Research Project Descriptions

Primary tabs

Elucidating Maize Diterpene Metabolism: Site-Directed Mutagenesis of Kaurene Synthase 2

Student Name: 
Eileen Toh
UCD Department: 
Plant Biology
UCD Mentor: 
Dr. Philipp Zerbe

As the most harvested crop in the United States, maize (Zea mays) serves as a source of food, livestock feed, and biofuel. Pests, pathogens, and abiotic stresses contribute to significant crop losses, and the stresses, particularly drought, have only been exacerbated by climate change and rising global temperatures. All higher plants including maize produce an array of specialized metabolites that coordinate the plant’s interaction with the environment. Among these metabolites, diterpenes constitute the largest and most diverse group of compounds and have critical functions in the defense of maize against pest and pathogens. Recently, two diterpene synthase (diTPS) enzymes were identified in maize and shown to play a role in these stress responses: kaurene synthase 2 (KS2) and kaurene synthase 4 (KS4). While both proteins utilize the same substrate, ent-copalyl diphosphate (ent-CPP), which is produced by the class II diTPS Anther Ear2 (An2), the two enzymes produce different products. Investigation of the structural-functional differences of these two enzymes through expression in Escherichia coli (E. coli) and activity analysis with gas chromatography/mass spectrometry (GC/MS) enabled the identification of several amino acid residues that are important for the distinct enzyme functions. These findings contribute to our understanding of the chemical diversity of plant diterpene metabolism, and may be an opportunity for improving stress resistance in maize.

Investigating Simulator Sickness during an Immersive Virtual Reality Navigation

Student Name: 
Elli Stogiannou
UCD Department: 
Psychology
UCD Mentor: 
Dr. Arne Ekstorm

Simulator sickness is a condition that has emerged along with the advancements in the field of Virtual Reality (VR). Simulator sickness originates from the incongruity between the motion of the simulation and the motion of the performer in the simulation. Simulator sickness (SS), also known as cyber-sickness, is characterized by multiple symptoms, clustered in three general categories: symptoms related to nausea, oculomotor disturbances , and disorientation (Kennedy, Lane, Berbaum & Lilienthal, 1993). However, there is deficient insight into what causes SS, and how it can be effectively prevented. This research investigates the factors that serve as indicators as to whether someone is susceptible to SS and further explores the possible ways to prevent the appearance of SS related symptoms. Peripheral SS data from a navigation experiment using a head-mounted VR display and an omnidirectional treadmill was coded and analyzed to determine which measures, collected by the experimenters, might be able to predict subsequent attrition in the study. Results obtained show that experience with video games and treadmill proficiency, as rated by the experimenter during a training phase on the VR treadmill, are critical factors that may predict SS. Based on this analysis, if these factors are rated poorly, the probability of SS occurring is high. These findings have major implications for both the private sector, where companies are producing VR for commercial uses, and for the public sector. In the public domain, this research is beneficial for services using VR interfaces for educational purposes, such as Army Institutes, and it contributes to the field of spatial cognition research.

Arabidopsis Thaliana Cell Plate Formation: an Interdisciplinary Approach to Characterizing ES7 Resistant Mutants

Student Name: 
Emily Dickinson
UCD Department: 
Plant Biology
UCD Mentor: 
Dr. Georgia Drakakaki and Destiny Davis

There is currently a lack of knowledge surrounding the signals and factors that lead to cell plate formation during cytokinesis. Although scientists in the field know the multistep process of the cell plate formation, there is still much to be learned about the molecular events occurring during formation. The Drakakaki lab at UC Davis is studying endomembrane trafficking and polysaccharide deposition at the cell plate. By using the chemical Endosidin 7(ES7), which inhibits cell plate maturation by specifically impeding callose deposition, the researchers have developed mutant strains of the Arabidopsis thaliana that are resistant (Park et. al 2013). Characterization of two mutants es7r-1 (ems 13) and es7r-3 (ems 70) by root length and subcellular effect in response to ES7 will yield the target gene and therefore a novel protein active during cell plate formation. In addition, a cell plate vesicle proteomics approach will lead to a collection of cell plate-destined proteins which to study further

Potential Tyrosine Sulfation Sites in Cadherins

Student Name: 
Emily Yang
UCD Department: 
NPB
UCD Mentor: 
Dr. Grace Rosenquist

Tyrosine sulfation is a permanent posttranslational modification to a protein that regulates protein-protein interactions. This project focuses on predicting potential tyrosine sulfation sites in type II cadherins, transmembrane proteins dependent on calcium-ion binding. Evidence from statistical data, 3-D protein modeling, and conservation data supports that tyrosine sulfation could occur in type II cadherins. Two of the predicted potential tyrosine sulfation sites showed to contain known calcium-binding sites. However, a study has shown tyrosine sulfation to decrease calcium-ion binding in a particular peptide hormone. If this study is true for all proteins, the location of tyrosine sulfation sites near calcium-binding sites would be impractical. Further research would be needed to clarify if tyrosine sulfation actually occurs in cadherins and the effect it might have on cadherin function. 

Determining the Affect of Diabetes on Rat Cells

Student Name: 
Eric Gu
UCD Department: 
Molecular Biosciences
UCD Mentor: 
Dr. Cecilia Giulivi

Examining how diabetes has affected the shape of certain parts of the cells of the rats. One group of rats has had a gastric bypass performed to delay the onset of diabetes, whereas the control group will develop diabetes normally without the surgery. The researchers will then harvest the cells from the heart and muscles of the rats after specific time intervals. Hopefully, by studying how the mitochondria are affected, the team will be able to provide more insight as to how diabetes affects the body.

The effect of microwave intensity and exposure on the carotenoid concentration of a cassava gari meal with added red palm oil.

Student Name: 
Ethan Udell
UCD Mentor: 
Dr. Betty Burri

Cassava gari is a staple food in Africa, which has been biofortified to help combat vitamin A deficiency. However, a correlation is often seen between the extent of gari preparation and a decrease in the carotenoid concentration of the gari. The objective is to find out if higher microwave intensities and longer duration of exposure to microwaves may decrease the carotenoid concentration in cassava gari.

Determining the role of endogenous auxin in sunflower heliotropism

Student Name: 
Faith Ajayi
UCD Department: 
Plant Biology
UCD Mentor: 
Dr. Stacey Harmer & Hagop Atamian

Sunflowers grow in response to sunlight in a movement called heliotropism, in which they track the sun. Their heliotropism has been proven to be regulated not by direct light stimulus, but by their circadian clock (Atamian et al. 2016). We now show the role of auxin, a naturally occurring plant growth hormone, in the clock’s regulation of sunflower heliotropism. Our experiments suggest that auxin is released at different times during the sunflower’s heliotropic cycle, causing stem elongation, which makes the plant grow in different directions.
 

The Identification of Bacteria Species in Vermicompost

Student Name: 
Gloria Liou
UCD Department: 
USDA Agricultural Research Services
UCD Mentor: 
Dr. Daniel Kluepfel

Standard microbial culture-based methods were used to study the composition and diversity of three vermicompost samples (Terra Vesco, Sonoma, CA, USA). Bacterial colonies were isolated from vermicompost using serial dilutions. The amplification and sequence analysis of 16S rDNA from 39 isolates showed a high percentage (79%) of Actinobacteria sp., especially Arthrobacter sp. (54%) and Streptomyces sp. (15%). Proteobacteria and Firmicutes sp. were also detected. The level of bacteria diversity in the soil supported the idea that microorganisms in vermicompost may be able to outcompete and reduce soil-borne pathogen populations, making vermicompost a viable disease-control method for the agriculture industry.

Chlorella sorokiniana Growth in Wastewaters

Student Name: 
Gregory Martin
UCD Department: 
Chemistry
UCD Mentor: 
Dr. Annaliese Franz

The algae species Chlorella sorokiniana was grown in dairy waste water (DWW) and in nitrogen reduced anaerobic digester effluent (ADE) at differing concentrations to find the optimal concentrations for growth. The effect the waste water had on the algae was measured by absorbance at 750nm, chlorophyll fluorescence, Nile Red lipid assay, and microscopy. Results indicated that the maximum concentration of DWW Chlorella sorokiniana can grow in while achieving robust growth is 56% and 100% for ADE. The most robust growth and lipid production were seen in the lowest concentrations of DWW and ADE at 10% and 50% respectively. The effect of additional ammonia in ADE on algal growth was also tested and demonstrated that Chlorella sorokiniana will not grow in concentrations over 10mM additional ammonium in 100% ADE.

Cloning and Preliminary Characterization of STY46 from Arabidopsis thaliana, a Candidate Protein Kinase Involved in the Plant Sugar Starvation Response

Student Name: 
Haishan Gao
UCD Department: 
Department of Plant Sciences
UCD Mentor: 
Diane M. Beckles

To study how plants respond to conditions under which the carbohydrates needed for growth and development are exhausted, this project focuses on cloning and functional characterization of a cytosolic protein kinase, STY46 that may potentially be involved in the sugar starvation response (SSR). Generating A. thaliana STY46 knockout (-KO) and overexpression (-OE) lines is the main method in this project to determine the function of the protein. A SALK line (SALK_116340) was confirmed to contain a T-DNA insert in the STY46 gene and the aim was to prove that this reduced the expression of this gene. Highly intact RNA was isolated and reverse transcription PCR performed to determine the level of transcript of STY46 in STY46-KO. However the results were inconclusive. This may be due to not enough amount of RNA use for the cDNA reverse transcription. To develop an overexpression line, STY46 was cloned from wild type Arabidopsis genotype. Primers were designed to flank the open read frame of the STY46. They also contained restriction enzyme recognition sites and a myc-tag engineered at their 5’ ends to facilitate subsequent synthesis of a plant transformation construct. A cDNA fragment of the expected size was successfully amplified by PCR. 

Spatio-temporal dynamics and physiological characterization of post harvest chilling in tomato fruit.

Student Name: 
Hansalia Sahil
UCD Mentor: 
Dr. Diane Beckles

Magnetic resonance imaging was used to spatially and temporally examine physiological changes in tomato fruit (S. lycopersicum var. cerasiforme cv. sweet 100) caused by exposure to chilling temperatures. Measurements for respiration and ethylene production showed the development of chilling injury as indicated by the chilling injury index. The MRI was used to calculate the apparent diffusion coefficient (ADC), a measure of water mobility in tissues, for different regions of interest (ROI) in the fruit.

An Investigation into the Buffering capacity of foodstuffs

Student Name: 
Henry Harrigan
UCD Department: 
Biological & Agricultural Engineering
UCD Mentor: 
Dr. Gail Bornhorst

While many studies have been conducted into the various buffering capacities of feed and cheese, no comprehensive study has ever been conducted into buffering capacity of protein and carbohydrate in the gastric environment. One specific area of interest is into how buffering capacity affects larger scale digestive processes in the stomach, such as gastric emptying and enzymatic secretion. To understand this, we first need a understanding of buffering capacity in the gastric environment. In this study we examined the buffering capacities of a variety of different mixtures of basic carbohydrate and protein. The two constituents were Whey protein isolate, and granulated cane sugar. These were dissolved in water as well as apple juice depending on FDA determined values for what average Americans consume. The difference in the buffering capacity between these repetitions will help us understand how the buffering capacity of foodstuffs changes with secretion of HCL. We found that buffering capacity of whey in water and juice is highly augmented in juice as opposed to water, and is further increased by the addition of whey protein, but little change results from the addition of sugar.

Creating Molecular Pesticides Against Olive Fruit Flies

Student Name: 
Irene Lin
UCD Department: 
Department of Chemistry
UCD Mentor: 
Dr. Dean Tantillo

Creating a pesticide against the olive fruit fly, which damages olives and affects the quality of olive oil. Irene is working on this project by using computer software to build molecules and test how well they work. An effective pesticide would have a large positive impact on the California olive oil industry, which produces a majority of American olive oil.

Two parental and 16 F2 offspring nematode lines were studied using polymerase chain reactions, restriction enzyme digestions, and agarose gel electrophoresis. Analysis of the final banding patterns allowed for comparison of parental and offspring mitochondrial DNA.

Results showed that paternal mitochondrial inheritance did not occur in any of the offspring lines. Even so, the limited sample size makes further experimentation necessary in order to conclude whether ever paternal inheritance occurs. Even more analysis is required to determine whether nematodes’ amoeboid sperm is responsible for this phenomenon.

 

Primary and Tertiary Trends of Tyrosine Sulfation

Student Name: 
Jack Youstra
UCD Department: 
Molecular and Cellular Biology
UCD Mentor: 
Dr. Grace Rosenquist

Tyrosine sulfation is a modification to tyrosine where sulfate ions are attached to the hydroxyl group at the end of the tyrosine. Primary structure trends in sulfated sites were revealed by comparing a sample set of 104 sulfated and 674 unsulfated tyrosine sites while tertiary structure trends were revealed by analyzing x-ray crystallography data from sulfated proteins. Primary structure analysis revealed the linkage between charge, hydrophobic nature, and proximity to a terminus with sulfation as well as the linkage between outliers, such as cysteine, with sulfation. Tertiary structure analysis revealed the linkage between hydrogen bonding and sulfation, especially with positively-charged amino acids. These tertiary characterizations reveal the increased stability brought by the increased hydrogen bonding network from tyrosine sulfation while the primary characterizations help provide refinement to tyrosine sulfation prediction when coupled with the existing PSSM method of prediction.

Role of Mitochondrial Inner Membrane Complex Organizing System in Fibroblasts from FMR1 Premutation Carriers

Student Name: 
Jacob Eisner
UCD Department: 
Molecular Biosciences: Vet Med
UCD Mentor: 
Dr. Cecilia Giulivi and Sarah Wong

FXTAS is an adult onset neurodegenerative disorder known to cause symptoms such as intention tremor and gait ataxia, which grow in severity with age. It is also possible to have the FMR1 premutation that causes FXTAS without experiencing symptoms of the disorder. In this study, fibroblast samples isolated from FMR1 premutation carriers with and without FXTAS and age and sex matched controls were tested through PCR in order to determine the gene expression of MICOS protein encoding genes and the FMR1 gene. Samples from male premutation carriers displayed a downward trend in expression of MICOS protein encoding genes and the FMR1 gene as age increased, whereas samples from female premutation carriers exhibited the opposite trend. Although this pilot study does not provide enough conclusive data to accurately and precisely justify any conclusions, it can be inferred from these data that males overexpress the genes tested while young in order to compensate for deficits associated with the premutation and resist pathogenesis until they grow too old to do so effectively, whereas FMR1 premutation heterozygous females underexpress the genes tested while young due to a compensatory response in the remaining unaffected allele.

Pages