Research Project Descriptions

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Determining the Interaction of Plants and Indigenous Fungus

Student Name: 
Nicky Meyer
UCD Department: 
Plant Sciences
UCD 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. 

The Effect of Stem Heliotropism on Sunflower Growth and Productivity

Student Name: 
Nicole Infantino
UCD Department: 
Plant Biology
UCD 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. 

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

Student Name: 
Nicolle Iacobacci
UCD Department: 
Psychology
UCD 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. 

Studying Tyrosine Sulfation as a Model for Cellular Response Activation

Student Name: 
Nikhil Kotha
UCD Department: 
Neurology, Physiology and Behavior
UCD 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! 

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

Student Name: 
Philip Hwang
UCD Department: 
Plant Pathology
UCD 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
UCD Department: 
Western Human Nutrition Research Center
UCD 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. 

 

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

Student Name: 
Rebecca Chang
UCD 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
UCD Department: 
Plant Science
UCD 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
UCD Department: 
MCB
UCD 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.

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

Student Name: 
Ryan Poon
UCD 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.

Potential of Tyrosine Sulfation in Voltage-Gated Sodium Channels

Student Name: 
Sabrina Liu
UCD 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.

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

Student Name: 
Sam Leitess
UCD Department: 
Plant Sciences
UCD 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.

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

Student Name: 
Sarah Hancock
UCD 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.

Prediction of Tyrosine Sulfation in Voltage-Gated Potassium Channels

Student Name: 
Savitri Asokan
UCD Department: 
Department of Neurobiology, Physiology and Behavior
UCD 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.

Determining the Role of Viruses in Bovine Respiratory Complex

Student Name: 
School of Veterinary Medicine
UCD Department: 
Jason Manley
UCD 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.

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