Difference between revisions of "Spring 2014 Synthetic Biology"

Revision as of 17:16, 8 January 2014

CH391L: Synthetic Biology (Spring 2014)

Mondays 2-5 PM MBB 2.456
Unique #: 53230

Instructors:

• Prof. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
• Dr. Dennis Mishler <dennis PERIOD mishler AT gmail DOT com>

Course web page: The course web site on SynBioCyc.org will host course handouts, readings, and assignments.

Course Syllabus

Previous year's websites:

• CH391L Synthetic Biology Topics (Spring 2012)
• CH391L Synthetic Biology Topics (Spring 2013)

Useful links:

• 2012 iGEM Competition
• 2013 iGEM Competition
• 2014 iGEM Competition

CH391L Users

Motivation

The purpose of this course is to become familiar with the techniques, biological parts, accomplishments, problems, and challenges of synthetic biology. For the most part, we will focus on E. coli and yeast. Participants will be expected to individually contribute to OWW pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. Then, they will be expected to create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an outstanding problem with technological or societal impact.

Assignments

Coursework will consist of in-class oral presentations on scientific papers or research proposals and a "written" component consisting of Wiki page edits on OpenWetWare. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.

Instructions for Wiki Editing

Class Assignments

Grading Rubric for Wiki Pages, Presentations, and Participation

Grading Rubric for Final Project

Topics

Topics

Week 1: Introduction

• Introduction to Synthetic Biology

Week 2: What is a part?

• BioBricks and Restriction Enzymes (undergrad)
• Biological Parts and the iGEM Registry
• CAD systems - TinkerCell

Week 3: Assembling the parts

• Genome Synthesis
• Gibson Assembly

Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization

• GFP (Green Fluorescent Protein)
• Ancestral Sequence Reconstruction
• Directed Protein Evolution

Week 5: Parts I: Chassis

• Host organisms and Plasmids/origins
• Selectable and Counter Selectable Markers (undergrad)
• Biocontainment

Week 6: Parts II: Basics of Gene Expression

• T7 Polymerase and Orthogonal Parts
• Transcriptional terminators, RBS, and gene expression

Week 7: Parts III: Reporter Genes and Gene Regulation

• Protein Regulators and Stochastic Expression
• Nucleic Acid Selections and Riboswitches
• Spinach RNA

Week 8: Parts IV: Environmental sensing and responses

• Quorum Sensing
• Motility and Taxis
• Light Sensing (optogenetics)

Week 9: Systems I: Circuits

• Oscillation
• Cell Counting and memory
• Edge Detection

Week 10: Genome Editing Techniques

• MAGE (Multiplex Automated Genomic Engineering)
• CRISPR (Dennis?)

Week 11: Systems II: Whole Organisms

• Refactored T7 and Yeast
• GMOs, Polio Virus, Dual-Use research, and Ethics

Week 12: Systems III: Metabolic Engineering

• Nitrogen Fixation Refactoring
• Artemisinin
• Bioremediation and caffeinated coli

Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics

• Synthetic Ecology
• Consortia
• Other Topics?

Ideas for Topics

• Use COPASI to model circuits (like repressilator) and switches, changing parameters to tune behavior.