John A. Bryant Jr

PhD Candidate • Biological Systems Engineering • Virginia Tech

jbryant2@vt.edu • https://jbryantvt.github.io/

 

Automated cloning workflows and modular DNA parts enable synthetic biologists to engineer specialized molecular systems for chemical synthesis, environmental response, pharmaceutical manufacturing, etc. I build software packages for automating synthetic biology with liquid handling robotics. I also design custom DNA parts that integrate with existing modular cloning toolkits to facilitate rapid multigene plasmid assembly. With these paired approaches, I am expediting synthetic biology design cycles, improving laboratory throughput, reducing training demands, and promoting reproducibility. I have four years of experience using automation and synthetic biology approaches to study the auxin signaling pathway in plants.

 

PhD, Biological Systems Engineering, Virginia Tech, GPA: 3.94                                                                                                                                       2019-Spring 2024

Thesis: An automated and high throughput framework for recapitulation and characterization of

regulatory plant genetics,

Advisor: R Clay Wright

BS, Biology (Chemistry minor), Samford University, cum laude, GPA: 3.57                                                                                                                2015-2019

 

Graduate Research Assistant, BioFoundry Laboratory, Virginia Tech                                                                                                                           2019-

                Advisor: R Clay Wright

Bayer B4U Mentee                                                                                                                                                                                                                         2023-

Program providing 1:1 mentoring with an industry scientist.                                                             

Davenport Leadership Fellow, Virginia Tech                                                                                                                                                                          2019-2020

Alabama Power Research Fellow, Samford University                                                                                                                                                      2018

University Fellow (Honors scholarship), Samford University                                                                                                                                           2015-2019

 

1.       Bryant, JA, *Kellinger M, *Longmire C, Miller R, and Wright RC (2023). AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots, Synthetic Biology, Volume 8, Issue 1, 2023, ysac032, https://doi.org/10.1093/synbio/ysac032

2.       Bryant, JA, *Longmire C, *Sridhar S, *Janousek S, *Kellinger M, and Wright RC (2023). TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 lab robots, SLAS Technology, ISSN 2472-6303, https://doi.org/10.1016/j.slast.2023.08.007

3.       Morffy N, Van den Broeck L, Miller C, Emencker RJ, Bryant JA, Mahatma S, Wright RC, Holehouse AS, Staller MV, Sozzani R, and Strader LC (2023). Plant Activation Domain Identification, Nature, In review.

4.       Bryant, JA, Taylor J, Bargmann B, and Wright RC (2023). A modular toolkit for engineering auxin response circuits in yeast, ACS Synth Biol, In preparation for submission.

5.       Bryant, JA and Wright RC (2023). Methods for Golden Gate assembly using AssemblyTron and Opentrons OT-2 lab robots. In: Schindler, D. (ed.) Golden Gate Cloning: Methods and Protocols, vol TBD. Humana Press, New York, NY, In preparation for submission. (Invited book chapter)

 

(*undergraduate mentee author)

 

1.       Bryant JA and Wright RC, AssemblyTron: Flexible automation of DNA assembly with OT-2 lab robots and DIVA. Opentrons Webinar. 2023 September 13th; Virtual. Link

2.       Bryant JA, Blazing a trail towards orthogonal auxin transcriptional regulation. Plant Biology 2023 (American Society of Plant Biologists national meeting), 2023 August 6th; Savannah, GA.

3.       Bryant JA, AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots. Process Development Symposium, 2023 Jun 14th; Vancouver, BC.

4.       Bryant JA, AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots. Translational Plant Sciences Center 2023 Symposium, 2023 Jan 27th; Blacksburg, VA.

5.       Bryant JA, DNtegrAte: An Open-Source Python Package for Performing DNA Assemblies with the OT-2 Liquid Handling Robot (Rapid Fire Talk). 2022 Synthetic Biology: Engineering, Evolution, and Design (SEED), 2022 May 2nd; Washington, DC. ID: 641420.

6.       Bryant JA, Overview of plant synthetic biology. Virginia Tech BSE Graduate Student Recruitment Weekend, 2020 February 26; Blacksburg, VA.

 

1.       Wright RC, Neres DF, Chaisupa PC, and Bryant JA (2023). Protein engineering and plants: the evolution of sustainable agriculture. Biochem (Lond) 10 March 2023; 45 (1): 12–17.

https://doi.org/10.1042/bio_2023_101

 

1.       Bryant JA, *Kellinger M, *Longmire C, Wright RC, DNtegrAte: An Open-Source Python Package for Performing DNA Assemblies with the OT-2 Liquid Handling Robot. 2022 Synthetic Biology: Engineering, Evolution, and Design (SEED), 2022 May 2nd; Washington, DC. ID: 641420.

2.       Bryant JA, Bargmann B, Taylor J, Wright RC, Finding molecular targets for engineering auxin signaling with synthetic interaction domains. 5th International Conference on Plant Synthetic Biology, Bioengineering, and Biotechnology, 2021 November 15-17; Virtual.

3.       Bryant JA, Bargmann B, Taylor J, Wright RC, Finding molecular targets for engineering auxin signaling with synthetic interaction domains. 38^th Mid-Atlantic Plant Molecular Biology Society Meeting, 2021 August 16; Virtual.

4.       Bryant JA, Bargmann B, Taylor J, Wright RC, Finding molecular targets for engineering auxin signaling with synthetic interaction domains. Virginia Tech Translational Plant Sciences Center Symposium, 2020 February 26; Virtual.

 

1.       Python: AssemblyTron, TidyTron

2.       R: Flow cytometry data analysis pipeline, custom scripts for TidyTron

3.       HTML and JavaScript: https://jbryantvt.github.io/TidyTron/Savings.html

 

Alpha Epsilon Agricultural and Biological Engineering Honor Society Inductee, Virginia Tech                                                                           2020

Order of Omega Leadership Honor Society, Samford University                                                                                                                                   2019

Gamma Sigma Alpha Honor Society                                                                                                                                                                                         2019

Dean’s List                                                                                                                                                                                                                                           2016-2019

 

1.       Spatial and temporal specificity of plant-hormone-induced gene expression and plant development                                      2019-

·         Goal: To characterize auxin signaling dynamics and rationally engineer gene expression.

·         Approach: Quantify the extent to which binding specificity between signaling proteins regulates gene

expression.

·         We built synthetic variants of auxin signaling proteins to quantify transcriptional specificity of these variants

on gene expression.

·         Expression data will allow us to generate a molecular model that informs rational engineering of pathway

dynamics.

 

2.       AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots                                                                   2020-

·         Github: https://github.com/PlantSynBioLab/AssemblyTron

·         Goal: To automate the error-prone DNA assembly process.

·         Approach: Develop protocols for Opentrons lab robots to assemble plasmids beginning from primers and

DNA templates.

·         This package automatically generates PCR parameters, dilution factors, output files, etc. for any DNA

construct designed with the J5 algorithm.

 

3.       Expediting rootstock and scion breeding for cold and drought tolerance by predicting hormone signaling interactions               2022-                    

·         Goal: To develop high throughput molecular assays for functional characterization of hormone

perception in apple.

·         Approach: Infiltrate Abscisic acid response element reporter into apple leaves.

·         We have developed an effective agroinfiltration protocol for transient expression of reporters in

apple leaves.

 

Alternate, Virginia Space Grant Consortium Graduate Research Fellowship                                                                                                            2023

                AssemblyTron 2.0: a software platform for automating continuous directed evolution.

Fellowship for Graduate Student First-Author Papers, Virginia Tech College of Engineering                                                                             2023

Graduate and Professional Student Senate Spring 2022 Travel Fund Program Award                                                                                          2022

(funding for SEED Meeting 2022)

Excellence Fund (funding for ASB Meeting 2018)                                                                                                                                                                2018

 

Bioprocess Engineering Lab (TA)                                                                                                                                                                                                BSE 4534

Undergraduate and high school Research Mentor                                                                                                                                                             2021-

                High school mentee won Blacksburg regional science fair.

Black Engineering Excellence at Virginia Tech (BEE VT)                                                                                                                                                     2023

                Building with Biology Seminar

 

American Society of Plant Biologists, graduate member                                                                                                                                                  2021-

American Institute of Chemical Engineers                                                                                                                                                                             2023-

                Society for Biological Engineering

Association of Southeastern Biologists, undergraduate member                                                                                                                                 2018-2019

 

Vice President for Bioprocess Engineering, Biological Systems Engineering                                                                                                             2020-2021

Graduate Student Organization, Virginia Tech

President, Tribeta Biological Honor Society, Samford University                                                                                                                                  2018-2019

 

Civil and Environmental Consultants, Inc., Bat surveys Intern                                                                                                                                        2018

Dynamic Biosciences, Intern                                                                                                                                                                                                        2017

Analytical Industrial Research Laboratories, Inc., Analyst                                                                                                                                                 2016