Seminar in Synthetic Biology

Fall 2015 | Pass/Fail | 1 Credit
Mondays/Wednesdays 1:30 - 2:45
BIO 196-06

Introduction to the basics of synthetic biology and the design and development of research proposals, led in part by undergraduate members of Tufts’ Synthetic Biology team with faculty guidance. Overview of essential molecular biology principles, using primary literature and software. Topics include DNA assembly, protein purification, cell culture, genetic and metabolic engineering, biological circuits and the creation of synthetic life, and the broader technological and ethical implications of synthetic biology. Proposals written in class may be carried out in lab and possibly entered in the international synthetic biology competition (iGEM). Pass/Fail. 1 credit.

Expectations and Goals

It is expected that each student will attend and participate in each class. At the end of the semester, each student will submit his or her own research proposal on the topic of their choosing and present the proposal to the class. Through this course, students will learn the basics of synthetic biology and understand how to develop a research proposal.

Grading: Pass/Fail

 Participation: 40% -- This includes asking and answering questions, discussing your ideas and opinions about research papers with the class or smaller groups, and debating proposal ideas.
 Attendance: 30% -- Two missed classes are permitted without reason. Any more than that and the attendance grade will drop 10% for every missed class. Two late classes equals as one missed class.
 Proposal: 30% -- Outline for the proposal paper and presentation is below.
 o Written proposal: 20%
 o Proposal presentation: 10%

Course Materials

Required Text
Regenesis by George Church

Recommended Text
If you would like to learn more about synthetic biology, these two books are great resources We will be reading two chapters from the first.
Synthetic Biology: A Primer by Geoff Baldwin, et al.
Synthetic Biology: Tools and Applications by Huimin Zhao

Other Materials
All research papers will be uploaded to Trunk.

Journal Club

Students will be split into three groups, and each group will present for one of the three journal club days.


Speaker Schedule


Date
Speaker
Lesson
Work Due
Wed 9/9/15 Kate Mirkin Lecture: DNA (basic chemistry) None
Mon 9/14/15 Kate Mirkin Lecture: DNA (applications) Read chapters 1 and 2 of Regenesis.
Wed 9/16/15 Kate Mirkin Lecture: Research paper reading workshop Read the paper to be discussed.
Mon 9/21/15 Kate Mirkin Lecture: RNA Read chapters 3 and 4 of Regenesis.
Wed 9/23/15 Kate Mirkin Lecture: Proteins Read chapters 5 and 6 of Regenesis.
Mon 9/28/15 Karen Vagts presentation;
Proposal day: Introduction to proposals.
Read chapter 7 of Regenesis.
Wed 9/30/15 Robert Citorik Engineering bacteriophage for antibiotic resistant bacteria. Read guest lecture paper.
Mon 10/5/15 Kate Mirkin Lecture: Proteins Read chapter 8 of Regenesis.
Wed 10/7/15 Proposal day: Discuss/work on ideas to help choose best option. 3 proposal ideas,
0.5 pages each
Mon 10/12/15 Kate Mirkin Lecture: Host systems (prokaryotes) Read chapter 9 of Regenesis.
Wed 10/14/15 Jifa Qi Engineering bacteriophage to create nanomaterials. Read guest lecture paper.
Mon 10/19/15 Kate Mirkin Lecture: Host systems (eukaryotes) Read chapter 10 of Regenesis.
Wed 10/21/15 Journal Club 1: Discuss research paper Read research paper. Finalized idea and outline.
Mon 10/26/15 Velia Siciliano Biomedical applications of synthetic biology. Read guest lecture paper.
Wed 10/28/15 Journal Club 2: Discuss research paper. Read research paper.
Mon 11/2/15 Nikhil Nair Lecture: Biological circuits/networks and biosensors. Read chapter 11 of Regenesis.
Wed 11/4/15 Lab day: PCR Read Appendix I in Synthetic Biology: A Primer.
Mon 11/9/15 Jonathan Scheiman CRISPR/Cas9 and synthetic biology. Read guest lecture paper.
Tue 11/10/15 Lab day: Assemble PCR fragments with HiFi. Read technique paper.
Mon 11/16/15 Proposal day: edit paper. First draft of paper.
Wed 11/18/15 Alec Nielsen Genetic circuit design automation. Read guest lecture paper.
Mon 11/23/15 Proposal day: Start presentations Second draft of proposal paper.
Mon 11/30/15 Nikhil Nair Organisms as factories (producing biofuels, proteins), metabolic engineering. Read chapter 5 of Synthetic Biology: A Primer
Wed 12/2/15 Proposal day: Look over presentations, make edits, and finalize. Presentation draft.
Mon 12/7/15 Journal Club 3: Discuss research paper. Read research paper.
Wed 12/9/15 Proposal Presentation Day Final presentation.
Tue 12/15/15 Proposal Paper Due Date Final proposal paper due to Dr. Mirkin.

Proposal

Proposal Paper
The proposal paper should be written in groups of 2 or 3. The paper should be between 15 and 20 pages long, double spaced, including figures. The sections for the paper are: Abstract, Introduction, Materials and Methods, Rationale, Expected Results, Applications, Literature Cited. It will constitute 2/3rd of the overall proposal grade.
Proposal Presentation
The proposal presentation should be completed after the paper is written. It should last about 15 minutes and give a brief overview of all sections of the proposal, including relevant figures. The presentation is 1/3rd of the overall proposal grade.