CH391L/S12

CH391L: Synthetic Biology

Spring 2012

Mondays 2-5 PM MBB 2.204

Instructor: Dr. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>

Course web page: The course web site on OpenWetWare.org http://openwetware.org/wiki/CH391L/S12 will host course handouts, readings, and assignments.

Course Syllabus (PDF)

2012 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 systems as chassis. 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 Topic Writeups and Presentations

Synthetic Biology Seminars at UT

Upcoming

• Michelle Chang (UC Berkeley) - Friday, Feb 3, 3:30 PM, WEL 2.122 webpage
• Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 webpage
• Roger Tsien (UCSD) Burdette Lecture, 2008 Nobel Prize in Chemistry - Tuesday, Feb 7, 2:30 PM, SAC 1.402 webpage

Past

• Erik Winfree (Caltech) - Thursday, Feb 2, 3:30 PM, ACES 6.304 webpage
• Lulu Qian (Caltech) - Wednesday, Feb. 1 4:00 PM, WEL 2.122 webpage
• Sang Yup Lee (Korea Advanced Institute of Science and Technology (KAIST)) - Tuesday, Jan. 31 3:30pm, CPE 2.218 webpage

Synthetic Biology News

Here is a collection of recent news articles related to current synthetic biology. Please feel free to add anything you feel is relevant to the class and any appropriate comments or descriptions.

Topics

Introduction - Barrick

• Definitions of synthetic biology
• A short history of synthetic biology
• Ethical issues in synthetic biology
• Challenges and open problems

Methods

(Approximately 3 class periods)

Week 1: Making or finding parts

• iGEM Registry
• Bioprospecting new parts using Metagenomics
• Directed evolution / in vitro selection
• Ancestral Sequence Reconstruction

Week 2: Assembling parts into systems

• PCR and advanced PCR techniques
• Restriction enzymes and BioBricks/BglBricks assembly standards (RFCs)
• Gene/genome synthesis/Gibson assembly

Parts

(Approximately 6 class periods)

• Chassis (organism)
• Replication origins (plasmids and artificial chromosomes)
• Transcriptional promoters
• Ribosome binding sites
• Codon optimization (other factors controlling protein expression)
• Transcription terminators
• Selectable and counter-selectable genetic markers
  • Toxin-Antitoxin genes
• Reporter genes
• Sensor genes (quorum sensing, light)
• Transcriptional regulatory proteins / riboswitches
• Locomotion/chemotaxis

Systems

(Approximately 6 class periods)

• Refactored T7 (Endy)
• Represillator (Elowitz and Leibler)
• Toggle switch (Collins)
• Counter (Church and Collins)
• Edge detection (Ellington, Voigt, etc.)
• Yeast producing artemisinic acid (Keasling)
• Atrazine seek and destroy (Gallivan)
• Synthetic chromosome arms in yeast (Boeke)
• Synthetic ecologies
• MAGE increased lycopene production (Church).
• And many more...