Research Project Descriptions

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The corC Gene Influences Bacterial Sensitivity to Two-Peptide Bacteriocin Plantaricin EF

Student Name: 
Alice Gevorgyan
UCD Department: 
Food Science and Technology
UCD Mentor: 
Maria Marco

Plantaricin EF is an antimicrobial peptide produced by Lactobacillus plantarum to eliminate competition for food and resources. The exact mechanisms through which Plantaricin EF (plnEF) causes cell death are not known, but research in this lab (manuscript pending) has suggested that plnEF binds to magnesium channels on a cell’s surface to cause membrane leakage and cell death. The objective of the current study was to provide evidence that corC, encoding a putative magnesium efflux pump, serves as the molecular receptor for plnEF. In order to determine if there was a connection between the corC gene and plnEF susceptibility, two strains of L. plantarum and nine strains of L. pentosus, all of which are very closely related to the plnEF producer L. plantarum strain 8826, were isolated and used for DNA extractions. The corC genes from these isolates were sequenced and their sensitivities to plantaricin were measured using 96-well microtiter plate assays. By combining the data from the sequencing and the sensitivity assay, it was found that sequence divergence of the corC gene was associated with altered sensitivities to plnEF. This research can help clarify the mechanisms through which plnEF acts and fill in some of the immense gaps in knowledge that exist in the understanding of bacteriocins. Eventually, this research can help other researchers turn bacteriocins into a new class of antibiotics and aid in the incorporation of plantaricin into the food industry to provide safer, cleaner food.

Determining conserved motifs that distinguish high-expressed introns from low-expressed introns with a genetic algorithm on the C. elegans genome

Student Name: 
Allen Mao
UCD Department: 
Molecular & Cellular Biology
UCD Mentor: 
Ian Korf

In a wide variety of eukaryotes, some introns elevate mRNA accumulation to increase gene expression. However, the biological mechanism for this process is not well understood and it is unknown why some introns have this effect while others lack it. In this research, the object is to have a better understanding of intron function to gain greater control over gene expression by creating a genetic algorithm that identifies sequence motifs that are more commonly found in introns of high expression than introns of low expression. The approach for creating the genetic algorithm consists of generating random motifs, selecting fit motifs as per an objective and fitness function, and randomly mating and mutating motifs in order to yield high surviving motifs against the objective and fitness function.

The Effect of Mutations in Tropomyosin on Their Susceptibility to Protease-Facilitated Digestion

Student Name: 
Amy Du
UCD Department: 
Department of Neurobiology, Physiology, and Behavior
UCD Mentor: 
Dr. Aldrin Gomes

Tropomyosin works in conjunction with the troponin complex to regulate muscle contraction and relaxation. It is an alpha-helical protein that extends over the actin’s myosin binding sites. When calcium binds troponin, troponin interacts with tropomyosin in a way that changes tropomyosin structure, allowing myosin to bind to actin. Tropomyosin mutations are known to cause hypertrophic and dilated cardiomyopathy. However, the pathway for this is unknown. Preliminary studies conducted on tropomyosin studied the presence of phosphorylation sites and the up or down regulation of their phosphorylation, suggesting a structural change in the mutants. The presence of phosphorylation sites on tropomyosin were recently found but the functions of these sites are not known. Altered phosphorylation levels are usually important in protein function. To explore if mutations or phosphorylation of tropomyosin affect its conformation digestion of different tropomyosins was carried out. Trypsin digestion of tropomyosin mutants compared to the wild type suggest that the change of a single amino acid sequence affects digestion, which may be related to the structure. Since structure dictates function, a change in shape suggests a change in function. The implications of these results allow us to see the potential mechanism (structural change) for which mutated tropomyosin proteins may cause cardiomyopathy.

The Effects of Varying Concentrations of Different Chemicals on the Growth Rates of Microcystis aeruginosa

Student Name: 
Andrew Chen
UCD Department: 
Department of Anatomy, Physiology, and Cell Biology
UCD Mentor: 
Dr. Swee Teh

Microcystis aeruginosa is a unicellular, colonial cyanobacterium that produces a potent class of hepatotoxins called microcystins (MCs). During harmful algal blooms (HABs), Microcystis populations can drastically increase and release substantial quantities of microcystins into the surrounding waters upon cell death. These toxins can compromise environmental and human health. Therefore, it is important to understand what factors inhibit or stimulate Microcystis growth. In this study, Microcystis cultures were exposed to Roundup (glyphosate), bisphenol A (BPA), Diuron, and lab-created microplastic solution in a 96 well plate. Growth of the cultures were tracked daily by measuring the absorbance of chlorophyll in each well with a spectrophotometer. After three days, treatments that exhibited substantial growth inhibition or stimulation from the control group were scaled up to 250 mL flask exposures. A more concentrated microplastic solution was created for the flask exposure in order to explore the effect of a more concentrated exposure. The results of this study revealed that exposure to Diuron severely inhibited the growth rates of Microcystis. BPA and glyphosate inhibited growth in the well plates, but stimulate growth in the 250 mL flasks. Exposure to the microplastic solution inhibited growth more severely in the flasks than in the 96 well plate.

The Role of Tyrosine Sulfation in Liver Regeneration

Student Name: 
Archita Bhattacharya
UCD Department: 
Department of Neurobiology, Physiology, and Behavior
UCD Mentor: 
Grace L. Rosenquist

Tyrosine sulfation, the posttranslational modification of the amino acid tyrosine, has been discovered in countless major proteins in the body, and this study has predicted new sites in the proteins essential to liver regeneration. Liver proteins associated with regeneration were scored in a PSSM calculator. A wide variety of these proteins, including Fibroblast Growth Factor Receptors, Transforming Growth Factorsere found to have high scores, and a collection of predicted sulfation sites were found to also have natural variants. A total of 45 predicted sites were found with scores over the high cutoff of 2.42. In addition, 5 protein sites with high scores were found in clusters. The information on predicted sites could be used to understand regeneration of organs in other organisms and to develop methods aiding the natural process of liver regeneration.

Synthetic and natural auxin plays a major role in solar tracking for sunflowers

Student Name: 
Breana Lee
UCD Department: 
Department of Plant Biology
UCD Mentor: 
Stacey Harmer

Sunflowers undergo heliotropism, the dynamic form of phototropism, which is the directional growth of a plant towards a source of light. The goal of this project is to investigate how sunflowers adjust its growth patterns and respond to changes in the environment to better understand the solar tracking behavior of sunflowers. Hormones, such as auxin, play an important role in plant growth and cell elongation.  In Stacey Harmer’s lab, heliotropism has been studied by testing synthetic and natural types of auxin, identified as 2,4-D and IAA, respectively. In this experiment, IAA, a natural form of auxin, was applied to the east or west sides of sunflower stems at dawn or dusk. To investigate the movement of sunflowers in response to the application of IAA, images were collected measuring the angle between the apex of the plant with respect to the horizon line. Graphical analysis of the angles of curvature showed that when treated with IAA, sunflowers exhibited similar changes from natural heliotropic movement as when 2,4-D was applied. These findings confirm that when applied, auxin, in both its synthetic and natural forms, is responsible for the change in the natural movement of sunflowers and thus proves that auxin has a profound effect on sunflower heliotropism during the day. The knowledge gained by studying heliotropism in sunflowers can be applied to other economically important  plants and may improve the growth and maintenance of these plants for the agricultural industry.

Synthesis of amorphous molybdenum disulfide and tungsten disulfide to be used as a catalyst for carbon dioxide reduction

Student Name: 
Camille Killeen
UCD Department: 
Department of Chemistry
UCD Mentor: 
Jesus Velazquez

Atmospheric carbon dioxide can be used in the carbon dioxide reduction reaction to produce fuels such as 1-propanol, methane, acetate, ethylene glycol and formate from the CO2 reduction using amorphous molybdenum disulfide (MoS2) and tungsten disulfide (WS2) as catalysts. Wet chemical synthesis of these catalysts has been performed and their efficacy for this reaction has been investigated. The MoS2 and the WS2 were characterized to confirm their chemical composition and that they were amorphous. The catalysts were tested as thin films on silicon wafers at a potential of -1.6 V for 15 coulombs (24 hours), testing the efficacy through nuclear magnetic resonance spectroscopy (NMR) to discover the products of the CO2 reduction. While all of the previously mentioned products are useful, the most impressive was 1-propanol. This research may lead to a practical, cost-effective way to produce these fuels from atmospheric CO2 as a renewable source of energy.

Characterization of the effects of inhibiting fatty acid beta-oxidation in Breast Cancer Cells

Student Name: 
Carl Gibson
UCD Department: 
Department of Molecular Biosciences, School of Veterinary Medicine
UCD Mentor: 
Cecilia Giulivi

Differences in the metabolism among a population of breast cancer cells leads to difficulty in fully destroying the tumor. This metabolic heterogeneity was found in glucose-specific pathways and seemed to rely on interdependence among the tumors. This study hypothesized whether cancer cells, within a single tumor, could be separated based on their oxidation of glucose over fatty acids as a fuel source. This was accomplished by utilizing MDA-231 breast adenocarcinoma cells with two different, but directed to the same target (carnitine palmitoyltransferase I or CPT-1), inhibitors of fatty acid beta-oxidation: etomoxir and 4-hydroxy-L-phenylglycine (HPG). Cells were grown for 4-5 weeks on these inhibitors to ensure selection, and then different parameters were evaluated: mitochondrial respiration, cell proliferation, metastasis, pluripotency, and differentiation. The cells that were grown in etomoxir were more metastatic than the control, but had no effect on the other aspects measured in the cells. HPG increased metastatic capacity of the cells, ATP production with octanoate, and cristae density (cytochrome c oxidase over citrate synthase activities), whereas decreased cell differentiation (as judged by ESR1). Neither etomoxir nor HPG had an effect on cell pluripotency. Neither of the treatments affected cell viability or proliferation (evaluated as doubling time). The differences between inhibitors could be due to the presence of the CPT-1b form in breast cancer cells (mainly inhibited by HPG) vs. CPT-1a which is more inhibited by etomoxir. In conclusion, breast cancer cells forced by HPG to grow on glucose oxidation tend to have more metastatic capacity and decreased differentiation, suggesting a shift towards stemness, and developed more active mitochondria, whereas etomoxir-induced glucose oxidation only led to more metastatic capacity.

Comparing and Contrasting the Aspects of PCR and Taqman Assays

Student Name: 
Chelsea Mai
UCD Department: 
Mouse Biology Program Center for Comparative Medicine
UCD Mentor: 
Dr. Joshua Wood

The Mouse Biology Program is a production lab that specializes in producing transgenic and KO mice. To identify whether or not the initial founder mice contain the correct DNA modification, a screening process must take place (Garibyan, Avashia 2014). In retrospect, Sanger sequencing is a method that occasionally can give inconclusive results because the possibility of mosaicism arising due to the inherent multiple mutagenic nature of CRISPR modified genes. Taqman and PCR are more efficient in screening DNA, but due to slightly higher costs of Taqman, PCR vs. Sanger sequencing and the need for accurate data, traditional PCRs and Taqman assays require additional research to discover where they are best applied (Applied Biosystems). This project included the comparison of two pieces of biotechnology: Taqman QPCR and traditional PCR, in order to optimize the efficiency of the screening methods used to look at DNA insertions. Analyzing these screening methods helped provide MBP with the most effective way to produce gene edited mice thus furthering scientific research. The Taqman QPCR and traditional PCR screened a Knock In (KI) of SNPs and of loxP/CRE of the gene mir29a. By analyzing a gel and amplification curve of the screenings of this gene, it can be determined whether a Taqman or PCR is better suited for a particular method.This research contributed to enhancing the efficiency of this production lab. It is essentially a chain reaction: with better accuracy in screening DNA , MBP has more resources to produce gene edited mice at a faster rate thus providing research labs with more mouse models. By creating a library of mouse models, research labs looking for a certain gene function will have easy access to a mouse model with the desired gene function.

Search for a Homozygous Mutation of the LUX Gene in Sunflowers

Student Name: 
Cheryl Liang
UCD Department: 
Department of Plant Biology
UCD Mentor: 
Stacey Harmer

Sunflowers track the sun during the day, moving from east to west from dawn to dusk respectively. However, at night, they move back towards the east in anticipation of the sunrise despite a lack of sunlight. It is known that the circadian clock plays a role in regulating this heliotropism that increase plant fitness. Seeds from a heterozygous mutant plant were planted in an attempt to find a homozygous recessive mutation of the LUX gene that represses day-phased genes in the circadian clock of Arabidopsis thaliana. Using DNA extraction, PCR, and restriction digestion, no plants of the twenty samples were found to be a homozygous recessive mutant. Future research includes performing the experiment again with more samples, and once a mutated plant is found, planting the homozygous mutant plant in a field to observe any phenotypic differences from typical behavior. Understanding how a disrupted LUX gene affects the circadian clock and solar tracking may help future research in improving plant adaptations to increase plant productivity on a molecular level.

Implications of early loss of vision on tactile discrimination and motor capabilities in Monodelphis domestica

Student Name: 
Chris Iyer
UCD Department: 
Center for Neuroscience
UCD Mentor: 
Leah Krubitzer

Loss of vision at an early developmental stage results in profound anatomical and functional alterations in the brain. These neural changes result in cross-modal cortical plasticity, the process by which the deprived cortex is co-opted or taken over by the spared sensory systems. In this study, we investigated the extent to which the neocortex of the short-tailed opossum (Monodelphis domestica) can compensate for the lack of visual input by augmenting somatosensory and motor systems. We examined behavioral correlates of this plasticity by comparing the gross and fine motor capabilities of enucleated and control opossums in a skilled reaching task. Furthermore, we explored the impact of housing conditions on the extent to which visually-deprived brains can adapt and compensate. Our results indicated that the enucleated opossums significantly outperformed the control opossums in both the light and dark conditions, and that tactilely-enriched opossums could potentially demonstrate superior motor control, likely due to enhanced tactile and olfactory capabilities. These results imply that cross-modal reorganization can not only compensate for blindness but allow the animal to outperform normal animals in some sensory-mediated behavioral tasks, offering a foothold for further research into the exact mechanisms involved in plasticity, the brain’s full capacity for remodeling, and potentially improved therapies for sensory-impaired patients.

Physical and Chemical Property Changes during In-vitro Gastric Digestion of Boiled and Fried White Potatoes

Student Name: 
Daniel Kim
UCD Department: 
Department of Biological and Agricultural Engineering
UCD Mentor: 
Gail Bornhorst

As the physical properties of foods are linked to the processes and the functionalities of the digested materials, a demand for the knowledge of how food behaves during gastric digestion from the public has increased. The main objective of this study was to compare two contrasting cooking methods, frying and boiling, that were utilized in order to investigate the differences between the physical property of the boiled and fried white potatoes. The data collected will be part of a broader system that classifies food based on digestive properties: The Food Breakdown Classification System. This classification system aims to predict a food’s digestive behaviour based on its physical properties measured after in vitro digestion. The physical property that was measured from the white potatoes in this experiment was hardness. A Texture Analyzer was used to measure the hardness. The pH and the brix of the digestive fluids were also accounted for. Potato cubes were digested in simulated saliva and gastric juice for six time points of varying length. It was hypothesized that the potato cubes digested for longer time points were to have lower hardness values overall. Also, the pH and the brix of the digestive fluids were expected to increase as the digestion time increased. At the end of the investigation, it was concluded that the fried potatoes had an overall lower hardness than the boiled potatoes. LIkewise, the pH and the brix of the digestive fluids of both boiled and fried white potatoes increased as the digestion time increased.

The relationship between enzyme structure, thermostability, catalytic efficiency of threepoint-mutations in theβ-glucosidase B enzyme

Student Name: 
Darren Wang
UCD Department: 
Department of Chemistry
UCD Mentor: 
Justin B. Siegel

The ability to accurately view a protein in 3 dimensions is very new. Although the images are accurate, the data the models give are faulty due to lack of background data. With a massive database, scientists can compile an algorithm that will greatly help future enzyme engineers. In the future, they no longer need to test every mutant they find interesting in a wet lab, scientists will only need a laptop and a few minutes instead of a weeklong process. So far, the Siegel lab has collected data for 129 mutants of beta-glucosidase enzyme, also known as BglB. For this research, 6 original enzymes are designed using the current computational model, also known as the Rosetta Model, to mutate BglB. Other mutants of the BglB enzyme were grown simultaneously. Lastly, a positive control was used as a benchmark. After the cells were induced with the desired DNA, assays were executed to calculate the thermostability and the Michaelis-Menten constants (kcat, KM, and kcat/KM). Although the research has no short-term results, the small amount of data we can provide is still valuable for the development of a better predictive algorithm. As seen from the data we collected, we can see a general trend of lowering of catalytical efficiencies and a rise in thermostability for the three specific mutants.

The effect of somatostatin on mRNA expression in mouse pancreatic beta cells

Student Name: 
Eleanor Goh
UCD Department: 
Department of Neurobiology, Physiology, and Behavior
UCD Mentor: 
Mark O. Huising

Healthy mature beta cells secrete the peptide hormone Urocortin3 (Ucn3) to regulate insulin secretion through a negative feedback loop involving somatostatin, which suppresses insulin secretion. In the beta cells of diabetic mice and humans, Ucn3 levels are significantly lower than those in healthy individuals. The resulting low levels of somatostatin lead to sustained insulin secretion, where insulin production rate lags significantly behind release rate. The stress induced by sustained secretion may then lead to beta cell dysfunction. Adding somatostatin may induce beta cell rest, restoring beta cell function. This study shows the potential of somatostatin in amplifying the beta cell’s acute insulin response, suggesting a key role of somatostatin in the regulation of beta cell maturation markers under high glucose conditions. Finding new methods to provide beta cell rest could lead to new treatments in which beta cell dysfunction can be reversed.

The Emergent Nature of Alignment Effects in Spatial Learning and Memory

Student Name: 
Elliot Clark
UCD Department: 
Center for Neuroscience and Department of Psychology
UCD Mentor: 
Dr. Arne D. Ekstrom,

Alignment effects were found to have an emergent nature. Individual differences in the data across participants of two spatial memory experiments were analyzed to find an accurate period in which alignment effects begin to occur. In Experiment 1, participants navigated to goals in a large-scale, virtual environment interspersed with a pointing task to assess spatial memory. The procedure for Experiment 2 was identical to that of Experiment 1, but added an additional task in which participants learn the environment to criteria with a map before exploring the environment. In both experiments, there was a significant difference in performance levels on the pointing task between aligned trials and misaligned trials, but only after repeated exposure to the environment. Though alignment effects are well documented in the literature, little is known about brief period when they manifest. The results confirm that alignment effects are not expected initially, after brief experience, but rather that they arise after learning.

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