Participants work one-on-one with a research mentor, including faculty, post-doctoral researchers, and doctoral students in state-of-the-art UC Davis laboratories on an individual project.

Past projects included hands-on bench research, field research, or computer-based research.

Each participant will prepare a journal quality paper and a symposium presentation about their work.  Participants are supported in the preparation of their paper and symposium presentation through checkpoints and assignments throughout the six week program, as well as support from their counselors. After completion of the program, participants will receive five (5) units of University Group Study Credit.

Below are the abstracts of past papers written by participants.

2023 Research Projects

Student Name: Andrew Chao
UC Davis Department: Plant Sciences
UC Davis Mentor: Dave Tseng

Suppressing Starch Branching Enzyme Gene Expression in Tomato Fruit by CRISPR-Cas9

Starch branching enzymes (SBEs) are a critical component to starch biosynthesis and starch structure in plants.  Because of their influential nature, they have been widely studied in horticultural crops such as tubers and cereal crops to improve the qualities that benefit human health.  Surprisingly, starch branching enzymes have not been studied in tomatoes, which consist of a large percentage of starch during the young fruit.  Our aim is to study the roles of SBEs in tomato plants by generating tomato plants that have mutations in the SBE I and SBE II gene, in an attempt to knock down the SBE I and SBE II protein function.  We propose that with this change there will be changes to the starch structure of tomato, which could lead to altered developmental processes as well as biochemical and physiological changes that will influence fruit quality.

Student Name: Vincent Cheung
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

The Validity of Electrical Impedance Spectroscopy (EIS) in Determining Water Stress of Walnut (Juglans regia)

Given the state of California’s water supply, it is important that agricultural water consumption is reduced while increasing the quality of product that is produced. Electrical impedance spectroscopy (EIS) is a new method of measuring plant water stress; by sending electrical current through plant tissue & determining the impedance, one could theoretically determine the best time to water depending on  changes in impedance. The goal of this study was to determine if there was a relationship between electrical impedance measurements obtained from EIS and measurements from the Scholander pressure chamber & Florapulse microtensiometer. It was determined that a non-linear, inverse hysteresis loop relationship existed between the standard water potential as measured by the microtensiometer & impedance as measured by EIS in field conditions, while a strong correlation existed between impedance & Scholander pressure chamber measurements in laboratory conditions. Future study should aim to increase the duration of measurements, and should aim to investigate the impact environmental factors have on EIS results. 

Student Name: Chloe Choi
UC Davis Department: Plant Sciences
UC Davis Mentor: Jiaqi Zhou

Understanding the Effects of Modifying RIN Gene Expression in Tomato Fruits with CRISPR/Cas 9

Tomatoes are widely consumed globally due to their health benefits and culinary versatility. My project aims to extend the shelf life of tomatoes by editing the promoter region of the RIN (Ripening Inhibitor) gene, a transcription factor that regulates the biochemical processes of ripening in tomato fruits. If the perfect tomato, one with an extended shelf life and high quality, is found then hopefully it can be sold to consumers in their local grocery stores. 

Student Name: Alyssa Cholwell
UC Davis Department: Entomology and Nematology
UC Davis Mentor: Anil Mantri 

Plasma Activated Water Evaporation Rates

In the Nansen lab we worked with a relatively new field of Plasma Activated Water. We observed the evaporation rates of Plasma Activated Water (PAW)  in order to try to see if   PAW evaporated faster than tap water which means it confirms PAW has less surface tension and we wanted to find a safer pesticide to use. 42 We also looked to see if different concentrations of plasma in water has any correlation with evaporation rates. We analyzed the color of filter papers treated with different concentrations of PAW and one treated with tap water. We then compared the colors to 85 the negative control of a dried filter paper. Our data came back inconclusive due to flaws in our experimental design, such as not taking photos for long enough time and the room not having consistent lighting.

Student Name: Dany Comparan
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Weiyi Sun

Acid and Moisture Uptake in Different Foods and Associated Texture Changes During in Vitro Gastric Digestion

A Food Break Down Classification System (FBCS) was proposed by Bornhorst et al., in 2016 and is used to list food functionality and predicted gastric digestive behavior. By adding different solid foods to this list the California food industry can have a better idea of how to create innovative food products that meet consumer needs (Bornhorst et al., 2016). This experiment studied four different foods: cantaloupe, chickpea, rice-flour pellet, and white bread. These foods underwent the process of in vitro static gastric digestion then were analyzed for their structural changes (moisture, texture, and acidity). It was found that rice pellets and white bread have a weaker structure which allows for their structural properties to change quickly during digestion. Cantaloupe had a more resilient structure so their structural properties changed moderately. Finally, it was discovered that chickpeas had the firmest structure therefore would need more digestion time to see notable changes in the structural properties. 

Student Name: Neha Dinesh-Kumar
UC Davis Department: Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Chang-il Hwang

The Effect of the YAP Inhibitor on EN1 Expression in Pancreatic Cancer Cells

Student Name: Arnav Godavarthi
UC Davis Department: Microbiology and Molecular Biology
UC Davis Mentor: Judith Fishburn

The Downstream Consequences of a Loss of Senataxin Mutation: Role of Reactive Oxygen Species in Innate Immunity

Senataxin is a genome stabilizing protein responsible for resolving R-loops, DNA:RNA that form as byproducts of transcription. A loss of Senataxin mutation can cause genome instability, resulting in multiple downstream consequences including DNA damage, innate immune activation, and elevated reactive oxygen species (ROS) production. Increased DNA damage contributes to cellular degradation and innate immune induction produces inflammation and auto-aggression. In addition, excess ROS production produces oxidative stress. DNA damage and ROS have been hypothesized to contribute to innate immune induction in cells lacking Senataxin. In order to evaluate this hypothesis, we evaluated the differences in ROS production between wild-type (WT) and Senataxin knock-out (Setx -/-) mouse embryonic fibroblasts (MEFs). We manipulated ROS levels by introducing excess H2O2 and beta lapachone (BLP) as ROS inducers and sodium pyruvate as a ROS scavenger. We found that WT and Setx -/- cells are differentially impacted by ROS inhibition and induction. We were unable to test these conditions impact to innate immune activation. However, these results suggest that genome instability from loss of Senataxin may contribute to changes in ROS production.

Student Name: Soren Granlund
UC Davis Department: Energy Graduate Group
UC Davis Mentor: Farhana Sharmin

Designing a More Sustainable Transportation System

In order to analyze the US transportation system as a whole, a life cycle assessment (LCA) was conducted to discover what systems or products are responsible for emitting the most greenhouse gasses (GHGs). In 2018 the transportation system accounted for 25% of GHG emissions in the US [6]. This research covers most of the US transportation system and takes into account the GHG emissions of internal combustion engine vehicles (ICEVs), electric vehicles (EVs), internal combustion engine buses (ICEBs), electric buses (EBs), and the alternative fuel choices for aviation and bus transit systems. The carbon footprint of these topics are analyzed from cradle to grave: including raw material production, manufacturing, transportation, operation, and decommissioning. Through our research, we found that EVs emitted considerably less GHG than ICEVs with 363.2 gCO2-eq/km and 469.1 gCO2-eq/km respectively [5]. Similarly, EBs had fewer emissions than ICEBs, emitting approximately 1,000 tons of CO2-eq (carbon dioxide equivalent) compared to the ICEBs 2,750 tons CO2-eq. Alternative fuel for transit buses concluded that electric and hybrid were the most efficient, emitting 1,000 tons CO2-eq and 1,400 tons CO2-eq respectively. In regard to GHG emissions, solar, wind, and hydropower based hydrogen fuel have the lowest global warming potential (GWP) with 0.042, 0.025, and 0.023 kgCO2eq/tkm respectively. This shows how if the US focused on replacing ICEVs and ICEBs with EVs and EBs in addition to using more sustainable fuel options in bus transit and aviation, it would be well on its way to achieving a more sustainable transportation system.

Student Name: Ram Jhawar
UC Davis Department: Animal Science
UC Davis Mentor: Dr. Patrycja Kurowska

Exploring the Impact of Obesity on Mammary Gland Development and its Effect on Estrogen Receptors and pSTAT5 Expression in Adolescent Pigs

Adult obesity is linked to an increased risk of breast cancer that can be attributed to the excessive levels of estrogen in obese individuals. As part of normal development, estrogen mediates breast growth by binding to estrogen receptors that then indirectly activates phosphorylated Signal Transducer and Activator of Transcription 5 (pSTAT5). However, excessive estrogen can also upregulate proto-oncogenes, promoting cancer development. Despite this explanation, a paradox exists wherein adolescent obesity reduces the risk of breast cancer development. We used the pig to model this complexity, as mammary gland development in pigs is highly similar to that in the human mammary gland. The goal of this study was to compare pSTAT5 and ER expression between mammary gland sections from obese adolescent pigs and healthy weight adolescent pigs. Data were expressed as average scores for the percent of the alveoli stained and the staining intensity determined by immunohistochemistry. Our data reveal lower amounts of pSTAT5 expression and fewer estrogen receptors in the obese adolescent pigs compared to the healthy weight adolescent pigs. These results suggest that underdeveloped mammary glands in obese adolescent pigs is due to reduced signaling through pathways that stimulate mammary gland growth.

Student Name: Gisselle Jimenez
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Weiyi Sun

Initial Microstructure and Structural Breakdown During in Vitro Gastric Digestion

The distribution of food’s particle size during gastric digestion reveals how much of the food is physically broken down due to the peristaltic movement of the stomach walls, in addition to the initial breakdown during oral processing. The objective of this study was to determine the relationship between initial texture and the texture changes during in vitro gastric digestion. The techniques were used to quantify moisture content, acidity, and texture in cantaloupe, white bread, rice-flour pellets, and chickpeas. Data was examined through a vacuum oven, texture analyzer, and a pH meter probe to determine how much Sodium hydroxide (NaOH) is required to increase the starting pH which reveals the effective diffusivity of acid of the sample. Hardness of individual cubes and 0.5 inches of the food sample were completed before and after digestion. Our research concluded that digestion time significantly influenced moisture and acid uptake associated with  the change of texture during digestion. 

Student Name: Lauren Kane
UC Davis Department: Veterinary Medicine: Anatomy, Physiology, and Cell Biology
UC Davis Mentor: Dr. Kent E. Pinkerton

DIfferential Pulmonary Effects of Size-Specific, Source-Oriented Particulate Matter from Fresno, CA in a Mouse Model

Air pollution is contaminated air that contains gaseous, liquid, and/or solid particles that have been emitted into the atmosphere through natural or anthropogenic processes. Particulate Matter (PM) is the complex liquid and solid fraction of air pollution that has been associated with adverse cardiorespiratory effects. Particulate Matter differs in many aspects, including chemical composition, size, and source. The overarching hypothesis for this study is to analyze the differential effects that size-specific, source-oriented particulate matter has on the lungs through histopathological scoring and cell differentials. There are four PM sources which each have two PM sizes to create nine experimental groups including the control group. The strain of BALB/c mice were exposed to their respective PM sizes and sources and then twenty-four hours later were euthanized and necropsied. Bronchoalveolar lavage fluid (BALF) was extracted, cytospin slides prepared, and examined for leukocyte cell differentials. The left lung was inflation-fixed in paraformaldehyde, processed with paraffin wax, embedded, sectioned, stained, and finally examined under a microscope. Identifying specific components of air pollution that drive pulmonary inflammation would provide better insights for future air pollution regulation policies and awareness for the dangers of air pollution. In conclusion, both sizes of regional background PM and ultrafine gas/diesel PM produced the most robust inflammatory responses. Residential heating PM and submicron fine gas/diesel produced the least amount of inflammation in the overall lung. 

Student Name: Dory Kawauchi
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Gabriela Rivera

The Effect of Long-Term Acetaminophen Use on Proteasome in the Liver

N-acetyl-para-aminophenol, or acetaminophen, is often used for treating moderate pain and reducing fever. We aim to study the effects of acetaminophen on the molecular mechanisms of proteostasis using eight 6-month-old female mice models, of which four were given water and five were dosed with 100 mg/kg of acetaminophen per day for seven days. We observed no statistically significant difference in the expression of the RPT-6 subunit of the 26S proteasome between our control and acetaminophen-treated mouse heart and liver models. Targeting ubiquitin in our western blots, we found a decrease in the relative amount of expression of these proteins in the acetaminophen-treated samples, suggesting greater proteasome activity and possible cellular stress. However, the proteasome assay of the β-5 subunit indicated no significant change in proteasome activity, acetaminophen may cause a decrease in the ubiquitination pathway. In addition, previous research has suggested that the long-term use of acetaminophen increases the amount of reactive oxygen species (ROS) which results in oxidative stress on the body. This research provides better knowledge to medical professionals so that acetaminophen is not overprescribed.

Student Name: Vaaruni Khanna
UC Davis Department: Cell Biology
UC Davis Mentor: Dr. Ian Korf

Relationship Between Gene Expression Profiles and Chromosomal Locations in Arabidopsis Thaliana

Enhancers are sequence elements that are thought to control nearby genes by altering local chromatin structure. One prediction of this model is that genes that are expressed similarly should be physically located near each other on a chromosome. In this paper, we tested whether genes with similar expression profiles were clustered together in a genome. We found that the genes in the Arabidopsis thaliana genome appear to be randomly distributed on a chromosome.

Student Name: Mio Khuyag
UC Davis Department: Evolution and Ecology
UC Davis Mentor: Jon Aguiñaga

Within- and Between-Species Differences in m=Motivation to Feed in Two Poeciliid Fish

Mixed-species groups are composed of animals from a variety of species, usually two species or more. Even though these groups are common, their function within individuals remains largely unknown. These behavioral differences within- and between-species can create complicated interactions between group members. In a standard decision-making y-maze assay, we individually tested 39 unique Poeciliid fish from two species, Poecilia formosa and Poecilia mexicana. We evaluated their decision time, and each fish was trialed twice to assess their behavior changes after repeated experiences. Our findings highlight the importance in understanding how animals interact with their environment to make decisions at an individual level. Future work should consider studying animals that have already been characterized individually to evaluate whether they retain their asocial behaviors in a social setting.

Student Name: Alistair King
UC Davis Department: Chemical Engineering
UC Davis Mentor: Siddharth Sonti

Conformational Structures of pMMO Through Molecular Dynamics

Methane-to-methanol catalysis has long been explored due to the economic potential of an efficient methanol fuel source and the benefits of removing methane from the environment. Because of the strength of the C-H bond in methane, an effective catalyst that can convert at a low temperature is essential. This has led to the exploration of enzymes and zeolites for this purpose. Particulate methane monooxygenase (pMMO), found in methanotrophs, is an enzyme whose mononuclear and dinuclear copper active sites can convert methane to methanol at ambient temperature. Molecular dynamics (MD) simulations can provide insight into conformational structures pMMO takes without its copper active sites, giving a broader picture for new materials and future use. Additional efforts can be made into exploring various forms of simulation of pMMO, such as machine-learned force fields which will allow for a higher level of accuracy at a low computational cost.

Student Name: Huali Liao
UC Davis Department: Cell Biology
UC Davis Mentor: Dr. Ian Korf

Cryptogenes: The Search for Unidentified Genes in the Caenorhabditis Elegans Genome

Genomes and the genes they contain are a foundation for modern biology. While determining the sequence of a genome is relatively straightforward, identifying the location of all the genes remains a difficult problem. Even though the complete sequence of the Caenorhabditis elegans genome was determined in 1998, the complete catalog of genes is still unknown. Technology for finding genes continues to improve meaning there may be some genes that are yet to be discovered. In this paper, we examine regions of the C. elegans genome that may harbor unidentified genes by looking for outliers in intergenic length and RNA expression. We find that there are several regions that are likely to contain unidentified genes and create a score that allows us to prioritize which regions are most interesting, therefore most worthy of further investigation.

Student Name: Jayden Lim
UC Davis Department: Ophthalmology and Vision Sciences
UC Davis Mentor: Tzu-Ni (Mini) Sin

Cell-Specific Gene Expression Correlations with CNV Morphology In Wet Macular Degeneration Mice Models

To determine cell-specific gene expression related to choroidal neovascularization (CNV) morphology in wet age-related macular degeneration (AMD) in two mouse models including the JR5558 mutant mouse and a laser-induced CNV mouse, in order to identify important gene expression and morphology changes in wet AMD etiology that may be targeted for gene editing treatments in the future. Mice genomic DNA (gDNA) was obtained through tail snipping and DNA extraction. Subsequent polymerase chain reaction (PCR) and restriction enzyme digest (RED) tests were run in order to amplify the Jak3 gene in the JR5558 strain mice. Gel electrophoresis on reacted DNA was also performed. Mice were euthanized and eyes were enucleated. Eyes underwent cryoembedding and then sectioned by a cryostat  for immunohistochemistry staining (IHC). Finally, fluorescent microscopy was performed on the stained sections. Gel electrophoresis imaging showed whether mice were homozygous dominant, recessive or heterozygous for the Jak3 gene allele pair. Mice eyes were also imaged in vivo to track CNV and lesion developments, showing morphological effects on a structural level of the retinal disruption. Eyes were enucleated and sectioned to undergo immunohistochemistry staining and finally fluorescent imaging, which showed photoreceptor disruption as well as a higher glial cell and microglia cell response for both spontaneous CNV mice and laser CNV mice models. 

Student Name: Kaitlyn Lourenco
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation Sites in Complement Proteins

Speeding up enzymatic reactions, specifically in Complement proteins through the process of tyrosine sulfation, has the potential to benefit the well-being of the immune system. Proteins were acquired through the website UniProt. We input these proteins into the Position Specific Scoring Matrix (PSSM) to find the likelihood of tyrosine sulfation. From there we used Multiple Sequence Comparison by Log-Expectation (MUSCLE) to analyze amino acid sequences and their conservation across species. We did further research on the known sulfated site of Complement C4: the PSSM scores we obtained showed a high likelihood of sulfation in its scores. We also saw conservation and clustering of tyrosine residues within the amino acid sequences of C4, serving as additional evidence of its sulfated sites. Additionally, C4 contained sites that were located on the outer part of the protein, which was also indicative of tyrosine sulfation. Among the many other Complement proteins, Complement C9 in particular had a promising indicator of tyrosine sulfation, with 100% conservation across different mammals at positions 342 and 347. Our goal was to find possible tyrosine sulfation sites based on acidity, clustering, and location.

Student Name: Mario Machado
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Gabriela Rivera

How Does Acetaminophen Affect the Proteasome in Mouse Liver?

Acetaminophen (APAP) is one of the most common and well-known painkillers, however, past research has shown that acetaminophen has negative effects on mice liver cells and also humans. In this research, we explored if APAP has any other adverse effects on mouse liver. We specifically investigated if APAP would have any negative effects on proteasome subunit expression and activity. The liver samples used to get these results were from 6 month old female mice. The APAP treated mice were treated with a 100 mg/kg dosage of APAP everyday for 7 days. This type of dosage is about the same as 480 mg dosage everyday for 30 days in humans. Western blots done to see if APAP would have any statistically significant effect on proteasome subunits were done with antibodies which bind to the following proteasome subunits: α6, PSMA-1, β2i, α3, and anti-ubiquitin. None of these western blots showed any statistically significant effect APAP could have had on the subunits. The beta 5 proteasome activity assay also showed no statistically significant results. These results suggest that acetaminophen was not significantly affecting the proteasome.

Student Name: Vivian Mai
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Julia Fan

Sythesizing Potassium Cellobionate Towards Converting it to Cellobionic Acid 

The pretreatment of biofuel is essential for biofuel generation, breaking down hemicellulose and lignin in the feedstock’s cell wall to enhance enzyme access to cellulose. Cellobionic acid is used for pretreatment, and potassium cellobionate is synthesized as an intermediate compound. Various methods, such as adjusting water levels and substituting ethanol for methanol, are explored to optimize potassium cellobionate production. High-performance liquid chromatography (HPLC) is used to analyze the effects of these modifications on yield and purity. Accidental water contamination in the methanol solution results in higher potassium cellobionate yield and reduced cellobiose presence in the precipitation, while incorporating water improves cellobiose reaction efficiency and potassium cellobionate yield. However, the purification process using methanol and acetone leads to substantial cellobionic acid loss. Further research is needed to achieve cellobionic acid production. Nonetheless, this study advances the understanding of cellobionic acid synthesis, enzyme reactions, and biofuel production optimization, contributing to eco-friendly biofuel production methods and waste reduction efforts for a greener and more sustainable world.

Student Name: Christian Majalca
UC Davis Department: Plant Sciences
UC Davis Mentors: Elia Baeza, Adrian Sbodio

Examining the Effects of Environmental Stressors on the Early Stage Development of Pistachios

We worked with pistachios in their early stage of development in order to attain data that will ultimately be used to create prediction methods for farmers. We gathered data on the firmness of pistachios shell, hull, and kernel. The data pool of pistachios was derived from a variety of locations, which had unique environmental conditions. The prediction methods will be used by farmers so they can understand whether to continue applying treatment to pistachios, or whether they’ve developed to a sufficient degree.

Student Name: Alice Mardanian
UC Davis Department: Biomedical Engineering
UC Davis Mentor: Dr. Yi Xue

Software Developments in Light-Optic Microscopy

In a rapidly changing health environment, the need for improvement in biomedical imaging is growing. Though light-optic microscopy has been useful in past years, its relevance is decreasing as a result of the natural scattering of light in deep tissues. Therefore, images created by light-optic methods are blurry, sparse, and contain little useful information. Some circumventions have included using shorter wavelengths, like x-rays, but these do damage to human tissue and should be used with caution. Our proposed solution utilizes software, such as interpolation and compressed sensing algorithms, in order to infer the lost aspects of microscopic images while maintaining the non-invasive nature of light microscopy. Throughout the investigation, we have found that signals up to 96% sparse are able to be reconstructed by the CS algorithm, and that cubic interpolation performs nearly identically to linear interpolation, whilst nearest interpolation produces incredibly patchy images.

Student Name: Matthew Mullaney
UC Davis Department: Veterinary Medicine: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giulivi

Increased Defense Response in the Female Salivary Proteome with Age

Salivary proteomics is a relatively new field with much undocumented territory, specifically in regards to the changes in protein concentrations with age. This study seeks to expand the general body of literature regarding the change of protein concentration with age in women, explore the possibility of using protein concentrations in saliva as biomarkers of age in women, and to communicate any possible health effects of our findings. We tracked the changes in the concentrations of 87 different proteins in 26 healthy women of ages 21 through 60. We created single linear regression models for each protein along with stepwise regression models for the entire dataset, using JMP Statistical Software for all statistical analyses. The proteins SLPI, LEG1, LYZ, and CRISP3 all had individually statistically significant (p < 0.05) negative correlations with age. We selected two of the six generated stepwise regression models for analysis.The decreases in the 4 individually statistically significant may lead to greater risk of infections. The decreases in LYZ and SLPI specifically appear to implicate less neutrophil degranulation with age, but increases in other salivary immune proteins implicate increased immune defense with age.

Student Name: Macey Naritomi
UC Davis Department: Plant Biology
UC Davis Mentor: Cece Nguyen

N NLR Immune Receptor Role in Defense Against Pathogen Infection 

The N gene found in Nicotiana glutinosa codes for nucleotide-binding leucine-rich repeat (NLR)  protein that confers immunity against Tobacco mosaic virus (TMV). We are interested in understanding how N NLR confers immunity to TMV infection.  For this, N NLR protein interaction studies were conducted and a number of N immune receptor-interacting proteins (NRIP) were identified. Here, our research focuses on knocking out the gene that encodes NRIP5 to test its function in the N-mediated immunity pathway using CRISPR/Cas9-based gene editing approach. For this, we used the Tobacco rattle virus (TRV) to deliver the guide RNAs targeted to NRIP5 and a marker gene Phytoene desaturase (PDS) into SpCas9 nuclease expressing Nicotiana benthamiana transgenic plants. Editing of PDS leads to photobleaching of the leaves as the TRV delivers the guide RNAs and hence could be used to monitor the editing of NRIP5. Plants infiltrated with TRV expressing guides against NRIP5 and PDS showed photobleaching spots on the leaves in two weeks post-infiltration indicating that editing has been successful.

Student Name: Branden Ngo
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation in Toll-like Receptors

Recognizing that ligand binding is a critical function of toll-like receptors, we hypothesized that toll-like receptors (TLRs) may also contain tyrosine sulfation, given the effects of tyrosine sulfation on receptor binding. We used a Position Specific Scoring Matrix to assign each tyrosine site a score that represented the likelihood of each site to be sulfated. We used the MUSCLE program in order to align TLR sequences. Using these programs, we found that tyrosine sulfation is likely to occur in toll-like receptors, given their high PSSM scores as well as the conservation of tyrosine sites across the toll-like receptors of different species. Additionally, our findings highlighted similarities between the TLR 1, 6, and 10 family and illustrated the differences between protostomian toll proteins and deuterostomian toll-like receptors. This study has predicted specific tyrosine sites in the various TLRs which can be further researched. If these tyrosine sites are sulfated as we predict and play a role in ligand binding, further research may be able to use this knowledge and discover how to prevent ligand binding of TLRs through the manipulation of these tyrosine sites, in hopes of stopping adverse inflammation.

Student Name: Joshua Richardson
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation in Viral Chemokine Receptors

The chemokine system induces the migration of immune cells, primarily leukocytes (white blood cells), to a point of infection. Tyrosine sulfation in those chemokine receptors has been proven to increase the receptor to ligand binding affinity 5 – 100 fold. Both Herpesviruses and Poxviruses have been found to encode various chemokine receptor homologs in order to better avoid immune detection and viral replication. However, there has not been previous research on the presence of tyrosine sulfation in these viral chemokine receptor homologs. The average poxvirus chemokine receptor had 1.22 more high interest sites (sites with a tyrosine sulfation score exceeding 2.42) than the average herpes virus chemokine receptor. The existence of acidic groupings within these receptors was also uncovered, and herpesvirus chemokine receptor US28 was found to have sequence similarities to CCR1 and CX3CR1 in their tyrosine sites. By understanding the presence and role of tyrosine sulfation in viral chemokine receptor homologs, we could develop new drugs that target the tyrosine sulfation in those receptors and damage the virus as a whole. 

Student Name: Ashbi Rivera
UC Davis Department: Entomology and Nematology
UC Davis Mentors: Anil Mantri, Isabel Lee-Park

Evaporation Rate of Plasma-Activated Water Versus Other Liquids

Though plasma-activated water, or PAW, has only been researched in the past few decades, it is already showing great promise as a sustainable agricultural technology. To properly utilise PAW for commercial farming, more research needs to be performed as to further our understanding of PAW as a liquid. The evaporation rate of PAW may be able to provide important insight as to how it operates. If PAW has a quicker evaporation rate, it may be due to its lower surface tension as highlighted in previous studies done by Low [1]. A lower surface may imply that PAW could spread pesticides over a larger area, in turn allowing us to use less pesticides than we currently do. Evaporation rates were not able to be examined for any of the liquid treatments included due to several flaws in the experimental set up. If this experiment is to be repeated, it is important that the observation time for treatments is lengthened, and photographs are taken in a place with consistent lighting conditions. Continuing to deepen our understanding of PAW is crucial if we plan on applying it to sustainable commercial agricultural practices. 

Student Name: Tony Shen
UC Davis Department: Ophthalmology and Vision Sciences
UC Davis Mentor: Carol Villafuerte

Analyzing Drusenoid Deposit Morphology in Age-Related Macular Degeneration

This study aimed to characterize the behavior of punctate dots in the retinal pigment epithelium (RPE) of rhesus macaques resulting from a lipid-rich diet. We utilized cryosection, immunohistochemistry, and histology to analyze the RPE with punctate dots and compared it to a negative control RPE without such dots. The punctate dots were highlighted in red using ORO staining, while the control samples were treated to remove any punctate dots.
In our examination through a microscope, we observed punctate dots across multiple retinas in the RPE, exclusively highlighted by the ORO staining. The control samples, on the other hand, exhibited no punctate dots throughout the RPE. The study concludes that the punctate lesions consist of lipids and behave similarly to drusen, but are just located in a different region
Considering the resemblance to drusen, it is inferred that these punctate lesions may have risk factors like a lipid-rich diet and smoking potentially contributing to their formation, as seen in the case of drusen associated with dry age-related macular degeneration. Consequently, these findings suggest that patients can be advised to make dietary changes to decrease the likelihood of developing punctate lesions in the RPE.

Student Name: Arshiya Singh
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

Chemically Analyzing Walnut Exudate to Identify High Molecular Weight Solutes

One of the methodologies utilized for evaluating water requirements involves employing sensors to measure water tension levels. Walnut trees pose a challenge in this context due to their tendency to exude fluid, which we call “bleeding fluid,” which prevents effective connection between the xylem and sensors. By subjecting the bleeding fluid to chemical analysis, valuable data can be acquired regarding the solutes responsible for disrupting the sensor connection. The existing research on the chemical composition of walnut bleeding fluid is rather limited, as no substantial identification of compounds in the exudate has been achieved. In light of this, we hypothesized that the fluid primarily comprises high molecular weight solutes, which also generate the high osmotic pressure we observe. Interestingly, our dimensional analysis revealed that the average molecular weight of the solutes is approximately 60g/mol, contradicting our initial hypothesis of high molecular weight solutes. ICP OES indicated that K+ accounts for 43% of the dry weight of the bleeding fluid. Additional research is crucial to identify the remaining compounds in the exudate, possibly anions like Cl- in relation to K+. 

Student Name: Jessie Song
UC Davis Department: Chemistry
UC Davis Mentor: Frank Cerasoli

Simulating Specific Properties of Water Through the TIP4P/Ice Model

Water plays a significant role in our lives and on this planet. Therefore, exploring and understanding how water functions and behaves is important. It may be surprising to many that water has a number of anomalous properties in its liquid phase. Using molecular dynamics simulations, this research explored three thermodynamic properties of water: density, isothermal compressibility, and the heat capacity. The TIP4P/Ice potential was the model used throughout the study to determine the maximum density, the minimum compressibility, and the heat capacity. From the simulations, we found that the maximum density of water occurs at around 300K, and that the minimum compressibility of water occurs at around 340 K. We then used this data to compare with a previous study that used the TIP4P/2005 model to determine the same properties. Our data shows that the TIP4P/Ice model has a lower maximum density that occurs at a higher temperature, and a higher minimum compressibility that occurs at the same temperature when compared to the TIP4P/2005 model. 

Student Name: Tanyamon Sriprapundh
UC Davis Department: Biomedical Engineering
UC Davis Mentors: Dr. Yi Xue and Daniel Zepeda

Modulating Light Intensity Using Experimental Setups to Determine the Optimal Pattern for Image Reconstruction

In biomedical imaging, light is employed due to its non-invasive nature. Light scattering is the diffraction of light waves as they propagate through an uneven medium, producing multi-scattered waves rather than singular-scattered waves. The high probability of producing multiple scattered waves poses a significant obstacle in imaging biological tissue and cells. Biomedical engineering has constantly improved in the past decades, focused on addressing this pressing issue through modulating light and its properties. In our lab, we designed new approaches for high-speed image correction by modulating light intensity using experimental setups to discover the optimal pattern for image reconstruction. We imaged scattering media slides made up of random arrangements of glass beads that simulated the uneven makeup of biological tissue using a setup of digital micromirror devices, cameras, photomultiplier tubes, and microscopes. This process consists of three main sections: hardware setup, imaging, and image processing. Our research concluded that a greater aperture size and lower sparsity are the optimal parameters due to its abundance of open channels and highest light intensity, which is reshaped for image reconstruction.

Student Name: Ritika Surana
UC Davis Department: Plant Sciences
UC Davis Mentor: Toshisangba Chiba

Genotyping and Phenotyping β-1-3 Glucan Hydrolase and Callose Synthase Genes Involved in Plant Cytokinesis

Callose, a complex β-1-3 Glucan polysaccharide, is an instrumental component of cell plate formation during plant cytokinesis. The callose hydrolase 17 gene is involved with the hydrolysis of callose, and callose synthase-like genes (GSL) are involved in the biosynthesis of callose. Our study aims to investigate the functional mechanism of these genes involved in callose remodeling during cell plate formation. We started by genotyping the callose hydrolase 17 gene and the GSL gene T-DNA insertion lines of Arabidopsis thaliana. Through PCR and gel documentation, we identified both heterozygous and homozygous mutants. We also phenotype wildtype and GSL complementation lines in the presence of an ES7 chemical that inhibits plant cytokinesis. By doing this, we aim to investigate the effect of ES7 on root elongation of the wildtype and GSL complemented lines. Our study led to the confirmation of T-DNA insertion mutant plants and it helps to pave the way for future research on the effect of the callose hydrolase 17 gene and its relationship with GSL, a callose synthase gene.

Student Name: Shrawani Thapa
UC Davis Department: Veterinary Medicine: Anatomy, Physiology, and Cell Biology
UC Davis Mentor: Dr. Kent E. Pinkerton

Assessing the Impacts of House Dust Mite Allergen and Particulate Matter on the Lungs of Pregnant Mice

In this research study, there was a group of 16 BALB/C (Bragg Albino) female mice. They were exposed every other day for a total of three times to house dust mite allergen and particulate matter. Following this five-day period, they were mated over a breeding period of four days. On gestational days 12 and 15, the mothers were challenged by intranasal inhalation of HDM or Phosphate Buffered Saline (PBS) under sedation. Four hours following the challenge on gestational day 15, a necropsy was performed on the pregnant mice. Their lungs were collected, inflation-fixed, embedded, sectioned, placed on glass slides, and stained with Hematoxylin and Eosin (H&E) or Alcian Blue Periodic Acid Schiff (AB/PAS). These slides were examined using a Zeiss microscope to assess the condition of the pregnant mothers’ lungs post-exposure to the air pollutants. This study discovered that the lung tissue of mice treated with HDM displayed signs of severe inflammation. The lung tissue of mice treated with PM did not display as many signs of inflammation. It was noted that the lung tissue of mice treated with HDM + PM displayed the greatest degree of inflammation compared to the HDM and PM treatment groups. This research project will further our understanding of the impact of air pollution exposure on the lungs. It can also help explain the link between complications that may occur in the mother and the children of mothers exposed to air pollution. Future studies could use our assessment to research why inhaled particles cause inflammation specifically in the airways and blood vessels and whether the mice lung tissues in this study had fibrosis, a condition in which the lung tissue becomes thickened or scarred by excessive collagen deposition (Mayo Clinic, 2018). Future studies could also research the impact of exposure to air pollution during pregnancy on the unborn child and see how they were affected. 

Student Name: Yen Tran
UC Davis Department: Plant Biology
UC Davis Mentor: Veronica Thompson

Molecular Complementation of ELF3 in Arabidopsis Thaliana by Two Alleles of a Sunflower Homolog

In Arabidopsis thaliana (Arabidopsis), ELF3 has been shown to be a master regulator of growth and temperature response. In sunflowers (Helianthus annuus), an alternative allele of a homolog of Arabidopsis ELF3, Haelf3, has previously been shown to correlate with longer hypocotyls under low levels of constant red light. Additionally, we show that Haelf3 sunflowers flower earlier than WT plants at lower temperatures, but at 35° C they flower at the same time as the wildtype. Here we seek to characterize whether these two sunflower ELF3 alleles, HaELF3  and Haelf3 complement Arabidopsis plants differently. We will use Arabidopsis plants stably expressing these alleles to quantify differences in their function. The effects of the transgenes on flowering time, growth phenotypes such as hypocotyl elongation, and circadian function will be quantified. We found that across different temperature conditions, differences in  hypocotyl length are consistent for our molecular complementation lines. Future work will be done to characterize flowering time and clock phenotypes in these molecular complementation lines.

Student Name: Alan Wang
UC Davis Department: Veterinary Medicine: Molecular Biosciences
UC Davis Mentor: Cecilia Giulivi

Increased Defense Response with Age in the Female Salivary Proteome

Saliva contains many functions and proteins that can also be found throughout the body. Thus, saliva has potential to indicate systemic health. Our objective is to explore the  changes between the female salivary proteome and aging to identify possible health implications. Salivary proteomic data of 87 proteins from 26 individual healthy women ages 21-60 were analyzed by linear and stepwise regression analyses using JMP Statistical Software. LOG transformation was performed on the data to account for exponential patterns. Linear regression revealed four proteins to significantly decrease with age in healthy women: SLPI, CRISP3, LEG1, and LYZ. Stepwise regression showed 9 proteins to be statistically significant within our data set. Decreases in each of the four individually statistically significant proteins from linear regression models: LYZ, SLPI, and CRISP3, specifically appear to implicate a decrease in neutrophil degranulation and an overall weaker immune presence in the oral cavity with age. Stepwise regression proteins were involved in immune response and shown to increase with age. In conclusion, our results suggest an increase in salivary immune activity and a decrease in neutrophil degranulation.

Student Name: Ruomeng Wang
UC Davis Department: Integrative Genetics and Genomics
UC Davis Mentor: Sunkyung Lee

RNF212 Ensures Crossover Formation and Promotes Fertility in Male Mice.

Meiotic recombination is essential in facilitating accurate chromosomal segregation. It occurs every time a cell undergoes meiosis, and is fundamental in the formation of gametes for successful reproduction. When animal models undergo defective meiotic recombination, they display signs of meiotic arrest, DSB accumulation, and spermatocyte apoptosis, all of which are leading causes of miscarriages, birth defects, and infertility. Thus, understanding the mechanism behind meiotic recombination is crucial for advancements in the research and treatment of these diseases and conditions. The SNPs within the RNF212 (RING Finger Protein 212) allele have been connected with male crossover rates through a GWAS study, and the orthologs of the RNF212 protein, ZHP-3 and Zip3, were identified to be meiotic pro-crossover factors in C. elegans and S. cerevisiae. However, the function of mouse RNF212 in meiotic recombination remains largely unknown. In this paper, we provide evidence to show that mouse RNF212 also plays an essential role in the generation of crossovers. These findings give insight into the molecular pathophysiology of non-obstructive azoospermia and prompt inquiry into the effects of the RNF212 protein on human infertility.

Student Name: Isabella Wu
UC Davis Department: Chemical Engineering
UC Davis Mentor: Celeste Wan

Using Molecular Dynamics to Study Interactions Between Paramagnetic Amyloid Ligands and α-synuclein to Treat Parkinson’s Disease

Intrinsically disordered proteins (IDPs) are proteins that have an undefined three-dimensional structure and create aggregations that lead to neurodegenerative diseases. For example, the aggregation of α-synuclein will lead to overproduction of reactive oxygen species and further cause oxidative stress in neurons. Recent studies showed that a type of small molecule, paramagnetic amyloid ligands (PALs), can inhibit this kind of pathogenicity. However, the specific question of how PALs interact with α-synuclein remains unclear. Therefore, this re-search studies the binding and blocking interactions between PALs and α-synuclein. Using molecular dynamics (MD), the simulations run in our study have allowed us to visualize the binding sites of PALs and indicate the areas in which the interactions are more or less likely to occur. Future findings from this study will contribute to a potential treatment for Parkinson’s disease.

Student Name: Cindy Xing
UC Davis Department: Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Chang-il Hwang

The Effect of YAP Inhibitor on EN1 Expression in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDA) ranks third in cancer deaths in the US, owing to its aggressive metastasis to vital organs before diagnosis. This hampers effective treatment and results in low survival rates. The Engrailed-1 (EN1) protein has been linked to PDA’s metastatic traits, facilitated by the Yes-Associated Protein 1 (YAP) and TEA domain family member 1 (TEAD) interaction, upregulating EN1 expression in fibroblasts. Thus, using a YAP inhibitor like Verteporfin can decrease EN1 expression. My study on BxPC-3, MIA PaCa-2, and SUIT2 human PDA cell lines with YAP inhibitor treatment revealed downregulation of EN1 in BxPC-3 and MIA PaCa-2, but not clearly in SUIT2. EN1 downregulation was dose-dependent on YAP inhibitor concentration, suggesting YAP inhibitors as a potential therapeutic strategy to reduce metastatic capabilities in PDA.

Student Name: Julia Xu
UC Davis Department: Cell Biology
UC Davis Mentor: Dr. Ian Korf

Leveraging Conservation Level and Palindrome Content to Find Novel Regulatory Sequences

Within genomes, regulatory sequences are often sites of protein interactions. Specifically, palindromic sequences are thought to be functionally important sites for DNA binding proteins because their symmetry allows for efficient recognition by dimeric proteins. Multiple binding sites are important for gene regulation, and thus the palindrome content is directly related to the chance of protein interaction. Sequence conservation is also usually indicative of biological function. We hypothesize that combining conservation and palindrome content will yield DNA sequences which act as regulatory elements. We created programs to calculate the conservation levels and palindrome content of the Caenorhabditis elegans genome. We discovered two regions within the first 5 million base pairs on the first chromosome that had both high conservation and palindrome count, while also being non-coding sequences. We labeled these two areas as regions of interest, and future investigations may discover their purpose and importance.

Student Name: Evelyn Zhao
UC Davis Department: Plant Sciences
UC Davis Mentor: Toshisangba Chiba

Investigating the Effects of ES7 on Callose Deposition My Using Callose Hydroplane Mutant Lines.

Cytokinesis, a fundamental process governing cytoplasmic division during cell division, plays a crucial role in plant growth. Callose, a complex carbohydrate, is known to be involved in the formation of the cell plate during cytokinesis. This research aims to investigate the impact of ES7, an inhibitor of callose deposition, in Arabidopsis mutant plants. Through genotypic processes, we conducted a thorough screening of transgenic mutant lines to study the relationship between the hydrolase gene, callose deposition, and cytokinesis. Our findings demonstrate that disruption of the callose hydrolase gene results in shorter root lengths, indicative of impaired cytokinetic processes. Through genotyping analysis, we successfully identified callose hydrolase mutant lines, which hold promise for future phenotypic assays to unravel the critical role of this gene in regulating callose deposition during cytokinesis in Arabidopsis plants. This enhanced understanding of the underlying mechanisms governing callose synthesis and its interplay with the hydrolase gene could potentially hold significant implications for enhancing crop yield and improving overall plant development.

Student Name: Emily Zheng
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Aldrin V. Gomes

Impact of Long-Term Ibuprofen Usage on Cardiac Signaling Pathways

Ibuprofen, a common over-the-counter drug, is taken worldwide to alleviate pain and reduce inflammation. While the recommended dosage is generally regarded as safe for consumption, complications arise when the drug is taken chronically, even in the prescribed quantities. Previous research conducted in the Gomes Lab suggests that ibuprofen alters the productivity of various signal transduction pathways throughout the body and stimulates the production of reactive oxygen species (ROS) in cardiac tissue, ultimately leading to an increased risk of stroke. Our research aims to determine the changes in protein quantities of enzymes involved in life-enabling processes within cardiac tissue as a result of chronic ibuprofen usage. The study involved eight female mice divided amongst two treatment groups: control and ibuprofen. Mass spectrometry spectra analysis and Western blotting experiments yielded results that suggest long-term ibuprofen consumption results in the upregulation of aerobic respiration, the nucleotide metabolic process, and muscle cell development pathways. A possible implication of the observed upregulation of enzymes and pathways is the alteration of cell metabolic processes, which may lead to a variety of diseases.

2022 Research Projects

Student Name: David An
UC Davis Department: Evolution and Ecology
UC Davis Mentor: Dr. Samantha Worthy

Evaluating Functional Trait Differences between Streptanthus and Caulanthus Species and their Relationships with Environmental Conditions

Biomass allocation is the process by which plants allocate their finite resources to specific organs in order to grow and survive in response to their environment. Functional traits are one way to indicate this allocation by tracking the plant’s morphological traits. The relationship of plant functional traits with the outside environment is a topic area that has been extensively researched throughout the past; however, there has been little research done on the functional traits of plants in the Streptanthus and Caulanthus genera. These plants are native to California and are important for ecological research due to their environmental diversity and wide differences in geographic range. Not only would an understanding of these species’ functional trait development in response to the environment help provide valuable information in conservation efforts for these species and knowledge in ecosystem dynamics, but these plants can also provide information on closely related Brassicaceae vegetables which are eaten by people. Herein, the morphological functional traits of 8 different species (11 different populations) from the two genera were calculated, including the specific leaf area, specific stem length, and more. These data were then put alongside climate data averaged over 30 years containing precipitation, temperature, and elevation measurements to draw correlations between environmental factors and traits, as well as between traits, and discover differences between species. We found that Caulanthus species have significantly larger leaf sizes but shorter stems than Streptanthus species. Also, we discovered that, across all species, the precipitation has a significant, negative relationship with the leaf mass fraction and a significant, positive relationship with the root mass fraction. The maximum temperature has a significant, negative relationship with the stem mass fraction. Our results indicate how different environmental conditions can significantly influence biomass allocation and adaptation patterns in Streptanthus and Caulanthus seedlings in differing ways.

Student Name: Michelle Andal
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation in Voltage-Gated Potassium Channels

Tyrosine sulfation may occur at the extracellular regions of voltage-gated potassium channels which may impact their overall function of selectivity. This study utilized computational matrices in order to predict the likelihood of sulfation at a tyrosine site, then analyzed those sites based on location within the channels and conservation among species. Tyrosine sulfation is predicted to occur in channels Kv1.1, Kv1.3, and Kv6.3. Mutagenesis data of Tyr-447 of Kv1.3 revealed that cell proliferation may be abolished without sulfation at the site. Methods to target and confirm tyrosine sulfation at these sites can be developed to regulate cell proliferation, target mutations due to voltage-gated potassium channel malfunctions, and ultimately improve the regulation of signaling cascades via protein-protein interactions of these channels.

Student Name: Alex Chang
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Predicting Tyrosine Sulfation Sites in Voltage-Gated Sodium Channels

Tyrosine sulfation is the addition of a sulfate onto a tyrosine residue. It is known to enhance protein activity, especially proteins’ interactions with other binding partners. However, minimal studies have been done on finding sulfated tyrosine sites, and none on voltage-gated sodium channels. To find high probability tyrosine sulfation sites, this study used computational methods, such as a PSSM scorer, sequence conservation, 3D imaging, and mutagenesis. Using these methods, three main extracellular tyrosine sites were predicted to be sulfated in the voltage-gated sodium channel. Evaluating the correlation of the predicted sites with the function of the protein and any possible diseases can help develop new drugs and diagnoses, particularly to neurological diseases.

Student Name: Andrew Chen
UC Davis Department: The Genome Center
UC Davis Mentor: Ashley Vater, M.S.

Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: Q19M, N157D

Computational enzyme engineering has proven to be an efficient and cost effective method to build new biocatalysts for use in healthcare or industry. Existing enzyme design algorithms fail to accurately predict the effects of mutagenesis on the stability and activity of enzymes. In order to improve the prediction algorithm for the enzyme β-glucosidase B (BglB), a catalytic hydrolase for β-glycosidic linkages in oligosaccharides, this study analyzes two mutants of BglB: Q19M and N157D. Designed through FoldIt Standalone and synthesized in E. Coli cells, the two protein variants were assayed for their thermal stability ™ and catalytic efficiency (kcat/KM). The predicted Rosetta Energy Score had a weak positive correlation with thermal stability and a negative correlation with catalytic efficiency. We entered this data into the Design2Data database, which holds the experimental data of over 200 mutants of BglB, and will be used to train increasingly accurate prediction algorithms that capture the relationship between enzyme structure and function. Eventually, this ability to accurately predict the effects of enzyme mutations will lead to optimized biocatalysts with a broad range of applications in society.

Student Name: Andrew Chu
UC Davis Department: Molecular and Cellular Biology
UC Davis Mentor: Dr. Ian Korf

Exploring the conservation of non-canonical splice sites in nematodes

Canonical splice sites at intron-exon boundaries follow the GT-AG rule, in which GT dinucleotides are found at the donor (5’) end of the intron and AG dinucleotides at the acceptor (3’) end. However, the biological significance of non-canonical splice sites, such as GC-AG or AT-AC, is unclear. In this paper, we investigated whether these non-canonical splice sites are simply random biological noise or features that are conserved across multiple species. We used Caenorhabditis elegans (C. elegans) and related nematodes as our model system, analyzing sequence and annotation data from the WormBase online database. We identified and classified non-canonical splice sites within C. elegans, then examined orthologous genes to investigate if the non-canonical splice sites had been conserved. We found that the non-canonical splice signal GC-AG was conserved from C. elegans to related species at a rate higher than random chance in four related nematodes, indicating a biological significance of this non-typical feature in the genome. Specifically, the relatively small proportion of GC-AG introns that were conserved from C. elegans indicates that a particular class of genes require non-canonical splicing for normal function.

Student Name: Daniel Deng
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Aldrin V. Gomes

Improving the antibody incubation buffer in western blotting

The processes of primary and secondary antibody incubation are vital components of the western blot, allowing for fluorescent and chemiluminescent protein detection. Over the course of incubation, protein stained membranes are incubated in buffer solutions, usually consisting of TBS or TBST combined with a blocking agent. Little research has been conducted specifically on the compositions of these solutions, and their potential effects on overall western blot performance with respect to background noise, signal strength, and required incubation time. Consensus on an ideal antibody incubation buffer is thus sparse and often based on anecdotal evidence.

In this study, we perform a series of western blot experiments, varying the concentrations of the components in oft-used incubation solution recipes. A novel signal-enhancing reagent, polyvinylpyrrolidone (PVP40), was also introduced to certain experiments. The performance of blots performed with these modified solutions is then compared to a control performed in identical conditions, with the exception of the incubation buffers. Through these experiments, we demonstrate the necessity of blocking reagents, due to the high noise exhibited by experiments performed without them. Furthermore, the tendency for Tween-20 to enhance signal strength is observed. PVP40 also appeared to increase signal, but to a lesser extent than Tween-20, and whether it ought to be included in western blot protocols may require further experimentation. A potentially improved solution for antibody incubation is also determined.

Student Name: Kelly Gan
UC Davis Department: Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Su-Ju Lin

A Study in NAD+ Metabolism: Yeast Provides a Model System

NAD+ (Nicotinamide adenine dinucleotide) is a coenzyme found in all living cells and a central molecule in biological functions, being involved in redox reactions, cellular respiration, and protein modification. Abnormal levels of NAD+ have proven to play important roles in the emphasis of age-related diseases, which is why NAD+ precursor treatments are a potential therapeutic target to slow cell aging or to alleviate aging-associated disorders. However, the complicated connections between NAD+’s biosynthetic pathways makes such mechanisms currently unclear. Budding yeast, Saccharomyces cerevisiae, was used as a model system to discover what factors may contribute to the regulation of NAD+ homeostasis. In order to do so, the lab has attempted to identify elements that affect the three pathways of NAD+ metabolism, which include the de novo, NA/NAM and NR salvage pathways. This study also investigated how the pathways are interconnected and how the overexpression of certain genes can influence the NAD+ pathway yields by performing a cross-feeding spot assay. Specifically, the overexpression of the BNA1 gene has shown a small increase of QA from the de novo pathway, and an unexpected large increase of NA/NAM from the NA/NAM salvage pathway, which could mean that this gene may be connected to secondary mechanisms or other intermediates indirectly. These possibilities may lead to other experiments uncovering the ways NAD+ pathways are connected and to further research in NAD+ precursor treatments.

Student Name: Saanvi Ganesh
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

Utilizing Image Analysis to go ‘Back to the Future’ in Measuring Nonpareil Almond Fruit Growth

From the spring to summer season, Nonpareil almonds undergo the main stages of nut development. This research tests whether all almond flowers develop into fruit by closely following bloom (floral stage) to hull split (nut exposure). This study observes and analyzes almond growth with image analysis tools. Images were collected using a digital camera. ImageJ analysis enabled image scrubbing to go back and forth in time and track the growth phases of the almonds that complete development. The findings indicate that fruit growth is linear for about one month and then flatlines, and unsuccessful almonds stop developing in mid-March. Future research can quantitatively compare flowers that make it to almond development to flowers that do not. Additionally, measurements of almonds done on the field can allow for more accurate results.

Student Name: Skylar Granlund
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Weiyi Sun

Effect of Chickpea Ultrasound Treatment on In-Vitro Digestion

My project’s objective is of observing the effect of ultrasound of low versus high power on the texture and moisture of chickpeas during the process of in-vitro gastric digestion.

The research process started with separating 33-34g chickpeas into three sieving bags. Then ultrasound was done for 5 minutes each on each of the sieving bags with the treatments of soak, 100W, and 300W. After the ultrasound treatments, the sieving bags were soaked for 1 hour and then boiled for 40 minutes. Then the chickpea skins were removed and a total of 9 chickpeas were removed (3 for moisture content using a scientific scale and vacuum oven and 6 for texture analysis using a texture analyzer), then mass leftover was measured to calculate the needed amount of gastric juice and saliva. After this, the digestion process started in a shaking water bath and at 30-minute intervals from 0 to 180 minutes intervals 9 chickpeas were removed for analysis.

The analysis from each time point was then compared in order to answer the objective.

Student Name: Alyssa Halvorsen
UC Davis Department: Land, Air and Water Resources
UC Davis Mentor: Madison Mathers

Plant Fingerprints: Characterizing wetland plants in the Sacramento–San Joaquin Delta with a two biomarker approach

The lower food web of the  Sacramento–San Joaquin Delta is suffering due to anthropogenic causes. Wetland restoration may be the key to solving this issue, as detrital material in particulates are likely a supplementary food source for reviving the lower food web. Before we can assess the prevalence of wetland material in Delta particulates, we must first establish wetland source signatures from which we can use for characterization. To generate a relevant Delta wetland endmember database, plant samples were collected from Liberty Island, a Northern region of the Delta, and analyzed for lignin and elemental carbon and nitrogen. Cumulation of data helps to create references for future particulate studies, but comparisons with historical data also reveals an unexpected deviation from past research. As wetlands are crucial to the health of the Delta, accurately characterizing  prevalent plant material in wetland regions may assist in understanding carbon dynamics pertinent to the health of the ecosystem.

Student Name: Kayli Huang
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

Modeling the Viscoelastic Properties of Grapes and Olives

Fruits are biological materials that present viscoelastic behaviors when subjected to an external pressure. It is not well understood the reason behind this behavior, but viscoelastic models can be used to predict how fruits and vegetables will react in different circumstances, such as during a compression or drop. It is difficult to investigate the reasoning behind this characteristic of fruits and vegetables as there are many aspects that can contribute to a plant cell acting as a viscoelastic material. Therefore the focus of this research paper is to understand the viscoelastic models that fruits and vegetables fit. The Grape-Grabber, a device, was used to measure the reaction force from a fruit through a force transducer. Springs and rubber balls were used to represent the standards for elastic and viscoelastic materials, respectively. A Statistical Analysis Software, SAS, program was then used to analyze the collected data from the Grape-Grabber to fit the behavior of immature olives and grapes to the Maxwell and standard linear solid (SLS) viscoelastic models. The immature olives and grapes fit the SLS model for stress relaxation and the graphs of the initial reaction forces had a hysteresis between the forward and backward movement of the Grape-Grabber, a component of viscoelastic materials. This data can be used to help engineer more effective and efficient transportation containers to increase the accessibility of fresh, high quality produce.

Student Name: Kylie Huang
UC Davis Department: Plant Biology
UC Davis Mentor: Aleczander Young, Dr. Angelica Guercio, Shelly Lee, and Linyi Yan

Structure-Function Investigation of Hormone Biosensor RMS3 in Plants

Strigolactones (SLs) are a class of plant hormones which act as signaling compounds to affect both plant architecture and development. The DWARF14 (D14) strigolactone receptor is a part of the superfamily of α/β-hydrolases which not only perceives but also cleaves SLs (3). Here we investigate the structure and function of specific D14 strigolactone receptor by using site directed mutagenesis to alter its catalytic activity and perception. We also found that SL receptor bound to GR24 (SL analog) can be crystallized, meaning that the ligand bound form and the function of the receptor can be studied in atomic resolution. These findings can aid in the breeding of nutrient efficient plants and the prevention of the germination of parasitic plant seeds, both of which contribute to an increase in food stability and security around the world.

Student Name: Justin Jeng
UC Davis Department: Mouse Biology Program
UC Davis Mentor: Dr. Joshua A Wood

Effect of zygote harvest time on embryonic yield of c57b/6n mice

The Mouse Biology Program facility focuses on creating animal models using various methods, including CRISPR-EZ technology to alter the mice genome within embryos.  These animal models can be used to model human diseases to understand their underlying mechanisms and develop novel therapies.  By studying the effect that zygote harvest time has on embryonic yield and fertility in C57/B6N mice, the efficiency of zygote production can be maximized, leading to decreased animal consumption rates, decreased costs, and more mice models to work with.  The increased production of animal models allows for more research for therapeutics and medicine to be tested against these diseases.

Student Name: Sophia Jin
UC Davis Department: Evolution and Ecology
UC Davis Mentor: Jonathan Aguiñaga

Amazon mollies, P. formosa, associate more closely with conspecifics in response to predation risk

The social behaviors of animals have long been known to be influenced by different environmental stimuli. Social associations with others can confer strong anti-predator benefits which can enhance individual fitness such as survival and reproductive output. However, whether social behaviors are consistent throughout ecological contexts such as in the absence or presence of predation risk remains poorly understood. Here, we evaluate the effect of exposure to predation risk on consistent individual differences in social behavior of a highly social species, the Amazon molly (P. formosa). Amazon mollies (n = 10) were assayed using a standard sociability test while in the presence and absence of predator cues. We found that sociability increased significantly when fish were in the presence of risk compared to in the absence of risk. Additionally, we observed that sociability decreased over multiple exposures to the same treatment, indicating that individuals may trade-off time spent exploring their environment with time spent near conspecifics. Overall, these results suggest that individuals may adaptively adjust time spent with others depending on level of environmental risk.

Student Name: Chelsia Kwon
UC Davis Department: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giulivi

Differential Biological Pathways in Carriers and Noncarriers of the Fragile X Messenger Ribonucleoprotein 1 Premutation

Fragile X Syndrome is a genetic disorder caused by a mutation of over 200 CGG nucleotide repeats in the 5’ untranslated region of the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Those who are unaffected have under 55 CGG repeats, and those with the premutation have 55-200 CGG repeats. FMR1 codes for a protein called FMRP, which plays a significant role in neurodevelopment. Male carriers of the premutation are likely to develop Fragile X-associated Tremor/Ataxia Syndrome, which is characterized by disabilities in movement and cognition. To investigate the differential biological pathways in carriers and noncarriers of the FMR1 premutation, amniotic fluids were taken from 24 pregnant mothers with the premutation. All fetuses were male, with 12 being carriers and 12 being noncarriers of the premutation. These samples were analyzed for the abundance of 2934 detected proteins. The data were analyzed with bioinformatics tools and it was determined that pathways related to neural dysfunction were upregulated in carriers. By understanding the pathological mechanisms that underlie this mutation, scientists will be able to design therapies to improve the pathways associated with neurological problems and help symptoms of neurological conditions.

Student Name: Katie Lam
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Amisha Poret-Peterson

Life History Strategies and Identification of Bacteria from High and Low Nutrient Environments

Soil is composed of extensive microbial communities that vary with the availability of different nutrients. Nitrogen is a common agricultural soil nutrient applied in synthetic fertilizers and carbon is often added through organic amendments suchs as compost.  Microorganisms can utilize the added nitrogen or carbon as energy sources. The prevalence of Central Valley California almond orchards necessitates a method to dispose of orchard’s that are no longer productive. Whole Orchard Recycling, a management practice to dispose of tree biomass onsite, which may increase nutrient retention and carbon retention in soils, presents a system where relationships between carbon and nitrogen soil concentrations and microorganism populations can be assessed. Simulations of various nutrient applications are represented through soils with high carbon (Whole Orchard Recycling) or low carbon (untreated soils) and high or low nitrogen fertilization treatment. This study aims to determine differences between Whole Orchard Recycling and untreated soil microorganism populations through indicators of culturability and life history strategy on a copiotrophic or oligotrophic continuum, determined using rRNA gene copy number. This will be conducted through culture dependent methods that rely on isolate data – such as GEN III identification – and culture independent methods that utilize community data – such as microbiome sequencing. Results exhibit distinct differences in microbial composition between Whole Orchard Recycling and untreated soils – determined through trends of carbon utilization among communities, beta diversity measures, and rRNA gene copy number of cultured samples. Analyzing patterns of microbial communities increase understanding of microorganisms’ roles in biogeochemical cycles and soil nutrient retention, which may allow adjustment of agricultural nutrient management methods by determining ideal amounts of necessary nutrient amendments.

Student Name: Maegan Matchett
UC Davis Department: Plant Sciences
UC Davis Mentor: Isabel Ortega-Salazar

Postharvest Quality Measurements of Fresh-market Tomatoes Stored at Different Temperatures

With California being a leading producer of tomatoes in the USA, it is important to perform studies in postharvest because it can help to find strategies that may minimize food waste and losses. There are different methods to evaluate postharvest quality. Determining the best parameters used on the different post harvest measurements is key to obtaining accurate results. Several studies were conducted in order to find and test the best ways to measure these postharvest parameters on a fresh-market tomato variety. Fruit Firmness, ethylene production, CO2 production, weight, water loss, and visual qualities were assessed in order to characterize the shelf life of these tomato fruits. First, settings and probe attachments for a texture analysis machine were tested. A second study was done to see if running a firmness test on the fruit triggered excessive ethylene or CO2 production. A final study was performed on tomatoes stored in different temperatures to test the effectiveness of the chosen parameters and ways of measuring. This experiment was run on store bought tomatoes with no knowledge of the growing and handling processes.  These findings were limited by the fruit’s postharvest conditions at the moment of starting the measurements. More optimal results may be obtained through measurements taken directly after harvesting.

Student Name: Matthew Mullaney
UC Davis Department: Veterinary Medicine
UC Davis Mentor: Dr. Cecilia Giulivi

Decrease in Immune Defense in the Female Salivary Proteome with Age

Introduction: Salivary proteomics is a relatively new field with much undocumented territory, specifically in regards to the changes in protein concentrations with age. This study seeks to expand the general body of literature regarding the change of protein concentration with age in women, explore the possibility of using salivary protein concentrations as biomarkers of age in women, and to communicate possible health effects of our findings.
Methods: We tracked the changes in the concentrations of 87 different proteins in 26 healthy women of ages 21 through 60. We created single linear regression models for each protein along with stepwise regression models for the entire dataset, using JMP Statistical Software for all statistical analyses.
Results: The proteins SLPI, LEG1, LYZ, and CRISP3 had individually statistically significant (p < 0.05) negative correlations with age. We selected two of the six generated stepwise regression models for consideration in the discussion section.
Discussion: The decreases in each of the 4 individually statistically significant may lead to greater risk of, bacterial infections, fungal infections, and viral infections. The decreases in LYZ, SLPI, and CRISP3 specifically appear to implicate a decrease in neutrophil degranulation and an overall weaker immune presence in the oral cavity with age.

Student Name: Youngseo (Esther) Na
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Gabriela Rivera

Improving western blotting: optimal washing solutions and times that increase the efficiency and accuracy of western blots

Western blotting is a popular method for research involving protein analysis and for the clinical diagnoses of diseases and viruses. However, the technique takes several hours, and the long, multistep nature of the process can lend itself to errors and irreproducible results. Many studies have sought to decrease the time length and increase the accuracy of western blots; however, these studies tend to focus on the main steps, such as sample preparation and antibody incubation, rather than on the smaller steps such as washing. This study sought to find the optimal washing method for western blots to increase the efficiency and accuracy of the process using means that are accessible to most labs. In order to do this, western blots were run on the proteins of mice liver cells, and the washing solution used and time spent washing were tested. Specifically, the concentrations of Tween 20 and PVP-40 were varied or added, and the time length was shortened. However, due to the limited time frame and limited number of experiments, the study produced inconsistent results. Future studies need to be conducted to confirm or disprove the effectiveness of the tested variables.

Student Name: Matthew Naidu
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Gabriela Rivera

Optimization of Blocking Agent to Maximize Signal-to-Noise Ratio in Western Blotting

Western Blotting is a laboratory technique that is essential to research on proteins, which is a major subject of research in many fields such as cell biology, biochemistry, and molecular biology. However, western blotting is a lengthy process involving various procedures and much human interaction, resulting in a significant chance of yielding irreproducible and invalid results. This disadvantage makes research concerning protein identification and analysis incredibly time-consuming and unproductive, as a single minor mistake in procedure can lead to irreproducible and invalid results. This project aimed to increase the validity and reproducibility of western blotting results through optimization of the blocking agent. Uncommon blocking agents were tested, such as the water-soluble polymer Polyvinylpyrrolidone (PVP-40) and yeast extract. The effectiveness of each blocking solution was determined by calculating a signal-to-noise ratio (SNR), a ratio of the signal strength of a target protein (signal) to signal strength of background proteins (noise). PVP-40 proved to increase SNR when paired with nonfat milk powder, and yeast extract in concentrations of 2% successfully yielded distinct target protein bands, distinguishing it as a viable blocking buffer replacement in the event of an absence of nonfat milk powder.

Student Name: Riyanka Narasimhan
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Predicting Tyrosine Sulfation Sites in Classical Cadherins

Tyrosine sulfation is the post-translational modification of tyrosine residues in proteins that enhance protein-protein interactions. This study utilized computational methods to predict potential tyrosine sulfation sites in classical cadherins. Results from tyrosine sequence scoring, conservation alignments, and mutagenesis data strongly suggest that tyrosine sulfation is relevant in the calcium binding functionality of cadherins. For instance, mutagenesis data at position 627 in the Cadherin-2 EC5 domain revealed that binding between cadherins may be impossible without sulfation at this site. Methods to promote tyrosine sulfation at such sites can be developed to regulate cadherin expression and ultimately target cancer metastasis due to cadherin malfunctions.

Student Name: Jaimie Nguyen
UC Davis Department: Psychology
UC Davis Mentor: Dr. Carlos Pineda

Effects of Early Blindness in Posterior Parietal Cortex and Sensory Function

Gray short-tailed opossums are researched to understand congenital blindness and the constraints of which its brain has evolved. Opossums are an ideal model for congenital blindness because their visual system develops after birth, allowing easier access to induce blindness. Using these animals to model the common mammalian ancestor and congenital blindness allowed us to observe how their neuroanatomy and behavior changes as a result of the loss of visual input. Past studies have indicated that other mammals, such as rodents and humans, have shown reorganization of the sensory input into the primary visual cortex after early blindness. We observed changes in the connections of the posterior parietal cortex (PPC) of opossums using neuroanatomical tracer injections and myelin stains. This study showed that early blindness in opossums correlates to a lack of connectivity to the primary and secondary somatosensory cortex and a change in intrinsic connections within the PPC. In addition, the behavior of early blind opossums had demonstrated altered compensatory behaviors. This study shows us that mammals may have reorganization in their connectivity that affects their sensory function, though further research must be conducted.

Student Name: Adaleiz Ore
UC Davis Department: Veterinary Medicine
UC Davis Mentor: Dr. Cecilia Giulivi

Correlation between FMR1 CGG repeats and Metabolic Pathways

This study sought to identify proteins and biomarkers that correlate directly with CGG repeats within the 5’-untranslated region (UTR) of the FMR1 gene, in order to identify key biological pathways affected by this genetic disorder.  The FMR1 premutation (defined as 55-200 CGG repeats), is associated with several cognitive and developmental disorders.  Older subjects, typically those over age 50, may develop fragile-X-associated tremor/ataxia syndrome (FXTAS).  This project evaluated the proteome of 24 amniotic fluid supernatant samples (AF) from carrier pregnant females (12 carrying a fetus that is a carrier and 12 that are non-carriers).  Statistical analysis controlling for possible confounding variables determined the association between CGG repeat size and several pathways associated with mitochondria, ATP production, prefoldin, and ubiquitin.  These results show similarities between the increase in CGG repeats and the proteomes of people diagnosed with other neurological diseases.  Additionally, significant downregulation of the Multivesicular Body Pathway was found in direct relation to the number of CGG repeats.  Abnormal upregulation of ATP synthase subunits D and E was also found, suggesting further disruptions in ATP synthesis.  Further understanding of the cellular and metabolic differences related to CGG repeat size can lead to improvement in diagnosis of the premutation, and prediction of its effects.

Student Name: Ishita Pesati
UC Davis Department: Evolution and Ecology
UC Davis Mentor: Jonathan Aguiñaga

Amazon mollies (Poecilia formosa) decrease aggressive behavior when in the presence of risk

Throughout the animal kingdom, individuals often have to defend their resources from others. Some animals might have higher resource holding potential due to inherent differences in size or competitive ability. However, sometimes smaller individuals may win animal contests against bigger individuals. Consistent individual differences in behavior (animal personality) such as in aggression, can help explain the occurrence of upsets in animal fighting contests. Here, Amazon mollies (Poecilia formosa) were tested in a personality assay measuring aggression behavior while individual fish are in the presence and absence of predation risk. We predicted that more incidences of aggressive behavior would occur in the presence of predatory risk because of the innate need to protect individual resources. Our analysis showed that the median number of mirror bites was greater in the absence of a predatory risk. Our prediction was not supported because aggression in Amazon mollies decreases in the presence of predation risk.

Student Name: Ashley Raffaeli
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Minmin Wang

Identification of the Genotypes of T4 plants and the Relationship Between GSL8 and Callose Deposition

Drakakaki Lab has generated gsl8-3/3xYpet-GSL8 lines for studying the role of Glycan Synthase like-8 (GSL8) during cytokinesis. The goal of the project is to identify homozygous plants  (plants grown from seeds) harvested from self pollinated T4 transgenic plants, of gsl8-3/3xYpet-GSL8 with fluorescent signals. We are also trying to phenotype their growth and cellular phenotypes. The question to answer is (1) the genotypes of T4 plants, and (2) the relationship between the localization of GSL8 and callose deposition. Confocal microscopy strategy is utilized to study the micro-phenotype of transgenic plants. Our research begins to indicate, but doesn’t completely, disprove the null hypothesis that the mother is heterozygous. In the future, using a Q5 enzyme or Phusion enzyme to amplify 5 to 10 kb fragments will confirm the homozygosity of individual lines. This research will affect our society because plant cytokinesis is a highly regulated cellular process responding to environmental signals and will be translated to growth and stress responses long term. Studying plant cytokinesis will help us to understand how plants respond to long-term abiotic stress and how they adapt to climate changes, leading to advancements in how stress causes diminishing nutrient uptake and affects the harvest season.

Student Name: Pratyush Rallapally
UC Davis Department: Plant Biology
UC Davis Mentor: Veronica Thompson

Effect of Circadian Synchronization on Sunflower Fitness

Successful pollination requires plants to have synchronized responses to their environment. Sunflowers are a notable example as they follow the Sun throughout the daylight cycle in their adolescent stage. This mechanism is regulated by their circadian rhythm. In this study, our goal was to evaluate the extent of the plant circadian rhythm’s role in plant physiology. We cultivated a group of sunflowers such that they became “jetlagged”, planted them in a field with control sunflowers, and compared the number of pollinator visits each group received through scheduled photos. We found that plants that did not open as a result of a very out-of-sync circadian rhythm will not receive any pollinator visits. This indicates that the circadian rhythm of the sunflowers plays a substantial role in pollination success and overall plant fitness, likely since sunflower development was much more synchronized to the day in control plants.

Student Name: Taro Ramacciotti
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Franklin Cerasoli

Structure and Thermal Properties of Diamond- Like Amorphous Carbon

As a disordered carbon that both is semiconductive and maintains a structural integrity similar to that of diamond, amorphous carbon is a substance of great interest whose structural and thermal properties remain largely unexplored. The substance has been shown to have a range of potential applications in a variety of industries, particularly when it comes to its diamond-like structural properties. Further examination of the structural and thermal properties of the substance may yield further potential applications, particularly in electronics, where a structurally stable and thermally conductive material is desirable; this in particular has made an exploration of the thermal properties of amorphous carbon of great interest. In this preliminary investigation, we create amorphous carbon in a 512-atom diamond model by melting the diamond, and equilibrate the liquid at different densities, within a LAMMPS molecular dynamics simulation utilizing Tersoff potentials. We then quench the liquids to produce amorphous carbon of variable density, and examine their structural and thermal properties. We then outline a range of the structural and thermal properties achieved at these densities, and discuss the impact of variable density upon these properties, as well as the implications of these findings and suggestions for further research.

Student Name: Julian Randolph
UC Davis Department: Plant Sciences
UC Davis Mentor: Dave Tseng

Editing Starch Branching Enzymes to change starch structure in tomatoes to change digestibility.

The goal of our project is to change the expression of two genes in the tomato genome to change the overall structure of starch in the plant which would result in a change in digestibility, facilitated by CRISPR/Cas-9. The genes are responsible for the branching of starch chain structure and when branches occur they create a special type of bond. The bonds are a result from a easily digestible sugar, so if the starch chains have more branches it is hypothesized that the plant would be more digestible as the sugar becomes more prevalent in the plant.

Student Name: Ella Jean Raymundo
UC Davis Department: Plant Biology and The Genome Center
UC Davis Mentor: Dr. Savithramma Dinesh-Kumar

Validating the delivery of two component Tobacco rattle virus using single Agrobacterium method for virus-induced gene silencing

Virus-induced gene silencing (VIGS) approach is used for reverse genetics by the scientific community. In this method, a partial sequence of a target gene is cloned in a viral vector used to infect plants. Once viral infection occurs, the host plant’s RNA silencing defense system generates small interfering RNAs (siRNAs) from viral double stranded RNA (dsRNA) produced during viral replication. These siRNAs will then target corresponding host gene transcripts inducing downregulation. Tobacco rattle virus (TRV)-based vector is used for VIGS in plant gene function studies. The current method of TRV-VIGS involves infecting host plants by introducing the two TRV-RNA components into separate Agrobacterium and then co-introducing them into plant leaves. We tested introducing both TRV components using a single agrobacterium-based delivery for VIGS. When both TRV components are delivered using single agrobacterium, all cells are expected to contain both TRV-RNA components and hence predicted to induce better silencing of the target gene of interest. Results from our first attempt indicate that inserting both TRV-RNA components carrying the target gene into the same Agrobacterium strain failed to induce silencing of the target gene, phytoene desaturase  (PDS) in Nicotiana benthamiana (N. benthamiana). However, future developments dedicated to creating a more efficient TRV-VIGS method can allow for high throughput gene function studies that can decrease time and fundings needed to understand the function of plant genes. 

Student Name: Nini Rhee
UC Davis Department: Plant Sciences

Fruit Quality and Consumer Likeability of LSL (Long Shelf Life) Melon Varieties

Long Shelf Life, also known as LSL melons, have been developed to have a longer shelf life capacity and to transport fruits to markets beyond the area of production. A major disadvantage of these fruits is that the growers do not know when to harvest them, and they tend to pick up fruit that is not ripe enough. Due to this factor, Syngenta, a leading agricultural company, has generated a new line of LSL melons with a harvest indicator. By working under Dr. Blanco-Ulate, the goal of this research is to determine fruit quality attributes of new LSL melon varieties and to see if the consumers prefer the new line of LSL melons, Type A, against the traditional LSL melons, Type B. Finally, its objective is to be applied to post harvest research and growers around the world. Qualities were observed through marketability, external color, internal color, volatile organic compounds, firmness, juiciness, and sugar level were measured. Throughout the 4 evaluation time points: 0 (at harvest or time of arrival), 7, 14, and 21 days after harvest, the fruit quality traits remained similar amongst the two lines of melons. Additionally, sensory evaluation results show that consumer preferences were similar as well. Although the Blanco Lab is only on the second trial out of the 3 trials proposed, the results seem advantageous to the new line of melons. With this study, farmers can find the proper time of harvest and improve their marketability. Companies like Syngenta can further advance and develop LSL melons with improved fruit quality traits and longer shelf life.

Student Name: Johnny Seo
UC Davis Department: Anatomy, Physiology and Cell Biology; Veterinary Medicine
UC Davis Mentor: Dr. Kent Pinkerton

How vaping can influence susceptibility to influenza infection in the respiratory system of the mouse

Despite the increasing number of vapers in the United States, we don’t know every aspect of vaping. It was not clear whether vaping affects susceptibility to influenza infection. Since vaping and influenza disease are both related to the pulmonary immune system, vaping has potential to affect susceptibility to influenza infection. In order to test if vaping affects susceptibility to influenza infection, there were 4 groups that were being studied: PBS(control) mice, nicotine vaped mice, influenza nasal-instilled mice, and both nicotine vaped and influenza nasal-instilled mice. After giving different treatment for each group, cell differential, a step to count the number of macrophages, lymphocytes, and neutrophils, was performed. With the data from the cell differential, statistical analysis was runned through Anova one way with the Tukey Multiple Comparison Test. After generating graphs with Anova, it was found that nicotine vaped mice showed no statistical difference in number of lymphocytes and neutrophils when compared to the PBS group. This indicates that  vaping does not affect the susceptibility to influenza inflammation to a significant degree. However, influenza nasal-instilled mice and both nicotine vaped and influenza nasal-instilled mice showed differences in number of lymphocytes and neutrophils when compared to the PBS group. This indicates that being virally infected with influenza through the nose affected the mouse pulmonary immune system.

Student Name: William Su
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Yuanyuan Bai and Zimin Zheng

Improved Chemoenzymatic Synthesis of Fucosylated Human Milk Oligosaccharides Through Benzyloxycarbonyl Tagging and Crystallization of the Precursor LacβNHCbz

Improved synthesis of human milk oligosaccharides (HMOs) has major applications in the development of better infant formulas and other research for improving the health of infants and adults. However, HMOs remain difficult to synthesize on industrial scales. We explored benzyloxycarbonyl (Cbz) tagging to improve the synthesis and purification of two human milk oligosaccharides 2’-fucosyllactose (2’-FL) and 3-fucosyllactose (3-FL) on hundred-milligram scales. This was performed by attaching a Cbz group onto lactose to form LacβNHCbz, a precursor from which all HMOs can be enzymatically produced. This study also established a procedure to efficiently crystallize pure LacβNHCbz with a yield of approximately 70% from the crude sample using a 1:1 mixture of 1-butanol and water by volume. The resulting LacβNHCbz showed a single peak on ultra-high performance liquid chromatography (UHPLC) analysis.

Student Name: Nathan Tang
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Yuanyuan Bai and Zimin Zheng

Benzyloxycarbonyl tagging of lactose and one-pot multienzyme systems for the synthesis of sialylated human milk oligosaccharides

Human milk oligosaccharides (HMOs) are important carbohydrates for infant development. These complex carbohydrates are found in large quantities in human milk. Evidence suggests that HMOs have numerous benefits for infants, including the support of their brain development. There are a variety of methods for synthesizing HMOs. The Chen lab has developed highly efficient one-pot multienzyme (OPME) systems and benzyloxycarbonyl (Cbz) tagging of lactose for improved synthesis of HMOs. LacβNHCbz (Figure 1) was synthesized from lactose (Lac) via a two-step procedure. A solution of 1-butanol and water was found to be the most effective in crystallizing LacβNHCbz for purification. Both CjCstII and Pd2,6ST were confirmed to be suitable enzymes for the production of sialylated HMOs when used in one-pot multienzyme sialylation systems. Applying more efficient methods of oligosaccharide synthesis on the commercial scale will streamline the designing and the production of improved infant formulas that matches the beneficial values of human milk.

Student Name: Tejas Thirumalai
UC Davis Department: Anatomy, Physiology and Cell Biology; Veterinary Medicine
UC Davis Mentor: Dr. Kent Pinkerton

Effect of Vitamin E Acetate Inhalation on Airway Club Cells and Club Cell Secretory Protein (CCSP) in Vaping Mice

Vaping in youth is commonplace and has led to a number of emergency room visits with acute lung injury known as vaping-associated acute lung injury (EVALI). A chemical associated with EVALI is vitamin E acetate (VEA). Concern has been expressed that VEA may be potentially dangerous when present in cigarette solutions and inhaled during vaping. The objective of this study was to determine the effect of aerosolized VEA on lung health when present in e-cigarette solutions. In order to evaluate the effect of VEA exposure on club cells, club cell secretory protein (CCSP) was analyzed. Club cells form a portion of the airway epithelium, are present in the lower airways of the tracheobronchial tree, and produce club cell secretory protein. Club cells and the protein they secrete (CCSP) are critical to the lung airways to form a protective fluid lining layer that neutralizes injurious agents. For this study, mice were exposed to either filtered air or aerosolized VEA. Lung samples were collected following being inflation-fixed with 4% paraformaldehyde. The left lung lobe was cut in four transverse slices, embedded in paraffin, and sectioned using a microtome. Lung tissue sections were placed on glass slides and stained for the presence of CCSP using the technique of immunohistochemistry (IHC). The largest airway in cross-section for each animal was selected for examination by imaging the airway at the 3, 6, 9 and 12 ‘o’clock position of the airway for the presence of CCSP using brightfield microscopy. The software program, ImageJ, was used to determine the percentage of club cell surface area within the epithelium containing CCSP. This analysis led to the observation of a significant reduction in the percentage of club cells containing CCSP within the epithelium of the airways in male mice exposed for 10 days to VEA. Female mice, also analyzed, demonstrated a similar, but not statistically significant reduction in CCSP, compared to filtered air control mice. These findings suggest vitamin E acetate has a marked effect on the CCSP in males, while its effect on females is less pronounced.

Student Name: Rohan Tirumala
UC Davis Department: Plant Sciences
UC Davis Mentor: Arnaldo Rios-Cruz

Confirmation of Loss-of-Function Mutations in Genes Responsible for ABA Biosynthesis in Tomato

Abscisic Acid (ABA) is a plant hormone that regulates many aspects of plant development and physiology. The levels ABA in the plants are maintained by its biosynthesis which is regulated by 9-cis-epoxycarotenoid dioxygenase or NCED genes. The functions of ABA in plants are very broad. During seed development, ABA induces primary dormancy in the seeds which prevents preharvest sprouting or vivipary. However, residual primary dormancy after seed harvest can result in slow and non-uniform germination, which results in variable stand uniformity and hence yield loss. Using CRISPR-Cas9 mediated gene editing, Dr. Khanday’s lab is modifying NCED1 and 4 genes in tomato to create loss-of-function mutants in these genes. These genes are expressed in seeds and thus these mutants are expected to have decreased ABA levels in seeds which should remove the residual dormancy and result in faster and uniform germination. Throughout this experiment, the lab sequenced different lines or samples of tomatoes to decipher the mutations in NCED1 and NCED4 genes. Sanger sequencing was utilized in order to obtain the exact sequence of the DNA at the mutation site and using online tools and other sequence analysis software, the sequences were analyzed to determine what the mutations were, if any. Over the different samples of tomatoes, we saw that there were different forms of mutations including deletions, insertions, and inversions. As this data is collected, it will prove useful as the lab creates gene-edited seeds with confirmed mutations, in order to allow for uniform germination of tomato crops internationally. Further, this research will be applicable to other common crops such as lettuce and peppers.

Student Name: Felix Tuchscherer
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Amisha Poret-Peterson

Identifying the difference between bacterial composition in high versus low nutrient soils

In this study we aim to identify bacterial composition in soils treated with and without wood chips, as well as high levels and low levels of Nitrogen. In order to do this, we used both culture dependent methods including plating, observing, and GenIII plates; as well as culture independent methods which include microbiome sequencing and EcoPlates. By doing this, we concluded that the bacterial communities did in fact differ between unamended and wood-chipped treated soils. Multiple differences were identified: rate of carbon consumption, species of bacteria diversity, rRNA copy number, and colony morphologies. Identifying the bacteria in wood-chipped soil will allow us to understand their effect on biogeochemical cycles, plant pathogens, and relationship with the trees(symbiotic/pathogen). Additionally, understanding the effect lower nitrogen levels have on the bacterial composition of soils can lead to reduction of synthetic fertilizer use, therefore lessening the environmental impact of Nitrogen.

Student Name: Karen Vo
UC Davis Department: Plant Biology
UC Davis Mentor: John Davis

Functional Trait Differences and their Relationships with Gene Expression

In recent years, the study of the differences between species has become more prominent to understand how species adapt to different climates and how they may be impacted by climate change. In this research, the germination behaviors of the Streptanthus and Caulanthus genera, known as the California Jewelflower, are impacted by genetic variation interacting with different environmental factors. Through the statistical computing program R, the analysis of phenotypic and gene expression data can be used to find the correlation between functional traits and the expression of genes at time of germination. This study analyzed the genomic RNA expression profiles of the different populations and species of the California Jewelflowers to find how patterns of gene expression relate to functional traits. Using annotated RNA sequence, we were able to identify clusters of genes correlated with functional traits to determine the biomass allocation patterns of these species. The main genes found in this cluster found to correlate with functional traits were the Delay of Germination 1 (DOG1) and Gibberellin 2-oxidase genes. The levels of expression in these genes aid in ensuring seeds germinate under appropriate conditions and utilize growth patterns designed for their environment. Using the analysis of the genetic data, the Streptanthus species were found to be taller with smaller leaves, while the Caulanthus species are shorter with larger leaves. Overall, we found that the variation in gene expression interacting with the environment drives the phenotype trait differences between species.

Student Name: Justin Wang
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Alisha Kar

Effect of Ultrasound on Gastric Digestion in Model Food Gels

With increasingly unhealthy diets and newfound connections between diet and disease, more light has come to understanding the digestion of foods. In this study, non-treated and ultrasound-treated gels were measured in three different categories after in vitro gastric digestion: hardness (texture analysis), absorbance of gastric juice (moisture analysis), and acidity. After digestion, the ultrasound gels were more firm, absorbed similar amounts of gastric juice, and less acidic. This suggests that it is more difficult for gastric juice to break down ultrasound-treated gels. Thus, because ultrasound seems to be not beneficial during in vitro gastric digestion, ultrasound may not be a viable path to develop new food products for easier digestion and nutrient absorption. However, it still has many applications in the food industry such as food preservation.

Student Name: Zijing Wei
UC Davis Department: Plant Sciences
UC Davis Mentor: Linyi Yan

Structure-function investigation of hormone breakdown in plants

Strigolactones (SLs) are a class of carotenoid-based phytohormones that regulate developmental processes in plants, such as shoot branching and root growth. While the mediators of SL biosynthesis and signaling pathways have been extensively studied, the key components of SL catabolism remain undiscovered. Previous studies have identified carboxylesterase, a member of the α/β-fold hydrolase (ABH) superfamily, as a hydrolase of SLs and potential mediator of SL catabolism. Members of the ABH family have a conserved hydrolytic active site composed of a catalytic triad, in which a nucleophilic serine attacks the ligand and initiates hydrolysis, however, little is known about the structure and function of SL catalyzed enzymes and their conformations. Here, we generated a mutant protein, which replaces the catalytic serine residue of the active site with alanine. We found that the hydrolytic activity of the mutant towards SLs is indeed abolished. Furthermore, the mutant shows minimum change in stability when exposed to SLs compared to wild-type enzyme, which indicates that binding affinity of the mutant towards SLs is impacted as well. The mutant enzyme also shows higher stability than wild type, which indicates suitability for crystallization and subsequent structure function analysis. Overall, our results have provided valuable insight and opened new research possibilities regarding the unsolved structure of these enzymes, which is crucial for future applications in SL pathway.

Student Name: Siena Yang
UC Davis Department: Plant Sciences
UC Davis Mentor: Rosalie Sinclair

Callose’s Role During Plant Cytokinesis

Plant cytokinesis is the primary division process that involves the construction of the new cell wall that will separate the two daughter cells. The development of the cell wall requires four membrane maturation stages to form that happen simultaneously with the most mature material at its center. The cell wall is made up of polysaccharides such as cellulose that solidify the cell wall. Other polysaccharides such as callose exist at the cell plate only for a short time before getting recycled and are not in the final wall. However, they also appear at the junction of the cell plate meeting the cell wall, in addition to being a matrix for the other polysaccharides such as pectin and hemicellulose to assemble in. Each one of these stages involve vesicle buildup and coalescence and membrane maturity, which simultaneously occurs with the accumulation of cell wall polysaccharides. Although it has been discovered that each polysaccharide must play roles in the assembly process, very little is known. Questions still remain about callose’s short but important role in the cell plate. However, with the use of a unique tool set, we put forward that under different conditions, callose played a valuable role in guiding the structure of the cell plate in a cellularly stable and favorable way during division. Further investigations on characterizing and improving the support of the cell wall could lead to better protection against ecophysiological and biological factors that are damaging to society.

Student Name: Ella Yee
UC Davis Department: Molecular and Cellular Biology
UC Davis Mentor: Dr. Ian Korf

Ultraconserved elements: a plant genome perspective

Ultraconserved elements (UCEs) are parts of the genome that have extreme conservation among a clade of organisms. UCEs were first discovered between human, mouse, and rat genomes, and most studies since then have been conducted on animals. Research on plant UCEs is still in the early phases. Studies have identified high conservation in regions of plant genomes, but these regions are generally less similar than the UCEs identified in research on animals. This study aims to explore whether conservation on the level of animal UCEs can be found in plants. Comparison of the Arabidopsis thaliana genome to the genomes of Brassica rapa, Populus trichocarpa, and Oryza sativa demonstrated that UCEs do not exist in the noncoding regions of these plant genomes. However, they do exist in coding regions as exon outliers, exons with unusually high conservation compared to other exons from the same gene. The results from this study point at a key difference between animal and plant genomes: While animals share both noncoding and coding UCEs, UCEs only exist in coding regions of plant genomes. It is suspected that noncoding UCEs serve as enhancers and gene regulators, whereas coding UCEs control splicing and individual genes or exons. A lack of noncoding UCEs in plants suggests that though some plant and animal genes may be controlled in the same way, large scale genome organization differs significantly between these two kingdoms.

Student Name: Danny Youstra
UC Davis Department: Genome Center
UC Davis Mentor: Dr. Ashley Vater

Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: H419Y, K413Q, and T267E

Enzyme engineering is a rapidly growing field that harnesses the potential of artificial catalysts undiscovered by natural mutations. However, the small size of current datasets linking structural composition to catalytic efficiency and thermal stability limits the accuracy, precision, and reliability of modern protein modeling algorithms. In this study, we introduce three mutations, H419Y, K413Q, and T267E to β-glucosidase B (BglB) and conduct a series of assays to determine how the mutants affected protein expression in E. coli, kinetic activity represented by Michaelis-Menten constants (kcat, KM, and kcat/KM) and denaturation temperature ™. Each mutant expressed at high levels and yielded kinetic and thermal results in accordance with our hypotheses. In aggregate, these results reflect well on the current iteration of the Rosetta Energy Function, which correctly factored changes to intermolecular forces and into its predictions. These mutants contribute to the growing Design2Data database, which will be used to train new accurate prediction algorithms for BglB and other family I glucosidases through machine learning. Improved computational enzyme modeling tools could allow breakthrough developments in biofuels, therapeutics, and waste removal.

Student Name: Sarah Yu
UC Davis Department: Genome Center
UC Davis Mentor: Dr. Ashley Vater

Design to Data: A mutagenesis study for 8 β-glucosidase B (BglB) variants

The aim of enzyme engineering is to be able to accurately predict enzyme functions using computational models and algorithms, though a key limiting factor is a lack of comprehensive datasets. In this study, three variants of β-glucosidase B (BglB) and their thermal stability ™ as well as their Michaelis-Menten kinetic constants (kcat, KM, and kcat/KM) are characterized. The mutants were designed using FoldIt and the variants were produced in E. coli cells and then purified. The resulting proteins were tested by kinetic and thermal stability fluorescence-based protein unfolding assays. Mutants K68H and L108M exhibited increased catalytic turnover rates and thermal stability, while W407D expressed minimally and displayed reduced kinetic activity. K68H and L108M also demonstrated increased substrate binding capabilities as compared to the wild type. These variants and their functional properties were added to the BglB database with the aim of improving predictive algorithms such as Rosetta for more accurate enzyme engineering. Enzymes could be engineered to solve a range of problems, from creating biofuels to degrading plastics.

Student Name: Aasiya Zaidi
UC Davis Department: Molecular and Cellular Biology
UC Davis Mentor: Dr. Ian Korf

Palindromes & Promoters: Reflecting on the Importance of Palindromes in DNA Sequences

A palindrome is a word or phrase that can be read the same forward and backward. Similarly, palindromic sequences in DNA can be read the same from the 5’ to 3’ end on one strand as on the reverse complement strand. These sequences frequently occur near transcription factor binding sites, and this study aimed to determine whether they also occurred more often near promoters, enhancers, and other key regions of the genome. We deployed an algorithm on the genome of C. elegans to calculate the overall palindrome richness and identify extremely palindrome-dense areas. Our findings indicate that palindromes have biological significance in the C. elegans genome, as they occur significantly more often than expected under a randomized model. In addition, intergenic regions were found to be the most palindrome-dense in the genome, indicating that palindromes may occur more frequently in close proximity to promoters and enhancers.

Student Name: Mary Zawalick
UC Davis Department: Center for Neuroscience
UC Davis Mentor: Fernando Gomez

The Influence of Environment of the Primary Motor Cortex and Motor Behavior of Rats

The importance of the environment, specifically environmental enrichment, has long been investigated for its role in the development of animals. Previous studies have shown that environmental enrichment and skilled tasks, which both involve novel movement, can increase the rate of motor cortex development and alleviate the effects of motor deficits, such as cerebral palsy (Marques et al., 2014; Young, Vuong, & Teskey, 2012). This study characterized the emergence of motor maps based on how Brown Norwegian rats developed in differing environments–one containing an abundance of enrichment and one lacking movement opportunities. The research investigated if the rats that developed in the different environments had different organizations of their primary motor cortex, as well as how the different environments affected motor behavior. Overall, we investigated the plasticity (ability of change) of the primary motor cortex. We assessed differences in primary motor cortex (M1) connectivity and organization, and behavior tasks were used to determine the rate of motor development and the level of motor coordination. When the rats reached adulthood (postnatal day > 60), tetrodes assessed the specificity of neurological responses to different textures. Our results indicate that rats reared in the field pens displayed a faster rate of motor development for exiting a circle and less errors when walking across a standard ladder rung. This conveys how the level of environmental enrichment can affect the development of motor behavior.

Student Name: Peter Zheng
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Dr. Mason Earles

Deep Learning and Fruit Detection to Improve Strawberry Yield Forecasting from Proximal Imagery

Yield forecasting is an essential tool for agricultural management. It can enable automation and optimization of variable-rate inputs such as water and fertilizer, allowing farms to reduce both expenses and environmental impact while increasing their productivity. Currently, the primary method for yield forecasting involves manually sampling a small portion of plants and extrapolating to the entire field; however, this is time-consuming and inaccurate.

2021 Research Projects

Student Name: Raya Amin 
UC Davis Department: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giulivi 

Using Meta-Analyses to Find Mitochondrial Dysfunction in Wilson’s Disease

Wilson’s Disease is a genetic disease that affects about 1/30,000 people. In this disorder, mutations in the ATP7B gene and the resulting ATPase protein prevent the liver from excreting copper properly, and also inhibit the ceruloplasmin from storing and transporting copper. As a result, copper overloads in the liver and other organs, resulting in cirrhosis, cell damage, liver failure, and neurologic symptoms. Although these symptoms are very recognizable, the pathogenesis of Wilson’s Disease and the copper toxicity is still largely unknown. A prevalent hypothesis is that the copper causes mitochondrial dysfunction within the liver and other organs, and this dysfunction leads to the symptoms seen in Wilson’s Disease. However, this hypothesis is still controversial due to conflicting evidence. Therefore, this study looked to perform a literary review on studies containing data about mitochondrial dysfunction in Wilson’s Disease. The studies were found in PubMed and SciFinder, and the ultimate objective was to perform a meta-analysis on the data about hepatic mitochondrial dysfunction. The meta-analyses were performed for these primary outcome variables: ATP production, Complex IV activity, Mn-SOD activity, mtDNA deletions, and mitochondrial copper content. Ultimately, the results showed that there was a decrease in complex IV activity and ATP production within Wilson Disease subjects compared to controls. In contrast, there was an overall increase in Mn-SOD activity and mitochondria copper content in Wilson Disease patients, and it was more likely that mtDNA deletions were present within Wilson Disease subjects. The results of the meta-analysis implied that the copper overload did lead to mitochondrial dysfunction within Wilson Disease patients, and that this mitochondrial dysfunction could lead to the damage of entire cells and organs. However, because the research was conducted in limited time, and with a limited amount of studies, the results simply suggest that additional research is needed to truly confirm the role of mitochondria in Wilson’s Disease.

Student Name: Jiayin Song
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Siobhan Brady

A “Shiny” Application made in R provides easy analysis of Ethiopian soil data

Striga hermonthica, a root parasitic weed, is one of the most yield-limiting biotic factors affecting sorghum in Africa (Reddy 2004). Sorghum ranks as the fifth most important cereal crop in the world. In Ethiopia, heavy Striga infestation is a major issue for farms, especially smallholders. Understanding the significance of soil in this problem is essential to solving it. Moreover, soil characteristics, microbe composition, and Striga and sorghum variation are crucial factors to consider when studying complex host-parasite-microbe interactions. Much research has been working to devise approaches to limit the harmful effects of Striga and other parasitic weeds. The Shiny application this project coded in the R language with various packages provides easy analysis of Ethiopian soil data for users without needing knowledge in coding. It aims to assist farmers who may otherwise not have the expertise to conduct these analyses themselves. They must learn about the properties, conditions, and quality of their native soil to be aware of possible Striga infestation and methods to combat it. The main features and functionalities of the application are Bubble Map, Pie Chart, Correlation Plots, Data Upload, Data Filtering, Check, Correlation Analysis, PCA Plot, and Heatmap. Using the app with the model dataset found pronounced variation in Striga distribution across Ethiopia. The second case study using three candidate samples and analytically comparing the soil composition between them proved the physical attributes vary exponentially even in close-ranged samples, whereas the nutrients did the opposite. It concluded that the two groups do not appear directly correlated, and their patterns may be regulated by other environmental factors instead. This app is the foundation for future studies on the effect of soil properties on host-parasite chemical signaling and a beneficial resource for developing countries struggling with Striga.

Student Name: William Wong
UC Davis Department: Computer Science
UC Davis Mentor: Dr. Stacy Harmer

Effects of elf3 and lhy mutations on sunflower heliotropism

Heliotropism is the process by which sunflowers orient themselves towards the sun throughout the day, and is essential to their ability to attract pollinators. Circadian clocks regulate this process and are driven by many genes, such as the ELF3 and LHY genes. This study examines the effects of elf3 and lhy mutations on heliotropic behavior in sunflowers. A software program called ImageJ was used to measure the stem angles of wild type (WT), elf3 mutant, and lhy mutant sunflower plants in field photos taken in 30-minute intervals. When the data was plotted using R, we found no statistical difference in the plants’ phenotypes. This suggests that the elf3 and lhy amino acid mutations did not modify the protein significantly, allowing for normal gene expression and heliotropism. Examining the effects of mutations on sunflower heliotropism may benefit future research predicting the possible effects of climate change on sunflowers and their circadian clocks.

Student Name: Emily Yang
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation in Metabotropic Glutamate Receptors

Tyrosine sulfation in the past has demonstrated the increased functionality of a certain protein in many cells. Being a post-translational modification, its impact on the protein’s folding is integral to ensure the overall efficacy of interactions with other biochemical molecules and proteins. In this research project, tyrosine sulfation was investigated in proteins classified as metabotropic glutamate receptors, which fall under the Type C G-protein Coupled Receptor category. Abbreviated as mGluRs, these receptors are involved with diseases like melanoma, while also providing possible drug targets for neurological disorders like schizophrenia, autism, and Parkinson’s. By using Position-Specific Scoring Matrix, MUSCLE alignment, and meta-analysis of mutations, predicted tyrosine sites are at Tyr236 in mGluR1, Tyr223 in mGluR5, Tyr216 in mGluR2, Tyr222 and Tyr569 in mGluR3, Tyr400 in mGluR4, and Tyr227 in mGluR8. If confirmed, these predicted tyrosine sites could provide further treatment options for neurodegenerative diseases and more. 

Student Name: Tabatha Stewart
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Prediction of Tyrosine Sulfation in 5-HT receptors

Tyrosine Sulfation was predicted in five 5-HT G-Protein Coupled Receptors using a position-specific scoring matrix. The predicted sites were highly conserved in vertebrates, and sites in 5-HT1B exhibited clustering. Multiple predicted sulfation sites were found to be highly involved in ligand binding and recognition, a commonly observed function in previously identified tyrosine sulfation sites. Therefore, if a sulfated tyrosine in one of these sites turned out not to be sulfated, it would prevent ligand binding and thus obstruct 5-HT receptor function. 5-HT receptors mediate neurotransmission and are associated with various cognitive and neurological diseases and disorders such as depression, migraine, schizophrenia, Alzheimer’s, etc. If these predicted sites are confirmed to be sulfated, more accurate agonists/antagonists could be produced that could aid in the treatment of these diseases.

Student Name: Amber Henny
UC Davis Department: MCB / Genome Center
UC Davis Mentor: Dr. Ian Korf

Lethal Phenotypes Are More Likely in Single-Copy Genes

Gene duplication is a major evolutionary factor that contributes to the diversity of phenotypes within organisms. Paralogs can take on new functions after a gene duplication event, adding variety to the pool of traits within a population. We sought to describe the relationships among gene copy number and phenotypes to better understand how the type of gene, single-copy vs. gene family, impacts the categories of observed phenotypes. In this paper, we show that lethal phenotypes are more likely to occur in single-copy genes than in gene families. Other categories of mutations more likely to occur in single-copy genes include protein metabolisms and nonsense mRNA accumulation. Gene families are more likely to result in subtle phenotypes, for example, those related to pathogenic responses. From a human health perspective, where the onset of disease is later in life, therapeutic targets are more likely to come from gene families.

Student Name: Joshua Xu
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Nitzan Shabek

Structure Function Investigation of KAI2 Biosensor in Plants

KARRIKIN INSENSITIVE 2, or KAI2, is an α/β hydrolase involved in seed germination and seedling development. KARs and KARs-like signals also regulate many aspects of plant growth and development not limited to species from fire-prone environments. It is essential for plant responses to karrikins, a class of butenolide compounds derived from burnt plant material found in smoke that are structurally similar to strigolactone plant hormones. The mechanistic basis for the function of KAI2 in plant development holistically remains unclear. Investigation of the rice KAI2 sequence in silico demonstrates that it encodes for a function protein. By isolating this functional protein and analyzing its crystal structure using PyMOL, it may be concluded that KAI2 gene duplication plays an adaptive role for diverse environments by altering the receptor responsiveness to specific KAI2 ligands. The structure and ligand-binding pocket of KAI2 is consistent with its designation as a serine hydrolase with enzymatic function, as well as previous data implicating the protein in karrikin and strigolactone signalling. Understanding plant responses to KARs may better assist the controlled germination of plant species. A more comprehensive structural comprehension of the KAI2 protein alludes to future investigations into resolving the mechanistic basis for KAI2 function in plants and similar receptor pathway reactions to various growth regulators.

Student Name: Jeewon Han
UC Davis Department: Chemistry, Genome Center
UC Davis Mentor: Dr. Justin Siegel

Redesigning Protein Minibinders for SARS-CoV-2 Variants

To provide therapy for the highly contagious SARS-CoV-2, a group of researchers from the University of Washington developed high-affinity binders that interact with the virus’ spike proteins that inhibit the viruses attachment and colonization of human cells (Cao et al 2020). However, as various COVID-19 variants rise (such as the beta, delta, or gamma variants), the previous minibinder design may not function as effectively as they were designed to fit the original COVID strain. Therefore, making a redesign of the binder may be necessary. This research investigates variations of three scaffold minibinders described in Cao et al 2020: LCB1, LCB2, and AHB1 as well as two COVID variants of concern: beta and gamma. The protein minibinders were hand designed using FoldIt Standalone, changes were visualized in PyMol and mutation favorability was computed with the PyRosetta FastDesign module, with the aim of redesigning the binders to more effectively bind to the spike of COVID variants and form a stable complex. Furthermore, through analyzing a suite of mutations collectively created by the research team, a “universal” minibinder that fitted multiple variants was developed.

Student Name: Parthiv Nair
UC Davis Department: Physics
UC Davis Mentor: Dr. Daniel Cox

Decoys to Bind with MP120 in Fighting HIV

We present a decoy that will act as a substitute for CD4 in the binding with MP120 on HIV. The model is derived from a molecular dynamics simulation of the binding between MP120 and CD4 in water. The decoy isolates a section of CD4 that contains the greatest amount of concentrated hydrogen bonds while taking into account considerations such as hydrophobia of amino acids, length of the decoy, and NIT sequences. Binding simulation results have shown that the surface area loss of the binding process using the decoy is similar to that of the binding process with CD4. Additionally, the binding strength of hydrogen bonds between MP120 and the decoy is similar to the binding strength of the hydrogen bonds between MP120 and CD4. Once grafted on β-solenoids and trimers, the decoys can be used for both therapeutic and diagnostic purposes in fighting HIV infections in humans.

Student Name: Ethan Tam
UC Davis Department: Center for Population Biology
UC Davis Mentor: Jon Aguiñaga

Effect of Individual Differences in Behavior on Collective Assessments of Environmental States

The effects of how individual differences affect collective behavior in animal groups remains a challenge to theoretical and empirical researchers across various disciplines. In this paper, we construct a theoretical mathematical model through the coding language R to investigate how social information and specific individual differences interconnect to form an overall group response. We consider differences in cognition such as aggression and passiveness to replicate the variations in real-life groups. The analyses constructed through mathematical equations display how social information impacts the accuracy of individuals’ assessments of their environmental mean, whether it be an increase, decrease, or constant. Weights and decision rules are assigned to the private and social assessments based on aggression and passiveness. The final result of the simulations shows that more social samples increase the accuracy for both aggressive and passive individuals. However, the simulations also show that more personal samples cause a decrease in accuracy for aggressive individuals and a constant for passive individuals. This model predicts the accuracy of collective group assessments of their environment, and thus their responses. Since the variables and code are flexible, empirical researchers can utilize this aspect to see beforehand what responses to expect in a group or run theoretical simulations to visualize responses for specific changes within the experiment.

Student Name: Raya Amin
UC Davis Department: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giulivi

A Meta-Analysis of Mitochondrial Dysfunction in Wilson’s Disease

Wilson Disease (WD) is characterized by copper overload in the liver, brain, and other organs. Copper toxicity can cause liver cirrhosis and failure as well as neurologic manifestations. Many studies have hypothesized that copper accumulation targets mitochondria, and the resulting mitochondrial dysfunction is at the core of the symptoms and progression of the disease. However, the information on the exact pathogenesis of WD and its link to mitochondrial dysfunction is limited and sometimes contradictory. Thus, the objective of this study was to consolidate functional and imaging data on the “types” of hepatic mitochondrial dysfunction in WD. A literary review was conducted on SciFinder and PubMed, limited to original research, resulting in >70 relevant studies. The meta-analysis indicated increases in mitochondrial copper content, mtDNA deletions, and MnSOD activity in WD animal models and patients, with an overall decrease in ATP production, especially in the copper-containing Complex IV. Based on these results, WD treatments would need to be targeted at removing the excess of mitochondrial copper-content with the possible aim of decreasing the morbidity or progression of WD.

Student Name: Callie Milner
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles

Investigating the Effect of Promoter DNA Methylation on Tomato Fruit Ripening

This work focuses on ways to counteract perishability of the tomato fruit (Solanum lycopersicum L.). Some postharvest methods often extend shelf life; however, they lessen fruit quality, making the tomatoes unsatisfactory. The goal of this project was to investigate techniques to increase tomato shelf life with successful postharvest methods while improving tomato quality and taste. Specifically, this project aimed to generate and characterize tomato lines with allelic mutations in the promoter of a key ripening gene, i.e., RIN (Ripening Inhibitor), which regulates tomato fruit ripening, using CRISPR/Cas9 genome editing. In this research, the dead CRISPR/Cas9 technology was utilized by designing a construct for transformation into the tomato. The gRNA that directed the ‘dead’ Cas9 protein to one of the methylated sites in the promoter was also selected for cloning into the construct. Expression of the dead Cas9 and gRNA altered the methylation status of the promoter region of RIN. Our hypothesis is that if methylation of the RIN promoter region inhibits RINs expression and therefore its regulation of ripening, then removal of RIN methylation sites will increase RIN expression, which in turn would promote faster ripening and perhaps better fruit quality. In conclusion, the goal of this project is to use epigenetic modifying to improve the quality of tomatoes postharvest and increase the shelf life of tomatoes.

Student Name: Sia Agarwal
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Stacy Harmer

Regulation of Sunflower Heliotropism by Circadian Clock Genes

Heliotropism, or solar tracking, is an organism’s ability to orient itself to the position of the Sun. Sunflowers perform this function, which is regulated by the plant’s circadian clock. This study aims to further prove that through genetics, the circadian clock regulates sunflower solar tracking. This study compares the solar tracking of wild type, elf3, and lhy sunflowers. ELF3 and LHY are both known genes of the circadian clock in sunflowers. Members of the Harmer Lab UC Davis grew elf3, lhy, and wild type sunflowers in Davis, California and imaged the plants over several days. We measured the angles of the plants’ stems to observe solar tracking. Measured in ImageJ and plotted in R, the progression of stem angles demonstrated minimal to no differences in phenotype of solar tracking between the three genotypes. Further research is needed to confirm the effect of elf3 and lhy mutations on sunflower solar tracking.

Student Name: Anakha Ganesh
UC Davis Department: Physics
UC Davis Mentor: Dr. Daniel L. Cox

Identification of the Best Binding Structure for the Decoy Protein for the Marburg Virus

Decoy proteins are sections of human receptor proteins that bind to foreign antigens. Decoy proteins have been shown to be as effective as antibodies at preventing harmful effects of viruses. They operate by binding with the virus instead of allowing the virus to bind to the cell and capturing the virus. This traps the virus in the decoy (Sokolowska, 2020). Decoy proteins also avoid issues with viruses mutating to escape antibodies since viruses do not evolve away from the receptor. The Marburg virus is a filovirus, the same family of virus as Ebola (Ng, 2015). It can cause the highly dangerous Marburg hemorrhagic fever. The purpose of this project is to find and test the strongest binding structure for a decoy protein to the Marburg virus excerpted from the receptor protein, NPC1. The NPC1 protein contains two disjoint binding regions. Using the YASARA molecular dynamics software, two decoys were tested: one that includes only one of the binding regions, and another decoy that included both binding regions. The decoy protein structure that included both of the disjoint binding regions of the receptor to the Marburg virus had the strongest binding structure of the two tested. Developing this decoy protein has potential diagnostic and therapeutic applications. A decoy protein attached to a beta solenoid protein can diagnose diseases outside the body. Attaching the decoy protein to a therapeutic trimer can neutralize the virus within the body.

Student Name: Giacomo Carter
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Julin Maloof and John Davis

The Effects of Light on the Expression of Genes Involved in Germination in Two Species in the Streptanthus Clade

The time a seed germinates determines the environmental conditions the plant will face throughout its life cycle. There are many environmental cues that trigger germination. Light, temperature, and water availability play the most important roles. Ultimately germination is controlled by the DNA within each individual seed, so what specific genes are affected by the presence or absence of light and play a role in germination? To explore how light affects gene expression, samples were taken from seeds in the Streptanthus clade at a predetermined time before germination. They were then sequenced using RNA-Seq technology. From there the RNA sequence data was mapped to a reference genome and the sequence data analyzed. Genes whose expression increased or decreased in the absence or presence of light were first discovered. After a Gene Ontology (GO) term analysis, those differentially expressed genes that are potentially related to germination, or the inhibition of germination were uncovered. The results from the analysis of this sequence data can give us clues as to how different plants will be affected by the changes brought on by global warming.

Student Name: Megan Yee
UC Davis Department: 
UC Davis Mentor: Dr. Cecilia Giulivi

A Systematic Review and Meta-Analysis on Mitochondrial Dysfunctions in Schizophrenia

A significant number of studies relating to mitochondrial dysfunction in schizophrenia has emerged over the last few decades. Here, we conducted a systematic review and meta-analysis of past and current literature to consolidate the information and identify the most prevalent type of mitochondrial dysfunctions in schizophrenia. In this work, 106 studies were eligible for the analysis (human, brain, access to full-text, control, and schizophrenic data). From these we selected brain regions with the most studies (prefrontal cortex and striatum) with 58 studies separated by brain region and mitochondrial dysfunctions. Prefrontal cortex studies showed a significant reduction in mitochondrial mass, NDUFV1 gene expression of schizophrenic patients was found. Data from studies also showed commonalities in mitochondria reduction in the prefrontal cortex and striatum, and observed an increase in mitochondrial metabolic protein expression in the prefrontal cortex. These findings suggest reduced synaptic activity, altered neural activity, and increased glutamate levels that could disrupt normal cognitive functions in schizophrenic brains.

Student Name: Milton Nguyen
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton

The Effect of Cigarette Smoke Exposure and Smoking Cessation on the expression of Club Cell Secretory Protein in Central Airway Epithelial Cells

Club Cell Secretory Protein (CCSP) is a protein expressed in the lungs which acts as a defense for the airway epithelium against exposures such as tobacco and cigarette smoke. Cigarette smoke can damage the airway epithelium and can lead to the development of Chronic Obstructive Pulmonary Disease (COPD) which is categorized by inflammation of the bronchi and enlargement of alveolar air spaces. Very few effective treatments exist for COPD, and smoking cessation has been hailed as the most effective treatment for COPD. In this study, the effects of smoking cessation are investigated as it relates to content of CCSP in airway epithelial cells. This research will help elucidate how CCSP, a line of defense for the lungs, interacts as it relates to smoke exposure and subsequent smoking cessation. This research was conducted using a smoke exposure and smoking cessation experiment with spontaneously hypertensive rats. Lung tissue from the rats was stained using immunohistochemistry for presence of CCSP. The ImageJ computer program was used to analyze and measure CCSP content in relation to the airway epithelial cells. The results of the study showed a positive correlation between CCSP volume per basal lamina area and length of smoking cessation for rats exposed to tobacco smoke. These results help further confirm smoking cessation as a mechanism to repair lung cells and can be used to help inform public health and health policy efforts to improve health outcomes for current smokers.

Student Name: Kaley Mafong
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

The Physiological Effects of Evapotranspiration in Almond Trees

The average almond tree uses 1.1 gallons of water for every almond that is produced. This makes almonds a big target for studying water stress in the scientific community. It has been found previously that drought water stress decreases carbon dioxide uptake and causes leaf rolling and wilting in almond trees. Also, early hull split was associated with higher stem water potential in the soil. However, a relationship has not yet been determined between an almond tree’s external appearance and internal physiological processes, during times of water stress. The objective of this study was to identify a relationship between the visual and physiological cues of water stress in nonpareil almond (prunus dulcis P. Mill) trees. A video camera, established in 2015, was used to collect continuous photographic footage of the almond tree located in the Kearney Agricultural Research Extension Center. This particular study analyzed the images in the interval from April 12 to April 20 of 2018 in the form of a timelapse. In order to quantify the visual data from the camera, Fiji ImageJ was used to measure the angle between the front branch and leaves during periods of leaf wilting. A weighing lysimeter (with D, W, L dimensions of 2m x 2m x 4m) was implemented to determine the almond tree’s water usage and gather the physiological data. The tree was irrigated accordingly using a double-line drip irrigation system. Visual data from the photographs was directly compared with physiological data such as the tree’s Midday Stem Water Potential, Evapo-Transpiration measurements, and the lysimeter weight. An effect of using a lysimeter was restricted root growth on the tree because the apparatus limited the tree’s underground space. A relationship was found between the visual and lysimeter data during the period April 12-20 of 2018. According to the Midday Stem Water Potential on April 12, the almond tree was significantly stressed (-12.6 bars) in comparison to the non-lysimeter trees and the non-stressed Stem Water Potential. On that same day, the visual data portrayed a loss of turgidity in the leaves with a 72° wilt (175° normally). Therefore, it could be concluded that a relationship exists between the visual and physiological lysimeter data of water stress in nonpareil almond trees. It is now known that physiological effects of water stress are reflected in the tree’s physical appearance, and this finding can help find more sustainable methods of irrigation for almond trees in the future.

Student Name: Timothy Liu
UC Davis Department: Land, Air and Water Resources
UC Davis Mentor: Dr. Peter J. Hernes

Particle Characterization in the Sacramento-San Joaquin Delta - Where Are the Plants?

The Delta is a crucial water resource of California, providing drinking water to 30 million Californians, irrigation water for 3 million acres of farmland, and habitats for fish and surrounding wildlife. However, declining native pelagic fish populations since the early 2000s have put the Delta ecosystem into crisis. Reduced primary productivity has tipped the energy balance in the Delta, causing heterotrophic energy demand to far outweigh the energy sources available. Although the principal food source for the lower food web is phytoplankton, new research has shown that particles made of wetland plants can also be a food source utilized by the lower food web. Knowing this, characterizing the amount and spatial extent of detrital wetland particles across the Delta can identify areas capable of bolstering the lower food web and in turn support pelagic fish. Lignin, an organic polymer resistant to microbial degradation and unique to vascular plants, is used as a biomarker for organic material across the Delta to characterize wetland detrital particles. Previously, eastern and southern sites have yet to have particles characterized, but now with the first wide-area mapping survey conducted of the Delta, seasonal hotspots for lignin were found further inland than one may expect, as well as wetland hotspots in the marshes. The newfound data emphasizes the importance of routine research in the Delta, especially when human activity is altering the environment faster than it’s being monitored.

Student Name: Ayaan Ali
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist

Predicting Tyrosine Sulfation in Laminin, Leukocyte-Specific, and RGD Receptor Integrins

Tyrosine sulfation is a post-translational modification that enhances ligand-binding specificity and protein-protein interactions. Many proteins that are likely sulfated remain unidentified, potentially including integrins. Integrins are crucial proteins with numerous roles in organisms, such as tethering cells to the extracellular matrix. Similar to other sulfated cell adhesion molecules, integrins are also likely sulfated. The results indicate sulfation is most likely in the αM subunit, β1 subunit, β3 subunit, and β4 subunit. Mutations to tyrosine sites in the αM, β3, and β4 subunits were accompanied by decreased ligand binding and linked to epidermolysis bullosa. The likelihood for sulfation in these subunits predicts sulfation in other subunits due to evolutionary relatedness. Confirming sulfation in these sites elucidates molecular characteristics of integrins, allows for improvement in drug development, and provides insight into integrin structure.

Student Name: Olaf Morski
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

The Physiological Effects of Evapotranspiration on Almond Trees

Almond Trees use a lot of water for every almond they produce. This is due to the fact that it takes a lot of energy to produce these almonds. Acknowledgment of different factors that may affect almond tree’s productivity in using water to grow almonds can help farmers be more productive and resourceful in growing almond trees with less water use. The specific research question that is trying to be answered in this research is, how do physiological and water stress data compare in an almond tree? Evapotranspiration (ET) is a process that previous researchers have found to correlate with water usage in plants. A lysimeter is useful in measuring the evaporation in plants. Comparing lysimeter data of the almond tree in question to lysimeter data of turf grass can be useful to find data that might be related to extensive water stress in almond trees. Turf grass data was used as a comparison to ‘standardize’ tree ET to the current weather effects. Pictures taken of the almond tree being analyzed can be used to determine physiological data that might have caused inconsistencies in ET data of the almond tree. It has been found that as the Water stress ratio between the Lysimeter Tree and the Turf Grass decreases the amount of green color in the trees leaves also decreases and as the ratio increases the green color in the leaves increases as well.

Student Name: Arnav Rao
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton

The Effect of f Nose-to-Brain Transport of Engineered Zinc Oxide Nanomaterials on Microglial Activation

Zinc oxide engineered nanomaterials (ZnO ENMs) are present in personal, commercial, and industrial products, which are often aerosolized. Current understanding of the deposition, translocation, and health-related impacts of ZnO ENM inhalation is limited. This study determined whether the presence of Zn in the olfactory bulb (OB) affects microglial activity. Male Sprague-Dawley rats were exposed nose-only to ZnO ENM for 6 hr. The nasal cavity and OB were examined for the presence of Zn and for biological responses up to 21 days post-exposure. Short-term inhalation of ZnO ENM results in the accumulation of zinc in the OB over time, with some differences according to nanoparticle size. Inhalation of ZnO ENM results in a trend of increased microglial cell activation in the OB observed on day 7 and day 21 post-exposure when compared to control rats. The results of this study show that after rats experience a 6-hr inhalation exposure to ZnO ENM, microglial activation in the OB differs depending on time since exposure.

Student Name: Anika Sagar
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Georgia Drakakaki

An Analysis of Callose and Cellulose Involvement in Late Stage Plant Cell Cytokinesis

The aggregation of vesicles and other materials into an intracellular cell plate characterizes the start of plant cell cytokinesis. Plant cytokinesis concludes with the maturation of the cell plate into a new cell wall. During the later stages of plant cytokinesis, polysaccharides such as callose and cellulose are synthesized and integrated into the cell plate. Callose is transient at the cell plate, and its contributions to cell plate maturation are largely unknown. In contrast, cellulose is a permanent member of the cell wall known to contribute to cell wall strength and architecture. Efforts to decipher callose’s specific contributions to cell plate development hint that the molecule participates in the spreading force that reorganizes the cell plate as it expands. However, few efforts have examined the potential for other late-stage cell plate polysaccharides, including cellulose, to contribute to the spreading force. This study observed callose inhibition via endosidin 7 and cellulose inhibition via isoxaben in seedlings of Arabidopsis thaliana to study the potential for cellulose participation in the spreading force. The data produced supports that cellulose has minimal involvement in the reorganization and expansion of the cell plate while recognizing the potential for the involvement of other molecules.

Student Name: Shaina Rahman
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Siobhan Brady

A “Shiny” Application made in R provides easy analysis of Ethiopian soil data

As the parasitic plant, Striga hermonthica, continues to decimate populations of sorghum crops in Africa, researchers have begun to study the interactions between this parasite and its host plant. Due to its versatile nature and ability to grow in dry places, sorghum is one the top five produced crops in the world; thus, different populations around the globe depend on this crucial crop. The issue of creating a widely applicable and accessible solution to Striga infestation has come to the forefront. Physical and chemical attributes of native soil may influence the complex chemical signaling between Striga and its host plant. By developing a user-friendly, Shiny-based, online application, currently called the Soil Data App, the Brady Lab offers a platform for furthering research on the issue of Striga infestation. Using data collected by the Brady Lab’s Ethiopian collaborators, the Ethiopian Institute of Agricultural Research, the Soil Data app provides a way for not only researchers but also farmers to view trends in soil attributes across Ethiopia. Additionally, they may upload their own datasets to be visualized with a myriad of graphical models. The main features of the application include a bubble map of the different samples, regression and correlation analyses using the dataset collected by the EIAR, as well as correlation plots, PCA plots and heatmaps of soil attributes using user-inputted data. While the app is written in the R coding language, users do not require any knowledge of R in order to analyze and create models using the app. Through the App, whether the amount of clay or the amount of silt within soil affected the amount of Striga per sorghum plant was investigated. After careful examination of correlation figures produced by the Soil Data App and running a Two Overlapping Correlations based on Dependent Groups statistical test and a Pearson hypothesis test provided by the R cocor package, it was determined that Overall, the Soil Data App provides a platform for users to answer questions about the relationships and trends of certain soil attributes, and guides them to further research these specific relationships and come closer to finding a solution to Striga infestation.

Student Name: Randy Cai
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Aldrin Gomes

Effects of acetaminophen at therapeutic dosage on the liver

Acetaminophen is the most common active drug ingredient in the US and has been available OTC for decades in unrestricted amounts in various types of stores around the US. It is well known that acetaminophen causes liver damage at high dosage, causing 57% of acute liver failure cases in the US. Yet, user knowledge of acetaminophen and its risks remains detrimentally low. In this study, the side effects of acetaminophen on the liver at therapeutic levels (≤6g/day) is explored with focus on levels within the recommended range (≤4g/day). Through extensive review and analysis of previous articles, it was observed that acetaminophen within recommended dosage may increase risk of liver injury due to association with elevated serum alanine aminotransferase levels. Increased risk when therapeutic acetaminophen is taken following consumption of alcohol and after fasting is also supported. While dangers of therapeutic acetaminophen doses may be perceived as low, they undeniably exist—we recommend more efforts to educate the public and consideration of acetaminophen sale quantity limits. We also speculate that acetaminophen within recommended doses may pose risk to adolescents due to association of increased risk with alcohol and fasting and recommend studies to be done on this age group.

Student Name: Ella Morton
UC Davis Department: Chemistry, Genome Center
UC Davis Mentor: Dr. Justin Siegel

Redesigning Protein Mini-Binders for SARS-CoV-2 Variants of Concern

SARS-CoV-2 variants increase COVID transmission to humans and may reduce vaccine and therapeutic efficacy. Their binding affinity to the human ACE2 receptor is changed, in large part due to the mutations located in the receptor binding domain (RBD). Protein mini-binders have been proposed as a way to combat the effects of the SARS-CoV-2 virus by blocking the site on the spike protein where the virus first attaches to human cells. Software packages Foldit and PyRosetta FastDesign were used to modify existing mini-binder designs to account for changes in the amino acid sequence of SARS-CoV-2 variants. A new potential mini-binder⁠⁠⁠—to bind with the wild type SARS-CoV-2 virus as well as the Gamma and Beta variants⁠—was designed using Foldit hand mutation and PyRosetta FastDesign.

Student Name: Natalie Oh
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Georgia Drakakaki

GOI1 Contribution to ES7 Tolerance in Arabidopsis Undergoing Cytokinesis

Plant cytokinesis is known to be crucial for plant growth and development, however, the specific genetic and trafficking mechanisms that drive this process are still unclear. The chemical probe Endosidin 7 (ES7) is a known inhibitor of callose deposition during plant cytokinesis and was used as a tool to test certain genotypes of Arabidopsis thaliana with varying expressions of Gene of Interest 1 (GOI1). Using ES7, this gene in question was evaluated for contributions to ES7 tolerance in plants, and thus for involvement in callose deposition at the cell plate during cytokinesis. The tolerance of these genotypes was evaluated by comparing and performing statistical analysis of the root lengths between genotypes, as well as through observing root tip cells using confocal microscopy. The genotypes that expressed the GOI1G710D point mutation displayed tolerance to ES7 as represented by longer root length and fewer numbers of cell wall “stubs” in comparison to the wild type and other lines without the point mutation. By identifying GOI1’s contribution to ES7 tolerance, this research reveals novel molecular and genetic players involved in plant cytokinesis, helping to uncover the detailed mechanisms behind cell plate formation.

Student Name: Ali Harcha
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles

Improving Nitrogen Use Efficiency within wheat plants

The research topic that is being investigated is to identify the physiological processes underlying nitrogen use that is controlled by a novel Quantitative Trait Locus (QTL) in wheat. Improving nitrogen use efficiency (NUE) within the wheat plant is of interest. Currently, Ensembl Plants, a bioinformatic tool, was used to learn more about candidate genes located in the QTL and their potential to contribute to N-use. Ensembl Plants is being used specifically for finding wheat orthologs in a gene called Ureide permease (UPS) in the Oryza Sativa Indica group (rice). The function of UPS is that it releases N and 90% of N are compromised within Ureides.

Student Name: Alexander Zhou
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Georgia Drakakaki

Callose as the Spreading Force in Late Plant Cytokinesis

While much has been discovered regarding the maturation process of the cell plate, there is still a general lack of understanding of the exact mechanisms that form and refine the plate into cell walls. One such mystery is the role of callose, a polysaccharide that is deposited in late stage cytokinesis and in tissue repair. Callose has been assumed to serve a structural role in supporting the cell plate. A biophysical model put forth by Jawaid et. al (2020), however, found that a “spreading force” is necessary for the cell plate to mature and suggested that callose may be responsible. To eliminate the possibility of other late stage polysaccharides such as cellulose, Arabidopsis thaliana seedlings were treated with Endosidin 7 (ES7) and Isoxaben (IBX) to observe the effects of inhibiting callose and cellulose deposition, respectively. After 5, 7, and 12 days of germination, root lengths were measured, and the root tips were imaged using confocal microscopy. Seedlings treated with either ES7 or Isoxaben displayed hindered root growth. At the cellular level, ES7 treatment disrupted cell plate maturation and resulted in cell wall stubs. IBX treatment resulted in a few enlarged and swollen cells, but the treatment did not disrupt cell plate maturation. These findings show that callose is more likely than cellulose to be the spreading force, but further research will be needed on whether callose is the sole polysaccharide or force responsible.

Student Name: Andrea Jia
UC Davis Department: Computer Science
UC Davis Mentor: Dr. David Doty

Improving Efficiency in dsd Library for DNA Sequence Design

DNA sequences used in DNA nanotechnology must often follow certain constraints. Currently, the most efficient method of DNA design with constraint consideration is stochastic local search. The dsd library developed by the UC Davis Molecular Computing Group provides a code library that uses stochastic local search to generate and find satisfactory DNA sequences. This project focuses on how to most efficiently design DNA sequences while also satisfying constraints, and specifically investigates the effectiveness of different forms of random search methods. Experimentation shows that the random step method is more efficient than the random jump method based on search algorithm iteration number. Future work may investigate efficiency based on time measurement and further details on search method combination.

Student Name: Daniel Zhu
UC Davis Department: MCB / Genome Center
UC Davis Mentor: Dr. Ian Korf

Theoretical and practical considerations for predicting miRNA targets

MicroRNAs (miRNA) are short, non-coding RNAs that regulate post-transcriptional gene expression by forming base-pair interactions with mRNA targets. In animals, miRNAs are thought to bind to the 3’UTR region of the mRNA target and either repress translation or induce mRNA decay through the 5’-3’ pathway rather than direct endonucleolytic cleavage. Using previous computational methods, each miRNA was predicted to have approximately 100 of these targets. This large number of predicted targets is due to animal miRNAs only needing to have partial complementarity to the 3’UTR regions of its targets. However, since miRNA single gene mutations usually result in no phenotypic changes, despite each miRNA being predicted to regulate so many targets, it is doubtful that all of these 100 “targets” are of biological significance. In this study, we evaluate the effectiveness of traditional sequence alignment in predicting miRNA targets. We find that traditional sequence alignment is not an accurate predictor for miRNA targets as it produces thousands of targets, rather than hundreds, burying actual targets under statistical noise. Surprisingly, we also find that some miRNAs and their putative targets are 100% identical over the alignments in both the 3’UTR region and coding region, suggesting that some C. elegans may use a direct endonucleolytic cleavage degradation pathway.

Student Name: Srinivasan Arumugham
UC Davis Department: Chemistry, Genome Center
UC Davis Mentor: Dr. Justin Siegel

Redesigning Protein Mini-Binders for SARS-CoV-2 Variants of Concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID- 19 pandemic, and some of its recent escape mutations have altered the shape of the spike protein. The global scientific community is observing the boosts in transmissibility and lethality that these mutations might contribute to. By redesigning the Receptor Binding Domain (RBD) minibinders from Cao et al. 2020 (8), we aim to develop minibinders tailored to relevant viral variants of concern and to suggest a therapeutic treatment for COVID-19. We observed that mutations L6N, M13A, R14V, D17F, E18K, H21D, S25A, M26L, R27K, S29A, I32L, Y33E, M36R, K37R, and G39D significantly reduced the free energy scores of the minibinder RBD system in the Wild type, Gamma and Beta variants.

Student Name: Catherine Liang
UC Davis Department: MCB / Genome Center
UC Davis Mentor: Dr. Gerald Quon

Gene Expression of Stomach Cells and its Effects on Gastritis and Stomach Cancer in Latinos

Gastritis and gastric cancer are prevalent diseases in developing countries, and specifically the Latino population of South and Central America. This research uses RStudio to analyze the largest accessible population of stomach single cell RNA sequencing data in order to expand stomach single cell atlas data, as well as estimate correlations of this data in relationship to genetic ancestry and environmental influence.

2019 Research Projects

Student Name: Chengrui Hou
UC Davis Department: 
UC Davis Mentor: Justin Siegel

Characterization of new mutations of the β-glucosidase B protein using thermal and kinetic assays

One of the most important goals of protein engineering is to accurately model the stability and enzyme activity of proteins. However, one major challenge with modern enzyme modeling algorithms is the weak correlation of computer predictions with experimental results, which can be attributed to the lack of large data sets to quantify the properties of enzymes. Here, the thermal stability and Michaelis-Menten constants (kcat, KM, and kcat/KM) of three novel mutations of the β-glucosidase B protein Q19T, F152G, W120R is quantitatively characterized. Enzyme stability was hypothesized using the FoldIt software and the soluble β-glucosidase B protein was synthesized in E. Coli cells. Testing is done through a kinetic assay and thermal stability fluorescence-based protein unfolding assay, where the mutated protein’s stability and catalytic efficiency are determined. Results from the assays have suggested that the F152G mutation had relatively decreased catalytic proficiency as compared to the wild type, while the W120R and Q19T mutations showed almost no signs of activity at all. Furthermore, thermal stability assays suggested that the W120R mutation is more stable than the wild type BglB and that the F152G mutation exhibited decreased thermal stability compared to the wild type. Meanwhile, thermal stability differences between Q19T and the wild type were negligible. In addition, the collected thermal stability and catalytic efficiency data is used to improve the Rosetta algorithm for modeling and predicting the interactions between biomolecules through a machine learning algorithm and facilitate the precise engineering of protein catalysts.
 

Student Name: Emma Hsu
UC Davis Department: 
UC Davis Mentor: Ali McClean 

Comparison of carbon substrate utilization by different California Agrobacterium tumefaciens isolates

Agrobacterium tumefaciens is a species of bacteria that has been known to cause crown gall disease for more than a hundred years. Crown gall disease has significant detrimental effects on the production of many tree crops, including cherry, almond, and walnut trees. The disease is a major problem for the walnut industry. The decrease in nut yield caused by this disease makes studying this pathogen important. Characterization of various A. tumefaciens isolates from California’s top walnut producing counties would help gain a deeper understanding of pathogen diversity and distribution and how to effectively handle the disease. Thirty isolates were characterized by their ability to use 4 different various carbon sources (D-Galactonic Acid-૪-Lactone, α-D-Lactose, D-Mannitol, and Glucose-1-Phosphate), general antibiotic resistance, resistance to biocontrol strain K1026, growth rate, and bacterial motility. 6 strains were identified that grew faster or more slowly that the other strains on 3-4 of the carbon sources. Differences in sensitivity to K1026 and growth on a minimal motility agar relative to control strains. Results from these experiments provide a glimpse into how diverse A. tumefaciens strains are. The differences observed in carbon substrate utilization also suggests that the A. tumefaciens isolates did not stem from a recent single progenitor. Continued characterization of walnut A. tumefaciens and cross referencing characteristics and geographical data will provide the background needed for developing solutions to treat crown gall disease.

Student Name: Elizabeth Ding
UC Davis Department: 
UC Davis Mentor: Eduardo Blumwald

Characterization of poplar mechanisms in adaptation to environmental stress

The expansion of corn-based biofuel occupies fertile land that could be otherwise utilized for food crops. Here, we focused on characterizing poplars growing in marginal lands, or lands under environmental stress. We genetically modified the pathways of these alternative constituents for biofuel. Candidate gene 35S:HSFA2 was previously identified to possibly increase heat shock response, or a cellular response to environmental stress. We tested the functionality of 35S:HSFA2 construct with in vitro-grown and ex vitro-grown poplars. After preparing the explants, we co-cultivated them with Agrobacterium strains carrying the construct with Acetosyringone added. We induced calluses, regenerated shoots and roots, and later transferred the in vitro poplars into soil pots. Analysis indicated mostly successful transformations; the resulting band size under DNA ladder 1kb plus was around the expected value of 612 bp. The implications of this study include helping eliminate the food versus biofuel space competition.

Student Name: Jonathan Ma
UC Davis Department: Chemistry
UC Davis Mentor: Jennifer Lien

Fundamental comparison of physical and magnetic properties for superparamagnetic, hard, and soft ferromagnets at the nano scale.

Physical and magnetic properties of ZnO:Cu, Fe3O4, and Co nanoparticles were investigated in order to determine the differences between different types of ferromagnetic behavior at the nano scale. These nanoparticles were analyzed for their efficacy in applications ranging from biomedicine to data storage. Magnetometry data demonstrated superparamagnetic behavior in Fe3O4 and ferromagnetism in ZnO:Cu. Furthermore, the saturation magnetism of each were compared as Fe3O4 demonstrated significantly higher saturation magnetism than the weak magnetism of ZnO:Cu. However, the temperature independence of ZnO:Cu provides promising potential for uses as a dilute magnetic oxide superconductors. The superparamagnetism of the Fe3O4 is qualitatively compared to that of the Co nanorods, differences being attributed to shape and crystallinity disparities resulting in different anisotropies. The magnetic property of superparamagnetism as well as the biocompatibility of Fe3O4 are ideal for applications in biomedicine, specifically with magnetic resonance imaging (MRI). The similar superparamagnetism in conjunction with the corrosion resistance allow Co nanorods to be applied in data media storage. Both theoretical and experimental comparisons of different nanomagnets provide the fundamental background upon which further optimization may be conducted

Student Name: Alexander Wu
UC Davis Department: 
UC Davis Mentor: Susan Lott

Investigating Evolutionary Adaptations in the Respiratory Structure of Cactophilic Drosophila Pupae

When a female mouse is mated with a vasectomized male, she becomes pseudopregnant–her body acts hormonally pregnant despite the absence of a fertilized egg. Scientists implant genetically-altered embryos in a pseudopregnant mouse so the mouse raises the embryos and gives birth to genetically-altered mice relevant to research. Pseudopregnant mice are important for research, but are challenging to produce because the mice need to be in a specific phase of their reproductive cycle to be receptive to mating and subsequently become pseudopregnant. This experiment tested the effect of administering cloprostenol (a hormone that affects the reproductive system) on the synchronization of the reproductive cycle in mice and the success in producing pseudopregnant mice. Cloprostenol is a hormone that resets the reproductive cycle in mice, so ideally, with the correct dosage and number of injections, it will synchronize the reproductive cycle in groups of female mice, causing them to all become pseudopregnant at the same time. Generating a high number of pseudopregnant mice in a short amount of time is optimal for research, but doing so is challenging. Traditional methods are unpredictable and ineffective, so a more efficient, reliable method to induce synchronization is desired. This experiment consisted of two parts: the first part compared the effectiveness of one vs. two dosages of cloprostenol, and the second part varied the dosage of cloprostenol. This experiment concluded that 20 ug of cloprostenol is the ideal dosage, while dosages of 2 ug and 10 ug have minimal effects. This study also suggests that the introduction of males to females–without any hormone–causes a large percentage of females to mate three days afterwards.

Student Name: Jason Chen 
UC Davis Department: 
UC Davis Mentor: Dr. Kent Pinkerton

Aerosol Treatment of Inflammatory Symptoms in Asthma Airways with an Inhibitor of Soluble Epoxide Hydrolase

Asthma is a prevalent chronic airway disease that results in harmful respiratory effects such as airway constriction, mucin production, coughing, and immune inflammation. Current steroidal treatments are ineffective because while they decrease respiratory symptoms, they often lead to negative side effects among patients such as growth velocity reduction and adrenal suppression. Soluble epoxide hydrolase inhibitors (sEH inhibitors) are enzymes that are responsible for hydrolyzing Epoxyeicosatrienoic Acids (EETs). EETs are bioactive lipids that are important due to their anti-inflammatory and anti-hypertensive properties in terms of physiological health. This study aims to examine the possibility of using TPPU, one particular sEH inhibitor, in reducing symptoms of asthma in mice. Mucin production and airway contraction, two of the main respiratory symptoms, were quantified and measured in TPPU-exposed and ovalbumin-exposed mice to see if TPPU exposure leads to a reduction in severity these two symptoms. Mice lung samples were captured with a microscope and analyzed with ImageJ, and my results demonstrate a correlation between TPPU exposure and both a decrease in mucin production and airway contraction reduction.

Student Name: Nathaniel Satriya
UC Davis Department: 
UC Davis Mentor: Dr. Cecilia Giulivi

Analysis of transmission electron microscope images of cortices from Wdfy3-deficient mice reveals abnormal mitochondrial morphology

In the human body, mitochondria are essential for maintaining proper function within the central nervous system due to their critical roles in neuron firing. Typically, mitochondrial function is preserved through mitophagy, the selective destruction of damaged or dysfunctional mitochondria. Impairments in mitophagy are associated with neurological disorders such as autism spectrum. Wdfy3 is a protein involved in mitophagy. Mutations in the Wdfy3 gene can impair neural mitophagy, lowering brain function overall. This project quantitatively assessed the impact of Wdfy3-mutancy on mitochondrial morphology by analyzing transmission electron microscope images of cortices from WT and Wdfy3-mutant mice. Image analysis performed with the help of statistical software revealed a significant decrease in the quality of cristae and a significant increase in the circularity (p=0.00742) and solidity (p<0.0001) of cortical mitochondria (p=0.00016) in Wdfy3-mutant mice. Healthy mitochondria are typically peanut-shaped (i.e., somewhat tubular and slightly concave); hence, the obtained results suggest that Wdfy3-deficiency negatively impacts mitochondrial morphology. Morphology is closely associated with mitochondrial functionality. Thus, the abnormal morphology observed in Wdfy3-mutant mice suggests dampened mitochondrial and neural function overall. Understanding the impact of Wdfy3 on neural mitophagy furthers comprehension of neurological disorders associated with Wdfy3 or mitophagy in general, which could potentially lead to new forms of diagnoses or treatments for such disorders in the future. Future studies on Wdfy3 should aim to study its impact in humans in vivo and differentiate its specific effects on neuronal and glial mitophagy.

Student Name: Phoebe Loo
UC Davis Department: Plant Sciences
UC Davis Mentor: Georgia Drakakaki

A tDNA artificial construct can influence GSL8 mutations and callose synthesis at the cell plate during mitosis

The gene that is most involved in cell plate formation during mitosis is GSL8, as mutations in the GSL8 gene result in dysfunctional cytokinesis and dwarfism. GSL genes are present in the model organism Arabidopsis Thaliana, which was used to study mutant plants. To rescue the function of the mutated gene, an artificial construct consisting of tDNA that complements the mutated gene was conjugated with the blooming flowers of mutated plants. In particular, we studied the third insertion site in the GSL8 gene (GSL8-3), which was also the location of the artificial construct insertion. The percentage of mutant plants in the cohort of offspring were calculated by phenotyping and genotyping the seedlings. Screenings executed at a confocal microscope were used to confirm the presence of callose tagged by a fluorescent protein (YFP) in the cell plates of conjugated plants. It was found that transformed mutant GSL8-3 plant lines did not show a decrease in the frequency of mutant GSL8 plants. As similar complements have worked in other GSL8 plants such as GSL8-4, we speculate that the ineffectiveness of the tDNA insertion in GSL8-3 plants is due to the potency of the GSL8-3 gene function.

Student Name: Qijia Liu
UC Davis Department: 
UC Davis Mentor: Dr. Ian Korf

Genes that make you go HMM – Errors in protein sequences propagated by heuristic conveniences can be fixed with probabilistic models

Student Name: Akshra Paimagam
UC Davis Department: 
UC Davis Mentor: Dr. Russell Hovey

Effect of prolactin on expression of calcium regulatory genes in porcine kidneys

Prolactin is a pituitary hormone that plays a role in mammary gland development and lactation. Since sows and dairy cows struggle with a dysregulation of calcium during gestation and lactation, there has been a growing focus on prolactin’s possible connection to maintaining calcium homeostasis during these states. Given that the levels of prolactin rise during gestation and lactation, we investigated the effects of prolactin (PRL) on the expression of calcium regulatory genes in porcine kidneys. Nine samples were derived from the kidneys of peripubescent gilts. Three porcine kidney explants were not cultured with any media, three explants were cultured with serum-free cell culture media for 24 hours, and three explants were cultured with serum-free cell culture media and 200ng porcine prolactin for 24 hours. Total RNA was extracted from the explants, reverse transcribed, and then subjected to polymerase chain reaction (PCR). Amplicons were loaded on 2% agarose gels and levels of gene expression were analyzed through band intensity. A pixel density assessment was used to quantify the gel results, by calculating the amount of pixels concentrated in each produced band. We found an increase in the gene expression of transient receptor potential vanilloid 5 (TRPV5), plasma membrane Ca2+ -ATPase (ATP2B1), sodium chloride cotransporter (SLC12A3), and claudin 2 (CLDN2). We found a decrease in the gene expression of calbindin 28k (CALB1) and sodium calcium exchanger (SLC8A1). In conclusion, there was both an increase and decrease of expression in calcium-regulatory genes under the effect of prolactin in porcine kidneys. This data suggests that prolactin has an influence on calcium regulation in the kidney, which points to potential treatments for hypocalcemia in sows and dairy cows in the future.

Student Name: Kaitlin Lim 
UC Davis Department: 
UC Davis Mentor: Ian Korf

laocoön: a tool for high-throughput automated cell counting

Motivation: There are current programs and plugins that exist to automatically count the number of cells in a given image. However, many of these processes are not entirely automatic, as they require user input to specify a region of interest, and are also frequently inaccurate.
Results: This project presents laocoön, a Python package specifically designed to automatically and efficiently count the number of Fucci-stained cells in images. This package not only allows for quick and reliable cell counting, but returns the proportion of cells in each cell cycle relative to all the cells in the DAPI channel, which can be used for clinical purposes.
Availability and Implementation: This package, its corresponding execution instructions, and further information about the underlying algorithms, are currently available in the GitHub repository https://github.com/edukait/laocoon under the MIT license and can be run on the command terminal of any operating system. Alternatively, laocoön is available in the Python Package Index (PyPi), so the user can use the pip command to immediately download the package.

Student Name: Yudong Zhang
UC Davis Department: 
UC Davis Mentor: Lin Tian

Genetically engineering a novel red fluorescent biosensor for imaging of deep brain glutamate transmission

Glutamate is an major excitatory neurotransmitter in the mammalian brain, and it plays an important role in neuronal communications, and functional tasks, such as learning and memory. However, abnormal concentration of glutamate and overly sensitive glutamate receptors can damage nerve cells and cause neurodegenerative diseases such as Alzheimer’s and Parkinson’s Disease. Currently, researchers are interested in new and accurate methodologies to study glutamate neurotransmission in the deeper sites of the brain than what is currently feasible. The aim of this project is to genetically engineer a new intensity-based glutamate sensing fluorescent reporter (iGluSnFR) that would allow for deep brain imaging of glutamatergic transmission. This new glutamate biosensor is made by coupling a glutamate binding protein (GltI), derived from bacteria, with a red emitting fluorescent protein (FusionRed) through molecular cloning. Optimization using site-directed random mutagenesis was performed, targeting the linkers that connect the two proteins. Using high throughput fluorescence-based screening, some interesting variants of this new biosensors were discovered, with differing colors and dynamic range of response. Researchers could eventually employ this new biosensor to noninvasively observe deep brain imaging in vivo, after further optimization to improve its features. Ultimately, it could be used to learn more about the relationship between glutamate and neurodegenerative diseases.

Student Name: Victor Johnson 
UC Davis Department: 
UC Davis Mentor: Diane M. Beckles

Understanding the molecular basis of Chilling Injury in CBF-1 overexpressing tomato during cold storage

While refrigeration is one of the best methods for preserving fruits, some species, at refrigeration temperatures, 0-12.5oC experience a physiological order called Postharvest Chilling injury (PCI). PCI reduces tomato fruit quality and increases spoilage; it affects consumers, and negatively impacts the fresh tomato industry. PCI makes it more difficult for industries to transport tomatoes over long distances to fulfil the market needs of different places. The injury caused by being in the cold promotes an array of symptoms after they are brought back into the room temperature, such as an inability to fully ripen, blotching, pitting, decay, among others 1. Previous work in this lab found that while overexpression of CBF1 may help tomato seedlings adapt to cold, it worsened PCI in the fruit. The aim of this work is to answer the question: “Why does the CBF1 gene cause damage to the tomato fruit, but allows the seedlings to survive better when exposed to cold stress?” Through experimentation, (i) the cold tolerance of the prechilled transgenic and Wild type seedlings, (ii) the expression of CBF1, (iii) the recovery of stunting in transgenics, and (iv) the susceptibility to disease in the transgenic fruit were tested. The results show that the transgenics displayed a faster adaptive response to cold than WT seedlings. Also, the plants can recover somewhat from the stunting that occurs. The transgenic fruits also did not show greater susceptibility to disease compared to the non-transgenic fruits.

Student Name: Edward Kim 
UC Davis Department: 
UC Davis Mentor: Dr. Maria Marco

Comparing novel metabolic processes amongst lactic acid bacteria

Lactic acid bacteria (LAB) are a group of gram positive bacteria that play an essential role in the production of numerous fermented foods including sauerkraut, kimchi, and pickles as well as in probiotics for human health. They have adapted to a wide variety of nutrient rich environments from decomposing plant matter to the cavities and digestive tracts of animals. Previous studies have investigated LAB for their role as food fermentors and human probiotics. In this study, novel metabolic pathways were investigated in LAB to see how certain LAB may be able to obtain energy and outcompete their microbial neighbors. The metabolic pathways used by certain LAB may help to refine the taste and safety of fermented foods in certain industries.

Student Name: Chloe Fuson
UC Davis Department: 
UC Davis Mentor: Dr. Beckles

Production of ‘CRISPR’ Potato for Increased Health Value and Postharvest Quality

Potatoes are the third most important crop worldwide as they are not only a major staple food for many countries, but are also consumed commercially on a massive scale by consumers and industries. The overall goal of this research is to produce a transgene-free potato germplasm that has higher health benefits for consumers and can maintain higher postharvest quality. This project is focused on using CRISPR/Cas9 technology in order to target genes within potatoes that have been found responsible for the production of an enzyme called the starch branching enzyme (SBE). SBEs are responsible for the production of the highly branched, easily digested starch glucan called amylopectin. By using CRISPR to inhibit the production of SBEs, the amount of amylopectin within potatoes will decrease, and thus the amount of the less branched, more difficult to breakdown glucan (called amylose) will increase. The specific goal of this research was to develop different methods of amylose and starch quantification experiments, suitable for high-throughput screening of germplasm produced by CRISPR. The concentration of amylose within potato leaves and stems was tested in order to determine whether the CRISPR modifications will have their desired effect. The new potato germplasm produced will serve as a healthy food option for consumers facing dietary restrictions and will maintain higher postharvest quality, as they will be less susceptible to cold induced sweetening (CIS) that occurs postharvest.

Student Name: Rushil Desai
UC Davis Department: 
UC Davis Mentor: Dr. Mohsen B Mesgaran

Using Image Analysis and Deep Learning to Differentiate Amaranthus palmeri Seeds

Image analysis and deep learning with the purpose of feature extraction can be utilized to find minute differences in extremely similar images that would be indiscernible to the naked human eye. The applications of this concept range from medical diagnoses to simple seed sorting. For this project, seeds were taken from a water-deficient Palmer amaranth plant (CA_WD) and a well-watered Palmer amaranth plant (CA_WW). The objective of this project is to write a software program in MATLAB that can correctly separate, analyze, and identify which plant these seeds came from in a fully autonomous procedure based off a photo on a computer screen. Using MATLAB, the images were successfully segmented into a greyscale format, masked, and cropped to obtain hundreds of individual seeds. Then, using AlexNet, a pretrained neural network, MATLAB learned to distinguish seeds from the two Palmer amaranth plants, and then attempted to correctly classify the seeds itself. The program was accurate in approximately 76.5% of its attempts. Deep learning’s ability to discern miniscule differences between images of similar objects based off pixel properties could be the key to preventing human error and standardizing procedures that involve observation such as distinguishing cancerous and normal cells or improving processes already involving object recognition such as facial recognition programs.

Student Name: Matthew Lee
UC Davis Department: 
UC Davis Mentor: Dr. Daniel Runcie

The Expression of FT in Mimulus guttatus

Timing of flowering in angiosperms is crucial for reproductive success, as flowering in suboptimal conditions could mean a failure to reproduce. For both short-day and long-day plants, FLOWERING LOCUS T, or FT, when transported from the true leaves to the shoot apical meristem, appears to play a crucial role in activating key transcription factors for transformation into floral meristem. The levels of FT expression as well as expression levels of other similar proteins and mRNA transcripts throughout a photoperiod for long-day plant have been well defined by the “classical” model of FT expression in Arabidopsis Thaliana, notably featuring a peak of FT expression prior to the transition from the light period to the dark period. However, it has not been determined as to whether or not the expression levels defined by the classical model can be generalized for all long-day plants. Therefore, the purpose of this study was to explore the expression patterns of FLOWERING LOCUS T in Mimulus guttatus, which is also a photoperiod-sensitive long-day plant, to observe FT expression levels Mimulus guttatus. Furthermore, this study aimed to observe expression levels from leaf to leaf, trying to observe differences in expression levels and timing for each leaf. An analysis of expression levels from true leaves sampled from different time points throughout the light period revealed different FT expression peaks for each leaf. However, as very few of these peaks seemed to corroborate the classical model of FT expression, more research would be necessary to investigate FT expression patterns for long-day plants fully.

Student Name: Aditya Mehta
UC Davis Department: 
UC Davis Mentor: Dr. Daniel Runcie

The Expression of FT in Mimulus guttatus

Timing of flowering in angiosperms is crucial for reproductive success, as flowering in suboptimal conditions could mean a failure to reproduce. For both short-day and long-day plants, FLOWERING LOCUS T, or FT, when transported from the true leaves to the shoot apical meristem, appears to play a crucial role in activating key transcription factors for transformation into floral meristem. The levels of FT expression as well as expression levels of other similar proteins and mRNA transcripts throughout a photoperiod for long-day plant have been well defined by the “classical” model of FT expression in Arabidopsis Thaliana, notably featuring a peak of FT expression prior to the transition from the light period to the dark period. However, it has not been determined as to whether or not the expression levels defined by the classical model can be generalized for all long-day plants. Therefore, the purpose of this study was to explore the expression patterns of FLOWERING LOCUS T in Mimulus guttatus, which is also a photoperiod-sensitive long-day plant, to observe FT expression levels Mimulus guttatus. Furthermore, this study aimed to observe expression levels from leaf to leaf, trying to observe differences in expression levels and timing for each leaf. An analysis of expression levels from true leaves sampled from different time points throughout the light period revealed different FT expression peaks for each leaf. However, as very few of these peaks seemed to corroborate the classical model of FT expression, more research would be necessary to investigate FT expression patterns for long-day plants fully.

Student Name: Kimberly Liu
UC Davis Department: 
UC Davis Mentor: Dr. Mohsen B. Mesgaran

Evaluating the Effects of Spent Coffee Grounds on Amaranthus Palmeri Seed Germination

Lab experiments conducted in 2019 at the UC Davis Plant Science Department evaluated the response of Amaranthus palmeri (A. palmeri) to different concentrations of coffee solution (CS). Used coffee grounds were collected from the Coffee House on UC Davis campus. A stock coffee solution was extracted from the coffee grounds and then diluted into five different concentrations: 0%, 25%, 50%, 75%, 100%. Forty A. palmeri seeds were placed into petri dishes with varying concentrations, and each concentration was replicated five times before being placed in an incubator at alternating 30oC/22oC 14 hour photo/dark periods. As the concentration of CS increased, significantly fewer seeds germinated. In 0% CS, about 90% of all seeds germinated and grew cotyledons. In contrast, less than 50% of seeds germinated in 100% CS, few cotyledons were visible, and root length was approximately 80% shorter than that of 0% CS. After three days, the petri dishes with 50% CS or greater displayed mold growth, which indicates that the seeds have died. These promising results suggest that a coffee-based herbicide can simultaneously repurpose used coffee grounds and also contribute to the fight against harmful weeds.

Student Name: Eric Ma
UC Davis Department: 
UC Davis Mentor: Xi Chen

Expression, purification, and crystallization of polysaccharide synthase NmSiaDW-135

Glycosyltransferases (GTs) are a class of enzymes found in a wide variety of organisms. GTs catalyze the formation of a glycosidic linkage using dehydration reaction to form a glycoside, which is a saccharide bonded to the functional group of another molecule. Neisseria meningitidis is a leading cause of bacterial meningitis, and crucial virulence factor of the bacteria is its unique polysaccharide capsule created by an enzyme NmSiaDW-135. NmSiaDW-135, or Neisseria meningitidis capsular polymerase, is an enzyme that creates polymers from sialic acid and carbohydrates, and is responsible for creating the capsule that strongly resists most complement immune systems. NmSiaDW-135 was expressed using E. coli with recombinant DNA plasmids inserted encoding the gene. The cells were lysed to obtain the NmSiaDW-135 protein and the lysate was then purified using chromatography techniques to obtain a homogenous protein solution. Finally, commercial crystal screens were used to find conditions that would create NmSiaDW-135 crystals. Initial crystal hits were sent to the Advanced Photon Source at Argonne National Laboratory for X-ray diffraction facility to test its diffraction.

Student Name: Celeste Do
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Aldrin V. Gomes

Improving the Western Blotting Technique

One of the most common ways to identify specific proteins from biological tissue samples is a multistep, 6+ hour procedure called Western blotting. The procedure involves the use of primary and secondary antibodies that fluoresce and bind to proteins for their detection and analysis. However, this protocol involves multiple time-consuming steps, meaning that making even a single mistake can seriously affect an entire Western blot, producing inaccurate results. This, in turn, often deems Western blot procedures irreproducible and inefficient. Preliminary research on Western blots has already shortened procedural times to a little over 1.5 hours by using different solutions that allow for higher antibody-binding sensitivity and decreased nonspecific antibody binding. Yet, due to its immense popularity in biology labs, the aim of this research is to find a way to shorten the time spent on each step even more in order to condense the procedural time to one hour and produce a more efficient Western blot protocol.

Student Name: Elizabeth Krolicki
UC Davis Department: 
UC Davis Mentor: Dr. Clare Casteel

The Impact of Potato Virus Y Infected Tomatoes on Potato Aphids

Potato Virus Y (PVY) is a potyvirus that is transmitted primarily by aphids. In this study we will focus in on how PVY infection positively influences the growth and reproduction of aphids on tomato. This mutualistic virus-vector interaction will be studied in correspondence with both wild and domesticated tomato plant, most likely showing a positive relationship between the spread of PVY and aphid population size. Focusing in on Macrosiphum euphorbiae (potato aphids), their fecundity rates will be studied in order to measure the tomato plant species’ susceptibility to PVY. Fecundity rates will be a clear use of measurement as preliminary results have shown a massive difference in nymph population sizes between tomato plants infected with PVY and tomato plants without PVY. Using Solanum pennellii and two different varieties of Solanum lycopersicum (UC82 & Moneymaker) to test PVY’s ability to impact the fecundity of PA on different tomato species. UC82 and S. pennellii crosses will also be tested for aphid fecundity rates. The results from these crosses will help give an insight into finding a better crop that is more resistant to not only PVY but also aphid pests. This will be accomplished by further understanding the mechanisms of the PVY and aphid relationship within this experiment. The results from this experiment showed that aphid fecundity and survival increased on UC82 infected with PVY as expected. However fecundity and survival was unaffected on S. pennellii infected with PVY.

Student Name: Valerie Fu
UC Davis Department: 
UC Davis Mentor: Dr. Aldrin Gomes

The Effects of Aging on the Proteostasis of Mice Cardiac Tissues

The proteasome — a protein complex that is responsible for the selective degradation of obsolete and oxidatively-damaged intracellular proteins — has been proven to play a significant role in the maintenance of proteostasis. Proteostasis, which can only come about through the efforts of a healthy, working proteasome, is essential to the preservation of critical bodily functions, especially as certain functions decrease in quality with age. Oxidative stress and the aggregation of obsolete proteins, which ultimately lead to a downturn in the overall function of mammalian organisms, are the main markers of aging. Since the proteasome plays a large role in the clearance of obsolete and damaged proteins, further understanding of the exact functions affected by oxidative stress could potentially assist in attenuating the adverse effects of age on bodily function. Increased efficiency of the proteasome has been linked to increased resistance to proteotoxic stress, metabolic capacity, and longer lifespan (1). In specific regard to the role of the proteasome in the lifespan of mice, we have used the widely used Western Blotting method in order to identify, compare, and quantitatively analyze the expression of specific proteins and cells in 3 month and 22 month old mouse cardiac tissue. Through this study, we aim to quantitatively determining the exact effects of age-related oxidation on specific proteins and their respective functions. The proteins investigated were the HSP 70 protein, the E3 ubiquitin-ligase enzyme (CHIP), and relative concentrations of ubiquitinated proteins and nitrotyrosine through the Fk2 mouse monoclonal and anti-nitrotyrosine mouse monoclonal antibodies, respectively. The p-53 tumor suppressor protein and the ubiquitin-like alpha-ISG15 protein were also investigated through the use of a Western Blot, but no usable results were yielded by the experiment. It was found that the expression of CHIP was significantly increased in older mice cardiac tissue compared to younger tissue; however, despite the discovery of multiple trends, no significant data was collected regarding the expression of ubiquitinated proteins, nitrotyrosine, and HSP 70 proteins in older versus younger mouse hearts. This could most likely be due to insufficient sample size and lack of time for additional data collection.

Student Name: Micheal Tu
UC Davis Department: Computer Science
UC Davis Mentor: Stacy Harmer

Examining Sunflower Disc Floret Development Under Different Environmental Conditions and Biological Factors to Assess Circadian Regulation.

The circadian clock is a biological timekeeper that runs on a 24-hour rhythm, regulating many processes, including environmental responses. Sunflowers are composite flowers, meaning the head or the capitulum of the sunflower is made up of tiny clusters of flowers called inflorescences. Sunflower inflorescences comprise disc florets that make up the capitulum and ray florets that sit on the outskirts. The timing of sunflower disc floret development, which includes the release of pollen and elongation of a floret’s style, is being studied to determine its regulation, whether by the environment or the circadian clock, or both. Sunflower disc florets were studied in the Harmer Lab under different thermocycles, photoperiods, and plant hormones to assess their circadian regulation. To investigate circadian regulation, images of individual sunflower heads and disc florets in agar plates were recorded every 15 minutes. Gradual movement occurring in these centripetal sequences of florets, called whorls, was measured based on corolla swelling, anther elongation, and style elongation in sunflower heads. Data from disc florets in agar plates were measured in floret length. Data analysis of the timings of floret development showed that disc floret development is regulated by environmental cues and the circadian clock. These findings can be applied to the creation of plant mathematical models and the development of sunflower lines more attractive to pollinators.

Student Name: Tracy Zhao
UC Davis Department: 
UC Davis Mentor: Jacqueline Barlow

Implications of R-loop accumulation on genome instability at common fragile sites and early replicating fragile sites

When replication forks collide with transcription complexes, the favorability of R-loop formation increases. R-loops are a triple stranded nucleic acid structure composed of a DNA:RNA hybrid and the non-template single-stranded DNA (ssDNA) that have serious implications on genome integrity and stability, but may also play a key role in the regulation of gene expression. These structures occur naturally as a by-product of transcription, but a persistence can produce detrimental effects. Accumulations of R-loops interfere with vital cellular functions including replication, transcription, and homologous recombination. Mutant genotypes of mouse B lymphocytes were used to perturb R-loop removal mechanisms, and replication stress was induced to evaluate their DNA damage response in the presence of elevated levels of R-loops, specifically at fragile sites. We provide insights into the sensitivity of the mutant cells to DNA replication inhibitors, the sensitivity of fragile sites to R-loops, and the effectiveness of enzymes at R-loop removal.

Student Name:  Charles Ding
UC Davis Department: 
UC Davis Mentor: Gail Bornhorst

Effects of Surface Area and Time of Digestion on Buffering Capacity

Buffering capacity is the characteristic of foods to resist changes to pH during digestion, and has been observed to affect the physicochemical breakdown of food by influencing the rate of gastric acid secretion. A more thorough understanding of different factors that can influence buffering capacity is needed to further improve the standardized method of measuring buffering capacity by incorporating more variables. This may help provide a better estimation of gastric acid secretions by taking into account the relationships between those factors and buffering capacity.

The objective of this research project was to observe the effects of surface area and time of digestion on the buffering capacity using protein-based model foods. Surface areas were modified by preparing spheres and cubes that had similar volumes but different surface areas, with the cubes having a higher surface area than spheres. Times of digestion were controlled by subjecting 20% whey protein-based gels to varying times of in vitro digestion, ranging from 0 to 180 min. In vitro digestion was accomplished using a shaking water bath preheated to 37.0 C and at 100 rpm. Buffering capacity was analyzed by titrating 0.2 M HCl to 20% whey protein gels in 0.5 mL increments and recording the amount of mL added for the pH to drop to 1.5. Calculated parameters from buffering capacity experiments included total acid added, area under the curve, and total buffering capacity. Understanding how surface area and time of digestion influences buffering capacity may influence the way foods are manufactured to better adapt to individual consumers’ nutritional needs.

Student Name: Katharine Jacobs
UC Davis Department: 
UC Davis Mentor: Dr. Grace Rosenquist

Tyrosine Sulfation in Voltage Gated Sodium Channels

Tyrosine sulfation is a post-translational modification that has the primary function of enhancing protein-protein interactions. Voltage gated sodium channels are found throughout the body and help transmit messages to the brain and control heartbeats by regulating membrane potentials. Predicted tyrosine sulfation sites in voltage gated sodium channels were found at conservation sites 1, 2 and 3, defined as position 360 in Nav 1.1, 790 in Nav 1.1, and 1458 in Nav 1.1, respectively, as well as position 1228 in Nav 1.5. Mutations at these sites cause severe neurological and cardiac disorders. There are currently no known tyrosine sulfation sites in human voltage gated sodium channels. More research is required to confirm these tyrosine sulfation site predictions. If these predictions are confirmed, drugs can be better designed to target these tyrosine sulfation sites in voltage gated sodium channels.

Student Name: Mia Wesselkamp
UC Davis Department: 
UC Davis Mentor: Kent Pinkerton

Effects of Perinatal Exposure to Environmental Tobacco Smoke on Club Cell Secretory Protein Expression and Susceptibility to Infection.

Club cells are nonciliated epithelial cells that line the respiratory bronchioles and produce crucial proteins and substances that aid in protecting the bronchioles and smaller airways of the lungs. The Club cell secretory protein (CCSP) is one of the most abundant proteins expressed in the lung. This study evaluates the effects of perinatal exposure to smoke and immune challenges on the expression of CCSP to provide greater insight into the health implications of perinatal exposure to second hand tobacco smoke and consequently the ability to recover from viral and bacterial challenges. In this study, mice were perinatally exposed to environmental tobacco smoke with controls exposed to filtered air. These mice were then divided into specific test groups and challenged with either a murine-adapted influenza A viral strain, the human bacterial pathogen Staphylococcus aureus, or both in order to test if environmental tobacco smoke affects resistance to viral or bacterial infection. Lung tissue samples were stained using immunohistochemistry (IHC) and analyzed with a curvilinear lattice overlay to calculate the volume of Club cell secretory protein per surface area of basal lamina. Analysis showed a significant decrease in Club cell secretory protein expression in the groups exposed to the virus and virus/bacteria combination. There was no statistically significant difference in Club cell secretory protein expression between the filtered air and environmental tobacco smoke treatment groups.

Student Name: Joyce Huang
UC Davis Department: 
UC Davis Mentor: Peishan Huang

Testing Kinetic Activity and Thermal Stability of Beta-glucosidase B Enzymes to Refine Enzyme Modeling Programs

Siegel Lab is focused on refining enzyme modeling programs by collecting data from mutant Beta-glucosidase B (BglB) enzymes. Currently, enzyme modeling programs have shown inaccuracies. In order to tackle these discrepancies between predictions and experimental data, Siegel Lab uses kinetic assays and fluorescence-based protein unfolding assays to collect quantitative data on the catalytic efficiency and thermal stability of the enzymes. To prepare for assays, the mutant enzymes undergo Kunkel mutagenesis, DH5a transformations, Mini-prep procedures, and BLR transformations for E. coli to express the protein. While past research has considered thermodynamic stability and catalytic efficiency to be trade-offs, Siegel Lab shows that these two traits can be separately designed in BglB, thus allowing for the possibility of a more efficient, stable BglB protein. The Michaelis-Menten constants have shown that the three mutants demonstrate decreased kinetic activity, and the Tm values show decreased thermal stability compared to the wild-type. These data sets can improve enzyme modeling programs, thus benefitting clinical and industrial applications such as engineering, medicines, and tools involving enzyme compatibility.

Student Name: Annabelle Ju
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel

Functionality and damage cause identification of a novel plant water stress sensor

In the agricultural field, the water status of crops is often utilized as an indicator to determine their proper irrigation treatments. Traditionally, plant water stress has been measured with devices such as pressure chambers, tensiometers, and porometers. All of these current tools, however, are either invasive to the plant or are only capable of taking instantaneous measurements. In recent years, the Bosch company in Germany has developed a supposed solution for these problems. Their telemetric leaf sensor (TLS) is a probe that is meant to measure water status continuously without damaging the plant it is used on. Despite the device’s potential, however, several previous studies cite observations of questionable TLS data under certain conditions as well as instances of leaf necrosis where the sensor is attached. Thus, this study investigates the cause of this leaf damage as well as the reliability of the TLS as an indicator for plant water stress. Identifying the source of sensor damage and confirming the functionality of this sensor is significant for irrigation management in agriculture and ultimately the environment as well.

Student Name: Kate Blanchard
UC Davis Department: Neurobiology, Physiology and Behavior
UC Davis Mentor: Grace Rosenquist

Predictions of Tyrosine Sulfation in Class C G-protein Coupled Receptors

Tyrosine sulfation is an irreversible post-translational modification that increases protein-protein interaction. With only 102 known sulfated sites and many of them in GPCRs, it is likely other GPCRs have sulfated tyrosines as well. Specifically, sulfation is likely in Class C which are known for their long extracellular domain, the primary location for tyrosine sulfation. One site that is well-conserved across different receptor types and across species also scores high on the Position-Specific-Scoring Matrix. Additionally, the site has protein dysfunction when the tyrosine is mutated to other amino acids. This evidence suggests tyrosine sulfation occurs, giving scientists more information on the structure of Class C GPCRs to better design pharmaceutical drugs.

Student Name: William Yuan
UC Davis Department: 
UC Davis Mentor: Savithramma Dinesh-Kumar

Engineering Split Cas9 for Gene Editing in Plants

The CRISPR-Cas9 system has been used in recent years to edit or modify genes of interest in plants. The successful editing of gene depends on the effective delivery of CRISPR tools. Compared to transgenic-based delivery of CRISPR, virus-mediated delivery could potentially offer benefits such as multiplexing and non-transgenic delivery. However, the small size of viral genomes limits the amount of heterologous genetic materials that can be inserted into the viral genomes. One approach to reduce the payload into the viral genome is splitting Cas9 gene. Under the control of a constitutive promoter, split Streptococcus pyogenes Cas9 (SpCas9) gene fragments were inserted into a transfer DNA (T-DNA) vector to demonstrate feasibility of gene editing in plants through mutating the phytoene desaturase (PDS) gene. Significant activity rates of split Cas9 proteins could demonstrate applicability in a viral delivery system to induce non-transgenic gene editing.

Student Name: Kira Sterling
UC Davis Department: 
UC Davis Mentor: Cecilia Giulivi

Impact of Wdfy3 on neural mitochondrial morphology

The Wdfy3 gene, also known as Alfy, was previously found to play a key role in the processes of selective autophagy and mitochondrial homeostasis. The gene encodes for an eponymous adaptor protein that connects selected cellular cargoes to the lysosome for degradation. Mutations in this gene have been shown to increase the risk of developmental delay or of developing an intellectual disability. Using image processing software to analyze transmission electron micrographs, we investigated the effects of Alfy in regulating mitochondrial morphology and accumulation in mouse cerebellum tissue. We found that in the cerebellum, mutations in the Alfy gene are associated with an increase in size and number of neural mitochondria and a decrease in the number of synapses, while mitochondrial shape remained unchanged. These findings elucidate the impacts of Alfy mutations on mitophagy and mitochondrial homeostasis with implications to help researchers better understand the mechanisms of this mutation, as well as how to better diagnose and treat the disorders that arise from it.

Student Name: Skylar Fong
UC Davis Department: 
UC Davis Mentor: Helen Raybould (professor), PI (KP Huang)

Effect of the Deletion of the Leptin Receptor in VAN on the Morphology of Jejunum

The human digestive tract controls and processes all the food that is eaten every single day. The gut has a complicated neuronal feedback loop which prevents humans from overeating. Leptin is involved in informing the body of the status of energy storage in adipose tissue and helps control appropriate changes in metabolism, appetite, and nutrient partitioning. We tested the hypothesis that the deletion of the LepR in the vagal afferent neurons (VAN) will lead to the decrease in proliferation in jejunum cells. The jejunum cells were the choice of interest because the jejunum is the main site of absorption. To measure the proliferation in jejunum cells we measured the length of the crypts which contain stem cells, which later turn into all the other cells that make up the jejunum. In this experiment there were four groups of mice: (wildtype control, knock out control, wildtype high fat diet, knockout high fat diet). The knockout mice were genetically bred with the deletion of the LepR in VAN. The results showed that when mice were fed the low fat diet, the deletion of the leptin receptor did not statistically differ from the wild type control mice. In contrast, in the knockout mice the high fat diet leads to a decrease in the average crypt length in comparison to the wildtype high fat diet. We conclude that the deletion of the LepR in the VAN leads to a decrease in proliferation of the jejunum cells for mice on a high fat diet. The knowledge gained by studying the jejunum cells in response to the deletion of the LepR could be applied to a new medication for diabetes and obesity or it could be used to see how it affects other body systems.

Student Name: Alex Gao
UC Davis Department: 
UC Davis Mentor: Dr. Kenneth Shackel

Evaluating the Reliability of the Bosch Telemetric Leaf Sensor and Potential Factors Causing Leaf Damage

The Bosch Telemetric Leaf Sensor (TLS), a magnetic sensor that attempts to monitor plant water status non-invasively and continuously, has been found to cause leaf damage when used. The goals of this study were to determine what factor or factors were causing this leaf damage and if the TLS is a reliable monitoring tool. Multiple experiments were planned and conducted so that each evaluated a specific factor that could potentially cause leaf damage. These factors included sensor weight, shading caused by the sensor, and damage from sensor installation. From the leaf samples of these experiments, leaf sections were prepared. To evaluate the conditions of these leaf sections, microscopy and staining with fluorescein diacetate (FDA) were used. Under a special blue light microscope, stained cells that were alive would fluoresce green while damaged ones would be much darker. Photos were taken of these leaf slides and analyzed to determine how much damage a certain factor caused. Another experiment was organized to test the reliability of the TLS. This was done by comparing the data measurements of the TLS to those of proven tools like the micro tensiometer and Scholander pressure chamber. These experiments showed that installation damage seems to be the main factor behind leaf damage caused by the TLS and that the TLS is not a reliable plant water status monitor. But, further research is needed to confirm the results of these experiments. Regardless, the findings of this study have implications in irrigation work and the related sensor industry. Continued research on tools for measuring plant water status will lead to optimized water use and improved agriculture.

Student Name: Alton Sturgis 
UC Davis Department: 
UC Davis Mentor: Doctor Rebecca Parales

Understanding Chemotaxis through Hybrid Proteins in E.coli

Previous studies have demonstrated that chemotactic responses are possible in many forms of bacteria. In general, chemotactic responses are mediated by cell surface receptor proteins. The goal of this study was to develop functional hybrid receptors that allow the identification of specific chemoattractants. We first needed to develop a rapid and easy screen to evaluate the function of hybrid chemoreceptors. We tested three different methods to assay for β-galactosidase activity and we also used a Green Fluorescent Protein (GFP) screen in order to further evaluate the functionality of the hybrid. Variants of a non-functional chemoreceptor hybrid, McpC – NarQ, were created and investigated through blue-white screening, assays and GFP screens, resulting in the possibility of improved hybrid functionality. Overall, the experiments indicate that although the β-gal screening methods were unusable, assays and fluorescent screens have potential for use in identifying functional hybrid receptors.

Student Name: Linda Wu
UC Davis Department: 
UC Davis Mentor: Alexandra San Pablo

Effect of MICP Stimulation Treatment on Pipeline Metals

Liquefaction is a process that makes soil take up a liquid state, which poses as a threat to infrastructure and the general public. The central focus of this experiment is Microbially Induced Calcite Precipitation (MICP), a process stimulating bacteria in soil to perform calcification. This process aids in further binding the soil particles together with calcite to prevent liquefaction and making soil more stable. This experiment works to identify the optimal chemicals to use in treatment to cause minimal damage to the surrounding environment. Chloride based solutions have been developed to select bacteria for performing calcification and encourage their reproduction. Since chloride is a corrosive chemical that can induce damage to nearby pipelines, this experiment aims to compare its damage to those of an acetate based treatment to recognize if acetate is a beneficial substitute.

Student Name: Sydney Hwang
UC Davis Department: 
UC Davis Mentor: Kristin Grimsrud

The effect of cloprostenol on the synchronization of the estrous cycle in female mice

When a female mouse is mated with a vasectomized male, she becomes pseudopregnant–her body acts hormonally pregnant despite the absence of a fertilized egg. Scientists implant genetically-altered embryos in a pseudopregnant mouse so the mouse raises the embryos and gives birth to genetically-altered mice relevant to research. Pseudopregnant mice are important for research, but are challenging to produce because the mice need to be in a specific phase of their reproductive cycle to be receptive to mating and subsequently become pseudopregnant. This experiment tested the effect of administering cloprostenol (a hormone that affects the reproductive system) on the synchronization of the reproductive cycle in mice and the success in producing pseudopregnant mice. Cloprostenol is a hormone that resets the reproductive cycle in mice, so ideally, with the correct dosage and number of injections, it will synchronize the reproductive cycle in groups of female mice, causing them to all become pseudopregnant at the same time. Generating a high number of pseudopregnant mice in a short amount of time is optimal for research, but doing so is challenging. Traditional methods are unpredictable and ineffective, so a more efficient, reliable method to induce synchronization is desired. This experiment consisted of two parts: the first part compared the effectiveness of one vs. two dosages of cloprostenol, and the second part varied the dosage of cloprostenol. This experiment concluded that 20 ug of cloprostenol is the ideal dosage, while dosages of 2 ug and 10 ug have minimal effects. This study also suggests that the introduction of males to females–without any hormone–causes a large percentage of females to mate three days afterwards.

Student Name: Erik Hanson
UC Davis Department: 
UC Davis Mentor: Dr. Joshua Wood

Optimizing Electroporation For Inserting Large Strands of DNA

I have been working at the UC Davis Mouse Biology Laboratory, and the project I was a part of focused on finding a more efficient way to implement the genome editing technology CRISPR in a mouse embryo. The current way to genetically alter a mouse is to inject CRISPR reagents into an embryo using a microscopic needle, which is technically challenging, time consuming, and less successful than ideal. As a result, CRISPR-EZ, an electroporation-based technology, has been developed. Rather than puncture a hole, this technology uses a series of electrical pulses to expand the natural pores present in the embryo, allowing the CRISPR regents to enter in a more natural, less disruptive way. For small strands of DNA, CRISPR-EZ technology dramatically increases the chance of embryo survival and increases the success rate of the desired mutation to nearly 100%. However, it is not so effective for larger strands of DNA, so the goal of this project was to optimize CRISPR-EZ technology to make it applicable to DNA strands of all lengths. Once this is accomplished, CRISPR-EZ technology will likely become the new standard mouse genome editing tool across the United States and The World.

2018 Research Projects

The responses of insect vectors to potyviruses

Student Name: Aaron Lin
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Clare Casteel
The infection of plants by potyviruses is effects the localization of different proteins like the Nuclear Inclusion a Protease (NIa Pro). In addition, the overall phenotype of the plant can be observed through the effects of the potyvirus on the fecundity of insect vectors on the plant. It has previously been shown that infecting plants with Turnip mosaic virus (TuMV) increases insect attraction and reproduction on host plants. Using previous research that sequenced Turnip mosaic virus (TuMV), Potato virus Y (PVY), and Soybean mosaic virus (SMV) as well as observing their varying effects on fecundity, we were able to identify amino acid sequences of interest within the NIa Pro sequence. We performed fecundity tests on Tobacco etch virus (TEV) and Pepper mottle virus (PepMoV) infected Nicotiana benthamiana to further categorize amino acids within NIa Pro. Tobacco etch virus (TEV) did not significantly increase fecundity, likely due its coinfection with Potato virus Y (PVY), which would increase the fecundity for both of them. Pepper mottle virus (PepMoV) significantly increased fecundity, likely due to its similar homology to Potato virus Y (PVY), which also increases fecundity. The focus of our research was making a 90 amino acid deletion from the N-terminus in Turnip mosaic virus (TuMV)  We observed that the NIa Pro sequence from the mutant TuMV was transported around the cell by vesicles, suggesting that the 90 amino acid deletion from the N-terminus affected the ability of the NIa Pro to relocate to the vacuole

Contribution of sorghum root aerenchyma to Striga susceptibility

Student Name: Alexander Chen
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Dorota Kawa, Dr. Siobhan Brady
Sorghum bicolor is an essential cereal crop that is extensively parasitized by plants of the Striga genus, leading to yield loss and exacerbating food insecurity in sub-Saharan Africa.  Previous research has suggested that soil microbes may reduce the degree of Striga penetration into host roots. This study focused on examining the effect of natural soil microbes on the formation of root aerenchyma by studying possible patterns of formation in different cultivars of S. bicolor under various conditions, including soil sterility and Striga treatment. Seeds of Striga-resistant genotype SRN39 and Striga-susceptible genotype Shanqui Red (SQR) were germinated in vitro and grown in a greenhouse environment. After two weeks, cross-sections of the plant roots were taken and analyzed. Images of root cross-sections were electronically processed and quantified based on the amount of aerenchyma formation.  An initial analysis found that SQR grown in natural soil saw significantly more aerenchyma formation than those grown in sterile conditions. Meanwhile, a second comparison found that aerenchyma was completely absent in SRN39 regardless of soil sterility. In addition, this analysis found that the crown and seminal root tips of S. bicolor grown in sterile soil had significantly less aerenchyma compared to those grown in non-sterile soil. This suggests that soil microbe therapy may prove useful to certain sorghum cultivars, such as SRN39, that already exhibit natural Striga tolerance properties. The insight gained through these findings can be potentially applied to building a Striga-resistant yet affordable and productive sorghum cultivar. 

The Evolutionary History of Tyrosylprotein Sulfotransferases

Student Name: Alvin Zhang
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Tyrosylprotein sulfotransferases (TPSTs) are responsible for catalyzing the sulfation of peptidyl tyrosine residues. Tyrosine sulfation is a post-translational modification that strengthens a variety of protein-protein interactions, including leukocyte adhesion to endothelial cells and host-pathogen interfacing. We sought to elucidate the evolutionary history of TPST in order to understand the function of sulfation in a wide range of organisms. By comparing the homology of TPSTs across lineages through multiple sequence alignments, the conserved mechanism of substrate recognition and sulfation in both eukaryotes and prokaryotes was elucidated. Binding motifs for the universal sulfate donor 3’-phosphoadenosine 5’-phosphosulfate (PAPS) were found to be conserved in nearly all sulfotransferases, and residues involved in interactions with substrates were found to be highly consistent as well. Molecular visualization software was used to identify trends, as well as nonconserved regions at a level beyond the primary sequence in the catalytic domains of the two isoforms of TPST, TPST-1 and TPST-2. These structural differences may implicate distinct roles for the two isoforms of TPST.

Evaluation of the mitochondrial DNA copy number and deletions in fibroblasts from subjects with the FMR1 premutation

Student Name: Ashwin Kumar
UC Davis Department: MIND Institute
UC Davis Mentor: Dr. Cecilia Giulivi
Fragile X syndrome occurs in subjects with >200 CGG repeats in the 5’ untranslated region of the FMR1 gene. Premutation carriers (55-200 CGG repeats) were originally thought to be asymptomatic but some have psychological and metabolic issues among others, and with age some develop the neurodegenerative disease called Fragile X-associated tremor/ataxia syndrome (FXTAS). Studies have been done which have shown that people with FXTAS tend to have mitochondrial functionality problems. However, the exact reason for why this occurs is still elusive. The overall goal of our research was to evaluate the mitochondrial DNA copy numbers (mtDNA) and deletions in fibroblasts from individuals with the FMR1 premutation by qPCR utilizing dual-labeled probes. To measure the mtDNA and deletions, we evaluated the Ct values for each DNA sample provided from Real Time Quantitative-PCR (qPCR).  Our data shows that there was not a significant difference between the mitochondrial DNA copy numbers in fibroblasts from individuals with FXTAS and without it. Our data also shows that non-affected FXTAS carriers had a lower mitochondrial gene ratio, signifying that they had more deletions.

Comparative Genomics of M. stipitatus Cyclase Proteins

Student Name: Brian Lee
UC Davis Department: Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Mitchell Singer and Dr. Gaurav Sharma
Cyclases are proteins involved in signal transduction pathways. These proteins help in catalyzing vital intracellular chemical processes such as gene transcription, cellular metabolism, and cardiac function. Myxobacteria such as Myxococcus stipitatus are unique because they display multicellular-like social behaviour in densely grouped populations. Cyclases might be involved in coordinating this type of social behaviour by organizing cell-to-cell communication via various signaling pathways, but the exact mechanism is not yet known. Here, in silico studies were used to identify 14 cyclase proteins in M. stipitatus and explored their architecture, origins, phylogeny, and putative functions. After identification using Pfam domains, the domain architecture of myxobacterial cyclase proteins were compared using different sequence databases. In addition, multiple sequence alignments and phylogenetic trees were used to analyze conserved regions and evolutionary relatedness among the cyclases. This research is focused on understanding the probable evolution and structure of M. stipitatus cyclases, which would be the foundation of further characterization and identification of their unique roles in regulating cell-to-cell communication.

Prediction of Possible Tyrosine Sulfation Sites in Complement Factors

Student Name: Carolyn Lai
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Three tyrosine sulfation sites are known in complement C4, and sulfation of C4 influences its activity in the complement cascade. Since tyrosine sulfation usually occurs within a group of proteins, this research focuses on whether there are additional tyrosine sulfation sites in complement proteins. The Position-Specific Scoring Matrix (PSSM) reports high scores at tyrosine sites in all of the complement proteins. Some of the complement proteins, such as complement C5, have tyrosine residues located on the exterior of the protein, showing an increased likelihood of becoming sulfated. An increased understanding of tyrosine sulfation contributes to the development of pharmaceutical drugs that could treat diseases related to mutations of complement-mediated immune responses. These diseases include macular degeneration, angioedema, systemic lupus erythematosus, and other complement deficiencies that greatly impact the lives of affected people.

Soil Stabilization and MICP

Student Name: Cat Acuff
UC Davis Mentor: Dr. Jason T. DeJong & Alex San Pablo
Soil Stabilization and MICP, microscopically induced calcite precipitation, was an engineering focused project in the Department of Civil and Environmental Engineering, under Dr. Jason T. DeJong that included building large scale structures to test soil stability and comparing calcite levels in small scale samples. This research is important in events of earthquakes where liquefaction can easily occur.

Engineering optimal introns

Student Name: Clara Wang
UC DavisDepartment: Genome Center
UC Davis Mentor: Dr. Ian Korf
Background: Intron mediated enhancement (IME) is the phenomenon in eukaryotic organisms in which an intron improves gene expression. Creating new introns that boost gene expression beyond observed introns would be useful in biotechnology applications.
Results: Introns near the promoter are compositionally distinct from those farther down the transcript. This difference in composition is used in an algorithm called the IMEter, which can be used to predict the effectiveness of an intron. Creating artificial introns that simply maximize the IMEter score results in introns that are almost entirely GC. In order to create more natural introns we propose a genetic algorithm, MIA, that simultaneously maximizes IMEter score and the relative entropy compared to average introns. We also propose MIA+, which adds a motif-scoring function to the fitness function.
Conclusions: MIA creates high scoring introns as well as introns with repeated motifs which have previously been shown to be effective in increasing IME. Command line options allow the user to tune the algorithm for IMEter score or motif density. Based on previous experimental data, introns created by MIA are expected to increase gene expression 20-fold or more.

Identification of brighter genetically encoded fluorescent indicators of dopamine and opioids

Student Name: Clara Wu
UC Davis Department: Biochemistry and Molecular Medicine
UC Davis Mentor: Dr. Lin Tian
Neurotransmitters and neuropeptides are significant to a number of neurological functions. Understanding how these chemicals act in living cells and animals in real time is made possible with genetically encoded fluorescent indicators that light up neuronal membranes upon binding with their corresponding ligand (trigger chemical). . The goal of our study was to determine if we could further optimize the brightness of our recently developed red dopamine indicator (dLight 1.1 red) and green opioid indicator (KOR 1.1) by altering their genetic codes. After one round of screening, we have determined our current variants to be the highest performers. These sensors show great spatiotemporal resolution when expressed in mammalian cells. These tools provide scientists with a better understanding of dopamine and opioid-related disorders, which will aid in the development of targeted treatments for ADHD, addiction, depression, anxiety, Parkinson’s Disease, schizophrenia, and many others.

Ibuprofen and proteasomal dysfunction in the kidney

Student Name: Colette K. O’Grady
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Aldrin V. Gomes
Ibuprofen is a nonsteroidal anti-inflammatory drug that is used worldwide to inhibit pain and inflammation. Ibuprofen has been shown to have negative side effects in the cardiovascular system, but there has been significantly less research on the side effects in the kidney. The goal of this research is to determine if ibuprofen causes proteasomal dysfunction in the kidney. The proteasome is a complex that is critical for removal of unwanted and oxidized proteins. Proteasome levels were observed through western blotting and proteasome assays, and no significant difference was found in proteasome levels between the ibuprofen and control samples. The proteasome activity was significantly decreased in samples treated with ibuprofen. It was also determined that automated western blot machines are not as effective as manual western blotting methods.

Impacts of Complex Formation Between Chromophoric Dissolved Organic Compounds on UVvisible Absorbance

Student Name: Coral Chen
UC DavisDepartment: Land, Air, and Water Resources
UC Davis Mentor: Dr. Peter Hernes
Absorbance data on chromophoric dissolved organic matter (CDOM) in the UV-visible band is a popular proxy for biomarkers in aquatic systems.  However, these direct correlations between absorbance and other properties of DOM may be flawed if the absorbance data does not accurately reflect the CDOM concentration.  In this study, the impact of synergistic effects between dissolved compounds on CDOM UV-visible absorbance is examined to demonstrate the need to account for these effects when analyzing CDOM absorbance data.

This study looks at various combinations of lignin model compounds, amino acids, and condensed purified tannins, demonstrating that when combined, the absorbance behavior of these compounds is not accurately predicted by Beer’s Law.  The interactions found in this study indicate that any calculations based on CDOM absorbance of water samples should be adjusted for synergistic effects between the compounds present in the sample. In the future, a database of synergistic effects would be important to accurately interpret data from any remote sensing systems that may be developed to monitor DOC in relation to climate change.

Mesoporous Silica Nanocage (MSN) Uptake in Macrophages After Inhalation in MiceMesoporous Silica Nanocage (MSN) Uptake in Macrophages After Inhalation in MiceMesoporous Silica Nanocage (MSN) Uptake in Macrophages After Inhalation in Mice

Student Name: Dana Jung
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton
Mesoporous silica nanocages (MSNs) are inorganic-based nanocarriers containing porous channels. These channels can be filled with medicinal compounds and utilized to target various diseases in the respiratory system. The purpose of this study is to determine the frequency of MSN uptake, retention and fate in macrophages after deposition in the lungs following a single, acute period of inhalation. Macrophages, highly phagocytic cells of the lungs, appear to uptake MSNs at different rates and to different degrees following inhalation into the lungs. The actual MSN uptake by these cells over time was done by calculating the volume of MSN in alveolar macrophages at 1, 7, and 21 days post-inhalation. In previous studies, mice were exposed to MSNs and harvested after 1, 7, and 21 days to show macrophages as the dominant cell type in the lungs to sequester MSN following inhalation. Using cells recovered from the lungs by bronchoalveolar lavage (BAL), as well as examining lung tissues to determine the location of these cells in lungs, MSN with either a positive or negative surface charge to determine its effect on uptake were used to determine the relative frequency of uptake in the macrophages. The results show that the area of MSNs within the macrophages both slightly decrease over time. However, overall it indicates that the MSNs are not clearing out from the lungs or the macrophages.

The Importance of Mutations on Structure and Function of Legionella Pneumophila CMP-N,N’-Diacetyllegionaminic Acid Synthase

Student Name: Echo Tang
UC Davis Department: Chemistry
UC Davis Mentor: Dr. John McArthur
Sialic acids are important molecules that are present during cell-to-cell interactions, immunological processes, and pathogenic processes. Their role as markers in pathogens and cancer cells are well understood, but the reason that nature favors some mutations is largely unknown. It has been found that mutations help with sialic acid enzyme substrate binding, specifically in sialic acid synthases that synthesize sialic acids. However, it is difficult to incorporate sialic acid analogs with modifications on the positions C7 to C9 onto glycans using enzymatic methods. The enzyme Legionella Pneumophila CMP-N,N’-Diacetyllegionaminic Acid Synthase (LpCLS), which synthesizes legionaminic acid present in Legionnaire’s Disease, was found to have high structural homology to the human enzyme CMP-sialic acid synthase, N. meningitis CMP-sialic acid synthase (NmCSS). Thermal shift assays also concluded that the stabilizing conditions for LpCLS includes an ideal pH of 8.5 and the presence of the stabilizing ligands CTP and legionaminic acid. 

Characterization of one new variant of β-glucosidase B with kinetic and thermal analysis

Student Name: Enya Xing
UC Davis Department: Genome Center
UC Davis Mentor: Dr. Justin Siegel
With a deeper knowledge and understanding of the effects of point mutations on amino acid interactions and protein functions, the objective is to create a database to store the collected data and add on to computational learning. Currently, through the FoldIt software, a Rosetta score is provided to serve as a frame of reference for the stability of a mutation. However, only a small amount of designs and mutations engineered achieve the desired function. The database would allow for an increased accuracy and level of knowledge on the prediction on how different point mutations would affect protein stability and efficiency through altered amino acid interactions. The current project focuses on the already well understood β-glucosidase B (BglB) enzyme with a known crystal structure and reports the Michaelis-Menten kinetics and thermal stability of purified mutants. [Insert part about important results]. Through the analysis of the results and the accumulation of data points within the database on BglB, there can be an improved understanding toward point mutations that can be applied to other proteins. The research currently does not have immediate short term results but the data that is collected continues to grow and better the predictive algorithm and protein redesign.

Induction of N immune receptor TIR domain dimerization yields no cell death in N. benthamiana

Student Name: Eric Vuong
UC Davis Department: Plant Biology and Genome Center
UC Davis Mentor: Dr. Savithramma P. Dinesh-Kumar
The N resistance gene, which encodes the N protein and confers resistance to tobacco mosaic virus (TMV), is a member of the Toll-interleukin-receptor (TIR) class of plant nucleotide binding leucine rich repeat (NLR) immune receptor . Previously, the N NLR has been shown to dimerize through its TIR domain upon infection with TMV. Here, we attempted to artificially induce dimerization of the N TIR domain in the absence of TMV to see if the oligomerization can induce hypersensitive response (HR-PCD), a form of programmed cell death (PCD) defense response, in Nicotiana benthamiana. The TIR domain was fused to green fluorescent protein binding protein (GBP) and mCherry fluorescent protein binding protein (ChBP). Through the use of Agrobacterium-mediated transient expression, we co-expressed TIR-GBP and TIR-ChBP with GFP-mCherry fusion in N. benthamiana leaves in order to create a  TIR domain homodimer. Our initial results suggests that artificially induced TIR domain dimerization using this approach fails to induce cell death.

Characterization of a Diterpene Synthase in Grindelia robusta

Student Name: Esha Chawla1
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Philipp Zerbe
Plants have a diverse set of defense mechanisms in order to protect themselves against external stressors. Among these defense mechanisms is a class of 20-carbon molecules called diterpenoids. Diterpenoids are key in the structure and function of plants, as they protect the plants against pests/insects, excessive UV radiation, and drought [3].  In order to better understand how diterpene synthase, the enzyme that aids in the production of diterpenoids, function in plantae, site-directed mutagenesis was performed near the active site of the diterpene synthase, diTPS. In this study, E. coli bacteria was used as a transient expression system via transformation of E. coli with mutants of GrTPS2 by inducing mutations into GrTPS2 observing the difference in metabolite formation via gas chromatography mass spectrometry analysis (GC-MS). Using this analysis, we can identify which amino acids are key in the structure and function of diterpene synthases.

Ultra-conservation identifies exons missed by traditional annotation

Student Name: Gabrielle Berman
UC Davis Department: UC Davis Genome Center
UC Davis Mentor: Dr. Ian Korf
Motivation: Multi-species genomic alignments show that there are numerous regions that retain 100% nucleotide identity even in organisms that last shared a common ancestor more than 300 million years ago. Such extreme conservation is indicative of molecular function, although it is not always clear what that function is. Where such conservation overlaps exons found in another organism, it can be inferred that the underlying sequence is from a gene. In this paper, we sought to discover highly conserved exons missed by previous annotation efforts.

Results: Using a bioinformatics approach, non-human exons were aligned from the Ensembl database to the human genome and proteome. Exons that are highly conserved in the genome but not found in the proteome represent missed exons. Some of the missed exons turned out to be errors in annotation. The most common case was exons that Ensembl failed to annotate even though they were found in other databases. Another source of error were small RNAs that were not masked in the non-human genomes. We also found several cases where the human genome is missing an exon that other related genomes clearly contain. Since these exons are identical to the human genome, it’s highly likely they continue to function. The reason they are unannotated is probably because the expression profile is highly limited, for example, from an early developmental stage.

Modeling Theoretical Plant Systems with Asynchronous Populations

Student Name: Garrett Gould
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Mohsen B. Mesgaran
Modeling reproductive asynchrony and developing a framework to calculate seed production is very crucial need not only in the further understanding of how asynchronous species reproduce but also in the controlling of asynchronous invasive species. To model reproductive asynchrony, four probability distributions are employed, representing the population density of the male or female of the species that are reproductively active at a given time. This framework models the percent of the population mating, the total amount of seed production, and how these quantities are affected by varying the distribution parameters. By knowing how many seeds will be germinated, given reproductive timing data, further methods of controlling invasive species can be proposed, leading to agroeconomic growth.

Genome-wide Association Study of Plant Development in Arabidopsis thaliana

Student Name: Gaurav Ghosal
UC Davis Mentor: Dr. Daniel Runcie
Plant development and its influences are relevant to a variety of applications and research questions. However, plant development is multi-faceted as it involves genetics, the environment, and different stages of development. A genome-wide association study (GWAS) was conducted to identify quantitative trait loci (QTL) which control the vegetative development in Arabidopsis thaliana, using a panel of 70 worldwide accessions. Previously collected plant images were fed through a computer vision pipeline in order to extract measurements which, along with existing reproductive trait measurements, were used for association. Established single locus association models were used in addition to a newer, multi – loci model. Afterwards, the relationships between the QTL and traits observed during both developmental stages were analyzed.  Gene annotation was conducted to further investigate the QTL identified in this study and validate the results. This study identified significant QTL for traits in both the developmental stages analyzed. Gene annotation revealed that two QTL associated with vegetative development had overlap with previously found development related genes. Ultimately, the path model indicated a significant indirect effect between a region controlling vegetative development and traits measured during the reproductive stage.

The effects of environment stress on the genetic diversity of Agrobacterium tumefaciens

Student Name: Hanlin Sun
UC Davis Mentor: Dr. Dan Kluepfel
For over a hundred years, Agrobacterium tumefaciens has been known to cause crown gall disease in trees around the world. Because the Agrobacteria operate under similar conditions, it would logically follow that it would have a narrow genetic diversity. However, Bosmans et al. (2015) has proven through a variety of tests that Agrobacterium contains a uniquely large genetic pool. To gain a glimpse into the factors that create this uncommon genetic and phenotypic variation, the 186r strain of Agrobacterium, a real-world infectious strain that exists today, was placed under a variety of environmental stresses. The Agrobacteria were cultured for two weeks in a soil environment, a water environment, a minimum medium (M9), and a rich medium (TSB). These stress environments would illustrate if the different biotic and abiotic factors of varying habitats cause genetic changes in the Agrobacteria. In addition to these stress environments, strains of 186r Agrobacterium that were stressed for two years in fallow and orchard soil environments were also included for DNA analysis. This would illustrate how long it takes for the environment to instill DNA changes. To show if environmental factors played a role in creating genetically different Agrobacteria, the stressed Agrobacteria underwent a variety of single gene and complete genome scans that show DNA changes at the base level. Not only would this offer explanations for the creation and plasticity of Agrobacterium’s genetic diversity, this would also contribute towards finding a potential solution for Agrobacterium.

Effect of Ibuprofen on Murine 26S Brain-Specific Proteasomes in Cytosol

Student Name: Henry Huynh
UC Davis Department: Neurobiology, Physiology, and Behavior, & Physiology and Membrane Biology
UC Davis Mentor: Dr. Aldrin Gomes & Dr. Celena Lozano
Ibuprofen, a NSAID (non-steroidal anti-inflammatory drug), is a popular over-the-counter analgesic and antipyretic, which functions by non-specifically inhibiting the COX-1 (cyclooxygenase-1) and COX-2 (cyclooxygenase-2) pathways. The temporary inhibition of the COX (cyclooxygenase) pathways by ibuprofen reduces the formation of prostaglandins, which are lipids necessary for inflammatory processes. It has been hypothesized that ibuprofen and other NSAIDs could endanger the functionality of the proteasome in the brain. The UPS (ubiquitin-proteasome system) is essential for intracellular protein degradation in mammalian cells. It has been further speculated that ibuprofen could target pathways crucial for proteasome function and cause dysfunction. Misfolded protein aggregates and oxidative stress due to proteasomal dysfunction are intimately linked to aging, neurodegenerative diseases, and cancer.  To determine if ibuprofen induces proteasomal dysfunction in brain tissue, we performed semi-quantitative western blotting and proteasome activity assay analysis on mice brain homogenates to determine the effect of ibuprofen on brain homogenates. The β5 and β2 subunit proteasome activity was found to be statistically significantly reduced in brain tissue derived from ibuprofen treated mice. The heat shock protein 70 (HSP70), which sometimes is upregulated during stress, and β1 are both potential correlates with proteasome function and their activity was not increased in ibuprofen treated mice.

A Study on the Effects of Ibuprofen on Murine 26S Liver-Specific Proteasomal Dysfunction

Student Name: Joon Y. Park
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Aldrin Gomes
Ibuprofen is one of the most common type of nonsteroidal anti-inflammatory drugs used for moderating pain in human body by inhibiting the production of both COX-1 and COX-2. More than 30 million Americans use them to soothe discomforts and pains everyday, according to American Gastroenterological Association (Griffin, 2015). Ibuprofen is well known to show detrimental effects in damaging cardiac and gastrointestinal cells, but no research has yet conclusively demonstrated the clear effect of ibuprofen on the liver. Thus, the goal of this research is to determine the effect of ibuprofen on proteasomal function in liver. Proteasome serves as a useful indicator, as it is responsible for degrading most of the protein in the eukaryotic cells (Budenholzer et al. 2017). Through western blotting technique, the relative amount of proteasome and antioxidant protein was measured. Through proteasome assay, the proteasomal activity was measured. These two approaches showed that ibuprofen caused proteasomal dysfunction in the specific proteins and beta-subunits: PSMA6, β1, and β2. Overall, the ibuprofen was part of the causing factor of 26S liver-specific proteasomal dysfunction. These results suggest that people with liver problems or people at age 45 or older should be cautious about the use and dosage of ibuprofen. This research also suggests that investigation of other NSAIDs, such as aspirin, using similar approaches should be carried out to accurately evaluate hazards on the human body.

Expanding the Database of Single Point Mutations of the β-glucosidase B Protein Using Kinetic and Thermal Analysis

Student Name: Lauren Fu
UC Davis Mentor: Dr. Justin Siegel
The well-documented crystal structure of Beta-glucosidase B, or the BglB protein, leads to its common usage in studies done on site directed mutagenesis. In terms of this project, the predictions of a computational enzyme design program is assessed using the experimental data BglB mutations. Using a combination of dry and wet lab techniques, three mutations are studied in how changes in enzyme structure affect amino acid interaction. FoldIt is used to predict the changes brought to the wild type BglB protein by the each of the mutations, and the kinetics and thermodynamics are determined through assays on proteins containing the mutant DNA. The data points are evaluated against the projections of the algorithm in order to examine its accuracy. The data reveals that the H206R mutation is more stable than the wild type, as it denatures at a higher temperature than the wild type. [insert kinetic data analysis here]. As the database expands, the predictions of FoldIt can be improved through machine learning.

Effects of Tactile Enrichment in Sensory Cortex and Behavior of Early Blind and Sighted in Monodelphis Domestica

Student Name: Luyan Zhang
UC Davis Department: Center for Neuroscience
UC Davis Mentor: Dr. Leah Krubitzer
Compensatory cross-modal plasticity is the ability for the brain to alter neural connectivity and functionality, and it is highly experience-dependent. Rearing animals in enhanced environments has been shown to ameliorate deficits caused by neurological diseases and promote the development of the visual system. The goal of this study was to determine the effects of tactile enrichment on the behavior and cortical area size of early-blinded and sighted short-tail opossums (Monodelphis Domestica), seeking to find the extent enhanced environment can affect cross-modal plasticity. The opossums performed two naturalistic behavior tasks: the variable ladder task and skilled forelimb reach task. While the variable ladder task tests the ability of tactile discrimination, the skilled reach task tests the motor ability and sense of smell. The brains were then extracted from enucleated and sighted animals from enriched-reared animals and standard reared cages. The experiment then involved histological tests to determine the size of primary visual and somatosensory cortices. This study showed that opossums reared in tactile enriched environment made significantly less error in the variable ladder task and skilled reach task, and performed generally better in the behavioral tasks. While the area of primary somatosensory and visual cortices stayed relatively the same for both enriched-reared animals and the standard-reared animals, the density of neurons, their firing rates, or receptive field sizes may have changed. The findings of this research may promote better rehabilitation methods for blind patients.

A Semiquantitative Fluorescent Method to Assess Genome Editing Efficiency and Knock-in Rates using CRISPR/Cas9 and a single stranded DNA oligo

Student Name: Nathaniel Kim
UC Davis Department: Mouse Biology Program
UC Davis Mentor: Dr. Joshua Wood
One method for generating animal models for precision medicine applications is to insert pieces of DNA that code for changes in that animal to more closely mimic disease conditions. At the UC Davis Mouse Biology Program, a method has been developed for generating a single stranded DNA (ssODN) construct that can be used in combination with CRISPR/Cas9 to generate mutant animals with DNA insertions. We have employed this method to generate a Cy3 (red) fluorescently labeled ssODN that encodes green fluorescent protein (GFP) and engrafts via small homology arms downstream of exon 1 in the embryonic development gene, Platr 14. To test the durability of the ssODN, we evaluated its structural integrity under repeated freeze/thaw cycles and/or electroporation conditions. By evaluating the resilience of the single stranded DNA to withstand common procedures used in generating the mutant animals, we provide evidence that this method for generating ssODNs is a reliable platform for generating mutant animal models by DNA insertion. Further, by testing the Cy3 fluorescently labeled ssODN that encodes GFP and integrates into a gene that is active on embryo days 4-5, we will be able to measure the relative efficiency of ssODN entry into mouse zygotes and its ability to integrate into the genome by culturing the embryos ex vivo. This innovative tool allows us to rapidly assess the relative efficiency of two electroporation methods in comparison to traditional pronuclear microinjection. Our results showed that only zygotes which underwent BioRad electroporation glowed green on day 5 which shows that integration of the ssODN was successful into the Platr 14 gene. This ultimately shows that the mean fluorescent intensity method is a reliable way to rapidly determine successful integration of DNA using CRISPR/Cas9 and targeted integration of a relatively large ssODN (1692bp) into the mouse genome using CRISPR-EZ.

Relations of Organs and Water Potential to Bent Neck in Roses

Student Name: Nitya Kotha
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel
Bent neck is a common phenomenon seen in roses when the top part of the rose bends over, contributing to a significant monetary loss in the horticulture industry. Bent neck is caused by loss of pressure in the peduncle, but it is unknown what leads to this change in water pressure. In this project, four experiments were conducted, in which water potential was determined by using pressure chambers. The first experiment was conducted to test which organ has the greatest effect on the loss and gain of turgor pressure. The water absorption, content, and loss of each rose was calculated and the water potential of the peduncle, stem, and leaf of each rose was measured. The bud was seen to contribute greatly to water loss in the roses. A second experiment was conducted to test if the presence of the rose bud affects equilibration of the flower by having two flowers without buds and three with buds and proceeding to measure the water potentials of the peduncle, leaf, and stem after equilibrating the roses for three hours. It was found that on average the leaves had great stress values than the peduncle, which was greater than the stem regardless of the presence of the bud. The third experiment tested the presence of the rose bud in relation to the presence of water, having four conditions in total. Using three roses per condition and letting them sit overnight, water potential measurements were taken of the peduncle and leaves of each rose, showing that the bud only plays a role in water stress when a water source is present. The final experiment tested if the presence of leaves affected water loss based on the findings of experiment 1. Using the cultivar Frederic Mistral, it was found that the presence of leaves contributes to more water loss. Further research must be conducted to test the applications of the research.

Application of the hydrotime model to germination in invasive weeds and emergence from various burial depths

Student Name: Quin Wai Wong
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Mesgaran M. Matzrafi
The hydrotime model is a common system for predicting seed germination in response to water availability. Developed after the thermal time model, its functionality lies in accounting for the environmental conditions of seeds in a statistical fashion. The hydrotime method focuses on water potential: the ability of a plant to take in water. By comparing water potential to germination rates, more data can be gained by applying the hydrotime model to various stressors. The seeds are germinated at nearly optimal temperature with varying water potentials through incubation. Since Palmer amaranth has high genetic variability in its population, and hence, varied times for seed germination, it is important to understand whether the hydrotime system can be applied. Through analysis on hydrotime for Palmer amaranth, more questions arise as to whether either the hydrotime or thermal time model have applications to other environmental conditions. Analysis of emergence in terms of seed burial depths with similar modeling techniques is approached. The hydrotime model best matched the emergence studies on seed depth. However, use of the logistic distribution and a separate emergence equation were required. From this, the amount of parameters required to express emergence are decreased for seed depth by examining trends in the data. As a result, this study benefits growers in managing invasive weeds while providing insight on the implications of burial depth modeling.

Observing the Influence of the Presence of Rose Leaves, Flowers, and Peduncles on Water StressThrough Water Potential

Student Name: Rhea Cho
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel
The floriculture industry experiences losses due to premature wilting by flowers during transport every year. Water potential has been recently proposed as an effective and accurate indicator of plant stress levels in a variety of crops, including flowers. The primary objective of this study was to observe the water relations of roses (Rosa) with respect to the presence of certain rose organs in detail through four experiments. ANOVA tests were conducted to detect overall significance of data, and the Tukey Test was used to make direct comparisons between treatment groups. In the first experiment, ten roses of two different cultivars (‘La Perla’ and ‘Ingrid Bergman’) were cut in five ways to create different organ combinations. A pressure chamber measured the water potential values of the stems, leaves, and peduncles of these roses after four days. It was concluded that organ combinations with flowers exhibited more negative water potential values under conditions of water stress. The second experiment involved observing the influence of the presence of a flower on water equilibration of roses of one cultivar. No significant difference in water potential values was seen between stem to stem, peduncle to peduncle, and leaf to leaf comparisons between roses with flowers and roses excluding flowers. The third experiment investigated the differences of water potential values of the stems, leaves, and peduncles of twelve roses subjected under four different treatments: with flower and with water, with flower and without water, without flower and with water, and without flower and without water. A statistically significant difference was found between with water and without water treatments, but not between with flower and without flower treatments. The fourth experiment was essentially a repeat of the first experiment with a greater focus on observing the influence of the presence of leaves on water potential values. A statistically significant difference was found in water gain in rose, uptake, and water potential values. These findings indicate that the presence of flowers and leaves negatively impacts rose water potential values in post-harvest conditions. Practical applications for this research involve further exploring which pre-harvest growth conditions for roses reveal more negative water potential values for assessing the effectiveness of specific water or soil treatments. 

Markers of Mitochondrial Dysfunction in FMR1 Premutation Carriers

Student Name: Roshni Varma
UC Davis Department: MIND Institute
UC Davis Mentor: Dr. Cecilia Giulivi
A premutation in the fragile X mental retardation-1 (FMR1) gene is characterized by 55 to 200 repeats of the trinucleotide CGG in the 5’-untranslated region of the gene. Some premutation carriers will develop a late-onset neurodegenerative disease known as fragile X-associated tremor/ataxia syndrome (FXTAS). The mechanisms that induce FXTAS in premutation carriers remain elusive, but mounting evidence points to age-dependent accumulation of mitochondrial damage, which is exacerbated by the CGG expansion. Past research reported decreased citrate synthase activity and mitochondrial DNA (mtDNA) copy numbers, coupled with increased mtDNA damage in premutation carriers with and without FXTAS. However, the link between citrate synthase and the mtDNA copy number (both usually used as surrogate markers of mitochondrial mass) has not been investigated in detail in premutation carriers with and without FXTAS. This is relevant in the context that a higher mtDNA copy number may be associated with oxidative stress, whereas a lower copy number may be associated with issues of mtDNA maintenance and replication. To this end, this study evaluates citrate synthase activity and mtDNA copy numbers per cell in skin fibroblasts from nine premutation carriers, six of which were diagnosed with FXTAS. The majority of carriers (5 of 9) showed lower mtDNA copy numbers than the 95% confidence interval (CI), whereas only one of nine showed lower citrate synthase activity. While more research is needed within a larger dataset, these results indicate that lower than control values of mtDNA are present in carriers.

Enhancing Determinants of Tyrosine Sulfation Site Predictions

Student Name: Samarth Kamle
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
The post-translational modification of tyrosine sulfation is thought to be recognized when the sulfating enzyme tyrosylprotein sulfotransferase exhibits specific properties. However, with the recent discoveries of new sulfated sites, recognition features to identify tyrosine sulfation require modifications. Thorough analysis of amino acid sequences using the Position-Specific-Scoring-Matrix (PSSM) emphasizes that the consensus features do not possess updated information essential to predict tyrosine sulfation. The amino acid residues surrounding the tyrosine site affect the condition of the tyrosine as sulfates tyrosines are typically found near acidic or mutagenesis sites. New sulfated tyrosines with low PSSM scores indicate alternate factors contributing to the status of the tyrosine site as the cutoff score has decreased. This view implies that current consensus features to recognize TPST substrate may not be essential as reevaluation of the factors contributing to prediction of tyrosine sulfation have revealed lower sensitivity values for the dataset of known sulfated tyrosine sites (p114n551).

Optimization of RAFT-forming Drug Formulations

Student Name: Sarah Suriano
UC Davis Department: Biological and Agricultural Engineering
UC Davis Mentor: Dr. Gail Bornhorst
Gastroesophageal reflux disease, or acid reflux, causes 25-100 million people to experience heartburn in the US alone. Treatments available include antacids, raft-forming drugs, and combinations of the two, which consist of sodium alginate, calcium carbonate, and sodium bicarbonate, which react together to form a raft that floats to the top of the stomach contents to prevent acid from entering the esophagus. The purpose of this study is to investigate the effects of the composition of the formulation on pH and raft formation. Each of the different formulations was tested in vitro in HCl solutions of pH 1 and pH 2. The mass of the raft and the pH of leftover solution were measured and the effects of the ratios and composition of the formulations on the pH and raft were analyzed. The results suggest that 4.5 g of sodium alginate is the optimum level because it always forms a gel.  

Optimization of AtCBF1 ectopic expression in harvested tomato fruit using a chemically-inducible transgenic system

Student Name: Sarah Wornow
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles
Tropical and subtropical fruit, such as the tomato, experience postharvest chilling injury (PCI) when stored at low temperatures, accelerating deterioration and reducing shelf-life, resulting in losses for the agricultural industry and consumers. CBF genes (CBF1-3) code for transcription factors which regulate the expression of cold responsive genes that confer tolerance in the model plant Arabidopsis thaliana. Overexpressing a CBF gene from this plant (AtCBF1) in tomato fruit during postharvest refrigeration may increase PCI tolerance and better preserve quality. The goal of this project was to optimize the application of the glucocorticoid dexamethasone (Dex) in transgenic Micro-Tom tomato fruit containing a construct to chemically-induce AtCBF1 expression during periods of refrigeration. Transgenic tomato fruit were harvested, soaked in a Dex solution, and refrigerated for specific times. RNA was extracted to quantify the relative expression of AtCBF1. A physiological characterization found control seeds (no AtCBF1) had a higher germination percentage than the transgenic seeds at Day 8. The optimal concentration of Dex to induce gene expression was found to be fifty micromolar and the optimal soaking time to be one hour. In conclusion, the Dex system successfully induced AtCBF1 expression in harvested fruit, a novel finding.

Refinement of quantification methods for Sporosarcina pasteurii

Student Name: Sarah Yun
Aims: Sporosarcina pasteurii is a bacterium used to precipitate calcite in sands, creating a sandstone-like material. As it has been difficult to attain a viable count of S. pasteurii comparable to that of direct counting methods, this project aimed to refine quantification methods for S. pasteurii.

Methods and Results: S. pasteurii cultures were serially dilute and viably plated on various medium to compare the ability of the medium to facilitate efficient cell recovery. It was found that agar media containing nutrients mixed for longer periods of time facilitated the best recovery. Additionally, the relationship between S. pasteurii optical density and total direct count by acridine epifluorescence microscopy was compared across spectrophotometers to find significant discrepancies.

Conclusions: Agar media containing nutrients mixed for longer periods of time and low optical density inoculums can be used to meet expected recovery. Further studies should aim to verify these findings. The discrepancies across spectrophotometers suggest researchers must not solely rely on data from outside spectrophotometers and must instead develop a correlation for each spectrophotometer.

Significance and Impact of Study: This project enables the accurate physiological study of soil bacteria and improvement in their utilization by demonstrating proper quantification.

The ROG2 Protein Interacts with Arabidopsis TRAPPIII Tethering Complexes and is Involved in SYP61 Trafficking

Student Name: Sean Fu
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Georgia Drakakaki
It is known that cell wall components are trafficked by vesicles that fuse to plasma membranes mediated by SNAREs and tethering complexes. Highly conserved tethering complexes such as TRAPP complexes are known to guide vesicles and fuse them to the plasma membrane. In Planta, TRAPPIII complexes have been identified. Recently, research done has shown a new protein called ROG2 within the complex. Here, the initial characterization and interaction between ROG2 and other well-known TRAPP complex proteins is investigated. One component of this characterization was done by analyzing the relationship between ROG2 and known TRAPPIII complex components such as TRS33 and BET3. The presence of ROG2 in TRAPP complexes was demonstrated by creating biomolecular fluorescence complementation (BiFC) using a 2-in-1 plasmid containing ROG2 along with a potential TRAPPIII binding partner (such as TRS33 and BET3). The interaction between ROG2 and the TRAPPIII proteins was analyzed using confocal microscopy. The images revealed that ROG2 does interact with (insert which one it interacted with), suggesting that ROG2 is part of a new TRAPPIII-like complex. Two mutant Arabidopsis lines, rog2-1 and rog2-2, had their rog2 genes knocked out to better understand the role of ROG2 in cell wall component trafficking. The mutations resulted in the disruption of normal trafficking conducted by SYP61 vesicles. Work was primarily done with rog2-2 and the two recovery Arabidopsis lines CFP-SyP61xROG2-2 Dipped w/UB-YFP-ROG2 and CFP-SyP61xROG2-2 Dipped w/Rog2-YFP-ROG2. The rescues of these mutants verified the lack of the ROG2 protein was responsible for the cell dysfunction.

Magnetophoresis of Iron Oxide Spherical Nanoparticles and Anisotropic Nanorods

Student Name: Sean Wu
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Jennifer Lien
Two competing morphologies of iron oxide (Fe3O4) nanoparticles, spherical and rod shaped, were synthesized via established solvothermal and three-step (hydrolysis, reduction, and ligand exchange) reaction methods, respectively. Single crystal spherical particles averaging 30.8 nm in diameter and nanorods averaging 40.3 nm in length and 9.9 nm in diameter were synthesized and dispersed into an aqueous biofluid model solution, under a magnetic field gradient. The field strength of a permanent magnet was measured and found to fall off quickly past 2 cm. Movement experiments were conducted between 0-1 cm away from the magnet, with a field of 3180 Gauss at the surface and down to 750 Gauss 1 cm away from the magnet. It was anticipated that despite similar size and component materials, the anisotropic characteristic of nanorods would attribute to the faster induced magnetization movement in media relative to its spherical counterpart, suggesting a necessary shift of focus towards anisotropic magnetic nanostructures. Further work is needed to improve crystallinity and size matching in the rods used in this work to realize the improvement in magnetic response compared with equivalent spheres. The preliminary results with 40.3 nm 9.9 nm rods which are smaller in material volume and less crystalline than the spheres point towards the anticipated results.

Comparing the Breathing Structures of Cactophillic Drosophila Larvae and Pupae to Other Species

Student Name: Serena Wong
UC Davis Mentor: Dr. Susan Lott
Evolutionary adaptations in many species of organisms prove to be protective mechanisms against predators and prey alike. Like many other species, cactophillic Drosophila have developed adaptations, such as long epithelial breathing tubes, that enable them to survive in harsh desert climates. However, the cause for developmental differences in Drosophila breathing tubes is not clearly understood by the scientific community. This research project studied 4 different species of Drosophila: three cactophillic species and one non-cactophillic species as a control. Specimen were first imaged using a stereoscopic microscope and linear measurements were taken of different pupal body segments. Using specialized computer software, the measurements were analyzed and comparisons were conducted between anterior and posterior spiracles against full body lengths. The results show that there is little to no difference between the length of the two anterior spiracles on each pupa, while there is a difference between the two posterior spiracles of each pupa in either cactophillic or non-cactophillic Drosophila. Ratios between anterior or posterior arm segment lengths and whole body lengths were mostly uniform within species, but vary between species.

The function of the homologous recombination Dmc1 protein during zebrafish meiosis

Student Name: Tina Li
UC Davis Department: Molecular and Cellular Biology
UC Davis Mentor: Dr. Sean Burgess
Meiotic recombination is necessary for generating genetically unique gametes, homologous chromosome pairing, and segregation. Recombination initiates with programmed DNA double strand breaks (DSBs). These DSBs are resected to reveal 3’ single strand DNA, which are bound by recombinases Dmc1 and Rad51. These recombinases mediate DNA homology search and strand invasion, which results in chromosome pairing. However, when recombination defects occur, it can lead to chromosomal abnormalities or miscarriages.

To test the function of the dmc1 gene, a dmc1 knockout strain in zebrafish was created. Then, the dmc1+/- zebrafish were crossed together. The offspring from the heterozygous dmc1 zebrafish  were genotyped and separated into three categories: dmc1+/+, dmc1+/- or dmc1-/-. It is discovered that in the dmc1-/- group, the majority of the progeny was female. Another discovery was made after crossing the female offspring with wild type males. The survival rate, which was 98.120%, was the highest after crossing the dmc1+/- and WT fish. The survival rate of the two other crosses were 93.671% (dmc1+/+ and WT cross) and 93.130% (dmc1-/- and WT

High-amylose resistant starch mutant wheat (Triticum turgidum) shows a change in germination pattern under cold stress

Student Name: Tomo Yoshino
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles
High-amylose wheat is highly desired because it resists digestion to sugars and thus acts as fiber with all the associated health benefits. A mutant wheat (abAB) with twice the amylose content of normal wildtype (WT) wheat was engineered by disabling a starch branching enzyme. The hypothesis is: wheat germination will not adapt to high resistant starch as it would not be able to digest enough starch for use. The germination of these variants was compared over 12 days at room temperature ® and in the cold (C) at 15°C. Low temperatures slowed germination at 4 days. By day 12, accelerated growth in WT-C made coleoptile and radicle length, water uptake, and biomass distribution the same as in the non-stressed WT-R seeds. In contrast, the mutant showed greater defects in the cold; it only adapted its coleoptile and radicle length at day 12. There was surprisingly, a higher amount of both sugars and starch in cold-treated abAB seeds at day 8, suggesting altered metabolism of these carbohydrates in the mutant. Overall, wheat germination adapted to high levels of resistant starch and low temperatures by day 12, since there were few differences in physiological and biochemical parameters assayed compared to the control.

Ablation of somatostatin-secreting Delta cells and its effect on the maturation of Beta cells

Student Name: Vivek Annadata
UC Davis Mentor: Dr. Mark O. Huising & Jessica L Huang
The islets of Langerhans in the pancreas consist of alpha, beta, and delta cells. The focus of this research is to understand the paracrine interaction between the pancreatic delta and beta cells and how their impaired interaction contributes to diabetes development. Specifically, our goal is to determine the effect of somatostatin secreted by delta cells on the maturation of beta cells in the Islets of Langerhans. We studied this by comparing the levels of Urocortin 3 (Ucn3) secreted by mature beta cells in normal mice with levels of Ucn3 in mice whose delta cells have been ablated. Compared to the wild type normal mice, we found negligible levels of somatostatin but the equivalent levels of Ucn3 in the specimens with delta cells ablated. These results offer an explanation that either somatostatin has no effect on the secretion of Ucn3 and thereby on the maturation of beta cells or for somatostatin to exhibit an effect, the pancreas has to be acquired after waiting for a longer duration than 6 days, as was done in this study. 

Effects of Multi-walled Carbon Nanotubes on the Lung Cells of Mice and Rats

Student Name: Younkyung Oh
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton
As advancements in nanotechnology are drastically improving consumer products in recent years, the human health effects and environmental safety issues associated with nanomaterials remain widely unknown. The primary objective of this study is to determine whether multi-walled carbon nanotubes (MWCNTs) inhaled into the lungs 1) cause harm to the respiratory system via inflammation, 2) can be cleared from the lungs over time and 3) if not cleared, where in the lungs they can be found. Inhalation methods used for this study include the exposure of mice and rats to three different concentrations (0.06, 0.2, 0.6 mg/m³) of aerosolized MWCNTs in exposure chambers each weekday (Monday-Friday) for approximately one month. Following end of inhalation exposure, B6C3F1/N mice and Harlan Sprague Dawley rats were examined at two different periods of time post exposure (PE), at approximately one and five weeks. Our findings demonstrate a dose-dependent acute inflammatory response that subsides by the 4-5 week PE time. Continued retention of MWCNTs raises concerns regarding possible long-term effects.

2017 Research Projects

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

Student Name: Alice Gevorgyan
UC Davis Department: Food Science and Technology
UC Davis 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
UC Davis Department: Molecular & Cellular Biology
UC Davis 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
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis 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
UC Davis Department: Department of Anatomy, Physiology, and Cell Biology
UC Davis 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
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis 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
UC Davis Department: Department of Plant Biology
UC Davis 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
UC Davis Department: Department of Chemistry
UC Davis 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
UC Davis Department: Department of Molecular Biosciences, School of Veterinary Medicine
UC Davis 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
UC Davis Department: Mouse Biology Program Center for Comparative Medicine
UC Davis 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
UC Davis Department: Department of Plant Biology
UC Davis 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
UC Davis Department: Center for Neuroscience
UC Davis 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
UC Davis Department: Department of Biological and Agricultural Engineering
UC Davis 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
UC Davis Department: Department of Chemistry
UC Davis 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
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis 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
UC Davis Department: Center for Neuroscience and Department of Psychology
UC Davis 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.

Analysis of TAD calling Algorithms for Hi-C Data Analysis

Student Name: Eric Tang
UC Davis Department: Biochemistry and Molecular Medicine
UC Davis Mentor: Fereydoun Hormozdiari
Hi-C, a form of chromosome conformation capture (3C), is a method that is used to create an accurate 3D model of the genome using methods that reveal chromatin structures. However, Hi-C data alone is not enough to produce a stand alone model. Processing steps involving various algorithms are necessary in order to use the read pairs within the Hi-C data to generate the most accurate images of chromatin interactions and topographically associating domains (TAD). The specifications of each of these algorithms, and the disparate results they produce as a result thus require further research. Research within the Hormozdiari lab used statistical and qualitative analyses to look at the different TAD’s produced by the algorithms Arrowhead, Armatus, HiCseg, TADtree, TADbit, InsulationScore, and DomainCaller in order to assess which of them was the most accurate and effective. Although the results of the research revealed the differences in the size, shape, and proximity of the TADs that were found by the algorithms, concrete conclusions regarding the accuracy of the algorithms could not be made

The Q324H Variant of the DNA Repair Glycosylase MUTYH May Predispose CRC

Student Name: Garrett Ma
UC Davis Department: Department of Chemistry
UC Davis Mentor: Dr. Sheila David
MutY is a bacterial DNA repair glycosylase that cleaves a mismatched adenine across the oxidatively damaged guanine base, 8-oxo-7,8-dihydroguanine (OG), via base excision repair (BER). Unrepaired DNA damage may cause disease-inducing mutations, including changes in transcription regulation or a resultant translated protein. When germ-line mutations occur in the gene of the human homolog, MUTYH, it can lead to a condition called MUTYH associated polyposis (MAP), a colorectal cancer (CRC) subtype. Some variants associated with MAP exist in the interdomain connector (IDC) that joins the N-terminal domain responsible for catalysis to the C-terminal domain necessary for OG recognition. The Q324H variant is located in the IDC in a critical binding domain of several downstream repair proteins. Initial studies with this variant demonstrated reduced OG:A repair in vivo yet maintains wild type (WT) activity in vitro. In this study, we employ the mouse Mutyh homolog of Q324H, Q306H, to better characterize Q324H activity due to difficulties in assessing human MUTYH activity in vitro. Although these studies with the mouse homolog variant may also show WT OG:A repair in vitro, due to the location of this variant in the IDC, it’s CRC association may be caused by perturbations in downstream repair.

Investigating the spatial and temporal response of tomato fruit to oxidative damage during postharvest chilling injury

Student Name: Gurpaul Basra
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: Dr. Diane Beckles
One of the most frequently used and effective methods to preserve postharvest produce is low temperature management. Refrigeration of fruits and vegetables is beneficial as it can prolong shelf life as well as maintain the overall quality of the product; however, tropical and subtropical produce often do not reap the same benefits as they are not suitable for lower temperatures. These fruits, vegetables and herbs are negatively impacted by low temperature storage, a disorder called postharvest chilling injury (PCI). Tomato fruit represents an important part of human diet, and is also susceptible to PCI, which manifests as a series of physiological, biochemical and molecular changes, such as alterations in the  redox state of the cell (reactions involving the transfer of electrons) and the production of reactive oxygen species (ROS). The accumulation of ROS to toxic levels is harmful to the cell and can accelerate its overall rate of deterioration. Although PCI has been studied for more than 200 years, the development of oxidative damage caused by ROS has not been extensively characterized in the different tissues that compose a tomato fruit. This article will investigate  two different parameters associated to oxidative stress during postharvest cold storage in the columella and pericarp tissues of cherry tomatoes.

Localization of Plant Pathogen Effectors and Plant Innate Immunity

Student Name: Hilal Morrar
UC Davis Department: Department of Plant Biology
UC Davis Mentor: Savithramma Dinesh-Kumar
The world loses some food crops to pathogenic infections, and investigating how pathogens infect plants would help reduce how much crop is lost. In turn, this leads to the development of new pesticides and pathogen resistant plants. Plants have two main defense systems, which are Pattern Triggered Immunity and Effector Triggered Immunity. The first system includes the plant’s receptors on the outside that trigger the immune response after detecting a pathogen effector. These extracellular receptors act like plants first layer of defense against invading pathogen. Pathogens have evolved sophisticated means to compromise this primary layer of defense by delivering effector protein inside the plant cells. Plant employ a second layer of defense through intracellular Nuclear Binding – Leucine Rich Repeat (NLR) receptors that direct the Hypersensitive Response after detecting an effector. In nature, these effectors are injected into a plant host cell via the Type Three Secretion System. The secretion system complex protrudes out of the bacterial cells and is comprised of a transmembrane base and a long, narrow needle to directly release effectors into a host. Here we explore the localization of these effectors using confocal microscopy. We engineered effector proteins fused to a fluorescent protein by molecular cloning, resulting in a chimeric protein that was delivered into tobacco leaves through Agrobacterium mediated transformation.  Our data reveals that the pathogen effectors localize to the plasma membrane, chloroplast, and mesophyll cells of the tobacco plant leaves.

Biocatalyst Discovery for the Chemoenzymatic Synthesis of Lacto-N-Tetraose

Student Name: Ivy Tang
UC Davis Department: Department of Chemistry
UC Davis Mentor: Xi Chen
Researchers desire an affordable synthetic route for forming human milk oligosaccharides absent in cow milk to study their functions and incorporate them into infant formula. These compounds are believed to provide the protective properties of human milk for preterm infants from necrotizing enterocolitis and other diseases. Many of these compounds can be synthesized with purified enzymes and substrates or microbial cells engineered for their production. However, those containing Galβ1-3GlcNAc linkages, such as lacto-N-tetraose, are generated in low yield and are expensive due to the lack of a encoding β1-3-galactosyltransferase known to express well in suitable hosts. Eight genes encoding β1-3-galactosyltransferases were unsuccessfully cloned into pET-22b(+), an E. coli expression vector. If successful, the vector would be transformed into E. coli BL21(DE3) cells. Enzyme expression titers, optimal reaction conditions, and catalytic properties of the β1-3-galactosyltransferase will be determined. The most suitable enzyme will then used in the total enzymatic synthesis of lacto-N-tetraose from lactose with excellent yield. Affordable synthetic procedures for the preparation of human milk oligosaccharides such as lacto-N-tetraose may lead to improved baby formulas that reduce infant mortality rates.

The Significance and Misforecast of the 15 May 2018 New England Severe Thunderstorm Outbreak

Student Name: Jacob Feuerstein
UC Davis Department: Land, Air, and Water Resources
UC Davis Mentor: Dr. Kyaw Tha Paw U
The severe thunderstorm outbreak of 15 May 2018 devastated large portions of the Northeast with huge swaths of damaging wind up to 110 mph and a dozen tornadoes up to EF2 in strength. Five people were killed and 1.4 billion dollars in damage were caused by the event, making it among the costliest and deadliest severe thunderstorm outbreaks in the history of the Northeast. However, the storm prediction center (SPC) failed to forecast the severity of the event in the days before it occurred, potentially leaving many residents of impacted areas uninformed of the dangerous conditions soon to occur. This case study attempts to answer both why this event was relatively severe and why the SPC failed to forecast the event’s severity. This was accomplished by analyzing synoptic conditions, significant mesoscale events, and model data associated with SPC forecasts. The outbreak was also compared to a previous significant Northeastern outbreak that occurred on 31 May 1998. The current analysis concludes that the severe weather event was an unusual combination of an elevated mixed layer and very high wind shear, due to a split stream pattern (in which the jet stream branches into two different components) and a 700mb trough over the West Coast. This is a synoptic setup that matches the one in 1998 very closely. Model and NWS text data suggests that ample evidence of incipient severe weather existed preceding the event, implying that the SPC could have forecast its severity. It was also determined that the event should be classified as a derecho using procedures outlined in Johns and Hirts, 1987. The split stream setup, when taken with its similarity to past significant severe outbreaks over the Northeast, introduces a better understanding of Northeast severe weather that can aid in forecasting of severe thunderstorm potential.

GESI Constructs in PDGFR-N-ARCLIGHT Scaffold

Student Name: Janet Han
UC Davis Department: Department of Biochemistry and Molecular Medicine,
UC Davis Mentor: Lin Tian
The recent increase in the number of behavioral diseases with neurobiological bases has increased the effort to find biosensors to monitor neural connections in the brain. Neural biosensors may be used to monitor brain disease progression by tracking neural activity. Current neural biosensors, such as the genetically encoded calcium sensors (Li, Q. et al.) lack the ability to show how frequently the neuron is firing because calcium levels do not have perfect correlation to neural activity. However, neural activity can be tracked by monitoring the activity of potassium ion channel proteins because action potentials rely on these channels to re-polarize the membrane. By cloning a specified peptide (termed GESI, genetically encoded small illuminant) into the potassium ion channel (Kv2.1) protein that activates the dye bromocresol purple (BCP) upon exposure a biosensor that can track neural activity can be created. The peptide will be cloned in an area that will only be exposed to the BCP in solution when the potassium ion channel is active. As a pilot experiment, the Tian Lab at UC Davis has identified several GESIs that can be cloned into PDGFR-N-Arclight, a smaller and easier to manipulate voltage sensitive protein. While this experiment does not directly clone GESIs into the Kv2.1 voltage-gated potassium channel, the PDGFR-N-Arclight scaffold does provide the possibility of developing a voltage-sensitive biosensor used for tracking neural activity due to its similarities to Kv2.1. Furthermore, the PDGFR-N-Arclight scaffold provides insight into how to achieve a Kv2.1 based biosensor.

Metabolites Produced from Bifidobacterium Consumption of Breast Milk Oligosaccharides Suppress the LPS Induced Inflammatory Response in Macrophage Cells

Student Name: Jason Own
UC Davis Department: Anatomy, Physiology & Cell Biology
UC Davis Mentor: Dr. Helen Raybould
Macrophages play a key role in maintaining adipose tissue homeostasis, yet recently these cells have become extensively associated with adipose tissue inflammation upon the development of obesity, a disease that affects 2.1 billion people in the world today. In response to the chronic lipid overloading of adipose tissue during the development of obesity, adipose tissue macrophages increase in number and change their localization. This newly attained knowledge shifts medical approaches away from targeting the inflammatory traits of adipose tissue macrophages, towards targeting their metabolic programming. Mediations directed at increasing metabolic capacity might be used to reprogram macrophage metabolism, allowing macrophages to better deal with metabolic challenges during obesity, in order to maintain adipose tissue homeostasis. Taking this into account, the aim of this study was to determine which metabolites produced by Bifidobacterium grown on specific milk oligosaccharides will suppress inflammation induced by the inflammatory stimuli, LPS, in macrophage cells. RAW-Blue cells, a macrophage-like, Abelson leukemia virus transformed cell line derived from BALB/c mice, were cultured and exposed to various Bifidobacterium supernatants produced from Bifidobacterium consumption of lactose, bovine milk oligosaccharides, 2′-Fucosyllactose, and 3′-Sialyllactose. These cells were then induced with LPS, activating the transcription factor, NF-kB. Upon activation of NF-kB in these RAW-blue cells, a secreted embryonic alkaline phosphatase was secreted into the cell supernatant. After overnight incubation, a QUANTI-blue macrophage inflammatory assay was executed in order to detect the levels of alkaline phosphatase. This study provides the first evidence that high concentrations of lactose and 2-FL metabolites were found to significantly decrease NF-kB activation. Therefore, it was concluded that metabolites produced from Bifidobacterium consumption of lactose and 2-FL suppress the LPS induced inflammatory response in adipose tissue macrophages.

Evolutionary history and genetic basis for elongated posterior spiracles in cactophilic Drosophila species

Student Name: Jerry Liu
UC Davis Department: Population Biology, Evolution and Ecology
UC Davis Mentor: Dr. Susan Lott
Developmentally constrained traits are robust to perturbations, including genetic change, environmental change, and internal noise, likely because variation may be detrimental to the organism. However, the interactions between genetic and environmental perturbations and developmental variation are poorly understood. Can traits that are essential for the proper development of the organism change over evolutionary time? If so, do they change in small frequent steps or rare big jumps? In this paper, the evolutionary history of the posterior spiracles in twelve cactophilic Drosophila species spanning about 20 million years of evolution is examined. Position of each abdominal segment was determined at the 1st instar larval stage from each of the species using denticle belts as a proxy. The positions of the denticle belts were measured in proportion to the entire larval body length and analyzed using linear models. The results show that robust traits do evolve, as there are small but significant changes in body plan within the group of cactophilic species, and larger differences between cactophilic and non-cactophilic species. All cactophilic species examined in this paper were shown to have significantly longer posterior spiracles than that of the outgroup species, suggesting that this trait may have arisen as an adaptation to the desert climate. Finally, when comparing the segment position of each species to the mean segment position, it was found that closer segments tend to shift together, which suggests that the genetic changes underlying the observed segment position changes may lie in the late embryonic stages.

Effect of Differences of Shell Thickness and Pressures on the Cracking of Grapes

Student Name: Justin Semelhago
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: Kenneth Shackel
Grape splitting has affected the grape and wine industry greatly. Thousands of dollars are spent yearly to cover the cost of grapes that split because they cannot be sold to the consumers or wine companies. Past research only indicates that cracking could be a cause of unevenness of skin surface or the irregularities of pressures within the grape. To inhibit cracking, grapes were spray-painted with white dots randomly on the surface and were then placed in water with randomly spray-painted white dots and analyzed over time. The analysis process consisted of running the images taken of the grapes through MATLAB to produce eigenvalues. The eigenvalues track the percent movement of a centroid of three white dots over time. The eigenvalues were then plotted using SAS and patterns were drawn from the graphs. It was found that eigenvectors in the cracking area were growing in a nonuniform way the moment before the crack. The eigenvectors would become larger in both directions indicating an increasing strain adjacent to where the crack would eventually form. Eigenvectors that were not directly beside the crack but in the cracking area showed a decreasing strain perpendicular to the crack. However, within the same eigenvector there would be an increasing strain perpendicular to the crack. This is caused by the crack pushing the centroids of the dots closer to other dots on the same side of the crack which could be a result of either differences of pressure in that area or an unevenness of skin thickness.

The Location of Mesoporous Silica Nanoparticles Over Time in Mouse Lungs Following Acute Inhalation

Student Name: Krysta Zmich
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Kent E. Pinkerton
Mesoporous silica nanoparticles (MSNs) are a new and effective method of drug delivery in the body, with the ability to be tailored for continuous or triggered drug release. Past research has shown MSNs to be highly efficient at targeting specific cells in the body, with greater specificity  than chemotherapy treatments for cancer. Previous research has also shown that once MSNs are taken up by the body through inhalation, the particles do not leave the lung one (1), seven (7), and twenty one (21) days after exposure. To identify the location of MSNs in the lung once inhaled, and the potential consequences of these MSNs on the body, immunofluorescent staining of the lung epithelium coupled with confocal scanning fluorescence microscopy was done to identify the precise nature of MSN uptake and retention in the lungs over a period of 21 days post-exposure. Researchers at the Center for Health and the Environment at UC Davis had previously exposed mice (n = 53) to MSNs and removed the lungs for histological sampling. These lung samples were embedded and sectioned for staining and subsequent confocal microscopy imaging. To determine the cell type associated with MSNs, staining with antibodies for CDH1 (epithelial cell surface protein), CD11c (macrophage and dendritic cell surface protein) and Siglec F (macrophage specific surface protein) was performed. No MSNs were found to be present in the epithelial cells of the lung, but instead were found in cells outside of the epithelium and in the airspaces of the lungs. This suggests MSNs are most likely uptaken by cells of the immune system, macrophages or dendritic cells. Future investigation is needed to confirm this theory

Characterization of Breast Cancer Cells Growing on Mitochondria-Driven Metabolism

Student Name: Lindsay Tao
UC Davis Department: Department of Molecular Biosciences
UC Davis Mentor: Cecilia Giulivi
Intra-cell heterogeneity in breast tumors may confer resistance to conventional cancer treatments. Certain types of cells may be resistant to a certain treatment, thus allowing cancer to persist. We hypothesized that the heterogeneity of  cancer cells can be evidenced in multiple ways, including the identification of discrepancies in their metabolic processes. To this end, we sought to select and characterize a subpopulation of cells that only utilize mitochondrial metabolism to obtain energy from fuels. Adenocarcinoma breast cancer cells (MDA-MB-231) were grown in a galactose or glucose media. The cells in galactose were selected for the ability to use mitochondrial metabolism, while the cells in glucose served as the control. Cell proliferation, phosphorylating capacity, and markers for differentiation, pluripotency, and metastasis were evaluated in cells grown in galactose versus those in glucose. Cells grown in galactose (cells that rely on mitochondrial metabolism including fatty acid oxidation) were found to proliferate slower, have higher ATP production, and were less pluripotent and less differentiated. Thus, breast cancer cells which were forced to generate ATP from mitochondria displayed unique morphological and metabolic characteristics that seem to include a transition towards stemness.

Studies Towards a Synthesis of 4,10,15-(1-4)tristetrafluorobenzena- 1,7-diazabicyclo[5.5.5]heptadecaphane, a Potential Macrobicyclic Fluoride Receptor

Student Name: Matthew Nemeth
UC Davis Department: Department of Chemistry
UC Davis Mentor: Mark Mascal
The detection and monitoring of chemical levels in bodily and environmental systems is a growing objective in the field of synthetic chemistry, following the increasing ability of scientists to synthesize specific chemical receptors. Most artificial anion receptors target phosphate ions or a range of the larger halides: chlorine, bromine, and iodine. This report describes progress in the synthesis of a macrobicylic molecule as well as a macrocyclic intermediate that could act instead as a fluoride receptor. The feasibility of synthesis of 1,4-Bis(carboxymethyl)-2,3,5,6-tetrafluorobenzene 1,4-Bis(cyanomethyl)-2,3,5,6-tetrafluorobenzene were verified with moderate yields, but more time is needed to synthesize 1,4-Bis(ethylamine)-tetrafluorobenzene and carry out the full macrocyclization.

Comparing and Contrasting the Aspects of PCR and Taqman Assays

Student Name: Mehr Sahota
UC Davis Department: Mouse Biology Program Center for Comparative Medicine
UC Davis Mentor: Dr. Joshua Wood
A human and a mouse both have 3.1 billion base pairs which makes a mouse’s genome ideal for genetic research (Importance of Mouse Genome 2017). This project will include the comparison of two important pieces of biotechnology: Taqman assays and traditional PCR, in order to discover which is more cost efficient and accuracy of the screening methods when looking DNA insertions. Analyzing these screening accurate will help provide MBP with the most effective way to produce transgenic and Knockout mice thus furthering scientific research. The Taqman assay and traditional PCR will screen a large Knock in of GFP, a Knock in SNP (single nucleotide polymorphism), and a knock in of loxP/CRE which is a site specific recombinase consisting of around 30 base pairs (Valenzuela et. al., 2003). A Taqman assay is initially more expensive, but it is hypothesized to perform better than traditional PCR when working with small changes in the number of base pairs (Redig 2014). On the other hand, traditional PCR is better suited to find a large insertion than a Taqman assay (Valenzuela et. al., 2003). To investigate whether a Taqman assay or PCR is more effective in certain screening methods, time measurements and cost calculations must be taken into consideration for each of the methods. The quality of the screening must also be taken into consideration to ensure that quality is not being sacrificed for cost or time efficiency.

Thermal and kinetic characterization of β-glucosidase B mutants reveal structural and functional relationships

Student Name: Michelle Tong
UC Davis Department: Department of Chemistry
UC Davis Mentor: Justin B. Siegel
Predictive algorithms for mutant enzyme activity are important for facilitating enzyme selection in industrial projects. But, due to the lack of a large data set collected on mutant enzymes, current Rosetta programs are not accurate in predicting the kinetic activity and thermal stability of mutants. In order to expand the data set documenting mutant activity, the effect of BglB point mutations on its Michaelis-Menten constants and its thermal stability was looked at in this study. The research revealed an increase in the thermal stability of point-mutations when hydrogen bonds were added and a decrease in catalytic efficiency when packing around the side-chain was increased. By characterizing mutants based on their kinetic activity, binding affinity, thermal stability, and catalytic efficiency, this quantitative data will advance understanding of how enzyme structure relates to function.

Effects of Acetaminophen on Proteasome Activity in Cardiac Cells

Student Name: Mitra Pourmehraban
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Aldrin Gomes
The use of nonsteroidal anti-inflammatory drugs (NSAIDs) which are commonly prescribed to patients as pain relievers have recently been associated with cardiovascular disease (CVD). Acetaminophen (Tylenol), which is not an NSAID but has similar pain relieving effects, is not known to induce CVD. The effects of acetaminophen on proteasome activity in H9C2 rat cardiomyocytes was investigated. Proteasomes are enzymes in the body that degrade intracellular protein. These proteasomes are essential for the body to function. The known effects of acetaminophen include liver damage, but the effects of the drug on the heart have not yet been studied. Using rat cardiac cells and proteasome assays acetaminophen was found to have no significant effect on the proteasome proteolytic activity of all three substrates. These results suggest that acetaminophen is not likely to cause as significant an increase in the risk of developing cardiovascular disease as NSAIDs.

RNA Sequencing data analysis between two of Brassica napus F1s

Student Name: Mizuki Kadowaki
UC Davis Department: UC Davis Genome Center Plant Biology
UC Davis Mentor: Julin Maloof
Climate change has deemed it necessary for various crops to adapt to the fast changing environment in order to produce yields. To increase profit, Brassica napus plants must be bred to not only produce more oil but to be less susceptible to climate change. In order to study the gene expression of Brassica napus and apply that information to breeding, RNA sequencing data were analyzed for two different F1 progenies, F1 414 and F1 415, which were created by swapping maternal and paternal parent. Four different tissue types at different stages of the plant’s life were studied. Expression analysis was conducted between these two F1s to see whether genes were differentially expressed between F1 414 and F1 415 throughout the plant’s lifetime and what biological functions are differentially expressed. Single Nucleotide Polymorphism (SNP) identification (allele analysis) between the two F1 generations were correlated with the expression analysis to confirm that gene expression is affected by specific alleles inherited from maternal and paternal parent plants.

Tracking the dynamics of mesoporous silica nanoparticles using fluorescent immunohistochemistry and confocal microscopy

Student Name: Raj Ajudia
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton
Mesoporous silica nanoparticles (MSNs) could possibly become one of the best vehicles for drug delivery created to date. The unique characteristics of MSNs allow for the packaging of medicines into miniscule particles that, once inhaled, allow drugs to be accurately and efficiently delivered to deeper-than-ever target sites in the lung. Much is still unknown about the long-term dynamics of deposition of MSNs in the lungs following initial exposure. In efforts to close this knowledge gap, lab mice were exposed to MSNs for 5 hours, andlung tissues were collected at 1, 7, or 21 days post-exposure. These tissue samples were collected andprepared for examination in a process called fluorescent immunohistochemistry. In this study, epithelial cells in the lungs were tagged with primary antibodies binding to CD11C—e-cadherin proteins. Once fluorescent secondary antibodies and DAPI stain were applied to the tissues, the epithelial cells, alveolar macrophages, and auto-fluorescent MSNs were seen using confocal microscopy. The images confirmed that MSNs were located in and surrounding the alveolar macrophages; however, they were not found in the epithelial cells. Future research may utilize these same methods to search for MSNs in other possible cells of interest in the lungs, such as dendritic cells.

Kinetic and Thermal Characterization of β-glucosidase (BglB) Mutants to Evaluate Effects on Michaelis-Menten Constants and Thermal Stability

Student Name: Raushun Kirtikar
UC Davis Department: Department of Chemistry
UC Davis Mentor: Dr. Justin Siegel
Advents in technology are leading to a revolution in the biological research industry, particularly the field of molecular medicine and genomics. A major goal of these advancements is the creation of a predictive software that will determine what effect an enzymatic mutation will have on the protein and the potential applications of such a mutation. The manipulation of proteins has applications ranging from pharmaceuticals to biofuels to wine-making. Using a design-build-test-learn setup, point mutations were first chosen using the computational software, FoldIt. Then, the mutant DNA was inserted into E. coli cells. The protein produced by the cells was then kinetically characterized to determine Michaelis-Menten constants and analyzed for thermal stability by observing the melting temperature. The results of the kinetic and thermal assays did not match the predictions, likely due to the inaccuracy of the current predictive software. This supports the fact that there is a need for more data collection in order to develop a better predictive software.

Predicting Tyrosine Sulfation Sites in Pattern Recognition Receptors

Student Name: Ria Arora
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis Mentor: Grace L. Rosenquist
Tyrosine O-sulfation, a post-translational modification, plays a crucial role in cell signaling and protein-protein interactions. This phenomenon was demonstrated to be essential in the binding of some pattern-associated molecular patterns (PAMPs) to pattern recognition receptors (PRRs). PRRs activate downstream signal cascades, which generate the innate immune response. However, it is not known whether PRRs are tyrosine O-sulfated. In this study, computational methods were used to predict tyrosine O-sulfation sites in PRRs by using a position-specific scoring matrix to examine the similarity of tyrosine sites in PRRs to that of known sulfated sites. Tyrosine O-sulfation was predicted to exist in 57 PRRs observed, with 130 positive sites found. Furthermore, five predicted tyrosine sites were conserved between Toll-like receptors, an important family of PRRs. Predicting tyrosine O-sulfation sites in PRRs could elucidate the prevalence of tyrosine O-sulfation in the innate immune response and assist with developing drugs that target innate immunity.

Sensitivity and Specificity of the PSSM Tyrosine O-Sulfation Calculator

Student Name: Richard Cheng
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis Mentor: Grace L. Rosenquist
One significant but still not completely understood modification of proteins is tyrosineO-sulfation. Because it is expensive and time-consuming to detect O-sulfated tyrosines, computational tools like the position-specific scoring matrix (PSSM) and the Sulfinator have been developed to predict tyrosine O-sulfation. Using a documented set of tyrosines, both sulfated and unsulfated, the sensitivity, specificity, accuracy, and Matthews Coefficient of computational tools for predicting tyrosine O-sulfation were evaluated at various cutoffs. Although the PSSM was found to have relatively high sensitivity and specificity, Jackknifed resampling demonstrated the need for additional O-sulfated tyrosines to be identified to improve the PSSM further. The Sulfinator was found to have lower sensitivity, specificity, accuracy, and Matthews coefficient than the PSSM, and thus is not recommended to be the primary tool for computational studies of tyrosine O-sulfation.

Effects of Motor Oil Extracts on Medaka Fish

Student Name: Shelley Jersey
UC Davis Department: Department of Anatomy, Physiology, and Cell Biology
UC Davis Mentor: Dr. Swee Teh
Oil from motor vehicles can leak onto roads. This oil is flushed into nearby water bodies when it rains, potentially harming aquatic life. The purpose of this study is to determine the effect of various dilutions of motor oil extracts on the embryonic development of Japanese Qurt Medaka fish (Oryzias latipes). The first batch of embryos was exposed to four different dilutions of motor oil extract and a field sample obtained from the UC Davis VP56 parking lot. A second batch was treated with 0.01% dimethyl sulfoxide (DMSO) to increase the permeability of the embryo’s chorion and subsequently exposed to an undiluted extract and four different dilutions of motor oil extract. All embryos were placed in a 96-well plate with 200 uL of their respective dilutions. Both batches were monitored for changes in morphology, delayed growth, and mortality. Some deformities were observed in the embryos but did not seem to be consistent with any particular group. However, embryos exposed to the field sample and the undiluted extract showed delayed growth and high mortality rates. The groups exposed to higher concentrations of motor oil extract seemed to have higher mortality rates. The data suggests that motor oil extracts may be harmful to aquatic life, but further studies and analysis would need to be conducted to determine if an imminent threat exists.

X-ray Induced Förster Resonance Energy Transfer between Quantum Dot-Nanoporphyrin Conjugates to Generate Singlet Oxygen

Student Name: Susan Garcia
UC Davis Department: Department of Chemistry
UC Davis Mentor: Dr. Jennifer Lien
X-rays combined with Förster Resonance Energy Transfer, can produce singlet oxygen, a reactive oxygen species (ROS), through the conjugation of Quantum Dots encapsulated in Nanoporphyrins. This type of ROS can be used in health applications such Photodynamic therapy and Photothermal therapy. Enhanced singlet oxygen through this process can progress towards a new type of treatment for tumors that will only eradicate malignant cells rather than healthy cells. In this research, a previous experiment was conducted and was found unrepeatable,  presumably, due to material changing over time. The goal of this paper was to attempt to replicate this experiment to present replication and consistency. However, results indicated that the production of enhanced 1O2 is higher when Quantum Dots are encapsulated in Nanopohyrins than not being encapsulated. The replicating experiment presented the enhanced production of 1O2 lower than the first experiment. It is hypothesized SOSG was quenched and that is why the fluorescence signal decreased, however, this is up for further study.  This is significant because the replication of the experiment has added new data that demonstrates X-ray combined with FRET and the conjugation of Quantum Dots produces more enhanced  1O2  than Nanoporphyrin itself. Concluding, that 1O2  is enhanced through combination of X-rays and FRET conjugating Nanoporphyrin and Quantum Dots, leading to alternative treatments for tumor reductions.

Finding the Genetic Diversity of Juglans microcarpa

Student Name: Taoyi Li
UC Davis Department: Plant Pathology Department
UC Davis Mentor: Dr. Daniel Kluepfel
Rootstocks are genetically distinct from the scion, the fruit producing portion of the commercial walnut. Rootstocks are generally better suited to the environmental conditions present in the rhizosphere, often providing resistance to soil borne pests that may otherwise affect the scion and decrease walnut production. Regarding the rootstocks of commercial walnut plants, a better rootstock needs to be developed because a greater resistance to soil borne microbes and pests is desired by the walnut industry. The Texas walnut tree Juglans microcarpa has demonstrated resistance to the crown gall disease causing microbe Agrobacterium tumefaciens. To facilitate rootstock development, we evaluated recent USDA acquisitions of J. microcarpa germplasm for genetic diversity. A sample of 272 individual genotypes were analyzed, originating from Texas, Oklahoma, Kansas, and New Mexico. Population structure and genetic diversity analyses were carried out with adegenet and Poppr packages in R using multilocus microsatellite genotypes. Within the sample groups, little population structure was found with principal component analysis. Analysis of molecular variance showed little differentiation in population. Hardy-Weinberg and F-statistics test showed the groups to be in Hardy-Weinberg disequilibrium for most loci.

Studying the Relationship Between the Stretching of a Grape’s Skin and Cracking

Student Name: Trevor Zinky
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: Kenneth Shackel
Berry cracking in a grape is a common problem that is unable to be predicted. Grape cracking causes an exposure of the inside of the grape, leading to an increased susceptibility to disease. In this project, existing data consisting of timelapse pictures was studied to determine whether a cause of grape cracking can be predicted based on the stretching of the grape’s skin. Random patterns of spray paint dots were applied to each grape, which were then submerged in water and photographed periodically to capture water-induced absorption and expansion. Each photo was analyzed and positional data was created based on the tracking of each dot, which was then converted into graphical representations. Initial observations revealed that fractures in the dots of paint were observed before cracks in the skin of the grape. Examination of the area change of the dots showed that dots of paint can stretch and increase their area over time without fracturing. Visual observations of dot fracturing also indicated that a crack may form in the skin of the grape before it is visible on the surface in areas without paint dots. These results show that an irreversible state of cracking could occur in the grape far before the point where the crack is visible on the grape’s surface. However, more research is needed to determine if fracturing in the dot occurs at the same time of cracking in the skin of the grape.

Information theory suggests that long introns splice via exon definition in C. elegans

Student Name: Veronica Lee
UC Davis Department: Molecular & Cellular Biology
UC Davis Mentor: Dr. Ian Korf
Pre-mRNA splicing, a process in which introns are removed and exons are ligated, is an essential part of gene expression. Revealing more about the process of splicing in eukaryotic DNA can lead to a greater understanding of and control over gene expression, which yields advancements in medicine, health, and food/agriculture. This research project hopes to answer the question: are long and short introns in eukaryotic DNA spliced in fundamentally different ways? In this project, a bioinformatics approach (Unix operating system, text editor Notepad++, and programming language Perl) was used to analyze k-mer distributions of long and short introns and their flanking exons. Results showed that introns similar in length have similar k-mer distributions, while long and short introns have significantly different k-mer distributions. It was also shown that short-flanked exons have k-mer distributions that are more similar to other short-flanked exons than to long-flanked exons. This may indicate different protein binding sites for spliceosomal snRNPs during the splicing of long and short introns, providing further evidence for intron and exon definition.

Organic soils influence tomato resistance to insect attack

Student Name: Victoria Yang
UC Davis Department: Department of Plant Pathology
UC Davis Mentor: Clare Casteel
Studies have shown that organic farming techniques applied on soil leads to increased health and microbiota diversity. The optimal management of multitrophic interactions between soil microbial communities, crops, insect pests, and pathogens has the potential to increase plant health and agroecosystem productivity, resilience, and sustainability. However, the underlying mechanisms are unclear, and the impact of soil health-building management practices on pest and virus resistance remains to be quantified in economically relevant crops. Experiments using soil from three field locations in Northern California and from the Russell Ranch Century Experiment investigated the effect of soil health and microbial community composition on processing tomato (Solanum lycopersicum) plant growth and nutrition, induction of defense compounds, and attractiveness to insect vectors. These results support the hypothesis that organic practices decrease pest populations. The findings of this experiment pave the way for the next generation of insect control, leading to a cleaner future in which the natural defense systems of plants are utilized, instead of an over-reliance on chemical insecticides.

Using Algae to Investigate Cytokinesis Conservation

Student Name: Yolanda Shen
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: Siobhan M. Brady
Little is known of the details of plant cytokinesis, despite it being one of the fundamental processes in plant biology. Endosidin 7 (ES7), a highly specific probe, has been shown to prevent cell cytokinesis by inhibiting the synthesis of callose in Arabidopsis thaliana. This research utilized Penium margaritaceum, an algae with a cell wall that is structurally and developmentally similar to that of land plants. Immunofluorescent tagging of cell plate-related polymers created an understanding of ES7’s effects on unicellular algae in comparison to complex plants. ES7 was found to affect the size of the isthmus zone, while JIM5-labeled pectin particles were also detected in the isthmus. In this experiment, the phenotypic observations of ES7-treated algae serve as preliminary data for future analysis of the target of ES7. If the target can be discovered, it will indicate the presence of a conserved component of cytokinesis between algae and plants. Ultimately, this research laid a foundation for a comprehensive understanding of the evolutionarily conserved pathways of cytokinesis.

2016 Research Projects

Interactions Between Candidatus liberibacter and Potato Virus Y in Russet Burbank Potatoes

Student Name: Alex Kuang
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Clare Casteel
Liberibacter candidatus (LSO) is a bacteria causing extensive damage to potatoes. Potato Virus Y (PVY) one of the most prominent viruses affecting all potato crops grown in America. The insect vectors for both pathogens are often found on the same harvest at different times, and this study seeks a relationship between LSO and PVY in which one may be facilitating the other. If such a connection is found, treatment for one pathogen may remedy the other as well. Further research may lead to a lesser need for pesticides and an increased crop yield.

Examining Automated Methods of Boxing in EMAN for 3-D Reconstruction

Student Name: Alexander Xu
UC Davis Mentor: Dr. R. Holland Cheng
Selecting individual virus particles in micrographs, or boxing, is done frequently by hand, but the automation of this process would allow for greater efficiency during the process of 3-D reconstruction. Two methods of semi-automated boxing, autoboxing and autoboxing from references, were tested, both of which are two automatic boxing settings found as a part of the program Electron Micrograph Analysis (EMAN), version 1.9. Autoboxing from references appears to pick up slightly less undesirable particles, each of which were reviewed manually after automatic selection. After boxing, selected virus particles can then be used to form a 3-D reconstruction of the virus, whose accuracy is dependent on the quality of particles selected, and help with both virus analysis and virus-like particle (VLP) creation. Particles selected from autoboxing from references, however, appear to form less accurate reconstructions of viruses after 3-D reconstruction and 10 cycles of refinements.

The Synthesis of 2,3,4,5,6-pentafluorobenzene Diazonium Tetrafluoroborate and its Possible Function as a P-type Dopant=

Student Name: Alexandra Li
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Mark Mascal
Recently, organic semiconductors have gained more attention as an alternative to inorganic semiconductors. Organic electronics are lighter, more flexible, and more low-cost than inorganic ones and have many possible applications, including thinner OLEDs (Organic Light Emitting Diodes) and cheaper solar cells. Organic polymers can become more efficient with the help of a more efficient dopant, an agent that allows a semiconductor to conduct current by either adding an isolated electron (n-type) or creating a hole in a sea of electrons (p-type). The goal of the project was to create an electrophilic diazonium salt in order to test whether it will be a more efficient p-type dopant than standard ones. A new procedure to make the diazonium salt was created, which led to successful synthesis of the compound, PFBDT. Critical data of the general chemical properties of PFBDT was provided to chemical engineers, who will perform further analysis of the compound’s role as a dopant.

Measuring and Predicting Syringe Hub Loss

Student Name: Allison Mayes
UC Davis Department: Mouse Biology Project
UC Davis Mentor: Dr. Kristin Grimsrud
The design of a conventional syringe includes a dead space between the needle and barrel of the syringe called the hub. This space collects liquid that once drawn up, cannot be plunged out. As a result, the substance remaining in the hub is inevitably wasted and difficult to account for. Little information is known about the true amount of hub loss that is expected from a given vial of controlled substances. We calculated and measured the hub volume using a variety of different syringes and vial volumes to determine the anticipated substance loss. Additionally, we tested the effects of interpersonal variability, number of syringes used per vial, volume drawn up in each syringe, and other real world conditions. Prior to finding the hub loss per vial, we calculated the hub volume of three different syringe and needle types. The two conventional 1ml syringe types used had means of 0.068ml and 0.066ml of hub loss. The hubless tuberculin syringe had a mean of 0ml of hub loss. After calculating the hub volume of each syringe, we tested expected hub loss from 10ml and 20ml vials. The trend of these tests showed an increase in hub loss as the number of syringes used increased. When 50 syringes were used to draw out half of a 10ml vial, there was a mean of 3.3ml of hub loss. When 10 syringes were used to draw out half of a 10ml vial, there was a mean of 0.5ml of hub loss. Of the recorded hub loss, the range of all datasets ranged from 0.1 to 2.9. These wide ranges display inconsistent amounts of hub loss per vial. The inconsistency may have been due to real world variables such as imprecise starting vial volumes, interpersonal variability, air bubbles, and unstable pressure within vials. The aim of this study was to establish a reasonable range of hub loss to monitor the usage of controlled substances. Based on our data, a reasonable range of hub loss depends on the number of syringes used to draw from a single vial, with the volume per draw not significantly affecting hub loss. As an example, a reasonable amount of hub loss from a vial when 10 syringes are used is 0.1ml-1.07ml. When 50 syringes are used, 1.99ml-4.53ml. The study may also be used to improve laboratory protocols so hub loss can be minimized.

A Study on the Effectiveness of Different Carbon Sources on Anaerobic Soil Disinfestation (ASD) and Characterization of Soil Fungi Associated with ASD

Student Name: Anne Chamberlain
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Daniel Kluepful
Anaerobic soil disinfestation (ASD) is an environmentally sustainable alternative to soil fumigation that has been shown to be effective for controlling a broad range of soil phytopathogens, including the crown gall causing bacterial walnut phytopathogen, Agrobacterium tumefaciens. This research focuses on specific aspects of the ASD process, particularly on evaluating a variety of different agricultural waste products as carbon sources (C-sources), and using culture and molecular-based methods to identify microbes present in ASD treatments.

Developing CAPS Markers for Genotyping Sunflower Mutant Populations

Student Name: Benjamin Caswell
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Stacey Harmer
While a great deal is known about the effects of plant circadian clocks on general biological functions, the molecular mechanisms behind this regulation are somewhat uncertain. Sunflowers with known point mutations were obtained, primers were designed, and restriction enzymes selected for each mutant. The primers were tested on wild-type DNA to determine whether they effectively amplified DNA fragments around the desired point mutations. Since the mutations are in genes associated with circadian clocks, this work will help facilitate experiments in this field in the future.

Exploration of a New Barium Antimony Selenide Compound as a Thermoelectric material

Student Name: Chang Hwan Kwak
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Kirill Kovnir
Study in the field of thermoelectricity, the conversion of heat energy into electrical energy and vice versa, He explored a new barium antimony selenide compound, Ba6Sb7Se16.11, that has been previously determined to have a high potential as a thermoelectric material. Bryan became the pioneer to study the thermal conductivity, resistivity, and Seebeck coefficient of the barium antimony selenide compound. These components are required to calculate the figure of merit, which determines how good a thermoelectric material is. He synthesized the compound via high-temperature solid-state reactions, using a furnace and a Spark Plasma Sintering (SPS) device. With a Rigaku-600 Miniflex powder X-ray diffraction machine, the phase of the compound was determined. Bryan hopes to continue his research by keeping in contact with his mentor for further results.

Understanding Crop Immunity for Increasing Crop Yields

Student Name: Christian Mojica
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Dinesh-Kumar
In order to defend itself from various pathogens, plants use various methods including ROS secretion by RbohD in order to eliminate pathogens. Various signaling cascades and protein interactions can lead to ROS secretion, yet only few have been studied. Some of the unstudied protein interactions are the ones between RLCKs and RbohD, yet here we provide this information through a method known as yeast two hybrid. These findings will highlight the direct roles that RLCKs play in ROS secretion.

Determining fertility in Mus musculus eggs for pronuclear injection should be optimized to prevent wastage

Student Name: Darren Tong
UC Davis Department: Mouse Biology Project
UC Davis Mentor: Josh Wood
The new CRISPR-Cas9 system, when combined with pronuclear injection, is capable of inducing specific mutations in mice. However, this process has a low mutation rate, around 15% [1]. The aim of this study is to determine if alterations to the timing of the pronuclear injections will improve the aforementioned mutation rate. Based on the results, it seems that around 32.8% of eggs thought to be unfertile are actually fertile. Because they are not used, the embryos are disposed of. This leads to a large amount of waste, and more importantly, a large amount of mice needed. These mice must be fed, and taken care of. Using embryos efficiently means that fewer mice will be needed as a lower total of eggs will be necessary.

Distinguishing C. elegans chromosomes through amplicon size polymorphisms

Student Name: David Wang
UC Davis Department: Molecular and Cellular Biology
UC Davis Mentor: Dr. Ian Korf
The worm C. elegans is a transparent, free-living nematode that has shown to be an efficient and effective model organism. Since 65% of human disease genes have homologues on the C. elegans genome, it has great potential to be an invaluable research organism in the health and biomedical sciences. Researchers studying the C. elegans worm, however, have no cost-effective method of distinguishing homologous chromosomes. This becomes a problem when investigating its reproductive processes such as chromosomal loss in aneuploid individuals. In our project, we propose a cost-effective method of distinguishing homologous chromosomes through size differences on specific regions on the genome which are the result of indel polymorphisms. These size differences can be amplified through PCR and distinguished through gel electrophoresis. We analyzed a dataset of all indel polymorphisms referenced to the N2 strain on significant number of C. elegans strains. We were able to find six strain pairs which had size polymorphisms on all six chromosomes. Laboratory work confirmed our method as a viable, cost-effective solution to distinguishing homologous chromosomes. Our research aids in better understanding the reproductive processes of C. elegans worms which may increase our capacity to utilize it as an effective research organism.

The Influence of Surface Charge on Engineered Nanoparticle Delivery and Retention in the Respiratory Tract

Student Name: Delaney Buskard
UC Davis Department: Vet Med
UC Davis Mentor: Dr. Kent Pinkerton
Mesoporous silica nanoparticles (MSNs) are inorganic-based nanocarriers that have porous channels. Their channels can be filled with medicinal compounds and can be utilized to target various disease of the respiratory system. The purpose of the study is to determine what the MSNs do after being deposited in the lungs following a single, acute period of inhalation. Mice were exposed to aerosolized MSNs or filtered air through a nose-only exposure system for 5.5 hours. They were examined 0, 1, 7, and 21 days post exposure and bronchoalveolar lavage was performed. The lung tissue was sectioned and the bronchoalveolar lavage fluid was used to prepare cytospin slides. DAPI or Hematoxylin and Eosin (H&E) were stains that were used to detect the presence of MSNs or inflammatory or structural changes in the respiratory system, respectively. It was discovered that neither positively or negatively charged MSNs do not cause an inflammatory response in the respiratory systems of mice. It was also discovered that the positive MSNs have a better retention rate than the negative ones do. Over time, the negative ones were being released from the macrophages that engulfed them. Overall, MSNs show potential to be a good drug delivery system.

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

Student Name: Eileen Toh
UC Davis Department: Plant Biology
UC Davis 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
UC Davis Department: Psychology
UC Davis 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.

Potential Tyrosine Sulfation Sites in Cadherins

Student Name: Emily Yang
UC Davis Department: NPB
UC Davis 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 role of endogenous auxin in sunflower heliotropism

Student Name: Faith Ajayi
UC Davis Department: Plant Biology
UC Davis 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.

Chlorella sorokiniana Growth in Wastewaters

Student Name: Gregory Martin
UC Davis Department: Chemistry
UC Davis 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.

An Investigation into the Buffering capacity of foodstuffs

Student Name: Henry Harrigan
UC Davis Department: Biological & Agricultural Engineering
UC Davis 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.

Primary and Tertiary Trends of Tyrosine Sulfation

Student Name: Jack Youstra
UC Davis Department: Molecular and Cellular Biology
UC Davis 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.

Comparison of apoE4 and its 61T mutation and lipid-bound stability of apolipoproteins

Student Name: Jacquelin Ho
UC Davis Department: Biochemistry & Molecular Medicine
UC Davis Mentor: Dr. John Voss
Amyloid beta (Aβ) is a protein commonly found in the membranes of neurons. Because of its tendency to misfold and oligomerize, the transport of Aβ out of the brain is crucial to cognitive health. The apolipoprotein E (apoE) is responsible for the transport of Aβ; consequently, its gene is the sole genetic cause of Alzheimer’s that has been widely agreed upon. Of the three alleles E2, E3, and E4, the apoE4 protein is the most closely associated with increased Alzheimer’s risk. ApoE4 differs from ApoE3 at the 112th amino acid; in this study, the positively charged 112 arginine of ApoE4 was mutated into a 112 serine to resemble the uncharged 112 cysteine in ApoE3. Six drugs still under development were obtained, and as a result their manufacturers and details must remain confidential; they will be referred to as drugs A through F. To determine whether the effects of drugs A-F on the ApoE4 mutant were significant, the EPR spectra for the E3-like mutant and the E4 clone were scanned and compared. The greatest difference between the E3-like and E4 spectra was found with the drugs D and F, indicating that the drugs may have changed the protein’s structure. To further observe the behavior of apolipoproteins, the stability of lipid-bound nanodiscs of apolipoprotein A with diameters of 7.8 nm, 8.4 nm, and 9.6 nm were observed through comparison of samples in SDS-PAGE gels, EPR, and Coomassie Assays in the second phase of this project. In general, the SDS-PAGE gels showed that the lipid-bound samples retained shape better than their lipid-free counterparts.

Confirming Arabidopsis Mutants Hypersensitive to ES7

Student Name: John Almazan
UC Davis Department: Plant Science
UC Davis Mentor: Dr. Georgia Drakakaki
Cytokinesis is an essential developmental process for plants. Currently, scientists have limited knowledge on the processes that occur within cytokinesis. John Almazan is researching the effects of Endosidin 7, a chemical that inhibits the cytokinesis phase of plant cell replication, on Arabidopsis Thaliana mutant seedlings. The primary goal of his research is to confirm whether the mutant seedlings are hypersensitive to Endosidin 7. Studying ES7 and its hypersensitivity effects on the mutant seedlings will confirm that there are additional proteins involved in callose deposition at the plant cell plate. Callose deposition is a significant process for the later stages of cytokinesis when a polysaccharide called callose is deposited at the cell plate, providing mechanical support to the membrane network before the plant cell splits into two daughter cells. Using a software called ImageJ and confocal microscopy, John will monitor the seedlings’ growth and observe ES7’s effects on the plant cells. This research can potentially lead to the identification of the specific proteins that assist the callose deposition process.   

“Using a Dairy Relevant Bacterial Mock Community to Compare Quantitative PCR, High-Throughput Sequencing, and Culture-Based Cell Enumeration Methods ”

Student Name: Kane Tian
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Maria Marco
A study that will contribute toward the improvement of quantification methods for bacterial profiling. This study is comparing high-throughput sequencing, plate counting, and Quantitative PCR using a bacterial community with dairy-associated bacterial species in order to assess whether current methods produce consistent and similar results. Using these three methods, this mock community is also testing the biases introduced by PCR and DNA extraction kits.

Changes in M1 and M2 Macrophage Phenotype Numbers following Long-term Smoking Cessation in Spontaneously Hypertensive Rats

Student Name: Katie Li
UC Davis Department: Vet Med
UC Davis Mentor: Dr. Kent Pinkerton
Smoking leads to increased susceptibility to heart attack, stroke, lung cancer, and other respiratory complications, such as chronic obstructive pulmonary disease (COPD), emphysema, bronchitis and persistent cough. COPD is the third leading cause of death in the world today (1). Previous findings on smoker rats show increased epithelial volume, mucin content, and also consistent inflammation in the form of high numbers of macrophages. The purpose of this project was to determine whether macrophage numbers in rat tissues after a period of smoking cessation could be used as a unbiased marker of former smoking. In addition, this study was designed to determine the relative proportion of M1 or M2 phenotype macrophages (markers of active inflammation or lung repair, respectively) in the lungs of old rats as well as former smoker rats as a possible marker of continued lung inflammation or repair. The lungs of 12 male spontaneously hypertensive (SH) rats were examined using histological methods. There were significantly more M1 macrophages found in the tobacco smoke (TS) group compared to the filtered air (FA) group. In the TS group, large numbers of foamy macrophages were observed in the subpleural and terminal bronchial regions. Meanwhile in the FA group, the macrophages found were more dense and scattered throughout the tissue. Findings suggest certain changes in rat lungs due to tobacco smoke are still present after long-term cessation- some changes are irreversible and result in chronic damage. The cellular changes that occur in the cell due to TS exposure are important to consider when designing treatments for those who have stopped smoking.

Gene Expression Differences Between Fayoumi and Leghorn Chicken and their Impact on NDV Infection Resistance.

Student Name: Kevin Yang
UC Davis Department: Animal Science
UC Davis Mentor: Dr. Huaijun Zhou
NDV, Newcastle Disease Virus, is a negative sense single RNA strand virus that infects many wild Avian species. While NDV poses no major threat to humans directly, it causes major losses in the poultry industry and disrupts the poultry food supply. It has been shown that differences in immune response has associated genetic factors that can affect susceptibility or resistance. Determining what those genetic factors are in chicken response to NDV can greatly increase our knowledge of host-pathogen interaction, but also improve genetic selection for resistant birds. And so, the goal of this project was to determine difference in gene expression between two distinct chicken breeds, Fayoumi and Leghorn. Past research has demonstrated that Fayoumi are more resistant to viral infections while Leghorn are more susceptible (Wang, 2014). Chickens were hatched and subjected to heat treatment and viral infection. Samples were collected at 3 different time points: 2 dpi, 6 dpi, and 10 dpi and mRNA was extracted. cDNA was generated and analyzed using qPCR. Analysis of the data demonstrates that Fayoumi gene expression for TLR3, TLR7, IRF7, CD8A in spleen and TLR3, PRKCD, and CD8A in lung is greater when compared to Leghorn. The difference in expression of these genes between these two lines are possibly associated with why Fayoumi has a greater resistance to NDV infection, however further studies must be conducted to show a direct connection between this difference in gene expression and the genetic mechanism used to cause the difference in resistance between Fayoumi and Leghorn.

Recommended Methods Such As Folding, Recutting, and Bagging Techniques on Leaves to Measure Stem Water Potential in Cherries, Walnuts, Pistachios, and Grapes

Student Name: Lisa Xinying Wu
UC Davis Mentor: Dr. Kenneth Shackel
According to the soil-plant-atmosphere-continuum (SPAC) model, water from soil is under tension within a plant, which allows for water to be transported from the root to the leaf of a plant. Water potential is a way of quantifying the tension in the plant, which directly correlates to its water stress. The Scholander pressure chamber was used to test different methods of finding stem water potential in plants and its impact on the measurement taken. This research was done on adjacent leaves, testing for the difference in stem water potential in leaves that were folded and unfolded, and between those cut directly from a branch by its petiole and those with petioles recut after being pulled off a branch. Additionally, research was done on pistachio trees by comparing branches versus individual leaflets, as there is a problem with latex being mistaken for water. Adjacent leaves were placed into light-proof bags and placed into a pressure chamber, where pressure was slowly added until water visibly left the xylem of the leaf. It was found that folding and recutting generally did not have an impact on the measured stem water potential, which will allow farmers to adapt these methods to their convenience instead of worrying about whether or not they need to fold their leaves or cut a leaf only once to fit into the pressure chambers. With pistachio trees, bagging an entire branch produces very close results to bagging just a terminal leaflet, which will allow agriculturalists to pick which method to use that would produce the clearest measure of water potential. In the future, this research can possibly be used to determine a universal and most accurate method of finding stem water potential.

The Effects of Indomethacin on Cardiac Protein Degradation

Student Name: Logan Samuel
UC Davis Mentor: Dr. Aldrin Gomes
NSAIDs are the most commonly used drugs around the world. They are linked to many side effects such as heart attack and stroke. More specifically, NSAIDs affect the proteasome, a multimeric enzyme that degrades damaged and old protein. Without proteasomes, the body would not be able to function. Indomethacin is a common NSAID used to treat pain, inflammation, arthritis, and patent ductus arteriosis. It has been shown to cause gastrointestinal problems, however, the effects of the drug on proteasomes has not been studied. Due to the high abundance of proteasome activity in the heart, eight mice were injected with indomethacin to investigate the effects of the drug on proteasome activity in the heart. Using western blots, biological assays, and data analysis on homogenized heart samples, it was determined that the control mice and indomethacin injected mice had similar proteasome activity levels. However, trends suggest that proteasomes were being slightly effected by the drug.

Development of UBQ10pro tRFP-WIP1 plasmid for Plant Cell Immunity Studies.

Student Name: Maken Horton
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Dinesh Kumar
Plant innate immunology introduces a new plasmid containing a promoter, UBQ10pro, which does not react with 35Spro. Previously, two 35Spro promoters on different plasmids inside the plant arabidopsis co-silenced each other and prevented fluorescent proteins from being produced. This fluorescent nucleic membrane marker protein allows her to see how chloroplasts and stromule extensions interact with the nucleus in the immune responses. Majken transferred the gene tRFP-WIP1 from a vector containing 35Spro to a vector with UBQ10pro. This allows the cell to produce both proteins in large quantities that allow the organelles to be studied. In the future, this research and plasmid will help farmers and agricultural scientist protect and understand plant health leading to increased crop yield and quality.

Analyzing the Role of the Protein Kinase, STY46, in Regulating the Sugar Starvation Response in Arabidopsis thaliana

Student Name: Marlene Goetz
UC Davis Mentor: Dr. Diane Beckles
When plants undergo environmental stresses, they experience sugar starvation (SS), causing a shift in carbon fluxes and signal transduction cascades to alter the plant’s metabolism and growth processes. This series of events, called the sugar starvation response (SSR), is crucial in determining plants’ survival under diminished carbon levels. It is speculated that the protein kinase, STY46, is a potential master regulator of the sugar starvation response. Compared to wild type plants, Arabidopsis with genetically altered levels of STY46 are expected to have differences in carbon use and plant growth. To meet this objective, four transgenic Arabidopsis thaliana lines (knockout, complementation, inducible overexpression and constitutive overexpression) will be generated to examine carbon partitioning and allocation under sugar starvation. The specific aim of this paper was to generate construct for a STY46 complementation line and discuss future research to be performed using the constructs. Positive results were obtained in preliminary gel electrophoresis, since restriction enzyme digest of the transformed plasmid construct appeared accurate. However, when the STY46 gene was sequenced, the results were inconclusive due to the inability of the primers to bind onto the plasmid. This most likely occurred due to either incorrect primer design or untransformed plasmids sent to sequencing.

Biomarkers to Signify Early Detection of a Spontaneous Mouse Mutation In the Palmitoyl Transferase Zdhhc13 Gene

Student Name: Matthew Xie
UC Davis Department: VM: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giulivi
The Zdhhc13 gene in mice is partly responsible for the encoding of palmitoyl acyltransferase (PAT) enzymes in mice. A naturally occurring recessive mutation in the mice causes a nonsense base substitution, leading to a truncated form of the Zdhhc13 protein. Mutant mice experienced an increased susceptibility to tumor multiplicity and malignant progression of papillomas after chemically induced skin carcinogenesis. Our goal in this research is to identify potential biomarkers that signify early detection of mutation in the Zdhhc13 gene. This is mainly done through MetaboAnalyst, a metabolite analysis program used to identify possible biomarkers, achieve group separation, and analyze pathways of metabolites to see their role in a functional gene. After the metabolite concentrations from three groups of mice are normalized, statistical procedures are conducted, and significant compounds are identified. Our graphs showed fair separation between homozygous WT, heterozygous, and homozygous mutant mice, with heterozygous mice showing characteristics closer to homozygous mutant mice than homozygous WT mice. Significant biomarkers identified include cysteine, taurine, L-pyroglutamic acid, and L-glutamic acid, which all have a direct role or a connection to processes in the skin.

Kinetic Analysis of Three Glycoside Hydrolase Mutants to Discover Associations Between Michaelis-Menten Constants and Protein Structure

Student Name: Michael Tan
UC Davis Department: Med: Biochemistry & Molecular Medicine
UC Davis Mentor: Dr. Justin Siegel
The need to process and analyze novel enzymes is exponentially growing; meanwhile the rate to do so has not kept up. Therefore, computational methods are necessary to continue to explore an ever increasing amount of new enzymes. This project intends to enhance computational methods through the collection of experimental data from mutant proteins to further determine how protein structure affects enzyme efficiency. To do so, the Michaelis-Menten kinetic constants, Kcat and KM values, will be gathered on three different glycoside hydrolase mutants; subsequently, the data will be contributed to an algorithm that will better predictions of kinetic constants based on protein structure through computational modeling.

“Understanding the molecular basis of Postharvest Chilling Injury in tomato fruit: Generation of RD29A::CBF1 transgenic construct ”

Student Name: Michelle Jiang
UC Davis Mentor: Dr. Diane Beckles
For decades, consumers have been purchasing refrigerated produce and storing it in refrigerators at home. Although this approach helps to preserve the produce for a certain period of time after harvest, many fruits and vegetables are damaged by the cold in a disorder called Postharvest Chilling Injury (PCI). Although PCI has been extensively studies, the molecular basis of its early events still remain poorly understood. The general goal of this project was to study those processes in tomatoes. The C-binding factor 1, or CBF1 gene, regulates cold tolerance, and the objective is to introduce CBF1 from a cold tolerant species, Solanum habrochaites, into the cold-sensitive cultivated tomato, Solanum lycopersicum. The aim of this work was to synthesize RD29A::CBF1 gene constructs which will be transformed into S. lycopersicum to assess cold tolerance in fruit after harvest. The two constructs created were RD29A::ShCBF1 using CBF1 from S. habrochaites and RD29A::SlCBF1 using CBF1 from S. lycopersicum. RD29A, ShCBF1, and SlCBF1 were amplified using Assembly Polymerase Chain Reaction (PCR). After purification, RD29A::ShCBF1 and RD29A::SlCBF1 constructs were spliced into pCAMBIA1300 vector plasmids and transformed into competent E. coli cells which copied the plasmids after multiple rounds of replication. The plasmids were extracted and diagnostic restriction digest was conducted with the EcoRI enzyme which yielded positives in colony #1 of RD29A::ShCBF1 and colony #21 of RD29A::SlCBF1. These were then sent for sequencing. This portion of the project culminated without the corroboration of the identities of the two engineered gene constructs due to time constraints. Even so, this brings research one step closer to reducing PCI in produce and decreasing the overall losses in agriculture.

Computational Design of Single Point Mutations on the Beta-Glucosidase B (BglB) enzyme

Student Name: Michelle Zhou
UC Davis Department: Med: Biochemistry & Molecular Medicine
UC Davis Mentor: Dr. Justin Siegel
Enzymes play a fundamental role in catalytic functions integral to many biological processes. The use of computational design to engineer the structure and predict enzymatic function hold the potential to enhance catalytic efficiency. Here, 3-D protein-folding simulators were used to structurally mutate the BglB enzyme’s primary structure for three mutants. The computationally designed mutants, then produced and purified, were analyzed according to Michaelis-Menten kinetics that provided further insight on the mutants’ catalytic efficiency (Kcat/Km). The compiled data will be important for developing and refining computational algorithms that can successfully predict correlations between structure and function.

Observing the Different Stress Tolerances of Lactobacillus plantarum

Student Name: Nathan Lee
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Maria Marco
In today’s fermented foods industry, a single harmful type of bacteria can destroy a whole crop yield. However, the presence of lactic acid bacteria can kill these detrimental types of bacteria because of its acidic nature. Nathan’s experiment focuses on testing the different stressful environments LAB can endure so as to give more concrete data on the environments in which LAB can grow and be of service to farmers and agricultural companies.

The Effects of Restrictive Cardiomyopathy R145W Mutation on Signaling Pathways and Proteasome Function

Student Name: Rebecca Chang
UC Davis Mentor: Dr. Aldrin Gomes
The leading cause of sudden cardiac death (SCD) in young adults is familial hypertrophic cardiomyopathy (FHC), but the incidence of SCD in restrictive cardiomyopathy is even higher. Restrictive cardiomyopathy is a heart condition where the ventricle walls do not thicken but become stiff and cannot relax. Although restrictive cardiomyopathy is the least common of the cardiomyopathies, it has the highest mortality rate. However, how restrictive cardiomyopathy affects the heart is not well understood. The goal of this study was to determine the effects of the restrictive cardiomyopathy R145W mutation on signaling pathways and proteasome function in the heart. In the experiment, hearts with the mutation as well as control wild type hearts were homogenized in urea, centrifuged, digested with trypsin, and tagged with TMT isobaric mass tags for mass spectrometry. Statistical analysis showed that six proteins from the Parkinson’s pathway were present in the R145W hearts in significantly lower levels than in the wild type hearts. These proteins were proteasome subunits and heat shock proteins and were responsible for protein degradation and stress response in the cell. The lower amounts of these proteins suggests that the mutated hearts were likely subjected to higher amounts of oxidative stress due to the lack of response from the heat shock proteins and lack of proteasome activity that would normally help to prevent stress. With this research suggesting that R145W hearts are likely to experience more stress, future tests can be done to detect levels of oxidative stress, reactive oxidant species, ER stress related proteins, and determine the antioxidant status of animals.

Comparing the Targeting of Toc75 and OEP80, two Transmembrane Chloroplast Proteins, Through the Construction and Expression of a Chimeric Gene Involving Portions of Toc75 and OEP80.

Student Name: Renee Radusewicz
UC Davis Department: Plant Science
UC Davis Mentor: Dr. Kentaro Inoue
According to the endosymbiotic theory, chloroplasts descend from a cyanobacterial ancestor that was engulfed by a eukaryotic cell. Within the chloroplast’s outer membrane are paralogous transmembrane proteins known as Toc75 and OEP80. The two proteins evolved from a cyanobacterial protein, which inserted proteins into the outer membrane of the chloroplast’s cyanobacterial ancestor. Toc75 has evolved to function in protein import into the endosymbiont, which was required for the evolution of chloroplasts. The molecular function of OEP80 remains unknown, but is hypothesized to retain the function of its cyanobacterial ancestor. We are interested in how Toc75 evolved its novel function. One aspect of Toc75 and OEP80 that may contribute to their different functions is how they are targeted to the outer membrane of the chloroplast. Much is known about the targeting mechanism of Toc75, but not that of OEP80. Preliminary results of the Inoue lab indicate that Toc75 and OEP80 have distinct targeting mechanisms. To compare the targeting mechanism of OEP80 and Toc75, polymerase chain reactions (PCR) and gel electrophoresis will be utilized to construct a gene that incorporates portions of Toc75 and OEP80. The section in Toc75 that is responsible for targeting will replace the corresponding portion of OEP80. After Gateway cloning, plasmid isolation, transformation of agrobacteria, and infiltration of the bacteria into Nicotiana benthamiana, this transgene will be expressed in plants. The chloroplasts of the mutant plant cells will then be isolated and undergo SDS-PAGE and a Western blot, enabling this project to verify where the protein produced by the new gene is located within the chloroplast. This will determine if difference in targeting mechanisms between the two transport proteins contributed to distinct functions, hinting at how chloroplasts evolved through endosymbiosis.

Computational investigation of peculiarly-conserved elements between the C. elegans and C. briggsae genomes

Student Name: Richard Yu
UC Davis Department: MCB
UC Davis Mentor: Dr. Ian Korf
We define peculiarly-conserved elements (PCEs) as regions of DNA at least 100nt long and conserved at unusually high levels between multiple organisms. In the genomes of the C. elegans and C. briggsae nematodes, we found a total of 385 PCEs. We computationally investigated and analyzed these PCEs and found that most of them are protein-coding, lie on genes, lie on exons or intron-exon junctions, code for mRNA, and have richer G+C content than DNA of typical conservation. All intergenic PCEs were found to lie on the X chromosome. These unique properties may facilitate identification of unusually high DNA conservation in nematodes. Furthermore, these findings introduce new areas of study in nematode, organismal, and evolutionary biology.

Potential of Tyrosine Sulfation in Voltage-Gated Sodium Channels

Student Name: Sabrina Liu
UC Davis Mentor: Dr. Grace Rosenquist
Tyrosine sulfation is known to be a key process in many organisms but the lack of an efficient way to figure out which tyrosines are sulfated means that the sites need to be predicted. Voltage-gated sodium channels have many potential tyrosine sulfation sites, especially GRNPNYGYTSF, MAMEHYPMTDH, and YEESLYMYLYF, that have evidence based on homology, mutagenesis, and toxin binding that support their sulfation. Their connection to various muscle and nervous system conditions can help the development of new drugs. However, more research will be needed to confirm sulfation in these sites.

Canopy and leaf temperature, stomatal conductance, and stem water potential in greenhouse tomato plants sensitive to water stress

Student Name: Sarah Hancock
UC Davis Mentor: Dr. Kenneth Shackel
Examines how greenhouse tomato plants respond to water stress by measuring different physiological responses of the plants, including leaf and canopy temperature, evapotranspiration, stomatal conductance, and water potential. The long term goal of this research is the development of a sensor that manages irrigation for field crops based on their water needs. While there currently exists many methods for gauging plant water stress, none of them are particularly accessible, especially in the context of the large-scale agriculture of modern society. This experiment is designed to affirm the link between canopy temperature and water stress by comparing canopy temperature trends to trends measured with conventional techniques, so that canopy temperature can be used to detect water stress across a large agricultural area.

Modifications to Brush Border Enzyme Glycosylation Decreases Enzymatic Activity

Student Name: Sithara Menon
UC Davis Department: Vet Med
UC Davis Mentor: Dr. Helen Raybould
Glycosylation is an important modification to cell surface proteins. The brush border of intestinal epithelial cells (IECs) contains many glycoproteins that are key to intestinal function. This study tested how changes to glycosylation affects the function of cell surface glycoproteins in IECs. Specifically, how removing N-glycans with exoglycosidases, such as those secreted by intestinal bacteria, affects the function of brush border enzymes, such as Intestinal Alkaline Phosphatase and Dipeptidyl Peptidase IV. This was tested in Caco-2 cells, a human cell line derived from colon adenocarcinomas that is used as a model for intestinal function. Caco-2 cells were cultured for 12 days, and their expression of IAP was tracked throughout the differentiation process. Once they were fully differentiated, the cells were then treated with glycosidases, and the enzymatic activity of IAP and DPP IV was measured. The results showed that changing the glycosylation caused enzymatic activity to decrease. Removing all the N-glycans with the glycosidase PNgase F decreased IAP activity to about 40 %, confirming that glycans are key to the function of the enzyme. Of the individual monosaccharides, removing mannose had the greatest effect, and removing sialic acid and fucose also affected the enzymatic activity. However, removing individual sugars did not cause any large decreases in activity, especially compared to removing the entire glycan.

A Mechanistic Insight on Chemical Enhancement of Gold Nanoparticles through Electron Paramagnetic Resonance

Student Name: Sonny Huynh
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Jennifer Lien
Nanoparticles are capable of enhancing reactions under X-ray irradiation. In order to utilize this enhancement and apply it to other reactions, further knowledge of the enhancement mechanism is required. The experiment was performed in two parts, the first involving the quantification of chemical enhancement using a fluorometer to test the fluorescence of the hydroxylation of coumarin carboxylic acid in the presence of various concentrations of gold nanoparticles. The second part of the experiment involved understanding the hydroxyl radical, reactive oxygen species (ROS), pathway of the reaction using electron paramagnetic resonance (EPR). It was found that the surface of gold nanoparticles catalytically facilitates conversion 3-OH radical adduct to 7-OH-CCA in the presence of oxygen. Also the amount of hydroxyl radicals found in solutions with varying concentrations of gold nanoparticles was constant, implying that ROS generation is not a part of the catalytic process.

Detecting Mutations and Heteroplasmy in Mitochondrial DNA with Surveyor Endonuclease.

Student Name: Sung Bin (Sean) Roh
UC Davis Department: VM: Molecular Biosciences
UC Davis Mentor: Dr. Cecilia Giuvili
Due to the susceptibility of mitochondrial DNA to insertions, deletions, and point mutations and the existence of multiple copies of mitochondrial DNA in each organelle, a phenomenon called heteroplasmy arises. High levels of heteroplasmy are known to be a factor in the development of mitochondrial diseases. Sung Bin “Sean” is optimizing a procedure to detect low levels of heteroplasmy. Applications of this research include future studies into heteroplasmy as well as diagnosis of risk of mitochondrial diseases.

The Effect of Computationally Designed Point Mutations on Structure and Kinetic Characteristics of Glycosidase Hydrolase Enzymes

Student Name: Willy Fan
UC Davis Department: Med: Biochemistry & Molecular Medicine
UC Davis Mentor: Dr. Justin Siegel
The importance of predicting an enzyme’s function and rate of function based on its structure. Due to the inaccuracy of current predictive algorithms, there is a need for large and comprehensive databases from which more accurate predictions can be made. Three mutants of the beta glucosidase B enzyme were tested for expression and then kinetically characterized through Michaelis-Menten kinetics. The ultimate goal of this project is to be able accurately mutate an enzyme for a specific purpose (i.e increased or slowed activity) and even create novel enzymes from scratch with the intended chemical activity.

Salinity stress, a key factor affecting almond tree stem water potential

Student Name: Zhiren (George) Ye
UC Davis Department: Plant Science
UC Davis Mentor: Dr. Patrick Brown
Almond trees are particularly sensitive to salt; their perennial nature allows the damage to the tree to cumulate over time. An estimated 10% of almond acreage is salt impacted and an additional 30% is at immediate risk. Research was conducted to investigate how NaCl applications affect the plant water status of almond trees. It was hypothesized that addition of salts would decrease stem water potential over time. The experiment consisted of two trees: one under balanced nutritional conditions and the other under salinity stress. Five leaves were collected from each tree around noon daily and stem water potential of each leaf is measured using a pressure chamber. Data collected showed that there was no significant decrease of stem water potential for the first 10 days. However, stem water potential values after 10 days showed a decreasing trend. Results were consistent with the hypothesis after 10 days of NaCl applications. Addition of salts indeed decreases stem water potential over time. Different salt concentration may be applied to evaluate the change in almond tree growth and yield in the future. Ion toxicity of almond trees may also be investigated by comparing the effect of polyethylene glycol and sodium chloride.

2015 Research Projects

Structure-Seq Influenced RNA Secondary Structure Prediction

Student Name: Aditya Bollam
UC Davis Department: Biomedical Engineering
UC Davis Mentor: Sharon Aviran
Current life on earth is believed to have descended from self-replicating RNA molecules, and evidence of its deep history is apparent in its diversity of function. Discerning the structure of RNAs will help inform our understanding of RNA function as well as develop future tools in medicine. The most basic structural information lies in its secondary structure, the first level of structural organization within an RNA molecule. Techniques such as crystallography, comparative analysis, and computational algorithms have been developed to predict secondary structure of RNA, though performance becomes hindered when analyzing longer RNAs. In order to find a more efficient method of predicting the structure of long RNAs, we combine data gathered from DMS probing experiments (Structure-Seq) and input subsections of the RNA into the RNAStructure prediction algorithm. By dividing the structure into smaller sections, we find that predictive capabilities can be vastly improved, though inclusion of DMS probing data has varying effects in improving prediction accuracy. We test this subdividing of RNA of prediction in both a user-directed and naive manner in the 18S RNA in Arabidopsis thaliana. Overall, these improvements in computation and experimentation suggest a more efficient and accurate strategy to predict RNA secondary structure in long RNAs.

Biochemical Characterization of MAPK6 Enzyme in Regards to Plant Innate Immunity Response Pathways

Student Name: Alex D. Doan
UC Davis Department: Department of Plant Biology and The Genome Center
UC Davis Mentor: S.P Dinesh-Kumar
Plants and animals have evolved and developed different methods of immunity to defend themselves against various attacking pathogens. One technique is by recognizing such pathogens through recognition receptor proteins located on the extracellular membrane and then signaling a response pathway. In this lab, the MAPK6 enzyme of the MAP/ERK pathway in Arabidopsis thaliana was studied and biochemically characterized. The gene for the protein was cloned, expressed in bacteria and the protein then purified through extraction. By running an analytical gel exclusion chromatography, MAPK6 was then determined to be monomeric structurally. Also, through an in vitro reaction with ATP, the protein was determined to be an active kinase that utilizes phosphorylation to transmit immune responses within the cascading pathway.

A Plant-based Evaluation of Landscape Irrigation Efficiency

Student Name: Brian Glucksman
UC Davis Department: Department of Pomology
UC Davis Mentor: Ken Schackel and Maya Lopez-Ishikawa
To accommodate a rapidly drier climate, Californians need to cut water from landscaping. The goal of this study is to evaluate the effectiveness of adding extra water to young frontier elms (Ulmus “Frontier), using hydration bags on young valley oaks, and irrigating young valley oaks with MP rotators and hydration bags. The plant-based measurement of water stress, midday stem water potential (MSWP), was collected in the early afternoon through the process of pressure bombing. This study found that adding extra water did not reduce the water stress of frontier elms and had no prolonged effect, that using hydration bags was three times as water efficient as using MP Rotators at watering the young valley oaks, and that removing hydration bags increased water stress in young valley oaks.

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

Student Name: Emily Dickinson
UC Davis Department: Plant Biology
UC Davis 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

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

Student Name: Haishan Gao
UC Davis Department: Department of Plant Sciences
UC Davis 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.

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

Student Name: Jacob Eisner
UC Davis Department: Molecular Biosciences: Vet Med
UC Davis 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.

Quick Screening of Chemoreceptor Functions

Student Name: Jimmy Kim
UC Davis Department: Department of Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Rebecca Parales and Watumesa Tan
Chemotaxis allows some organisms like Pseudomonas bacteria to move in response to chemical stimuli. Methyl-accepting chemotaxis proteins (MCPs) are membrane-bound chemoreceptors that facilitate this process. Understanding MCPs could lead to potential application of chemotaxis in fields like bioremediation, where it could improve efficiency since bacteria could not only break down pollutants but seek them out as well. In order to characterize the MCPs of species like Pseudomonas putida F1, hybrid sensor proteins comprised of the sensory domain of bacterial MCPs and the signaling domain of a 2-component regulator were used in the optimization of a screening method. By using a filter paper disk to diffuse potential attractant/repellants in a plate, bacteria with these hybrid sensor proteins will show an inhibition of growth if they sense the compound. This screening method was optimized by testing various concentrations and volumes of compounds as well as plate media content. This method will allow for quick screening of MCP functions in P. putida F1 and other bacteria.

Buffering Capacity of Foods and its Effects on Digestion

Student Name: Jonathan Liu
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Bornhorst, Dr. Ferrua, and Dr. Singh
The buffering capacity of foods plays a pivotal role in food breakdown during gastric digestion. The ability of foods to resist changes in pH alters the acidity of the stomach, influencing acid secretion, enzyme function, and chyme viscosity[SO1] . All of these properties directly influence the stomach’s ability to break down foods. Therefore, a comprehensive and replicable method to determine the buffering capacity of foods would prove beneficial for helping to predict and compare digestive properties [SO2] of different foods. We have developed a preliminary methodology for determining the buffering capacities of certain categories and subcategories of undigested foods, and used these to determine buffering properties of certain semisolid foods before digestion.

Cocrystallization of C60 and C70 Mixture with Sulfur

Student Name: Karen C. Guo
UC Davis Department: Department of Chemistry
UC Davis Mentor: Alan L. Balch
Research and application of fullerenes have been limited by the work and cost of separation and purification. This paper studies sulfur as a separation agent with C60 and C70 solutions. Crystal tubes were made of sulfur and 1:1 molar ratio mix of C60 and C70. Resulting crystals were tested with HPLC and single crystal X-Ray diffraction. It was found that sulfur cocrystallizes with both C60 and C70, but the two fullerenes crystallize separately. The results of this experiment can be used to develop new separation methods for fullerenes and adds to existing knowledge of sulfur as a cocrystallizing agent with fullerenes.

Determining the Role of OEP80tr in Plant Germination and Growth

Student Name: Katie Chung
UC Davis Department: Plant Biology
UC Davis Mentor: Kentaro Inoue and Philip Day
The outer membrane protein 85 (Omp85) family proteins found in the outer envelope of chloroplasts are remnants of ancestral cyanobacterium protein since their endosymbiosis by eukaryotes.  Flowering plants in particular have an additional beta barrel protein in the outer membrane of their chloroplasts, OEP80tr, whose exact function is unknown.  This study attempts to determine the function of OEP80tr by investigating the effects of null expression mutations of the gene.  Through analysis of germination and plant growth (in roots, hypochotyl, and leaves), this study compares the phenotypes of wild type plants with the functioning gene to plants without the gene.  The resulting observations could then be used to determine the role in development of the OEP80tr protein.

Reconciling Cost Efficiency and Biodiversity by Native Seed Dispersal

Student Name: Lauren Lee
UC Davis Department: Plant Sciences
UC Davis Mentor: Aubrianne Zamora and Emilio Laca
Restoration of native grasslands in California is expensive, mostly due to the high cost of seeds. Although restoration can increase biodiversity and ecosystem services, ecosystem services do not generate revenue. In order to reconcile economics and the need for biodiversity in California annual grasslands, this study focuses on discovering how a grass species’ status as an annual or perennial plant affects biodiversity and relates to cost. We studied several restoration methods based on strip seeding, where strips of various widths were alternatively seeded or left unseeded. We hypothesized that over time seeds from the seeded strips would establish in the unseeded strips, a cost-efficient means of restoration. Requiring $825 and $1250 respectively, the 33% seeded and 50% seeded (wide) treatment demonstrated potential as cost efficient means of habitat restoration. The 33% treatment resulted in approximately 12.5 species at the plot level for species richness, while the 50% wide treatment yielded 12.4 species. Botanical composition of seeded and unseeded strips indicated that strip seeding is a successful low-cost method for Elymus glaucus, but other native perennial grasses failed to establish in unseeded strips.

Understanding the Structural and Molecular Basis of Postharvest Chilling Injury in Tomato Fruit (Solanum lycopersicum L.)

Student Name: Leona Lee
UC Davis Department: Plant Science and Food Science
UC Davis Mentor: Diane M Beckles and Michael McCarthy
Postharvest Chilling Injury (PCI) is a devastating disorder that leads to loss of produce. In this study two approaches were taken to better understand the development of PCI in tomato (Solanum lycopersicum L.) a species susceptible to PCI. First, the spatio-temporal development of PCI symptoms in developing fruit was assessed using Magnetic Resonance Imaging (MRI). Second, the CBF1 gene from Arabidopsis thaliana was cloned so that the gene may be engineered into tomato fruit to improve the tomato fruit response to chilling. MRI data indicates that chilling injury affects each tomato tissue type (the pericarp, the locular tissue and the columella) differently with greater effects seen in green fruit due to their continuation of ripening and various metabolic processes. A 780 bp fragment corresponding to the coding sequence (CDS) of CBF1 was amplified from Arabidopsis genomic DNA and attempts to sub-clone into pGEM-T Easy Vector® are underway.

Optimization of Homogenization Protocol for Analysis of TPPII in Heart Samples

Student Name: Meera B. Ganesh
UC Davis Department: Department of Neurobiology, Physiology and Behavior
UC Davis Mentor: Dr. Aldrin V. Gomes
The primary function of proteasomes is to degrade mis-folded and unwanted proteins. Tripeptidyl peptidase II (TPPII) is a newly discovered protease that works downstream of the ubiquitin-proteasome system. It is required in eukaryotic cells for cleaving of larger protein degradation products. However, little is known about its function in other cellular processes. TPPII’s responses to stress and DNA damage could be areas of research for cancer therapy, if TPPII can be studied better.  Homogenization is a process used to break down cells for subsequent analysis or purification of proteins. Accurate analysis of protein expression and protease activity in the cell can be studied by good homogenization procedures and sample preparation. This study investigated the effect of various homogenization and assay buffers to determine the optimal buffer for homogenization and activity assays of cardiac TPPII. The results demonstrated that a homogenization buffer containing polyvinylpyrrolidone and glycerol produced more desirable results compared to buffers currently used for TPPII analysis

Structural and kinetic analysis of hydrolase mutants and subsequent impact on predicting functionality with Michaelis-Menten mechanics

Student Name: Michael Hsiu
UC Davis Department: Department of Chemistry
UC Davis Mentor: Justin Siegel and Ryan Caster
Understanding about enzymes has grown due to the use of computational algorithms in predicting the correlation between structure and function. These algorithms have had critical roles in the redesign and reengineering of native enzymes to enhance catalytic behavior. In this paper, front-end programs were used to model, interact with, and redesign a glycoside hydrolase enzyme. The structural model was coupled with Michaelis-Menten kinetics to yield the Kcat and Km kinetic constants for three mutants. The compiled dataset will be essential to tracking patterns and trends across enzyme families. It may also be useful in future efforts to redesign enzymes using predictive methods.

The Effect of Stem Heliotropism on Sunflower Growth and Productivity

Student Name: Nicole Infantino
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Stacey L. Harmer and Dr. Hagop Atamian
Heliotropism, also known as solar-tracking, is the diurnal motion of plant leaves and flowers in response to the direction of the sun.  Many studies of solar-tracking plants indicate that heliotropism is correlated with higher light absorption, photosynthetic efficiency, and crop productivity.  Sunflowers undergo this process by orienting their leaves, as well as their stem toward the sun throughout the day.  The flowers continue to move at night in order to readjust their direction in preparation of the sun’s rise in the east the next day.  This paper reports two experimental tests of the hypothesis that disrupting the normal solar cycle of the sunflower will slow the rate at which the plant develops and decrease yield.  In the first experiment, 83 HA412 inbred line sunflowers were planted in a field.  Half of the plants were treated by being tethered to bamboo stick in order to restrain heliotropic stem movement.  In the second experiment, 28 HA412 inbred line sunflowers were planted in 3 gallon pots placed in the field.  Half of the plants were rotated 180 degrees at sundown to face the other direction.  Leaf area, leaf count, and plant height was measured for all plants in both experiments.  The angle of head movement was also measured for the plants in the second experiment.  The results of both experiments show that plant growth and development was less in treated plants then the control plants, indicating that heliotropism plays a part in plant growth.  However, more research and trials are needed to confirm this.  The objective of this study is to determine the effect of stem heliotropism on sunflower growth and productivity in order to arbitrate whether genetically modifying other crop-bearing plants to elicit stem heliotropism would be beneficial to crop yield.

Prediction of Tyrosine Sulfation in Voltage-Gated Potassium Channels

Student Name: Savitri Asokan
UC Davis Department: Department of Neurobiology, Physiology and Behavior
UC Davis Mentor: Grace L. Rosenquist
Tyrosine sulfation is a protein modification which causes a tyrosine residue to gain a sulfate group and become negatively charged.  So far, 102 tyrosines have been shown to be sulfated, but no voltage-gated potassium channel proteins contain confirmed sulfated sites.  Using a Position-Specific-Scoring-Matrix, the selectivity filter GYGD and pore helix site MYP were predicted to likely be sulfated. Sequence alignment of these motifs across 40 potassium channel proteins showed that both motifs are conserved to a high degree, indicating some likely functional role.  Past mutagenesis experiments on the two sites were collected to determine the effect of the GYGD and MYP residues on toxin binding.  GYGD and MYP appear to be critical sites for cation binding, but no evidence of a strictly ion bond is available.

The Effects of Anaerobic Soil Disinfestation Treatments With Different Carbon Sources on Agrobacterium tumefaciens

Student Name: Shanti Gurbuxani
UC Davis Department: Plant Pathology Department
UC Davis Mentor: Daniel Kluepfel
As the worldwide restrictions for soil chemical fumigants increase, growers need alternatives to eradicate soilborne plant pathogens. Anaerobic soil disinfestation (ASD), developed in Japan and the Netherlands in the 2000s, is one of these alternative techniques that can control certain soilborne plant pathogens, plant-parasitic nematodes, and weeds in specialty crop systems. To utilize the technique, the soil has to have a carbon source applied, covered with plastic, and mixed with water to generate anaerobic conditions in the soil. The point of this experiment was to see the effects of different carbon sources such as ethanol, almond hulls, almond shells, and rice bran on the soilborne plant pathogen Agrobacterium tumefaciens, which causes crown gall disease in walnuts. The results showed that ethanol was the most effective ASD treatment at suppressing A. tumefaciens. However, the most anaerobic treatment was the almond shells, but it was also the treatment with the greatest abundance of A. tumefaciens. The anaerobic environment created by ASD may not be the only driving mechanism behind suppression of A. tumefaciens. The ethanol treatment did not have anaerobic conditions, but volatile compounds produced through ASD in the ethanol treatment could have suppressed the A. tumefaciens instead.

Determining the Signaling Pathways Regulated by Chaperone-Mediated Autophagy

Student Name: Sriya Lingampalli
UC Davis Department: Department of Neurobiology, Physiology, and Behavior
UC Davis Mentor: Aldrin V. Gomes
Chaperone-mediated autophagy (CMA) is a process that maintains cellular homeostasis and degrades dysfunctional or damaged proteins. It functions by transporting proteins to the lysosome for degradation with the help of the HSC70 and LAMP-2A molecules. Research demonstrating a five residue amino acid sequence and several substrate proteins has resulted in many proteins being identified as potentially CMA regulated. We analyzed all proteins in the genome of several species including humans, and concluded that many proteins and signaling pathways are likely CMA regulated. Using a novel prediction program, we have also found that a greater percentage of proteins (46.5%) in the human protein sequences possess KFERQ-like motifs than previously thought (30%). Testing of lysosomes from starved H9c2 cells showed that the three proteins, which are predicted to have KFERQ-like motifs, are present in the lysosome.

Understanding The Role Of Salicylic Acid Signaling Pathway In Stromule Induction During Plant Innate Immunity

Student Name: Sydney Collier
UC Davis Department: Department of Plant Biology and the Genome Center
UC Davis Mentor: Eunsook Park, and Savithramma Dinesh-Kumar
Stromules are plant cell specific structures that extend out from the chloroplast. The role of the stromule is not known, however, a recent publication from the Dinesh-Kumar lab suggests that they are involved in the plant’s immune response to protect the plant from pathogens. More detailed studies regarding the regulation mechanism about the stromule induction is crucial to understand their contribution in the plant immune response. The Dinesh-Kumar lab studies have suggested that the stromule induction pathway might be regulated through the plant hormone Salicylic Acid (SA) pathway that is essential to the plant immune response. Key genes in this pathway are SID2/EDS16 and ATG5. To obtain a better understanding of the role of SA in stromule induction, the sid2/eds16 and atg5 mutants were crossed to make sid2/eds16 atg5 double mutant. sid2/eds16 atg5 double mutant was identified by genotyping using polymerase chain reaction (PCR). The results show that there was a double mutant and we will introduce a stromule marker later to observe stromule induction. Characterization of stromule induction in single and double mutants will provide insights on how stromule induction is regulated during the plant immune response.

Investigating the Effect of Mutations on the Enzymatic Activity of Beta-glucosidase B

Student Name: Victor Lee
UC Davis Department: Department of Chemistry
UC Davis Mentor: Dr. Justin Siegel, Ryan Caster, and Alex Carlin
Beta-glucosidase B is an enzyme found in every organism that breaks down the glycosidic bondages of polysaccharide molecules. Currently, there is a lack of understanding of how enzymes work, partly because databases on how point mutations affect this enzyme are incomplete. In this study, we investigated the effects of how three specific point mutation affects the enzyme’s effectiveness by using kinetic constants to characterize the enzyme’s effectiveness. One mutation has significantly improved enzymatic activity, but the other mutations have caused the enzyme to be less effective. Investigations such as these could lead to an understanding of how enzymes work, which has many applications, such as the biofuels industry.

2014 Research Projects

A Comparison of Tripeptidyl-Peptidase II in Akita and common mice using western blotting

Student Name: Angie Chen
UC Davis Mentor: Dr. Aldrin Gomes
The activity and expression levels of tripeptidyl-peptidase II (TPP-II), a proteolytic protein complex, is unknown in diabetic muscle tissue. To investigate TPP-Iwestern blotting and biological assays were employed to answer the questions: 1) Do TPP-II levels differ in Akita mice versus wild-type mice? and 2) Is TPP-II activity different in Akita and wild-type mice? Before responding to these questions, however, the common western blotting technique used was optimized to improve the sensitivity of the blot. The optimal conditions for western blotting were determined to be 5% PEG-8000 + 0.01% Glutaraldehyde + 75% TTBS and overnight primary antibody incubation. Using this optimized western blotting, TPP-II levels were determined to be the same in Akita and wild-type mice. TPP-II activity was also determined and found to be similar between hearts from Akita and wild-type mice.

Understanding the Influence of Multiple Contextual Features During the Encoding of Episodic Memory

Student Name: Bethany Hung
UC Davis Mentor: Dr. Arne Ekstrom
The ability to form complex memories is a well studied yet not well understood mechanism of the brain. Several studies have been performed on the creation of episodic memories from object representations, but none have examined the effect of multiple types of contextual cues and how they are prioritized during memory encoding. In this study, we examined the creation of episodic memories via the integration of multiple different elements. Sixty-four subjects, all of normal health, navigated a system of virtual reality rooms and answered questions about the room and music’s emotional effect during a study phase. During the testing phase, they once again navigated the hallway but answered questions that tested for recall of details in rooms that they entered. We then quantified this data by counting corrects versus false alarms and analyzed the data using a one-way ANOVA. We examined three model effects: delay between the study and test phases, the subjects’ type of recall – spatial, musical, or both – as determined by the questions, and the interaction between delay and recall type. Our findings indicate that music, as a lone contextual cue, provides an advantage over spatial cues during encoding that later presented itself in retrieval. However, this effect dissipated after one week. It therefore appears that the impact of varying types of contextual details changes differently over time, although a combination of multiple details is always better than a single type of detail.

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
UC Davis 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.

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

Student Name: Hansalia Sahil
UC Davis 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.

Analyzing Lipid Structure on Oxidized Gold as a Function of Vesicle Size and Solution

Student Name: John Rodgers
UC Davis Mentor: Dr. Donald Land
Small unilamellar vesicles (SUVs) aptly model cell membranes.  In fact, vesicles are currently a major area of focus.  They are being used to study biological functions through the incorporation of various molecules into the vesicle membrane . In this research, the structure of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) 30 and 100 nanometer vesicles were studied in phosphate buffered saline (PBS) and water. The lipid samples were adsorbed on an oxidized gold surface on a germanium crystal and studied with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). In both PBS and water, 30 and 100 nm vesicles adsorbed intact. However, deformation of the SUVs varied with the size of the vesicles and solvent.  This study shows that DMPC vesicles reacted differently based on changes to these two factors.  These observations will help advance surface chemistry research and the development of better cell bilayer models.

Predicting Tyrosine Sulfation in GPCRs

Student Name: Kevin Ma
UC Davis Mentor: Dr. Grace Rosenquist
The posttranslational modification of tyrosine sulfation is critical for the binding affinity and peptide specificity of many G-protein coupled receptors (GPCRs). Using a log-odds position specific scoring matrix (PSSM), 64 tyrosine sulfation sites in 31 different peptide binding GPCRs were scored. Higher scores indicated a higher degree of similarity between confirmed sulfation sites and that tyrosine. While our PSSM did not account for characteristics such as clustering and conservation, the sites nonetheless exhibited these characteristics. Most predicted sites were located in the binding pockets of GPCRs, which is also consistent with confirmed tyrosine sulfation sites. Binding affinity or peptide specificity decreased when our tyrosines were mutated into alanine or phenylalanine, indicating the important role of the tyrosine in ligand binding.

The Role of Protein Ferritin in Plant Immune Responses to a Pathogen

Student Name: Lila Balakrishnan
UC Davis Mentor: Dr. Dinesh-Kumar
In N.tabacum, chloroplastic protein NRIP1 mediates the innate immune receptor recognition of p50, the viral effector protein of the Tobacco Mosaic Virus. The presence of stromules was observed  extending from the stroma of the chloroplasts towards the nucleus. Researchers discovered that ferritin, another chloroplastic protein, does not complete a similar process to NRIP1, instead, it is always located in small quantities in the nucleus that do not appear to change during N-mediated defense.

Comparing Glutathione S-Transferase Mu 1 in Akita Mice and Wild-Type Mice

Student Name: Madelyn Wang
UC Davis Mentor: Dr. Aldrin Gomes
The goal of this project was to determine if Glutathione S-Transferase Mu 1 (GSTM1), a key antioxidant enzyme, is altered in diabetes. We compared GSTM1 levels between hearts of type I diabetic Akita mice and wild-type mice using Western blotting. Western blotting for GSTM1 had previously been unsuccessful because of the low amounts of this enzyme in the heart. The Western blotting procedure was optimized through experiments to determine if treatment of the membrane prior to blocking and during primary and secondary antibody incubation increased the sensitivity of the blot. We found that treatment of the membrane in 0.01% glutaraldehyde for 20 minutes before blocking and incubating with the primary antibody in the presence of 75% TTBS (Tris-buffered saline with Tween 20) increased band intensity by 8.92-fold when compared to the control. In addition, the addition of 5% PEG-8000 and the use of 1% BSA in the primary and secondary antibody incubations increased Western blot sensitivity. The improved Western blotting procedure allowed for the detection and quantification of the GSTM1 in the Akita and control samples. After quantifying and normalizing the protein loaded, we found that GSTM1 levels were similar in Akita mice than in normal mice. Hence, the levels of GSTM1 do not seem to be affected in type 1 diabetic heart dysfunctions.

The Effects of Carbon Sources on Anaerobic Soil Disinfestation

Student Name: Matt Wang
UC Davis Mentor: Dr. Daniel Kluepfel
Greenhouse studies were performed to examine the effects of two carbon sources on Anaerobic Soil Disinfestation (ASD) of Agrobacterium tumefaciens and Pseudomonas synxantha inoculum. The first experiment was performed using Yolo silty clay loam soil from the UC Davis Armstrong Field Facility, which will be referred to as clay soil. The experimental design was composed of treatment pots in a controlled greenhouse environment, each with an irrigated soil amended with rice bran at a rate of 9, 7, or 5 tons/acre, or molasses at a rate of 4.5, 2.25, or 1.125 tons/acre. Inoculum bags containing the bacteria A. tumefaciens and P. synxantha were buried in these pots, which were then covered with an impermeable tarp. The second experiment only considered the treatment of 9 tons/acre of rice bran, but used soil with a Hanford fine sandy loam texture, which will be referred to as sandy soil. Untreated control pots were also present for comparison in both experiments. At three and seven days after initiating Anaerobic Soil Disinfestation, three pots from each treatment were taken to enumerate the bacteria through dilution plating on selective media. Populations of A. tumefaciens in the 1.125 tons/acre molasses treatment tended to decrease with time, but the populations at seven days were not significant different from time zero across treatments. Populations of P. synxantha in the 9 tons/acre rice bran treatment also tended to decrease with time, but the populations were also not significantly different from time zero across treatments. Anaerobic conditions were lost after five days for both the 1.125 tons/acre molasses 2.25 tons/acre molasses, with lower efficacy of ASD over time for molasses compared to the rice bran treatments. A. tumefaciens populations decreased to undetectable levels by seven days in the sandy soils exposed to ASD conditions. These data indicate that soil texture may play a major role in ASD efficacy which will affect where ASD will be used commercially in the state of California. Overall, the comparison of rice bran and molasses as carbon sources for ASD was inconclusive; however, it was clearly shown that rice bran at rates below commercial levels of 9 tons/acre were effective at inducing anaerobic conditions in the soil.

Refining the metagenomic approach used to study sanitizer-treated sludge microbiota and orange peels with limonene

Student Name: Ryan Poon
UC Davis Mentor: Dr. Christopher Simmons
To maximize biofuel methane production from food processor waste, our research sought to develop a system that could be used to genetically examine methanogens that are resistant to industrial and natural sanitizers. We especially focused on the orange juice processor waste, which contained the natural sanitizer limonene and the protein pectin that inhibited DNA extraction. Hermetic bioreactors filled with tomato pomace and sludge were connected to a respirometer, which quantified the gases they released. After testing factors such as the nutrient medium, it was found that higher volumes (>100 mL) of brand new sludge taken straight from refrigeration was needed for reliable results. The results of the following test trials showed that methanogens were increasingly hindered by increasing sanitizer concentrations above 30 mg/L, signifying that the system functioned properly. In another experiment, DNA was best extracted from a mixture of orange peels and limonene by lysing the samples without centrifuging or bead beating and using pectinase to digest the pectin. The concentration of DNA was qualitatively analyzed using spectrophotometry and Qubit®. For polymerase chain reaction (PCR) amplification, bovine serum albumin (BSA) was used to enhance the compatibility of the DNA strand as well as to prevent inhibitors from interfering with the process. Such a systematic procedure could not only be utilized to discover the genes coding for sanitizer resistance, but also potentially be applied to test a wide variety of variables that may affect methane generation.

2013 Research Projects

Towards Understanding the Importance and Divergence of the OMP85 homologs Toc75 and OEP80

Student Name: Aditya Srinivasan
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kentaro Inoue
This study focuses on the relationship between two OMP85 homologs, Toc75 and OEP80, derived from an ancestral cyanobacterial protein. These two homologs are present within modern-day chloroplasts. OEP80 is hypothesized to play an important role in seedling development much like its sister protein – Toc75. This study attempts to determine the function of OEP80 as well as its necessary expression time (in either the seed, germination, or seedling stage). By creating mutants without a properly functioning OEP80 gene and rescuing these mutants using genetic constructs, this study compares the functional sequences of OEP80 and Toc75. These constructs can then be used to determine the exact time (stage of plant development) and role that the OEP80 plays in functioning and normal development of plants.

Prediction of Tyrosine Sulfated Sites in Integrins

Student Name: Allan Zhou
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Tyrosine sulfation is a post-translational modification of proteins that is important to protein-protein interactions. We show that integrins, a family of trans-membrane receptors found in animals that link cells to the Extracellular Matrix, have a high number of likely tyrosine sulfation sites. Particularly, likely tyrosine sites in integrins are often found near ligand binding or recognition sites. Our data also show a high degree of conservation between likely sulfated tyrosine sites, suggesting their functional importance to the integrin.

Effects of Dof1 Transcription Factors on Tomatoes

Student Name: Annabel Chem
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles
Nitrogen is a nutrient essential to plant growth and development. Improving a plant’s ability to uptake and metabolize nitrogen is essential to preserving plant productivity and agricultural viability under low nitrogen growing conditions, but is difficult to achieve due to the complicated nature of the nitrogen assimilation pathway. Because transcription factors often regulates the coordinated expression of genes involved in a pathway, modification of transcription factors is a powerful and promising approach towards modifying complicated pathways. This experiment focuses on the effects that the Dof1 transcription factor has on nitrogen assimilation in tomato plants in hopes to design a tomato that can maintain high crop yield without requiring added nitrogen from fertilizers. Plant length, fresh weight, dry weight, root length, and PEP-Carboxylase expression were higher under low nitrogen conditions in plants overexpressing Dof1, showing that the Dof1’s role in regulating nitrogen metabolism in plants has a positive impact on nitrogen assimilation in transgenic tomato plants under low nitrogen conditions. Although this project evaluates the NUE of a transgenic tomato plant, the ultimate goal is to create a non-transgenic line that has similar properties.

Roles of Arabidopsis thaliana Na+/H+ Antiporters NHX2 and NHX3 in Potassium Ion Homeostasis

Student Name: Athena Kan
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Eduardo Blumwald
Antiporters are generally responsible for ion homeostasis in the model organism Arabidopsis thaliana by exchanging hydrogen ions (H+) for sodium (Na+) or potassium (K+). However, information regarding the role of NHX2 and NHX3 in this process is scarce; therefore, this study aims to investigate the effect of overexpression of NHX and NHX3 genes individually when the plant is grown in Spalding media with varying concentrations of potassium: 30mM (high), 1mM (medium), and 0.1mM (low). After ten days of growth, root length was measured and then expression of HAK5 and AKT1, which correlate with low levels and high levels of potassium, respectively, were measured using comparative qPCR analysis. The results indicated that though overexpression of the NHX2 gene had little to no effect in any concentration of potassium media, overexpression of the NHX3 gene significantly impacted growth and development. Specimens with an overexpressed NHX3 gene exhibited shorter roots, increased expression of HAK5, and decreased expression of AKT1 in low levels of potassium. Not only do these results present a better understanding of Arabidopsis thaliana, but they may also guide the process of developing better stress response capabilities in crops; abiotic stress is the primary cause of crop loss worldwide.

Effect of developmental stage on viability of medusahead seeds

Student Name: Catalina Zhao
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Emilio Laca
Medusahead (Mh, Taeniatherum caput-medusae, (Sim). Nevski, Elymus caput-medusae), a noxious, invasive, annual grass, has invaded millions of acres in west coast states and is destructive to the natural ecosystem. Mh invasions decrease biodiversity, commercial and wildlife grazing value, and the capacity and recreation value of rangeland. Mh has a maximum period of susceptibility in the spring to control methods, but the start and end point are unknown. Thus, control methods, such as mowing, grazing, fire and herbicides, are ineffective or not feasible. The purpose of this project is to find the end point in that period to improve the timing of controls. First, a classification of partial Mh phenology, from post-pollination to complete maturity, was constructed. Then, seeds of different life stages from three different regions in California were germinated to find the germination percentages of each stage. The data, along with the results of a 1957 seed germination experiment, was then analyzed to identify the end point and to examine regional differences in Mh viability. The latest phenological stage at which Mh is still susceptible to control was found to be Intermediate 2. Also, differences in germination among the regions were identified.

Tyrosine Sulfation in Voltage-Gated Potassium Channels

Student Name: Christina Ji
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Tyrosine sulfation is a posttranslational modification of a protein in which the hydroxyl group of the amino acid tyrosine is changed into a sulfate group. This modification strengthens protein-protein interaction. Tyrosine sulfation is prominent in the signature sequence of the conserved selectivity filter of voltage-gated potassium channels. The functionally similar KcsA from bacteria Streptomyces lividans shares this signature sequence. Positively charged toxin binding sites interact with negatively charged sulfated tyrosine sites. Voltage-gated potassium channels function in repolarization of action potentials in the brain, heart, and muscles. Tyrosine sulfation plays a critical role in the conduction of these channels.

The Identification of Bacteria Species in Vermicompost

Student Name: Gloria Liou
UC Davis Department: USDA Agricultural Research Services
UC Davis 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.

The Role of Genotype and Water Availability in Storage Carbohydrate Distributions in Grapevines

Student Name: Jennifer Chen
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel and Dr. Mark Matthews
Perennial crop plants like grapevine (Vitis vinifera L.) use stored carbohydrates (CHO) from the previous season to sustain early season growth and flower development.  Water deficits inhibit current season growth and yield of the current season and following season, but the effects on stored CHO are not known.  CHO assays were performed on two grapevine genotypes, Grenache and Syrah, across three different irrigation treatments. Specifically, CHO concentrations in basal nodes and internodes were assayed just after the onset of veraison, the onset of ripening, which has been shown to be the annual low point in storage CHO concentrations in grapevine. A series of hot ethanol baths were used to extract soluble sugars. After extraction, CHO samples were digested into glucose using an alpha-amylase and amyloglucosidase solution. A PGO enzyme o-dianisidine dihydrochloride solution was added to each sample for a color reaction. The plate was read using a spectrometer and optical density numbers were recorded and analyzed with a standard starch calibration curve. In general, Syrah had higher storage CHO concentration than Grenache, which suggested that it was more efficient with water. Across both varieties and all three irrigation treatments, internodes contained higher concentration of storage CHO. CHO distribution in internodes supported the hypothesized relationship: decreased water availability results in decreased concentrations of storage CHOs. These data suggest that water deficit and storage CHO concentrations are positively correlated in perennial crop plants like grapevine (Vitis vinifera L.).  CHO in the nodes did not show the predicted distribution. Syrah vines had lower midday leaf water potential than Grenache vines which can be attributed to their anisohydric tendencies. This information on CHO distribution and genotypic variation in response to water deficits is important for identifying water-efficient grapevines and for water-conservation in agriculture.

A Home Use Descriptive Analysis Study to Evaluate Body Washes

Student Name: Jennifer Mou
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Michael O’Mahoney and Dr. Rie Ishii
Panelists were given blind samples of body washes to evaluate at home on a seven point scale. They received sufficient training to be able to distinguish between product differences for each attribute of the body washes. The goal of this study was to improve on the current methods of analytical product assessment with a home use descriptive analysis study to reflect more realistic home use situations of body wash products.

Evolution of 2-Nitrotoluene 2,3-dioxygenase and Gene Manipulation of Catechol 2,3-dioxygenase in Acidovorax sp. Strain JS42

Student Name: Jessica Li
UC Davis Department: Microbiology and Molecular Genetics
UC Davis Mentor: Dr. Rebecca Parales
Acidovorax (formerly Pseudomonas) sp. JS42 is able to use the compounds 2-nitrotoluene (2NT) and nitrobenzene as carbon, nitrogen, and energy sources. In the first step of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase (2NTDO) converts 2NT to 3-methylcatechol with concomitant nitrite release. 2NTDO has three component proteins, and although it can break down all three mononitrotoluene isomers, JS42 cannot grow on 3-nitrotoluene (3NT) or 4-nitrotoluene (4NT). However, it is possible to force JS42 to adapt to 3NT and 4NT with resulting changes to 2NTDO. In this study, we evolved 4NT+ JS42 strains to grow on 3NT using long-term selection. Sequencing of the ntdAc gene encoding the α subunit of 2NTDO oxygenase revealed substitutions at the amino acid position 204 on the active site. Mutations at positions 238 and 248 were conserved from the parent 4NT+ strain and no other mutations were present, supporting the hypothesis that the amino acid position 204 is crucial for the evolution of JS42 to utilize new substrates. The next step of the 2NT degradation pathway involves catechol 2,3-dioxygenase (CDO). Both ctdE1 and ctdE2 encode CDO, and each has an associated regulatory gene (ctdR1 and ctdR2). Based on the phenotype of a mutant strain with deactivated ctdE1, ctdE1 seems critical to the degradation pathway. We will complement the ctdE1 mutants to verify the role of the enzyme in 2NT degradation. It is not yet known whether ctdR1 encodes an inducer or repressor, so ctdR1 inactivation will be used to determine the function of the regulatory protein.

Effects of Cage Density on the Microenvironment and Health of Mice

Student Name: Jessica Ye
UC Davis Department: Anatomy, Physiology, and Cell Biology (Vet Med)
UC Davis Mentor: Dr. Kent Lloyd and Dr. Kristin Evans
According to the Institutional Animal Care and Use Committee (IACUC), Public Health Services (PHS), and Office of Laboratory Animal Welfare (OLAW), institutions must follow guidelines set by the Guide for the Care and Use of Laboratory Animals in their animal care and use programs when establishing mice populations within a cage to maintain the health and welfare of the laboratory mice2. The effects of mouse-caging density were studied in this project to determine the maximum number of mice that could be housed in a cage and maximum time between cage changes while maintaining the health and welfare of the mice. The CO2 level, Ammonia level, change in air flow, temperature, humidity, and any social, behavioral, or physical changes of the mice were evaluated. Seventy cluster of differentiation 1 (CD-1) outbred female adult mice were divided into four groups, with a minimum of two mice and a maximum of five mice per cage. Each week measurements of the microenvironmental gases in the cage, observations of the behavior and physical changes in the mice, cage temperature, cage humidity, cage airflow, and weights of the mice were recorded, for three weeks.

The Effect of Restoration on Soil Organic Carbon in Californian Grasslands

Student Name: Kaitlyn Gee
UC Davis Department: Plant Science
UC Davis Mentor: Dr. Emillio Laca
The atmospheric carbon sequestration abilities of plants, and in specific of grasses, are important on a local and global scale. However, little is known about the difference in carbon sequestration rates of perennial and annual grasses. The goal of this study is to discover if and to what extent grassland restoration, which is commonly achieved by seeding native perennial grasses, increases carbon sequestration through the analysis of soil organic carbon (SOC) stocks. Two sets of soil samples were taken, one set with samples from restored and nearby unrestored sites, and one with pairs of adjacent annual and perennial samples. The soils were processed and analyzed for carbon content in external laboratories. Statistical analysis using JMP revealed that the unrestored sites generally have higher amounts of SOC, although there is a positive relationship between perennial grasses and carbon presence. We conclude that the varying management practices and land use histories greatly shape SOC stocks in grasslands and that there is preliminary evidence that perennial grasses are more effective than annuals in storing carbon.

Purification of Functional Milk Oligosaccharides for Human Health Improvement

Student Name: Kevin Chen
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Daniela Barile
Milk oligosaccharides play a prebiotic role in the growth and establishment of a balanced gut flora in infants, selectively enriching the beneficial and protective bacteria that promote healthy immune and cognitive development. By acting as anti-pathogenic agents, milk oligosaccharides hold great promise as high quality supplements that can help support the health of any population with comprised immune systems. In order to provide sufficient quantities of oligosaccharides for clinical and functional testing, this work optimized several steps of activated carbon oligosaccharide filtration from human milk permeates. For measurement of process efficiency, a carbohydrate assay was first developed by treating milk products treated with Carrez clarification. Carbohydrate adsorption tests on activated carbon followed by total carbohydrate and lactose quantification showed that ratios of activated carbon to carbohydrate from 5-10 had better carbohydrate retention. In addition, permeates filtered with finer mesh charcoal (20-500) at a charcoal/carbohydrate ratio of 10 had the majority of carbohydrates adsorbed. Optimized conditions found in this study can be applied to purification from bovine milk whey permeate, a dairy industry waste stream. With further refinements to other steps of the purification technique, activated carbon filtration can be adapted as an effective method for mass extraction of health promoting oligosaccharides.

Optimization of gram-scale synthesis of UDP-galactose via one-pot multienzyme approach

Student Name: Kevin Feng
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Xi Chen
Uridine 5’diphopho-α-D-galactopyranoside (UDP-Gal) is a sugar nucleotide commonly used by animals, plants, and bacteria as the activated donor of galactose (Gal).   The salvage pathway is the simplest route to synthesize UDP-Gal and involves three different enzymes: Streptococcus pneumoniae TIGR4 galactokinase (SpGalK), Bifidobacterium longum UDP-sugar pyrophosphorylase (BLUSP), and Pasteurella multocida inorganic pyrophosphatase (PmPpA)1.  The optimum conditions for the entire reaction pathway in a one-pot multienzyme system were determined.  Then, using these conditions, synthesis of UDP-Gal was scaled-up to the gram-scale.  Production of UDP-Gal was successfully attempted using 1 g of Gal and a reaction yield of 70% was obtained.  No isolation yield was determined because of incomplete purification.

The Investigation of the Genetic Basis of the Shade Avoidance Response in Arabidopsis thaliana

Student Name: Kisha Thayapran
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Julin Maloof
Shade avoidance is a series of plant responses elicited when a plant experiences a reduced ratio of red to far-red (R:FR) light. In this study we investigate the genetic basis of shade avoidance by examining hypocotyl and root growth of Arabidopsis thaliana in four natural variants and three mutant lines. The four natural variants were Columbia (Col), Kondara (KON), KNO-18, and RRS-10. The three mutant lines, numbered 19, 38, and 52, were TDNA lines with insertions in the gene of interest. The average hypocotyl length was found to be longer in the shade conditions for every genotype. From the difference between the average hypocotyl length in sun and shade conditions, it was found that 19 may be a high responder, 38 responds similarly to wild-type Col, and 52 may be a low responder. After 3 days of shade treatment, there was little difference between the average root length between genotypes or between plants grown in sun or shade conditions. However, primary root length measured after 10 days of light treatment revealed that the average root length was longer in the shade conditions for every genotype. This suggests that roots show increased growth in response to shade. These results are relevant because knowledge gained from this experiment can be utilized in the agricultural industry when deciding crop spacing and land conservation.

Examination of posttranscriptional regulation and de novo transcription during early embryonic development using RNA-Seq

Student Name: Krishna Bharathala
UC Davis Department: Animal Science
UC Davis Mentor: Dr. Pablo Ross
Background: Embryonic genome activation (EGA) is a critical time during mammalian development during which an embryo initiates transcription of many important genes after a long period of transcriptional silence and dependence on stored transcripts in the oocyte. In bovine, EGA typically occurs at the 8-16 cell stage. Before EGA, the oocyte and early embryo regulate protein production using post-transcriptional mechanisms like cytoplasmic poly-adenylation.  The global targets of this regulation are not very well understood. Despite the fact that the oocyte is mostly transcriptionally silent, there is some evidence of de novo transcription between fertilization and EGA.  In fact, it has been suggested that there is a minor EGA earlier in development at the 4-cell stage. This study focuses on that transcription and on the post-transcriptional regulation of stored maternal mRNAs. Results: Our results support and characterize the notion of EGA. They yielded inconclusive results with respect to cytoplasmic poly-adenylation and post-transcriptional modification. They also suggest that androgen receptors that play a role in oocyte maturation may also play a role in signaling between embryos and the mother during early embryonic development.

Identification and Quantification of Fusarium oxysporum f. sp. vasinfectum Infestation in Soil with a Real Time Polymerase Chain Reaction Assay

Student Name: Lauren Banks
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Mike Davis
A real-time PCR protocol was developed to detect specific concentrations of Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 in soil samples, using publicly available primers specific to FOV race 4. Environmental samples of equivalent spore concentrations from a range of 10^3-10^6 spores/ml were detected with this protocol. Soispore concentrations in this range have been shown to cause Fusarium wilt; this protocol detected both artificially spiked samples as well as environmental samples within this critical range. Pending further validation, this protocol will serve as an appropriate means of testing soil and determining soil spore load.

Determining the Pathway in which a Precursor Imports Through the Chloroplast Membranes

Student Name: Maya Lopez-Ichikawa
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Stephen Theg
Proteins transport across the chloroplast membrane through the translocon of the outer and inner membranes (Toc and Tic, respectively). In previous studies, the translocon was successfully plugged with a biotinylated precursor, RSSU-HC, bound to a large avidin molecule. Recently, the precursor was systematically shortened to find the minimum number of amino acids for a protein to span both membranes. From this, researchers can determine the protein import pathway and whether they import in a linear or folded manner.

Exploring MAP Kinases’ Role in Stress Response

Student Name: Neil Shieh
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Katie Dehesh
Plants are subject to many stresses daily.  In order to efficiently deal with all of these stresses, plants have devised a general stress response which allows them to immediately respond before executing a specialized response to deal with the stressor.  Multiple biological pathways in cells have been observed to activate the Rapid Stress Response Element (RSRE), which is the cis-element that plays a part in activating the general stress response.  Previous research conducted on the effects of various chemicals on RSRE activation indicated a possible relationship between Mitogen Activated Protein Kinase (MAPK) pathways’ and RSRE activation.  The individual effects of MAPK inhibitors on wound response, pathogen response, and basal response in one week old Arabidopsis thaliana seedlings will give a clearer picture of how MAPK pathways are utilized in those responses. This study shows that MAPK modulating chemicals are able to enhance specific stress responses. Additionally, one MAPK modulator was able to delay all RSRE induction.  Since MAPK pathways are conserved in animals, studying MAPK pathways’ role in plants could be applicable to human stress responses.

The Relation Between Memory Functioning and Anxiety and Depressive Symptoms in Children

Student Name: Nicolle Iacobacci
UC Davis Department: Psychology
UC Davis Mentor: Dr. Simona Ghetti
Previous studies have demonstrated a correlation between anxiety and depressive symptoms and memory functioning ability in adults (Castaneda, Tuulio-Henriksson, Marttunen, Suvisaari, & Lönnqvist, 2008). However, these studies have not yet been conducted on children ages 7 – 11, thus it is unclear as to whether or not there are any correlations between these symptoms to memory ability. This study will observe and examine how both anxiety and depressive symptoms correlate between memory ability and functioning in children. These data supported a relationship between both increased atypical internalizing behaviors and decreased memory abilities and they explore a possible relationship between externalizing behaviors and memory ability, but ultimately did not support any existing link between them. This new research gives parents a broader insight for their young children, so they can be aware of the many ways in which anxiety, depression, and other internalizing problems may affect seemingly unrelated areas of their child’s growth and development.

Tobacco mosaic virus modifies the host gene expression and methylation in Arabidopsis

Student Name: Philip Hwang
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Bryce Falk
The mutants being used in this research are named based on the gene that does not function in the plant. These mutants include the MET-1 mutant, RDR2 mutant, DCL3 mutant, and DDM1 mutant. These mutants are bing used because they are suspected of playing a part in A. thaliana’s virus-induced methylation pathway. The control being used in this research is known as the Columbia ecotype or Col-0. Arabidopsis thaliana is being used as the experimental plant because it is essentially the model plant for genetic research. The Tobacco Mosaic Virus (TMV) and Cucumber Mosaic Virus (CMV) were inoculated into A. thaliana in order to determine which virus can work with the Arabidopsis. First, a virus screening was used to determine which virus would work with the Arabidopsis thaliana with the use of a TMV and a CMV primer. Then after determining the virus strain that is most useful for the continuation of this research, total RNA is extracted and used to create cDNA. These cDNA sequences were then amplified using PCR with primers designed for certain genes in an analysis for gene expression in each of the Arabidopsis mutants. DNA is then extracted from the mutants and methylation sensitive PCR is then used to locate areas and patterns of virus-induced methylation.

Effects of Non-Steroidal Anti-Inflammatory Drugs on Cell Oxidation and Proteasome Phosphorylation in Striated Muscle Cells

Student Name: Rajeev Parvathala
UC Davis Department: Western Human Nutrition Research Center
UC Davis Mentor: Dr. Betty Burri
Cassava is a root vegetable that is a primary source of energy for millions of people.  Unfortunately, the cassava root does not contain many nutrients, but it does contain varying levels of cyanide. Many cassava consumers are negatively affected by prolonged consumption of cyanide which can result in paralysis, ataxia, and other undesirable consequences to health. Current methods of cyanide reduction are too expensive or inefficient for the impoverished people that eat large amounts of cassava. This study focuses on trying to find inexpensive and feasible methods of cyanide reduction through pH treatments. The cassava was treated, rinsed and then tested for cyanide by diffusion into water. The water was then tested for cyanide using the La Motte Cyanide in Water Test Kit. It was discovered that weak acids and bases cause the greatest loss in cyanide. This research can be used for innovation of new cassava processing methods.

Effect of Leaf Water Potential and Irrigation on Stomatal Conductance in Grape Vines

Student Name: Sam Leitess
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Kenneth Shackel and Dr. Mark Matthews
Deficit irrigation, the practice of purposely providing plants with less than ample water, is used in some cultural practices. Deficit irrigation is believed by some to cause favorable conditions in vine yield and water use efficiency (Shackel 2011). This study aimed to plot the reaction of grape vines to varying irrigation treatments, specifically stomatal conductance (Gs) against transpiration rate (T) and midday Stem Water Potential (SWP). Gs was taken from three leaves on each vine at noon with a L-Cor 1600 porometer, T was taken every thirty seconds and averaged for each ten minutes with load cells, and SWP was taken once per day from each plant with a pressure bomb. Results indicated the time delay between last irrigation and vine reaction varies from vine to vine, but a general pattern of a sudden and large decrease in Gs several days after last irrigation was noted.

The Investigation of the Pathway and Production of Sugar Alcohols in Lactobacillus florum

Student Name: Sean Thomas
UC Davis Department: Food Science and Technology
UC Davis Mentor: Dr. Maria Marco
Erythritol is a naturally occurring, zero calorie sweetener produced by fermentation and is used as an additive in many foods and beverages. Erythritol is produced commercially through yeast fermentation using an expensive filtration process. The discovery of a microbe that could produce erythritol in comparable amounts could provide an alternative to this process, especially if it is a food grade microbe that could remain in the finished product. Lactobacillus florum is a novel, heterofermentative, lactic acid bacteria that has been found to produce erythritol making it a potential candidate.  Two strains of Lactobacillus florum, 8D and 2F, previously isolated from an unripe king palm fruit and a Valencia orange leaf, respectively, were tested for their ability and efficiency in producing erythritol when given glucose, fructose, or a combination of the two. Other metabolites, such as mannitol, acetic acid, lactic acid, and ethanol were also measured for. Since the erythritol pathway is not known in L. florum, enzyme assays were conducted to measure for the activity of enzymes responsible for erythritol production in Oenococcus oeni and yeast, erythritol 4-phosphate dehydrogenase and erythrose reductase, respectively. The results described will increase our knowledge of Lactobacillus florum, the pathway by which it can produce erythritol, and lead to areas of study for an alternative means of erythritol production. Both 8D and 2F were found to be capable of erythritol production when provided glucose, fructose, and the glucose-fructose combination, with 8D producing more than 2F.

Prediction of Sulfated Tyrosine Sites in Human Rhodopsin

Student Name: Shaan Somani
UC Davis Department: Neurobiology, Physiology, and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Tyrosine sulfation is a post-translation modification that has been proven to strengthen protein-protein interactions. In this study, we examine the potential for tyrosine sulfation in the human G-protein coupled receptor rhodopsin, the prototypic GPCR which plays a role in the visual phototransduction pathway in the rod cells of the eye. Through the position-specific scoring matrix, tyrosine sites Y26, Y29, Y30, and Y191 were found to have a high likelihood of sulfation in human rhodopsin. These sites were all well aligned in other forms of rhodopsin and cone opsins found throughout the animal kingdom. Y191, which is involved in a hydrogen bond network on extracellular loop 2 between E181 and Y192, was demonstrated through site-directed mutagenesis studies to function in the proper maintenance of Metarhodopsin II, the active state of photo-activated rhodopsin. Therefore, we find that sites Y26, Y29, Y30, and Y191 are consistent with sulfation.

Chlorpyrifos triggers mitochondrial dysfunction in mouse striatal neurons

Student Name: Viran Batth
UC Davis Department: Molecular Biosciences (Vet Med)
UC Davis Mentor: Dr. Cecilia Giulivi
Chlorpyrifos (CPF) is an organophosphate found in common pesticides that inhibits the enzyme acetylcholinesterase. Chronic exposure of CPF in humans results in neurological defects, developmental and autoimmune disorders, probably due to the generation of reactive oxygen species (ROS). Furthermore, CPF has been shown to have an effect on the dynamics and movement of mitochondria in rat cortical neurons and to decrease the activity of Complex I in PC12 cells. In this study, precursor neural cells from mouse brain were treated with 10 and 80 µM CPF for 24 hours. ATPase activity was found to be 20% lower on average compared to non-CPF-treated cells, with no changes in citrate synthase activity. Mitochondrial morphology and distribution were also analyzed through confocal microscopy. CPF-treated cells showed a significant decrease in the amount of tubular mitochondria (9% of untreated cells) accompanied by an 80% increase in the number of circular and fragmented mitochondria. Our results demonstrate that CPF exposure affects mitochondrial function suggesting its potential to produce oxidative stress and its involvement in oxidative stress-related neurodegenerative disease.

Prebiotics Help B. infantis Proliferate and Help Regulate Body Weight

Student Name: Won Park
UC Davis Department: Anatomy, Physiology, and Cell Biology (Vet Med)
UC Davis Mentor: Dr. Helen Raybould
The gastrointestinal tract (GI tract) of humans is colonized by immense amounts of microorganisms. They significantly affect the epithelial cells’ role of balancing the absorption of the necessary nutrients, ions, and water with the protection against potentially harmful toxins and pathogens. However, specific populations of microbiota tolerate only a certain range of conditions. Change in diet and nutrients (e.g. the consumption of prebiotics) can drastically change the population of microbiota present and consequently, the effects these microorganisms have on the GI tract.  This study suggests that inulin is able to help nurture B. infantis up to a certain point , that microbiota may play a role in regulating body weight, and that BMO may also be a prebiotic that helps microbiota proliferate.

2012 Research Projects

Investigating the Dof Gene in Tomato Plants

Student Name: Aditya Gupta
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Diane Beckles
Aditya Gupta is researching the Dof gene in tomato plants. His research takes place in Asmundson Hall, which is one of the many buildings with the UC Davis Plant Sciences Department. His research will involve a series of tasks, such as amplifying the Dof gene and identifying the location where the gene is expressed on the tomato plant. Aditya’s research will eventually allow tomatoes to grow with 25% more yield and help tomatoes have higher nitrogen use efficiency.

Understanding the Breakdown of Man Made Pollutants in Motile Bacteria

Student Name: Christie Ho
UC Davis Department: Department of Microbiology
UC Davis Mentor: Department of Microbiology
The lab seeks to understand the breakdown of manmade pollutants in motile bacteria, which are able to move towards the source of the pollutant and degrade the compound. Specifically, Christie is researching how a certain strain of bacteria can detect the presence of a specific compound, known as phenylacetate – a common compound found in many plastics and perfumes. Applications of this research include reducing the accumulation of environmental pollutants and minimize the effects of pollutants, helping preserve the planet.

Detecting Viruses in Grape Leaves

Student Name: Divya Bhaskar
UC Davis Department: Plant Science
UC Davis Mentor: Vicki Klassen
Viruses in grapevine plants tend to be unevenly distributed which means a virus may be located in the basal (lower leaves) of the grapevine, or in younger leaves. This is a major problem for farmers all throughout California, because they do not know how many samples must be sent to the lab in order to be sure the results of the test are accurate.  The purpose of Divya’s project is to determine the incidence of false negatives in grapevines infected with one or more of the five viruses. Divya will collect infected plant samples on the UC Davis vineyards, and then she will process these samples in the lab using a variety of techniques and machines such as real-time PCR in order to extract the plants’ RNA. Divya’s project will occur in the Foundation Plant Science Department regarding viticulture under the guidance of researcher Vicki Klaasen.

Plant Mechanisms for Recognizing Invading Pathogens

Student Name: Kimberley Berg
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Dinesh-Kumar
For this project, Kimberley is working with Dr. Dinesh-Kumar in the Plant Biology department at the University of California, Davis. The lab studies the mechanisms by which plants recognize invading pathogens, initiate a signaling pathway, and execute a defense response. In general, the research aims to gain a better understanding of plant immunity. This information could be used to prevent plant disease in the agricultural market, promoting higher productivity of food products for the ever-growing human population.

Investigating Plant-Pest Interactions in Alfalfa

Student Name: Nikhil Jois
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: Dr. Dan Putnam
Nikhil’s research involves alfalfa plants and plant-pest interactions, looking to control plant pests through the synthesis of novel phenolic compounds. It is currently hypothesized that these phenolic compounds found in plants deter pests by acting as prooxidants in the guts of the pests and causing cell damage. This work has a direct effect on forage production and pest control in an agricultural setting. The research may lead to further application in fruit and vegetable production as well

Determining the Effects of Environmental Tobacco Smoke on Rats

Student Name: Sarah Dukes-Schlossberg
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton
Sarah Dukes-Schlossberg is working at the Center for Health and the Environment at the University of California, Davis. She is working with Kent EPinkerton, Ph.D. of the School of Veterinary Medicine. She is researching the effects of environmental tobacco smoke (ETS) on the lungs of rats. Dukes-Schlossberg is comparing the lung tissues of spontaneously hypertensive rats (SHR) with those of control rats, SHR is a model for cardiovascular disease in humans. The results of the study will be used to better understand the effects of ETS on the lungs of humans and to develop better preventative measures and treatments.

Evaluating Symptoms of BRDC in Bovines

Student Name: Amy Kim
UC Davis Department: Department of Pathology, Microbiology, and Immunology
UC Davis Mentor: Dr. Laurel Gershwin
Kim is participating in a study on the bovine respiratory disease complex (BRDC), a deadly disease which costs the US cattle industry at least $3 billion dollars each year. Amy’s work in the lab, mainly involving virology, animal science, and molecular biology, will also include introducing different viruses to bovine steers for the evaluation of symptoms and for the search of traits that show resistance to this deadly bovine disease. In the end, not only will she will accumulate hours and hours of relevant lab experience, Amy will also help to find a cure to this costly disease

Determining the Structural Changes in Proteins During Staph Infections

Student Name: Andrew Kim
UC Davis Department: Chemistry
UC Davis Mentor: Dr. Donald Land
Andrew’s project is to determine the structural changes of the protein responsible for staph infections when incorporated in lipid vesicles that mimic cell membranes.  After creating the vesicles, he determines if the lipids maintain their spherical shape and the protein structure using infrared spectroscopy, a technique that analyzes absorbed light.  This project will allow researchers to gain a better understanding of how proteins interact with cell membranes.

Determining the Affect of Diabetes on Rat Cells

Student Name: Eric Gu
UC Davis Department: Molecular Biosciences
UC Davis 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.

Creating Molecular Pesticides Against Olive Fruit Flies

Student Name: Irene Lin
UC Davis Department: Department of Chemistry
UC Davis 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.

Determining the Effects of Allergens and Air Pollution on Mice

Student Name: Kelsey Green
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Kent Pinkerton
Studying the effects of allergens and pollution on mice. Since asthma is actually the body attacking itself through an immune response of antibodies to allergens, Kelsy will be able to dose mice with allergens and pollution to see their effects on the lungs. She will look at slides of exposed mice lungs with a microscope, analyze mice for indications of inflammation, and analyze a specific protein using immunohistochemistry to determine the damaging effects of air pollution in the lungs and how this may exacerbate allergic asthma. The results will be to see how these two factors of allergens and particulate matter affect those with asthma and the mechanism of asthma.

Investigating and Characterizing Protein Synthesis in Cardiovascular Disease

Student Name: Kunal Shah
UC Davis Department: Neurology, Physiology and Behavior
UC Davis Mentor: Aldrin Gomes
Protein synthesis is an important facet of any biological process. In the cardiac muscle, it is especially important in determining the state and condition of the muscle. One cardiovascular condition that is closely related to protein synthesis is cardiac hypertrohy. Cardiac hypertrophy is a thickening of the heart muscle, which results in a decrease in size of the chamber of the heart, including the left and right ventricles. This hypertrophy is a common known response to the increased workload of the heart that is associated with hypertension. The larger heart and cardiac cell mass means that more protein is necessary to make up the additional mass of the heart. This project investigated which proteins are specifically synthesized for the sake of contributing to cardiac hypertrophy and exactly how the rate of protein synthesis increases when cells are induced with hypertrophy by the cancer drug Doxorubicin. Using Click-iT AHA Protein Labeling Kits, and SDS-PAGE Gels, we were able to determine that the rate of protein synthesis increases by an average of 30.26%. In addition, we determined that Meclofenamate sodium, a Non-Steroidal Anti-Inflamatory Drug (NSAID), decreased the rate of protein synthesis in cardiac cells while simultaneously decreasing protein degradation, an important step in determining how exactly NSAIDs affect cardiotoxicity and induce cardiovascular disease.

Using Brachypodium as a Model for Drought Tolerance in Monocots

Student Name: Lucy Cui
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Eduardo Blumwald
Lucy Cui is working with Professor Eduardo Blumwald in the Plants Science Department to genetically engineer crops to be more drought and salt tolerant.  A model plant, Brachypodium, is used in place of wheat, rice, corn, barley, oats, and other monocots, to determine which genes to turn on in order to prolong crop life and produce greater yields with less water.  Another model plant,Arabidopsis, is used to understand the effect of genes that control pH in dicots, or flowering plants, on plant development. With the growing human population and loss of quality agricultural land, it is important to create these crops in order to continually feed the demanding population despite the harsh, arid conditions and to efficiently use the limited amount of agricultural land. 

Exploring the Effects of Photodegradation on Soil Organic Matter

Student Name: Nelson Chou
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Johan Six
Nelson Chou conducts a research project in the Department of Plant Sciences. The mentors of this young scholar are Dr. Johan Six and Dr. Sandra Yanni of the Agroecology Lab group. The objective the research is to explore the effects of photodegradation on littler and soil organic matter and its magnitude and rate in a California grassland. Photodegradation is an abiotic process in which sunlight, composed of both ultraviolet and visible light, degrades organic materials and can therefore facilitate subsequent microbial decomposition of organic matter. The carbon and nitrogen amounts of soil, grass litter, light effect on decomposition will be strategically analyzed. These understandings will form a basis of accurate prediction of annual decomposition rates of highly sun-exposed ecosystems such as the California grasslands.

Synthesizing the Protein MUC1

Student Name: Nicholas Andrew
UC Davis Department: Department of Chemistry
UC Davis Mentor: Dr. Xi Chen
Synthesizing MUC1, an important protein in human epithelial cells that protects cells from external disease. This protein is overexpressed in the cancer cells of the colon, ovaries, lung, and pancreas. By synthesizing various forms of this protein, Nicholas and his co-workers hope to begin developing a vaccine that can target and help the immune system destroy cancer cells while leaving normal cells intact.

Determining the Interaction of Plants and Indigenous Fungus

Student Name: Nicky Meyer
UC Davis Department: Plant Sciences
UC Davis Mentor: Dr. Sharon Strauss
Determining the interaction between plants and the fungus that live inside of plants. Through various experiments in the field, Nicky is looking to determine what impact the fungus has on the plant’s health, as well as its effect on the entire plant and animal community. Understanding the interaction between fungi and plants could lead to advances in agricultural techniques and environmental sustainability.

Studying Tyrosine Sulfation as a Model for Cellular Response Activation

Student Name: Nikhil Kotha
UC Davis Department: Neurology, Physiology and Behavior
UC Davis Mentor: Dr. Grace Rosenquist
Some viruses have a special family of proteins (GPCRs) on their coat which sense specific molecules and bind to them thus activating a response inside the cell. Tyrosine sulfation is a modification to a tyrosine amino acid in the DNA sequence which strengthens this interaction between the protein and its target. As part of the Physiology Department at UC Davis and under the guidance of Dr. Grace Rosenquist, I am using methods such as 3-D modeling, programming, DNA sequence alignment, and an algorithm matrix in order to find the probability of a tyrosine amino acid, in the DNA sequence that codes for this protein, being sulfated and the importance and function of this protein. If a tyrosine site in a protein sequence has a high chance of being sulfated, this means that the protein and consequently the virus strength are being enhanced by tyrosine sulfation. I am investigating over 5 different viruses for identifying and pinpointing this phenomenon and future applications of my research involve potential drug research and development in order to stop tyrosine sulfation at the specific place where it happens and thus inhibit the virus from doing any further damage!

Determining the Role of Viruses in Bovine Respiratory Complex

Student Name: School of Veterinary Medicine
UC Davis Department: Jason Manley
UC Davis Mentor: Dr. Laurel Gershwin
Manley’s research project deals with a bovine respiratory disease complex, a group of diseases that together kill millions of cows in the United States each year. Jason is studying a specific virus in this disease complex, called BRSV, to see whether a drug works as scientists hope in combatting the virus. If this drug is effective in cattle, further research could be pursued to determine whether the drug would work successfully against a similar virus that infects humans.

Characterizing the Efficiency of Catalysts

Student Name: Stacey Jeong
UC Davis Department: Department of Chemical Engineering and Materials Science
UC Davis Mentor: Dr. Bruce Gates
The research work is based on finding the characterizations of different catalysts to determine the most effective and appropriate catalyst. This will be done through various methods, such as IR spectrometry with unreactive gases to observe how much the spectra of the catalysts change. This work can be applicable to industrially used catalysts, which accelerate production and creation of other chemical-based materials.

Determining the Health Effects on Human Lungs Due to Air Pollution Exposure

Student Name: Tiankun Lu
UC Davis Department: Center for Health and the Environment
UC Davis Mentor: Dr. Laura Van Winkle
Tiankun’s project uses animal models to simulate health effects of exposure to air pollution on human lungs and involves the quantification and comparison of cellular damage caused by certain particulate matter (PM) between animals with different ages and between different compartments of lungs. Based on the previous work of his professor and through his own research, he might be able to determine the harmful portion of air pollution and potential biomarkers for susceptibility to PM that could be used either to identify or to treat afflicted individuals. The findings might also serve as reference and guidance to the government in regard of making environmental regulations and health policies.

Determining Biocontrol Methods for Bot Fungi

Student Name: Tommy Chiou
UC Davis Department: Plant Pathology
UC Davis Mentor: Dr. Doug Gubler
Tommy is currently working with Dr. Doug Gubler at the UC Davis Department of Plant Pathology, and his research involves several strains of fungi from the genus Botryosphaeria. His project tests several potential biocontrols, or methods of controlling pathogens through natural means, against the Bot fungi and seeing if any of them have inhibitory effects on the fungi. Fungi in the genus Botryosphaeria have been known to cause tree and shrub diebacks and diseases in grapes, apples, and pears. Each year, millions of dollars in revenue are lost in the agricultural industry because of damages by the fungi. Finding a cost-efficient and environmentally friendly method to control these organisms will greatly benefit the agricultural community.

Determining the Role of microRNA During Early Embryonic Development

Student Name: Tony Hua
UC Davis Department: Animal Sciences
UC Davis Mentor: Dr. Pablo Ross and Juan Reyes
Researching the role of microRNA during early development of embryos. MicroRNAs are small RNA molecules that regulate gene expression post-transcriptionally and play a key role in diverse biological processes, including development, cell proliferation, differentiation, and apoptosis. Consequentially, altered microRNA expression is likely to contribute to human disease, including cancer and HIV. By studying the mechanisms that are caused by microRNA function, additional insight and a deeper understanding of related processes will allow for the pursuit of further research and possibly more efficient treatments or cures. Currently, the success rate of In Vitro Fertilization or fertilization outside the body is only at a 30% success rate for females age 35. By studying the regulatory roles of microRNA, processes such as In Vitro Fertilization could potentially benefit from increased success rates from a greater insight of correlated processes and techniques

Determining the Gene Control of Stress Hormones in Plants

Student Name: Yuki Koide
UC Davis Department: Plant Biology
UC Davis Mentor: Dr. Dehesh
Locating a gene that controls the expression of stress hormones in plants. This research will help current understanding of various stress responses in plants and what they have in common. It might be applied in the future to genetically engineer plants that are resistant to multiple stresses, such as drought or insect attacks.

2011 Research Projects

De novo Assembly of Loblolly Pine (Pinus taeda) Transcripts obtained from RNA-Seq

Student Name: Charles Zhang
UC Davis Department: Department of Plant Sciences
UC Davis Mentor: David Neal
Forest trees provide a host of benefits to both humans and the biosphere. In order to better understand them, it is helpful to sequence their genetic information. In this project, RNA-Seq was performed on the needle transcriptome of four loblolly pine (Pinus taeda) individuals. The data was then assembled using Velvet and Oases de novo assemblers. The assembled transcripts were then analyzed using a combination of BLAST and Gene Ontology. The data from RNA-Seq was assembled using two different sets of parameters, and the results of these runs were compared. Sequencing the transcriptome is often the first step in a large enome-sequencing project. The results gained here will improve the overall understanding of the diversity of genes within the transcriptome as well as provide a foundation for assembling the much larger genome.

Movement of dissolved reactive phosphorous from soils to bodies of water in relation to eutrophication

Student Name: Kristen Chinn
UC Davis Mentor: Emily Carlson
Dissolved reactive phosphorous (DRP), or soluble reactive phosphorous (SRP), is a nutrient that can flow from agricultural land to bodies of water, causing eutrophication, which poses a threat to the health and efficiency of waterways. In order to prevent eutrophication from harming bodies of water, it is crucial to understand the movement of these nutrients, which was the main objective of this research.

Levels of DRP/SRP were analyzed by studying the sorption and desorption capacities of soils from different areas using the Bridgham et al (2001) method. This study found that sorption and desorption capacities varied between soil samples taken at different locations, indicating the level of effectiveness of different areas at retaining high amounts of phosphorous while releasing very low levels.

The information from this study can be used to evaluate potential areas for restoration based on the soil’s sorption and desorption abilities. In restoring wetland buffers, it is possible to benefit the environment by protecting water quality, using agricultural land more efficiently, managing waterways, and reducing or preventing eutrophication.