BFS GOTChAs, April 2010: Difference between revisions

Revision as of 00:29, 29 April 2010

This page contains some GOTChA charts for possible rotation projects in the lab this summer.

The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.

Design a transcriptional regulator that uses feedback to compensate for changes in load and changes in context and thus provides consistent performance independent of downstream loading or cellular context (cell strain, growth media)
Example: A -| B, designed so that transfer curve is maintained across changes in downstream reactions involving B, cell strain, growth media

Characterize the performance of existing transcriptional regulators across 3 cell strains, 3 growth media and 3 loading conditions.
Design a compensation circuit that measures output level and regulates device performance to compensate for uncertainty
- Idea: use RNA-based feedback in 5' UTR sequences to measure transcription and compensate
- Note: feedback dynamics should be 5-10X regulatory dynamics to allow for use in non-equilibrium circuits
Measure the performance of one or more compensation circuits and compare to existing regulators
Regulation circuitry should be "internal" to device, so that inputs and outputs are the same as traditional regulator

Design a set of devices for implementing feedback circuits that have timescales measured in seconds instead of minutes

Identify the mechanisms and timescales of various feedback mechanisms in natural systems
- Example: feedback mechanisms involved in chemotaxis
Use models to estimate the bandwidth of regulators based on transcriptional feedback, post-transcriptional feedback, translational feedback, post-translational feedback, and covalent modifications
Formulate a test setup that can be used to characterize the speed of response of one or more circuits using different mechanisms
Implement a fast-feedback mechanism using one of the following methods:
- RNA-based feedback using anti-sense interference
- RNA-based feedback using secondary structure
- Programmable scaffolds for phosphorylation cascades
Measure the response speed of one or more regulation mechanisms and demonstrate seconds-timescale response

Design, synthesize and characterize a circuit that provides robust transcriptional regulation
Win the 2011 CAGEN competition

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-This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer.
+This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__
 == Device Projects ==
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 The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.
-=== Integrated Load and Context Compensation ===
+=== Integrated Load and Context Compensation (RMM) ===
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 |- valign=top
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 |}
-=== Fast Mechanisms for Biomolecular Feedback ===
+=== Fast Mechanisms for Biomolecular Feedback (RMM) ===
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 |- valign=top
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 == Robustness Projects ==
-=== CAGEN ===
+=== CAGEN (RMM) ===
 {| width=100% border=1
 |- valign=top
 | width=50% |
 ==== Goals ====
+* Design, synthesize and characterize a circuit that provides robust transcriptional regulation
 * Win the 2011 [[CAGEN]] competition
 |