UC Davis Young Scholars Program

This summer, Caden researched the importance of lysis buffer choice in Dr. Aldrin V. Gomes' lab.

"Western blotting, also known as immunoblotting, is a process in which specific proteins are able to be detected and quantified. Despite having existed for several decades, further refinement in order to increase repeatability and clarity is still needed, as variability in sample preparation remains an important source of experimental inconsistency. My work concentrated on how different formulations of radioimmunoprecipitation assay buffers (RIPA buffers) affect the final western blot signal and protein extraction. Five commonly used commercial RIPA buffer formulations were compared using liver tissue from 5-month-old female mice (n=3). Following tissue homogenization, protein quantification, SDS-PAGE, electrotransfer to nitrocellulose membranes, and enhanced chemiluminescent detection, protein bands for PSMA1 and Rpt6 were quantified with ImageJ and normalized to total protein via Ponceau S staining. One-way ANOVA showed a significant effect of buffer formulation on Rpt6 signal, but not on PSMA1 signal, suggesting that the influence of buffer composition may depend on the target protein. Overall, findings demonstrate that RIPA buffer composition can measurably influence immunoblot signal."

This summer, Zoe researched the synthesis of 4NH2Neu5Ac in Dr. Xi Chen's lab.

"Seasonal Influenza poses a large health and economic threat to human society and continues to pose a barrier in healthcare and drug development today. Glycans are complex carbohydrates that are used for a variety of roles in biological systems. Sialic acids are sugars typically located at the ends of glycans, allowing glycans to communicate with other cells. Sialic acids are most commonly found as Neu5Ac on human cells. 4NH2Neu5Ac, a derivative of Neu5Ac, has been shown to bind to neuraminidases. Neuraminidases are enzymes used by influenza viruses that cleaves sialic acids. Here we synthesize 4NH2Neu5Ac in order to use the important molecule for later applications with glycan-binding proteins and forming other sialic acid derivatives."

Hasini spent the summer investigating the interactions between flavonoids, copper(II), and albumin in Dr. Marie Heffern's lab.

"Flavonoids are chemicals that naturally occur in all plants and nearly every food and are famed for their antioxidant abilities. They have been observed to neutralize free radicals and reactive oxygen species but little research has been done to examine their interactions with metals in the human body. Flavonoids can chelate metals like iron or zinc, preventing them from undergoing Fenton reactions and forming harmful radicals. Our lab studies the interactions between flavonoids, copper 2+, and albumin--a protein found in blood serum. We’re focusing on the shape and binding of the 3 complexes producible and their influence on diseases."

Walker's summer research was on paroxysmal sympathetic hyperactivity following traumatic brain injury in Dr. Cecilia Giulivi's lab.

"Traumatic brain injury (TBI) can result in paroxysmal sympathetic hyperactivity (PSH), a syndrome characterized by episodic surges of sympathetic nervous system activity. This study combined a systematic review and quantitative synthesis of the literature with proteomic analysis of cerebrospinal fluid (CSF) and plasma to examine the association between PSH, neurological outcomes, and biological pathways associated with recovery following TBI. The primary meta-analysis demonstrated a nonsignificant trend toward more favorable neurological outcomes among patients without PSH. Exploratory proteomic analyses of CSF and plasma suggested that proteomic variation was more strongly associated with neurological outcome than with PSH status alone. Favorable outcomes were associated with broader enrichment in immune, vascular, extracellular matrix, and metabolic pathways, whereas poor outcomes were associated with more restricted enrichment in signaling and repair-related pathways. Moderate concordance between CSF and plasma pathway enrichment was observed in the favorable-outcome, no-PSH phenotype."

This summer, Taiyo worked in Dr. Stacey Harmer's lab identifying genes that regulate circadian clock pace in plants.

"XAP5 CIRCADIAN TIMEKEEPER (XCT) is a key gene for the function of the circadian clock in Arabidopsis Thaliana. Loss-of-function XCT mutants have a short circadian period defect (Martin-Tryon and Harmer, 2008). While XCT functions in pre-mRNA splicing, this function is separable from its role in circadian period regulation (Zhang et al., 2023). This raises the question: what pathway does XCT operate on to control the clock? To identify genes acting downstream of or in parallel with XCT, we performed a forward genetic suppressor screen in the short period xct-1 background, using EMS mutagenesis and a luciferase based bioluminescence reporter to screen M2 populations for circadian periods restored to wild-type levels. Across three usable screening runs, we identified 15 suppressor candidates and one enhancer candidate with a period shorter than xct-1. Restriction enzyme digest confirmed that six suppressor candidates and the enhancer had the xct-1 genetic background rather than being Col-0 contaminated. These results provide targets for future bulked segregant analysis and sequencing to determine target genes that may act within the XCT pathway or independently to regulate the plant circadian clock."

This summer, Nora researched the effects of pH and concentration on almond protein dispersibility in Dr. Gail Bornhorst's lab.

"The development of plant-based protein has increased in recent years, the aim of which to replicate or even replace animal-based counterparts. While extensive research has been done on many types of plant proteins, almonds remain a mystery. To overcome this knowledge gap, this study investigated the effects of pH and concentration on almond protein behavior, particularly dispersibility (the capability of particles to form stable suspensions within a solvent). Six different solutions of protein concentrations (0.5%, 1%, 3%, 6%, 9%, and 12%) were each calibrated to five separate pH levels between 3 and 7, and the mass of dispersed protein was determined. It was strongly supported that a minimum concentration of protein is required to create a stable network that resists phase separation. Additionally, a proposed isoelectric point was determined through a significant drop in dispersibility."

This summer, Amaira researched Paroxysmal Sympathetic Hyperactivity after a Traumatic Brain Injury in Dr. Cecilia Giulivi's lab.

"The project I worked on this summer explored the subcondition called Paroxysmal Sympathetic Hyperactivity (PSH) after a Traumatic Brain Injury (TBI). We examined previous literature that addressed these conditions in order to examine whether there were links between PSH and clinical outcomes. We used forest plots in order to examine that there was an insignificant correlation between the two, but also identify outliers that could have changed this. The second aspect of our project was a proteomic analysis that was conducted on CSF and plasma proteins using mass spectrometry to identify the proteins. The proteins examined data from three clinical patient profiles, each with three distinct patient profiles. JMP software was used to preform hierarchal clustering on the data and establish that outcomes determined proteins and biological pathways more than PSH presence. Plasma proteins were also analyzed to draw conclusions that more proteins were examined in patients with poor outcome and PSH. There was also overlap between biological pathways in this clinical outcome only. Overall, our study works towards an increase in PSH standardization and diagnosis."

Snaps from the Bay Area and beyond with the scholars!