CH391L/S13

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(New page: Category:CH391L_S13 ==CH391L: Molecular Mechanisms of Genome Maintenance== Spring 2013 Instructor: Dr. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu> Course web page: The ...)
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[[Category:CH391L_S13]]
[[Category:CH391L_S13]]
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==CH391L: Synthetic Biology (Spring 2013)==
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==CH391L: Molecular Mechanisms of Genome Maintenance==
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Mondays 2-5 PM  MBB 2.204
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Spring 2013
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Instructor: Dr. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
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Course web page: The course web site on OpenWetWare.org http://openwetware.org/wiki/CH391L/S13 will host course handouts, readings, and assignments.
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Instructor: Dr. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
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[[Media:CH391_S13_Syllabus.pdf|Course Syllabus]]
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Course web page: The course web site on OpenWetWare.org http://openwetware.org/wiki/CH391L/S12 will host course handouts, readings, and assignments.
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Last year's website: [[CH391L/S12 | CH391L/S12]].
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[[Media:CH391L_S12_Syllabus.pdf | Course Syllabus (PDF) ]]
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[[CH391L/S13/Topics | Suggest Topics!]]
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[http://2012.igem.org/Main_Page 2012 iGEM Competition]
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[http://2013.igem.org 2013 iGEM Competition]
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[[CH391L/S12/Users | CH391L Users]]
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[[CH391L/S13/Users | CH391L Users]]
== Motivation ==
== Motivation ==
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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.
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.
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[[CH391L/S12/WikiEditing|Instructions for Wiki Editing]]
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[[CH391L/S13/WikiEditing|Instructions for Wiki Editing]]
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[[CH391L/S12/Assignments|Class Assignments]]
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[[CH391L/S13/Assignments|Class Assignments]]
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[[CH391L/S12/TopicGradingRubric|Grading Rubric for Topic Pages and Presentations]]
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[[CH391L/S13/TopicGradingRubric|Grading Rubric for Wiki Pages, Presentations, and Participation]]
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[[CH391L/S12/FinalProjectRubric|Grading Rubric for Final Project]]
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[[CH391L/S13/FinalProjectRubric|Grading Rubric for Final Project]]
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==Synthetic Biology Seminars at UT==
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===Upcoming===
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===Past===
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*Frances Arnold (Caltech) Gottlieb Lecture - Friday, Mar 2, 2:00 PM,  ACE 2.302 [http://cheme.che.caltech.edu/groups/fha/ webpage]
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*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]
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*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]
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*Douglas Fowler (U Washington) - Monday, Feb 6, 3:30 PM, WEL 2.122 [http://depts.washington.edu/sfields/staff.html webpage]
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*Michelle Chang (UC Berkeley) - Friday, Feb 3, 3:30 PM, WEL 2.122 [http://chem.berkeley.edu/faculty/chang_m/ webpage]
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*Erik Winfree (Caltech) - Thursday, Feb 2, 3:30 PM, ACES 6.304 [http://www.dna.caltech.edu/~winfree/ webpage]
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*Lulu Qian (Caltech) - Wednesday, Feb. 1 4:00 PM, WEL 2.122 [http://dna.caltech.edu/~lulu/ webpage]
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*Sang Yup Lee (Korea Advanced Institute of Science and Technology (KAIST)) - Tuesday, Jan. 31 3:30pm, CPE 2.218 [http://www.che.utexas.edu/event/pirkey-systems-metabolic-engineering-of-microorganisms-for-chemicals-fuels-and-materials-by-dr-sang-yup-lee-korea-advanced-institute-of-science-and-technology-kaist/ webpage]
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==Synthetic Biology News==
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Here is a [[CH391L/S12/RecentNews | 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.
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== Topics ==
== Topics ==
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===Introduction===
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=== Week 1: Introduction ===
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[[:Category:CH391L_S12 | Index of All CH391/S12 Pages]]
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[[Special:RecentChangesLinked/Category:CH391L_S12 | View Recent Changes to CH391/S12 Pages]]
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==== Week 1: Introduction ====
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* [[CH391L/S12/Introduction | Introduction to synthetic biology]]
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===Methods===
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====Week 2: Making or finding parts====
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* [[CH391L/S12/iGEM Registry | iGEM Registry]]
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* [[CH391L/S12/Bioprospecting | Bioprospecting new parts using Metagenomics]]
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* [[CH391L/S12/In vitro Selection | ''In vitro'' selection]]
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* [[/CH391L/S12/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]
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====Week 3: Assembling parts into systems====
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* [[CH391L/S12/Restriction_enzymes_and_BioBricks_assembly_standards | Restriction enzymes and BioBricks/BglBricks assembly standards (RFCs)]]
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* [[CH391L/S12/PCR and advanced PCR techniques | PCR and advanced PCR techniques]]
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====Week 4: Parts assembly, metabolic engineering, and choosing a chassis====
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* [[CH391L/S12/GeneandGenomeSynthesis | Gene and genome synthesis]]
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* [[CH391L/S12/MetabolicEngineering | Metabolic Engineering]]
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* [[CH391L/S12/HostOrganisms | Chassis (Host organisms)]]
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=== Parts ===
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====Week 5: Chassis and Backbones====
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* [[CH391L/S12/Selectablegeneticmarkers | Selectable genetic markers]]
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* [[CH391L/S12/ToxinAntitoxins | Toxin/anti-toxins, plasmid addiction systems]]
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* [[CH391L/S12/CounterSelection| Counter-selectable genetic markers]]
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====Week 6: Basic Gene Construction====
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* [[CH391L/S12/TranslationRBSandCodons | Ribosome Binding Sites and Codon Optimization]]
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* [[CH391L/S12/TranscriptionPromotersandTerminators | Transcriptional Promoters and Terminators]]
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* [[CH391L/S12/SpinachRNA | Spinach Aptamer]]
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====Week 7: Gene regulation ====
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* [[CH391L/S12/Origins of Replication | Origins of Replication]]
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* [[CH391L/S12/LightSensors | Light Sensors]]
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* [[CH391L/S12/Protein_regulators_of_transcription | Protein regulators of transcription]]
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====Week 8: Reporter Genes====
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* [[CH391L/S13/Introduction | Introduction to Synthetic Biology]]
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* [[CH391L/S12/Pigments | Pigments]]
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* [[CH391L/S12/Fluorescent Proteins | Fluorescent Proteins]]
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====Week 9: Complex parts====
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===Week 2: Making or finding parts/ethics/DIY Biology===
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* [[CH391L/S12/Unnatural_Amino_Acids | Unnatural Amino Acid Incorporation]]
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* [[CH391L/S12/Locomotion | Locomotion]]
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* [[CH391L/S12/Quorum_Sensing | Quorum Sensing]]
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===Systems===
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*[[CH391L/S13/Ethics | Ethics of Synthetic Biology]]
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*[[CH391L/S13/DIY_SyntheticBiology | DIY Synthetic Biology]]
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*[[CH391L/S13/BioBricksAndRegistry | BioBricks and the Registry of Standard Biological Parts]]
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====Week 10: Systems I====
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===Week 3: DNA Assembly===
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*[[CH391L/S12/Pattern Formation | Pattern Formation]]
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*[[CH391L/S12/Toggle Switches, Repressilators, and Counters | Toggle Switches, Repressilators, and Counters]]
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*[[CH391L/S13/CAD | CAD in Synthetic Biology]]
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*[[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]]
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*[[CH391L/S12/Refactoring Genomes | Refactoring Genomes]]
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===Week 4: Chassis Engineering and Making Parts===
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====Week 11: Systems II====
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*[[CH391L/S13/CleanGenomes | Minimal "Clean" Genomes]]
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*[[CH391L/S13/In vitro Selection of FNAs | In vitro selection of FNAs]]
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*[[CH391L/S12/Artemisinic Acid Engineering | Artemisinic Acid Engineering ]]
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===Week 5: Finding and Improving Parts===
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*[[CH391L/S12/Synthetic Cooperation | Synthetic Cooperation ]]
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*[[CH391L/S13/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]
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*[[CH391L/S12/MAGE lycopene production, CAGE "Amberless" E. coli | MAGE lycopene production, CAGE "Amberless" E. coli ]]
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*[[CH391L/S13/MetagenomicBioprospecting | Metagenomic Bioprospecting (old version)]]
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*[[CH391L/S13/Metagenomics & Bioprospecting | Metagenomics & Bioprospecting]]
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====Week 12: Systems III====
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===Week 6: Genetic Engineered Technologies===
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*[[CH391L/S12/Bacterial Odor Engineering | Bacterial Odor Engineering ]]
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*[[CH391L/S13/DirectedProteinEvolution | Directed Protein Evolution]]
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*[[CH391L/S13/Optogenetics | Optogenetics]]
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*[[CH391L/S13/Riboswitches | Riboswitches]]
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===Week 7: Communication and Containment ===
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*[[CH391L/S13/QuorumSensing | Quorum Sensing]]
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*[[CH391L/S13/Biocontainment | Biocontainment]]
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*[[CH391L/S13/GeneticMarkers | Selectable Genetic Markers]]

Revision as of 10:54, 4 March 2013

Contents

CH391L: Synthetic Biology (Spring 2013)

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/S13 will host course handouts, readings, and assignments.

Course Syllabus

Last year's website: CH391L/S12.

Suggest Topics!

2013 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 Wiki Pages, Presentations, and Participation

Grading Rubric for Final Project

Topics

Week 1: Introduction

Week 2: Making or finding parts/ethics/DIY Biology

Week 3: DNA Assembly

Week 4: Chassis Engineering and Making Parts

Week 5: Finding and Improving Parts

Week 6: Genetic Engineered Technologies

Week 7: Communication and Containment

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