This fall, Tufts Synthetic Biology has partnered with the Tufts Biology Department to offer a full credit, pass/fail course to expose prospective iGEM students to the essential theories and practices of synthetic biology. Although developed by current iGEM members, lectures are delivered by Dr. Kate Mirkin of the Biology Department and Dr. Nikhil Nair of the Chemical and Biological Engineering Department. It will also feature guests lectures from experts in the fields of bacteriophage engineering, biomedical research, genetic circuitry, and CRISPR-Cas9 genome editing. The class will culminate in a group project that asks students to envision and design a biological system to address a real-world problem. The course is already underway with 10 very engaged and inquisitive students.
Seminar in Synthetic Biology
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 GoalsIt 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%
Required Text Regenesis by George Church
Recommended TextIf 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 MaterialsAll research papers will be uploaded to Trunk.
Journal ClubStudents will be split into three groups, and each group will present for one of the three journal club days.
|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.|