Shelby Anderson is a first year graduate student in Chemical and Biomolecular Engineering (CBE). This Fall she is taking core courses in CBE and will start her CBI rotations in the Winter and/or Spring terms.
Teresa Cruz is a first year graduate student in Biological Sciences (BISC). This Fall she is taking courses and doing lab rotations.
Angel D’Oliviera (CBC) works in Dr. Jeff Mugridge’s lab studying RNA-modifying enzymes. She is investigating the structural and biochemical basis for substrate specificity by RNA demethylases and establishing a link between their function and the progression of Glioblastoma, a severe brain cancer with low prognosis.
Rachael Gill (BISC) is working in the Jessica Tanis lab characterizing the biogenesis of extracellular vesicles (EVs) from the ciliated sensory neurons in C. elegans. Currently, this project focuses on the role of lipid translocases in altering plasma membrane lipid composition for EV release. Additionally, she is seeking to determine the localization of EV marker proteins in the cilia before EV budding.
Summer Hackenburg (BISC) is a 3rd year Ph.D. student working in Dr. Ramona Neunuebel’s lab. She is currently working on unfolding the mechanisms behind Legionella pneumophila infection, the causative agent of Legionnaires disease. These works include characterizing 1 of the over 350 effector proteins that Legionella secretes to aid in infection of human lung macrophages. Additionally, she is interested in learning new techniques for protein characterization.
Eli Learn is a first year graduate student in Chemistry and Biochemistry (CBC). He is taking courses and doing his lab rotations.
Chris Mayhugh is a first year graduate student in Chemical and Biomolecular Engineering (CBE). He is taking core courses in CBE and will begin rotations in Winter/Spring terms.
Ellie Meck a first year graduate student in Chemistry and Biochemistry (CBC). She is taking courses and doing her lab rotations.
Vadesse L. Noundou (BISC) is working in Dr. Thomas Hanson’s lab. The Hanson laboratory focuses on photosynthetic bacteria, using Chlorobaculum tepidum as a model organism for green sulfur bacteria. Because it is autotrophic and oxidizes reduced sulfur compounds, it may be useful to make products from CO2 while consuming toxic hydrogen sulfide or large amounts of waste elemental sulfur produced in industrial processes. The principal question my research is trying to answer is how does membrane metabolism shape C. tepidum’s energy metabolism? Currently, I am investigating two topics, the potential role of outer membrane vesicles in S(0) globule metabolism and the biogenesis of chlorosomes, a light harvesting complex made from the cell membrane.
Rachel Putnik (CBC) s working in the lab of Dr. William Chain.
Stephanie Tsang is a first year graduate student in Chemistry and Biochemistry (CBC). She is taking courses and doing her lab rotations.
Cameron Twitty (CBC) is working in the M. Watson lab developing cross-couplings of lysine-derived pyridinium salts for the generation of unnatural amino acids. New synthetic methodologies to prepare unnatural amino acids are of particular importance because such molecules are critical for preparation of peptides with biorthogonal handles for labelling and for peptide-based drugs, which have become increasingly prevalent as pharmaceuticals due to their unique activities and low toxicity.
Elorm Awuyah (CBC) works for Dr. Laure Kayser synthesizing soft organic electronic polyelectrolyte materials. These materials will be used in the development and fabrication of organic electrochemical transistors (OECTs), which will be implemented into devices for the treatment of neurological disorders.
Patrick Beardslee (CBC) is working in the Karl Schmitz (Advisor) lab developing novel high-throughput screening methods to identify terminal sequences that promote proteolysis in bacteria. Bacteria possess multiple ATP-dependent proteases to carry out regulated destruction of damaged or unwanted proteins in the cytosol to maintain protein homeostasis. These proteases can selectively discriminate substrate from non-substrate proteins, minimizing wasteful or harmful off-target proteolysis. Bacteria have evolved various different ways to regulate substrate recognition, including directly via short unstructured terminal sequences termed degrons. However, the overarching rules governing this sequence-based recognition remain largely unknown. Our screening approaches will allow us to systematically interrogate degron specificity and uncover these rules that allow ATP-dependent proteases to discriminate degrons from the millions of possible terminal sequences.
Ashlyn Cantrel (CBC) is working in Dr. Joseph Fox’s lab to develop a new generation of dihydrotetrazines with increased shelf-life and stability toward background oxidation, as well as increased ligation rates when oxidized to their corresponding tetrazines. A library of these dihydrotetrazines will be synthesized to be used in targeted drug delivery utilizing the tetrazine ligation initiated by photocatalyzed or enzymatic oxidation of dihydrotetrazine prodrug molecules.
Alyssa Conner (CBC) is working in the Don Watson (Advisor) Lab developing phosphine pre-catalysts to further understand the oxidative addition processes of the silyl-Heck reaction and utilize cheaper, previously inaccessible silyl-chloride electrophiles. Developing practical synthetic methodology to prepare silicon-containing small molecules is of particular importance as such molecules are critical intermediates in the synthesis of bioactive compounds, and silicon compounds themselves are increasingly recognized as bioisosteres of biologically active compounds that possess altered selectivities and pharmacokinetic profiles. Allyssa is also working to develop a palladium-catalyzed Hiyama-Denmark-type cross coupling that utilizes un-activated vinyl silanes to generate tetrasubstituted alkenes, an important moiety in medicinal molecules – such as Tamoxifen, an anti-cancer drug used in the treatment of breast cancers.
Geneva Crump (CBC) Microbial Interactions Important for Human Health: Uncovering Bacterial-Fungal Crosstalk in the Human Microbiota through Molecular Recognition
Megan Dang (CBE) is working in Emily Day’s lab developing RNA and antibody nanocarriers to enable high precision treatment of triple negative breast cancer. High precision gene regulation is achieved via on-demand NIR light triggered release of miRNA and delivery of siRNA via specific antibody receptor binding.
Marina Grossi (CBC) is currently investigating mechanisms that the bacterial pathogen Legionella pneumophila uses to escape detection and degradation during replication in human alveolar macrophages, such as the hundreds of effector proteins that it secrets during the infection. Primarily, she is interested in how L. pneumophila effectors can recognize and bind to specific phosphoinositides, and in doing so hijack host vesicular trafficking in a way that is advantageous to the bacterium’s replication. One key effector of interest, Lpg2409, has previously been demonstrated to bind specifically to phosphatidylinositol-3-phosphates and is secreted late during the infection, a period of time not well characterized in the literature. Additionally, Lpg2409 harbors a putative F-box like domain, suggesting that it could participate in host E3 ubiquitin ligase complexes. An overarching question would be if Lpg2409 is manipulating host processes during late Legionella infection, such as protein quality control, autophagy, or apoptosis, through its putative participation in E3 ligase complexes. Her advisor is Dr. Ramona Neunuebel.
Sadia Islam (BISC) is working in the lab of Dr. Velia Fowler to characterize the role of actin regulation in fiber cell morphogenesis and biomechanism in mouse lens. The transparency and mechanical flexibility of the eye lens tissue is required for normal vision. Loss/alteration of transparency and biomechanical properties of lens leads to 1) cataracts, the leading cause of blindness and 2) presbyopia, an age-dependent increase in lens stiffness reducing ability to change shape (accommodation) to focus from near to far. Sadia’s current project is to characterize how F-actin is disrupted in the Cap2-/- mouse lens, and how this affects lens fiber cells, leading to loss of lens transparency and potentially altered biomechanics.
Joshua Jachuck (CBE) completed his CBI rotations in the labs of Terry Papoutsakis and Catherine Fromen. In the Papoutsakis Lab, he studied the production and function of extracellular vesicles (EVs) produced from CHRF-288-11, an immortalized megakaryocytic cell line. In the Fromen Lab, he investigated the properties of supernatant from particle-treated macrophages to improve primary T-cell longevity.
Andrew “AJ” Jemas (CBC) (Advisor: Joseph Fox). AJ is working on utilizing the tetrazine ligation to develop novel chemical biology tools. This bioorthogonal reaction is the fastest of its kind and has myriad biological applications both in vitro and in vivo with minimal perturbation of the native cellular environment. His current projects are focused on utilizing a light-activated tetrazine for on demand, spatiotemporal control of bioorthogonal reactivity for protein labeling and redox monitoring. AJ has successfully applied this tool to label proteins with fluorophores in both bacterial and mammalian cells, and is currently collaborating with Pfizer on using it to probe extremely low abundant endogenous proteins for drug discovery.
Esther Roh (CBE) is working in the Epps and Sullivan groups to develop formulations with controlled co-delivery of multiple cargoes using a stimuli-responsive polymer. We aim to understand how polymer design, nanoparticle composition, and stimulus application modulates nanoparticle stability, which ultimately defines the release and activity of multiple cargoes in both space and time for maximum synergy between cargoes.
Christine Rourke (BISC) is working in the lab of Dr. Aimee Jaramillo-Lambert, characterizing the differential role of DNA topoisomerase II in male and female meiosis.
Brittany Shimanski (CBC) is working in the Mugridge lab, obtaining a biochemical understanding of mRNA demethylation intermediates and products by FTO in the cell. Brittany plans to characterize the stability of the intermediates and develop probes to trap them; thenuse the probes with RNA seq to map the demethylation sites on RNA and characterize the cellular roles of the intermediates.
Zachary Stillman (CBE) current research focuses on developing pulmonary drug delivery vehicles, primarily in the form of metal-organic frameworks (MOFs). I have optimized the synthesis of UiO-66 MOF nanoparticles to independently control particle size and missing linker defects and have performed studies to confirm its biocompatibility, ability to load and release small molecule cargo, and capability for aerosolization. We are continuing to refine this system and explore its and other MOFs’ capabilities as pulmonary drug delivery vehicles.
Erica Green (CBE) is working in the Kelvin Lee lab to develop a mammalian cell expression platform for adeno-associated virus (AAV) vector production. Prior to coming to UD, she worked on projects in both upstream and downstream bioprocessing while working at Merck and doing undergraduate research at Carnegie Mellon University.
Stephen Hyland (CBC) is working in the Grimes lab to develop new chemical probes to decorate the peptidoglycan cell wall with various bioorthogonal functionalities. The human innate immune system defends the body from pathogens with macrophages. These macrophages differentiate between commensal and pathogenic bacteria through recognition of the breakdown of their peptidoglycan into fragments. Specific fragments signal for different immune responses and misrecognition can lead to the development of Crohn’s disease, inflammatory bowel disorders, and gastrointestinal cancers. We hijack the natural peptidoglycan biosynthesis pathway to incorporate chemical handles onto N-acetylmuramic acid which will subsequently allow for labeling and visualizing.
Michaela Jones (CBE) is working in the Kunjapur Lab to improve non-standard amino acid for in vivo protein bioconjugation. Non-standard amino acids (nsAAs) allow for the introduction of unique chemistries into specific sites in a protein. Various click chemistries are of particular interest for the development of novel synthetic biology tools; however, nsAA incorporation efficiencies are too low to pursue such technologies. So the Kunjapur Lab is investigating several different approaches for improving nsAA incorporation of multiple nsAAs at distinct, genetically encoded sites.
DeVonte Moore (CBC) is working in the April Kloxin lab to study the role of cellular autophagy in breast cancer cell dormancy and recurrence. Research within the April Kloxin group focuses on the development of novel biomaterials that can be utilized as flexible platforms for asking fundamental questions about the influences of the extracellular environment surrounding a cell. My project aims to use engineered hydrogels, in combination with cutting edge bioinformatics techniques and biochemical assays, to create 3D breast cancer cell culture model systems that will allow us to effectively interrogate cellular autophagy as a mechanism by which breast cancer cells exploit to endure periods of high metabolic stress, specifically, during chemotherapeutic treatment. Understanding these processes will allow for discovery and characterization of autophagy inhibitors for use in more robust chemotherapeutic treatment options.
Jessica O’Brien(CBC) is working with Dr. Joseph Fox to study the mechanism of diazirine photoaffinity labeling, which is commonly used to covalently tag proteins. Understanding the mechanism will allow us to develop better probes, both with higher labeling efficiency and selectivity. We currently have several probes in development that we believe will be useful for chemical biologists.
Brielle Hayward-Piatkovskyi (BISC) is working in the Gleghorn lab to study the role donor sex plays in cardiovascular development. Cells in culture, including those isolated from cardiovascular tissue, retain a memory of their donor sex that result in differential gene expression. The intent is to investigate how the molecular mechanisms that result from these differences influence cardiovascular developmental programming. The focus of this research is on cardiovascular diseases where one sex has higher risk than the other with an aim to understand how these underlying sex dependent molecular mechanisms contribute to the sex dependent risk factors.
Michael Lynn Dahle (CBE) is working in the Antoniewicz lab to study metabolism’s role in microbial ecology. Naturally occurring microorganisms are often auxotrophic: it is more efficient for an organism to over-produce one metabolite in exchange for essential metabolites supplied by community partners. To identify and quantify what is exchanged, an organism is grown on sugars labeled with 13C. The labeling patterns of biomass constituents are measured using GC/MS. From these data, metabolic flux analysis (MFA) calculates the flux for each intercellular and intracellular pathway. Co-cultures of auxotrophic E. coli knockouts (and other model organisms) are used to model natural microbiomes. Relationships in microbial ecology can be understood with insights from economics and game theory.
Katherine Nelson (CBE) is working in the Gleghorn and Sullivan labs to develop a method to treat women with pre-eclampsia. Using a targeted drug delivery system, the goal is to develop a system to safely deliver drugs that are harmful to the developing baby to the mother.
Julia Rosenberger (CBC) is working in the Fox lab on the development and application of the photocatalytic activation of tetrazines. One application utilizes near-IR (NIR) light to trigger the release of a drug from a dihydrotetrazine-based prodrug. Another involves in situ generation of electrophiles for tagging proteins of interest. Our goal is to create a system in which small molecule drugs or probes can be released, or “turned-on”, in a spatiotemporally controlled manner.
Phillip Taylor (CBE) is working in the Jayaraman and Kloxin labs to develop molecular models of responsive biomaterials, specifically biomimetic materials such as collagen-like peptides (CLP) and elastin-like peptides (ELP) which mimic the body’s extracellular matrix. We aim to use a combination of atomistic and coarse-grained molecular dynamics simulations to study the self-assembly and phase transitions of these thermoresponsive biopolymers, including but not limited to, their melting transitions and lower critical solution temperature (LCST) transitions. Moreover, our simulations will guide experiments and the development of biomaterials for biomedical applications such as thermoresponsive ELP- and CLP-based nanocarriers for on-demand drug release, and thermally stable CLP hydrogels which can be used for in vitro cell culture models and tissue engineering applications.
Kimberly Wodzanowski (CBC) is working in the Catherine Grimes and April Kloxin labs to develop a three-dimensional bacteria-macrophage co-culture hydrogel system to use as an invasion assay. We aim to utilize this system to study bacterial peptidoglycan fragments generated during an immune response.. This will give us insights into how our bodies respond to bacteria in natural and diseased states like Crohn’s disease.
Michael Clupper (BISC) is working in the Tanis lab to understand how biological cargo is sorted into extracellular vesicles (EVs). EVs are membrane-wrapped particles that mediate cell-cell signaling in numerous physiological and pathophysiological contexts. The Tanis lab uses the model organism C. elegans to answer basic questions of EV biology in vivo, using genetic tools, super-resolution imaging, and biochemical techniques.
Allyson Dang (CBC) is working in the Gleghorn lab to develop a biocompatible and synthetic self-healing hydrogel with user-defined spatiotemporal control to create structured cellular microenvironments for multi-dimensional culture. We aim to integrate this system with with microfabircation technologies to create structured hydrogel networks and complex hierarchical tissues.
Nate Hamaker (CBE) is working in the Kelvin Lee lab to improve the productivity and stbility of recombinant Chinese Hamster Ovary (CHO) cell lines. The intent is to develop a reporter system to screen sttrategies for increaseing the efficiency of site-specific integration (SSI) of transgenes into the CHO genome, as well as explore the potential of SSI to enhance productivity stability. At the same time, a proteomic approach is being taken to determine the effect of cell age on stability and host cell protein profile of an industrially relevant, monoclonal antibody-producing cell line.
Ophelia Ukaegbu (CBC) is working in the Grimes lab to stabilize Nod2 Chrohn’s associated mutants. The development of chaperones will be used to stabilize Nod2 and restore signalling as a therapeutic for Crohn’s disease.
Victoria Hunt (CBE) is working in the Wilfred Chen/Kelvin Lee labs with the goal to develop a temporally controlled gene regulation program utilizing CRISPR-Cas9 and toehold mediated strand displacement technologies. CRISPR (clustered regularly interspaced palindromic repeat)/Cas (CRISPR-associated systems) is found in nature as an adaptive immune defense for bacteria and archaea against invading foreign nucleic acids. Type II CRISPR/Cas9 systems have been engineered for gene regulation, either repression (CRISPRi) or activation (CRISPRa) with success in bacterial and mammalian cells. Using an engineered gRNA, it is possible to show conditional gene regulation using toehold-mediated strand displacement. This type of temporal control has successfully shown gene repression in bacterial cells. This technology provides inducible control over gene expression based on the presence of a trigger strand. The innovation of this technology is the potential for creating an autonomous cell network. Based on transcriptomic data, the trigger strand can be designed to be virtually any endogenous mRNA that is responsive to some nutrient, product, or process condition within the cellular network. This type of technology could be engineered to affect changes in cellular phenotype by allowing temporal control of gene expression in relevant pathways affecting cellular productivity, product quality, apoptosis, cellular growth, or metabolism.
Jodi Kraus (CBC) is working in the Polenova lab investigating the structure and dynamics of various cytoskeletal-associated protein assemblies by magic angle spinning (MAS) solid-state NMR, as well as magnetic resonance methods development.
Alexander Mitkas (CBE) is working in the Wilfred Chen lab developing synthetic CRISPR scaffolds to provide dynamic comtrol of metabolic fluxes in vivo. The scaffolds will help assemble proteins of interest to increase reaction rates and dynamically assemble and disassemble proteins based on the relative metabolite levels in the cell.
Rebecca Noll (BISC) is working in the Neunuebel lab with the overall goal of characterizing the functions of Legionella pneumophila effector proteins. Her current focus is to understand how this pathogen uses its effectors to exploit phosphoinositide lipids for intracellular survival.
Baruch Turniansky (CBC) is working in the Koh Lab on developing and investigating small-molecule catalytic acetylation of enzymes, including DHFR. Acetylation is a common post-translational modification that modifies the activity of enzymes, and many drug targets can be targeted with this system.