways combined with the experimentally-focused gas chromatography-mass spectrometry (GC-MS). The development of transformation pathways for all model phenolic compounds were performed successfully via the cytochrome P450 catalyzed reaction. This allowed for the determination and postulation of both reactive and non-reactive metabolites for use as biomarkers when assessing human health from exposed individuals. Many of these products were related to both the ketone and alcohol families of chemical compounds. Future work will involve the use of GC-MS to confirm and characterize our theoretical findings. This work in not only novel from a scientific method approach, but also unique in that it will allow for greater screening capacity of phenolic-related compounds for human health assessment. 

The Anti-Cancer Effects of Berberine on Primary Canine Cells and Its Role in Apoptosis

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Chad Barber Ph.D, Biology
Student: Nicholas Arredondo

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The anti-cancer properties of natural compounds such as curcumin and berberine have been studied on cancer cells in vitro showing that berberine has valuable properties that make it a possible supplement to enhance the effects of chemotherapy drugs. On its own, berberine has been observed to decrease cell proliferation and increase apoptosis in cancer cells in vitro. The objective of this study is to isolate primary cancer cells from donated canine tumors or from known cancer cell lines, to determine the effects of berberine on specific cancers, as well as observe caspase activation to determine if a caspase-dependent pathway is responsible for the observed effects. In order to observe the effects of berberine in this study, cancer cells isolated from either canine tumors or cell lines will be studied with varying amounts of berberine in vitro, compared to positive controls. Additionally, using western blotting, the activation of caspases will be measured in comparison to the controls on samples that exhibit decreased growth, to determine if a caspase-dependent pathway is responsible for these effects.

            This study will contribute to the understanding of berberine as a supplemental treatment for different types of cancers. Future studies can include the treatment of berberine in other cancer cell types or even in combination with a variety of chemotherapeutic drugs, to determine if effects are enhanced.

The Effect of Hesperidin on a Rotenone-induced Model of Parkinson’s Disease in Lymnaea stagnalis

Program: Swenson Science Summer Research Fellowships
Faculty: Kenneth Long, Biology
Student: Ariana Espinosa

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Parkinson’s Disease (PD) is the second most common neurodegenerative disease which is characterized by a selective loss of dopaminergic neurons in the substantia nigra due to oxidative stress. Symptoms such as cognitive decline, tremors, and loss of motor function are common in those afflicted with the debilitating disease. In PD, mitochondrial dysfunction – such as a decrease in complex I activity – leads to an increase in reactive oxygen species which leads to oxidative stress and ultimately apoptosis. With no current cure, research into possible treatments for PD is important in discovering a treatment to help the approximately six million people affected. Previous research has explored the use of hesperidin in cellular and animal models of PD and has revealed the ability of hesperidin to reduce the damaging effect of oxidative stress. The objective of this study is to unravel the potential positive effects the antioxidant hesperidin has on the rotenone-induced PD model in the freshwater snail, Lymnaea stagnalis. In L. stagnalis, rotenone is a complex I inhibitor that is used to induce PD. In this study, one control group and three treatment groups of L. stagnalis of the same age will be tested. One treatment group will be exposed to 0.05 µM rotenone, another will be exposed to 0.05 µM hesperidin, and another will be exposed to a mixture of both the rotenone and hesperidin. After being exposed to their solution for a set period, the subjects will be removed from solution. Observations of the feeding response, memory, and lifespan will be taken to determine if hesperidin reduces the harmful effects of rotenone. Immunocytochemistry using antibodies to tyrosine hydroxylase will identify dopaminergic neurons in isolated ganglia. Western blots will be performed to determine the effects that rotenone and hesperidin have on the concentration of tyrosine hydroxylase. It is expected that pairing rotenone with hesperidin will decrease the detrimental effects of rotenone. There should be a decrease in behavioral deficits, longer lifespans, and a decrease in dopaminergic cell loss. Since working in lab was not possible this summer, my focus was on reading relevant research and expanding my knowledge on the techniques that will be used once we are able to return to campus.

The Effects of Heel Strike Loading Magnitude on Hip and Lumbar Spine Bone Mineral Density in Male Distance Runners

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Michele LeBlanc, Exercise Science
Student: Allison Burdullis

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Previous research has reported that while male long-distance runners have normal bone mineral density (BMD) at their hip, their lumbar spine BMD values are lower than that of the general population (Fredericson et al., 2007; Hind et al., 2006). In fact, about 40% of the runners in these studies have lumbar spine T-scores < -1.0. Ground reaction forces and tibial stress fractures have been investigated, but an understanding of how their early loading characteristics may influence lumbar spine BMD values is lacking. The purpose of this study was to examine the effects of early impact loading rates on hip and lumbar spine BMD in male long-distance runners. Forty injury-free male runners aged 18-30 years were recruited. Participants ran across a Kistler force plate (1000 Hz) at a self-selected pace with each foot making contact for three trials per foot. Whole-body, hip, and lumbar spine scans were completed with a Hologic dual-energy X-ray absorptiometry machine. Participants who consistently exhibited a heel-striking pattern were divided into two groups (n = 16 each) based on their average early loading rate (ELR) values obtained with Bioware software. The Low and High group ELR values were statistically different (86.0 ± 18.3 kN/s vs. 175.3 ± 48.9 kN/s; p < 0.001). There was no difference between the two group’s mass, weekly mileage, or normalized peak active vertical force. The normalized peak impact force, stance time, time to peak vertical impact force, and time to peak vertical active force were different between the two groups. The High ELR group had greater BMD values at all anatomical locations analyzed, significantly so at the Ward’s triangle and total lumbar regions (p=0.023 and p=0.002, respectively). The lumbar spine T-scores were significantly different (p = 0.003) with 14 subjects in the Low group and 2 subjects in the High group having T scores < -1.0. The results suggest that a higher early impact loading rate may be desirable to obtain adequate BMD for the spine and thus prevent future osteoporic injuries.

The Production of a Newsletter and Review Article

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Dr. Jesus Cordova Guerrero, Chemistry
Student: Alexia Rangel

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The questions that I researched are, “What are the most current reports on the synthesis of alkenes?” and “Identify how many research projects are going on at CLU.” Another research student and I worked on the review of alkenes project under the guidance of Dr. Cordova Guerrero, and this project is the result of the product of a collaboration with another research group from the University of Tampa. We are writing a review on alkenes to better understand how they are formed and behave under various reaction conditions. The first step of conducting literature searches to find the most current reports in the synthesis alkenes followed by the analysis and discussion of the reports by the type of transformation, as a way to write a coherent review article for subsequent publication has already been completed. We used Scifinder Scholar as the scientific database to obtain the peer-reviewed articles, and Chemdraw as the software to draw chemical structures included on the manuscript. We are currently in the process of formatting all the articles into the desired template of the scientific journal where we will be publishing the review article. The expected outcome is the publication of a review article that possess recent reports for the synthesis of alkenes as a strategy to further the knowledge in the scientific community based on their unique characteristic structure. We plan to submit the article to the European Journal of Organic Chemistry. It is important to gather the most recent reports in the field to facilitate the process of finding information and learning more about alkenes. For the second project that I worked on, I helped create CLU’s first STEM Newsletter. The newsletter will highlight many Professors in the STEM field and the research they are conducting. The newsletter is important because it will be the first one at CLU that only focuses on STEM. This will help educate students about STEM research being conducted on campus and will also help students that are interested in becoming involved with research to see which types of projects there are and which Professors are conducting each project.

The Use of Neural Network Platforms for Chemical Characterization and Toxicity Prediction

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Grady Hanrahan, Ph.D, Chemistry
Student: Bianca Flores

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Artificial neural networks (ANN’s) are computerized models that mimic the brain, in that they can be trained for a specific purpose, and eventually, learn on their own. Optimized models can detect trends and make predictions with remarkable accuracy and robustness. The purpose of this study was to create a neural network and test it for accuracy. In this study, an enhanced neural network platform was created in a MATLAB format, including assessing network functionality, nodes, and related model factors. Using a model data set, neural network functionality was tested, trained, and optimized. High correlation between model predicted and experimental results was observed, as well as low model error and discrepancies. This newly developed neural network was proven useful and accurate. We will begin to examine chemical data sets from the GC-MS analysis of urine and blood samples in future work. This ANN will be used to assess these correlations and predictive capabilities. In consideration of how the structure of phenolic related compounds correspond to the chemical toxicity properties, human health consequences will be evaluated, and thus help establish a stronger basis for further research.

Understanding the Experiences of LatinX Community Members as Negative Media Portrayals Impact Higher Education Attainment

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Aaron Heresco, Communication
Student: Maria Barragan

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Under  President Trump’s administration, mainstream media has presented various perceptions of the Latinx community, at times painting a negative narrative. These negative perceptions have impacted this marginalized community as more racial and discriminating behaviors have risen in media coverage. Media coverage on controversial remarks made by the President about these ethnic groups have forced many to take a stand for those who cannot legally. 

The purpose of this study is to examine how negative portrayals of LatinX community  members through the media determine their  educational goals as students. This research intends to find if factors such as fear of deportation or stereotypes within media plays a role on the decision of undocumented and documented 12th grade and/or high school graduates in pursuing higher education. This study provides more information about the experiences of students who are currently or were under DACA as well as the implications it may have on their educational journey. The research intends to answer the following questions:What are some of the misrepresentations of LatinX community members seen through the media?How  have these experiences shaped the way  young LatinX adults see higher education?, and finally, How can DACA and immigration laws be revised to improve the educational opportunities and public perception of LatinX young adults?

Upper Extremity Angular Kinematics of an American Football Long Snap

Program: ALLIES in STEM Summer Research Fellowship
Faculty: Travis Peterson, Exercise Science
Student: Samuel Balentine

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Upper extremity kinematic variables have been strongly related to the resultant initial ball velocity of an American football long snap (Chizewski & Alexander, 2015). Understanding the relationship between these measures and long snap velocity can provide evidence-based principles for football players to produce faster long snaps. This study aimed to determine which angular kinematic variables are most strongly related to long snap velocity. Ten experienced football long snappers (5 high school; 5 collegiate) participated in the study. Athletes performed six long snaps directed at the Wizard Kicking Solo-Snap net placed 13.3 meters (15 yards) behind the anterior tip of the football. Trials were video recorded from a sagittal view placed on the left side of the subject (30 Hz). Ankle, knee, hip, shoulder, and elbow joint angular kinematic variables were tracked throughout the snap (Kinovea v0.8.27). Correlational analyses were conducted between angular kinematic variables and initial ball velocity (α=0.05). The timing of peak elbow flexion was significantly correlated to ball velocity for the whole group (r=0.829, p=0.002) and for just the college players (r=0.907, p=0.020). Additionally, college athletes produced larger ball velocities when the elbow maximum angular velocity was larger (r=0.881, p=0.032). For high school snappers, more extended elbow release angles were correlated with larger ball velocities (r=0.970, p=0.002). Shoulder angle prior to the snap initiation was not significantly correlated to ball velocity for high school (r=0.666, p=0.197) or college athletes (r=0.313, p=0.599). Therefore, football long snappers should focus on maximally extending their elbow at release from the most flexed position later in the snap. This allows for larger elbow angular velocity as the elbow extends through a larger range from the flexed position over a shorter duration to release the ball. This study found higher long snap horizontal velocities under those conditions and has the potential to increase overall long snap performance.

Using Bioinformatics to Analyze Surface Proteins on Coronaviruses

Program: Ronald E. McNair Post-baccalaureate Achievement Scholar
Faculty: Paloma Vargas, Biology
Student: Zsa Zsa Gabor

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SARS-CoV-2 the virus that causes novel Corona-virus disease (CoVID-19) is an enveloped RNA virus that is thought to have originated in bats. The current COVID19 pandemic likely started when the virus was able to jump and establish infection in a new host, a pangolin, before undergoing a mutation that enabled it to jump hosts once again to establish infection in humans. From the time that the 2019-2020 pandemic began, there have been at least three strains of SARS-CoV-2 isolated from patients. Infection with CoVID-19 begins when viral particles enter the upper respiratory tract via virus-laden droplets. Similarly to SARS-CoV, the SARS virus, SARS-CoV-2 encodes two major proteins that facilitate entry into host cells, S1 and S2, which coat the outer envelope of the virus and bind the host-cell receptor, ACE2. Changes to S1 or S2 in the novel coronavirus could lead to a higher affinity for the ACE2 receptor, increasing the ability of SARS-CoV-2 of infecting the human host. Without a proper understanding CoVID-19’s structure a vaccine is more difficult to create. To remedy this we will closely examine the mechanisms of the virus and identify what selective pressures create a more virulent strain.We will use bioinformatic software such as CLUSTAL OMEGA and MEGA to compare known bat coronaviruses, to known human-infective coronaviruses MERS, SARS and SARS-CoV-2. We will pay specific attention to the S1 and S2 RNA sequences and their predicted amino acid sequence to evaluate mutation sites that could increase affinity of S1 or S2 for the human ACE2 receptor. As of now we have identified complete lines of amino acid conservation in SARS 1& 2. Future work for this project includes identification of mutated residues, development of three-dimensional and correlation analyses to determine the role of these mutations on infection rates and disease outcomes. Specifically, we will be obtaining data from publicly available CoVID patient data to assess the relationship between any identified mutation and disease outcome based on sex, age, socioeconomic status and race/ethinicity. 

Using Recombination to Separate Genetic Components of the extra eye Mutation in Drosophila melanogaster

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. David Marcey, Biology
Student: Devin Romines

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The extra eye (ee) mutation in Drosophila melanogaster produces head deformities which range from missing and/or duplicated bristles and head cuticle to supernumerary compound eyes and antennae.  It is incompletely penetrant and conditionally dominant.  Marcey (personal communication) has developed an epigenetic, two-component model to explain the exotic genetic behavior of ee. The first component centers around a transposable P-element inserted in the 5′ exon of the Cytochrome p450 reductase (Cpr) gene in a reverse orientation with respect to the transcriptional polarity of Cpr.  This reverse-transcriptional orientation causes for an RNAi-based tightly packaging of DNA, heterochromatization, at the site of the anti-sense P-element and all other P-elements in the genome.  The second component of the model predicts that there is a P-element that exists near the Su(var)2-10 gene, which is important for normal eye development.  The RNAi-induced heterochromatization of this P-element subsequently suppresses the expression of Su(var)2-10, causing for the observed extra eye phenotypes.  In order to test the model’s validity, the present study is proposed to isolate these two components in ee lines by splitting the chromosome on which both components reside, the 2nd chromosome, through recombinational means.  It is expected that the resultant recombinationally-generated descendants with split extra eye chromosomes will not produce any phenotypes characteristic of the extra eye mutation in any capacity.  To conduct this project, ee flies will be mated to flies with a heavily mutated 2nd chromosome, a mapping chromosome, so as to track where recombination events take place.  Resultant progeny will be assayed for desirable recombination events.  Such offspring will then be mated with balancer stocks to preserve the split chromosome and then preserved into a line of flies for studying potential extra eye phenotypes.  This project is important as it provides further insight into the mechanisms of animal development, especially in understanding the role of transposable elements in gene expression.

Variations in Oral Microbiota May Explain Potential Racial Differences in Cardiovascular Diseases

Program: Aperture Summer Research Fellowship
Faculty: Dr. Allan Knox, Exercise Science
Student: Giselle Fernandez

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Previous research has discovered that the oral cavity is home to a wide diversity of bacteria that is present subgingival, on the dorsal of the tongue, and in the saliva. The oral microbiota consists of healthy and pathogenic bacteria that are known to cause different oral diseases. Oral diseases have been associated with cardiovascular health due to the inflammatory response caused by bacterial abscesses in the teeth.

Purpose: The purpose of this study was to conduct a literature review to determine the current data regarding the influence of the oral microbiota on cardiovascular risk between racial groups.

Methods: Existing literature was identified through the electronic databases: PubMed, ScienceDirect, Research Gate, and Pearson Library.

Results: The oral microbiome cannot be distinguished by race or ethnicity due to the wide diversity of bacteria. However, the oral microbiome is influenced by dietary and lifestyle habits. Racial differences in dietary habits were seen where Blacks ate higher quantity of fatty food than fruits and vegetables when compared to Hispanics and Whites. Tobacco and alcohol use was more prevalent in Blacks in adulthood when compared to Whites and Hispanics. Smoking tobacco reduces the diversity of  gram positive bacteria and revealed high levels of pathogenic bacteria at the expense of lower nitrate reducing bacteria. Pathogenic bacteria is linked to chronic bacterial infections that lead to an elevated-level of C-Reactive Protein. CRP is a key systemic health marker that predicts CVD risk. Elevated CRP levels indicate a higher risk of developing cardiovascular diseases.

Conclusion: The current data suggests that lifestyle habits are the main influencers of the oral microbiota. Racial differences exist in cardiovascular risks which may be reflective of differences in lifestyle habits. Objective comparisons of oral microbiota compositions between racial groups is absent from the current literature and is necessary to improve our understandings between the association of oral health and cardiovascular risk.

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