Participants work one-on-one with
researchers in state-of-the-art UC Davis laboratories on an
individual project. 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.
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.