Spring 2014 Synthetic Biology
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: This course web site on SynBioCyc.org will host course handouts, readings, and assignments.
CH391L Spring 2014 Course Syllabus
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 SynBioCyc pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. As the course progress, students will create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an existing problem with technological or societal impact.
Grading and 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 SynBioCyc. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.
Grading Rubric for Wiki Pages, Presentations, and Participation
Grading Rubric for Final Project
Previous year's websites
Topics
Key Papers for the semester
Week 1: Introduction
Week 2: What is a part?
- BioBricks and Restriction Enzymes (Ella)
- Biological Parts and the iGEM Registry (Alex)
- CAD systems (Gabo)
Week 3: Assembling the parts
Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization
- SPEAKER: Dr. Randy Hughes
- GFP (Green Fluorescent Protein) (Mindy)
- Ancestral Sequence Reconstruction (Cindy)
Week 5: Parts I: Chassis
- SPEAKER: Dr. Chris Yellman
- Selectable/Counter Selectable Markers (Ashley)
- Biocontainment (Liz)
- Host organisms and Plasmids/origins Not covered...Maybe later in the semester
Week 6: Parts II: Basics of Gene Expression
- SPEAKER: Mike Hammerling and ncAA's <---Moved to....
Tinker Cell in class Catch up day.
Week 7: Parts III: Reporter Genes and Gene Regulation
- Stochastic Gene Expression and Noise (Chen)
- Nucleic Acid Selections and Riboswitches (Dennis)
- Spinach RNA and Benner Bases (Drew)
Week 8: Parts IV: Environmental sensing and responses
Week 9: Systems I: Circuits
Week 10: Genome Editing Techniques
- MAGE (Multiplex Automated Genomic Engineering) (Jorge)
- CRISPR (Gabo)
- GMOs, Polio Virus, Dual-Use research, and Ethics (two people: one undergrad and one grad student) (Jordan) PART I
Week 11: Systems II: Whole Organisms
April 7th
- SPEAKER: Mike Hammerling and Amber-less E. coli
- GMOs, Polio Virus, Dual-Use research, and Ethics (two people: one undergrad and one grad student) PART II
Week 12: Systems III: Metabolic Engineering
Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics
- SPEAKER: Professor Hal Alper
- Synthetic Ecology
- Consortia (Colin)
- Other Topics?
- Benner (Drew) date to be determined
- Protocells Date to be determined