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[[Category:CH391L_S12]] | [[Category:CH391L_S12]] | ||
=CH391L: Synthetic Biology= | ==CH391L: Synthetic Biology== | ||
Spring 2012 | Spring 2012 | ||
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[[CH391L/S12/WikiEditing|Instructions for Wiki Editing]] | [[CH391L/S12/WikiEditing|Instructions for Wiki Editing]] | ||
[[ | [[CH391L/S12/Assignments|Class Assignments]] | ||
[[CH391L/S12/ | [[CH391L/S12/TopicGradingRubric|Grading Rubric for Topic Pages and Presentations]] | ||
[[CH391L/S12/ | [[CH391L/S12/FinalProjectRubric|Grading Rubric for Final Project]] | ||
==Synthetic Biology Seminars at UT== | ==Synthetic Biology Seminars at UT== | ||
| Line 37: | Line 37: | ||
===Upcoming=== | ===Upcoming=== | ||
===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] | *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] | *Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 [http://depts.washington.edu/sfields/staff.html webpage] | ||
| Line 54: | Line 56: | ||
===Introduction=== | ===Introduction=== | ||
[[:Category:CH391L_S12 | Index of All CH391/S12 Pages]] | |||
[[Special:RecentChangesLinked/Category:CH391L_S12 | View Recent Changes to CH391/S12 Pages]] | |||
==== Week 1: Introduction ==== | ==== Week 1: Introduction ==== | ||
* [[CH391L/S12/Introduction | Introduction to synthetic biology]] | * [[CH391L/S12/Introduction | Introduction to synthetic biology]] | ||
===Methods=== | ===Methods=== | ||
====Week 2: Making or finding parts==== | ====Week 2: Making or finding parts==== | ||
| Line 79: | Line 84: | ||
* [[CH391L/S12/MetabolicEngineering | Metabolic Engineering]] | * [[CH391L/S12/MetabolicEngineering | Metabolic Engineering]] | ||
* [[CH391L/S12/HostOrganisms | Chassis (Host organisms)]] | * [[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]] | |||
====Week 9: Complex parts==== | |||
* [[CH391L/S12/Unnatural_Amino_Acids | Unnatural Amino Acid Incorporation]] | |||
* [[CH391L/S12/Locomotion | Locomotion]] | |||
* [[CH391L/S12/Quorum_Sensing | Quorum Sensing]] | |||
===Systems=== | |||
====Week 10: Systems I==== | |||
*[[CH391L/S12/Pattern Formation | Pattern Formation]] | |||
*[[CH391L/S12/Toggle Switches, Repressilators, and Counters | Toggle Switches, Repressilators, and Counters]] | |||
*[[CH391L/S12/Refactoring Genomes | Refactoring Genomes]] | |||
====Week 11: Systems II==== | |||
*[[CH391L/S12/Artemisinic Acid Engineering | Artemisinic Acid Engineering ]] | |||
*[[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.
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.
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
View Recent Changes to CH391/S12 Pages
Week 1: Introduction
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
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
Week 8: Reporter Genes
Week 9: Complex parts
Systems
Week 10: Systems I
Week 11: Systems II
- Artemisinic Acid Engineering
- Synthetic Cooperation
- MAGE lycopene production, CAGE "Amberless" E. coli
