Immuno-Protein Engineer
Resume:
Zachary Frye, PhD
**A Anderson St.
Boston, MA **114
*****@***.******.***
Profile / Summary
I am seeking a Biology Scientist position with an emphasis on biotechnology, cellular and protein engineering, and process development.
My graduate research aimed to develop a systems-level understanding of thymocyte (T-cell) development and the selection of the T-cell receptor (TCR) by using high-throughput sequencing, structural analysis and modeling, protein engineering, and cell-based assays.
Technical Experience and Skills
Molecular biological techniques: library generation, DNA and mRNA isolation, cloning, and mutagenesis
Antibody and single chain TCR binding measurement by ELISA and SPR
Cell-based cytometry, sorting (FACS), and confocal fluorescent microscopy for data acquisition & analysis
Mouse handling and tissue harvesting for primary cell isolation and analysis
Mammalian cell, bacterial cell, and bacteriophage culturing
Transient and stable cell line generation for protein expression in T-cell and CHO hybridoma cells
T-cell activation and cytokine release assays
Protein expression, purification, and characterization: affinity, anionic, & size exclusion column chromatography (ӒKTA FPLC), TFF, SDS-PAGE, and Western blot.
Expertise in programming languages: Python, R, Perl, and SQL Education
The University of Texas at Austin (2015) Ph.D. Chemical Engineering Adviser: Dr. Jennifer Maynard
Virginia Tech (2009) B.S. Chemical Engineering
Summa cum laude and Honors Scholar B.S. Biochemistry Minor: Chemistry
Scientific Training and Industrial Experience
Graduate Research, Doctoral student in immune-protein engineering lab (2009- August 2015)
Generated transient and stable T-cell hybridoma lines to display reconstituted engineered TCRs and CARs in the native membrane immune complex for cellular binding, activation, and cytokine release assays.
Utilized Python and Perl to analyze over 250 TCR structures to identify key shape determining residues within epitope-binding regions and model the intermolecular interactions of low affinity proteins.
Analyzed bioinformatics data from Roche 454 and Illumina MiSeq high-throughput sequencing experiments with Python and SQL to identify antigen-specific TCR repertoire shifts including biases in gene frequency and hypervariable junction sequences.
Cloned, expressed, and purified TCRs generated from repertoire analyses and T-cell hybridomas for affinity maturation and specificity studies. Variants tested using soluble protein, bacterial phage display for library screening and TCR reconstitution for T-cell activation studies.
Designed and implemented immunological challenges in mice with lymphoid organ harvesting, cellular isolation, FACS, and subsequent downstream single-T-cell cloning, sequencing, and activation assays.
Validated an OptCDR model with a protein database search for antibody variable region framework and complementarity-determining region structures for de novo structure modeling of engineered chimeric and hybrid antibodies.
Frye, Page 2 of 2
Co-op, Dow Chemical Company, Biocide and New Products Division, Midland, MI (2007)
Characterized product off-spec coloration and efficacy due to biocide additives. Developed a formulation strategy with high throughput compound screening for additive stabilization. Co-op, Dow Chemical Company, Chloropyridines, Pittsburg, CA (2007)
Work on multiple plant improvement projects: steam-vent reroute, pump replacement, seismic anchorage, two-phase chute design, crystallizer optimization, and Layers of Protection Analysis tool. Co-op, Dow Chemical Company, Poly Ethylene Plant, Plaquemine, LA (2006)
Develop plant operation process graphics, installed nitrogen gas for shell-side blowback of glycol water in heat exchangers, and wrote ethylene-recovery resource documents. Internship, Novozymes Biologicals Inc., Fermentation Development, Salem, VA (2007)
Developed gene quantification techniques with qPCR and other biological markers for monitoring batch fermentation and overall product integrity.
Analyzed and modeled the parameters involved with predatory bacteria challenges to treated biofilm surfaces to determine synergistic characteristics required for bio-control. Undergraduate Research, Advisers: Dr. Nancy Love and Dr. John Novak (2006-2009)
Designed and tested carbon nanotube substrates used in microbial biofilm fuel cells for electricity generation during wastewater treatment.
Characterized methanogenesis inhibition kinetics from long chain fatty acid wastewater feed stocks in bioreactors.
Publications
Frye ZP & Maynard JA. Canonical loops in T-cell receptors: predicting structure and function from sequence
(manuscript in preparation)
Entzminger KC, Frye ZP, Pantazes RJ, Hughes RA, Ellington AD, Maranas CD & Maynard JA. (2014) De novo antibody design by complementarity determining region modeling. Protein Engineering, Design and Selection. (manuscript in preparation)
Entzminger KC, Frye ZP, Roy BM, Fogarty JA, Stevens CA, Leonard EK, & Maynard JA. Single-chain T cell receptor affinity modulation by phage display (manuscript in preparation) Acquaye EA, Frye ZP, & Maynard JA. (2014) Immunotherapeutic approaches to prevent CMV-mediated disease. Rino Rappuoli, JE Crowe and Diana Boraschi, ed. Antibodies for Infectious Diseases. ASM press. Microbiology Spectrum.
Presentations and Talks
Invited talk, Chemistry Department Lecture Series, Southwestern University (2014) Title: Mapping Adaptive Immunity: Antibodies, T-cell Receptors, and Protein Engineering Talk, Biomolecular and Biophysical Processes, American Chemical Society (2014) Title: Surface expression of customized T-cell receptors to study the binding affinity and downstream immunological stimulation
Talk, High Throughput Sequencing Session, American Institute of Chemical Engineering annual meeting (2012) Title: Finding murine TCR shifts due to ovalbumin challenges with high throughput sequencing. Mentoring and Teaching Experience
Teaching assistant, The University of Texas at Austin (2010, 2012, 2014)
University Honors First Year Excellence Mentor, Virginia Tech (2008-2009)
Colloquium leader for University Honors Courses, Virginia Tech (2006-2009)
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