Brown Synthetic Biology

BIOL 1940T (CRN 14871) Synthetic Biological Systems

Mondays and Wednesdays 3.30pm - 5.00pm, CIT Room 227

• First class is Wednesday August 5th.

• Taught by interdisciplinary faculty
• Opportunity for individual or group practical projects in Spring 2008.
• Join the Google group for announcements about this course.
• Open to juniors or seniors with relevant backgrounds in one of the key areas, or with instructors permission.

Outline

A multidisciplinary course that combines seven areas of science and engineering giving undergraduates a solid foundation in a cutting edge field of biological engineering. Synthetic biology is a mixture of biology, chemistry, engineering, genetic engineering and biophysics. It builds on recent work in systems biology which involves the modeling of biological systems, but goes further in that it involves the construction and standardization of biological parts, that fit together to form more complex systems.

Background

In 1978 the Nobel Prize in Medicine was awarded to Daniel Nathans and Hamilton Smith and it was predicated that "the new era of synthetic biology” had arrived , where genes could be cut up, changed around and put back together again to form novel function. However it was not until 2000 that the first examples of an engineered biological circuits were published in Nature. One was a synthetic oscillator; an engineered strain of E.coli capable of cyclic expression of green fluorescent protein, the other was a bacterial toggle switch capable of switching the protein to be expressed into one of two states. Since then engineers’ interest and contributions to biology have created a completely new field of ‘synthetic biology’.

Synthetic biology is a mixture of biology, chemistry, engineering, genetic engineering and biophysics. It builds on recent work in systems biology which involves the modeling of biological systems, but goes further in that it involves the construction and standardization of biological parts, that fit together to form more complex systems. One of the key factors that is making synthetic biology a reality is the falling cost of two key technologies, sequencing of DNA (now just $7 per read) and synthesis of novel DNA (now $0.69 per base pair). This fall in price continues to halve about every 18 months and was recently compared to the doubling of the number of processors being put onto computer chips which also happens every 18 months. If this pace of development continues then not only is a new field of science and engineering forming but also a new industrial revolution, based on smaller, cleaner biological machines.

Course aim

This course will aim to you a thorough grounding in the theory and current literature of synthetic biology as well as provide you with an up-to-date framework in modeling and systems biology. It will include the fundamental principles of engineering such as abstraction, modularity, standardization and composition and how these are being applied to biology. You will get an overview of the biological techniques specific to experts in biology and engineering at Brown. The course will also include a number of visiting lectures, experts in the field from outside of Brown.

Assessment:

• Synthetic Biological System 1: Part Design (Group project)
• Synthetic Biological System 1: System Design (Individual project)
• Primary literature class presentation
• Synthetic society paper, ethics and impacts
• Computer modeling labs/problem sets.

            Date                     Instructor                                                 Topic
1.      Sept 5 (W)    Gary Wessel  ( Brown, MCB  Introduction, perspective and ethical implications    
2.     Sept 10 (M)  Tom Knight  Foundations of synthetic biolog,  MIT, Computer Science and AI Laboratory
3.     Sept 12 (W)       John Savage      Nanocomputing,  Brown, Computer Science
4.     Sept 17 (M)      John Cumbers      The engineers approach, modularity, abstract hierarchy, Brown, BioMed    
5.     Sept 19 (W)             Jamie Gagnon           Synthetic biology literature review, Brown, MCB
 Ethics essay due
6.     Sept 24 (M)       Jeff Morgan          Techniques in synthetic biology Brown,   Biomedical Engineering 
7.     Sept 26 (W)            John Cumbers               Isolation, characterized behavior, interfaces  Brown, Biomed
8.       Oct 1 (M)               Wolfgang Peti                                   Protein engineering 1  Brown, MPPB
9.      Oct 3 (W)              Hasan Demirci        Protein engineering 2        Brown, MCB
     Take Home exam 1 given out
Oct 8 (M)                               Columbus Day, no class
10.    Oct 10 (W)  Sherief Reda       Cellular logic motifs, Brown, Engineering
 Take Home exam 1, Due at beginning of class
11.    Oct 15 (M)       Nicola Neretti     Deterministic models 1 Brown, Physics
12.    Oct 17 (W)     Nicola Neretti            Deterministic models 2   Brown, Physics
13.    Oct 22 (M)     Anubhav Tripathi        Microfluidics  Brown, Engineering
14.    Oct 24 (W)    Literature review       Literature review
   Modeling exercise due
15.    Oct 29 (W)       Pam Silver  Designing Biological Systems  Harvard, Systems Biology
16.    Oct 31 (M)                Jason Sello              Metabolic engineering        Brown, Chemistry
17.     Nov 5 (M)     Christina Smolke      Metabolic engineering and RNA logic devices,   Caltech, Chemical Engineering
18.     Nov 7 (W)   Jim Collins   Engineering Gene Networks: BU,    Integrating Synthetic Biology & Systems Biology
1 page outline of final project due
19.    Nov 12 (M)   Suzanne Sindi        Stochastic Modeling  Brown, Applied Math
Take home exam 2 given out
19.    Nov 14 (W)      Suzanne Sindi    Stochastic Modeling    Brown, Applied Math
21. Nov 19 (M)   Chris Voigt    Programming bacteria: wiring synthetic sensors - Pharmaceutical Chemistry, UCSF              and circuits to heterologous outputs
       Take home exam 2 due
       Nov 21 (W)                               Thanksgiving, no class
22.    Nov 26 (M)        Jay Tang     Biophysics of bacteria  Brown, Physics
23. Nov 28 (W)                           Group Presentations and Discussion
24. Dec 3 (M)     Marc Johnson             Bioenergetics and biofuels  Brown, MCB
25. Dec 5 (W)        Jim Head      Exploring Planetary Environments:   Brown, Geology     Earth and the Solar System
26. Dec 10 (M)                           Final project oral presentations 1
27. Dec 12 (W)                           Final project oral presentations 2

       faculty  	 Topic   	                                                Department / area
1 	Gary Wessel 	 Overview and Bioethics 	                                MCB

10 	Jim Head         Exploring Planetary Environments: Earth and the Solar System   Geology

20     Dec 14 (F)       Final written project due     

       The course outline will be finalized over the summer