IGEM:IMPERIAL/2009/Assays Protocols/Testing ConstructsOLD: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
 
(21 intermediate revisions by 4 users not shown)
Line 1: Line 1:
=== Ligation Summary===
== Ligation Summary==


- Running total of number of ligations required for the assembly of testing constructs.
- Running total of number of ligations required for the assembly of testing constructs.
Line 14: Line 14:
5) Restriction Enzymes (12 ligations)
5) Restriction Enzymes (12 ligations)


<b>Running total</b> = 29-30
6)Encapsulation (15 ligations)


=== Promoter Testing===
<b>Running total</b> = 45-46
 
== Testing Construct Summary==
 
 
Determine input protocol by looking at this paper:
http://www.nature.com/nbt/journal/v26/n7/extref/nbt1413-S1.pdf
 
 
<table border=1>
<tr>
<td><b>Assay</b></td>
<td><b>Input (Variable PoPs)</b></td>
<td><b>Protocol (Reporter Quantification)</b></td>
<td><b>Biobricks Required</b></td>
</tr>
 
 
<tr>
<td>PAH</td>
<td>AHL concentration</td>
<td>Indirect spectrophotometric detection of L-tyrosine</td>
<td>F2620, RBS, PAH, TT</td>
</tr>
 
<tr>
<td>Cellulase</td>
<td>AHL concentration</td>
<td>Indirect spectrophotometric detection of glucose</td>
<td>F2620, RBS, Cellulase, TT</td>
</tr>
 
 
<tr>
<td>Colanic acid</td>
<td>AHL concentration</td>
<td>Volumetric measurement of packed cell volume (PCV)</td>
<td>F2620, RBS, RcsB, TT
 
F2620, RBS, RcsB, RBS, Waal, TT
 
F2620, RBS, RcsB, RBS, B3023, TT
 
F2620, RBS, RcsB, RBS, B3023, RBS, Waal, TT
</td>
</tr>
 
 
<tr>
<td>OtsA</td>
<td>AHL concentration</td>
<td>Indirect colorimetric measurement of trehalose-6-phosphate</td>
<td>F2620, RBS, OtsA, TT</td>
</tr>
 
 
<tr>
<td>OtsB</td>
<td>AHL concentration</td>
<td>Measurable by the indirect  spectrophotometric detection of trehalose</td>
<td>F2620, RBS, OtsB, TT</td>
</tr>
 
<tr>
<td>Trehalose</td>
<td>Induction (dependent on promoter)</td>
<td>PrMeasurable by the indirect  spectrophotometric detection of trehalose</td>
<td>Promoter, RBS, OtsA, RBS, OtsB, TT</td>
</tr>
 
 
<tr>
<td>CI Repressor</td>
<td>Temperature (CI conformation)</td>
<td>Measure POPs output from λCI promoter by fluorescence detection of GFP expression.</td>
<td>J23114, RBS, CI, TT, λCI, E0240</td>
</tr>
 
 
<tr>
<td>Restriction Enzyme</td>
<td>Arabinose concentration</td>
<td>Cell death measurable by colony count assay</td>
<td>BBa_I0500, RBS, DpnII, TT
BBa_I0500, RBS, Taq1, TT
BBa_I0500, RBS, DpnII, RBS, Taq1, TT
 
BBa_I0500, RBS, DpnII, RBS, Taq1, TT, BBa_J23103,RBS,DAM,TT (in DAM –ve strain)
</td>
</tr>
 
<tr>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</table><br>
<br>
 
== Promoter Testing==


We aim to use a generic promoter testing system, however we are unsure of the exact promoters that we are using at this stage becuase of the timer situation.
We aim to use a generic promoter testing system, however we are unsure of the exact promoters that we are using at this stage becuase of the timer situation.
Line 39: Line 140:
[[Image:II09_E0240.png]]
[[Image:II09_E0240.png]]


=== Module 1===
== Module 1==




Line 73: Line 174:
<B>Parts Required:</B> BBa_F2620, RBS, Cellulase, TT
<B>Parts Required:</B> BBa_F2620, RBS, Cellulase, TT


===Module 2 ===
==Module 2 ==


====RcsB  ====
====RcsB  ====


[[Image:II09_RcsB_ClonStrat.png]]
[[Image:II09_RcsB_ClonStrat.png]]
 
*'''[[User:James Chappell|James Chappell]] 04:26, 4 August 2009 (EDT)''':I would join the RBS-Gx to the T first, think about the type of modules we want to submit to the registry. Think having a module that takes pops in and gives out G4 output is a good module to submit.


[[Image:II09_RcsB_Assay.png]]
[[Image:II09_RcsB_Assay.png]]
Line 128: Line 229:
Parts: BBa_F2620, RBS, OtsB, TT <br>
Parts: BBa_F2620, RBS, OtsB, TT <br>


===Module 3 ===
==Module 3 ==


====1)The thermoinduction system=====
====1)The thermoinduction system====
[[Image:items.jpg |700px]]
[[Image:items.jpg |700px]]


Line 165: Line 266:


====2) Restriction Enzymes====
====2) Restriction Enzymes====
<b>CHANGE IMAGE - NO LONGER USING pBAD!</b><br>
In total there will be 12 ligation steps.<br>
In total there will be 12 ligation steps.<br>
<br>
<br>
[[Image:REligations1.png |500px]]
[[Image:REligations1.png |500px]]<br>
<br>
<br>
We will test using a non-leaky pBAD promoter in order to utilise the GFP reporter cell death assay (see [http://openwetware.org/wiki/IGEM:IMPERIAL/2009/Assays_Protocols/M3_Assays here]).<br>
An alternative to the GFP assay is to measure [http://openwetware.org/wiki/IGEM:IMPERIAL/2009/Assays_Protocols/M3_Assays colony forming units].<br>


===DpnI===
===DpnI===

Latest revision as of 11:25, 18 August 2009

Ligation Summary

- Running total of number of ligations required for the assembly of testing constructs.


1) Promoter Testing (4-5 ligations)

2) PAH (3 ligations)

3) Cellulase (3 ligations)

4) Thermoinduction (7 ligations)

5) Restriction Enzymes (12 ligations)

6)Encapsulation (15 ligations)

Running total = 45-46

Testing Construct Summary

Determine input protocol by looking at this paper: http://www.nature.com/nbt/journal/v26/n7/extref/nbt1413-S1.pdf


Assay Input (Variable PoPs) Protocol (Reporter Quantification) Biobricks Required
PAH AHL concentration Indirect spectrophotometric detection of L-tyrosine F2620, RBS, PAH, TT
Cellulase AHL concentration Indirect spectrophotometric detection of glucose F2620, RBS, Cellulase, TT
Colanic acid AHL concentration Volumetric measurement of packed cell volume (PCV) F2620, RBS, RcsB, TT

F2620, RBS, RcsB, RBS, Waal, TT

F2620, RBS, RcsB, RBS, B3023, TT

F2620, RBS, RcsB, RBS, B3023, RBS, Waal, TT

OtsA AHL concentration Indirect colorimetric measurement of trehalose-6-phosphate F2620, RBS, OtsA, TT
OtsB AHL concentration Measurable by the indirect spectrophotometric detection of trehalose F2620, RBS, OtsB, TT
Trehalose Induction (dependent on promoter) PrMeasurable by the indirect spectrophotometric detection of trehalose Promoter, RBS, OtsA, RBS, OtsB, TT
CI Repressor Temperature (CI conformation) Measure POPs output from λCI promoter by fluorescence detection of GFP expression. J23114, RBS, CI, TT, λCI, E0240
Restriction Enzyme Arabinose concentration Cell death measurable by colony count assay BBa_I0500, RBS, DpnII, TT

BBa_I0500, RBS, Taq1, TT BBa_I0500, RBS, DpnII, RBS, Taq1, TT

BBa_I0500, RBS, DpnII, RBS, Taq1, TT, BBa_J23103,RBS,DAM,TT (in DAM –ve strain)



Promoter Testing

We aim to use a generic promoter testing system, however we are unsure of the exact promoters that we are using at this stage becuase of the timer situation.


At this present moment in time, we are estimating using 4-5 different promoters in our system. Since each will need to be characterised, 4-5 ligations will be required to faciliate the assembly of the testing constructs.


Testing Construct Assembly:


Input: POPs

Output: GFP

Parts Required: BBa_E0240, Each promoter to be characterised.


BBa_E0240 (RBS-GFP-TT):

Module 1

Testing Construct Assembly

We must test both cellulase and PAH, both testing constructs can be made using a total of 6 ligation steps.



PAH Assay:

Input: HSL (POPs)

Output: PAH (Tyrosine)

Parts Required: BBa_F2620, RBS, PAH, TT



Cellulase Assay:

Input: HSL (POPs)

Output: Cellulase (Glucose)

Parts Required: BBa_F2620, RBS, Cellulase, TT

Module 2

RcsB

  • James Chappell 04:26, 4 August 2009 (EDT):I would join the RBS-Gx to the T first, think about the type of modules we want to submit to the registry. Think having a module that takes pops in and gives out G4 output is a good module to submit.


Inputs : HSL (POPs)
Outputs : Colanic Acid Production
Parts: BBa_F2620, RBS, RcsB, TT

B30237


WaaL


Inputs : HSL (POPs)
Outputs : WaaL Ligase
Parts: BBa_F2620, RBS, WaaL, TT

OtsA : Trehalose–6-Phosphate Synthase Assay


Inputs : HSL (POPs)
Outputs : Trehalose 6-phosphate Synthase
Parts: BBa_F2620, RBS, OtsA, TT
Assay Method

OtsB


Inputs : HSL (POPs)
Outputs : Trehalose 6-phosphate Phosphatase
Parts: BBa_F2620, RBS, OtsB, TT

Module 3

1)The thermoinduction system

Total number of ligations: 7

cI repressor


Input: HSL (F2620)
Output: Amount of cI protein


Plambda


Input: HSL (F2620)
Output: Fluorescence


cI and Plambda


Input: HSL (F2620)
Output: (visual) cI physically binding to Plambda


cI and Plambda(GFP reporter)


Input: HSL (F2620)
Output: Change in fluorescence

2) Restriction Enzymes

CHANGE IMAGE - NO LONGER USING pBAD!

In total there will be 12 ligation steps.



We will test using a non-leaky pBAD promoter in order to utilise the GFP reporter cell death assay (see here).
An alternative to the GFP assay is to measure colony forming units.

DpnI



Input: HSL (F2620)
Output: Change in fluorescence

TaqI



Input: HSL (F2620)
Output: Change in fluorescence

DpnI & TaqI



Input: HSL (F2620)
Output: Change in fluorescence

Retrieved from "https://openwetware.org/mediawiki/index.php?title=IGEM:IMPERIAL/2009/Assays_Protocols/Testing_ConstructsOLD&oldid=339970"