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

July 22, 2016

SEED 2016

July 22, 2016/ Patrick Caveney

I presented a poster titled “Effects of Resource Sharing on Gene Expression Dynamics” at the 2016 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference in Chicago.

Dr. Julius Lucks, Associate Professor at Northwestern University, won the ACS Synthetic Biology Young Investigator Award and presented “Uncovering How RNA Molecules ‘Make Decisions’ On the Fly: Towards Understanding and Engineering CoTranscriptional RNA Folding." This was an amazing lecture about visualizing RNA folding as it is being transcribed. He described their SHAPE-Seq technology to protect RNA from degradation and measure the reactivity with nucleotide resolution. This allowed them to see hairpin loops fold and unfold as the RNA was transcribed.

Watters, Kyle E., et al. "Cotranscriptional folding of a riboswitch at nucleotide resolution." Nature structural & molecular biology 23.12 (2016): 1124.