Spring 2014 Synthetic Biology
CH391L: Synthetic Biology (Spring 2014)
Mondays 2-5 PM MBB 2.456
Unique #: 53230
- 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
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
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 spoke about some of the methods used to create large DNA sequences in yeast and the advantages of this organism.
Follow ups on GFP and Ancestral Sequence Reconstruction
Week 6: Parts II: Basics of Gene Expression
- Directed Protein Evolution (Nathan)
- Selectable/Counter Selectable Markers (Ashley)
- Biocontainment (Liz)
- 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 (Drew)
- Non-canonical Nucleotides (Drew)
Week 8: Parts IV: Environmental sensing and responses
Week 9: Systems I: Circuits
Tinker Cell II: Group projects
Week 10: Genome Editing Techniques
- MAGE (Multiplex Automated Genomic Engineering) (Jordan)
- CRISPR (Gabo)
- GMOs, Polio Virus, Dual-Use research, and Ethics (two people: one undergrad and one grad student) (XXXXXXX) PART I
Week 11: Systems II: Whole Organisms
April 7th FINAL PROJECT OUTLINES DUE
- 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
April 21st FINAL PROJECTS DRAFTS DUE
- SPEAKER: Professor Hal Alper
- Ethics (Ashley)
Week 14: FINAL PROJECT PRESENTATIONS
AFTER.... May 13th: Revised final projects due
[The above date is not correct]
It was announced in class and when meeting with Dennis that final projects are due on Friday, May 9th by 5:00pm.
If there is some confusion, please e-mail Dennis.
[Update: 5/7/2014, 2:30 pm]