BIOTECHNOLOGY TRAINING PROGRAM

Doctoral Research Project:  Water contamination remains a pressing global issue, yet current detection methods rely on expensive laboratory instruments or hand-held devices, limiting accessibility in low-resource settings. Cell-free biosensors offer a promising alternative—freeze-dried cell-free reactions produce measurable signals when rehydrated with water samples, are low-cost and field-deployable. To improve these biosensors, researchers have incorporated riboswitches, RNA structures that activate reporter gene expression upon ligand binding. However, natural riboswitches are difficult to engineer because their ligand-binding and gene-expression domains must overlap in sequence. Recently, the Lucks Lab discovered tug-of-war (TOW) riboswitches, which use competing RNA structures instead of sequence overlap, enabling independent tuning of ligand-binding affinity and output strength. My research project combines AI-guided sequence design with high-throughput, automated screening to optimize TOW riboswitch sensitivity and response time in cell-free systems to detect major water contaminants.

Doctoral Research Project:  With an estimated 24 million tons of plastic waste released into environmental systems each year, plastic pollution poses a threat to human and environmental well-being. Plastics composed of aromatic functional groups, such as polystyrene (PS) and polyethylene terephthalate (PET), tend to be particularly recalcitrant due to their hydrophobicity and high thermal stability. Biological recycling of plastics offers a sustainable method for mitigating pollution and recovering carbon from this waste feedstock. Microbial processing of plastic materials and derivatives can facilitate the conversion of complex aromatic polymers into commodifiable chemicals and biopolymers, like polyhydroxyalkanoates (PHAs). Comamonas testosteroni KF-1, a wastewater bacterium, presents a novel, non-model host for this, as it can catabolize recalcitrant aromatics derived from PET and PS and produce PHAs from these plastic-derived carbons. However, the metabolic networks and regulatory mechanisms required for tandem aromatic processing and PHA biosynthesis have not yet been characterized. Through a comprehensive multi-omic analysis with flux modeling of C. testosteroni carbon metabolism, I aim to build a metabolic roadmap to inform strain engineering for improved aromatic carbon allocation to PHA biosynthesis. This work will aid in the design of a biotechnological platform capable of converting mixed plastic waste streams into valuable biopolymers, increasing the circular nature of our carbon economy.

Doctoral Research Project:  Interleukin-2 (IL-2) is a cytokine that has shown strong promise in cancer immunotherapy by activating and expanding T cells and natural killer (NK) cells to better destroy cancerous cells. However, the therapeutic delivery of IL-2 often causes severe toxicities for patients, taking the form of adverse reactions that limit IL-2's viability in high doses. These limitations have motivated my research to develop an IL-2 mimic that can be selectively deactivated after delivery to mitigate or stop adverse reactions to IL-2's signaling pathways. This mimic will take the form of a megamolecule, based on a novel protein fusion platform developed by the Mrksich Lab that uses custom synthetic linkers to bridge protein domains in multi-specific constructs. The IL-2 construct will include a click-reactive synthetic linker that can cleave the megamolecule after delivery of a secondary compound, allowing us to turn off IL-2 signaling on command. This approach aims to produce a more translatable IL-2 analogue that takes advantage of this powerful cytokine signaling mechanism in a more controlled manner that is safer for patients.

Doctoral Research Project:  Translation is the process by which ribosomes decode messenger RNA (mRNA) into proteins. While translation typically initiates at an optimal start codon (AUG), ribosomes can also initiate at upstream AUGs or near-cognate codons (codons that differ from AUG by one nucleotide), leading to the translation of upstream Open Reading Frames (uORFs). uORF expression inhibits canonical protein expression and can lead to the expression of new micropeptides with downstream biological roles. 2’-O-methylation (Nm) is a chemical modification of RNA guided by small nucleolar RNAs (snoRNAs) and catalyzed by methyltransferases like Fibrillarin (FBL). Preliminary data has shown that Nm at start codons can inhibit uORF initiation while enhancing downstream canonical protein expression. I aim to 1) investigate whether Nm is an adaptive mechanism of uORF regulation during stress and 2) program inhibition of pathogenic uORFs via targeted 2-’O-methylation. For the former, I will develop a novel method to simultaneously map Nm, the transcription start site (TSS), and the translation initiation site (TIS) on the same mRNA. This method will overcome one of the major obstacles in post-transcriptional RNA regulation by simultaneously capturing RNA modifications and their consequences during both transcription and translation. For the latter, I will engineer and test artificial snoRNAs on a dual-reporter system to identify optimal snoRNA systems that can be used to target pathogenic uORFs. These findings will enable the development of new therapeutics with scalability across multiple disease types involving aberrant translation.

Doctoral Research Project:  Organisms have evolved cellular stress response mechanisms to maintain homeostasis and function in the face of diverse intrinsic and environmental challenges. Dysregulation of these pathways contributes to numerous human diseases, including cancer. Therefore, defining how these cytoprotective programs promote cellular resilience and how cells adapt to stressful environments is increasingly important for understanding cancer development and identifying novel therapeutic vulnerabilities. Our current knowledge of cellular stress responses is largely based on studies employing acute and severe stressors that are incompatible with continued proliferation. Cancer cells, however, must proliferate despite persistent stress, suggesting that they engage distinct adaptive mechanisms that remain poorly understood. To address this gap, my project integrates chemical-genetic functional genomics and transcriptomics to identify factors required for proliferation under stress and to define the transcriptional programs that enable this adaptation. Using these data, I will construct a comprehensive cellular stress atlas to define the functional networks that coordinate cellular adaptation to persistent stress. I will then combine mechanistic studies with multiomic profiling to determine how these adaptive programs are regulated. Together, this work will provide new insights into how cancer cells adapt to persistent stress and reveal potential therapeutic strategies arising from their dependence on these mechanisms.