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=CH391L: Synthetic Biology=
[[Category:CH391L_S12]]
 
==CH391L: Synthetic Biology==


Spring 2012     
Spring 2012     
Line 17: Line 19:
== Motivation ==
== 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.
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 ==
== Assignments ==
Line 27: Line 29:
[[CH391L/S12/Assignments|Class Assignments]]
[[CH391L/S12/Assignments|Class Assignments]]


[[CH391L/S12/TopicGradingRubric|Grading Rubric for Topic Writeups and Presentations]]
[[CH391L/S12/TopicGradingRubric|Grading Rubric for Topic Pages and Presentations]]
 
[[CH391L/S12/FinalProjectRubric|Grading Rubric for Final Project]]


==Synthetic Biology Seminars at UT==
==Synthetic Biology Seminars at UT==


===Upcoming===
===Upcoming===
*Michelle Chang (UC Berkeley) - Friday, Feb 3, 3:30 PM, WEL 2.122 [http://chem.berkeley.edu/faculty/chang_m/ webpage]
 
*Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 [http://depts.washington.edu/sfields/staff.html webpage]
 
*Roger Tsien (UCSD) Burdette Lecture, 2008 Nobel Prize in Chemistry - Tuesday, Feb 7, 2:30 PM, SAC 1.402 [http://www.tsienlab.ucsd.edu/ webpage]


===Past===
===Past===
*Frances Arnold (Caltech) Gottlieb Lecture - Friday, Mar 2, 2:00 PM,  ACE 2.302 [http://cheme.che.caltech.edu/groups/fha/ webpage]
*Frank M Raushel (Texas A&M University) - Friday, Feb 17th, 1:30pm, WEL 2.122 [http://www.chem.tamu.edu/faculty/faculty_detail.php?ID=65/ webpage]
*Roger Tsien (UCSD) Burdette Lecture, 2008 Nobel Prize in Chemistry - Tuesday, Feb 7, 2:30 PM, SAC 1.402 [http://www.tsienlab.ucsd.edu/ webpage]
*Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 [http://depts.washington.edu/sfields/staff.html webpage]
*Michelle Chang (UC Berkeley) - Friday, Feb 3, 3:30 PM, WEL 2.122 [http://chem.berkeley.edu/faculty/chang_m/ webpage]
*Erik Winfree (Caltech) - Thursday, Feb 2, 3:30 PM, ACES 6.304 [http://www.dna.caltech.edu/~winfree/ webpage]
*Erik Winfree (Caltech) - Thursday, Feb 2, 3:30 PM, ACES 6.304 [http://www.dna.caltech.edu/~winfree/ webpage]
*Lulu Qian (Caltech) - Wednesday, Feb. 1 4:00 PM, WEL 2.122 [http://dna.caltech.edu/~lulu/ webpage]
*Lulu Qian (Caltech) - Wednesday, Feb. 1 4:00 PM, WEL 2.122 [http://dna.caltech.edu/~lulu/ webpage]
Line 47: Line 55:
== Topics ==
== Topics ==


=== [[CH391L/S12/Introduction | Introduction - Barrick]] ===
===Introduction===
 
[[:Category:CH391L_S12 | Index of All CH391/S12 Pages]]


* Definitions of synthetic biology
[[Special:RecentChangesLinked/Category:CH391L_S12 | View Recent Changes to CH391/S12 Pages]]
* A short history of synthetic biology
 
* Ethical issues in synthetic biology
==== Week 1: Introduction ====
* Challenges and open problems
 
* [[CH391L/S12/Introduction | Introduction to synthetic biology]]


===Methods===
===Methods===
(Approximately 3 class periods)


====Week 1: Making or finding parts====
====Week 2: Making or finding parts====


* [[CH391L/S12/iGEM Registry | iGEM Registry]]
* [[CH391L/S12/iGEM Registry | iGEM Registry]]
* [[CH391L/S12/Bioprospecting | Bioprospecting new parts using Metagenomics]]  
* [[CH391L/S12/Bioprospecting | Bioprospecting new parts using Metagenomics]]  
* [[CH391L/S12/In vitro Selection | Directed evolution / ''in vitro'' selection]]
* [[CH391L/S12/In vitro Selection | ''In vitro'' selection]]
* [[/CH391L/S12/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]
* [[/CH391L/S12/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]


====Week 2: Assembling parts into systems====
====Week 3: Assembling parts into systems====


* [[CH391L/S12/Restriction_enzymes_and_BioBricks_assembly_standards | Restriction enzymes and BioBricks/BglBricks assembly standards (RFCs)]]
* [[CH391L/S12/PCR and advanced PCR techniques | PCR and advanced PCR techniques]]
* [[CH391L/S12/PCR and advanced PCR techniques | PCR and advanced PCR techniques]]
* [[CH391L/S12/Restriction_enzymes_and_BioBricks_assembly_standards | Restriction enzymes and BioBricks/BglBricks assembly standards (RFCs)]]
* [[CH391L/S12/GeneandGenomeSynthesis | Gene/genome synthesis/Gibson assembly]]


===Parts===  
====Week 4: Parts assembly, metabolic engineering, and choosing a chassis====
(Approximately 6 class periods)
 
* [[CH391L/S12/GeneandGenomeSynthesis | Gene and genome synthesis]]
* [[CH391L/S12/MetabolicEngineering | Metabolic Engineering]]
* [[CH391L/S12/HostOrganisms | Chassis (Host organisms)]]
 
=== Parts ===
 
====Week 5: Chassis and Backbones====
 
* [[CH391L/S12/Selectablegeneticmarkers | Selectable genetic markers]]
* [[CH391L/S12/ToxinAntitoxins | Toxin/anti-toxins, plasmid addiction systems]]
* [[CH391L/S12/CounterSelection| Counter-selectable genetic markers]]
 
====Week 6: Basic Gene Construction====
 
* [[CH391L/S12/TranslationRBSandCodons | Ribosome Binding Sites and Codon Optimization]]
* [[CH391L/S12/TranscriptionPromotersandTerminators | Transcriptional Promoters and Terminators]]
* [[CH391L/S12/SpinachRNA | Spinach Aptamer]]
 
====Week 7: Gene regulation ====
 
* [[CH391L/S12/Origins of Replication | Origins of Replication]]
* [[CH391L/S12/LightSensors | Light Sensors]]
* [[CH391L/S12/Protein_regulators_of_transcription | Protein regulators of transcription]]
 
====Week 8: Reporter Genes====
* [[CH391L/S12/Pigments | Pigments]]
* [[CH391L/S12/Fluorescent Proteins | Fluorescent Proteins]]


* Chassis (organism)
====Week 9:  Complex parts====
* Replication origins (plasmids and artificial chromosomes)
* [[CH391L/S12/Unnatural_Amino_Acids | Unnatural Amino Acid Incorporation]]
* Transcriptional promoters
* [[CH391L/S12/Locomotion | Locomotion]]
* Ribosome binding sites
* [[CH391L/S12/Quorum_Sensing | Quorum Sensing]]
* 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===
===Systems===
(Approximately 6 class periods)


* Refactored T7 (Endy)
====Week 10: Systems I====
* Represillator (Elowitz and Leibler)
*[[CH391L/S12/Pattern Formation | Pattern Formation]]
* Toggle switch (Collins)
 
* Counter (Church and Collins)
*[[CH391L/S12/Toggle Switches, Repressilators, and Counters | Toggle Switches, Repressilators, and Counters]]
* Edge detection (Ellington, Voigt, etc.)
 
* Yeast producing artemisinic acid (Keasling)
*[[CH391L/S12/Refactoring Genomes | Refactoring Genomes]]
* Atrazine seek and destroy (Gallivan)
 
* Synthetic chromosome arms in yeast (Boeke)
====Week 11: Systems II====
* Synthetic ecologies
 
* MAGE increased lycopene production (Church).
*[[CH391L/S12/Artemisinic Acid Engineering | Artemisinic Acid Engineering ]]
* And many more...
*[[CH391L/S12/Synthetic Cooperation | Synthetic Cooperation ]]
*[[CH391L/S12/MAGE lycopene production, CAGE "Amberless" E. coli | MAGE lycopene production, CAGE "Amberless" E. coli ]]
 
====Week 12: Systems III====
*[[CH391L/S12/Bacterial Odor Engineering | Bacterial Odor Engineering ]]

Latest revision as of 18:57, 15 April 2012


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

Upcoming

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

Methods

Week 2: Making or finding parts

Week 3: Assembling parts into systems

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

Parts

Week 5: Chassis and Backbones

Week 6: Basic Gene Construction

Week 7: Gene regulation

Week 8: Reporter Genes

Week 9: Complex parts

Systems

Week 10: Systems I

Week 11: Systems II

Week 12: Systems III

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