Endy:F2620: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
 
(37 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Image:ReceiverIcon.png|Receiver Device]]
__NOTOC__
==Introduction==
[[Image:F2620.de2.jpg|right|thumb|200px|Drew's datasheet]]
We are working to comprehensively characterize a receiver device to enable cell-cell communication.  F2620 is a receiver device that responds to the presence of a signaling molecule in the extracellular media by activating transcription from a regulated promoter.  Our aims are to provide a well-characterized receiver device to the biological engineering community and secondly to develop a framework for device characterization that can be adapted to characterize other devices that can be used to build modular biological systems.  Further details about this work can be found on the [http://parts2.mit.edu/registry/index.php/Featured_Parts:Cell-Cell-Signaling cell-cell signaling page] of the [http://parts.mit.edu/registry registry].


==Receiver Devices==
==Characterization data==
We define a receiver device as a set of genetic elements that responds to an extracellular input signal by changing the [[PoPS]] output from the device.  That input signal might be the concentration of a small molecule or a piece of DNA or peptide.  The only limitation on the signal is that it must be capable of being produced by other cells growing in the same environment.  While we can envisage a number of families of receiver devices we are currently developing a family based on the Lux System of ''V. Fischeri''.  This device family is specified below.
{|{{Table}}
!Experiment
!Protocol
!Data
|-
|[[Endy:F2620/Transfer Curve|Transfer Curve]]
|[[Endy:F2620/Transfer Curve/Protocols|protocol]]
|[[Endy:F2620/Transfer Curve/Data|data]]
|-
|[[Endy:F2620/Specificity|Specificity]]
|[[Endy:F2620/Specificity/Protocols|protocol]]
|[[Endy:F2620/Specificity/Data|data]]
|-
|[[Endy:F2620/Latency|Latency]]
|[[Endy:F2620/Latency/Protocols|protocol]]
|[[Endy:F2620/Latency/Data|data]]
|-
|[[Endy:F2620/Stability|Stability]]
|[[Endy:F2620/Stability/Protocols|protocol]]
|[[Endy:F2620/Stability/Data|data]]
|}


==Lux Receiver Family ([http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=Signalling Registry page])==
In this device family the input signal is the concentration of an acyl homoserine lactone (AHL).  More information on these molecules can be found under [[Cell to Cell Signal Carriers]]. Homoserine Lactone molecules with varying length acyl side chains can be used to produce different device behavior or to permit different signaling channels to be used in the one system. 


A schematic of device operation is shown below.  The AHL molecule is recognized by a member of the LuxR protein family.  This AHL-LuxR complex can bind to an operator site upstream of a [http://rosalind.csail.mit.edu/r/parts/partsdb/view.cgi?part_id=192 Luxp<sub>R</sub>] family promoter and activate transcription.  The exact mechanism and stoiciometry of this activation have not been fully resolved. The degree of transcriptional activation can be set by varying the specific receiver protein, signaling molecule or promoters used.  In the second figure, the part specification for a member of this device family ([http://model.mit.edu/endipedia/images/4/45/F2620_Data_Sheet.pdf F2620]) is shown.
*[[Endy:F2620/Experiments Pending|Experiments Pending]]
*[[Endy:F2620/Calibration|Calibration]]
*[[Endy:F2620/Machine variation|Machine variation]]
*[[Endy:F2620/Data Processing|Data Processing]]
*[[Endy:F2620/Data/Archive|Old data plots and discussion of data-processing methods]]


[[Image:ReceiverSchematic.jpg|Device Diagram for a Member of the Lux Family of Receivers]]
==Communications==
*[[Endy:F2620/Nature Biotech draft|Nature Biotech. draft]]
*[[Endy:F2620/Figures]]
*[[Nat Biotech Guidelines]]
*[[Endy:F2620/Miscellaneous communications|Other communications]]


[[Image:F2620Parts.png| BioBrick Part Specification for a Lux Receiver]]
==F2620 Data Sheets==
*[http://model.mit.edu/endipedia/images/7/7b/F2620.bc1.ppt Barry's first draft (.ppt file)]
*[http://model.mit.edu/endipedia/images/2/25/F2620.de2.ppt Drew's improved version (.ppt file)]
*[http://parts.mit.edu/registry/index.php/Part:BBa_F2620 F2620 Registry page]
*[[Endy:F2620/Data sheet versions|Other data sheet versions]]


==Device Characteristics==
<math>
 
P_{out} = \frac{P_{max}[3OC_6HSL]^n}{K^n+[3OC_6HSL]^n}
===Transfer Function===
</math>
The transfer function describes how the output [[PoPS]] varies with the input concentration of the AHL molecule.  A representative transfer function is shown graphically below.  Transfer curves for members of the family have been measured using fluorescence output that we expect is proportional to [[PoPS]] output.  Experiments are planned to measure the [[PoPS]] levels directly for members of the device family.  The parameters of interest that can be derived from the transfer curve are the input and output Hi/Lo values and the switch point of the device.  Transfer curves for the specific members of the device family can be found on their individual data sheets.  Transfer functions should also indicate the level of variation that can be expected in a genetically identical population of cells carrying the device.
 
[[Image:TransferFunctionSchematic.png|Schematic of a Transfer Function for the Lux Receiver Family]]
 
===Device Latency===
Latency is defined as the time lag between a change in input concentration and the output level reaching 95% of its final value.  While these measurements have not yet been made accurately. we expect that the Lux family of receivers will have very low latencies.  Since the receiver protein is being constitutively produced, the only time lags are for transport of the AHL molecule through the media and into the cell, and the fast time-scale binding reactions between the receiver protein, the signaling molecule and the promoter operator site.  As there are no feedback loops in the device, the response is first order.
 
[[Image:LatencySchematic.png|Schematic of a Latency Measurement for the Lux Receiver Family]]
 
===Load===
These devices contain two [[PoPS]] generators.  The [[PoPS]] load of these generators has yet to be measured.  The devices contain one [[RiPS]] generator.  The [[RiPS]] load of this generator has also not been measured.  Once these measurements have been made, it will be possible to quote the NTP/s.copy, the AA/s.copy and the machinery load of these devices.
 
===Specificity===
While each receiver protein will optimally bind to one AHL molecule it has been documented (ref.) that there is varying amounts of cross-talk between different protein-AHL pairs.  Where possible, device data sheets list those signaling molecules that a device is compatible or incompatible with.
 
===Genetic Stability===
The retention of function over long culture intervals is an important characteristic of all devices.  Where known, this data is reported on the device data sheets.
 
==Data Sheets==
 
[http://model.mit.edu/endipedia/images/7/7b/F2620.bc1.ppt Barry's receiver datasheet (.ppt file)]
 
[http://parts2.mit.edu/r/parts/partsdb/view.cgi?part_id=5114 Randy's online receiver datasheet]
 
[http://model.mit.edu/endipedia/images/2/25/F2620.de2.ppt Drew's receiver datasheet (.ppt file)]
 
JPEG of Drew's datasheet...
 
[[Image:F2620.de2.jpg]]

Latest revision as of 09:26, 11 February 2008

Introduction

Drew's datasheet

We are working to comprehensively characterize a receiver device to enable cell-cell communication. F2620 is a receiver device that responds to the presence of a signaling molecule in the extracellular media by activating transcription from a regulated promoter. Our aims are to provide a well-characterized receiver device to the biological engineering community and secondly to develop a framework for device characterization that can be adapted to characterize other devices that can be used to build modular biological systems. Further details about this work can be found on the cell-cell signaling page of the registry.

Characterization data

Experiment Protocol Data
Transfer Curve protocol data
Specificity protocol data
Latency protocol data
Stability protocol data


Communications

F2620 Data Sheets

[math]\displaystyle{ P_{out} = \frac{P_{max}[3OC_6HSL]^n}{K^n+[3OC_6HSL]^n} }[/math]

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Endy:F2620&oldid=185653"