Laboratory Fundamentals of Synthetic Biology
Syllabus
Class Format
The Class will meet twice a week, one 2 hour classroom session, and one 3 hour lab session. Problem sets will be assigned weekly for the first eight weeks. A midterm exam will cover the classroom material and the first several weeks of lab instruction. Lab exercises will be assigned, and cover the lab techniques taught. A small project to assemble and measure a BioBrick system follows the lab instruction. Finally, students will design, build and analyze their own BioBrick system.
Grades
The final grade will be as follows: 20% Problem Sets 30% Midterm Exam 20% Lab Evaluations 30% Final Project
Schedule
- Introduction - Synthetic Biology: History, current applications and future directions
Assignments: Endy Article and Comic Strip
- The Biology (4 sessions)
- Cells, DNA, RNA and Protein
- DNA - information encoding, structure, sequencing and synthesis
- RNA - encoding, structure, function (RNA Enzymes, RNA Aptamers)
- Proteins - Crystallography, functions, scaffolds
Introductory packet about DNA, RNA, Protein. Ron Weiss paper on Vibrio Fischerii quorum sensing (decompose into parts). Artemisnin overview article. Hellinga Paper on protein sensors.
- Foundational Technologies (4 sessions)
- BioBricks - Definition of a BioBrick, black-box encapsulation, PoPs and RiPs
- The Registry of Standard Biological Parts
- Analytical -omics tools - Proteomics, Genomics, Metabolomics
- Simulation tools - stochastic simulators, BioJADE, matlab
Create a biobrick out of a sequence (force them to re-optimize a coding region into e. coli and remove a biobrick incompatibility). An introductory packet on PCR and cloning.
- Basic Lab Techniques (8 sessions)
- Introductory Lab - PCR Primer Design
- Lab 2 - PCR, Restriction Digestion, Gel electrophoresis
- Lab 3 - Insert Preparation, Gel Extraction, Ligation and Transformation
- BioBrick Discovery and Creation Technique
- Cloning Basics - restriction enzymes, running analytical gels, QiaPreps
- Sterile Technique - autoclaving, flaming technique,
- Competent Cells - Production & QC
- PCR - About PCR, Polymerases, Primer design
- Screening - Antibotics, Blue/White screening
- Growth Curves
- Metabolite measurement
- Standardized Measurements for BioBricks
- Trial Project (2 weeks)
- Assembly and Measurement of a BioBrick system
- Final Project
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