Bredesen Center for Interdisciplinary Research and Graduate Education

I am a PhD student at the University of Tennessee, Knoxville and Oak Ridge National Laboratory with a Bredesen Center Fellowship. I research noise in protein expression at under the guidance of my advisors Mike Simpson in the DOE sponsored Center for Nanophase Material Science and Mitch Doktycz in BioSciences Division.

Cell-sized, cell-free reactions are increasing in complexity and imitating many functions of living cells. They have membranes, the ability to make proteins, form pores, grow, metabolize glucose, and communicate with cells. However making protein, the basis for every living cell, is highly variable in these reactions. Identically prepared reactions often show order of magnitude differences in the amount of protein made chamber-to-chamber. Understanding the causes of this variability will allow greater functionality for cell-sized, cell-free reactions.

I became interested in biology and genetics after creating transgenic, green fluorescent bacteria in high school AP biology. As an undergraduate junior, I worked with Dr. Mingjun Zhang to model the Young’s modulus of a silicone matrix filled with dispersed nanoparticles. Senior year, I worked with Dr. Cong Trinh to create a collection of plasmids with different copy numbers and antibiotic resistances. These plasmids were then incorporated into other work being done in the lab for better control over enzyme production and the associated metabolic processes. I graduated with a Bachelor of Science in Biomedical Engineering with a minor in Engineering Entrepreneurship from the University of Tennessee, Knoxville.

My ORNL profile is here.

My Google Scholar profile is here.

Awards:

2018 Extraordinary Professional Promise - Chancellor’s Citation Awards - Chancellor’s Honors Banquet

Bredesen Center Energy Science Engineering Fellowship

Summa cum laude 2013

Deans list Fall 2009 - Spring 2013

Alcoa Engineering Study Abroad Fellow

Tau Beta Pi member

Research Publications:

Norred, S. Elizabeth, Patrick M. Caveney, Gaurav Chauhan, Lauren K. Collier, C. Patrick Collier, Steven M. Abel, and Michael L. Simpson. "Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns." ACS synthetic biology 7, no. 5 (2018): 1251-1258.

Boreyko, Jonathan, P. Caveney, Sarah L. Norred, Charles Chin, Scott T. Retterer, Michael L. Simpson, and C. Pat Collier. "Synthetic Biology in Aqueous Compartments at the Micro-and Nanoscale." MRS Advances 2, no. 45 (2017): 2427-2433.

Caveney, Patrick M., S. Elizabeth Norred, Charles W. Chin, Jonathan B. Boreyko, Brandon S. Razooky, Scott T. Retterer, C. Patrick Collier, and Michael L. Simpson. "Resource Sharing Controls Gene Expression Bursting." ACS Synthetic Biology (2016). [PDF]

Norred, S. E., Caveney, P. M., Retterer, S. T., Boreyko, J. B., Fowlkes, J. D., Collier, C. P., et al. Sealable Femtoliter Chamber Arrays for Cell-free Biology. J. Vis. Exp. (97), e52616, doi:10.3791/52616 (2015).

Lijin Xia, Zhonghua Xu, Leming Sun, Patrick M. Caveney, Mingjun Zhang. (2013) “Nano-fillers to tune Young's modulus of silicone matrix.” Journal of Nanoparticle Research. v. 15 pg. 1570. [PDF]

Graduate Courses Taken

LFSC 507 - Programming for Biological Data Analysis

STAT 537 - Statistics for Research I

ESE 597 Bioenergy Journal Club

MSE 578 Advanced Biomaterials/Nanomaterials

PHYS 642 BioPhysics

ESE 697 Stochastic Processes Bio/Sys

CBE 691 Biomolecular Kinetics and Cellular Dynamics

MATH 527 Stochastic Modeling

ESE 593 Independent Study

ESE 593 Independent Study: Entrepreneurship

ESE 593 Entrepreneurship Studies

ESE 511 Introduction to Energy Science & Technology I

ESE 512 Introduction to Energy Science & Technology II

March 28, 2019

Dissertation Defense

March 28, 2019/ Patrick Caveney

I passed my dissertation defense! My presentation is here. It starts with the importance of biological solutions to increasing energy needs. Then dives into how these biological energy solutions depend on accurate control of protein expression. I covered important background topics including noise in protein expression, gene expression bursting, resource sharing, cell-free protein expression, microfluidics, and artificial vesicles. Finally, the purpose of my dissertation is to investigate how gene expression bursting and variation is affected by expression resources being shared among genes. I specifically answer:

How are gene expression characteristics altered by the size of resource pools?
Can membrane permeability be tuned to enhance gene expression?
How are the dynamics of gene expression affected by resource transport across permeabilized membranes?

My parents and grandmother were there to support me. Afterward we celebrated with dinner at J.C. Holdway in downtown Knoxville.