Keasling: Synthetic Biology Class

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (15:49, 5 April 2006) (view source)
(Tentative Schedule)
 
(36 intermediate revisions not shown.)
Line 1: Line 1:
-
Draft September 9, 2005
+
=Implications and Applications of Synthetic Biology=
-
T. Kalil/J. Goler
+
-
This is a wiki for a proposed course: “Implications and Applications of Synthetic Biology”
+
==General Info==
-
Feel free to edit if you have something productive to say!
+
__TOC__
 +
Spring 2006
-
'''Goals''':
+
Instructors: Jay Keasling, Adam Arkin
 +
GSIs: Howard Chou, Yasuo Yoshikuni. 
-
Explore strategies for maximizing the economic and societal benefits of synthetic biology and minimizing the risks.
+
Logistics: 
 +
Lecture: 2 hours, 8-10 AM Wednesdays
 +
Discussion: 1 hour per week date/time TBA
-
Create “seedlings” for the future research projects in synthetic biology at UC Berkeley.
+
Grading: Group Project 90%, Class Participation 10%
-
Increase multidisciplinary collaboration at UC Berkeley on synthetic biology.
+
Office hours: TBA
 +
==Tentative Schedule==
 +
Course Modules:
 +
#Introduction to Synthetic Biology
 +
#*1/17 Introduction, Basis for Synthetic Biology - Jay Keasling
 +
#**Synthetic circuits, Elowitz' repressilator, foundations of genetic engineering, cloning.  Enabling technologies: synthesis and sequencing.
 +
#*1/25 Synthetic Biology and Intellectual Property - Steve Maurer
 +
#**Working Systems, iGEM competition projects, successes in artemisinin project. 
 +
#**[[Keasling: Synthetic Biology Class/Slides|Slides]] [[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#*2/1 Modeling and Design of  Synthetic Systems - Adam Arkin
 +
#**Genetic models, stochastic and continuous simulations, adaption of circuit methods to SB.  BioJADE design tool.
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#*2/8 Projects: Challenges and Techniques - Keasling
 +
#**Artemisinin project, prostratin, and bio-energy.
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#Applications of Synthetic Biology
 +
#*2/15 Synthetic Biology in Production - Building Artemisinin - Neil Renninger
 +
#**Amyris will discuss the development of Artemisinin and related compounds, their discovery and commercialization approach.
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#*2/22 Synthetic Biology for Energy Production - Alex Farrell
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#**Current and future platforms for synthetic energy, economic and thermodynamics of energy production and distribution.
 +
#*3/1 Bioshield - Steve Maurer
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#*3/8 Marine Derived Compounds and Development -  William Gerwick
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#** Discovering and synthesizing marine-derived anti-cancer drugs.
 +
#*3/15 "Dual-Use" approaches - Lisa Conte, Napo Pharmaceuticals
 +
#**Pathway development for high-value products, and for easy, cheap deployment in the developing world.
 +
#**[[Keasling: Synthetic Biology Class/References|References]] [[Keasling: Synthetic Biology Class/Questions|Questions]]
 +
#*3/22  Final Project Planning and Discussions
 +
#**Spring Break
 +
#Ethical, Legal and Policy implications of Synthetic Biology
 +
#*4/5 Blue Heron - John Mulligan [[Media:mulligan.ppt]]
 +
#**DNA Synthesis technology, government and self regulation of synthesis technology.
 +
#*4/12 Pilar Ossorio
 +
#**Ethics and Synthetic Biology
 +
#*4/19  Rogert Brent, Molecular Science Institute and Michael Nacht GSSP
 +
#**National security implications of genetically-engineered pathogens
 +
#*4/26, 5/3 Final Project Presentations
-
'''Logistics''':
+
==Group Project Ideas==
 +
#Dual-use strategies: Identify a synthetic biology “platform” or product with “dual-use” applications for both developed and developing country markets
 +
#Energy: What is the energy balance of proposed schemes to produce biofuels from genetically-engineered organisms? What are the relevant technical targets that would need to be met for bioenergy to make sense from an economic and thermodynamic point of view?
 +
#Marine biotechnology: Marine natural products represent a largely untapped and promising resource for drug development. As scientists with the Harbor Branch Oceanographic Institution observe:
-
Instructor:  Keasling, Arkin
+
The marine environment may contain over 80% of the world's plant and animal species, and during the past decade over 5000 novel compounds have been isolated from marine organisms. The diversity of chemical compounds in the marine environment may be due in part to the extreme competition among organisms for space and resources … It is hypothesized that sessile marine organisms (for example, sponges, octocorals, tunicates and algae), have developed a diverse array of chemical compounds known as "secondary metabolites" or natural products for defense and competition.
-
TAs: Howard, Yasuo, Goler(?)
+
-
Listing: BioEngineering, ChemE, (MOT)
+
-
+
-
Composition of class:  How diverse (in terms of subject area) should the students be for this class?  In addition to science/engineering – would it make sense to have law, public policy, business, ERG, etc. students?  Make sure we have a strategy for recruiting those students.  (2/3 Science 1/3 biz/policy)
+
It is worth noting that this research group alone has discovered 235 bioactive compounds and has had over 117 patents issued over the last 10 years.
-
+
-
Resources:  What resources are required to make
+
-
the course successful? 
+
-
Lead In - Observe and pick people for iGEM 06
+
Researchers in synthetic biology may be in a position to increase the payoff from this research. Once pharmaceuticals (or possibly specialty chemicals) have been derived from marine natural products, “synthetic biology” approaches developed at Berkeley could lower the cost of producing them at high volumes. This, in turn, would increase the economic and social value that we place on marine biodiversity, in addition to its incalculable intrinsic value. Potential projects:
 +
a. Develop a list of the most promising pharmaceuticals, specialty chemicals, etc. that could be biosynthetically derived using genes from marine organisms. Identify current stage of commercialization. [Examples discussed in the literature include: a cancer therapy made from algae; a painkiller derived from the toxins in cone snail venom; anti-viral drugs Ara-A and AAZT and anti-cancer agent Ara-C developed from a Caribbean coral reef sponge; and Dolostatin 10 (extracted from an Indian Ocean sea hare and undergoing clinical trials for the treatment of breast cancer, tumours, and leukemia. A publication called Natural Products Report has review articles on marine and other natural products. See http://www.rsc.org/Publishing/Journals/NP/index.asp
-
'''Three modules'''
+
b. Determine whether any of these are candidates for cost-effective biosynthesis using existing platforms (e.g. pathways for isoprenoids)?
 +
c. Does an analysis of possible high-value marine products for biosynthesis suggest new pathways that would produce precursors for a broad range of them?
-
1. Introduction to synthetic biology (Keasling, Arkin, et. al) – primarily on current and future capabilities, as opposed to technical details
+
d. What models exist to re-invest some of the revenue generated from marine products into marine biodiversity efforts?
-
+
==Group Project Information==
-
2. Applications of synthetic biology
+
-
+
-
a.                    energy – Tad Patzek
+
-
+
-
b.                    energy – JGI termite gut project?
+
-
+
-
c.                    “Dual-use” approaches (developed/developing country markets) – Lisa Conte – Napo Pharmaceuticals
+
-
+
-
d.                    pharmaceuticals, specialty chemicals – Amyris
+
-
+
-
e.                    Marine biotech - ?
+
-
+
-
f.                      Other company talks (e.g. Diversa, Genecor, etc.)
+
-
+
Each group will consist of 3 or 4 people and will hand in a 10-15 page (before the addition of figures) single-spaced paper on the last day of classEach group will also give a 10-15 minute presentation about their project during one of the final discussion sections.
-
3. Ethical, legal, and policy implications of synthetic biology
+
-
+
-
a.                    Steve Mauer (Goldman School) Open Source Biology
+
-
+
-
b.                   Blue Heron – Regulation of gene synthesis
+
-
   
+
-
c.                    Steve Block, Stanford, Rogert Brent, MSI – National security implications of genetically-engineered pathogens
+
-
+
-
d.                   Gerry Sussman – How can synthetic biology be harnessed for biodefense?
+
-
+
-
e.                    John Wilbanks – Executive Director, Science Commons
+
-
+
-
f.                      What should a national strategy for synthetic biology look like?  Drew Endy
+
 +
The format of the paper will be similar to that of a grant.  Each group will pick a project idea related to synthetic biology and include discussions about the following topics in their report:
-
This is a list of possible student projects. Please add to it!
+
1) Give a brief overview of the project idea.
-
1.  Dual-use strategies:  Identify a synthetic biology “platform” or product with “dual-use” applications for both developed and developing country markets
+
2) What has already been done related to your project ideaDiscuss past or existing research related to your idea.
-
+
-
2.  Energy: What is the energy balance of proposed schemes to produce biofuels from genetically-engineered organismsWhat are the relevant technical targets that would need to be met for bioenergy to make sense from an economic and thermodynamic point of view?
+
-
3.  Marine biotechnology:  Marine natural products represent a largely untapped and promising resource for drug development.  As scientists with the Harbor Branch Oceanographic Institution observe:
+
3) What are you trying to accomplish? What is the purpose/goal of your idea?
-
The marine environment may contain over 80% of the world's plant and animal species, and during the past decade over 5000 novel compounds have been isolated from marine organisms.  The diversity of chemical compounds in the marine environment may be due in part to the extreme competition among organisms for space and resources … It is hypothesized that sessile marine organisms (for example, sponges, octocorals, tunicates and algae), have developed a diverse array of chemical compounds known as "secondary metabolites" or natural products for defense and competition.
+
4) Why is your project important? Remember, this is a grant, and you are trying to persuade the board to fund your project.
-
It is worth noting that this research group alone has discovered 235 bioactive compounds and has had over 117 patents issued over the last 10 years.
+
5) How would you go about trying to achieve your idea?  Discuss experimental protocols or how you would develop platform technologies to test/build your idea.
 +
 
 +
6) Discuss what parts of your project will be hardest to achieve.
-
Researchers in synthetic biology may be in a position to increase the payoff from this research.  Once pharmaceuticals (or possibly specialty chemicals) have been derived from marine natural products, “synthetic biology” approaches developed at Berkeley could lower the cost of producing them at high volumesThis, in turn, would increase the economic and social value that we place on marine biodiversity, in addition to its incalculable intrinsic value.  Potential projects:
+
7) Discuss the timeframe required to achieve your projectFeel free to provide milestones - try to be realistic. Could your project be achieved with existing technologies or would you require new technologies (which may extend the time required to achieve your idea)?
-
a.  Develop a list of the most promising pharmaceuticals, specialty chemicals, etc. that could be biosynthetically derived using genes from marine organisms.  Identify current stage of commercialization.  [Examples discussed in the literature include: a cancer therapy made from algae; a painkiller derived from the toxins in cone snail venom; anti-viral drugs Ara-A and AAZT and anti-cancer agent Ara-C developed from a Caribbean coral reef sponge; and Dolostatin 10 (extracted from an Indian Ocean sea hare and undergoing clinical trials for the treatment of breast cancer, tumours, and leukemia.  A publication called Natural Products Report has review articles on marine and other natural products.  See  http://www.rsc.org/Publishing/Journals/NP/index.asp
+
8) What are potential applications for your idea?
-
b.  Determine whether any of these are candidates for cost-effective biosynthesis using existing platforms (e.g. pathways for isoprenoids)?
+
9) What are the ethical/social issues/impacts of your idea?
-
+
-
c.  Does an analysis of possible high-value marine products for biosynthesis suggest new pathways that would produce precursors for a broad range of them?
+
-
+
-
d.  What models exist to re-invest some of the revenue generated from marine products into marine biodiversity efforts?
+
-
'''Advertising Poster''':
+
You are not limited to topics above, but you should cover all of them in your paper. Please provide references.
-
[[image:UCB_class_poster_1.0.jpg]]
+
Please email howardc@berkeley.edu with your groups and project ideas by March 8.

Current revision

Implications and Applications of Synthetic Biology

General Info

Contents

Spring 2006

Instructors: Jay Keasling, Adam Arkin GSIs: Howard Chou, Yasuo Yoshikuni.

Logistics: Lecture: 2 hours, 8-10 AM Wednesdays Discussion: 1 hour per week date/time TBA

Grading: Group Project 90%, Class Participation 10%

Office hours: TBA

Tentative Schedule

Course Modules:

  1. Introduction to Synthetic Biology
    • 1/17 Introduction, Basis for Synthetic Biology - Jay Keasling
      • Synthetic circuits, Elowitz' repressilator, foundations of genetic engineering, cloning. Enabling technologies: synthesis and sequencing.
    • 1/25 Synthetic Biology and Intellectual Property - Steve Maurer
    • 2/1 Modeling and Design of Synthetic Systems - Adam Arkin
      • Genetic models, stochastic and continuous simulations, adaption of circuit methods to SB. BioJADE design tool.
      • References Questions
    • 2/8 Projects: Challenges and Techniques - Keasling
  2. Applications of Synthetic Biology
    • 2/15 Synthetic Biology in Production - Building Artemisinin - Neil Renninger
      • Amyris will discuss the development of Artemisinin and related compounds, their discovery and commercialization approach.
      • References Questions
    • 2/22 Synthetic Biology for Energy Production - Alex Farrell
      • References Questions
      • Current and future platforms for synthetic energy, economic and thermodynamics of energy production and distribution.
    • 3/1 Bioshield - Steve Maurer
    • 3/8 Marine Derived Compounds and Development - William Gerwick
    • 3/15 "Dual-Use" approaches - Lisa Conte, Napo Pharmaceuticals
      • Pathway development for high-value products, and for easy, cheap deployment in the developing world.
      • References Questions
    • 3/22 Final Project Planning and Discussions
      • Spring Break
  3. Ethical, Legal and Policy implications of Synthetic Biology
    • 4/5 Blue Heron - John Mulligan Media:mulligan.ppt
      • DNA Synthesis technology, government and self regulation of synthesis technology.
    • 4/12 Pilar Ossorio
      • Ethics and Synthetic Biology
    • 4/19 Rogert Brent, Molecular Science Institute and Michael Nacht GSSP
      • National security implications of genetically-engineered pathogens
    • 4/26, 5/3 Final Project Presentations

Group Project Ideas

  1. Dual-use strategies: Identify a synthetic biology “platform” or product with “dual-use” applications for both developed and developing country markets
  2. Energy: What is the energy balance of proposed schemes to produce biofuels from genetically-engineered organisms? What are the relevant technical targets that would need to be met for bioenergy to make sense from an economic and thermodynamic point of view?
  3. Marine biotechnology: Marine natural products represent a largely untapped and promising resource for drug development. As scientists with the Harbor Branch Oceanographic Institution observe:

The marine environment may contain over 80% of the world's plant and animal species, and during the past decade over 5000 novel compounds have been isolated from marine organisms. The diversity of chemical compounds in the marine environment may be due in part to the extreme competition among organisms for space and resources … It is hypothesized that sessile marine organisms (for example, sponges, octocorals, tunicates and algae), have developed a diverse array of chemical compounds known as "secondary metabolites" or natural products for defense and competition.

It is worth noting that this research group alone has discovered 235 bioactive compounds and has had over 117 patents issued over the last 10 years.

Researchers in synthetic biology may be in a position to increase the payoff from this research. Once pharmaceuticals (or possibly specialty chemicals) have been derived from marine natural products, “synthetic biology” approaches developed at Berkeley could lower the cost of producing them at high volumes. This, in turn, would increase the economic and social value that we place on marine biodiversity, in addition to its incalculable intrinsic value. Potential projects:

a. Develop a list of the most promising pharmaceuticals, specialty chemicals, etc. that could be biosynthetically derived using genes from marine organisms. Identify current stage of commercialization. [Examples discussed in the literature include: a cancer therapy made from algae; a painkiller derived from the toxins in cone snail venom; anti-viral drugs Ara-A and AAZT and anti-cancer agent Ara-C developed from a Caribbean coral reef sponge; and Dolostatin 10 (extracted from an Indian Ocean sea hare and undergoing clinical trials for the treatment of breast cancer, tumours, and leukemia. A publication called Natural Products Report has review articles on marine and other natural products. See http://www.rsc.org/Publishing/Journals/NP/index.asp

b. Determine whether any of these are candidates for cost-effective biosynthesis using existing platforms (e.g. pathways for isoprenoids)?

c. Does an analysis of possible high-value marine products for biosynthesis suggest new pathways that would produce precursors for a broad range of them?

d. What models exist to re-invest some of the revenue generated from marine products into marine biodiversity efforts?

Group Project Information

Each group will consist of 3 or 4 people and will hand in a 10-15 page (before the addition of figures) single-spaced paper on the last day of class. Each group will also give a 10-15 minute presentation about their project during one of the final discussion sections.

The format of the paper will be similar to that of a grant. Each group will pick a project idea related to synthetic biology and include discussions about the following topics in their report:


1) Give a brief overview of the project idea.

2) What has already been done related to your project idea? Discuss past or existing research related to your idea.

3) What are you trying to accomplish? What is the purpose/goal of your idea?

4) Why is your project important? Remember, this is a grant, and you are trying to persuade the board to fund your project.

5) How would you go about trying to achieve your idea? Discuss experimental protocols or how you would develop platform technologies to test/build your idea.

6) Discuss what parts of your project will be hardest to achieve.

7) Discuss the timeframe required to achieve your project. Feel free to provide milestones - try to be realistic. Could your project be achieved with existing technologies or would you require new technologies (which may extend the time required to achieve your idea)?

8) What are potential applications for your idea?

9) What are the ethical/social issues/impacts of your idea?


You are not limited to topics above, but you should cover all of them in your paper. Please provide references.

Please email howardc@berkeley.edu with your groups and project ideas by March 8.

Personal tools