Schedule of Events
Science Showcase: Poster Session
Friday, April 23, 2021
11:00 am - 1:00 pm
Soiland Gym
Students from disciplines in the Natural Science Division will present their results in an in-person, interactive poster format. The featured research comes from honors and Capstone projects, class assignments, and faculty-directed collaborative efforts.
Student Abstracts
Solving the Structure of NIS Synthetase DesD Variant R306Q
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. DesD is a possible drug target due to being an essential enzyme in certain virulent bacteria. The DesD variant R306Q has had Arginine (R) replaced with Glutamine (Q) at amino acid residue 306. 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. 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. 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 R Free 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.
Student(s):
Raquel Barnard
Faculty Mentor:
Dr. Katherine Hoffmann
How many Sprint Trials is Enough? Avoiding Bias when Estimating Maximum Sprint Performance in Western Fence Lizards
The objective of my research is 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 focused on the locomotor performance of sprinting in S. occidentalis because it is a key measure of whole-organism performance in this species. 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 its 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 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. 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. 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.
Student(s):
Robin Bedard
Faculty Mentor:
Dr. Kristopher Karsten
Comparision of Female and Male Golf Swing Kinetics and Force Production
Golf is a popular sport that is enjoyed by both men and women across the world. It is beneficial to understand if men and women perform the golf swing differently in order to properly match training techniques and golf equipment to 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) volunteered to participate 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 and normalized by body mass. 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 generated linear impulse over a longer duration of time (0.371 ± 0.032 s) than males (0.304 ± 0.051 s, p = 0.046). Females may be using 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.
Student(s):
Michele Birkner
Faculty Mentor:
Dr. Travis Peterson
Investigating the Genetic and Developmental Basis of the Racing Stripe Phenotype in Drosophila melanogaster
The Drosophila melanogaster compound eye consists of an arrangement of about 750 single eyes (ommatidia) on lateral aspects of the adult head. Each eye consists of a dorsal and ventral arrangement of ommatidia that occur as mirror images of one another across the polar plane, with the dorsal segment above the plane and the ventral segment below the plane. The phenotype “Racing Stripe” is caused by the insertion of a white+ transgene into the third chromosome. The transgene is primarily expressed in rows of ommatidia along the Dorsal-Ventral midline. In a white- mutant background this results in the “Racing Stripe” phenotype consisting of a midline stripe of red pigmentation in an otherwise pale yellow eye. This study will focus on whether the expression of this “Racing Stripe” phenotype is affected by either Suppressors of Variegation (SU(var)s) or Enhancers of Variegations (E(var)s), by crossing a line DM600, that expresses this “Racing Stripe” phenotype, with various lines that include both SU(var)s and E(var)s.
Student(s):
Claire Bjork, Nicolette Alvandian
Faculty Mentor:
Dr. David Marcey
The Effects of Heel Strike Loading Magnitude on Hip and Lumbar Spine Bone Mineral Density in Male Distance Runners
Previous research has reported that male long-distance runners have normal bone mineral density (BMD) at their hip but low lumbar spine BMD (Fredericson et al., 2007; Hind et al., 2006). An understanding of how the early loading characteristics of ground reaction forces 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 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). 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.
Student(s):
Allison Burdullis, Marcus McKinnon, Steven Hawkins, Ph.D., FACSM, Michele LeBlanc, Ph.D.
Faculty Mentor:
Dr. Michele LeBlanc
Postfire Succession in Ventura, California: Vegetation Monitoring Over a Thirteen-Month Period
The increasing prevalence and severity of climate-induced wildfires has necessitated further research into the effects wildfires have on plant communities and overall biological ecosystems. Drastic changes in plant species composition may have monumental effects on local terrestrial and aquatic wildlife, especially if an ecosystem relies on bottom-up control. I monitored and analyzed plant community succession in an area adjacent to the Ventura River that suffered burning in October 2019; monitoring took place between Spring 2020 to Spring 2021 using line-transect and quadrat sampling methods for data collection. This project aims to determine plant species richness and abundance after having been afflicted by fire. Plant species were categorized into groups based on origin, growth form, and general response to fire. Data and results will be reported at the time of the Festival of Scholars, as data collection and analysis are still on-going.
Student(s):
Tawny De Guzman
Faculty Mentor:
Dr. Bryan Swig
Quantification of Microfibers in the Gastrointestinal Tract of Loligo opalescens
Focus has been drawn to plastic waste in our oceans regarding items on a macro scale such as water bottles and plastic containers. Recently, attention has begun shifting to plastics on a micro-level. As studies on microplastics (MP) in our ecosystems have been garnering attention, a subset of this anthropogenic debris must also be addressed: microfibers. Microfibers (MF), a form of microplastic that is shed from synthetic clothing such as polyester, often pollute our food and water supply. Recent work has detailed the presence of MP in marine filter-feeding organisms such as mussels, while little research has been conducted on marine organisms on the tertiary level. We chose to study a tertiary organism that also plays a role as a key forage species for many marine mammals, birds, and fish along Southern California. The squid was selected as the organism of choice for this study as it is a key forage species that spawn year-round. This study aimed to identify whether MF was present in the gastrointestinal tract of Loligo opalescens (California market squid). Organs were removed and ground so that MF would be released. Following this, they would then be placed into 500 mL of saltwater solution and stirred so that MF would then be suspended in the solution. The saltwater solution would then go through a Buchner funnel filtration apparatus, and filter papers would be analyzed under a dissection microscope for quantification. Results to be presented at Festival of Scholars.
Student(s):
Alexandria De Leon
Faculty Mentor:
Dr. Andrea Huvard
Quantification of Microfibers in the Gastrointestinal Tract of Loligo opalescens
Focus has been drawn to plastic waste in our oceans regarding items on a macro scale such as water bottles and plastic containers. Recently, attention has begun shifting to plastics on a micro level. As studies on microplastics (MP) in our ecosystems have been garnering attention, a subset of this anthropogenic debris must also be addressed: microfibers. Microfibers (MF), a form of microplastic that is shed from synthetic clothing such as polyester, often pollute our food and water supply. Recent work has detailed the presence of MP in marine filter feeding organisms such as mussels while little research has been conducted on marine organisms on the tertiary level. We chose to study a tertiary organism that also plays a role as a key forage species for a number of marine mammals, birds, and fish along the coast of Southern California. Squid was selected as the organism of choice for this study as it is a key forage species that spawns year round. This study aimed to identify whether MF was present in the gastrointestinal tract of Loligo opalescens (California market squid). Specimens were dissected and microfiber content was quantified under a dissection microscope following filtration of selected organs. Results to be presented.
Student(s):
Alexandria De Leon
Faculty Mentor:
Dr. Andrea Huvard
Can a High Dietary Nitrate Intake Attenuate the Harmful Effects of Chronic Alcohol Consumption on the Vasculature?
Alcohol-related deaths are the 3rd leading preventable cause of death in the United States withexcessive alcohol consumption contributing to severe health risks. 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. 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 items included alcohol consumption, fruits & vegetable consumption, dietary nitrate, cardiovascular disease, and all-cause mortality. Numerous studies have reported cardioprotective benefits with “moderate” consumption of alcohol, mostly due to 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 queried. 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. Further research is warranted.
Student(s):
Michael Diaz
Faculty Mentor:
Dr. Allan Knox
The Effect of Hesperidin on a Rotenone-Induced Model of Parkinson's Disease in Lymnaea stagnalis
Parkinson’s Disease (PD) is a neurodegenerative disease characterized by a selective loss of dopaminergic neurons in the substantia nigra due to oxidative stress. Preventing and curing PD is a major goal of basic and clinical research. Previous research on cellular and mouse models of PD has revealed that hesperidin reduces the damaging effect of oxidative stress. The pesticide rotenone inhibits the mitochondrial respiratory chain and produces PD-like effects in animal models. The objective of this study is to determine whether the antioxidant hesperidin counteracts the effects of rotenone in the rotenone-induced PD model of the freshwater pond snail, Lymnaea stagnalis. Forty snails were treated with either rotenone, hesperidin, or a combination of both. On days 3, 6, 9 and 12, locomotion was measured. Central and buccal ganglia were dissected for future immunocytochemical studies on dopaminergic neurons. Separate acute exposure tests measured locomotion and feeding (lettuce consumption) in twenty snails. Snails were pretreated with 0 to 10 μM hesperidin for four hours followed by exposure to 5 μM rotenone. After 24 and 48 hours, locomotion and feeding were measured. Exposure to rotenone decreased mobility and feeding in most trials. While there was a trend suggesting that hesperidin reduced the effect of rotenone, the differences were not statistically significant (p=0.295). Additional trials are needed to determine whether hesperidin can block the effects of rotenone.
Student(s):
Ariana Espinosa
Faculty Mentor:
Dr. Kenneth Long
Solving the Structure of E467A DesD from Streptomyces coelicolor
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), with cofactor, adenosine triphosphate (ATP). This mutation was done because it is believed that Glu467 is a critical catalytic residue. To obtain crystals, the protein had to be transformed, overexpressed, and purified. Once pure protein was formed, the hanging drop vapor diffusion method was used to set up crystals in various conditions. Crystal hits were found in 20% glycerol and 5mM dfoG. X-ray diffraction data was then collected and used to solve and refine the structure using CCP4i2 and COOT software. The crystals were diffracted to 1.88Å and were assigned a space group of P21.Backbone errors were corrected in all four chains. R-factor is currently 24.9% and free R-factor is 26.9%. Once the structure has been solved, it will be published on the Protein Data Bank (PDB). Future studies include determining the kinetic activity of this mutant form of DesD in comparison to previous kinetic studies on Arg306Gln and Wild type DesD. This data will be the foundation for future drug tests to determine the efficacy of the drugs against DesD.
Student(s):
Eliana Goncuian
Faculty Mentor:
Dr. Katherine Hoffmann
Impact of Police Unionization on FBI Dataset Participation
The FBI collects data on police agencies through their Offesnses Cleared dataset, Hate Crimes dataset, and Law Enforcement Officers Killed and Assaulted dataset. Given that participation in collection of this data is not mandatory, the purpose of this analysis is to find the relationship between police agency unionization and participation in the dataset. Utilizing probit regression models, we find that unions are less likely to participate in the LEOKA dataset, and also comment on the inability to properly analyze non-participants in each other FBI dataset. Data on police is important for reform and accountability. This analysis adds to the breadth of literature on the differences and downfalls of police unionization, even at just the employee level.
Student(s):
David Hall
Faculty Mentor:
Dr. Kirk Lesh
Classifying Infrared Emission Line Stars Using Optical Spectroscopy
Massive stars are not expected to have solar-like magnetic fields because of differences in internal structure. However, a rare subset of these stars have large, stable magnetic fields, denoted Bp stars for their peculiar spectra, including strong emission lines. These lines, created by material trapped in the magnetic field, look similar to another group of B-type stars, Be stars, although the cause differs, as Be stars are not magnetic. This study aims to distinguish Bp stars from 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 a magnetic field. Using optical spectroscopy from the CFHT and Mercator telescopes, the rotational velocities of eight target stars were determined by applying best fit synthetic models for accurate stellar parameters to determine the rotational broadening of the helium absorption line at 4388 Å. We compared the computed rotational velocity of the star to the velocity of the orbiting material, which was measured from infrared hydrogen emission lines by a previous study. Our analysis suggests that two targets are Bp stars, while three are clearly Be stars. Another interesting result is the spectrum of SS 453, which clearly shows the star is actually a binary star system. Although our results require spectropolarimetry to confirm the presence of a magnetic field, this study points to the possible addition of two new Bp stars, increasing the small number of identified Bp stars.
Student(s):
Van Haslett
Faculty Mentor:
Dr. Mary Oksala
THE INFLUENCE OF JUMPING RATE OF FORCE DEVELOPMENT ON BONE MINERAL DENSITY IN RUNNERS
Bone strength and density are known to increase in response to both ground reaction forces (GRFs) and muscle forces (Beck, 2009). The purpose of the present study was to determine if the rate of force development (RFD) during a squat jump was a factor in hip and lumbar spine bone mineral density (BMD) values in male long distance runners. Forty male runners (ages 18-30) who ran at least 30 miles per week were recruited. Each participant performed three maximum effort vertical squat jumps off of a Kistler 9281CA force plate (1000 Hz). Dual X-ray absorptiometry (DXA) scans were performed on the lumbar spine and hip. GRFs were collected with the participant running at a self-selected pace across the force plate. Bioware software was used to determine the average RFD from the lowest position until the maximum vertical force during the jump. Two distinct groups of subjects were formed based on average squat jump RFD. The greater RFD for the High group was created by both a larger peak vertical force (1,454.4 ± 133.7 N vs. 1,238 ± 135.2 N; p = 0.001) and a shorter time to the peak force (p < 0.001). There were no significant differences in peak vertical GRFs (impact or active forces) during the running trials between the groups. DXA data revealed no differences in any of the BMD values between the two groups. It appears that the differences in the runners’ ability to generate during a jump does not affect their BMD values.
Student(s):
Abigail Hiller, Marcus McKinnon, Steven Hawkins, Ph. D., Michele LeBlanc, Ph. D.
Faculty Mentor:
Dr. Michele LeBlanc
Study of QCD Background of VBF Higgs at CMS in CERN
In 2012, using a particle collider at CERN in Switzerland, physicists found the Higgs Boson, which had been hypothesized but had eluded detection until then. A reason this particle is important is because the Higgs Boson is linked to the Higgs Field, which imparts most of the physical mass to fundamental fermion particles. There are 4 main processes that can produce the Higgs through a proton collision, the only one that has not been experimentally observed is Vector Boson Fusion (VBF). The focus of our research is to produce a machine learning algorithm that can clean our data: accepting VBF Higgs while rejecting background processes, e.g. ZZ production and decay. While Julian will present the work on our attempt to optimize the machine learning algorithm, I am presenting the work to select candidate events through kinematical selection cuts on Monte Carlo simulated Higgs and ZZ backgrounds. I will show comparisons of kinematical variables between prefiltered/filtered data for the Higgs signal and a Drell-Yan ZZ background samples. From these comparisons we will show the effect of our selection cuts in increasing the population of expected Higgs events while decreasing the population of ZZ events in our filtered data. A machine learning neural network is then trained on these filtered data and will further increase the ratio of signal/background. It is intended that this presentation be read first, and then followed by Julian’s presentation, though both were developed through cooperation of all members of our group.
Student(s):
Connor Hinthorn, Julian van Geest
Faculty Mentor:
Dr. Sebastian Carron-Montero
Crybaby Induction by Genetic Elements in the extra eye Strain of Drosophila melanogaster
This project is based on a model for production of head defects by extra eye (ee), an incompletely penetrant, variably expressed, and conditionally dominant mutation in Drosophila melanogaster. Ee maps to a P-element in the Cpr gene, inserted in reverse transcriptional orientation. The model posits P-element, RNAi-mediated transcriptional suppression of genes near P-element insertions implicated in embryonic eye establishment. Screens were conducted by crossing ee to wild-derived lines in attempts to generate inducible, epigenetic variants revealed by ee-Cpr anti-sense P-elements. One screen recovered a variant, crybaby (cby), a tear-drop eye shape caused by ventral eye development impairment. I conducted an important control experiment to test whether the cby phenotype is inducible by any P-element line, or whether this putative “epiallele” is induced exclusively by genetic components in the ee genotype. My results examine whether cby was induced by de novo hopping of a P-element into a gene in the course of our cross of JG1 (ee) to KW003 (Brazil), as opposed to genetic crypsis being revealed by the anti-sense P-element of the ee line. I predicted the cby phenotype only appears in crosses with JG1 and not inducible by other P-element lines (KW006). I also predicted the cby phenotype would not be induced in crosses of KW003 to a stock that lacks P-elements (Canton-S). As expected based on the original screen, the cby phenotype appeared in a line established from a cross of JG1 and KW003. No cby mutants were noted in crosses between KW006 and Canton-S to KW003.
Student(s):
Emily Jabourian
Faculty Mentor:
Dr. David Marcey
Review of Spirocyclic Compounds and an Organic Chemistry Textbook
Many complex molecules rely on their unique spirocyclic structure in order to function properly. Of particular interest to researchers is how to efficiently synthesize such molecules through cascade processes. Individual articles were written on published research to summarize the experiments completed and the experimental data was sorted into categories, such as the type of reactions and conditions used to synthesize each spirocyclic product. 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 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. A similar process was taken to create this textbook as compared to writing the aforementioned review; reactions were gathered from the scientific database SciFinderâ, the 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 mechanisms, and see novel methods in which the reactions they are studying have been utilized in research. Thus far, a majority of the material covered in the first semester of organic chemistry has been written.
Overall, the review will further knowledge in the scientific community on spirocyclic compounds and the textbook will enable students to better understand material within the scope of organic chemistry.
The other project completed this past summer focused on enhancing students’ experience in organic chemistry by creating a textbook of practice problems. A similar process was taken to create this textbook as compared to writing the aforementioned review; reactions were gathered from the scientific database SciFinderâ, the 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 mechanisms, and see novel methods in which the reactions they are studying have been utilized in research. Thus far, a majority of the material covered in the first semester of organic chemistry has been written.
Overall, the review will further knowledge in the scientific community on spirocyclic compounds and the textbook will enable students to better understand material within the scope of organic chemistry.
Student(s):
Kayla Klussman, Noah Shepard, Jessica Nasr
Faculty Mentor:
Dr. Jesus Cordova Guerrero
A Generalization of the Hardy Distribution for Golf Hole Scores
In golf, the likelihood of success for each shot is primarily dependent on theresult 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.
Student(s):
Ryan Kyaw
Faculty Mentor:
Dr. Christopher Brown
STEM Research: CLU Newsletter and Graduate Program Database
Undergraduate students are typically unsure about which field of research they would like to go into, 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 often inquire about a graduate school fit for them and spend an extensive amount of time reading up on it. Therefore, publishing a newsletter that highlights a variety of Cal Lutheran’s faculty research will strike the interest of potential student researchers. Approximately eight to twelve faculty members, of those who participated in the past three research symposiums, were assigned to each research member. Faculty were then contacted via email with a word document and photo/video release form to be completed. Once the documents were returned, a zoom interview was conducted to further discuss the formatting of their article. In terms of the database, an excel spreadsheet was created of all the California graduate programs that conduct STEM research at the Ph.D. level in Biology and Chemistry. The spreadsheet was divided by: institution, location, sector, department, field, faculty members’ biography, research website link, tuition cost, application requirements link, student salaries, STEM companies nearby, and admission rates of different minority groups. STEM research at the graduate level is conducted across 15 different counties; however, five of the counties do not participate in biological or chemical research. Research is vital to unlocking a student’s potential, allowing one to gain knowledge of a preferred subject and jumpstarting their career path.
Student(s):
Morgen Lakpour, Noah Shepard, Alex Rangel, Crystal Cendejas, and Lyndsey Zamora
Faculty Mentor:
Dr. Jesus Cordova-Guerrero
Catalysis Mechanism Proposal for DesD
DesD performs a unique and understudied chemistry and understanding the mechanism through which occurs is valuable as a model for the NIS Synthetase family of enzymes. 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 mechanism. Our proposed mechanism was informed by the mechanism of AcsD, a NIS Synthetase, in addition to our labs previous kinetic data from a well-established ITC protocol. We hypothesized that Arg306, His443, and Glu467 are necessary for catalytic turnover of the substrate. Our hypothesized mechanism is as follows. The adenylation step requires His443 to stabilize the carboxylic group of the substate which 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.
Student(s):
Nathan March, Dr. Kathrine Hoffmann
Faculty Mentor:
Nathan L March
The Comparison of Microfibers in Sand Sediment in Southern California Beaches, Harbors, and Bays
Microplastics have been an emerging environmental threat to terrestrial and aquatic habitats worldwide. The non-biodegradable waste we are drawing our attention to in this study is microfibers. Microfibers are a subcategory of microplastics deposited into the environment when textiles are produced from a synthetic material shed. Microfibers measure less than 5mm in length and make up 80% of all microplastic pollution, contributing to 35% of primary plastic pollution in ocean water. From there, they will remain in a suspended state until they eventually settle into the sediment. Our objective was to determine just how many of these fibers settle into the sediment. Locations of sediment range from San Diego, CA. moving up the coast to Morro Bay, CA. 100mL of sand was analyzed from each site. Samples were mixed with 200mL of instant saltwater in a 500mL beaker to suspended the microfibers. Each sample was filtered through a Buchner Funnel having a 5μm cellulose nitrate membrane filter. Filters were placed under dissection microscopes for quantification. Microfibers were detected in all study site samples, averaging between 42-59 microfibers per 100ml of sand sediment, while the harbor and bay areas had a higher concentration of microfibers than open water beaches.
Student(s):
Amir Mejia
Faculty Mentor:
Dr. Andrea Huvard
A Screen for Inducible Epigenetic Variation in Natural Populations of Drosophila melanogaster
We are conducting a large scale screen for novel sources of cryptic genetic variation (CGV) in natural populations of Drosophila melanogaster. The screen is based on a model for the production of head defects by the extra eye mutation (ee), which is incompletely penetrant, variably expressed, and conditionally dominant. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a key molecule in the JAK-STAT signaling cascade implicated in embryonic eye field establishment. In ee strains, a P transposable element insertion maps near a gene (Su(var)2-10), and is the putative target of RNAi-induced heterochromatization. The proposed epigenetic model predicts that new mutant phenotypes may be uncovered in crosses between ee lines and flies from natural populations that harbor P-elements at various genomic locations. Such novel mutants are predicted to be incompletely penetrant and variably expressed, caused by epigenetic silencing via RNAi-induced heterochromatization of genes residing at genomic positions near P-elements. In an initial study, 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.
Student(s):
Gabriella Moreno
Faculty Mentor:
Dr. David Marcey
Artificial Neural Network Platform Development for Chemical Toxicity Model Assessment
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.
Student(s):
Kieudiem Nguyen
Faculty Mentor:
Dr. Grady Hanrahan
Analysis of Microfibers Found in Sardina pilchardus and Rastrelliger kanagurta
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 grounded into a paste; which were 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).
Student(s):
Keury Ortez Hernandez, Steven Ortez Hernandez
Faculty Mentor:
Dr. Andrea Huvard
Improved Optimization and Chemical Characterization for Urinary Metabolite Screening
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.
Student(s):
Sara Ortiz Ramirez
Faculty Mentor:
Dr. Grady Hanrahan
NIS synthetases Structure Review of IucA and IucC
Iron is vital for living organisms since it plays a role to allow protein’s biological activity, 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.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 and then pull using Pymol program. DesD structure was obtained and overlay with IucA and IuC separately, helixes and missing sequence loops were label in the structures. 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, but DesD completes them. 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. 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.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.
Student(s):
Pablo Paredes, Estrella Palacios, Nathan March, Eliana Goncuian, Raquel Barnard
Faculty Mentor:
Dr. Katherine M. Hoffmann
Fasting and Cerebral Dynamics: A Systematic Review
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 maybe translated to augmented cognition. The aim of this investigation is to perform a systematic review of the existing literature concerning fasting and cerebral blood flow. The methods used to conduct this project included literature searches completed in the databses of 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.
Student(s):
Luke Rodarte
Faculty Mentor:
Allan Knox
Using Recombination to Separate Genetic Components of the extra eye Mutation in Drosophila melanogaster
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 in the 5’ exon of the Cpr gene in a reverse-transcriptional orientation to that 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 a P-element exists near the Su(var)2-10 gene, which is important for normal eye development. In order to test the model’s validity, the present study works to isolate these two components in ee lines by splitting the chromosome on which both components reside through recombinational means. It is expected that the resultant recombinationally-generated descendants with split chromosomes will not produce any extra eyes. To conduct this project, ee flies will be mated to flies with 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 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.
Student(s):
Devin Romines, Gabriella Moreno
Faculty Mentor:
Dr. David Marcey
Are Robots Responsible? Extended and Shared Moral Responsbility
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. 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 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 our actions for the future. Questions of moral responsibility will soon arise for non-human non-agents and non-human quasi-agents (higher-order intentional systems) that will not be easy to answer. Thinking through responsibility in these cases is essential within an increasingly technological world.
Student(s):
Rishabh Sarin
Faculty Mentor:
Prof. Lacey Davidson
STEM Research Newsletter and Organic Chemistry Textbook
STEM Research at CLU Newsletter: An equitable opportunity for undergraduate research is elusive to many students because these highly sought-after positions are limited and not widely promoted. The goal of this project 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.
Organic Chemistry Textbook: Practice Problems and Applications: 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 from peer reviewed research sources. The goal of this project 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, the student’s knowledge and comprehension of organic chemistry can be reinforced and easily remembered.
Organic Chemistry Textbook: Practice Problems and Applications: 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 from peer reviewed research sources. The goal of this project 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, the student’s knowledge and comprehension of organic chemistry can be reinforced and easily remembered.
Student(s):
Noah Shepard, Kayla Klussman
Faculty Mentor:
Dr. Jesus Cordova Guerrero
A Screen for Cryptic Epigenetic Variation in Natural Populations of Drosophila melanogaster
Transposable elements (TEs) are DNA segments that can transpose within a genome. This study aims to screen for epigenetic cryptic genetic variation (ECGV) in natural populations of Drosophila melanogaster which have been induced by P-transposable elements. P-transposable elements are a specific class of transposable elements that have high rates of transposition and are associated with genetic defects like high mutation rates and chromosomal abnormalities. Our 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 (Marcey, personal communication) suggests a gene encoding the repressor STAT, a molecule present in the embryonic eye field establishment, is silenced through RNAi-mediated heterochromatization induced by P-transposable elements. Prior PCR analysis indicated presence or absence of P-elements in 40+ lines of wild type flies collected from various worldwide geographical locations. Lines that harbor P-elements are being crossed to JG1, a highly penetrant ee stock, and their F1 progeny intercrossed to establish lines. Lines are being screened for possible cryptic variants that could be revealed as a product of RNAi induced heterochromatization of genes near P-elements.The implications of such crosses is relevant to both genetic and evolutionary biology, as the variation is one of the essential components which natural selection acts upon. This search may uncover what are known as "epialleles” which play a role for variation upon which natural selection can act.
Student(s):
Neha Soogoor, Madison Katz
Faculty Mentor:
Dr. David Marcey
Study of Drell-Yan Z Boson Decay Background in Context of the Search for VBF Higgs at CMS (CERN)
After the Higgs Boson was detected in the Large Hadron Collider (LHC), models that could describe the process of creation of Higgs particles where theorized and tested. One mechanism includes Vector Boson Fusion (VBF) production where the Higgs is created by the fusion of two W or Z boson virtual particles. We are studying the decay of a pair of VBF Higgs into four muons. This research project will develop an algorithm that can separate Monte Carlo samples of these VBF Higgs events from its background processes such as quark diffractive and ZZ boson Drell-Yan production. The aim is to enrich our sample data selection schemes while reducing the statistical contamination from these two background sources. This work was done in collaboration with student Connor Hinthorn. In particular, my part of this collaborative project is to develop a machine learning algorithm that can accomplish the increased statistical significance of the signal process. The data analysis on the samples is done with software we have collaboratively developed that uses the CERN CMS experiment standard Python and C++ based software package. Much of the work to condition our data analysis software was done, as well as setting up our algorithm framework. We have produced and filtered both signal VBF Higgs and background ZZ samples. We have also settled on the data analysis event selection criteria. We will present this work as well as our initial efforts to implement a Neural Network signal/background separation algorithm on our simulated signal and background filtered samples.
Student(s):
Julian Van Geest, Connor Hinthorn
Faculty Mentor:
Dr. Sebastian Carron Montero