University of Colorado Boulder

Tufts University

Scientist II at Amyris

Skills: Biochemistry · Molecular Biology · Metabolic Engineering · Genomics · JMP · Spotfire · DNA Extraction · Enzymology · Molecular Cloning

Amyris

Scientist II

Collaborated with chemists and material scientists to identify bio-reachable molecules with superior material properties, resulting in >10 early-stage research projects. To put these projects to practice, I designed, built, tested, and analyzed high-throughput strain libraries for production of these identified molecules.

Zymergen

Worked as part of an interdisciplinary team of biologists, chemists, and material scientists to discover new molecules with superior material properties that can be produced biologically. My work focused on discovering enzymes that can catalyze the novel reactions required to produce these new biomolecules. Responsibilities included in vitro enzyme assay development, genetic engineering, protein bioinformatics, high throughput data analysis, use of automation, and routinely interfacing with chemists and materials scientists during product research.

Scientist I

My dissertation research focused on the molecular mechanisms of protein evolution by gene duplication and divergence. I used a combination of laboratory evolution, genetics, molecular biology and enzymology to uncover how the entire genome, proteome, and metabolome evolve when a gene is under selective pressure. Visit https://www.colorado.edu/lab/copley/ for more info on the type of projects going on in the Copley lab. Some of my more specific accomplishments include:

–Initiated, designed, and led several laboratory evolution experiments to identify adaptive mutations that arise when growth of a microbe is limited by a bottleneck enzyme in a biosynthetic pathway, resulting in 4 high-impact publications with inter-disciplinary teams, presentations at several conferences, and a ~$1.5 million NIH grant
–Leveraged phenotypic data, Next-Gen sequencing, proteomics, and in vitro enzyme assays to reveal how certain mutations improve flux through a bottlenecked pathway, ultimately identifying altered enzyme kinetics, proteome changes, and RNA structure as the key mechanisms
–Built a continuous-culture device using self-taught skills in machining, engineering, and automation to evolve parallel microbe populations for directed evolution experiments
–Performing bioinformatics analyses and developing original in vitro enzyme assays to infer sites of contact between two enzymes that channel a labile substrate in a biosynthetic pathway helping guide rational library design for future directed evolution studies
–Collaborating with local biotech company in a cross-disciplinary team of 8 scientists to design, build, and test multiplexed mutagenesis libraries targeting >50,000 loci across the E. coli genome resulting in an unprecedented view of the synonymous mutation fitness landscape of E. coli

Copley lab, University of Colorado Boulder

Graduate Student Researcher

As a member of the analytical chemistry group, I play a key role in the operation and transfer of GC, HPLC, and titration assays in a high throughput environment. Some of my more specific roles include:
- Statistical analysis of large data sets using SQL queries, JMP, and Spotfire
- Development assistance and supervision of an odor assay to test commercial product
- Monitoring the performance and robustness of the assays
- Maintenance and troubleshooting of the instruments

Amyris Inc

Associate Scientist

I conducted original research comparing ion compositions of Martian soil and Mars analogues on Earth using ion chromatography, ultimately identifying key differences in the ion profile of a commonly-used Mars analogue to inform future studies

Andrew Morgenthaler