Endy:Screening plasmid

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'''This page is a work in progress.'''
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*[[test]]
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'''This project is in progress -- results described are preliminary.'''
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If you would like to keep up to date with this work, please subscribe to the [http://openwetware.org/index.php?filter=Endy:Screening_plasmid&feed=rss&title=Special:Recentchanges RSS feed].
==Introduction==
==Introduction==
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[[Image:ScreeningPlasmidSchematic.PNG|500px|left|thumb|Schematic of the screening plasmid design.]]
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Construction of engineered biological systems from collections of standard biological parts requires mechanisms for rapid and reliable characterization of parts.  Additionally, the difficulty of rational part design necessitates library screening systems that can be employed in service of tuning part performance. Here we describe pSB1A10, a system for both characterizing and screening transcription-based parts based on their input / output function.  We demonstrate the successful operation of this system by characterizing and tuning genetic inverters and transcriptional terminators.
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The screening plasmid is designed to enable fast characterization of PoPS-based parts and devices.  It consists of 4 components: (1) Tunable input (2) Input measurement (3) Part/Device insertion site (4) Output measurement.  
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[[Image:ScreeningPlasmidSchematic.PNG|500px|left|thumb|Schematic of the screening plasmid design.  It consists of 4 components: (1) Tunable input (2) Input measurement (3) Part/Device insertion site (4) Output measurement.]]
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==Screening Plasmid 1.0==
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[[Image:ScreeningPlasmid1.0.PNG|600px|left|thumb|'''Design of Screening Plasmid 1.0:''' We are using the Pbad arabinose-inducible induction system <cite>Khlebnikov</cite> as a tunable input.  GFP is a measure of input and RFP is a measure of output.  A Biobricks cloning site enables easy insertion of any Biobricks part.  RNase E sites create independence between the mRNA stability of the device being screened and the mRNA stability of the fluorescent proteins.  In particular, we suspect mRFP1 contains internal RNaseE cut sites and have added a hairpin 5’ of the coding region to slow degradation by RNase E. <cite>Smolke</cite>
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*[[Endy:Screening plasmid 1.0/Background|Background]]
 
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*[[Endy:Screening plasmid 1.0/Protocols|Protocols]]
 
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*[[Endy:Screening plasmid status|Status]]
 
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*[[Endy:Screening plasmid constructs|Constructs]]
 
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===Terminator Characterization via Screening Plasmid 1.0===
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==Current Experimental Work==
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[[Image:TermDotPLot.JPG|left|300px|thumb|'''Characterization of 6 terminators from the Registry of Standard Biological Parts''' inserted into the Screening Plasmid. The black line is the best fit to the empty screening plasmid, and serves as a standard for 0% termination efficiency.  Functional terminators should lie below the line, note that B0025 (red) is sometimes acting as a promoter.]]
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*[[Endy:Screening plasmid/Notebook]]
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*Construction of [[Endy:Screening plasmid/v1.5|Screening plasmid 1.5]] -- Andrzej
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*Construction of [[Endy:Screening plasmid/v1.0/Hairpin|hairpin test constructs]] -- jason
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*Development of [[Endy:Screening plasmid/RBS library|RBS library]] for tuning expression level -- jason
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*Characterization of [[Endy:Screening plasmid/v1.0|empty Screening Plasmid 1.0]] with different induction approaches. -- jason
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*[[Endy:Screening plasmid/Calibration beads|Measuring effectiveness of beads]] for normalizing flow cytometry data.
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[[Image:TermsCorrected.jpg|left|300px|thumb|Histogram of calculated termination efficiencies for each terminator.  Note that B0025 is mostly off scale.]]
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==Screening Plasmid 0.X==
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*[[Endy:Screening plasmid/v0.X]]
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*[[Endy:Terminator characterization/Protocols|Protocols]]
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*[[Endy:Terminator characterization/Analysis|Analysis]]
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===Inverter Characterization via Screening Plasmid 1.0===
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==Screening Plasmid 1.0==
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'''This is the current working version of the screening plasmid.  It is available from the MIT Registry of Standard Biological Parts as [http://parts.mit.edu/registry/index.php/Part:pSB1A10 pSB1A10].'''
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*[[Endy:Screening plasmid/v1.0]]
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[[Image:Q04740sp.PNG|thumb|400px|left|'''Characterization of Q04740: '''Dot plot of one replicate is shown in upper right.  Mean RFP expression for 3 replicates is plotted against GFP showing characteristic inverter transfer curve.]]
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==Screening Plasmid 1.5==
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This version of the screening makes use of an AHL-based induction system (<bbpart>F2620</bbpart>). 
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*[[Endy:Screening plasmid/Inverter characterization/Protocols|Protocols]]
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*[[Endy:Screening plasmid/v1.5|Screening plasmid 1.5]]
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*[[Endy:Screening plasmid/Inverter characterization|Inverters]]
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*[[Endy:Screening plasmid/Inverter characterization/Analysis|Analysis]]
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==Screening Plasmid 2.0==
==Screening Plasmid 2.0==
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==Documents==
==Documents==
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*[[/Registry technical report/]]
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*[[/Registry technical report/]] (''in progress'')
==References==
==References==
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#Smolke pmid=12402322
#Smolke pmid=12402322
</biblio>
</biblio>
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__NOTOC__
 

Current revision

This project is in progress -- results described are preliminary. If you would like to keep up to date with this work, please subscribe to the RSS feed.

Contents

Introduction

Construction of engineered biological systems from collections of standard biological parts requires mechanisms for rapid and reliable characterization of parts. Additionally, the difficulty of rational part design necessitates library screening systems that can be employed in service of tuning part performance. Here we describe pSB1A10, a system for both characterizing and screening transcription-based parts based on their input / output function. We demonstrate the successful operation of this system by characterizing and tuning genetic inverters and transcriptional terminators.

Schematic of the screening plasmid design.  It consists of 4 components: (1) Tunable input (2) Input measurement (3) Part/Device insertion site (4) Output measurement.
Schematic of the screening plasmid design. It consists of 4 components: (1) Tunable input (2) Input measurement (3) Part/Device insertion site (4) Output measurement.


Current Experimental Work

Screening Plasmid 0.X

Screening Plasmid 1.0

This is the current working version of the screening plasmid. It is available from the MIT Registry of Standard Biological Parts as pSB1A10.

Screening Plasmid 1.5

This version of the screening makes use of an AHL-based induction system (<bbpart>F2620</bbpart>).

Screening Plasmid 2.0

We are in the process of designing a new version of the screening plasmid to account for some of the shortcomings of the previous version. Details can be found here:

Documents

References

  1. Khlebnikov A, Skaug T, and Keasling JD. . pmid:12080425. PubMed HubMed [Khlebnikov]
  2. Smolke CD and Keasling JD. . pmid:12402322. PubMed HubMed [Smolke]
All Medline abstracts: PubMed HubMed
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