Research Project Descriptions

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Determining the Structural Changes in Proteins During Staph Infections

Student Name: 
Andrew Kim
UCD Department: 
Chemistry
UCD 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.

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

Student Name: 
Angie Chen
UCD 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.

Effects of Dof1 Transcription Factors on Tomatoes

Student Name: 
Annabel Chem
UCD Department: 
Plant Sciences
UCD 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. 

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
UCD Department: 
Plant Pathology
UCD 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. 

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

Student Name: 
Athena Kan
UCD Department: 
Plant Sciences
UCD 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.

Developing CAPS Markers for Genotyping Sunflower Mutant Populations

Student Name: 
Benjamin Caswell
UCD Department: 
Plant Biology
UCD 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.

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

Student Name: 
Bethany Hung
UCD 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.

 

A Plant-based Evaluation of Landscape Irrigation Efficiency

Student Name: 
Brian Glucksman
UCD Department: 
Department of Pomology
UCD 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. 

Effect of developmental stage on viability of medusahead seeds

Student Name: 
Catalina Zhao
UCD Department: 
Plant Sciences
UCD 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. 

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

Student Name: 
Chang Hwan Kwak
UCD Department: 
Chemistry
UCD 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
UCD Department: 
Plant Biology
UCD 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.

Tyrosine Sulfation in Voltage-Gated Potassium Channels

Student Name: 
Christina Ji
UCD Department: 
Neurobiology, Physiology, and Behavior
UCD 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.

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

Student Name: 
Darren Tong
UCD Department: 
Mouse Biology Project
UCD 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
UCD Department: 
Molecular and Cellular Biology
UCD 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
UCD Department: 
Vet Med
UCD 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. 

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