Here you will find my background, research & publications, teaching portfolio, CV, & contact info.
About
Dr. Courtney E. Gonzalez studied Chemical Engineering at the University of Utah (Salt Lake City, Utah) on a full academic scholarship. Her undergraduate research included internships at the Kimberly Clark Corporation and a research assistantship in the lab of Dr. Leonard F. Pease, developing a novel technique to detect eosinophilic esophagitis. She graduated cum laude with departmental honors from the College of Engineering and the Honors College in 2010.
She did her doctoral studies in Chemical and Biomolecular Engineering in the lab of Dr. Marc Ostermeier at Johns Hopkins University (Baltimore, Maryland). Her research focused on characterizing the fitness landscape of the antibiotic resistance protein, TEM-1 beta-lactamase, using next-generation DNA sequencing. In 2012, she was awarded the NIH Ruth L. Kirschstein National Research Service Award Predoctoral Fellowship.
A passionate teacher, she was awarded the George M.L. Sommerman Engineering Graduate Teaching Assistant Award for the Whiting School of Engineering in 2013, and received a Teaching Academy Certificate in 2016. She guest lectured in the Chemical and Biomolecular Engineering department and the Biology department. In Spring 2017, she was an instructor for MATLAB Made Easy, an introductory computer programming course for engineering students.
Her research interests include molecular evolution, protein engineering, antibiotic resistance, and metagenomics. She is particularly interested in using NGS technology and data science to solve problems that impact human health.
Courtney is currently working as a Bioinformatics Scientist at IDbyDNA in Salt Lake City, Utah.
Research & Publications
Courtney E. Gonzalez, Paul Roberts, and Marc Ostermeier, Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase, Journal of Molecular Biology, Volume 431, Issue 12, 2019, Pages 2320-2330 [Science Direct]
Short insertions and deletions (InDels) are a common type of mutation found in nature and a useful source of variation in protein engineering. InDel events have important consequences in protein evolution, often opening new pathways for adaptation. However, much less is known about the effects of InDels compared to point mutations and amino acid substitutions. In particular, deep mutagenesis studies on the distribution of fitness effects of mutations have focused almost exclusively on amino acid substitutions. Here, we present a near-comprehensive analysis of the fitness effects of single amino acid InDels in TEM-1 β-lactamase. While we found InDels to be largely deleterious, partially overlapping deletion-tolerant and insertion-tolerant regions were observed throughout the protein, especially in unstructured regions and at the end of helices. The signal sequence of TEM-1 tolerated InDels more than the mature protein. Most regions of the protein tolerated insertions more than deletions, but a few regions tolerated deletions more than insertions. We examined the relationship between InDel tolerance and a variety of measures to help understand its origin. These measures included evolutionary variation in β-lactamases, secondary structure identity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact number. We found secondary structure, weighted contact number, and evolutionary variation in class A beta-lactamases to be the somewhat predictive of InDel fitness effects.
Courtney E. Gonzalez and Marc Ostermeier, Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase, Journal of Molecular Biology, Volume 431, Issue 10, 2019, Pages 1981-1992 [Science Direct]
Interactions between mutations play a central role in shaping the fitness landscape, but a clear picture of intragenic epistasis has yet to emerge. To further reveal the prevalence and patterns of intragenic epistasis, we present a survey of epistatic interactions between sequential mutations in TEM-1 β-lactamase. We measured the fitness effect of ~12,000 pairs of consecutive amino acid substitutions and used our previous study of the fitness effects of single amino acid substitutions to calculate epistasis for over 8000 mutation pairs. Since sequential mutations are prone to physically interact, we postulated that our study would be surveying specific epistasis instead of nonspecific epistasis. We found widespread negative epistasis, especially in beta-strands, and a high frequency of negative sign epistasis among individually beneficial mutations. Negative epistasis (52%) occurred 7.6 times as frequently as positive epistasis (6.8%). Buried residues experienced more negative epistasis that surface-exposed residues. However, TEM-1 exhibited a couple of hotspots for positive epistasis, most notably L221/ R222 at which many combinations of mutations positively interacted. This study is the first to systematically examine pairwise epistasis throughout an entire protein performing its native function in its native host.
Hedieh Saffari, Jeffrey J. Krstyen, Courtney Gonzalez, Frederic C. Clayton, Kristin M. Leiferman, Gerald J. Gleich, Kathryn A. Peterson, Leonard F. Pease, 99mTechnetium-labeled heparin: A new approach to detection of eosinophilic esophagitis–associated inflammation, Journal of Allergy and Clinical Immunology, Volume 132, Issue 6, 2013, Pages 1446-1448 [Science Direct]
Teaching Portfolio
Statement of Teaching Philosophy
My interest in teaching began as an undergraduate at the University of Utah. I was asked to be a teaching assistant for Introduction to Engineering Computing, a Chemical Engineering course that gave students a background in programming, and Numerical Methods, a higher-level course on algorithms and numerical analysis. My experience teaching as an undergraduate tremendously influenced my decision to pursue graduate school. As a Ph.D. candidate at Johns Hopkins University, my interest in science education and pedagogy evolved into a passion.
At Johns Hopkins, I was a teaching assistant under Dr. Jeff Gray for the course Introduction to Chemical and Biological Process Analysis. In place of traditional TA recitations, we adopted the workshop-style, active-learning principles of Peer-Led Team Learning. Committed to creating an environment that included every student, I led students through engineering problems using innovative game-like strategies to foster teamwork and engaged learning. This experience significantly informed my teaching philosophy, as I observed how an environment of respect and encouragement fostered the development of communication skills, allowed students to integrate concepts, and ultimately led to better learning outcomes. At the end of this course, my students nominated me for the Graduate Teaching Assistant Award for the Whiting School of Engineering.
I continued to pursue teaching opportunities throughout my career in graduate school. I guest-lectured and developed course material for Applications of Molecular Evolution to Biotechnology and Introduction to Biological Molecules. From 2013-2016, I was involved in the JHU Teaching Academy certificate program, which includes workshops, courses, mentored teaching opportunities, and a capstone. In Spring 2017, I was the instructor of record for MATLAB Made Easy, an introductory programming class for engineering students. In this capacity, I had the opportunity to organize a course, utilize course management software, and write a full series of lectures, activities, homework assignments, and exams.
Whether giving a lecture or leading an informal workshop, creating a classroom environment that is welcoming and engaging is one of my top priorities. As a woman in engineering, I have some experience being the minority in a classroom. As a teacher, my goal is to make every student feel respected and essential to the classroom dynamic. I design learning objectives with Bloom’s Taxonomy in mind, looking for ways to help students progress from knowledge to synthesis and evaluation of concepts on a higher level. Ultimately, my goal as an educator is to not only help students develop practical skills for STEM careers, but also inspire them toward deep thinking and life-long education.
Statement of Teaching Responsibilities
EN.540.111.04 MATLAB Made Easy, Instructor of Record
Course Description: This course uses MATLAB to teach the fundamentals of programming, exploring such questions as: What is a program? How can we use loops and branches to accomplish a task? What exactly is MATLAB doing when it’s running a script? It builds upon the fundamentals of programming to tackle relevant engineering problems. This course is designed to help ChemBE students excel in subsequent engineering courses, such as Modeling and Statistics, Separations, and Chemical Kinetics.
Responsibilities: As the instructor of record for a section of 25 freshman and sophomore engineering students, I had the freedom to develop all aspects of the course based on some existing materials from the previous year. I developed learning objectives, created weekly lectures and active-learning exercises, and wrote homework, exam, and final project materials. I created grading rubrics and graded all homework assignments and exams. I utilized Blackboard to distribute materials and track grades. To supplement my lectures each week, I held office hours and homework help sessions.
AS.020.205 Introduction to Biological Molecules, Guest Lecturer
Course Description: This course presents an overview to biochemistry and molecular biology, especially focusing on biotechnology and medicine.
Responsibilities: I wrote and delivered four guest lectures for this course as my capstone for the JHU Teaching Academy certificate. I designed lectures from scratch, implementing a combination of blackboard-and-chalk-style lecturing, active-learning activities, in-class technology for mini-quizzes, and supporting media. I also wrote homework and exam problems drawing on Bloom’s Taxonomy to complement my lectures.
EN.540.202 Introduction to Chemical and Biological Process Analysis, Teaching Assistant
Course Description: This course provides an introduction to chemical and biomolecular engineering and the fundamental principles of chemical process analysis. It covers formulation and solution of material and energy balances on chemical processes, reductionist approaches to the solution of complex, multi-unit processes, and introduction to the basic concepts of thermodynamics and chemical/biochemical reactions.
Responsibilities: As the teaching assistant for this course, I was given tremendous freedom and responsibility to design my weekly TA sessions. I held two 2-hour workshop-style sessions each week wherein I reviewed lecture material, selected example problems to work, designed game-like strategies to facilitate balanced group involvement, and guided students toward solutions. I was also responsible for grading homework, writing solution guides, holding exam review sessions and weekly office hours, and helping to grade exams.
Curriculum Vitae
Bioinformatics scientist with 9 years of experience in molecular biology, antibiotic resistance, NGS technology, protein evolution, and metagenomics. Expertise in molecular cloning techniques, antibiotic resistance, deep-mutational scanning, and analysis of NGS datasets.
Education
Ph.D. Chemical and Biomolecular Engineering
Johns Hopkins University
October 2018
H.B.S. Chemical Engineering
University of Utah
May 2010
Research Experience
Bioinformatics Scientist
IDbyDNA
November 2019 - Present
Bioinformatics Postdoc
IDbyDNA
April - November 2019
Ph.D. Candidate
Ostermeier Lab, Johns Hopkins University
Fall 2010 - Fall 2018
Undergraduate Research Assistant
Pease Lab, University of Utah
Fall 2009 - Spring 2010
R&D Intern
Kimberly Clark Corporation
Summer 2009 & 2010
Teaching Experience
Instructor
MATLAB Made Easy
Spring 2017
Guest Lecturer
Applications of Molecular Evolution to Biotechnology
Fall 2015
Guest Lecturer
Introduction to Biological Molecules
Summer 2016
Teaching Assistant
Introduction to Chemical and Biological Process Analysis
Fall 2011 & 2012
Technical Skills
Molecular Cloning
Directed Evolution
PCR & RT-PCR
High-Throughput Mutagenesis
Bacterial Cell Culture
NGS Multiplexing
DNA Sequencing Analysis
MATLAB
Python
Bioinformatics
Honors & Awards
NIH Ruth L. Kirschstein National Research Service Award Predoctoral Fellowship, 2012-2016
George M.L. Sommerman Engineering Graduate Teaching Assistant Award, 2013
Whiting School of Engineering Deanʼs Fellowship, 2010
Nonresident Academic Full Tuition Scholarship, 2006-2010
Semnani Foundation Scholarship, 2009
Neelu Ramaswami Scholarship for Chemical Engineering Students, 2008
Lloyd E. Malm Memorial Award, Kennecott Scholar, 2007
Contact
I am most easily reached by my personal e-mail: courtney.gonzalez@gmail.com
Please feel free to contact me with any questions about my work, research interests, teaching portfolio, or CV.
