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. 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 Pages and Presentations

Grading Rubric for Final Project

Synthetic Biology Seminars at UT

Past

• Frances Arnold (Caltech) Gottlieb Lecture - Friday, Mar 2, 2:00 PM, ACE 2.302 webpage
• Frank M Raushel (Texas A&M University) - Friday, Feb 17th, 1:30pm, WEL 2.122 webpage
• Roger Tsien (UCSD) Burdette Lecture, 2008 Nobel Prize in Chemistry - Tuesday, Feb 7, 2:30 PM, SAC 1.402 webpage
• Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 webpage
• Michelle Chang (UC Berkeley) - Friday, Feb 3, 3:30 PM, WEL 2.122 webpage
• 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

Index of All CH391/S12 Pages

View Recent Changes to CH391/S12 Pages

Week 1: Introduction

• Introduction to synthetic biology

Methods

Week 2: Making or finding parts

• iGEM Registry
• Bioprospecting new parts using Metagenomics
• In vitro selection
• Ancestral Sequence Reconstruction

Week 3: Assembling parts into systems

• Restriction enzymes and BioBricks/BglBricks assembly standards (RFCs)
• PCR and advanced PCR techniques

Week 4: Parts assembly, metabolic engineering, and choosing a chassis

• Gene and genome synthesis
• Metabolic Engineering
• Chassis (Host organisms)

Parts

Week 5: Chassis and Backbones

• Selectable genetic markers
• Toxin/anti-toxins, plasmid addiction systems
• Counter-selectable genetic markers

Week 6: Basic Gene Construction

• Ribosome Binding Sites and Codon Optimization
• Transcriptional Promoters and Terminators
• Spinach Aptamer

Week 7: Gene regulation

• Origins of Replication
• Light Sensors
• Protein regulators of transcription

Week 8: Reporter Genes

• Pigments
• Fluorescent Proteins

Week 9: Complex parts

• Unnatural Amino Acid Incorporation
• Locomotion
• Quorum Sensing

Systems

Week 10: Systems I

• Pattern Formation

• Toggle Switches, Repressilators, and Counters

• Refactoring Genomes

Week 11: Systems II

• Artemisinic Acid Engineering
• Synthetic Cooperation
• MAGE lycopene production, CAGE "Amberless" E. coli

Week 12: Systems III

• Bacterial Odor Engineering