Our Training Approach
Synthetic biologists of the future will need to traverse and integrate disciplines and scales
At the core of our unique synthetic biology training approach is the concept of scales. Throughout its history, the field of synthetic biology has developed an inherently constructive approach, built off of the hypothesis that by understanding the rules of life we can deconstruct natural biological systems into ‘parts’ which we can re-combine to carry out customized, predictable, and useful functions. These ‘parts’ function on intrinsic length scales, combining together in a bottom-up fashion to create increasingly complex systems that have emergent behaviors across many different scales, from the molecular-level building blocks, to the cellular systems that encapsulate them, to the tissues, organisms, and communities that may eventually result, to the ethical considerations they create.
Our training approach is to embed this concept of scales from the beginning.
We train students to break down synthetic biology technologies along the scales of phenomena that they require. This approach informs how their research in a particular scale is part of a larger whole, allowing them to identify challenges that arise between scales that in turn drive further research questions. This approach allows students to think big from the beginning, incorporate societal-level considerations such as ethics into their work, and drive collaboration with other CSB labs to create impactful innovations.
For example, Nitrogen fixing bacteria as a more sustainable alternative to chemical fertilizers
Nitrogenase enzymes that fix nitrogen
Genetic pathways that regulate nitrogenase synthesis and assembly
Systems that are involved nitrogen, oxygen, and product transport
Cellular interactions that happen between microbes and plants in a soil ecosystem
Technology use by farmers, assessment of benefits, and technology access
We offer several courses with the scales in mind
We offer two introductory courses in synthetic biology. The first course introduces the field of synthetic biology and its natural scientific and engineering basis. In the second course, we break down how synthetic biology solutions integrate concepts across five spatiotemporal scales—molecular, network, cell/cell-free systems, biological communities and societal—using case studies in sustainability, biomanufacturing, and human health.
- CHEM_ENG 376: Principles of Synthetic Biology
- CHEM_ENG 378-0: Deconstructing Synthetic Biology – Biotechnology Case Studies Across Scales
Several of our courses exist along the scales
Molecular scale courses cover the physical, chemical and mathematical principles required for understanding the molecular basis of life and its use in biotechnology. Appropriate topics for these courses include biophysics of molecular folding, free energy landscapes, kinetic molecular folding, charge screening, molecular interactions, RNA folding, protein folding, enzymology and others. Courses that use these principles to teach concepts related to RNA and protein design and experimental strategies for RNA and protein engineering are encouraged.
- CHEM ENG 395: Molecular Folding and Function (preferred)
- CHEM ENG 375: Biochemical Engineering
- IBIS 410: Quantitative Biology
- BIOL SCI 361: Protein Structure and Function
- IGP 401: Biochemistry
Network/circuit scale courses enable students to understand biological, mathematical and biophysical principles underpinning the mechanisms that biological systems utilize to propagate information, coordinate physiological states, and implement control over those states. These courses cover topics such as genetic circuits, metabolism, dynamical systems, network theory and mechanisms for intracellular and intercellular signaling and communication.
- CHEM ENG 379: Computational Biology – Analysis and Design of Living Systems (preferred)
- ES APPM 495: Special Topics – Introduction to Network Science
- BIOL SCI 354: Quantitative Analysis of Biology
- Physics 465-0: Advanced Topics in Nonlinear Dynamics
- BMD ENG 311: Computational Genomics
Cell/cell-free systems scale courses cover biophysical and chemical principles involved in engineering biological parts within living and cell-free systems. These courses can include topics such as cellular and cell-free enzymatic biosynthesis, the implementation of genetic circuits in cell and cell-free systems, transport phenomenon at the cellular scale, interactions between cells/tissues and biomaterials, techniques for the manipulation of systems at this scale, and the use of cell-free systems as platforms for discovery and diagnostics.
- BME 395: Cell and Cell-Free Phenomena (preferred)
- IBIS 406: Advanced Topics in Cell Biology
- IGP 405: Cell Biology
Biological communities scale courses will cover the biological, biochemical and mathematical principles required for understanding the emergent behavior of cellular communities. These courses can include topics such as microbial ecology and metagenomics, prediction of emergent microbial community dynamics, interspecies metabolic interaction, tissue-scale phenomena such as tissue engineering, microbial ecology, and modeling of biological communities including agent-based models and nonlinear differential equation models.
- CIV ENV 442: Environmental Biotechnology for Resource Recovery
- CIV ENV 443: Microbial Ecology for Resource Recovery
- CIV ENV 447: Molecular Microbiology
- BMD ENG 343: Biomaterials and Medical Devices
- BMD ENG 346: Tissue Engineering
Societal scale courses will teach students the skills needed to quantitatively estimate the needs, market sizes and viability of synthetic biology technologies including frameworks of field trials, user testing, and stakeholder analysis. These courses can also be used to address topics such as bioethics related to synthetic biology.
- CHEM ENG 373: Biotechnology and Global Health (preferred)
- CHEM ENG 382: Biotechnology Regulatory Science
- BMD ENG 495: NUvention Medical (ETREP 470)
- ISEN 420: NUvention Energy
- MHB401: Foundations of Bioethics
- ENTREP 325/IEMS 325: Engineering Entrepreneurship
Methods/skills courses teach students technical approaches that are important for applying concepts learned in other courses to their research or future careers. These courses can cover both experimental and computational approaches.
- NICO 401-0: Introduction to Programming for Big Data
- IBiS 416-0: Practical Training in Chemical Biology Methods and Experimental Design
- IGP 486: Advanced Bioinformatics
This coursework is a launch pad towards impactful research in synthetic biology that allows students to use the scales framework to identify the most important scale to the success of a particular application and key engineering opportunities and challenges between scales for ultimate impact.