A longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design – allowing...
There is a need for alternative biomanufacturing solutions to produce novel medicines and help solve long-standing issues regarding difficult-to-treat diseases. Cell-free protein synthesis (CFPS) provides scientists with a new paradigm for producing proteins with an unprecedented freedom and control over the biomolecular machinery involved. In this document, I describe my...
Metabolic engineering of microorganisms to produce useful compounds from renewable substrates is a promising means for sustainable, on-demand production of chemicals. However, efforts to design and engineer microbial cell factories are constrained by costly and slow “build” times in which each genetic variation requires re-engineering a new strain for each...
Recent advances in cell-free synthetic biology have spurred the development of in vitro molecular diagnostics that serve as effective alternatives to whole-cell biosensors. However, cell-free sensors for detecting manmade organic water contaminants such as pesticides are sparse, partially because few characterized natural biological sensors can directly detect such pollutants. Here,...
It is pertinent now more than ever that we find sustainable alternatives to produce chemicals. For decades, scientists and engineers have turned to biological systems to help meet societal needs in energy, medicine, materials, and moreespecially when chemical synthesis is untenable. Often, biologically-produced small molecules are insufficient for production at...
Since their introduction nearly a century ago, protein vaccines and therapeutics have revolutionized our ability to prevent and treat human disease. However, existing production processes for biopharmaceuticals are technically complex and rely on living cells, which necessitates highly centralized manufacturing in large-scale production facilities, specialized equipment, and cold-chain distribution. With...
Proteins represent a critical class of biomolecules, universally employed by all living organisms to fulfill essential structural, functional, and enzymatic roles necessary to support life. In nature, these polymers are composed generally of twenty natural amino acid (AA) building blocks, which can be modified with covalent adducts known as post-translational...
The need to rapidly develop and produce life-saving vaccines and therapeutics is critical for overcoming pandemics in a global economy. Recent advances in automation and cell-free systems have opened new avenues for expediting optimization and production of biologic vaccines and therapeutics. A key consideration for the development of protein biologics...
This dissertation focuses on the development of quantitative approaches for characterizing endogenous signaling pathways and designing new pathways in mammalian cells. I demonstrate how mathematical descriptions that are formulated to explain gene expression patterns can also serve as a powerful springboard for deeper analyses into the properties and functions of...
By 2030, up to half of the world’s population is projected to suffer from water insecurity: a chronic scarcity of potable water due to rapidly warming temperatures, increased agricultural demand, and pollution. The health impacts of contaminated water are profound: hundreds of thousands of global deaths each year are ascribed...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...