Schedule of Events

Cryptic Epigenetic Variation (CEV) are hidden mutations that involve chromatin packaging in genes. Such mutations can alter the state of the gene through mechanisms, like heterochromatization, without changing the DNA sequence. The extra eye (ee) mutation in Drosophila melanogaster is an example of CEV and holds three epigenetic signatures: incomplete penetrance, conditional dominance, and variable expression. Introducing ee to the wild-type strain of D. melanogaster from Bahai, Brazil revealed a new eye mutation called, crybaby (cby). cby also exhibited the same three epigenetic signatures as ee. Our study aimed to locate the position of cby in the genome of D. melanogaster. Mapping which chromosome cby is on will not only provide information on the genes affecting cby but also allow us to gain insight into eye development in D. melanogaster. We expect the cby gene to be located on the X, 2nd, or 3rdchromosome. The cby line (DM37) was crossed to two separate lines containing balancer chromosomes (33821 and 36283). The F1 progeny were interbred and the resulting F2 were scored. Data was inconclusive but suggested that cby could be located on the second or third chromosome. Thus far, an altered genetic scheme was created to establish F1 progeny from 33821 and 36283 containing all three balancer chromosomes. The F1 progeny was then crossed with DM37. Further analysis is ongoing to uncover the location of cby.
 

Golf players must often hit shots from address positions that are different than playing shots off flat ground. Previous research found that golf ball trajectory is affected by ball speed, launch angle, and lateral spin (Wallace et al. 2007). This study aimed to determine the changes in ball kinematics when hitting golf shots from sloped address positions. Eight skilled golf players (handicap: 5.125 ± 4.123) volunteered for this study in accordance with the local institutional review board. Players performed 10 golf shots toward a target with their own 6-iron at their preferred distance when playing shots from the Flat, Uphill, Downhill, Incline and Decline conditions. A launch monitor calculated ball launch angle, lateral spin, and carry distance. Custom ramps oriented the force plates into the sloped address positions (increments of 5°). Differences between conditions were determined using repeated measures ANOVA (α = 0.05). Launch angle was greater in the Uphill condition (19.32° ± 3.32°, p < 0.029) than all other conditions and smaller in the Downhill condition (12.69° ± 2.59°, p < 0.024) compared to Flat, Uphill and Incline conditions. There was also a difference in lateral spin between Incline (-289.43 rpm ± 613 rpm) and Decline conditions (378.78 rpm ± 701.51 rpm, p = 0.008).Golfers were more likely to hit with a greater launch angle in an Uphill condition and a lower launch angle in a Downhill condition. Players also hit shots that spun more to the left when Inclined and more to the right when Declined.

The purpose of this project is to contribute to the ongoing multi-institutional effort (CLU, UCSB, CERN, and other institutions) in the search of yet undetected supersymmetric particles in the large Hadron Collider CMS (Compact Muon Solenoid) experiment on two different fronts: hardware and data analysis. Regarding hardware, we are contributing to the ongoing instrumentation improvement of the CMS calorimeter components by designing and currently building a coincidence particle scintillator to serve as the “trigger” to start data collection in test-beam experiments to characterize a particle calorimeter detector (The High Granularity Calorimeter-HGCal) being developed in a collaboration between our university, UCSB, The University of Minnesota, CERN and a few other institutions. This trigger will also be able to be used to test detectors in lab with minimum ionizing particles. Attached to this task, a mapping has been created and the plotting code has been modified to work specifically for the new 8in HGCal Silicon detector prototypes.
Regarding the data analysis, we are currently working on Montecarlo simulations of the Higgs decaying to charm-charm quarks. It is important to mention that the search for SUSY is a collaborative effort done by a very large community of scientists, and it will take several years. Nevertheless, the work done and soon to come from this project are aimed to be a small aid for this gigantic search.

The most common method of treating cancer is directly removing the mass of cells through surgery, with chemotherapy and radiation therapy being used post-surgery to ensure that any remaining cancerous cells are killed. Recent studies focusing on plant-derived treatment methods have proposed curcumin as a new anti-cancer agent for its multiple anti-proliferative and apoptotic properties. I hypothesized that as concentrations of curcumin within the cell culture media increased, both the migratory capabilities and cellular viability would decrease, and the total quantity of apoptotic cells would increase. I conducted migration assays, MTT assays, and flow cytometry to examine the anti-cancer effects of curcumin on a canine osteosarcoma (D17) cell line. The results have found that curcumin worked in both a time-dependent and dose-dependent manner. Treatments with less than 20 micromolar of curcumin, and trials that last less than 24 hours, seemed to have little impact on the migration and metabolic health of the cancer cells. But as both time and concentration increased beyond that point, the migratory capability and cellular viability decreased significantly, as shown by the migration assay (p<0.001) and the MTT assay data (p<0.05), respectively. Flow cytometry data showed that apoptotic rates of the D17 cells also increased as both dose concentration and time of exposure to curcumin increased (p<0.05). Together, these results show that curcumin can be an effective anti-cancer treatment, decreasing both the growth and health of canine cancer cells.

Microfibers are a fast-growing concern in environmental issues; they are a pollutant that are quickly accumulating in and affecting ocean ecosystems, and are present in most of the Earth’s watersheds, especially the U.S.. Microfibers are a form of microplastics shed by synthetic materials such as fleece when washed. Watersheds, particularly Ventura watershed, is an area riddled with microfibers. Ventura county, like most watersheds surrounding urban areas, leads off into the ocean through different rivers. Although microfiber research has begun to pick up speed over the past decade, little to nothing has been done in Ventura county. We decided to collect sediment samples from the watershed zones Ventura and Santa Clara. Sediment was then placed into 500 mL beakers and mixed with seawater. Once settled, the seawater was then poured into a Buchner Funnel filtration system with a filter paper. Each sample was mixed and filtered 3 times, in the hopes to clear the sample of microfibers, ultimately to no avail. Finally, the filter paper was then analyzed underneath a microscope to count the amount of microfibers present on the filter paper. In both areas we were able to see microfibers at every location sampled, and for the most part, the average amount of microfibers was the same, with the exception of the midpoint of Santa Clara zone. From this data, it is difficult to conclude that there was a significant difference  so more data both in and out of Ventura County will be necessary to draw decisive conclusions.

Legionella pneumophila (Lpn) is a gram-negative bacterium that occurs naturally in freshwater environments and man-made systems, including plumbing, misters, and air conditioning. Lpn is the causative agent of Legionnaires disease, which causes pneumonia-like symptoms in immunocompromised individuals. Disease onset is the result of inhaling Legionella-infected protozoa or the bacteria alone. Lpn uses a Type II Secretion System (T2SS) that pumps up to twenty-five effector proteins through the outer membrane into the environment, which is essential for optimal bacterial growth. While other secretion systems (Type IV) in Lpn have been studied extensively, the function of effectors secreted by the T2SS remains a mystery. One of the effector proteins secreted via the T2SS, novel type II A (NttA), has been implicated in the successful infection of amoeba; however, the function within the host-cell and structure is yet to be defined. In fact, NttA is so novel that it does not share sequence or domains with known proteins. The goal of this study is to overexpress and purify NttA protein, which will be used to elucidate structure using X-ray Crystallography methodology in future experiments. NttA was cloned into pET44b plasmid, transformed into BL21 overexpression cells, and purified using a nickel affinity column.

Previous reports have observed that high intensity aerobic exercise elicits hemodynamic changes in the cerebral circulation. Resistance exercise is a major component of both performance and therapeutic exercise prescription. Current exercise guidelines recommend participating in moderate intensity resistance-based exercise at least twice per week. High intensity resistance exercise has received increasing interest within the scientific community due to its performance and therapeutic potential. However, our understanding of the cerebral hemodynamic responses to high intensity resistance exercise is limited. The aim of this investigation was to explore the response of the cerebral hemodynamics following acute maximal effort resistance exercise. These data may provide insight into the optimal prescription of resistance exercise. Peak systolic blood velocity (PSV), end diastolic blood velocity (EDV), time averaged mean blood velocity (TAMEAN), time averaged maximum blood velocity (TAMAX), pulsatility index (PI), resistance index (RI), and blood volume flow (FLOW) of the brachial artery (BA), common carotid artery (CCA) and internal carotid artery (ICA) were calculated using Doppler Ultrasound. A one repetition maximum strength test (1RM) with the leg press machine in adherence to the National Strength and Conditioning Association standard. Resting hemodynamics were recorded prior to and following exercise in resting states. Both BA PI (p=0.029) and RI (p=0.022) reduced following exercise, as well as the ICA TAMEAN (p=0.035). The current data shows no significant changes in CCA hemodynamics (p>0.05 for all).These data suggest that peripheral and cerebral artery hemodynamics remain altered following the cessation of acute high intensity resistance exercise.

Typhoid fever is a dangerous diagnosis for many in developing countries, as poor sanitation and contaminated water sources provide the perfect environment for Salmonella enterica serovar Typhi to grow and infect a human host. In other animal models, the Rab32 dependent pathway can clear the infection by delivering an unknown antimicrobial compound to the Salmonella containing vacuole where S. Typhi grows in the macrophage. Another serovar, a related pathogen with a broader host range, Salmonella enterica serovar Typhimirium, has two effector proteins that can disrupt this pathway. Itaconic acid may be this antimicrobial compound, and the confirmation could lead to a deeper understanding of Salmonella and future treatments for typhoid fever. To test for this, we used knockout mouse models to compare how the bacteria grew in cells both expressing Irg1, the gene for itaconic acid, and in cells lacking Irg1. This preliminary study shows that itaconic acid may not be the compound delivered, but these methods may be flawed as using the safer relative S. Typhimirium may result in degradation of the itaconic acid present in the wild type macrophages. Regardless, it is shown that the expression of Irg1, the gene ultimately responsible for itaconic acid production, has no effect on S. Typhimirium growth. Further experiments will be to repeat these experiments both as it was done originally and using S. Typhi as opposed to S. Typhimirium.

Climate change has had devastating effects on most ecological populations, but the first populations to see substantial damage is marine mammal populations. Especially off of the coast of California near Channel Islands, strandings of many marine mammals and birds have increased in number. California sea lion (Zalophus californianus) pups have been discovered stranded on the California coastline for the past few years showing signs of malnutrition and illness. It is hypothesized that their mothers have been traveling further for food as the rising ocean temperatures force their prey north to cooler waters. The rehabilitation efforts using the antibiotic amoxicillin focused on Z. californianus pups is effective in some cases, but the overall survival rate is low. Continuing on work done by Dr. Theresa Rogers’ lab with sequencing of fecal samples by these sea lion pups, QIIME2 (Quantitative Insights Into Microbial Ecology) can reveal patterns in the surviving sea lion pups, possibly altering the current method of treatment. QIIME2 can take the incredibly large amounts of sequencing data and analyze the alpha and beta-diversity of the samples. We expect that the diversity between the pups will be high before rehabilitative antibiotic treatment, but that they will contain a core microbiome immediately before healthy release. With this knowledge, we can improve treatment of Z. californianus pups and reduce the use of broad-spectrum antibiotics, like amoxicillin.

High Intensity Aerobic Exercise (HIAE) is incorporated into training regimens at every athletic level. Previous research has reported that common carotid arterial hemodynamics following HIAE reduces blood flow. However, data is lacking on the hemodynamic response of the internal carotid artery (ICA) which is responsible for the blood supply to the Circle of Willis. These findings can potentially change the narrative when prescribing aerobic exercise. The aim of this study was to determine the response of the ICA hemodynamics following a single bout of HIAE. Peak Systolic Velocity (PSV), End Diastolic Velocity (EDV), Pulsatility Index (PI), Resistance Index (RI), Diameter, and Flow at rest were calculated by Doppler Ultrasound of the ICA. Participants then performed a maximal aerobic capacity test (VO2 Max) with baseline ICA hemodynamics being calculated once the participant returned to resting state. A total of five participants (22±3.21 years) participated in the study. No significant changes following HIAE were observed in the ICA PSV (p = 0.554), EDV (p = 0.391), PI (p = 0.694), and diameter (p = 0.156). However, statistical trends were observed suggesting a reduction in ICA blood flow (117.7ml/min, 95%C.I.: -86.87 – 322.27, p = 0.087) and an increase in RI (-0.11, 95%C.I.: -0.23 – 0.001, p = 0.051) following exercise. The current data shows no significant changes in ICA hemodynamics following HIAE. This suggests cerebral hemodynamics return to resting states when intense exercise has ceased. It is suggested that future studies enhance subject recruitment due to the evident statistical trends.

Variegating phenotypes can be caused by loosely packed euchromatin changing into heterochromatin, a state in which DNA is packaged tighter. This tight packaging causes the suppression of gene expression in some cells, leading to phenotypically mosaic individuals. When variegation is caused by the movement of euchromatic genes near heterochromatin, position effect variegation (PEV) occurs because of heterochromatic spreading. PEV can be suppressed or enhanced by a variety of mutations. Suppressors of variegation [Su(var)] decrease heterochromatization while Enhancers of variegation [E(var)] increase heterochromatization. The extra eye (ee) mutation in D. melanogaster demonstrates properties of variegation: incomplete penetrance and variable expression. Marcey (personal communication) reports that the ee line contains a P-element in the Cpr gene in a reverse transcriptional orientation, producing anti-sense P-element RNA within Cpr transcripts. The antisense RNAs may initiate RNAi-mediated heterochromatization of P-elements and adjacent genes. Since heterochromatization of a gene or genes near P-elements in the ee line may account for the mutant phenotype, we hypothesize that mutations that affect the heterochromatic state of the genome will affect the penetrance of the ee mutation. Here I report the effects of a variety of Su(var) and E(var) mutations on ee penetrance as well as the ee mutation acting as a weak Su(var). Although statistically significant differences in ee penetrance between genotypes with and without most heterochromatization modifiers were not found, Su(var)2-10 mutations have been noted to significantly enhance ee penetrance. The results are discussed in the context of a model for extra eye developmental defects involving RNAi-induced down regulation of key signal transduction genes.

Populations of minority identities have been disproportionately burdened by infectious diseases. This project aimed to measure the impact of infectious diseases on minority populations in order to suggest improvements in disease prevention strategies. The Infectious Diseases by Disease, County, Year and Sex dataset was obtained from the CA Open Data Portal, which contained data for 48 reportable diseases measured in California throughout 2001-2018. R was used to analyze disease incidence and correlations by sex, and socioeconomic status (SES) by measures of median income per county. Disease prevalence was measured in each of three regions of California, as defined by the California Continuing Education Association (CCEA). Results showed that five diseases were prevalent throughout California (CA): coccidioidomycosis (CM), campylobacteriosis (CB), shigellosis (SH), salmonellosis (SM), and giardiasis (GI). Current results show that CM was the most prevalent of all infectious diseases in CA, and was significantly correlated to SES in Southern CA (p=0.01318) and Central CA (p=0.00285), but no significant relationship for CM was found in Northern CA. All other diseases were significantly correlated to SES (p<0.001) in Central CA and Northern CA. ANOVA tests measured a significant difference between the female and male sexes for GI (p=0.0244) and CR (p=0.0965) in Southern CA, CM (p=0.0154) in Central CA, and SH (p=0.0368) in Northern CA. Future work includes analysis by age, race/ethnicity, and month/seasons of disease incidence.

 

Patterns of intersexual dominance vary within squirrel monkeys (genus Saimiri). Preliminary field observations on the species S. collinsi indicate that females may be dominant over males, while captive work suggests co-dominance between the sexes. Our study aimed to characterize intersexual dominance in S. collinsi by collecting behavioral data on wild social groups. We hypothesized that if females are dominant over males, they would win most of the aggressive interactions and have feeding priority. The study was conducted in Eastern Amazonia, Brazil, over six weeks. We systematically recorded social interactions between adults, noting the winner and the context. The order of arrival of the sexes to dense fruit patches also was recorded. Results show that 95.9% of the interactions between males and females (N= 293 observations) occurred in a mating context. Intersexual agonistic interactions were mostly initiated by females (80%, N=106) and females won most of these (95%, N=71). Intersexual affiliative interactions were mostly initiated by males (97.3%, N=187). Adult females and juveniles arrived in a first “wave” to fruit patches, with adult males reaching the patch after the females had fed (N=37). These results suggest that S. collinsi is characterized by female dominance, a relatively uncommon pattern in anthropoid primates.
 
 
 
 
 
 

Widespread antibiotic resistance is a growing concern for healthcare systems around the world. Frequent misuse of these drugs create antibiotic resistant bacteria, or “superbugs”, which threaten the potency of even the strongest antibiotics. Pharmaceutical companies are not contributing to the pipeline of novel antibiotics due to low investment returns and strict FDA regulations. For these reasons, the USDA and WHO, regard antibiotic resistant bacteria as potentially the most significant medical concern of our time. To combat this issue, Tiny Earth developed a crowdsourcing strategy to address the need for antibiotic research which is implemented in this study. The aim of this project is to optimize the transformation of a rescue plasmid via electroporation of an isolated ­Bacillus strain, WJF-45.A growth curve was created to determine the mid-exponential phase of WJF-45 which is the optimal length of incubation to prepare electrocompetent cells. WJF-45 was incubated for 6.5 hours and a record of the optical density was taken periodically. The results indicated that the optimal incubation time before electroporating WJF-45 occurs at 2.5 hours. Various electroporation buffer concentrations and cell densities were tested to determine which produced the highest electroporation voltage. An electroporation buffer consisting of ddH2O and 250x cell concentration was found to be optimal using our methods. The findings of this study will help improve the methods of identifying sequences involved in antibiotic biosynthesis in unknown Bacillus spp. and contribute to the mission of Tiny Earth.

Research suggests that the South Asian population possesses greater cardiovascular (CV) risks than Caucasians.  Resistance exercise has an inverse relationship with CV risk. The aim of this study is to determine if racial differences exist in the response to short-term resistance exercise between Caucasian and South Asian males. The findings may help determine the potential of resistance exercise on cardiac mechanics and provide evidence towards possible needs of revising current exercise guidelines. Myocardial strains and strain rates were determined using 2D echocardiography by Doppler Ultrasound. Peak LV longitudinal, circumferential, and twist mechanics were established using apical 4 and 2 chamber views. Data was recorded for offline speckle tracking analysis which involved tracking of cardiac tissue corresponding to the chamber walls. Subjects participated in a supervised progressive resistance exercise protocol, then baseline variables were repeated following their exercise completion. A total of 24 males participated (n=11 CAUC; n=13 SA). Group x time interactions were evident for circumferential peak strain (p = 0.006), circumferential peak early diastolic filling rate (p = 0.011), longitudinal time of peak strain rate (p < 0.001), longitudinal peak early diastolic filling (p = 0.037). Statistical trends were evident for group x time interactions for twist time of peak strain rate (p = 0.057) and twist time of peak systole (p = 0.057). The data suggests that short term progressive resistance exercise influences cardiac mechanics with racial differences. Future work could provide insight into potential clinical impact of exercise and race induced adaptations.

How do the electron interaction inside strontium ruthenate, Sr2RuO4, produce its superconducting properties? How can we better understand strontium ruthenate through improving our modeling techniques? The unusual superconducting state in strontium ruthenate  has long been viewed as being analogous to a superfluid state in fermi liquid He3, in which the paired particles form spin triplets. However, recent experimental evidence suggests that strontium ruthenate superconducts with spin singlets. We hypothesis that models based on the creation of spin singlets rather than spin triplets will match new experimental results. We propose a simple model to match some of the fundamental properties of strontium ruthenate superconducting with spin singlets. The model uses C++, GNU scientific libraries and Make Utility to calculate the Hamiltonian, magnetization and electron interactions.  Our model starts with the initial conditions of temperature, net magnetic field, potential energy, and number of atoms. The potential energy value allows for the lowest energy configuration to be electron singlet pairs. This is an early version of such a model, but we have successfully shown the suppression of paramagnetism due to spin singlets at temperatures below the superconducting temperature. In the future, we hope to add specific heat calculation and include the effects of stress on the strontium ruthenate. Through improving the modeling of strontium ruthenate, we better understand the odd phenomena and have a more complete theory of superconductivity. A better theoretical understanding of superconductivity will aid in the choice of materials could be used in the future to make new superconductors. 

Neurocognitive assessments including the Immediate Post-Concussion Assessment and Cognitive Test (ImPACT) use baseline concussion test scores to compare with scores acquired post-injury to aid in determining whether a concussion has been sustained. Numerous factors may lead to the production of an invalid score profile on the ImPACT, including failure to properly read test directions, difficulties with concentration, or intentional underperformance, among others. A 2009 study found although almost 95% of certified athletic trainers at the high school and collegiate level surveyed administered baseline neurocognitive testing to their athletes, only 51.9% reported examining the score’s validity. For this study, I hope to explore the effect of certain factors such as the presence of Attention Deficit Hyperactivity Disorder (ADHD) on the validity of an athlete’s baseline profile. Utilizing the validity indicators developed by the ImPACT, the goal of this study is to explore whether the presence of ADHD serves as a moderating variable in increasing the likelihood of an athlete producing an invalid baseline score profile. A data set of over 45,000 NCAA athletes and military cadets will be utilized to explore the hypothesis that ADHD does in fact increase the likelihood of an athlete producing an invalid score profile through the application of multiple regression data analysis. 

Previous research on magnetic massive stars has shown that the rotational velocity of these stars can decrease over time due to magnetic braking. The purpose of this research is to determine if there is a change in the rotational period of the magnetic O-type star Plaskett’s star, using long-term spectroscopic observations. The spectral data for this study came from 5 different telescopes over a period of 5 years. The reduced image data was converted to text format and then normalized. For this study, we focused on the hydrogen spectral line Hβ at 486.1 nm. The equivalent width (EW), or the measured total area above and below the normalized continuum was calculated for every Hβ profile. The EW measurements were then used to check for any changes in the period. Over time, the equivalent width measurements form a periodic pattern. Each time the pattern repeats itself, the star is beginning a new rotation. We have compared the timing of the pattern from each data set to check for a change in the rotational period, which would cause the pattern to shift in phase. The result is that there is a significant change in the phase. This implies that there are intense and complex interactions between the stellar wind and the magnetic field. This research will provide scientists currently working on this unique object improved models of the magnetic structure and a better understanding of the wind-field interaction and its consequences for the case of both a strong wind and high rotation.

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 model to explain the behavior of ee centered around a transposable P-element in the 5’ exon of the Cpr gene in a reverse-transcriptional orientation to that of Cpr. The model involves tightly packaging DNA at the site of the anti-sense P-element and all P-elements in the genome. To test the model, this study observed the effect of the anti-sense P-element on the singed and patch mutations, which involve P-element insertions in their regulatory regions. It was expected that the anti-sense P-element would induce offspring to exhibit changed phenotypes due to alterations in packaging the genes. Lines of flies containing singed and patch mutations were reciprocally mated to ee lines and a P-element containing wildtype control. Singed F1 virgin female offspring were backcrossed to ee males. Male F2 offspring were scored for abnormal singed phenotypes as they could express singed and ee. No significant difference was found between offspring and stock phenotypes. Patch F1 males were scored for abnormal patch phenotypes as they were heterozygous for patch and ee. Experimental results correlated strongly with the control, indicating that the observed effect was caused by P-elements, not ee. This project is important as it provides insight into mechanisms of development, especially in understanding P-elements in relation to gene expression.

The Hayflick limit phenomenon states that there is a limit to the amount of times (about 40-60 times) a cell may divide before senescence or apoptosis is induced. The cell division limit is due to telomeres, repetitive sequences at the ends of chromosomes, shortening after each cell cycle.  Telomerase is an enzyme that contains an RNA template and h.TERT that is able to regenerate telomeres at the ends of chromosomes. High levels of telomerase are present in stem cells and most human cancers. However, in vitro, cancer cells follow the Hayflick limit phenomenon and go through senescence. The purpose of this project is to create an immortalized cancer cell line through the process of transfecting a bacterial plasmid containing the human Telomerase reverse transcriptase (h. TERT) protein. E. coli containing the h. TERT plasmid was grown in LB plates, and the plasmid was isolated using QIAprep Spin Miniprep Kit. Transfection occurred using Lipofectamine Reagent on D17 (canine osteosarcoma derived from metastatic site: lungs) cells. Immortalization using telomerase allows for the growth of cancer cells in vitro without the occurrence of cell death. Immortalization of cell lines is an important tool in the field of biology. In theory, these cells are homogenous, which helps in producing replicative and stable results; this is extremely valuable in cell biology experiments.