A Primer in Biological Research at Tufts

Fall 2014

Biology and the life sciences have experienced extensive innovations over the last half century. Researchers at Tufts have been consistent contributors to these major advancements making their work pertinent teaching material for students interested in pursuing research opportunities. In this course, undergraduates will not only be able to explore the landscape of biological research performed at Tufts, but engage in discussions with the faculty behind it. Over the course of the semester, the students will become acquainted with various research publications by creating presentations, drafting proposals, and discussing the research with faculty and peers. The course will culminate in group proposals in which the students develop a potential research endeavor based on the principles examined throughout the course. Students will have the opportunity to have these proposals funded with the help of the Tufts Synthetic Biology team. The goal of the Tufts Synthetic Biology team has been to establish an undergraduate team of researchers who will work closely with select faculty to take part in an annual competition, learn about research on campus, discuss bioethics, and learn how to write a research proposal. We believe the best way to intellectually prime and train undergraduates who want to take part in this highly independent research project is through a class which exposes them not only to the technical aspects of the molecular biology techniques involved but also to the administrative necessities of running an independent lab. Students taking this course will be prepared to pursue undergraduate research in a professor’s lab or as a member of the Tufts Synthetic Biology team.

Speaker Schedule

9/26/14 Andrew Camilli 1. Cholera transmission: the host, pathogen and bacteriophage dynamic
2. Evolutionary consequences of intra-patient phage predation on microbial populations
3. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity
Cabot 703
10/3/14 Bacteriophage Conference None Cabot 701, 702, 703
10/10/14 Michael Levin 1. Bioelectrical Mechanisms for Programming Growth and Form: Taming Physiological Networks for Soft Body Robotics
2. Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration
3. Reprogramming cells and tissue patterning via bioelectrical pathways: molecular mechanisms and biomedical opportunities
4. The wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology and cancer
196 Boston Ave, Suite 2500
10/17/14 Fiorenzo Omenetto 1. Stabilization of vaccines and antibiotics in silk and eliminating the cold chain
2. Silk-Based Conformal, Adhesive, Edible Food Sensors
3. Implantable, multifunctional, bioresorbable optics
4. Optional: New Opportunities for an Ancient Material
Pearson 106
10/24/14 Nikhil Nair 1. Selective reduction of xylose to xylitol from a mixture of hemicellulosic sugars
2. Evolution in Reverse: Engineering a d-Xylose-Specific Xylose Reductase
Cabot 703
10/31/14 Jonathan Garlick None Pearson 106
11/7/14 Soha Hassoun Probabilistic Pathway Construction Cabot 702
11/14/14 David Walt None Pearson 106
11/21/14 Joshua Kritzer 1. Beyond discovery: probes that see, grab and poke
2. Comprehensive analysis of loops at protein-protein interfaces for macrocycle design
3. Peptide Bicycles that Inhibit the Grb2 SH2 Domain
Cabot 703

Intellectual Goals:

To impart familiarity and a thorough understanding of the components involved in the research, design, development, and experimentation associated with the life sciences, for real world experience and application. Students, particularly underclassman, taking the course will gain insight into the landscape of research at Tufts so that they may become involved more rapidly.
Specific Topics:
- Overview research in Life Sciences at Tufts
- Fundamental molecular biology techniques
- Current methods for genomic modification
- Ethical considerations of research
- Human practices

Recommended Readings:

Required readings are listed in the schedule. The below are additional readings for further knowledge on the topic of synthetic biology.
1) Geoff Baldwin, Kitney Richard I, Travis Bayer, Freemont Paul S, Tom Ellis, Karen Polizzi, Guy-Bary Stan. Synthetic Biology: A Primer
2) Bohannon, J. (2011). The Life Hacker. Science, 1236-1237.
3) Brent, E., Singh, R., & Winters, P. (2011). Synthetic Biology: Regulating Industry Uses of New Biotechnologies. Science, 1254-1256.
5) Church, G. (2012). Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. Basic Books.
6) David, G. (2009). The Machinery of Life. Copernicus.
7) Enriquez, J. (2005). As the Future Catches You. Crown Business.
8) Khalil, A., & Collins, J. (2010). Synthetic biology: Applications Come of Age. Nature, 367-379.
9) Schwille, P. (2011). Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World. Science, 1252-1254.
10) Steven, B., & Sismour, M. (2005). Synthetic biology. Nature Reviews Genetics, 533-543.

Student Involvement:

Before guest lectures, the class will receive papers written by the visiting lecturer. A one- page summary and reflection of the publication is to be completed for the following class during which discussion of the article will occur. All students must also be prepared for the question and answer session which will follow the guest lecture.
For a set amount of time each class, students will divide into their groups to discuss the semester project and pose questions to the instructors. Project checkpoints will also be required for the 4th, 7th, and 9th weeks of the course to ensure all students are progressing at a sufficient pace.

Final Project Description:

All semester projects include the following:
- 3 project checkpoints
- At minimum, a single page summary of the student’s role within and understanding of the project.
- A presentation to the class
Project Options:
- (Group) Synthetic Biology Proposals (7-10 pages)
- (Individual) Extended Proposals from Publications Review (3-5 Pages)
A final paper detailing a project proposal for a future synthetic biology project that could be pursued by the iGEM team.