Current Students

Bradley Biggs

Bradley Biggs

2012 B.S. Chemical Engineering, University of Southern California
Ph.D. Advisor: Keith Tyo

Doctoral Research Project:
I work in the laboratory of Prof. Keith Tyo in Chemical and Biological Engineering. My research focuses on protein engineering within the context of whole cells. This comes predominantly in the form of the introduction of new chemical functionality by way of novel ligand binding domains or protein-protein interactions for the output of either chemical signal transduction or chemical synthesis. To accomplish these output goals, I care about the free energy of each protein fold, using computational approaches to evaluate this parameter, and appreciate both promiscuous enzyme functionality and specific cell contexts (E. coli, S. cerevisiae, etc.).

Shannon Brady

2014 B.A. Biology, University of Kentucky
Ph.D. Advisor: Erik Andersen

Doctoral Research Project:
Many traits that were once believed to act in a simple Mendelian nature have been determined to be much more complex. Some complex traits that are of interest to the medical field are disease susceptibility and drug sensitivity in humans. My work in the Andersen lab focuses on correlating genetic variants to variation in drug response in Caenorhabditis elegans. Specifically, I will focus on understanding variation in sensitivity to bleomycin, a chemotherapeutic drug that results in highly variable efficacy and toxicity in human cancer patients.

Evan Buechel

Evan Buechel

2015 B.S. Biochemistry, University of Wisconsin - Madison
Ph.D. Advisor: Heather Pinkett

Doctoral Research Project:
The multiple drug resistance phenomenon that occurs in bacterial and fungal infections, as well as human cancer, is primarily the result of the upregulation of a set of ABC transporters that are capable of exporting a wide range of xenobiotics. In S. cerevisiae, the master regulator of this set of ABC transporters is the transcription factor Pdr1p, which has homologs in humans and in bacteria. Currently, it is known that Pdr1p is capable of binding xenobiotics, and what DNA sequences it binds to. Through structural and biochemical studies, I will answer how Pdr1p binds xenobiotics and identify what conformational changes it undergoes to upregulate transcription.

Janel Davis

Janel Davis

2014 B.S. Biomedical Engineering, University of Texas at Austin
Ph.D. Advisor: Hao F. Zhang

Doctoral Research Project:
Recent advances in super resolution imaging techniques have presented the opportunity to investigate new detection and diagnosis methods. Working with collaborators, the Zhang lab has developed a spectroscopic photon localization microscopy (SPLM) platform. SPLM utilizes extrinsic emission to locate and detect spectral signatures with high spatial and spectral resolution. My research will use bacterial drug resistance as a model to demonstrate how this nanoscopic imaging platform can be used to detect and study nucleic acids. This technology has the potential to have many applications in the discovery, detection and characterization of numerous diseases. Additionally, the improved resolution is ideal for studying the process of gene expression which will allow us to better understand how pathogens become drug resistant and virulent.

Do Soon Kim

2014 B.S. Chemical Egineering, The University of Texas-Austin
Ph.D. Advisor: Mike Jewett

Doctoral Research Project:
In the Jewett Lab, I am using oRibo-T, a recently developed synthetic ribosome with tethered subunits to promote production of novel biomolecules. Specifically, I will be focusing on engineering the ribosome's peptidyltransferase center (PTC) to promote new chemistries beyond the conventional alpha-peptide bond formation currently observed in wild-type ribosomes. The ability for the ribosome to accommodate unnatural monomers beyond the standard 20 amino acids as well as the ability to catalyzenew chemical bonds in its catalytic PTC would redefine the ribosome as a general polymerizing biomachine, opening up possibilities in the production of sequence-defined polymers with applications in therapeutics and biomaterials previously unobtainable.

Sophia Liu

Sophia Liu

2014 B.S. Chemistry, National Tsing Hua University in
Ph.D Advisor: Luis Amaral

Doctoral Research Project:
Metagenomic data from microbiomes are a treasure trove of data that have widespread applications in biotechnology, human health, and environmental protection. With current sequence analysis techniques, we are still unable to identify the majority of the sequences in these datasets. I propose that we can use ancestral genome reconstruction as a method to increase gene identification in these datasets, in order to mine for genes that can be engineered for biotechnological and biomedical applications.

Andres Martinez

2014 B.S. Chemical Engineering, Purdue University
Ph.D Advisor: William Miller

Doctoral Research Project:
My research focuses on studying ex-vivo platelet production from megakaryocytes by utilizing microfluidic bioreactors. The three aspects of the research include computational fluid dynamics modeling of bioreactors to understand the shear and velocity profiles generated ex-vivo so as to match the vasculature profiles experienced in vivo. The second aspect of the research includes fabricating and testing the bioreactors using live imaging microscopy to understand the platelet formation by analyzing release kinetics. Third, by probing the cytoskeletal rearrangement that occurs inside the megakaryocytes during platelet formation with the use of inhibitors of RhoA, Rac1 and Cdc42 GTPases, I hope to elucidate a novel mechanism of platelet formation and further integrate that into our bioreactors to study these inhibited cells under flow conditions.

Becky Sponenburg

Rebecca Sponenburg

2014 B.S. Chemistry, Gettysburg College
2014 B.S. Philosophy, Gettysburg College
Ph.D Advisor: Thomas Meade

Doctoral Research Project:
In the Meade lab, I work on the design of cobalt(III) Schiff-base complexes for protein inhibition. Previous complexes in our lab have demonstrated inhibition of α-thrombin via coordination to histidine residues in a pro-drug type strategy, but there are still many synthetic factors which must be addressed to make these complexes relevant for bio-medical applications.  My project seeks to fill this need by designing and synthesizing a series of electron donor species which are light-activated by near-infrared wavelengths and achieve efficient electron transfer.  Not only would this provide essential information about the electron transfer process in molecules of this type, but the finished agent will be able to be tested in-vivo for bio-compatibility.

Jimmy Su

2013 B.S. Biomedical Engineering, The Johns Hopkins University
Ph.D. Advisor: Ramille N. Shah and Jason Wertheim

Doctoral Research Project:
The kidney glomerulus is the initial site of fluid filtration of the nephron. Development and maintenance of the glomerular filtration barrier (GFB) relies upon specific interaction between endothelial cells and podocytes. The objective of my project is to elucidate how defined biochemical and structural boundaries within the extracellular matrix proteins (ECM) of the glomerular basement membrane (GBM) can direct podocyte and endothelial cell interactions to help understand regenerative processes within the glomerulus and develop new strategies for renal engineering and recovery of function. To investigate the importance of biochemical boundaries, I will decellularize kidneys from transgenic mice that exhibit conditional knockdown and knockout of vascular endothelial growth factor (VEGF) expression in podocytes and use the isolated ECM scaffold with altered VEGF retention levels for cell culture. To investigate the importance of structural boundaries, I will develop hydrogels and printable bioinks from isolated renal ECM to allow precise control and organization of fabricated scaffolds and printed cells using a 3D bioplotter.