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2021 Student Research Symposium - Oral PresentationsLocation: Program: ALLIES in STEM Undergraduate Research Fellowship ron 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, needing to map the binding site to determine which critical contacts will be necessary to maintain a future drug design. Overexpression of Glu445Ala is began from pellets of protein E445A starting from glycerol stock of E445A, which later is overexpressed to contain the bacteria with the desire DNA ready for use purification and crystal’s structure setup. Purification of E445A leads to the separation of cells and DNA of the protein via the FPLC. The FPLC will separate from one run in a HI salt to a second run of desalt of E445A. For crystal set ups of E445A it needs to be desalt in a Final Buffer that contains a higher pH of 8. Kinetics desalts in ITC Buffer which has a pH of 7.5 and contains MgCl2, Hepes, and TCEP. The glycerol amount of ITC buffer begins at 10% but then change to 25% after FPLC. Crystal structure E445A will be binding with AMP, HSC, DfoG, and DfoB. Kinetics would have the binding of ATP and DfoG E445A crystal set ups have been crashing from the protein beginning to precipitate quite faster than other DesD proteins and needing to change the amount of overexpression time and IPTG added to bacteria. Kinetics of E445A have yet to demonstrate the catalytic activity of E445A DesD. E445A is being remade with new DNA plasmids and pellets of the cell gone through overexpression. New pellet of E445A have presented DesD in the protein ready to be use for kinetics and crystal setup runs. An increase of the IPTG use in overexpression also increase the amount of DesD being purify in the FPLC and doubling the number of pellets use. Crystal set ups of E445A will contain higher glycerol percentage to have higher probability of appearing.
Program: Summer Undergraduate Research Fellowship The purpose of the current study was to explore how a defendant’s race/ethnicity and education level would impact a mock juror’s decision when looking at a murder case involving a false confession. A total of 536 MTurk participants were randomly assigned to read a short case file summary highlighting a murder, which varied by the defendant’s race /ethnicity (White / Black / Latino / Asian / Native American / Arab) and their education level (high school diploma / bachelor’s degree / graduate degree). Participants responded to items relating to the credibility of the defendant’s false confession as well as their perceptions and emotional reactions towards the defendant. It was found that participants felt the most anxiety towards an Arab defendant with a Master’s Degree as well as a Native American defendant with a High School Diploma. Participants were neutral when asked about police interrogation techniques and they found the confession to be more believable for defendants with a High School Diploma than a Master’s Degree. It was found that these factors did impact the mock juror’s perceptions and emotional reactions. According to these findings, training for jurors might be necessary in order to reduce negative reactions associated with the identities we studied. Program: ALLIES in STEM Undergraduate Research Fellowship PURPOSE: There is robust evidence presenting higher incidences of hypertension experienced by the African American (AA) population when compared with matched cohorts. Exercise has been shown to reduce the prevalence of hypertension, however, the cardiovascular recovery of exercise is associated with mortality. The purpose of the present study was to investigate the cardiovascular recovery between AAs, Hispanics (HSPs), and Caucasians (CAs). METHODS: VO2max was measured by indirect calorimetry. Body composition was measured by air displacement plethysmography (BODPOD). Brachial blood pressures were captured by automated cuff before exercise, immediately after exercise, and every 2 minutes following exercise for a total of 15 minutes in a supine position. RESULTS: 15 healthy volunteers (n=5 AA, n=5 HSP, n=5 CA) participated in the study. Participants were matched for age and all body composition measures (p>0.05 for all). No statistical effects of time were observed within-groups (p>0.05) or between-groups (p>0.05) for systolic (SBP) and diastolic (DBP) blood pressures. However, the AA maintained “elevated” SBP throughout the recovery phase. The HSP group maintained “elevated” SBP up to 10 minutes following the cessation of exercise. The CA cohort returned to “healthy” SBP within 2 minutes following VO2max. CONCLUSION: Young AA and HSP individuals may show varying recovery from VO2max when compared to CAs. These results need to be confirmed by a larger sample.
Program: ALLIES in STEM Undergraduate Research Fellowship The Drosophila melanogaster compound eyes consists of approximately 750 single eyes (ommatidia) arranged on the sides of the head. Each eye is separated horizontally by a Dorsal-Ventral (D-V) midline, an “equator,” with ommatidia dorsal to the equator having their photoreceptor cells arranged in a trapezoidal pattern that is a mirror image to those of ommatidia ventral to the equator. During development, the equatorial cells are an important signaling center for proper eye formation. Flies were obtained from Dr. Catherine McElwain (LMU) that incorporate an insertion of a white+ (w+) transgene into an as yet unmapped location on the third chromosome. The phenotype of this line is novel in that the w+ transgene’s expression pattern, visible in a w– genetic background and unlike most w+ transgene expressions, consists of low-level w+ (pigmented/wild-type) expression throughout the eye, with a much stronger expression of the transgene in the equatorial region, an expression named “Racing Stripe.” We have obtained variations of this expression pattern, modified in different genetic backgrounds (Pin Stripe, Wide Racing Stripe, Scythe). We have documented this variability, which is suggestive of epigenetic modification that alters the w+ transgenes’s expression by changing the parameters of heterochromatization in the transgene’s genomic locale. We are currently investigating whether its expression can be affected by mutations known to alter heterochromatin status, Suppressors of Variegation (Su(var)s) and Enhancers of Variegation (E(var)s). Crosses of the lines with variable w+ transgene expressions to certain Su(var) stocks show that changes in heterochromatin status can alter the expression of the w+ transgene. We are mapping the genomic position of this transgene in order to investigate its possible relationship with as yet unidentified genes that may also be expressed along the D-V midline. This work holds implications for genome engineering, as this field relies on appropriate expression of transgenes to cure disease or improve agricultural phenotypes. Program: ALLIES in STEM Undergraduate Research Fellowship The Drosophila melanogaster compound eyes consists of approximately 750 single eyes (ommatidia) arranged on the sides of the head. Each eye is separated horizontally by a Dorsal-Ventral (D-V) midline, an “equator,” with ommatidia dorsal to the equator having their photoreceptor cells arranged in a trapezoidal pattern that is a mirror image to those of ommatidia ventral to the equator. During development, the equatorial cells are an important signaling center for proper eye formation. Flies were obtained from Dr. Catherine McElwain (LMU) that incorporate an insertion of a white+ (w+) transgene into an as yet unmapped location on the third chromosome. The phenotype of this line is novel in that the w+ transgene’s expression pattern, visible in a w– genetic background and unlike most w+ transgene expressions, consists of low-level w+ (pigmented/wild-type) expression throughout the eye, with a much stronger expression of the transgene in the equatorial region, an expression named “Racing Stripe.” We have obtained variations of this expression pattern, modified in different genetic backgrounds (Pin Stripe, Wide Racing Stripe, Scythe). We have documented this variability, which is suggestive of epigenetic modification that alters the w+ transgenes’s expression by changing the parameters of heterochromatization in the transgene’s genomic locale. We are currently investigating whether its expression can be affected by mutations known to alter heterochromatin status, Suppressors of Variegation (Su(var)s) and Enhancers of Variegation (E(var)s). Crosses of the lines with variable w+ transgene expressions to certain Su(var) stocks show that changes in heterochromatin status can alter the expression of the w+ transgene. We are mapping the genomic position of this transgene in order to investigate its possible relationship with as yet unidentified genes that may also be expressed along the D-V midline. This work holds implications for genome engineering, as this field relies on appropriate expression of transgenes to cure disease or improve agricultural phenotypes. Program: Swenson Science Summer Research Fellowship
As daily life moves increasingly online, ensuring the security of data traveling over the internet becomes more important. However, when attempting to ensure that data sent over the internet is protected, it is equally important to ensure ease of use for the end user and ease of maintenance for the programmer. The goal of this project is to demonstrate, using a Java-based Client-Server System, that all of these goals can be achieved.
The base of this project, the Client-Server System, is a project that was completed in Fall Semester of 2020 for CSC 335: Software Engineering alongside a team of other students. This was an ideal foundation because many programs and apps are simply specialized client-server systems, thus demonstrating that this method can be used to secure a large percentage of communications over the internet. An interface class was added for encryption, and multiple classes implemented that interface class, each using a different type of encryption. The largest advantage of using an interface is to enforce uniformity and compatibility. A program that uses an interface class in Java will not be allowed to compile if the functions of the interface class are not fully implemented. This means that, when properly implemented, different types of encryption are easily interchangeable, therefore allowing the program to be easily maintained and updated over time and providing little disruption for either the programmer or the user.
The result of this project demonstrates that encryption can be used on any client-server system with little effort on the part of the programmer and no disruption on the part of the user. If a security module is designed in the system from the start, the effect that this addition has on the time to develop and implement the system is minimal. All of the libraries used in this project are readily available in the Java library and an interface class ensures that ease of maintenance and functionality are preserved. Integrating encryption in such a way is invisible to the end user, yet effectively protects their data.
Program: Swenson Science Summer Research Fellowship In 2012, using the largest particle collider in the world at CERN in Switzerland (the LHC), physicists found the Higgs Boson, a particle which had been hypothesized but had eluded detection until then. A reason that this particle is important is because the Higgs Boson is linked to the Higgs Field, a field which imparts most of the physical mass to some of the fundamental particles in our universe, known as fermions. There are 4 main processes that can produce the Higgs through a proton collision (the type of collisions being observed at the LHC), and the only one that has not yet been experimentally observed is called Vector Boson Fusion (VBF). The focus of our research is to produce a machine learning algorithm that can “clean” some of the LHC collision data: accepting VBF Higgs while rejecting background processes (such as ZZ production and decay). In my presentation I will show the comparisons of kinematical variables between prefiltered/filtered data for the Higgs signal and a Drell-Yan ZZ background samples. From these comparisons, we will be able to 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 was then trained on these filtered data and further increase the ratio of Higgs to ZZ events in our sample. I am presenting the work on our attempt to optimize the machine learning algorithm to more reliably select Higgs from the background through a variety of measures. Those measures include: smoothing the input files’ (Ntuples) kinematical variable distributions, experimenting with the structure of our neural network itself (manipulating the number of hidden layers), and experimenting with the exclusion of different kinematical variables from our network’s input, since they may be acting more as a source of noise than as a valuable distinguishing factor between Higgs and background. |
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2021 Student Research Symposium - Poster PresentationsLocation: Program: Ronald E. McNair Research Scholar In 1962, anthropologist Anthony Forge asserted that application of pigment activated the spirituality of cultural figures in Papua New Guinean sculpture, but no study has been done to establish whether the pigment or the act of applying it did so. We will present an X-ray fluorescence (XRF) investigation of possible difference in pigments used in 20 figures from CLU’s permanent collection, ranging from ancestor figures used in sacred ceremonies, to similar wood sculptures used for non-sacred purposes. X-ray fluorescence can qualitatively establish whether pigments are ochre-based or metal-based pigments, and further which metals are present in metal-based pigments. We will follow-up with statistical analysis to determine whether the differences in sacred vs. non-sacred pigments are significant, suggesting that the pigments themselves are associated with sacredness. Future researchers might benefit from utilizing Raman Spectroscopy or FTIR in order to further identify non-metal materials within Papua New Guinean art. Keywords: X-ray fluorescence, Pigment Identification, Papua New Guinea, Infrared Spectroscopy
Program: Swenson Science Summer Research Fellowship Edward L. Martinez Alex Mazaheri Abstract Over the past decade, the interest in marine microfiber research has grown substantially, along with the scientific understanding of its impact on various ecosystems. Microfibers are a type of microplastic that is shed from synthetic fabrics made from materials (i.e. nylon) that frequently pollute various waterways and their inhabitants. Despite the great amount of attention towards research on a multitude of fish and filter feeder species, we decided to shift our focus to Loligo opalescens (California market squid), a tertiary consumer and a keystone species for many marine and land species found along the coast of Southern California. The purpose of this study was to confirm the presence of microfibers in the gill tissue of the squid and to compare the findings with the quantities observed in the squid’s gastrointestinal tract (guts). The number of microfibers were quantified under a light microscope for each sample after the dissection and vacuum filtration of the guts and/or gill tissue. In our preliminary results, a larger quantity of microfibers have been observed in gut tissue samples in comparison to the gill samples observed. Although further research is needed to certify a conclusion, the results suggest that California market squid has been significantly impacted by microfiber pollution present in its ecosystem when compared to similar organisms, such as Argonauta nuoryi (Del et. al.). The squid’s role as a keystone species and the theory of microfiber trophic transfer may also be indicative of the similar impact that other members of its ecosystem may be enduring.
Keywords: microfiber, California market squid, gastrointestinal tract, gills, quantity Program: ALLIES in STEM Undergraduate Research Fellowship A screen for novel sources of cryptic epigenetic variation (CEGV) in Drosophila melanogaster is being conducted in the Marcey lab. CEGV may be a 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 (Marcey, personal communication) posits P transposable element-induced, RNAi-mediated heterochromatization of a gene that encodes a repressor of STAT, a molecule implicated in embryonic eye field establishment. We have predicted that new mutant phenotypes may be uncovered in crosses between ee lines and flies derived from wild, natural populations known to contain P-elements. Such novel mutants might represent RNAi-induced heterochromatization of genes near P-elements. Indeed, several new variants that display characteristics of inducible, epigenetic mutations have been recovered and are being subjected to analysis. Here I report a rescreen of the lines that yielded such variants in order to determine the repeatability of previous work and to determine if the variants represent genuine epigenetic inductions of mutations by components of the ee line or represent new insertions of P-elements into target genes. The following variants have reappeared in crosses of ee to particular wild strains: crybaby, beady, red belly, and Scythe. These results indicate that these heritable variations are inducible by genetic components in the ee strain, and may be concrete examples of cryptic epigenetic variation in nature. These results hold significance for the fields of both molecular and evolutionary biology. Additionally, my work has confirmed P-element induced, conditional dominance of the extra eye mutation, as evidenced by the ee phenotype appearing in the offspring of the crosses of ee to the various, wild type strains that contain P-elements. Program: Ronald E. McNair Research Scholar
The use of social media (SM) refers to interactive technological applications or networks allowing users to quickly communicate content and ideas. In the United States SM has increased at a vast rate yet, the lasting psychological effects due to social media use is uncertain. This study explores the association between social media usage in relation to self esteem and depression. Understanding the relationship between social media and depressions could allow for the development of interventions or preventative strategies for at risk populations which is why I have decided to investigate this. Further neglecting this issue could be detrimental to the next generation’s mental well being which is why it is so crucial to recognize and understand this relationship. Utilizing a quantitative correlational research design along with the Rosenberg self esteem scale we will assess a sample of 200 participants, ages 18-25 years throughout the United States. The participants will be recruited via Amazon Turk and given monetary compensation for their honest participation and time. To further test the association between social media and the psyche, depression will be tested using the Center for Epidemiological Studies-Depression (CES-D) scale. We hypothesize women will exhibit higher levels of depression and lower self-esteem compared to men. We hope this study will allow individuals to become more self aware of how social media use is impacting their mental health, specifically self-esteem and depression. Program: Swenson Science Summer Research Fellowship Age-related Effects on Behavioral Sexual Dimorphism in Squirrel Monkeys Amy Wilkerson and Anita I. Stone Sexual dimorphism (differences between males and females) in morphology and behavior is prevalent among non-human primates. However, less is known about the development of these behavioral sex differences. For example, patterns of dimorphism in activity budgets and social association may differ between adults and juveniles. Squirrel monkeys (genus Saimiri) are small neotropical primates (<1kg) that inhabit tropical forests of Central and South America. These primates live in large social groups, and have a long maturation period over which juveniles can develop sexually dimorphic behaviors. Our study investigated the development of behavioral sexual dimorphism in wild squirrel monkeys (Saimiri collinsi). Specifically, we used a multi-year data set to examine differences in activity budgets and association patterns in adult and juvenile squirrel monkeys. We hypothesized that due to higher reproductive demands, adult females would devote more time to foraging and feeding compared to males, who would invest more in resting and social behaviors. In addition, we expected that adult females would associate with juveniles more than adult males would. We predicted that these sex differences would be more evident in juveniles as they mature; that is, younger juveniles would show little to no sexually dimorphic behaviors, while older juveniles would mirror adult behavioral patterns. Data for this project were collected on two groups of squirrel monkeys, consisting of 40-50 individuals, in Eastern Amazonia, Brazil. Behavioral data were collected during June, July and August of 2017 and 2018. Using 10-minute focal animal sampling, we recorded the individual’s activity and its nearest neighbor within 3m, at every minute. Data were organized in Excel and analyzed in RStudio using unpaired Wilcoxon multivariate tests. We constructed activity budgets and nearest neighbor budgets for males and females, and compared the sexes within each age-class (adults, young juveniles, older juveniles). Our results showed that adult males traveled significantly more than adult females, but there were no sex differences in eating and foraging activities. Adult males spent more time alone and adult females spent more time near juveniles. As predicted, young juveniles showed no behavioral sexual dimorphism. Older juveniles showed some sex differences in behavior, but these did not mirror adult sex differences. This study supports that behavioral sexual dimorphism is present in adult and older juvenile squirrel monkeys, likely due to differences in reproductive investment and energy requirements. Program: ALLIES in STEM Undergraduate Research Fellowship The objective of this research is to determine the quantity of microfibers (MF) within Engraulis mordax and Leuresthes tenuis.The species organs ( digestive tract and gills) were extracted. The extracted tissues were measured and ground into a paste; which was then suspended in a brine solution. The solutions were then filtered through a vacuum pump, and the results were analyzed using light microscopy. When comparing the digestive tract and gills of E. mordax there were significantly more microfibers found in the digestive tract than the gills (t=0.0009, df=99, p≤0.05). Different gills and digestive tract sizes were also used to determine which size contains the most amount of microfibers. When small and large gills were compared, there was no significant difference found between the two gills sizes(t=0.46, df=99, p≥0.05). When small and large digestive tracts were compared, no significant differences were found between two digestive tract sizes (t=0.40, df=99, p≥0.05). Program: ALLIES in STEM Undergraduate Research Fellowship The objective of this research is to determine the quantity of microfibers (MF) within Engraulis mordax and Leuresthes tenuis.The species organs ( digestive tract and gills) were extracted. The extracted tissues were measured and ground into a paste; which was then suspended in a brine solution. The solutions were then filtered through a vacuum pump, and the results were analyzed using light microscopy. When comparing the digestive tract and gills of E. mordax there were significantly more microfibers found in the digestive tract than the gills (t=0.0009, df=99, p≤0.05). Different gills and digestive tract sizes were also used to determine which size contains the most amount of microfibers. When small and large gills were compared, there was no significant difference found between the two gills sizes(t=0.46, df=99, p≥0.05). When small and large digestive tract were compared, no significant differences were found between two digestive tract sizes (t=0.40, df=99, p≥0.05).
Program: ALLIES in STEM Undergraduate Research Fellowship Research shows the existence of large-scale, stable magnetic fields in ~10% of hot, massive (>8x the mass of the Sun) stars. In a subset of these, “centrifugal” magnetosphere (CM) stars, the star is rotating fast enough to keep outflowing material trapped, like swinging a bucket with water in it. Although rare, these magnetospheres have a stable structure that appears as emission in a star’s spectrum, and allows for calculation of the amount and location of material, as well as the star’s rotation period. The material trapped around the star is easily seen in the infrared (IR), where the star is less bright. Raw spectroscopy of one CM star, HD 23478, was taken with the IR spectrometer GNIRS on the 8-m Gemini Telescope (Mauna Kea Observatory, HI) over 9 separate nights. That data includes flats, arcs, and target and telluric spectra. Using these data products, the target and telluric star data were reduced using an astronomical software system, IRAF, with GNIRS-specific reduction routines to extract clean spectra for each night. Tasks were run to prepare various calibrations to clean the data, including building a flatfield, which cleans the images of any optical flaws or issues like dust rings on the mirrors or dead pixels in the detector. Atmospheric effects (due to water vapor) are a significant issue in the IR, and appear as smeared out regions or sharp absorption features, contaminating the data set. A program, XTELLCOR, was used to remove this absorption from the clean spectra, so a full analysis can be performed in the future. The goal is to measure various spectral lines to compare to each night, as well as optical data. Only a few CM stars have been studied with IR spectroscopy, and this is the first study to pair a large data set of both IR and optical spectroscopy, giving researchers a broader image of the effects of the magnetic field on the star and its surroundings. Massive stars are important to understand, as they greatly contribute to the energy and chemistry of their local environment, particularly as they will evolve to explode as supernovae. Program: Swenson Science Summer Research Fellowship Long snapping is found in American football. The goal is to have the ball reach the punter as quickly and accurately as possible so they can kick the ball downfield with little interference from the opposing team. PURPOSE: To describe differences in angular impulse between high school and college athletes during long snapping. METHODS: This study compared high school long snappers (n=5) and college long snappers (n=5). Whole group average age (18.9 ± 1.3 years), years of long snapping experience (5.1 ± 1.65 years), and body mass (99.6 ± 7.5 kg) were measured. One force plate was located under each foot (Kistler, 1200 Hz), and a left sagittal video (Apple, 30 Hz) was taken. Center of mass (CM) was calculated according to de Leva’s body segment parameters (1996). The interval of interest began with a rise in posterior force and ended as posterior force decreased to zero. Sagittal plane resultant force and kinematic data were used to calculate whole body moments about the center of mass. The area under the moment-time curve defined angular impulse and was normalized by mass. Independent t-tests were used to detect differences between college and high school athletes (α = 0.05). RESULTS: Angular impulse (p=0.98, college=0.019 ± 0.015 Nms/kg, high school=0.018 ± 0.033 Nms/kg) and average moment (p=0.61, college=113.99 ± 75.63 Nm, high school=133.46 ± 191.27 Nm) were similar between groups. There were differences in the distance from CM to center of pressure (p=0.02, college=0.79 ± 0.015 m, high school=0.84 ± 0.035 m), and in time (p=0.045, college=0.153 s ± 0.026, high school=0.139 s ± 0.026). CONCLUSION: The whole body angular impulse observed was positive, rotating the body counterclockwise to throw the ball posteriorly between the legs. There is a difference in how the two groups generated this motion. High school players had longer position vectors but took less time in the push phase compared to college players. Future research analyzing snap performance as it relates to long snap kinetics could provide insight into more effective strategies to long snapping. Program: John Stauffer Research Fellowship in the Chemical Sciences Artificial Neural Networks (ANNs) are mathematical computing systems that imitate how our brain analyzes and processes information. ANNs can be trained to classify information and recognize patterns in a complex data set. Remarkably, 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 developed in C++ to compare with prior results from Matlab to purposely optimize the predictive power of ANNs toward estimating the potential toxicity of selected herbal medicine via chemical structure and function. C++ was utilized to modify multiple parameters concomitantly, which are usually difficult to implement in Matlab. The ANN model was created with one hidden layer. Twelve data samples were chosen randomly for the training stage, and six data samples were chosen in the testing stage. The model was trained based on a linear function and compared to experimental results. Subsequently, the model performance was observed under percentage and square errors between the predictive and experimental responses. The average percentage error is 20.76, and the mean square error was 1.69237E+11. As a result, the C++ platform model will be further optimized to improve the accuracy of the predictive results and employ both platforms to access the toxicity of herbal medicine via chemical structure and LD 50 values. Program: Ronald E. McNair Research Scholar Siderophores are biosynthesized and excreted by microorganisms to find iron. Many siderophores are peptides that are biosynthesized by members of the nonribosomal peptide synthetase (NRPS) multienzyme family, which is also responsible for making a majority of microbial peptide antibiotics. Several other siderophores are not peptides but consist of alternating diamine and dicarboxylic acid building blocks linked by amide bonds; these are synthesized by pathways that include an NRPS-Independent Siderophore (NIS) synthetase. Desferrioxamines are well-known members of this nonpeptide hydroxamate siderophores, in which the last three bonds are made by NIS synthetase Desferrioxamine D (DesD). NIS siderophores are increasingly associated with virulent, pathogenic bacteria, and DesD is a model for a new antibiotic class targeted at NIS synthetases. To facilitate IC50 drug testing, we are developing a binding assay utilizing isothermal titration calorimetry. DesD variants will be overexpressed in E. coli and purified using Ni-affinity column chromatography. Isothermal titration calorimetry experiments will be performed using a Microcal PEAQ ITC instrument in triplicate to determine binding affinity. We have established that binding studies will be performed with the proteinat 20 μM in the cell and 200-300 μM cofactor in the syringe. Thirteen injections were done with various volumes with 2 minute intervals between and covering stoichiometric ratios from 0-3. Future binding studies will utilize variant R306A pre-bound to cofactor to test the substrate tolerance of DesD using this newly established protocol. Program: ALLIES in STEM Undergraduate Research Fellowship
Legionella pneumophila is a gram-negative, bacillus bacteria that is the causative agent of Legionnaires disease. This disease is a type of pneumonia that affects immunocompromised individuals (elderly, AIDS, etc.). There are more than 50 species of Legionella and 24 of them afflict humans. Legionella pneumophila is the most infectious but not the most abundant in the environment. This bacteria is prevalent in freshwater systems, including misters and air conditioning units. Legionella usually attempts to live within protozoans and in biofilms, which provide more protection than free-living bacteria. Legionella infect humans by inhalation and infection of alveolar macrophages, assisted by a type II secretion system. This system aids in motility, attachment, and many other functions in order to infect the host cells. The proteins that this system secretes are important in virulence and are being studied intently. There are more than 25 proteins involved in the T2SS, and many have different functions. We will be attempting to determine some of the structure and function of a few novel substrates that aid in the pathogenicity of the bacteria and its T2SS. This will be done by using bioinformatics software, including NCBI to identify sequence similarity and domain identification, String for protein-protein interactions, Artemis for gene localization, and OligoEvaluator for primer design. Interactions between genes were displayed in most substrates via String. Of particular interest, the substrate nttB returned zero interactions, posing the question of the true role of nttB. To further study the roles of T2SS effectors nttB, ChiA and other genes were isolated via PCR. Current work includes cloning and expression T2SS effectors using the plasmid vector (pet45b+)and E. coli cells. This will allow us to further observe the structure/function of select T2SS effectors. Future studies can be conducted in order to determine the interactions between the novel and the better known substrates of the T2SS via in silico protein modeling, gene location/interaction, and biochemical assays. Program: Swenson Science Summer Research Fellowship
Triathletes often complain about lower limb discomfort when running after cycling (Quigley,1996). Several studies have found differences in muscle activation (Chapman, 2009), kinematics (Rendos et al., 2013), and kinetic cost (Millet, 2001) during the transition run. These differences were also found to be more severe in less experienced triathletes (Chapman, 2008). PURPOSE: This study aimed to determine the kinetic differences between baseline and transition runs of inexperienced triathletes. METHODS: Twelve novice triathletes age: 29.4±12.15 y, mass: 71.2±10.3 kg, weekly running mileage: 24.4±16.7 mi/week volunteered to participate. Athletes completed a 20 min run during session 1, and a 20 min bike followed by a 20 min run during session 2, each conducted at 75-80% effort level. Cycling sessions occurred on a stationary trainer (Wahoo Kickr snap) allowing athletes to use their own bike or have a standard bike fitted to their preferred geometry. Running sessions occurred on an outdoor loop (~370m) where subjects passed through timing gates (Brower) and over two force plates (Kistler,1200 Hz). Sagittal view, right side video (Sony, 240 Hz) was also collected. Each running session was broken into 4 five-minute blocks. Duration of foot contact with the ground determined stance phase, while braking (-RFY) and propulsive phases (+RFY) were also defined. A two-way repeated measures ANOVA was used to determine differences between run type and time block (α = 0.05). RESULTS: During the stance phase, there was a main effect for time block of anterior linear impulse (F=3.03, p=0.043) and average +RFY (main effect F=3.37, p=0.03) and contact time (F=3.11, p=0.039). Similarly, there was a main effect for time of propulsive phase linear impulse (F=7.94, p<0.001) and average +RFY (F=7.95, p<0.001). Although post-hoc analysis did not reveal significant differences, it appears the later time blocks decreased anterior linear impulse as RFY decreased. CONCLUSIONS: Athletes displayed similar running kinetics between the baseline and transition run, however differences did occur between time blocks. This suggests that athletes fatigued similarly between the two run types. These findings may indicate that self-reported discomfort in the transition run may not be detected by measures of whole-body kinetics.
Program: Swenson Science Summer Research Fellowship Research has studied upper-body kinematics (Balentine 2020) and whole-body kinetics during the American Football long snap (Goldstein 2020). There are no studies describing lower extremity (LE) joint kinetics during this movement. PURPOSE: This study aimed to understand how players coordinate LE torques while completing a long snap. We hypothesized there would be plantarflexor torques at the ankle and extensor torques at the knee and hip. METHODS:Subjects included college-aged football players (n=5) and high school football (n=5) players with >2years experience. All subjects provided informed consent per local IRB. Average age of participants was 18.9±1.3 years, average mass was 99.57±7.49 kg, and average experience was 9.0±2.57 years. Sagittal plane video (30 Hz) was collected and digitized on the left side. Force data was collected with one foot on each force plate (Kistler, 1200 Hz). Torques at the ankle, knee, and hip were calculated using inverse dynamics. RESULTS: The group average extensor torques were generated at the hip (203.3±60.9 Nm) and plantar flexor torques were generated at the ankle (173.1±40.9 Nm) for all subjects[PT1] .[FC2] However, flexor knee torques were found for college athletes (55.4±50.2Nm), while an extensor knee torques were generated by high school athletes (-28.9±22.7Nm).[PT3] Knee joint torque magnitude was relatively small compared to the ankle and hip torques. This may occur because the posterior two-jointed muscles that cross flex the knee also work to extend the hip (e.g. biceps femoris) and plantarflex the ankle (e.g. gastrocnemius). The extension/plantarflexion at the hip and ankle may prioritize these posterior two-jointed muscles, while sacrificing extension torque at the knee in the college athletes. Whereas high school athletes may rely on more extension torque at the knee to successfully complete the long snap. CONCLUSIONS: Identifying LE torques provides information in determining joint coordination strategies of college and high school athletes during a long snap. This information can be helpful for athletes to target specific muscle sets and joint coordination strategies during training for better long snap performance. Program: Swenson Science Summer Research Fellowship Research has studied upper-body kinematics (Balentine 2020) and whole-body kinetics during the American Football long snap (Goldstein 2020). There are no studies describing lower extremity (LE) joint kinetics during this movement. PURPOSE: This study aimed to understand how players coordinate LE torques while completing a long snap. We hypothesized there would be plantarflexor torques at the ankle and extensor torques at the knee and hip. METHODS:Subjects included college-aged football players (n=5) and high school football (n=5) players with >2years experience. All subjects provided informed consent per local IRB. Average age of participants was 18.9±1.3 years, average mass was 99.57±7.49 kg, and average experience was 9.0±2.57 years. Sagittal plane video (30 Hz) was collected and digitized on the left side. Force data was collected with one foot on each force plate (Kistler, 1200 Hz). Torques at the ankle, knee, and hip were calculated using inverse dynamics. RESULTS: The group average extensor torques were generated at the hip (203.3±60.9 Nm) and plantar flexor torques were generated at the ankle (173.1±40.9 Nm) for all subjects. However, flexor knee torques were found for college athletes (55.4±50.2Nm), while an extensor knee torques were generated by high school athletes (-28.9±22.7Nm). Knee joint torque magnitude was relatively small compared to the ankle and hip torques. This may occur because the posterior two-jointed muscles that cross flex the knee also work to extend the hip (e.g. biceps femoris) and plantarflex the ankle (e.g. gastrocnemius). The extension/plantarflexion at the hip and ankle may prioritize these posterior two-jointed muscles, while sacrificing extension torque at the knee in the college athletes. Whereas high school athletes may rely on more extension torque at the knee to successfully complete the long snap. CONCLUSIONS: Identifying LE torques provides information in determining joint coordination strategies of college and high school athletes during a long snap. This information can be helpful for athletes to target specific muscle sets and joint coordination strategies during training for better long snap performance. Program: Undergraduate Research The study of protecting groups in organic synthesis is essential when it pertains to selective chemical reactions that contain multiple reactive functional groups, such as the hydroxylation of alkanes with borane in which borane can react with both the alkane and the carboxylic acid group if there is one present. In order to select a protecting group for the carboxylic acid group, there are three things to factor in. The protecting group has to be installed in a way that is able to produce the protected carboxylic acid in good yield, it needs to be stable under specified condition reaction, and it must be selectively removed in a way that will not affect the other functional groups. Our research focuses on developing a protecting group for a carboxylic acid via the formation of an ester. This is a well-known process; however, one of the most efficient methods of esterification is done via the reaction of carboxylic acids in the presence of diazomethane, a highly explosive reagent. Another method is through a reaction between carboxylic acids and benzyl chloroformate. The drawback to this technique is that the resulting benzyl alcohol isn’t stable under various conditions. In this experiment, we will be synthesizing two different protecting groups, one where R is an electron donating group and one where R is an electron withdrawing group, for a carboxylic acid without the use of diazomethane. This process is envisioned in three stages, synthesis of the carboxylic acid protecting group, followed by the synthesis of a functionalized ester. The carboxylic ester will then undergo a series of stability tests under various conditions including hydrochloric acid, reducing agents, and even under hydrogenolysis. It is also expected that carboxylic esters will be stable under all conditions except for trifluoracetic acid (TFA), where it will instead cleave the protecting group. These studies can then be used to further the progress made on anti-cancer therapies. Program: Summer Undergraduate Research Fellowship There are shifts in jury decisions when the defendant identifies within a marginalized community, leading to longer sentences, harsher convictions, and disproportionate prison populations when compared to national ratios (Pew Research Center, 2020). Purpose: The purpose of the study is to explore how the intersectional identities of race/ethnicity and religion of a defendant can impact the decision that mock jurors make in a murder case with different types of DNA evidence. Methods: Five hundred thirty eight subjects (52.6% male, 47% female) aged 19 to 79 years participated in this study through Amazon’s Mechanical Turk. Participants were randomly assigned to a murder case that varied in the defendant’s religion, race/ethnicity, and the type of DNA evidence given. All were instructed to judge the case as if they were on a jury. Then each participant was instructed to answer questions regarding verdict/sentencing, interpretation of the DNA evidence, and their emotions/perceptions towards the defendant. A 3-way ANOVA was used to analyze the impact of religion, race/ethnicity, and DNA evidence on the dependent variables. Results: Participants felt marginally more anger towards the White Muslim defendant as compared to the White Christian defendant. Participants felt more confident that the Black Muslim defendant committed the crime rather than the Black Christian defendant. Participants felt that the Black Muslim more likely fit the crime as compared to the Black Christian, as suggested by differences in the perceived reliability of the presented DNA evidence. Conclusion: The current study demonstrated bias towards a defendant based on their race/ethnicity and religion. In order to best achieve justice in the court system, jurors must be better educated in identifying their own pre-existing biases and given greater guidance through the jury process. Attorneys who enact jury selection should be further informed on how to spot potential biases in jurors during the voir dire process and make this their priority. Program: Ronald E. McNair Research Scholar RNA thermometers can turn gene expression on or off, depending on temperature. A specific type of thermometer, ROSE-like RNA thermometers, increase the expression of downstream genes in response to heat. ROSE-like RNA thermometers have been found in a few bacteria, but the number and how prevalent they are is unknown. The interest in this study revolves around the discovery of proteins that may be regulated by these RNA thermometers. Using RNArobo, a bioinformatics tool, potential thermometers DNA polymerase III subunit theta (PoLIII) and phosphoadenylyl-sulfate reductase(PsDS) were found directly upstream of the proteins. PoLIII plays a role in the duplication of chromosomal DNA and PsDS is an enzyme involved in the biochemistry and metabolism of adenosine. Thermometers were amplified by polymerase chain reaction (PCR) to attach ends that were complementary to a reporter plasmid containing GFP and RFP in order to perform HiFi Assembly. In order to test potential thermometers in bacteria, cloning was performed with a HiFi DNA Assembly kit and heat shock transformation. Thermometers were inserted downstream of GFP and upstream of RFP in order to measure expression by fluorescence. Colony PCR found that the insertion of thermometers had been successful. Clones were grown overnight, then incubated at different temperatures to test for a change of expression. Fluorescence of the clones was measured, there was no noticeable differences in gene expression between the conditions that were tested, however, additional conditions will be tested in the future. Program: Ronald E. McNair Research Scholar This research explored in depth the experiences of those living within underserved communities impacted by economic disparities to better understand how those disparities impact mental health and well-being among individuals, relationships and the community. In particular, participants were asked to reflect on how economic disparities and access to resources such as educational accessibility, healthcare, businesses meeting daily living needs (e.g. grocery stores, financial support, exercise facilities) and social support within the community affect them and the community as a whole. The study also comprised data on how the effects of COVID-19 has impacted these communities in the past year. The cost of living, sustainability crisis, and the differing wage gaps across racial groups of color compared to their white counterparts which all contribute to the experiences of chronic anxiety and external stressors within people of color in these communities (Brower & Michener, 2020), will be taken into consideration. By using nationwide ethnographic surveys to gather participants’ perspectives, this mixed method study aims to provide contextual analysis of the impact of these systematic disparities to better understand how to reduce the negative impacts of these discrepancies within underserved communities now and in the future Program: ALLIES in STEM Undergraduate Research Fellowship Antibiotics are inhibitors targeted towards essential biological functions, functionally stopping the reproduction of the bacteria, or killing the bacteria outright. Desferrioxamine Synthesis Protein D (DesD), a nonribsomal-peptide-synthase-independent siderophore (NIS) synthase protein from the species Streptomyces coelicolor, catalyzes the last three steps in a pathway that makes a siderophore called desferrioxamine E. DesD is a drug target in our research because it is a model for other NIS synthase family members, which are present in some of the most virulent and pathological bacteria, like MRSA and Anthrax. Understanding DesD and designing an inhibitor for it will hopefully lead to a new class of antibiotics. Previous work in the Hoffmann Lab determined the structure, and kinetic turnover of wild-type DesD. This work revealed that wild-type DesD bound fully with the nucleotide substrate in the active site of the dimer. We propose a binding study to quantify the binding interaction with DesD, but will need to use variant R306Q, which showed catalytic inactivity when performing kinetic assay, to avoid catalysis. We hypothesize that the nucleotide will fully bind in both active sites of the dimer, but the substrate dfoG or HSC will bind with substrate in only half of the active sites (a cooperative effect). The key methods in determining the binding of R306Q are overexpression and purification of the protein, as well as isothermal titration calorimetry (ITC). The protein is overexpressed in E. coli, then purified using Affinity Chromatography. After these first two steps we use ITC to determine the binding thermodynamics in triplicate. We have performed binding assays with different concentrations of ATP and 10 mM of R306Q and got preliminary results confirming the results with the wild-type DesD. We have also begun the developing the binding conditions with the product desferrioxamine E limiting, along with ATP, and 10mM of R306Q. Further research will be binding studies with substrate including desferrioxamine G and HSC with variant R306Q. Program: ALLIES in STEM Undergraduate Research Fellowship Freshwater coastal river corridors affect global biochemical processes, most notably carbon cycling. Sea level rise is expected to move tidal ends of coastal river corridors into freshwater regions, exposing freshwater habitats to high salinity levels. Previous studies have found that increasing salinity levels have a detrimental effect on the freshwater microbial communities, but the findings are inconsistent due to a lack of understanding of the underlying microbial mechanisms. The purpose of this study was to evaluate the composition, structure, and function of microbial communities in river sediments at the freshwater end of coastal river corridors. Field sediments were collected from Washington, Texas, Massachusetts, and California. Microbial DNA was extracted, and metagenomes sequenced prior to the start of my research project. Metagenome sequence analysis was conducted on The Department of Energy Systems Biology Knowledgebase (KBase), a software and data science platform. The three metagenomes were individually quality assessed, trimmed, assigned taxonomic classifications, scaffolded, and binned. The bins were assessed for quality and completeness then assembled. Taxonomy was assigned to specific metagenome-assembled genomes (MAG)and finally annotated. The annotated assemblies were evaluated for coverage of metabolisms including short-chain fatty acid and alcohol metabolism, carbohydrate-active enzymes (CAZY), and nitrogen metabolisms. The taxonomic classification of all samples resulted in the identification of novel bacteria, with the Eel River sample resulting in the highest percentage of reads classified at the genus level. The microbes demonstrated functional characteristics including antibiotic resistance, methane metabolism, metal reduction and the expected metabolic abilities for their environment. The microbes also demonstrated possible adaptations to salt stress. Comparative evaluation of the MAGs will be performed to detail location-specific functional potential characteristics. Program: John Stauffer Research Fellowship in the Chemical Sciences The main focus of this research was to examine both the theoretical and experimental aspects to elucidate the metabolic breakdown of the natural medicines or herbal remedies with their respected parent compounds or the active and reactive ingredients. There were two methodologies broken into smaller parts to help answer our research question. The first part of the method was theoretical, in which it was predicted the schematic mechanism of parent, active, and reactive compounds via cytochrome P450 metabolic breakdown. The cytochrome P450 is an metabolite enzyme in the liver that helps break down compounds. The second part of the experimental aspect focused on extraction using varying organic solvents and different separation techniques such as thin layer chromatography (TLC) and the gas chromatography mass spectroscopy (GC-MS). The different organic solvents used in this experiment were hexane, dichloromethane, diethyl ether, methanol, and dimethyl furan. The data was expected to show the products from the theoretical aspect will have the same results as the instrumental analysis, such as capillary electrophoresis (CE), GC-MS, and high-performance liquid chromatography (HPLC). The thin layer chromatography(TLC) plate showed the polarity of the active and reactive compounds present in the mixture from both the cerium molybdate stain and the potassium permanganate stain. For future work, HPLC will be used as an additional separation method to help quantify, identify, and separate these compounds. In addition, we will either work to find more qualified TLC ratios of each natural or herbal remedies’ parent compound or the active and reactive ingredients.
Keywords: Natural or herbal remedies, gas chromatography mass spectroscopy (GC-MS), thin layer chromatography (TLC), theoretical, experimental, high-performance liquid chromatography (HPLC), cytochrome P450, active ingredients, reactive ingredients Program: Ronald E. McNair Research Scholar Do people remember items better when they say them out loud as opposed to internally? This study investigates the idea that memory scores will be better for people when they rehearse out loud as opposed to rehearsing internally. People who speak aloud are using more processing (motor, and also auditory) as opposed to people who don’t speak aloud. To test this idea, we will ask participants to remember the numbers that are shown in front of them. They will either be told to read and rehearse aloud or in their head. Then after 10 seconds or 5 minutes (depending on if they are in the long term group or short term) they will be prompted to say the numbers they remember. In a second experiment, instead of having to remember digits, participants will be asked to remember coffee orders. We hope to show that participants that read aloud will score higher on memory than those who read in their head. In general, these results can be used by humans as another way to retain information. We predict that individuals that repeat the stimulus allowed will have better retention than the individuals that repeat the stimulus in their head. Program: The Louis W. and Gladyce Foster Family Foundation Summer Fellowship in Religion
Female physicians have a 140% greater likelihood of experiencing depression, anxiety, and suicidal ideations than the average female. Male physicians have a 70% greater likelihood of experiencing these same obstacles than the average male. The current pandemic contributed to the dramatic increase of this statistic. Even under these conditions, medical providers continue to put patient care as the top priority; the problem is setting the second priority: self-care for the medical providers who experience “moral distress”. Studies define moral distress as the emotional state that arises when the ethically correct action to take conflicts with the task one must undertake. Studies also show that faith practices and spiritual routines build resilience to moral distress. Over time, such religious and spiritual interventions significantly reduced clinical symptoms like anxiety. This study interviewed current physicians, current medical and residency students, undergraduate students interested in healthcare careers, and hospital chaplains. These individuals answered questions including what faith practices and routines, if any, helped alleviate their moral distress. 41% of participants reported using prayer, 25% used scripture reading, 16.7% used grounding methods, and 16.7% used meditation practices to counter moral distress. Using these self-reported results, and prior studies on the success of faith practices in building resilience, a follow-up study will construct an interventionist curriculum for undergraduate students preparing for the medical profession. This curriculum will teach the students to use a variety of faith practices to build habits of resilience, to equip them with the means to address moral distress. Program: ALLIES in STEM Undergraduate Research Fellowship The variably expressed extra eye (ee) mutation in Drosophila melanogaster produces head deformities that can include missing and/or duplicated bristles and head cuticle, and in its most severe expressions, supernumerary compound eyes and antennae. In addition to variable expression, the mutation possesses several other exotic features: ee is both incompletely penetrant and conditionally dominant. Marcey (personal communication) has developed a P-element induced, RNAi-based, epigenetic model to explain the exotic genetic behavior of ee that proposes a downregulation of a negative regulator of the JAK-STAT signaling pathway. JAK-STAT signaling is a potent inducer of dorsal eye field development, and overexpression of JAK in developing heads can produce extra eyes similar to the ones elicited by ee (Harrison, et al., 1995). This project aims to generate a line of ee flies that display very high penetrance of the mutation. This is being accomplished by a series of positive selections by breeding ee-bearing flies of each generation and monitoring the resulting penetrances. Starting with a line of ee flies ( JG1^SEL^2), both males and virgin females that demonstrate the extra eye mutation are collected and crossed. Flies will be screened for wild-type vs. extra eye mutation phenotype and scored accordingly. For each generation, only the flies that demonstrate the extra eye mutation are crossed to produce the next generation. Thus far, penetrances have increased from 45% in generation 1 to 63% in generation 3. Penetrance data from subsequent generations will be presented. Obtaining an extra eye line with very high penetrance of the mutation will aid a variety of experiments aimed at elucidating the genetic basis of extra eye. Discovering the mechanisms of developmental processes in Drosophila melanogaster has provided key insights into animal development in general, and human development in particular. For this reason, this model organism continues to play an important role in biomedical research. 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. Program: ALLIES in STEM Undergraduate Research Fellowship The variably expressed extra eye (ee) mutation in Drosophila melanogaster produces head deformities, which in severe expressions result in ectopic, supernumerary compound eyes. In addition to variable expression, the mutation possesses several other exotic features: ee is both incompletely penetrant and conditionally dominant. Marcey (personal communication) has developed an epigenetic model to explain the exotic genetic behavior of ee. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a signaling molecule implicated in embryonic eye field establishment. This project is testing the hypothesis that selection for increased penetrance of ee will yield a line, enriched for enhancers of the mutation, that displays very high penetrance values and that can be used to study the mutation more effectively. This selection is being accomplished by a series of positive selections over a number of generations. Beginning at generation 1 with a line of flies displaying approximately 45% penetrance, flies have been scored for the presence or absence of ee mutant phenotypes, the penetrances recorded, and virgins that bear the mutant phenotype mated to begin the next generation. Thus far, penetrances have increased from 45% in generation 1 to 63% in generation 3. Penetrance data from subsequent generations will be presented. Obtaining an extra eye line with very high penetrance of the mutation will aid a variety of experiments aimed at elucidating the genetic basis of extra eye. Discovering the mechanisms of developmental processes in Drosophila melanogaster has provided key insights into animal development in general, and human development in particular. For this reason, this model organism continues to play an important role in biomedical research. Incomplete penetrance characterizes many human disease genes and the study of this phenomenon in a model organism may therefore bear import for biomedical studies. Program: John Stauffer Research Fellowship in the Chemical Sciences DesD performs a unique and understudied chemistry and understanding the mechanism through which it occurs is valuable as a model for the NIS Synthetase family of enzymes. The intent of this study was to determine the role of H443 in your proposed reaction mechanism by ITC analysis. Preliminary analysis of the kinetic data shows the rate of the first reaction step or k1/k-1. The data showing only part of the kinetic turnover of wild type DesD. Thus, supporting our hypothesis that His443 is necessary for catalytic turnover of the substrate. In future work we will attempt to isolate the intermediate from the reaction vessels of the partially complete synthesis. Program: Ronald E. McNair Research Scholar Women in history have often been misrepresented or erased because of their gender. Regarding Latin America, specifically Mexico and the Spanish Conquista, one of the more prominent female figures that stands out is La Malinche. Generally when La Malinche is presented in historical texts she’s portrayed as a villain, victim and, in rare cases, as a heroine. Neglecting the struggles and challenges La Malinche faced as a woman limits how much she can truly be understood in her contributions to the Spanish Conquista despite her impediments. This study focuses on La Malinche as more than a folktale; feminist theories from the West and Latin America are used to examine how she was percieved and her contributions in the Spanish Conquista. Feminist theories allow us to take into account the realities and obstacles that she lived through, even though La Malinche’s past explains how she met the Spaniards and why she decided to help them. La Malinche and the role that she played in the Spanish Conquista was notable and should be acknowledged in order to have an accurate representation of women in Latin America’s history. Program: Swenson Science Summer Research Fellowship Abstract:
The extra eye mutation (ee) in Drosophila melanogaster is incompletely penetrant, conditionally dominant, and variably expressed; each of these factors lead us to believe that this mutation is caused by epigenetic mechanisms. An epigenetic model (Marcey, personal communication) hypothesizes that the ee mutation is due to transcriptional, epigenetic silencing of a gene, or multiple genes, near P-transposable element insertions. These insertions activate the RNAi pathway, which silences genes through heterochromatization due to the presence of P-elements. Due to P-elements insertion in the DNA, during transcription double-stranded RNA is formed by the sense and anti-sense RNA strands that are present, and double-stranded RNA is formed at every location that the P-element is located in the DNA. We believe there is a P-element located near genes that regulate the formation of eyes in Drosophila melanogaster that are the target of such RNAi-induced heterochromatization, which could potentially lead to head deformities such as extra eye. The flanking genomic sequences of P-element insertions in multiple lines have been acquired by means of Splinkerette PCR and sequenced via next generation DNA sequencing. Here I report the genomic positions of P-element insertions in one ee line, as well as an update to the previous protocol to the research which allows us to perform the process much faster. This research is vital to the lab’s research as it increases our understanding of epigenetically induced mutations such as extra eye as well as other mutations that may possibly be caused by P-transposable elements. Program: ALLIES in STEM Undergraduate Research Fellowship Introduction: Low-to-moderate intensity aerobic exercise has been reported to elicit changes in systemic hemodynamics. Recent evidence suggests that the cerebral circulation reacts independently to systemic circulations to the same physiological stimuli. The aim of this is to determine the influence of high-intensity aerobic exercise on common carotid artery (CCA) hemodynamics. Methods: Hemodynamic measurements were recorded before and following the cessation of a maximum oxygen uptake test (VO2max). One minute video of the CCA by Doppler ultrasound were recorded and used to determine peak systolic velocity (PSV), end diastolic velocity (EDV), time averaged mean blood velocity (TAMEAN), timed average maximum velocity (TAMAX), pulsatility index (PI), and resistance index (RI). CCA diameters were calculated by commercially available vessel tracking software. Results: A total of 29 individuals, 14 male and 15 females, participated in this study. Following the cessation of exercise, PSV (p<0.001), TAMAX (p=0.0085), RI (p<0.001), and PI (p=0.0032) significantly increased whilst the minimum diameter (p=0.005), and maximum diameter (p=0.020) decreased. Conclusion: The results show hemodynamic changes in the CCA following VO2max exercise. Specifically, increases in vascular resistance are likely due to the reductions in arterial diameter, which may be evident downstream of the CCA. Program: ALLIES in STEM Undergraduate Research Fellowship
A microfiber is a microscopic strand of plastic measuring under 5 μm long. Clothing made of synthetic fabrics such as polyester, nylon, and spandex are a main source of microfiber pollution. Thousands of plastic strands fall off our clothing during each washing machine cycle. The fibers are too small to be captured by our water treatment centers so they travel through our rivers and ultimately make their way to the ocean. In the ocean they can be 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 compared to the gills of the Anchovy fish, Engraulis mordax. In comparing the number of microfibers from the digestive tract and gills, it was expected there would be more fibers in the digestive system. This would be due to the fish ingesting more fibers than would pass through their gills. To test this hypothesis, the gills and digestive tract were removed and mashed up in a mortar and pestle. Both mashed organs were separately placed into a saltwater solution and allowed to sit for 24 hours. Leaving the samples in the saltwater allowed the microfibers to float to the top of the beakers, ensuring they would be captured on the filter paper. The contents of each beaker were filtered using a vacuum pump and examined under a microscope. The fibers 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. After conducting a t-test it was found that the results were statistically significant with a p-value of 0.00093 (p < 0.05). It is important to note that of the one hundred fish that were sampled, all contained multiple microfibers. The quantity of microfibers found in each fish shows the extreme pollution of the ocean these fibers have caused which may be damaging to the fish as well as their ecosystem. Program: ALLIES in STEM Undergraduate Research Fellowship A microfiber is a microscopic strand of plastic measuring under 5 μm long. Clothing made of synthetic fabrics such as polyester, nylon, and spandex are a main source of microfiber pollution. Thousands of plastic strands fall off our clothing during each washing machine cycle. The fibers are too small to be captured by our water treatment centers so they travel through our rivers and ultimately make their way to the ocean. In the ocean they can be 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 compared to the gills of the Anchovy fish, Engraulis mordax. In comparing the number of microfibers from the digestive tract and gills, it was expected there would be more fibers in the digestive system. This would be due to the fish ingesting more fibers than would pass through their gills. To test this hypothesis, the gills and digestive tract were removed and mashed up in a mortar and pestle. Both mashed organs were separately placed into a saltwater solution and allowed to sit for 24 hours. Leaving the samples in the saltwater allowed the microfibers to float to the top of the beakers, ensuring they would be captured on the filter paper. The contents of each beaker were filtered using a vacuum pump and examined under a microscope. The fibers 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. After conducting a t-test it was found that the results were statistically significant with a p-value of 0.00093 (p < 0.05). It is important to note that of the one hundred fish that were sampled, all contained multiple microfibers. The quantity of microfibers found in each fish shows the extreme pollution of the ocean these fibers have caused which may be damaging to the fish as well as their ecosystem. Program: ALLIES in STEM Undergraduate Research Fellowship Microfossils are an important tool in reconstructing past climate records. Foraminifera (single-celled marine organisms) are one of the most important paleoclimate tools because they have existed and evolved since the Cambrian period (541 million years ago (Ma)) and are widespread and abundant. More specifically, the tests, or shells of foraminifera can be used to reconstruct ocean temperature and sea levels of the past. This is possible because foraminifera build their tests in equilibrium with the surrounding ocean water and therefore provide a snapshot of the ocean chemistry during their lifespan. The oxygen isotope ratios (δ18O) measured in the tests of foraminifera provide ocean temperature information. Higher δ18O values represent cooler time periods and lower δ18O values indicate warmer time periods. These intervals are called glacial-interglacial cycles. When reconstructing these climate histories through geochemical techniques, it is important to use pristine, well-preserved foraminifera to limit inaccuracies. When a poorly-preserved foraminifera is used, the δ18O signature can be offset leading to skewed climate reconstructions. The amount of “offset” depends on the degree of preservation. Previous research by Poirier et al. (2021) quantifies the effects of different levels of test preservation on past climate records. Three types of preservation are defined: 1) glassy (nearly perfect preservation); 2) pseudo-frosty (moderate preservation); and 3) frosty (poor preservation). It is expected to see more poorly preserved microfossils during the interglacial (warmer) time intervals. In this study we expand on the work of Poirier et al. (2021) by increasing the sampling resolution during the Pleistocene (2.58 Ma-0.0117 Ma) at Site 846 (Pacific Ocean). 17 sediment core samples are washed through a 63 micron sieve to remove fine clays and foraminifera are analyzed under a microscope. The specific foraminifera taxa of interest are Cibicidoides and Uvigerina. These taxa are chosen due to their abundance within these samples and popularity in geochemical recontrustions. All specimens of Cibicidoides and Uvigerina in a sample are picked out and categorized by the level of preservation and breakage to determine a specific Foraminifera Preservation Index (FPI) value for each sample. Our preliminary results show more frosty and pseudo-glassy foraminifera which indicates an overall poorer preservation and is expected in an interglacial period. This is likely due to a more corrosive water mass in the Pacific ocean during this time period. Future work includes generating FPI and δ18O data and comparing these results with data at Site 926 in the Atlantic Ocean. This work is important because the FPI helps determine how much preservation can alter a δ18O value. A poorly preserved foraminifera can under or overestimate paleo temperature and paleo sea level records. As preservation is studied more, the accuracy of climate data increases. Program: Swenson Science Summer Research Fellowship Modeling Nickel Superconductors Matthew Hickerson Dr. John Deisz
Superconductors are materials that have zero electrical resistance for temperatures below the transition temperature. Many materials containing copper and iron are known to be superconductors. Since nickel is near these elements in the periodic table, this has led to a search for nickel-based superconducting materials which has recently been successful. Purpose: Nickelates - compounds that contain nickel and oxygen atoms bound together - have been shown to display superconducting properties at low temperatures, but the properties of nickelates suggest they may be a potential material for superconductivity at elevated temperatures. The purpose of this study was to model the subatomic and atomic properties of nickel compounds or nickelates to further characterize their properties so that researchers can have a better understanding of how these materials work and potentially be improved. Methods: I simulated a model for nickel compounds on a computer. I worked with square and cubic lattices of atoms. For nickel, the 3d orbitals are partially filled and therefore most responsible for its electrical properties. In particular, in this nickel-based superconducting compound, it is believed that the xy, x2-y2, and z2 orbitals are the most important and so I focused only on these in my model. Results: I calculated the Fermi level, the magnetization of the nickel compound in an external magnetic field, and the band structure. The simulation predicted that the magnetization decreases as temperature increases. The simulation highlighted how nickel’s three orbitals change in energy as we move through the different momentum states. The simulated results are consistent with the electron behavior suggested by previously published work. Conclusion: This study affirmed that we have a model that accurately describes electronic states in a nickel compound. This is a first step in examining superconducting behavior. Program: Ronald E. McNair Research Scholar To be Latinx means to be a person from Latin America specifically from Mexico, Central America, The Carribeans, and South America. In the 1970’s the population was 9.6 million and most recently as of 2020 it has reached 60.6 million, making them 18 percent of the U.S. population. The impact this power holds can already be seen as of the most recent presidential election. The 2020 presidential election about 1 in 10 voters was Latino. This is surprising news due to the fact that before the 2020 election eligible Latinx voters never passed 50 percent. This upward trend is predicted to continue. However, throughout the last half of the 2010s, many misconceptions arose towards immigrants, specifically for the Latinx community. The rhetoric president Trump used at the time skewed the perception of Latinx Immigrants to a negative one. This made the Latinx community, specifically, writers, project their voice to give a better perspective on what their community is truly experiencing. Latinx writers have always discussed immigration policies throughout the decade since Obama's mass deportation, but the recent scrutiny towards Trump's detention centers has only led to their work getting more attention. Given the Latinx community's struggles, progress, and lived experiences, their response to immigration policies' impact on their communities will be the study's primary focus. The dependent and independent model will be used to examine the U.S policies through the writing and voices within the Latinx community. In this study, the independent variable, the cause, will be immigration policies and laws implemented during the Obama and Trump presidencies. The dependent variable, the effect, will be Latinx writers' interpretation of said policies and laws. Poems were picked as the lens to view the Latinx community's response because their briefness allows for more voices to be examined and provides a lot of qualitative data. This study seeks to provide answers that quantitative data cannot provide by itself.
Program: Swenson Science Summer Research Fellowship Public Key Cryptography with Graph Theory Nicholas Drain Dr. John Villalpando Currently there are many different algorithms that can be used to encrypt information, however; evidence suggests that the advent of quantum computing could bring an end to many of these algorithms. Current research suggests that should a cryptographically relevant quantum computer be constructed, many current encryption standards will be made obsolete, and while the process of selecting an algorithm for widespread in a post quantum world has been started, there is currently no standard. The purpose of this project is to develop a public key encryption algorithm using the principles of graph theory. Properties common in public key cryptography were identified and graph theory concepts containing these properties were found. These graph theory concepts would then be explored further until one was able to encrypt data publicly without exploitable vulnerabilities. It was shown that most public key encryption standards used some question that had a high computational complexity, which could be reduced using some combination of private information and separate mathematical properties. Furthermore, most either encoded and decoded the information using separate methods or securely exchanged a key at the beginning. The problem of finding the maximum independent set of a graph was found to have all the requisite properties, while still being firmly in the world of graph theory. A method was developed in which a graph could be created such that it had a pre-determined maximum independent set and would therefore not need to be solved by the sender. On top of this, if sent in sufficiently large quantities solving all of them could be made infeasible. Brute force was found to be ineffective as there were Program: ALLIES in STEM Undergraduate Research Fellowship
Studies have shown that microfibers are a prevalent issue found in our oceans, marine sediments, and in filter-feeding organisms such as the common mussel and clam. With being no longer than 5 mm in length, over 2 million tonnes of these fibers are released into marine ecosystems yearly via domestic laundering, illegal landfills, dumping, and fragmentation of large plastics. The goal of this research was to quantitatively and qualitatively analyze the microfibers present in Emerita analoga (Pacific Mole Crab). This research aims to broaden our knowledge by examining if microfiber pollutants negatively impact the indicator species of Emerita analoga. Since Emerita analoga rely on filter-feeding techniques, it is expected that there will be the presence of microfiber pollutants inside the organisms tested. In total, 300 crabs were collected from Sycamore Canyon watershed in Ventura County California and were immediately put on ice in preparation for the filtration process. Dissection was performed on 15 crabs per-sample x4 through disembowelment and then were proceeded to be ground up using a Mortar and Pestle. Samples settled in 50% salinity water overnight and then a quantitative analysis was conducted the next day using a light microscope. Samples were washed three times and then were poured into beakers with filter paper. This filtration process made the microfibers easily visible for quantitative analysis to be performed. We were able to determine the total amount of microfibers present inside the crabs as well as the color of those fibers. A total of 217 microfibers were found in 300 crabs with the largest portion of fibers being black and blue. This research aims to improve our overall understanding of the impact that the transfer of these microfibers have on different trophic levels in the marine ecosystems. This is because Emerita analoga are one of the most important herbivores on the beach, and a vital link in the sandy beach food web. Program: ALLIES in STEM Undergraduate Research Fellowship Over the past decade, the interest in marine microfiber research has grown substantially, along with the scientific understanding of its impact on various ecosystems. Microfibers are a type of microplastic that is shed from synthetic fabrics made from materials (i.e. nylon) that frequently pollute various waterways and their inhabitants. Despite the great amount of attention towards research on a multitude of fish and filter feeder species, we decided to shift our focus to Loligo opalescens (California market squid), a tertiary consumer and a keystone species for many marine and land species found along the coast of Southern California. The purpose of this study was to confirm the presence of microfibers in the gill tissue of the squid and to compare the findings with the quantities observed in the squid’s gastrointestinal tract (guts). The number of microfibers were quantified under a light microscope for each sample after the dissection and vacuum filtration of the guts and/or gill tissue. In our preliminary results, a larger quantity of microfibers have been observed in gut tissue samples in comparison to the gill samples observed. Although further research is needed to certify a conclusion, the results suggest that California market squid has been significantly impacted by microfiber pollution present in its ecosystem when compared to similar organisms, such as Argonauta nuoryi (Del et. al.). The squid’s role as a keystone species and the theory of microfiber trophic transfer may also be indicative of the similar impact that other members of its ecosystem may be enduring. Keywords: microfiber, California market squid, gastrointestinal tract, gills, quantity Program: Swenson Science Summer Research Fellowship Studies have shown that microfibers are a prevalent issue found in our oceans, marine sediments, and in filter-feeding organisms such as the common mussel and clam. With being no longer than 5 mm in length, over 2 million tonnes of these fibers are released into marine ecosystems yearly via domestic laundering, illegal landfills, dumping, and fragmentation of large plastics. The goal of this research was to quantitatively and qualitatively analyze the microfibers present in Emerita analoga (Pacific Mole Crab). This research aims to broaden our knowledge by examining if microfiber pollutants negatively impact the indicator species of Emerita analoga. Since Emerita analoga rely on filter-feeding techniques, it is expected that there will be the presence of microfiber pollutants inside the organisms tested. In total, 300 crabs were collected from Sycamore Canyon watershed in Ventura County California and were immediately put on ice in preparation for the filtration process. Dissection was performed on 15 crabs per-sample x4 through disembowelment and then were proceeded to be ground up using a Mortar and Pestle. Samples settled in 50% salinity water overnight and then a quantitative analysis was conducted the next day using a light microscope. Samples were washed three times and then were poured into beakers with filter paper. This filtration process made the microfibers easily visible for quantitative analysis to be performed. We were able to determine the total amount of microfibers present inside the crabs as well as the color of those fibers. A total of 217 microfibers were found in 300 crabs with the largest portion of fibers being black and blue. This research aims to improve our overall understanding of the impact that the transfer of these microfibers have on different trophic levels in the marine ecosystems. This is because Emerita analoga are one of the most important herbivores on the beach, and a vital link in the sandy beach food web. Program: ALLIES in STEM Undergraduate Research Fellowship Purpose: The cardiovascular system is constructed of arteries and veins that carry blood and lythm throughout the body. Males’ and Females’ cardiovascular systems possess the same structural form of elements: circulation in the blood and vessels constructed of the same cell types. This similarity is seen in the anatomic location of the major vessels the hearts, lungs, the vertebral, and most other organs between sex differences. It is known that the cardiovascular system’s alliance of the elements do not fulfill the same functions between males and females, furthermore it is the result of achieving homeostasis. Is there a possibility to recognize that the cardiovascular system operates the same in males’ and females’ Common Carotid Artery (CCA) following intensive exercise. Therefore, the aim of this study is to determine if there is a sex difference in the Common Carotid Artery (CCA) in hemodynamic response to VO2 max test. Methods: 14 males and 15 females were recruited for this study. The participants underwent a BodPod test to determine anthropometrics. Once this test was concluded an ultrasound of their CCA was conducted, as well as blood pressure taken in their arm. Then the participants performed a VO2 test, which determines cardiovascular fitness. After the test was completed, a second ultrasound on their CCA was taken, along with their blood pressure. Results: There was no difference seen in males and females CCA in hemodynamic response to intensity exercise. However, the results demonstrated a significant difference in End Diastolic Velocity (ED) between males and females before intensity exercise was performed, p<0.001. The females also showed a significant difference in End Diastolic Velocity after performing intensity exercise, p<0.001. Conclusion: Males’ and females’ common carotid arteries in hemodynamic did not change in response to performing a VO2 max test. Furthermore, our data demonstrate a change in only the End Diastolic Velocity of the CCA before intensive exercise for both sex difference. Though it is interesting that the results obtained for females’ on their End Diastolic Velocity response to intensity exercise are different from the males’. Therefore, our data provides an important based for further study related to the Common Carotid Artery in hemodynamic response to exercise between sex differences. Program: Swenson Science Summer Research Fellowship In 2012, using the largest particle collider in the world at CERN in Switzerland (the LHC), physicists found the Higgs Boson, a particle which had been hypothesized but had eluded detection until then. A reason that this particle is important is because the Higgs Boson is linked to the Higgs Field, a field which imparts most of the physical mass to some of the fundamental particles in our universe, known as fermions. There are 4 main processes that can produce the Higgs through a proton collision (the type of collisions being observed at the LHC), and the only one that has not yet been experimentally observed is called Vector Boson Fusion (VBF). The focus of our research is to produce a machine learning algorithm that can “clean” some of the LHC collision data: accepting VBF Higgs while rejecting background processes (such as ZZ production and decay). In my presentation I will show the comparisons of kinematical variables between prefiltered/filtered data for the Higgs signal and a Drell-Yan ZZ background samples. From these comparisons, we will be able to 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 was then trained on these filtered data and further increase the ratio of Higgs to ZZ events in our sample. I am presenting the work on our attempt to optimize the machine learning algorithm to more reliably select Higgs from the background through a variety of measures. Those measures include: smoothing the input files’ (Ntuples) kinematical variable distributions, experimenting with the structure of our neural network itself (manipulating the number of hidden layers), and experimenting with the exclusion of different kinematical variables from our network’s input, since they may be acting more as a source of noise than as a valuable distinguishing factor between Higgs and background. Program: ALLIES in STEM Undergraduate Research Fellowship Macrolides are a type of natural products that consist of a macrocyclic lactone ring that is typically 14, 15, or 16 membered. There were three isocorniculane macrolides that were found to have anti-cancer activities. The plant in which these three macrolides were derived from is used in Southeast Asia to treat diarrhea, cholera, malaria, and viral diseases such as influenza. One of the macrolides, corniculatolide C, was reported to possess alpha-glucosidase inhibitory activity. It was reported that the hydroxy as well as methoxy substituents at C-11 and C-12 played a significant role in the α glucosidase inhibition. Therefore, corniculatolide C is the most favorable compound for total synthesis. Two separate wittig reactions were conducted first. The first Wittig reaction included 3-hydroxy-4-methoxybenzaldehyde and triphenylphosphorane to produce Ethyl 3-(3’-hydroxy-4’-methoxyphenyl)-2E-propenoate. The starting materials 4-bromobenzaldehyde and triphenylphosphoranylidene acetaldehyde reacted to produce (E)-3-(4-Bromophenyl)acrylaldehyde for the second Wittig reaction. The first reaction had a yield of 38% and the second reaction had a yield of 78%. Both reactions were repeated on larger scales. The two products were coupled using a CuI mediated Ullmann reaction to produce two aromatic rings connected via an oxygen forming an ether. This reaction was repeated three times under different conditions. Using NMR spectroscopy, it was determined that the final Ullmann coupling reaction was successful in producing the desired product. The next steps are to obtain more product from the Wittig reactions, in order to reproduce the Ullmann coupling reaction. Once that has been done, the Olefin produced will be reacted with H2 and Pd to reduce the C=C double bonds and esters, to alkanes. Using Fischer Esterification reaction the alcohol will attack the ester and combine to make one single ester forming a ring. The expected outcome is to produce corniculatolide C. Program: John Stauffer Research Fellowship in the Chemical Sciences
Previous research has shown the metal-organic frameworks (MOFs) have shown intrinsic anti-cancer activity. Purpose: The purpose of this study is to determine the effects of a MOF’s geometry on its cytotoxicity on cancer cells. Methods: Iron-based MOFs were synthesized, as they showed no toxicity in the body in previous research. These were done using an organic linker and a metal cluster for each MOF, and then stored in a Teflon-lined autoclave and heated in an oven. Once these MOFs were collected, they were subjected to XRD analysis. After confirming the expected crystallinity, they will be sent for anti-cancer cell line testing. Results: As of date, six different iron-based MOFs have been synthesized, and five have been XRD characterized. We are in the process of analyzing this data to make sure that the MOFs were accurately synthesized and have the correct geometries. Once this is done, we will send them for cell line testing. Future Work: Once we confirm the correct crystalline structures, the samples will be submitted for biological testing. Program: ALLIES in STEM Undergraduate Research Fellowship
The purpose of this study was to synthesize Metal-organic Frameworks (MOFs) to be used for drug delivery for anti-cancer therapies. Metal-organic Frameworks are hybrid materials that are composed of organic linking units and metal clusters that allow for customizable pore sizes and structures. MOFs have been used as vehicles for effective adsorption and controlled drug delivery. One of the main components of this research is to analyze the way these drugs can be released by light-responsive drug release delivery because of the controllability in time release. The MOFs organic components are biodegradable, provide low toxicity, and chemically modifiable but they are insufficient in controlling the drug release which is made up by the properties of the inorganic portion of the MOFs.The synthesis of the metal linker will involve a six-step reaction scheme bearing a substituted coumarin system as the pseudo-drug. The steps of the synthesis are nitration, reduction, mesylation, SN2, Sonogashira coupling, and hydrolysis. The metal linker is then crystallized to form a hybrid MOF and then the MOFs will undergo light-induced release to deliver the pseudo-drug from the MOF. The progress to date resulted in synthesizing large quantities of the first three steps to allow for more experimentation for the Sonogashira coupling. The steps were repeated with various reaction conditions to attempt to perfect the reactions. The nitration reaction had a yield of 33-40% with H2SO4 and HNO3 as reagents. The reduction reaction had a yield of 67-93% with THF, NaBH4, and H2O as reagents. Finally, the mesylation produced a yield of 27-100% with Et3N, mesyl chloride, and THF as reagents. Future research will include analyzing the products with NMR and improving the quality of the Sonogashira coupling reaction. Overall, the importance of synthesizing the organic linker is to allow for more improvements in current studies of MOFs for drug delivery systems and finding the most effective release method. Program: ALLIES in STEM Undergraduate Research Fellowship The variably expressed extra eye (ee) mutation in Drosophila melanogaster produces head deformities, which in severe expressions result in ectopic, supernumerary compound eyes. In addition to variable expression, the mutation possesses other exotic features: ee is both incompletely penetrant and conditionally dominant. Marcey (personal communication) has developed an epigenetic model to explain the exotic genetic behavior of ee. The model posits RNAi-mediated transcriptional suppression via epigenetic heterochromatization of a gene that encodes a repressor of activated STAT, a signaling molecule implicated in embryonic eye field establishment. The proposed epigenetic model predicts that new, inducible mutant phenotypes may be revealed 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. In one such cross, a new mutation, Crybaby (Cby), was recovered. Cby exhibits the properties expected of an epigenetically-triggered mutation, and its primary phenotype, a disruption in ventral eye development, resembles that of known mutations of the Lobe locus on the second chromosome. I have conducted complementation tests between Crybaby and various Lobe alleles in order to see if Cby represents a new Lobe allele. Cby females were mated to males from eight different Lobe lines, and the F1 progeny were screened to determine if they demonstrated a more severe phenotype than either Lobe or Crybaby (i.e. non-complementation). I determined that, in most cases, the F1progeny did indeed exhibit a more severe phenotype than either Cby or Lobe, suggesting that Cby is an allele of Lobe. Cby females were also bred with male Canton-S (wild-type) flies as a control. The appearance of Cby phenotypes in the F1 of this control cross establishes Cby as a dominant mutation, as are known Lobe alleles. My results will be employed to better understand aspects of genetic control of tissue development in a model organism. Program: Swenson Science Summer Research Fellowship OURCS Bontu Wako
Abstract
It was observed that the strain on the phosphate group and ATP was significant to induce a catalytic reaction. By removing the strain through the introduction of the variant we could potentially change the binding and kinetics of Des D. A series of protein over expression and purification was conducted to attain viable protein samples to study the binding and catalysis of variant R280 Des D. Multiple over expression and protein purification methods were carried out. However, an adequate amount of protein has not been attained to study binding and catalysis. The method of protein over expression was modified. If adequate amount protein is attained variant R280A will be observed to understand the role of ATP strain in binding and catalysis of Des D. Program: ALLIES in STEM Undergraduate Research Fellowship
There are several studies that cardiovascular diseases have a correlation with abnormal blood pressure. According to a research by Christopher J.A. Pugh only highly fit individuals exhibit elevated CCA, PCS and S-SR. The incidence of clinical manifestation of CVD differ substantially between racial groups. The African American (AA) population present double the levels of incident CVD than Caucasians (CAs) which is reflected in higher mortality rates experienced by AAs. Previous studies show higher systolic blood pressure in AA children compared to Caucasions children. On the other hand, there not much research on arterial recovery differences between male and female. In this research we are aiming to look if there is a difference between male and female in arterial recovery after a maximal exercise. We believed that there will be there will be a difference between the arterial recovery between males and females. This research Included 15 subjects (7 males and 8 females) between the ages of 20-23 years old. We used bod pod to measure the subject’s body compositions and after that we did an ultrasound imaging on the subject’s Common Carotid Artery. After that we preformed the ultrasound the subject preformed a VO2 max test, and right after that we preformed another set of ultrasound imaging. In a time period of 15 minutes we recorded 30 of ultrasound for every two minutes. The results that we found are that in the systolic BP male had and higher BP compared to female and that there is a significant (n=15, P value = 0.001) difference between male and female. In addition, male reached a BP Plato faster than females. In the results for the diastolic BP it was found that females reach a higher peak of diastolic BP right after maximal exercise, and that there is a significant difference (n=15, P value = 0,008) in the arterial recovery compared to males. The female diastolic BP reaches a Plato faster than the male diastolic BP. In the future I would like to complete the analysis of the diameter of the CCA. Also, I would like to expend the subject Pool size the achieve stronger evidence. Moreover, I would like to investigate how different diets will affect the arterial recovery time, and the difference between of full racial groups and mix racial group. Program: Ronald E. McNair Research Scholar Understanding how our dietary and lifestyle choices affect our cognitive function can help students perform better in school and other aspects of their life. For these experiments we will be using beetroot juice because it has high levels of nitrate and has been used in previous experiments dealing with cognitive functions. We will also be collecting various measures of vascular function that may provide insight into potential changes in neurovascular coupling as a result of nitrate supplementation.
The purpose of this study is to determine the effects of short-term dietary nitrate supplementation on vascular and cognitive function in college-aged individuals.
Each participant will have their heart rate, blood pressure, weight, height, vascular function, and cognitive function recorded in the beginning of the experiment. Participants will take two different cognitive tests: The Stroop test, and the California Verbal learning test. Participants will then be provided with nitrate supplementation on the same day and wait for an hour and 30 minutes, before baseline measures are repeated. Nutrient intake will be recorded 3 days prior to taking the beetroot juice. Program: Ronald E. McNair Research Scholar Starting new ventures is always a challenge. Based on extant research, frequently identified barriers to entrepreneurship are a lack of access to education, cultural factors, gender disparities, absence of funding, and a limited understanding of entrepreneurial finance, among others factors. Minority groups are at a particular disadvantage compared to majority groups when pursuing entrepreneurial opportunities. There is a commonly acknowledged lack of resources and support for minorities that hinders their likelihood of success when seeking true opportunity-based entrepreneurship. The consequence of this inequality is that minority entrepreneurs will fail to thrive in California’s business landscape. My research focuses on a specific subset of minority groups, the LatinX population, and it examines the barriers they face as entrepreneurs in California. The purpose of my research is to investigate, among others, differences in access to resources and support between Latinx entrepreneurs and non-entrepreneurs. An additional goal is to identify key differences and similarities between male and female LatinX entrepreneurs concerning their pathway to entrepreneurship. My investigation analyzes extant literature and secondary data. The data collected from this project confirms key factors, such as education, limited understanding of financial terminology, lack of support, and differences in gender roles are setbacks for LatinX entrepreneurs; in comparison to the experiences mentioned by non-LatinX entrepreneurs. The insights collected from my research raises awareness of the limitations for LatinX entrepreneurs in their pursuit of entrepreneurship, assist policy-makers, investors, and other stakeholders in the startup ecosystem in addressing this issue, and form the basis for the formulation of hypotheses for subsequent quantitative research. Program: Ronald E. McNair Research Scholar How do we distinguish morally condemnable from morally defensible violent political action? Is there a standard set of criteria that should be used when determining which acts of political violence warrant moral justification or should the permissibility of political violence be contingent on the circumstances that conditioned it? The purpose of this paper will be to examine two existing justificatory frameworks for political violence in efforts of answering the questions above. Drawing arguments from the Just War Theories and the criteria for defensive-harm, political theorist Avia Pasternak has developed an assessment which determines the appropriate moral response of political rioters to be one that adheres to the limitations of necessity, proportionality, and success. Warning that these limitations may be too stringent to vindicate the full range of acts of intuitively justified political violence, political theorist Edmund T. Flannigan developed a supplemental theory which emphasizes that the justification of political violence is dependent on its fittingness as a response to the circumstances that triggered it. In this paper, I will defend Pasternak’s assessment noting that principled accounts are superior to accounts that rely on moral intuition—such as the one proposed by Flanigan. I will additionally defend Pasternak’s account from Flanigan’s critiques to show that the concerns raised in his paper are generally unfounded.
Key words: Political Violence, Just War Theory, Ethics of Resistance Program: ALLIES in STEM Undergraduate Research Fellowship
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 at the Sycamore Watershed when compared to the coastlines of Western Australia, Hawaii Island, and San Miguel Island. It’s hypothesized that the number of microfibers present will be elevated in regions with increased commercial traffic and water discharge. Sediment samples were collected from the intertidal zone of the varying sample locations. 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. Sand sediment was then placed into 600 mL beakers (200 mL of salt water with 100 mL of sand) and mixed so that microfibers are suspended in water. Next, the surface water of the mixture was filtered over a 5 μm cellulose nitrate membrane filter. The filter was placed in a clean Petri dish for further observation under a microscope. All microfibers caught on the filter papers were examined, counted, and characterized under a dissecting microscope, and images were taken. A visual assessment was used to identify and record the microfibers based on their physical characteristics, such as color and size. The results revealed that Sycamore watershed had a noticeably higher number of microfibers when compared to the other locations like Hawaii, Australia, and San Miguel Island which are open, intertidal areas that would provide little time for microfibers to be deposited into sediments whereas the Sycamore watershed receives direct output from common microfiber sources. Supporting the hypothesis, our results revealed that more microfibers were found in the Sycamore Watershed sediments that are closer to sewage-sludge disposal sites where our washing machines are polluting the runoff water. In conclusion, microfibers are polluting the sediments along the coastlines of California, Australia, and Hawaii and this is negatively affecting all ecosystems as it spreads throughout the environment. Program: Swenson Science Summer Research Fellowship Microfibers, a subset of microplastics, are an increasingly concerning form of pollution that negatively affects all levels of marine food chains. These small (<5mm), synthetic fibers make their way to the ocean primarily from washing machines via wastewater runoff and collect in beach sediment. The goals of this study were to determine if microfibers would be found at all the locations surveyed, and if so, if the watershed location would have the most microfibers. It is expected that there will be microfibers at each location and that the watershed will have the most microfibers. To conduct this study, sand samples were collected from San Miguel Island and Sycamore Cove Watershed, both in California, as well as from Western Australia and The Big Island of Hawaii. 100mL of sediment was mixed with 200mL of seawater in a beaker to suspend the microfibers in the seawater. The seawater was then poured through a Buchner funnel filtration system, which caught the microfibers on a 5µm cellulose nitrate filter paper. The filter paper was analyzed under a dissecting microscope and the number, color, and approximate size of the microfibers was noted. The process was repeated six times per sample to ensure that the majority of the microfibers were caught. Sycamore Watershed had a higher average number of microfibers per sample than any other location, with 111.5 microfibers compared to the average of 20.6 from San Miguel Island, 34.5 from Australia, and 16.4 from Hawaii. Both hypotheses were supported, as there were microfibers present at all locations and the watershed had the highest number of microfibers. This difference in the average number of microfibers is indicative of the watershed being a source of marine pollution. Since washing machines and wastewater treatment plants are unable to remove all the microfibers before the water is released into the environment, there are more fibers present closer to runoff sites. It is imperative that we note heavily polluted areas and determine solutions to this problem before it affects any more marine organisms. Program: ALLIES in STEM Undergraduate Research Fellowship
Legionella pnuemophila (Lpn) is a gram negative bacteria that occurs naturally in freshwater and human-made water systems with over 60 species, half of which are disease causing. Lpn is an opportunistic pathogen known as the causative agent for Legionnaires Disease in immunocompromised patients, with symptoms presenting as pneumonia. This pathogen evades fusing with lysosomes and takes over host cell replication machinery forcing the cell to replicate the virus till its vacuole bursts open. Lpn grows in alveolar macrophages in infected lungs and relies heavily on the machinery of its type two secretion system (T2SS) which has shown to be responsible for fitness and growth in eukaryotic host cells. Based on Cianciotto 2013, 2019 we expect that the nttB, PlaC, LspF will have an effect on growth at temperatures outside of 37C. We will be testing Lpn mutants PlaC, NttA, and LspF against the wild type bacteria 130b. Based on previous research of (cianciotto 2019?), we hypothesize that water temperatures close to normal environmental temperatures will encourage growth of bacteria while low temperatures will present difficulty growing.130b and T2SS mutants were cultured overnight at 215 rpm, 37C. Three independent biological replicates were resuspended at OD 660 equal to 0.3 or 0.8 (lspF) in enriching BYE media (+/- Kan). Their optical densities were read using a Genesys spectrophotometer every 24hr for a total of 72h. The difference between the mutants and 130b is that some mutants hit their death stage much earlier than the wild type, this indicates that the mutants are not surviving well in higher temperatures than what is environmentally common for them to grow at. Future work will include testing more novel T2SS mutants at 25℃ and 17℃ to determine their role, if any, in Lpn survival in the environment, and using E. coli to clone and express T2SS novel effectors to further determine structure and function. Program: Ronald E. McNair Research Scholar In this study, herbal medicines such as ginkgo, feverfew, echinacea, hyssop, lobelia, astragalus and comfrey were identified and examined to analyze their parent compounds and active/reactive compounds both theoretically and experimentally. The prediction of these herbal/medicinal compound biotransformation pathways via cytochrome P450 were analyzed theoretically with schematic mechanisms. Experimentally, extraction using various organic solvents aided in extraction of active and reactive compounds from the products, therefore, allowing us to analyze via gas chromatography- mass spectrometry (GC-MS). As a result, methanol was shown as the best method for extracting active and reactive compounds of the medicinal products. The data from GC-MS are expected to be the same as the theoretical prediction to further examine their effects on human health in future research.
Keywords: Herbal medicines; metabolic transformation; gas chromatography-mass spectrometry (GC-MS); cytochrome P450; gingko; feverfew; echinacea; hyssop; lobelia; astragalus; comfrey.
Program: ALLIES in STEM Undergraduate Research Fellowship 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 is 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 works to isolate these two components in ee lines by splitting the chromosome on which both components reside, the 2nd chromosome, through recombinational means. It was expected that the resultant recombinationally-generated descendants with split extra eye chromosomes would not produce any phenotypes characteristic of the extra eye mutation in any capacity. To conduct this project, ee flies were mated to flies with a heavily mutated 2nd chromosome, a mapping chromosome, so as to track where recombination events took place. Resultant progeny were assayed for desirable recombination events. Such offspring were 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. Program: The Louis W. and Gladyce Foster Family Foundation Summer Fellowship in Religion
Youth in Double Cultures and Third Culture kids. Naomi Mbise. OURCS Research Abstract 2021.
Research Topic and Questions. At the age of 3-8, I got the chance to learn the Bible at home, attend Sunday school and talk about the word of God. I was a happy kid, making my own fantasies about heaven and always ready to be told another bible tale. I moved to a boarding school at the age of 9, it was actually a Seventh day Adventist school. A different denomination from my own, I am Lutheran. I noticed a few changes on the practices but I was in a brave space, still learning and being told on different Bible characters/tales. I loved it and I always felt fulfilled. In my teen years I moved to a different school where religion was not something we talked about at. I started to notice a change of things, ways of doing things: a life that God was not a topic as much. I went home for the holidays, went to church some Sundays and I did not at some. At the age of 16, I was navigating in both public(secular) and a life of faith (spiritual life). As a teen my culture had changed, I was living in two cultures one spiritual at home and church gatherings. The other secular when with friends, at school or other people in my community. I know this is a case to most teens, and more interesting that, at these years is a period of transition from childhood to adulthood. This is where I drive from the term “Youth in double Cultures”. Youth are at a point of curiosity and need to explore both a secular and the spiritual world. If the latter is not given proper consideration, answers or open space to discuss things in the outside world such as sexuality, politics and personal relationships with God and themselves. Youth feel unfulfilled in their spiritual life and leave the church to seek answers to their problems and questions. In this research work I explore how youth navigate in double cultures. From the realities to supporting systems and what the future looks like. In this research work I explore further, to Understanding Third Culture kids (TCK’s). A term used to define individuals who have spent a significant period of their developmental years outside their parents’ culture. They live a life experiencing three cultures; one, their parents’ culture; second host culture and three; a mix of other cultures. (Mai Bouchet, Madiso Zeller and Emi MacLeod). TCK’s are often assisted by adults to grow in their secular and spiritual life. Similarly, to above, in this research work I explore how youth navigate in triple cultures. From the realities to supporting systems and what the future looks like. Research questions 1.What are the challenges and realities of living in double or triple cultures? 2. What patterns exist between Youth in double Cultures and Third Culture Kids (TCK’s)? 3.What does/can individuals, institutions and the community as whole do to support youth to navigate in Double Cultures or Third Cultures? (Looking at Institutions like the Church, Higher-learning Institutions) Background and significance In this era of globalization, young adults have a varying experience in navigating and finding brave spaces to tap to their highest potential. Spirituality and religion have also been used to help youth seek their identity or define their identity. In this research work I will explore how the community, institutions and individuals can support young adults? How can they support young adults to learn and explore a secular and spiritual life? What can be used to help them live a double or triple cultural life. How can youth grow up in both cultures? Growing up in a life of faith/religious but yet be able to experience a secular/public life and find the balance without omitting the other. The knowing, transformation and moving from affirmation to practicality of raising youth in double and third cultures. Youth development in double and third cultures is not a one-person job! It is for the families, the community, the church and primary care-givers all play a very important role in spiritual development: King and Roeser (2009). Thus, to enable youth live in double and third cultures they all should be able to discuss issues that affect youth in both worlds such as sexuality, politics, science and religiosity. The quality of the relationship between young adults and young-adults is what will determine their genuine ability to live in a double and triple cultures. I personally believe that young-adult ministries should enable youth through advocacy and discussions on issues such as on-going political situations, sexuality tensions and spiritual diversity. I know that the Church for example the Evangelical Lutheran Church in America already has advocacy platforms for young -adults such as Peace Not walls to enable youth explore the world in a different eye. Ministries such as Compass ministries also work to enable youth navigate in Third Cultures. I would say this research is important to see the practicality of this and how further can we move to advocate and incorporate this in our institutions, communities and in the Church
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