Beckman Scholars Program

Emma Lang (2018) is majoring in Biology and Spanish, and will be studying “The role of the transcription factor Pdc2 in Ascomycota thiamine biosynthesis regulation” with her faculty mentor, Dennis Wykoff, Professor of Biology and Dennis M. Cook Endowed Gregor Mendel Chair in Genetics.

Thiamine (also known as vitamin B1) is essential for energy metabolism and, if cells do not have thiamine they die. Ms. Lang will examine how the Pdc2 transcription factor has evolved to upregulate the genes required for thiamine synthesis.

Saccharomyces cerevisiae, the fungus necessary for winemaking, baking and brewing, can make thiamine, but a similar, closely-related yeast, Candida glabrata, lacks the ability to produce thiamine. Both species regulate thiamine metabolism using the transcription factor Pdc2. However, in S. cerevisiae, Pdc2 also regulates sugar breakdown, and Pdc2 is essential for survival. C. glabrata is an emerging fungal pathogen that causes yeast infections, thrush, and most dangerously, in immunocompromised individuals, sepsis. Understanding the function of genes that regulate thiamine synthesis provides an appealing entry into designing antifungal medications against C. glabrata. Preventing C. glabrata growth by starving it of thiamine may help the 30% of individuals with systemic Candidiasis do not survive the fungal infection. Ms. Lang’s detailed study of the evolution of function of Pdc2 in these two yeast species, in addition to four other species will provide important new insights into antifungal drug research development. Ms. Lang will be determining which species’ Pdc2 are capable of performing the function of inducing the transcription of thiamine synthesis genes and which are capable of inducing the critical sugar breakdown genes. She will then use a mutant screen to attempt to convert the C. glabrata Pdc2 into a transcription factor that now regulates sugar breakdown genes as well. Ms. Lang’s work will identify how the specificity of Pdc2 has evolved over time and should clarify the role of Pdc2 in metabolism in C. glabrata.

Kali Carrasco (2019) is majoring in Biology and focusing her research on the molecular genetics and cellular biology of aging with her Faculty Mentor, Professor Matthew Youngman.   

Are aging humans fated to the same slow decline as older machines, suffering the ill effects of wear-and-tear? Not necessarily, at least according to studies of aging in roundworms called Caenorhabditis elegans, whose genetic makeup is remarkably similar to humans. Studies of older worms suggest that perhaps more than breaking down from long-term use, the functional decline of tissues that occurs later in life is  driven by lower expression levels of the genes responsible for maintaining cellular health and defending against environmental stresses—these genes are turned down or are completely off later in life. Along with its role in metabolism, insulin modulates gene expression by regulating the activity of a protein called DAF-16 in C. elegans, a close relative of the human FOXO3a protein, that functions as a transcription factor. Like light board operators at a Broadway show, transcription factors work inside the nucleus of cells where DNA is housed to flip the switches on genes, adjusting their level of expression (their “brightness”). The specific genes that DAF-16 controls are important for immunity and stress resistance, among other functions, and higher expression levels of these genes extend the worm’s lifespan. Understanding more about how DAF-16 functions during adulthood may one day lead to treatments to keep the protective genes turned on for longer, which could improve health in advanced age.  

In younger worms DAF-16 appears to wait for the cue of exposure to an environmental stress before it takes action. Work in Dr. Matthew Youngman’s lab in the Department of Biology, however, suggests that another cue seems to come during aging even in the absence of stress, as early in adulthood DAF-16 turns on at least some of the genes that it controls. Defining the nature of this age-dependent, constitutive activation of DAF-16 is the ultimate goal of a project undertaken by Kali Carrasco (Biology, ’19). Specifically, Kali will test the idea that in adult worms a protein called DAF-18 must counteract insulin’s inhibitory signal to allow DAF-16 to do its job. If her hypothesis is correct, adult animals without DAF-18 will lose the immune protection conferred by DAF-16 and will be more susceptible to bacterial infections. Accordingly, she expects to find that DAF-18 is necessary for DAF-16 to gain access to the light board—that is, to regulate its target genes. Since the human version of DAF-18, known as PTEN, plays a role in the development of prostate cancer, Kali anticipates that her studies will not only provide mechanistic detail regarding the control of gene expression during aging but they will also have implications concerning the molecular events that underlie tumor progression. 

Chris Braganca (2021) is majoring in Biochemistry and Neuroscience and is studying the correlation between ATP hydrolysis and protein degradation by the 26S Proteasome in eukaryotes with his Faculty Mentor, Dr. Daniel Kraut, Assistant Professor in Biochemistry.

Cells accomplish nearly all their intracellular and extracellular functions through the synthesis of specific proteins. Once a given protein has served its purpose, the cell degrades the protein so its components can be used again. In eukaryotic cells, this degradation is accomplished using the machinery of the 26S proteasome complex. Proteins to be degraded are first polyubiquitinated by a series of enzymes (E1, E2, and E3) that attach the C-terminus of a ubiquitin molecule to a lysine within the substrate, then polyubiquitinate by attaching ubiquitins to lysines within previous ubiquitins. Additionally, there are different ways to ubiquitinate a substrate, which can be controlled by using different E3 enzymes. This ubiquitinated substrate is then recognizable by the ATP-dependent proteasome and is able to be degraded. In Chris’ project, he will study the mechanochemical coupling between ATP hydrolysis and protein degradation by slowing down the rate of hydrolysis using ATP-gamma-S, a non-hydrolyzable ATP analog. If the rate of ATP hydrolysis is slowed down, how does that affect the unfolding of the substrate by the proteasome? How is this affected by different forms of ubiquitination, which have been shown to lead to different abilities of the proteasome to unfold substrates? Chris will initially use Green Fluorescent Protein as a model system.

Based on previous research on both the proteasome and the bacterial homolog ClpXP, Chris anticipates that reducing the ATP hydrolysis rate will decrease not just the rate of unfolding, but also the ability of the proteasome to successfully unfold the substrate.

Julianna Cresti (2021) is majoring in Biochemistry and Chemistry and her study is the "Investigation of the Conformational State of the 26S Proteasome and Protein Unfolding Ability Using FRET" with her Faculty Mentor, Dr. Daniel Kraut, Faculty Mentor, Dr. Daniel Kraut, Assistant Professor in Biochemistry. 

The 26S proteasome is an essential component of the eukaryotic cell, tasked with engaging, unfolding, and degrading a protein in the case that it is no longer of use to the cell or problematic, mitigating damage or greater consequences before the cell experiences adverse effects. First, a degradation signal called ubiquitin is attached to a target protein. Ubiquitin then binds to receptors (Rpn1, Rpn10 and Rpn13) that are part of the proteasome. The proteasome then engages the target protein with motor proteins that unfold it and pull it inside a degradation chamber. Engagement involves changes in the conformation of the proteasome as it moves from a substrate accepting state to a substrate processing state. The Kraut lab has found that ubiquitin binding to these receptors affects the proteasome’s ability to successfully unfold target proteins. Ms. Cresti’s research will be primarily focused on elucidating the relationship between the conformational state of the 26S proteasome and its ability to unfold and degrade ubiquitinated proteins through the use of the instrumental technique Fluorescence Resonance Energy Transfer (FRET).

Gillen Curren (2022) is majoring in Environmental Science and her study is "Heavy Metals in Estuarine Food Webs " with her Faculty Mentor, Dr. Nathaniel Weston, Associate Professor and Chair of the Department of Geography and the Environment.

Ms. Curren will be working to compare the heavy metal concentrations found in various plants, insects, fish, benthic infauna, and filter feeders from coastal tidal marsh systems in the Delaware Estuary (New Jersey and Delaware), the Plum Island Estuary (Massachusetts), and the York Estuary (Virginia). Heavy metals in estuarine soils are a result of natural rock weathering augmented by anthropogenic sources that are delivered from the watershed to the coastal zone. Anthropogenic sources of heavy metals to coastal systems have become a concern with the increase in development in many coastal watersheds. Research in Dr. Weston’s lab has previously found that these three coastal ecosystems represent a gradient of heavy metal contamination. Ms. Curren’s project will focus on the movement of these heavy metals into the food web in these estuarine ecosystems, using the prior research on heavy metals in marsh soils as a starting point. Samples from select plants, insects, fish, benthic infauna, and filter feeders will be collected from the three sites. Samples from each organism will be digested using a hot acid microwave digestion system and analyzed on an inductively coupled plasma mass spectrometer (ICP-MS), which will yield the concentrations of a suite of heavy metals in each sample. She will compare the heavy metal concentrations between organisms of the same species across the three estuaries to determine the relationships between heavy metal delivery to the coastal zone and heavy metals in the estuarine food web. In addition, she will compare the concentrations of heavy metals between different organisms within the same estuary to elucidate how the trophic level and location in the estuarine food web influences the heavy metal load of estuarine organisms. Estuarine food webs support the production of fish and shellfish that humans consume, and so understanding levels of potentially toxic heavy metals in estuarine organisms has implications for human health, along with ecosystem health. Should Ms. Curren discover that any of these organisms contain a level of heavy metals that rise to a level of concern for human health, she will contact regional stakeholders and managers for appropriate public notice.