Endy:Chassis engineering

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Specific Aims)
Current revision (08:42, 2 July 2008) (view source)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
 +
[[Image:DedicatedTubesW852.jpg|thumb|right|300px|Two orthogonal protein synthesis channels, one specific for engineered biological systems and one specific for normal cellular function.]]
==Abstract==
==Abstract==
-
The engineering of biological systems with predictable behavior is currently a challenging problem.  A major reason for this difficulty is the complexity and variation found in cells acting as a host to engineered biological systems and the numerous interactions between the host and system.  To make the future engineering of biological systems easier, I will study and optimize the interface between an engineered biological system and its host cell or '"chassis".  An optimal design of the host/system interface should essentially decouple system function from host function, such that newly designed systems work as predicted first time with less need for iterative design.  Ultimately this will lead to the development of a host engineering field to complement the system engineering field.  With a standardized and specified host/system interface any system will function in any host designed for the same interface.  This interchangeability of modules has been a powerful enabler in other engineering disciplines.  I will accomplish these overall goals by first specifying and testing the interaction between a host and an engineered system to better characterize the effects of one on the other.  I will then build dedicated transcription and translation systems, independent from the equivalent host systems.  The goal of these systems is to decouple system function from host function wherever possible.  Lastly, I will use the isolated systems as a tool to further examine the interactions between a system and its host.
+
The engineering of biological systems with predictable behavior is currently a challenging problem.  A major reason for this difficulty is the complexity found in cells acting as a chassis to engineered biological systems and the numerous interactions between the chassis and system.  To make the future engineering of biological systems easier, we are designing a standard interface between an engineered biological system and its host cell or "chassis".   
-
==Specific Aims==
+
An optimal design of the chassis/system interface should decouple system function from chassis function, such that newly designed systems perform as predicted first time with less need for iterative design. With a standardized and specified chassis/system interface any system will function in any chassis containing the same standard interface.
-
*[[Endy:Dedicated systems|Integrate dedicated transcription and translation systems into a chassis]]
+
 
 +
We are implementing a standard chassis/system interface using an orthogonal protein synthesis channel.  This orthogonal channel uses T7 RNA polymerase (RNAP) and mutant ribosomes to transcribe and translate coding regions and open reading frames that are not recognized by ''E. coli'' RNAP and ribosomes.
 +
 
 +
==Projects==
 +
*[[Endy:Dedicated systems|Implement orthogonal transcription and translation in ''E. coli'']]
 +
**[[Endy:Dedicated systems/Virtual machines|Virtual machine 1.0]]
 +
**[[/VM2.0|Virtual machine 2.0]]
 +
**[[User:Barry Canton/Notebook/T7 RNAP transcription of rRNA| T7 RNAP transcription of rRNA]]
*[[Endy:Chassis test systems|Develop test systems & measurements to evaluate chassis response to system demands]]
*[[Endy:Chassis test systems|Develop test systems & measurements to evaluate chassis response to system demands]]
-
*Evaluate the ability of a wild-type chassis and a dedicated system containing chassis to supply an engineered system
+
**[[Endy:Translation demand|Applying and measuring translation demand]]
-
*Investigate “porting” an engineered system between two chassis
+
**[[/Computational load modeling|Load modeling]]
 +
*[[/Paper|Paper]]

Current revision

Two orthogonal protein synthesis channels, one specific for engineered biological systems and one specific for normal cellular function.
Two orthogonal protein synthesis channels, one specific for engineered biological systems and one specific for normal cellular function.

Abstract

The engineering of biological systems with predictable behavior is currently a challenging problem. A major reason for this difficulty is the complexity found in cells acting as a chassis to engineered biological systems and the numerous interactions between the chassis and system. To make the future engineering of biological systems easier, we are designing a standard interface between an engineered biological system and its host cell or "chassis".

An optimal design of the chassis/system interface should decouple system function from chassis function, such that newly designed systems perform as predicted first time with less need for iterative design. With a standardized and specified chassis/system interface any system will function in any chassis containing the same standard interface.

We are implementing a standard chassis/system interface using an orthogonal protein synthesis channel. This orthogonal channel uses T7 RNA polymerase (RNAP) and mutant ribosomes to transcribe and translate coding regions and open reading frames that are not recognized by E. coli RNAP and ribosomes.

Projects

Personal tools