Research Project Descriptions

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Investigating the Dof Gene in Tomato Plants

Student Name: 
Aditya Gupta
UCD Department: 
Plant Sciences
UCD 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
UCD Department: 
Department of Microbiology
UCD 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
UCD Department: 
Plant Science
UCD 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
UCD Department: 
Plant Biology
UCD 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
UCD Department: 
Department of Plant Sciences
UCD 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
UCD Department: 
Center for Health and the Environment
UCD 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.

Structure-Seq Influenced RNA Secondary Structure Prediction

Student Name: 
Aditya Bollam
UCD Department: 
Biomedical Engineering
UCD 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.

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

Student Name: 
Aditya Srinivasan
UCD Department: 
Plant Sciences
UCD 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. 

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

Student Name: 
Alex D. Doan
UCD Department: 
Department of Plant Biology and The Genome Center
UCD 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.

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

Student Name: 
Alex Kuang
UCD Department: 
Plant Pathology
UCD 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
UCD 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
UCD Department: 
Chemistry
UCD 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.

Prediction of Tyrosine Sulfated Sites in Integrins

Student Name: 
Allan Zhou
UCD Department: 
Neurobiology, Physiology, and Behavior
UCD 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.

Measuring and Predicting Syringe Hub Loss

Student Name: 
Allison Mayes
UCD Department: 
Mouse Biology Project
UCD 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.

Evaluating Symptoms of BRDC in Bovines

Student Name: 
Amy Kim
UCD Department: 
Department of Pathology, Microbiology, and Immunology
UCD 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

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