Spring 2014 Synthetic Biology

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Contents

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.

Instructions for Wiki Editing

Class Assignments

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?

Week 3: Assembling the parts

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

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

  • SPEAKER: Mike Hammerling and ncAA's <---Moved to....

Tinker Cell in class

Catch up day.

Week 7: Parts III: Reporter Genes and Gene Regulation

Week 8: Parts IV: Environmental sensing and responses

Week 9: Systems I: Circuits

Tinker Cell II: Group projects

Week 10: Genome Editing Techniques

Week 11: Systems II: Whole Organisms

April 7th FINAL PROJECT OUTLINES DUE

  • SPEAKER: Mike Hammerling and Amber-less E. coli

Week 12: Systems III: Metabolic Engineering

April 14th

Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics

April 21st FINAL PROJECTS DRAFTS DUE

Week 14: FINAL PROJECT PRESENTATIONS

April 28th

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]

Useful links