Difference between revisions of "Spring 2014 Synthetic Biology"
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Course web page: This course web site on SynBioCyc.org will host course handouts, readings, and assignments. | Course web page: This course web site on SynBioCyc.org will host course handouts, readings, and assignments. | ||
| − | [http://www.synbiocyc.org/wiki/images/ | + | [http://www.synbiocyc.org/wiki/images/f/f0/CH391L_S14_Syllabus.pdf '''CH391L Spring 2014 Course Syllabus'''] |
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== Motivation == | == Motivation == | ||
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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. | 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 | + | 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. |
| − | == Assignments == | + | == 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 | + | 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. |
[[CH391L/S14/WikiEditing|Instructions for Wiki Editing]] | [[CH391L/S14/WikiEditing|Instructions for Wiki Editing]] | ||
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[[CH391L/S14/FinalProjectRubric|Grading Rubric for Final Project]] | [[CH391L/S14/FinalProjectRubric|Grading Rubric for Final Project]] | ||
| + | == Previous year's websites == | ||
| + | * [http://openwetware.org/wiki/CH391L/S12 CH391L Synthetic Biology Topics (Spring 2012)] | ||
| + | * [http://openwetware.org/wiki/CH391L/S13 CH391L Synthetic Biology Topics (Spring 2013)] | ||
== Topics == | == Topics == | ||
| + | |||
| + | * [[CH391L/S14/Users | List of CH391L/S14 Users]] | ||
| + | * [[:Category:CH391L_S14 | Index of CH391L/S14 pages]] | ||
| + | === [[CH391L/S14/KeyPapers | Key Papers for the semester]]=== | ||
=== Week 1: Introduction === | === Week 1: Introduction === | ||
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===Week 2: What is a part?=== | ===Week 2: What is a part?=== | ||
| − | *[[CH391L/S14/BioBricks | BioBricks and Restriction Enzymes (''' | + | *[[CH391L/S14/BioBricks | BioBricks and Restriction Enzymes ('''Ella''')]] |
| − | *[[CH391L/S14/BiologicalpartsandtheiGEMregistry | Biological Parts and the iGEM Registry (''' | + | *[[CH391L/S14/BiologicalpartsandtheiGEMregistry | Biological Parts and the iGEM Registry ('''Alex''')]] |
| − | *[[CH391L/S14/CAD systems | CAD systems | + | *[[CH391L/S14/CAD systems | CAD systems '''(Gabo)''']] |
===Week 3: Assembling the parts=== | ===Week 3: Assembling the parts=== | ||
| − | *[[CH391L/S14/Genome Synthesis | Genome | + | *[[CH391L/S14/Genome Synthesis | Synthetic Genome '''(Drew)''']] |
| − | *[[CH391L/S14/Gibson Assembly | Gibson Assembly]] | + | *[[CH391L/S14/Gibson Assembly | Gibson Assembly '''(Jordan)''']] |
===Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization=== | ===Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization=== | ||
| − | + | * SPEAKER: Dr. Randy Hughes | |
| − | *[[CH391L/S14/GFP | GFP (Green Fluorescent Protein)]] | + | *[[CH391L/S14/GFP | GFP (Green Fluorescent Protein) '''(Mindy)''']] |
| − | *[[CH391L/S14/Ancestral sequence | Ancestral Sequence Reconstruction | + | *[[CH391L/S14/Ancestral sequence | Ancestral Sequence Reconstruction '''(Cindy)''']] |
| − | + | ||
===Week 5: Parts I: Chassis=== | ===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=== | ===Week 6: Parts II: Basics of Gene Expression=== | ||
| − | *[[CH391L/S14/ | + | *2/24/2014 |
| − | *[[CH391L/S14/ | + | *[[CH391L/S14/Directed protein evolution | Directed Protein Evolution '''(Nathan)''']] |
| + | *[[CH391L/S14/SelectableCounterselectable | Selectable/Counter Selectable Markers ('''Ashley''')]] | ||
| + | *[[CH391L/S14/Biocontainment | Biocontainment '''(Liz)''']] | ||
| + | |||
| + | * 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 7: Parts III: Reporter Genes and Gene Regulation === | ||
| − | *[[CH391L/S14/ | + | *[[CH391L/S14/StochasticGeneExpression | Stochastic Gene Expression and Noise (Chen) ]] |
| − | *[[CH391L/S14/NucleicAcidsRiboswitches | Nucleic Acid Selections and Riboswitches]] | + | *[[CH391L/S14/NucleicAcidsRiboswitches | Nucleic Acid Selections and Riboswitches (Dennis)]] |
| − | *[[CH391L/S14/Spinach RNA | Spinach RNA]] | + | *[[CH391L/S14/Spinach RNA | Spinach RNA (Drew)]] |
| + | *[[CH391L/S14/Non-canonical Nucleotides | Non-canonical Nucleotides (Drew)]] | ||
===Week 8: Parts IV: Environmental sensing and responses === | ===Week 8: Parts IV: Environmental sensing and responses === | ||
| − | *[[CH391L/S14/ | + | *[[CH391L/S14/QuorumSensing | Quorum Sensing (Mindy)]] |
| − | *[[CH391L/S14/ | + | *[[CH391L/S14/MotilityandTaxis | Motility and Taxis (Jorge)]] |
| − | *[[CH391L/S14/ | + | *[[CH391L/S14/ApplicationsofOptogenetics | Applications of Optogenetics (Ella)]] |
===Week 9: Systems I: Circuits=== | ===Week 9: Systems I: Circuits=== | ||
| − | *[[CH391L/S14/Oscillation | Oscillation]] | + | *[[CH391L/S14/Oscillation | Oscillation (Ashley)]] |
| − | *[[CH391L/S14/Cellcountingmemory | Cell Counting and memory]] | + | *[[CH391L/S14/Cellcountingmemory | Cell Counting and memory (Alex)]] |
| − | + | Tinker Cell II: Group projects | |
===Week 10: Genome Editing Techniques=== | ===Week 10: Genome Editing Techniques=== | ||
| − | *[[CH391L/S14/MAGE | MAGE (Multiplex Automated Genomic Engineering)]] | + | *[[CH391L/S14/MAGE | MAGE (Multiplex Automated Genomic Engineering) (Jordan)]] |
| − | *[[CH391L/S14/CRISPR | CRISPR ( | + | *[[CH391L/S14/CRISPR | CRISPR (Gabo)]] |
| + | *[[CH391L/S14/PolioGMODualUseEthics | GMOs, Polio Virus, Dual-Use research, and Ethics '''(two people:''' one undergrad and one grad student) (XXXXXXX)]] PART I | ||
===Week 11: Systems II: Whole Organisms === | ===Week 11: Systems II: Whole Organisms === | ||
| − | * | + | April 7th |
| − | *[[CH391L/S14/PolioGMODualUseEthics | GMOs, Polio Virus, Dual-Use research, and Ethics '''(two people:''' one undergrad and one grad student)]] | + | '''FINAL PROJECT OUTLINES DUE''' |
| + | * SPEAKER: Mike Hammerling and Amber-less E. coli | ||
| + | |||
| + | *[[CH391L/S14/PolioGMODualUseEthics | GMOs, Polio Virus, Dual-Use research, and Ethics '''(two people:''' one undergrad and one grad student)]] PART II | ||
| + | |||
| + | *[[CH391L/S14/SmallRNAs | Small RNAs in metabolic engineering (Jorge)]] | ||
===Week 12: Systems III: Metabolic Engineering === | ===Week 12: Systems III: Metabolic Engineering === | ||
| − | *[[CH391L/S14/NitrogenFixationRefactoring | Nitrogen Fixation Refactoring]] | + | April 14th |
| − | *[[CH391L/S14/Artemisinin | Artemisinin ]] | + | *[[CH391L/S14/NitrogenFixationRefactoring | Nitrogen Fixation Refactoring (Nathan)]] |
| − | *[[CH391L/S14/Bioremediation&caffeinatedcoli | Bioremediation and caffeinated coli]] | + | *[[CH391L/S14/Artemisinin | Artemisinin (Liz)]] |
| + | *[[CH391L/S14/Bioremediation&caffeinatedcoli | Bioremediation and caffeinated coli (Chen)]] | ||
===Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics === | ===Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics === | ||
| − | *[[CHE391L/S14/ | + | April 21st |
| − | + | '''FINAL PROJECTS DRAFTS DUE''' | |
| − | *[ | + | * SPEAKER: Professor Hal Alper |
| + | *[[CHE391L/S14/Ethics | Ethics (Ashley)]] | ||
| + | |||
| + | ===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 == | ||
| + | * [http://2012.igem.org 2012 iGEM Competition] | ||
| + | * [http://2013.igem.org 2013 iGEM Competition] | ||
| + | * [http://2014.igem.org 2014 iGEM Competition] | ||
Latest revision as of 19:32, 7 May 2014
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.
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?
- BioBricks and Restriction Enzymes (Ella)
- Biological Parts and the iGEM Registry (Alex)
- CAD systems (Gabo)
Week 3: Assembling the parts
Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization
- SPEAKER: Dr. Randy Hughes
- GFP (Green Fluorescent Protein) (Mindy)
- Ancestral Sequence Reconstruction (Cindy)
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
- 2/24/2014
- Directed Protein Evolution (Nathan)
- Selectable/Counter Selectable Markers (Ashley)
- Biocontainment (Liz)
- SPEAKER: Mike Hammerling and ncAA's <---Moved to....
Tinker Cell in class
Catch up day.
Week 7: Parts III: Reporter Genes and Gene Regulation
- Stochastic Gene Expression and Noise (Chen)
- Nucleic Acid Selections and Riboswitches (Dennis)
- Spinach RNA (Drew)
- Non-canonical Nucleotides (Drew)
Week 8: Parts IV: Environmental sensing and responses
Week 9: Systems I: Circuits
Tinker Cell II: Group projects
Week 10: Genome Editing Techniques
- MAGE (Multiplex Automated Genomic Engineering) (Jordan)
- CRISPR (Gabo)
- GMOs, Polio Virus, Dual-Use research, and Ethics (two people: one undergrad and one grad student) (XXXXXXX) PART I
Week 11: Systems II: Whole Organisms
April 7th FINAL PROJECT OUTLINES DUE
- SPEAKER: Mike Hammerling and Amber-less E. coli
- GMOs, Polio Virus, Dual-Use research, and Ethics (two people: one undergrad and one grad student) PART II
Week 12: Systems III: Metabolic Engineering
April 14th
Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics
April 21st FINAL PROJECTS DRAFTS DUE
- SPEAKER: Professor Hal Alper
- Ethics (Ashley)
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]
