Spring 2014 Synthetic Biology

CH391L: Synthetic Biology (Spring 2014)
Mondays 2-5 PM  MBB 2.456 Unique #: 53230

Instructors:
 * Prof. Jeffrey Barrick 
 * Dr. Dennis Mishler 

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.

Instructions for Wiki Editing

Class Assignments

Grading Rubric for Wiki Pages, Presentations, and Participation

Grading Rubric for Final Project

Previous year's websites

 * CH391L Synthetic Biology Topics (Spring 2012)
 * CH391L Synthetic Biology Topics (Spring 2013)

Topics

 * List of CH391L/S14 Users
 * Index of CH391L/S14 pages

Week 1: Introduction

 * Introduction to Synthetic Biology

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

 * Synthetic Genome (Drew)
 * Gibson Assembly (Jordan)

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
Follow ups on GFP and Ancestral Sequence Reconstruction
 * SPEAKER: Dr. Chris Yellman spoke about some of the methods used to create large DNA sequences in yeast and the advantages of this organism.

Week 6: Parts II: Basics of Gene Expression

 * 2/24/2014
 * Directed Protein Evolution (Nathan)
 * Selectable/Counter Selectable Markers (Ashley)
 * Biocontainment (Liz)

Tinker Cell in class
 * SPEAKER: Mike Hammerling and ncAA's  <---Moved to....

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

 * Quorum Sensing (Mindy)
 * Motility and Taxis (Jorge)
 * Applications of Optogenetics (Ella)

Week 9: Systems I: Circuits
Tinker Cell II: Group projects
 * Oscillation (Ashley)
 * Cell Counting and memory (Alex)

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


 * Small RNAs in metabolic engineering (Jorge)

Week 12: Systems III: Metabolic Engineering
April 14th
 * Nitrogen Fixation Refactoring (Nathan)
 * Artemisinin (Liz)
 * Bioremediation and caffeinated coli (Chen)

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]

Useful links

 * 2012 iGEM Competition
 * 2013 iGEM Competition
 * 2014 iGEM Competition