Team:Bielefeld-Germany/Results/Characterization

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(K389015: VirA/G reporter device with luciferase)
(K389421, K389422, K389423: Sensitivity Tuner amplified Vir-test system)
 
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     <li><a href="/Team:Bielefeld-Germany/Results">Results</a></li>
     <li><a href="/Team:Bielefeld-Germany/Results">Results</a></li>
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     <li><a href="/Team:Bielefeld-Germany/Results/Tests">Tested</a></li>
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     <li><a href="/Team:Bielefeld-Germany/Results/Characterization">Characterization</a></li>
     <li><a href="/Team:Bielefeld-Germany/Results/Used">Used</a></li>
     <li><a href="/Team:Bielefeld-Germany/Results/Used">Used</a></li>
     <li><a href="/Team:Bielefeld-Germany/Results/Submitted">Submitted</a></li>
     <li><a href="/Team:Bielefeld-Germany/Results/Submitted">Submitted</a></li>
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     <li><a href="/Team:Bielefeld-Germany/Results/Unfinished">Unfinished</a></li>
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     <li><a href="/Team:Bielefeld-Germany/Results/Sequencing">Sequencing</a></li>
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=Tested BioBricks=
 
-
We tested the following BioBricks:
 
-
===<partinfo>K238008</partinfo>: ''virA''===
 
-
We made a restriction analysis and sequenced parts of this BioBrick. There were problems - more information within a short time.
 
 +
=<partinfo>K238008</partinfo>: ''virA''=
 +
We wanted to use this part in our project, but could only obtain unexpected/faulty restriction patterns. Finally we chose to sequence the part, hoping to find the cause for the maintained restriction patterns. Unfortunately we could not approve the sequence of <partinfo>BBa_K238008</partinfo> deposited in the parts registry so that we chose to design our own VirA BioBrick. I strongly recommend using our VirA since it has been approved by multiple means, e.g. restriction patterns and sequencing (<partinfo>K389001</partinfo>).
-
===<partinfo>BBa_K238011</partinfo>: ''vir''-promoter===
+
=<partinfo>BBa_K238011</partinfo>: ''vir''-promoter=
-
We made a restriction analysis and sequenced parts of this BioBrick.
+
We wanted to use this part in our project, but could only obtain unexpected/faulty restriction patterns. Finally we chose to sequence the part, hoping to find the cause for the maintained restriction patterns. Unfortunately we could not approve the sequence of <partinfo>BBa_K238011</partinfo> deposited in the parts registry so that we chose to design our own VirA BioBrick. I strongly recommend using our VirA since it has been approved by multiple means, e.g. restriction patterns and sequencing (<partinfo>K389003</partinfo>).
-
 
+
=<partinfo>P1010</partinfo>: ''ccdB''-gene=
-
===<partinfo>P1010</partinfo>: ''ccdB''-gene===
+
The ''ccdB'' gene targets the gyrase of ''Escherichia coli'' and is lethal for all ''E. coli'' strains without the gyrase mutation gyrA462 ([http://openwetware.org/wiki/CcdB Openwetware]). The ''ccdB'' BioBrick is used for the 3A-assembly as a positive selection marker.  
-
The ''ccdB'' gene targets the gyrase of ''Escherichia coli'' and is lethal for all ''E. coli'' strains without the gyrase mutation gyrA462 [1]. The ''ccdB'' BioBrick is used for the 3A-assembly as a positive selection marker.  
+
We transformed this BioBrick into ''E. coli'' JM109, DH5α, TOP10, XL1-Blue, EC100D and DB3.1. ''E. coli'' JM109, XL1-Blue and DH5α seem to be ''ccdB'' resistant because there were as much colonies after P1010 transformation as observed with DB3.1. The P1010 works as expected in ''E. coli'' TOP10, EC100D (no colonies after transformation) and DB3.1 (many colonies after transformation).
We transformed this BioBrick into ''E. coli'' JM109, DH5α, TOP10, XL1-Blue, EC100D and DB3.1. ''E. coli'' JM109, XL1-Blue and DH5α seem to be ''ccdB'' resistant because there were as much colonies after P1010 transformation as observed with DB3.1. The P1010 works as expected in ''E. coli'' TOP10, EC100D (no colonies after transformation) and DB3.1 (many colonies after transformation).
-
<center>
+
<center>Table 1: Results of the transformation of the cell-death gene ''ccdB'', BioBrick <partinfo>P1010</partinfo>, into different strains of ''E. coli''.  
-
Table 1: Results of the transformation of the cell-death gene ''ccdB'', BioBrick <partinfo>P1010</partinfo>, into different strains of ''E. coli''.  
+
{|cellpadding="10" style="border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000"
{|cellpadding="10" style="border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000"
|-
|-
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!style="border-style: solid; border-width: 1px"| Resistant to ''ccdB''?
!style="border-style: solid; border-width: 1px"| Resistant to ''ccdB''?
!style="border-style: solid; border-width: 1px"| Expected result?
!style="border-style: solid; border-width: 1px"| Expected result?
-
!style="border-style: solid; border-width: 1px"| Gyrase genotype [2,3]
+
!style="border-style: solid; border-width: 1px"| Gyrase genotype <br> ([http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-47PNXC3-F3&_user=2459438&_coverDate=01%2F28%2F1994&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=dfcdeab4c210c1f4ec70de318d013c15&searchtype=a Metcalf ''et al.'', 1994]; [http://openwetware.org/wiki/E._coli_genotypes Openwetware])
|-
|-
|style="border-style: solid; border-width: 1px"| DB3.1
|style="border-style: solid; border-width: 1px"| DB3.1
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It seems that not only the gyrase mutation gyrA462 is causing a ''ccdB'' resistance. Also the gyrase mutation gyrA96 gives ''E. coli'' a ''ccdB'' resistance. This should be kept in mind when assembling BioBricks with the 3A assembly.
It seems that not only the gyrase mutation gyrA462 is causing a ''ccdB'' resistance. Also the gyrase mutation gyrA96 gives ''E. coli'' a ''ccdB'' resistance. This should be kept in mind when assembling BioBricks with the 3A assembly.
 +
=<partinfo>K389004</partinfo>: Luciferase from pGL4.10[luc2]=
 +
[[Team:Bielefeld-Germany/Results/Characterization/K389004#mRFP vs. luciferase as reporter gene | For a comparison between mRFP and luciferase as reporter genes click here. ]]
-
===<partinfo>K389011</partinfo>: VirA screening device===
+
Some important parameters determined by the characterization experiments are shown in tab. 2. For more information concerning these experiments click on the corresponding link in tab. 2 or click here:
-
[[Image:IGEM-Bielefeld-LD50.jpg|600px|thumb|center|Ratio of surviving colonies of ''E. coli'' EC100D carrying unmutated <partinfo>K389010</partinfo> and <partinfo>K389011</partinfo> plated on PA agar plates with chloramphenicol, ampicillin and different concentrations of kanamycin. Comparison between cells that were induced with acetosyringone with cells that were not induced.]]
+
-
The ratio of surviving colonies ϕS was calculated like
+
<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/K389004">Detailed information...</a></div></html>
-
[[Image:IGEM-Bielefeld-formel-LD50.jpg|100px|center]]
 
-
with the number of colony forming units CFU, the concentration of kanamycin on the considered plate KanX and no kanamycin on the plate Kan0.
+
<center>Table 2: Parameters for <partinfo>K389004</partinfo>.  
 +
{|cellpadding="10" style="border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000"
 +
|-
 +
!style="border-style: solid; border-width: 1px"| Experiment
 +
!style="border-style: solid; border-width: 1px"| Result
 +
|-
 +
|style="border-style: solid; border-width: 1px"| [[Team:Bielefeld-Germany/Results/Characterization/K389004#Accumulation of luciferase | Behaviour during cultivation]]
 +
|style="border-style: solid; border-width: 1px"|
 +
* production is growth dependent
 +
* degradation in stationary growth phase
 +
|-
 +
|style="border-style: solid; border-width: 1px"| [[Team:Bielefeld-Germany/Results/Characterization/K389004#Kinetic of luciferin conversion | Kinetic of luciferin conversion]]
 +
|style="border-style: solid; border-width: 1px"| max. output between 20 - 40 s
 +
|-
 +
|style="border-style: solid; border-width: 1px"| [[Team:Bielefeld-Germany/Results/Characterization/K389004#Sensitivity | Limit of detection (LOD)]]
 +
|style="border-style: solid; border-width: 1px"| 162 RLU ~ 0.3 % of <partinfo>J23103</partinfo> output
 +
|-
 +
|style="border-style: solid; border-width: 1px"| [[Team:Bielefeld-Germany/Results/Characterization/K389004#Sensitivity | Limit of quantification (LOQ)]]
 +
|style="border-style: solid; border-width: 1px"| 306 RLU ~ 0.7 % of <partinfo>J23103</partinfo> output
 +
|}
 +
</center>
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===<partinfo>K389012</partinfo>: VirA reporter system with luciferase===
+
=<partinfo>K389011</partinfo>: VirA screening device=
-
coming more soon
+
-
===<partinfo>K389015</partinfo>: VirA/G reporter device with luciferase===
 
-
Control of BioBrick quality by capillar gel electrophoresis (GCE)
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<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/K389011">Detailed information...</a></div></html>
-
The quality of plasmid-conformation is crucial for following works such as transformation. A high content of covalent closed circular (ccc-type) pDNA indicates to high pDNA quality ([http://onlinelibrary.wiley.com/doi/10.1002/jgm.512/full Stadler ''et al.'', 2004]), ([http://www.eppendorf.com/script/cms-newspic.php?id=4966&col=DOWNLOADFILE Behrens B, Eppendorf AG]).
 
-
The representative tested BioBrick shows ccc-type of over 90 %, meaning pDNA quality is optimal.
 
-
[[Image:Bielelefeld_CGE_K389015_1.jpg|500px|center|thumb|STANDARD CGE ANALYSIS
+
[[Image:Bielefeld_LD50_Graph2.jpg|600px|thumb|center|Figure 1: Ratio of surviving colonies of ''E. coli'' EC100D carrying unmutated <partinfo>K389010</partinfo> and <partinfo>K389011</partinfo> plated on PA agar plates with chloramphenicol, ampicillin and different concentrations of kanamycin. Comparison between cells that were induced with acetosyringone with cells that were not induced.]]
-
SAMPLE ID: K389015 
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-
Run: 10/22/2010 8:00:07 AM
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-
REPORT: 10/25/2010 10:01:30 AM
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-
PLASMIDFACTORY GMBH & CO KG
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-
]]
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-
===<partinfo>K389016</partinfo>: VirA/G reporter device with mRFP===
 
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Control of BioBrick quality by capillar gel electrophoresis (GCE)
 
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[[Image:Bielefeld_CGE_K289016_3.jpg|500px|center|thumb|Standard CGE Analysis
+
=<partinfo>K389015</partinfo>: VirA/G reporter device with luciferase=
-
Sample ID: K389016
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Some important parameters determined by the characterization experiments are shown in tab. 3. For more information concerning these experiments click on the corresponding link in tab. 3 or click here:  
-
Lauf: 10/22/2010 12:55:04 PM
+
-
Report: 10/25/2010 10:03:46 AM
+
-
PlasmidFactory GmbH & Co KG
+
-
]]
+
-
===<partinfo>K389052</partinfo>: tightly regulated ''lac'' operon with mRFP readout===
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<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/K389015">Detailed information...</a></div></html>
-
Fails...more soon.
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-
===<partinfo>K389421</partinfo>, <partinfo>K389422</partinfo>, <partinfo>K389423</partinfo>: Sensitivity Tuner amlified Vir-test system===
 
-
By self designed PCR-Primer we excluded terminal GFP and the initial promoter pBAD/araC, for replacing our own VirB promotor and reporter gene luc (luciferase). Primers were designed for sensitivity tuner [http://partsregistry.org/Part:BBa_I746370 I746370], [http://partsregistry.org/Part:BBa_I746380 I746380] and [http://partsregistry.org/Part:BBa_I746390 I746390] so that standard assembly would be possible. Assembling of PCR-products took place by Silver Assembly.
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<center>Table 3: Parameters for <partinfo>K389015</partinfo>.  
 +
{|{{Table}}
 +
!Experiment
 +
!Characteristic
 +
!Value
 +
|-
 +
|rowspan="4"|[[Team:Bielefeld-Germany/Results/Characterization/K389015#Transfer function | Transfer Function]]
 +
|Maximum induction level
 +
|2.2 fold
 +
|-
 +
|Maximum induction level reached
 +
|200 µM acetosyringone
 +
|-
 +
|Hill coefficient
 +
|1.09
 +
|-
 +
|Switch Point
 +
|31.6 µM acetosyringone
 +
|-
 +
|rowspan="3"|[[Team:Bielefeld-Germany/Results/Characterization/K389015#Growth functions and Luciferase expression for BBa_K389015 | Doubling time / h]]
 +
|without plasmid
 +
|1.98
 +
|-
 +
|carrying K389015
 +
|2.24
 +
|-
 +
|carrying K389015 with 400 µM acetosyringone
 +
|2.67
 +
|-
 +
|rowspan="2"|Response time
 +
|Induction: [[Team:Bielefeld-Germany/Results/Characterization/K389015#Response time | exponential phase]]
 +
|>1 h
 +
|-
 +
|Induction: [[Team:Bielefeld-Germany/Results/Characterization/K389015#Data Analysis | begin of cultivation]]
 +
|max. induction at OD<sub>600</sub> = 1 +/- 0.5
 +
|-
 +
|rowspan="3"|[[Team:Bielefeld-Germany/Results/Characterization/K389015#Plasmid conformation analysis | Conformation analysis]]
 +
|ratio ccc monomer / %
 +
|91
 +
|-
 +
|ratio ccc dimer / %
 +
|3.7
 +
|-
 +
|ratio oc forms / %
 +
|5.3
 +
|-
 +
|}
 +
</center>
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'''Accomplishment'''
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=<partinfo>K389016</partinfo>: VirA/G reporter device with mRFP=
-
'''PCR-Primer Design'''
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Protocols for [https://2010.igem.org/Team:Bielefeld-Germany/Project/Protocols#Cultivation_for_measuring_mRFP_and_Luciferase_expression Cultivation] and [https://2010.igem.org/Team:Bielefeld-Germany/Project/Protocols#Measuring_of_mRFP Measurement]
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Primer forward activator phage P2:
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Some important parameters determined by the characterization experiments are shown in tab. 4. For more information concerning these experiments click on the corresponding link in tab. 4 or click here:  
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5`-GTT TCT TCG AAT TCG CGG CCG CTT CTA GAT GTT TCA TTG TCC TTT ATG CC-3`
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<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/K389016">Detailed information...</a></div></html>
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Primer forward activator phage PSP3:
 
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5`-GTT TCT TCG AAT TCG CGG CCG CTT CTA GAT GAT GCA CTG CCC GTT ATG- 3`
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<center>Table 4: Parameters for <partinfo>K389016</partinfo>.
 +
{|{{Table}}
 +
!Experiment
 +
!Characteristic
 +
!Value
 +
|-
 +
|rowspan="4"|[[Team:Bielefeld-Germany/Results/Characterization/K389016#Transfer function of BBa_K389016 | Transfer Function]]
 +
|Maximum induction level
 +
|2.6 fold
 +
|-
 +
|Maximum induction level reached
 +
|150 µM acetosyringone
 +
|-
 +
|Hill coefficient
 +
|1.67
 +
|-
 +
|Switch Point
 +
|26.5 µM acetosyringone
 +
|-
 +
|rowspan="4"|[[Team:Bielefeld-Germany/Results/Characterization/K389016#Growth functions and mRFP expression for BBa_K389016 | Doubling time / h]]
 +
|without plasmid
 +
|1.98
 +
|-
 +
|carrying K389016
 +
|2.57
 +
|-
 +
|carrying K389016 with 150 µM acetosyringone
 +
|2.77
 +
|-
 +
|carrying K389016 with 1000 µM acetosyringone
 +
|3.01
 +
|-
 +
|rowspan="3"|[[Team:Bielefeld-Germany/Results/Characterization/K389016#Plasmid conformation analysis | Conformation analysis]]
 +
|ratio ccc monomer / %
 +
|91.2
 +
|-
 +
|ratio ccc dimer / %
 +
|3.2
 +
|-
 +
|ratio oc forms / %
 +
|5.6
 +
|-
 +
|rowspan="5"|[[Team:Bielefeld-Germany/Results/Characterization/K389016#Different possible inducers | Inducers]]
 +
|Induction by
 +
|Acetosyringone
 +
|-
 +
|rowspan="4"|No Induction by
 +
|Capsaicin
 +
|-
 +
|Dopamine
 +
|-
 +
|Homovanillic acid
 +
|-
 +
|3-Methoxytyramine
 +
|}
 +
</center>
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Primer forward activator phage phi R73:
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=<partinfo>K389052</partinfo>: Tightly regulated ''lac'' operon with mRFP readout=
 +
This construct was plated for plasmid isolation in a ''lacI<sup>q</sup>'' negative ''E. coli'' strain after assembly - and we have never seen such red plates when working with constructs with mRFP downstream of a promoter. This ''lac'' operon definitely shows a very high basal transcription, so it is not tightly repressed. It seems that the ''lacI'' repressor <partinfo>BBa_C0012</partinfo> is not suitable for this purpose due to its LVA degradation tag or it does not work properly. Another indicator for this assumption is the experience page of <partinfo>C0012</partinfo>.
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5`-GTT TCT TCG AAT TCG CGG CCG CTT CTA GAT GCG CTG CCC TTT CTG-3`
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=<partinfo>K389421</partinfo>, <partinfo>K389422</partinfo>, <partinfo>K389423</partinfo>: Sensitivity Tuner amplified Vir-test system=
-
Primer backward Promotor PF from phage P2:
 
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5`-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TTC TCC TCT TTC TCT AGT AAG TGG- 3`
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<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/Sen_Tuner">Detailed information...</a></div></html>
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'''Characterization tests'''
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[[Image:ST Tuner.png|600px|thumb|center| '''Figure 2: Amplification factor of induced, 50 µM Acetosyringone (red) and not induced (green) modified Sensitivity Tuner <partinfo>K389421</partinfo>, <partinfo>K389422</partinfo> and <partinfo>K389423</partinfo>, Standard deviation shown.''']]
-
Cultivation was done by induction with Acetosyringone at 50 µM. Controls were not induced Sensitivity Tuner devices as well as induced and not induced nativ system ([http://partsregistry.org/Part:BBa_K389015 K389015]; without tuning elements). Induction was done upon inoculation.  Measuring point for amplification factor calculation was OD 1.0.
 
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'''Results'''
+
[[Image:Bielefeld_luc.jpg|600px|thumb|center| '''Figure 3: Vizualitation of induced (from left to right) <partinfo>K389421</partinfo>, <partinfo>K389422</partinfo> and <partinfo>K389423</partinfo> sensitivity tuner amplified vir-system.''']]
-
Three sensitivity tuned Vir-Gen sensing systems were obtained: [http://partsregistry.org/Part:BBa_K389421 K389421], [http://partsregistry.org/Part:BBa_K389422 K389422] and [http://partsregistry.org/Part:BBa_K389423 K389423] distinguishing by the amplification level of luc transcription.
 
-
----
+
=Mutated <partinfo>K389001</partinfo> (exemplary): Results of the directed mutagenesis=
-
'' Space Illustration''
 
-
----
+
<html><div style="font-size:20px; text-align:center; font-weight:bold;"><a href="https://2010.igem.org/Team:Bielefeld-Germany/Results/Characterization/Exemplary_results_DM">Detailed information...</a></div></html>
-
The amplification factor was received by apply [http://partsregistry.org/Part:BBa_K389015 K389015] as reference. Amplification calculation was done by normalizing relative light units emmitted from luciferase per OD.
+
[[Image:Bielefeld_results_screening.jpg|600px|thumb|center| '''Figure 4: Luciferase production rates of the exemplary clone “21” are shown under conditions of induction with acetosyringone (21-A), capsaicin (21-C) and in uninduced state (21-U). The right bar indicates the production rate of the native system without acetosyringone (212-U), all the values in the figure had been normalized to.''']]
-
Output-signal amplification is in the induced contructs (red) [http://partsregistry.org/Part:BBa_K389422 K389422] and [http://partsregistry.org/Part:BBa_K389423 K389423] 100 and respectively 200 fold higher than in not induced controls (green). An exception is K389422 were induced and not indiced system revealed analog results. Corresponding to data of iGEM Team, Cambridge 2009, K389423 (originated from [http://partsregistry.org/Part:BBa_I746390 I746390]) shows the highest amplification rate of all tested Sensitivity Tuners. Our results indicate to higher amplification rate of [http://partsregistry.org/Part:BBa_K389421 K389421] than [http://partsregistry.org/Part:BBa_K389422 K389422] of 100 fold under induced conditions. The controls also show high basal transcription rates.
+
-
Because there is small difference in induced and not induced system visible and basal transcription rates are high, we assume that the sensitivity tuning constructs are not well applicable for luciferase measurements.
+
=References=
-
 
+
-
For further theory click [https://2010.igem.org/Team:Bielefeld-Germany/Project/Theory#Read_out_system Read out system]
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-
 
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-
=Sequenced BioBricks=
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-
 
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-
 
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===Own BioBricks===
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-
 
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-
The sequencing of the following of our own BioBricks was succesful and lead to the expected results:
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-
 
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-
* <partinfo>K389001</partinfo> (not fully completed)
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-
 
+
-
* <partinfo>K389002</partinfo>
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-
* <partinfo>K389003</partinfo>
 
-
* <partinfo>K389004</partinfo>
 
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* <partinfo>K389005</partinfo>
 
-
* <partinfo>K389010</partinfo> (not fully completed)
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*Behrens B, Eppendorf AG, Laborpraxis, Nr.20, Reinste Plasmid-DNA in nur 9 Minuten.
-
 
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-
* <partinfo>K389011</partinfo> (not fully completed)
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-
 
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-
* <partinfo>K389012</partinfo> (not fully completed)
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-
 
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-
* <partinfo>K389013</partinfo> (not fully completed)
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-
 
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-
* <partinfo>K389015</partinfo> (not fully completed)
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-
 
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-
* <partinfo>K389016</partinfo> (not fully completed)
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-
 
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-
* <partinfo>K389050</partinfo>
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-
 
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-
 
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-
===Other BioBricks===
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-
 
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-
* <partinfo>K238008</partinfo> sequencing gave negative results - infos in registry are not correct!
+
-
 
+
-
* <partinfo>K238011</partinfo> sequencing gave negative results - infos in registry are not correct!
+
-
 
+
-
 
+
-
=References=
+
-
[1] http://openwetware.org/wiki/CcdB, CcdB (seen on 10.10.10).
+
-
[2] http://openwetware.org/wiki/E._coli_genotypes, E. coli genotypes (seen on 10.10.10).
+
*http://openwetware.org/wiki/CcdB, CcdB (seen on 10.10.10).
-
[3] Metcalf, W.W. ''et al.'' (1994) Gene 138, 1.
+
*http://openwetware.org/wiki/E._coli_genotypes, E. coli genotypes (seen on 10.10.10).
-
[4] Stadler J, Lemmens R, Nyhammar T, 2004, Plasmid DNA purification, ''The J. of Gene Medicine'',Vol.6, pp.54–S66
+
*Metcalf, WW ''et al.'' (1994) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-47PNXC3-F3&_user=2459438&_coverDate=01%2F28%2F1994&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=dfcdeab4c210c1f4ec70de318d013c15&searchtype=a ''Use of the rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6Kλ origin plasmids at different copy numbers''], Gene 138(1):1-7.
-
[5] Behrens B, Eppendorf AG, Laborpraxis, Nr.20, Reinste Plasmid-DNA in nur 9 Minuten.
+
*Stadler J, Lemmens R, Nyhammar T 2004, ''Plasmid DNA purification'', The J. of Gene Medicine,Vol.6, pp.54–S66

Latest revision as of 01:07, 28 October 2010

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Contents

<partinfo>K238008</partinfo>: virA

We wanted to use this part in our project, but could only obtain unexpected/faulty restriction patterns. Finally we chose to sequence the part, hoping to find the cause for the maintained restriction patterns. Unfortunately we could not approve the sequence of <partinfo>BBa_K238008</partinfo> deposited in the parts registry so that we chose to design our own VirA BioBrick. I strongly recommend using our VirA since it has been approved by multiple means, e.g. restriction patterns and sequencing (<partinfo>K389001</partinfo>).

<partinfo>BBa_K238011</partinfo>: vir-promoter

We wanted to use this part in our project, but could only obtain unexpected/faulty restriction patterns. Finally we chose to sequence the part, hoping to find the cause for the maintained restriction patterns. Unfortunately we could not approve the sequence of <partinfo>BBa_K238011</partinfo> deposited in the parts registry so that we chose to design our own VirA BioBrick. I strongly recommend using our VirA since it has been approved by multiple means, e.g. restriction patterns and sequencing (<partinfo>K389003</partinfo>).

<partinfo>P1010</partinfo>: ccdB-gene

The ccdB gene targets the gyrase of Escherichia coli and is lethal for all E. coli strains without the gyrase mutation gyrA462 ([http://openwetware.org/wiki/CcdB Openwetware]). The ccdB BioBrick is used for the 3A-assembly as a positive selection marker. We transformed this BioBrick into E. coli JM109, DH5α, TOP10, XL1-Blue, EC100D and DB3.1. E. coli JM109, XL1-Blue and DH5α seem to be ccdB resistant because there were as much colonies after P1010 transformation as observed with DB3.1. The P1010 works as expected in E. coli TOP10, EC100D (no colonies after transformation) and DB3.1 (many colonies after transformation).


Table 1: Results of the transformation of the cell-death gene ccdB, BioBrick <partinfo>P1010</partinfo>, into different strains of E. coli.
E. coli strain Resistant to ccdB? Expected result? Gyrase genotype
([http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-47PNXC3-F3&_user=2459438&_coverDate=01%2F28%2F1994&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=dfcdeab4c210c1f4ec70de318d013c15&searchtype=a Metcalf et al., 1994]; [http://openwetware.org/wiki/E._coli_genotypes Openwetware])
DB3.1 yes yes gyrA462
DH5α yes no gyrA96
EC100D no yes WT
JM109 yes no gyrA96
TOP10 no yes WT
XL1-Blue yes no gyrA96


It seems that not only the gyrase mutation gyrA462 is causing a ccdB resistance. Also the gyrase mutation gyrA96 gives E. coli a ccdB resistance. This should be kept in mind when assembling BioBricks with the 3A assembly.

<partinfo>K389004</partinfo>: Luciferase from pGL4.10[luc2]

For a comparison between mRFP and luciferase as reporter genes click here.

Some important parameters determined by the characterization experiments are shown in tab. 2. For more information concerning these experiments click on the corresponding link in tab. 2 or click here:

Detailed information...


Table 2: Parameters for <partinfo>K389004</partinfo>.
Experiment Result
Behaviour during cultivation
  • production is growth dependent
  • degradation in stationary growth phase
Kinetic of luciferin conversion max. output between 20 - 40 s
Limit of detection (LOD) 162 RLU ~ 0.3 % of <partinfo>J23103</partinfo> output
Limit of quantification (LOQ) 306 RLU ~ 0.7 % of <partinfo>J23103</partinfo> output

<partinfo>K389011</partinfo>: VirA screening device

Detailed information...


Figure 1: Ratio of surviving colonies of E. coli EC100D carrying unmutated <partinfo>K389010</partinfo> and <partinfo>K389011</partinfo> plated on PA agar plates with chloramphenicol, ampicillin and different concentrations of kanamycin. Comparison between cells that were induced with acetosyringone with cells that were not induced.


<partinfo>K389015</partinfo>: VirA/G reporter device with luciferase

Some important parameters determined by the characterization experiments are shown in tab. 3. For more information concerning these experiments click on the corresponding link in tab. 3 or click here:

Detailed information...


Table 3: Parameters for <partinfo>K389015</partinfo>.
Experiment Characteristic Value
Transfer Function Maximum induction level 2.2 fold
Maximum induction level reached 200 µM acetosyringone
Hill coefficient 1.09
Switch Point 31.6 µM acetosyringone
Doubling time / h without plasmid 1.98
carrying K389015 2.24
carrying K389015 with 400 µM acetosyringone 2.67
Response time Induction: exponential phase >1 h
Induction: begin of cultivation max. induction at OD600 = 1 +/- 0.5
Conformation analysis ratio ccc monomer / % 91
ratio ccc dimer / % 3.7
ratio oc forms / % 5.3

<partinfo>K389016</partinfo>: VirA/G reporter device with mRFP

Protocols for Cultivation and Measurement

Some important parameters determined by the characterization experiments are shown in tab. 4. For more information concerning these experiments click on the corresponding link in tab. 4 or click here:

Detailed information...


Table 4: Parameters for <partinfo>K389016</partinfo>.
Experiment Characteristic Value
Transfer Function Maximum induction level 2.6 fold
Maximum induction level reached 150 µM acetosyringone
Hill coefficient 1.67
Switch Point 26.5 µM acetosyringone
Doubling time / h without plasmid 1.98
carrying K389016 2.57
carrying K389016 with 150 µM acetosyringone 2.77
carrying K389016 with 1000 µM acetosyringone 3.01
Conformation analysis ratio ccc monomer / % 91.2
ratio ccc dimer / % 3.2
ratio oc forms / % 5.6
Inducers Induction by Acetosyringone
No Induction by Capsaicin
Dopamine
Homovanillic acid
3-Methoxytyramine

<partinfo>K389052</partinfo>: Tightly regulated lac operon with mRFP readout

This construct was plated for plasmid isolation in a lacIq negative E. coli strain after assembly - and we have never seen such red plates when working with constructs with mRFP downstream of a promoter. This lac operon definitely shows a very high basal transcription, so it is not tightly repressed. It seems that the lacI repressor <partinfo>BBa_C0012</partinfo> is not suitable for this purpose due to its LVA degradation tag or it does not work properly. Another indicator for this assumption is the experience page of <partinfo>C0012</partinfo>.

<partinfo>K389421</partinfo>, <partinfo>K389422</partinfo>, <partinfo>K389423</partinfo>: Sensitivity Tuner amplified Vir-test system

Detailed information...


Figure 2: Amplification factor of induced, 50 µM Acetosyringone (red) and not induced (green) modified Sensitivity Tuner <partinfo>K389421</partinfo>, <partinfo>K389422</partinfo> and <partinfo>K389423</partinfo>, Standard deviation shown.


Figure 3: Vizualitation of induced (from left to right) <partinfo>K389421</partinfo>, <partinfo>K389422</partinfo> and <partinfo>K389423</partinfo> sensitivity tuner amplified vir-system.


Mutated <partinfo>K389001</partinfo> (exemplary): Results of the directed mutagenesis

Detailed information...


Figure 4: Luciferase production rates of the exemplary clone “21” are shown under conditions of induction with acetosyringone (21-A), capsaicin (21-C) and in uninduced state (21-U). The right bar indicates the production rate of the native system without acetosyringone (212-U), all the values in the figure had been normalized to.

References

  • Behrens B, Eppendorf AG, Laborpraxis, Nr.20, Reinste Plasmid-DNA in nur 9 Minuten.
  • http://openwetware.org/wiki/CcdB, CcdB (seen on 10.10.10).
  • http://openwetware.org/wiki/E._coli_genotypes, E. coli genotypes (seen on 10.10.10).
  • Metcalf, WW et al. (1994) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-47PNXC3-F3&_user=2459438&_coverDate=01%2F28%2F1994&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=dfcdeab4c210c1f4ec70de318d013c15&searchtype=a Use of the rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6Kλ origin plasmids at different copy numbers], Gene 138(1):1-7.
  • Stadler J, Lemmens R, Nyhammar T 2004, Plasmid DNA purification, The J. of Gene Medicine,Vol.6, pp.54–S66