Keasling: Synthetic Biology Class/Questions

Questions for 1/25/2006:

Questions for Engineering E. coli to see light:

1. What is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

Questions for Engineering a mevalonate pathway in E. coli for production of terpenoids:

2. What is the purpose of the system? What are the "parts" of the system designed? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system?

3. What are the advantages of splitting the biosynthetic genes into multiple operons? What could be the disadvantages?

4. What were some of the problems encountered while engineering E. coli to produce amorphadiene? How did the authors overcome those problems? How was the system optimized for production of amorphadiene in E. coli?

5. What other types of applications could you build based on this system?

Questions for 2/1/2006:

Questions for Reconstruction of genetic circuits:

1. In Fig 2a, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

2. In Fig 2b, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

3. In Fig 2c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

4. In Fig 2d, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

5. In Fig 3a, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

6. In Fig 3b, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

7. In Fig 3c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

8. In Fig 1c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

Questions for 2/8/2006:

Questions for Programming cellular function:

1. What are some of the ethical issues associated with each of the applications for synthetic biology discussed in the paper? Are there some applications that might be easier to adopt than others from an ethical perspective? Which ones? Why?

2. For the applications you thought might be difficult to adopt, discuss some of the ways you might persuade policy makers to approve the application. If you do not believe that certain applications should be adopted, then discuss why you believe that the application should not be adopted.

Questions for Metabolic engineering for drug discovery and development:

3. Discuss some the issues (scientific, engineering, ethical, etc.) that make metabolic engineering challenging. How might one try to resolve these issues?

4. What are the limitations of metabolic engineering? Are there any disadvantages? Are there scenarios where chemical synthesis might be a better solution for producing a small molecule?

Questions for 2/15/2006:

Questions for A synthetic multicellular system for programmed pattern formation:

1. What is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system?

2. How did the authors control the distance between sender and receiver cells for receiver cell activation? What other parts can be introduced to the system to see the similar control effect? Can authors control band width too and how?

Questions for Directed evolution of a genetic circuit:

3. What is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system?

4. What kind of bug was Weiss nonfunctional construct associated? What methodology did authors used to debug the system? What was the expected change during the debugging? What other part can by modified to debug the system?

Questions for 2/22/2006:

1. How are the two types of riboregulators presented in the two papers different? Think about how the mechanisms of regulation differ and how the riboregulators themselves are regulated.

2. What are some applications where one riboregulation design (antiswitch or cis-trans) might be better than the other? For example, which design would you use to create a biosensor for anthrax? Why? What about for a common metabolite, such as lactose?

3. What are some problems with either/both designs that might make them difficult to use as engineering tools for controlling gene expression?

4. What accounts for the digital (switch-like) property of the antiswitch design? Do you think the cis-trans design behaves more like a digital or analog system? Why?

Questions for 3/1/2006:

1. Explain the methodology developed in paper 1. What is the strength and weakness of this methodology? What other application can you do using this methodology? How can you improve the methodology?

2. Explain the methodology developed in paper 2. What is the strength and weakness of this methodology? What other application can you do using this methodology? How can you improve the methodology?

3. Compare two methodologies, and identify advantages and disadvantages for each methodology over the other.

Questions for 3/8/2006:

1. What are some current limitations for using natural products for therapeutics?

2. What are some of the key technologies that made the use of natural products as therapeutics possible?

3. What are some technologies that would be required in the future in order for the use of natural products as therapeutics to be commercially viable?

Questions for 3/15/2006:

1. How did authors achieved to obtain AND-gate behavior? Although different kinds of gate behaviors were also observed in their constructs, how would you be able to interpret molecular mechanisms in each gate behavior?

2. In their switch model, the effective concentration is defined as the fold change in intramolecular association of one domain when the other is already engaged in intramolecular inter action. How would it affect the relative output activity if you increase the effective concentration, and vice versa. How would you be able to change effective concentration.

3. Explain proposed molecular mechanism of Ste5/Ste11/Ste7/Fus3 complex for mating signal transduction.