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August

rMFC

CO₂ fixation

Isobutanol

Biosafety

General

Week 1 08/04 - 08/10

Deletion of dcuB and integration of oprF into chromosome

This week we amplified and purified the pR6K-cassette again in order to connect it to oprF
- pR6K
Connection of the pR6K-cassette and oprF

PCR amplification to connect the pR6K-cassette and oprF
- Bands as expected (~3300 bp)
PCR product was purified out of the gel

Agarose gel from colony PCR. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.

Fum A

This week we assembled FumA it with the T7-Promotor as well as with several Anderson-Promotor using Biobrick-Assembly

BioBrick Assembly (Suffix)

Backbone (digested with SpeI, PstI)

pSB1A2_T7

Insert (digested with XbaI, PstI)

Fum A

BioBrick Assembly (Suffix)

Backbone (digested with SpeI, PstI)

Insert (digested with XbaI, PstI)

Fum A

Cultivation of E.coli with neutral red and bromphenol blue

This week we tested if neutral red and bromphenol blue have an influence on the growth of E. coli. Therefore we cultivated E.coli wildtype in M9 medium with glucose supplemented with 100 µM of neutral red or bromphenol blue. Samples were taken for OD₆₀₀ measurement to document the growth curve.

Week 2 08/11 - 08/17

Deletion of dcuB and integration of oprF into chromosome

This week we checked our first colonies to verify the deletion of dcuB

pR6K

The pR6K-cassette for the dcuB deletion was purified out of the gel

Transformation of pR6K-cassette for the deletion of dcuB with electrocompotetent cells

pRedET
- Transformation of RedET plasmid with electrocompotetent cells

dcuB

Colony PCR to verify the deletion of dcuB (dcuB_del_kon1, dcuB_del_kon2)

Annealing temperature: 55 °C
Bands not as expected (~2390 bp)

Fum A

This week we assembled FumA with different promotor

Transformation of
- BBa_J23101_FumA
- BBa_J23102_ Fum A
- BBa_J23104_FumA
- pSB1A2_T7 with electrocompotetent cells

Colony PCR (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Band as expected (~2200 bp)

Plasmid isolation of BBa_J23102_ Fum A

Sequencing of
- BBa_J23101_FumA
- BBa_J23102_FumA
- BBa_J23104_FumA
- pSB1A2_T7_FumA showed different mutations

Fum BCD

This week wie amplified FumBCD and its backbone

PCR amplification of Fum BCD-backbone (pSB1C3_pre_Fum_BCD , pSB1C3_pre_Fum_BCD)

Annealing temperature: 55 °C
Bands as expected (2070 bp)

The Fum BCD backbone was purified out of the gel

PCR amplification of Fum BCD (Fum_BCD_fwd , Fum_BCD_rev)

Annealing temperature: 55 °C
Bands not as expected (1579 bp)

ccm

This week we amplified the ccm-cassette and its backbone

PCR amplification of the ccm-backbone (pSB1C3_suf_ccm, pSB1C3_pre_ccm)

Annealing temperature: 65 °C
Bands as expected (~2070 bp) but slightly visible because of inappropriate annealing temperature
PCR amplification was repeated with an annealing temperature of 55 °C
Both PCR products were purified out of the gel

PCR amplification of ccm-cassette using a gradient (ccm_fwd, ccm_rev)

Annealing temperature: 61 °C appeared as the optimum
Bands as expected (~6281 bp)

PCR amplification of ccm-cassette (ccm_fwd, ccm_rev)

Annealing temperature: 61 °C
Bands as expected (~6281 bp)
PCR product was purified

Agarose gel from colony PCR. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.

GSU 3274

This week we amplified the GSU 3274 cytochrome and its backbone

PCR amplification of GSU 3274-backbone (pSB1C3_pre_pccH, pSB1C3_suf_pccH)

Annealing temperature: 65 °C
Bands not as expected (~2070 bp) because of inappropriate annealing temperature
PCR amplification was repeated with an annealing temperature of 55 °C

Bands as expected (~2070 bp)

PCR amplification of GSU 3274 using a gradient (pccH_fwd, pccH_rev)

Annealing temperature: 55 °C appeared as the optimum
Bands as expected (~453 bp)

PCR amplification of GSU 3274 (pccH_fwd, pccH_rev)

Annealing temperature: 55 °C
Bands as expected (~453 bp)
genomic DNA of G. sulfurreducens as well as the PCR product of the gradient-PCR was used as template
PCR product was purified

Agarose gel from colony PCR. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.

Week 3 08/18 - 08/24

Deletion of dcuB and integration of oprF into chromosome

This week we contninued to test colonies for the verification of the deletion if dcuB
- Connection of pR6K-cassette and oprF
  - PCR amplification to connect the pR6K-cassette and oprF
    - Bands as expected (~3300 bp)
  - PCR product was purified out of the gel
  - Colony PCR to verify the deletion of dcuB (dcuB_del_kon1, dcuB_del_kon2)

Fum A

This week wie tested some colonies for FumA

Colony PCR (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Bands as expected (1843 bp)

frd (E. coli)

This week we amplified and transformed frd (E. coli)

PCR amplification (T7_frd_Ec_fwd, T7_frd_Ec_rev)

Annealing temperature: 55 °C
Bands as expected (~3300 bp)
Additionally there were undefined bands at ~1200 bp
illiegal restriction sites were not removed yet

Gibson Assembly with frd (E. coli) and pSB1C3

Transformation with electrocompotetent cells of pSB1C3_frd

Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Bands not as expected (~3600 bp)

ccm

This week we transformed the ccm-cassette and tested colonies for it

DpnI-digest of ccm-backbone

Gibson Assembly with ccm and pSB1C3

Transformation with electrocompotetent cells of pSB1C3_ccm

Colony PCR of pSB1C3_ccm (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Bands not as expected (~6611 bp) probably because it was not completely amplified because of its length
To check whether one of the colonies is positiv a restriction digestion was done

Restriction digestion with EcoRI and PstI

Bands not as expected (~2070 bp and 6281 bp)

GSU 3274

This week we transformed the GSU 3274 and tested colonies for it

DpnI-digest of GSU 3274-backbone

Gibson Assembly with GSU 3274 and pSB1C3

Transformation with electrocompotetent cells of pSB1C3_GSU 3274

Colony PCR of pSB1C3_GSU 3274 (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Bands as expected (~783 bp)

Restriction digestion with EcoRI and PstI

Bands not as expected (~2070 bp and 453 bp)

Week 4 08/25 - 08/31

Deletion of dcuB and integration of oprF into chromosome

This week we tested the next colonies for the deletion of dcuB and performed the NPN-assay to verify the integration of oprF into chromosome
- oprF
- dcuB

FumA

This week we assembled FumA with different promotor

BioBrick Assembly (Suffix)

Backbone (digested with SpeI, PstI)

Insert (digested with XbaI, PstI)

FumA

Transformation of all contrsucts with electrocompotetent cells

Colony PCR with all contructs (VF-Primer, VR-Primer)

Annealing temperature: 55 °C
Bands as expected (~2100 bp) for BBa_J23101_FumA and pSB1A2_T7_FumA

frd (E. coli)

This week we transformed frd and checked several colonies for it
- DpnI digest of Gibson-Assembly of frd (E. coli) to remove the template
- Transformation of Gibson-Assembly with electrocompotetent cells
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- PCR amplification of frd backbone (pSB1C3_frd_pre, pSB1C3_frd_suf)
- frd backbone was purified out of the gel
- Gibson Assembly with frd and pSB1C3
- Transformation of pSB1C3_frd with chemocompetent cells
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Restriction digestion with EcoRI and PstI
- Plasmid isolation of pSB1C3_frd
- sequencing of pSB1C3_frd confirmed the correct construct

ccm

This week we performed Eckhardt gels as a new method besides Colony PCR to identify positiv colonies
- Eckhardt gel of ccm was performed two times

GSU 3274

This week we tested colonies for GSU 3274
- Colony PCR of GSU 3274 (VF-Primer, VR-Primer)
- Plasmid isolation of GSU 3274
- Restriction digestion with PstI and EcoRI

@@ Line 58: / Line 58: @@
 <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of <i>pR6K</i>-cassette and <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#DNAPurificationbyCentrifugation" target="_blank">Purification</a> out of the gel</li> </li>
 </ul>
+<div class="element" style="height:350px; width:120px; text-align:center">
+                      <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/3/37/Bielefeld-CeBiTec_2014-10-14_PR6K_PCR_08_19.png" height="230px"></a><br><font size="1">Agarose gel from colony PCR. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font>
+                    </div>
+</ul>
+<br>
 	<li>Connection of the <i>pR6K</i>-cassette and <i>oprF</i></li>
@@ Line 67: / Line 74: @@
 	<li>PCR product was <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#DNAPurificationbyCentrifugation" target="_blank">purified</a> out of the gel</li>
 </ul>
+<ul>
-	</ul>
+  <div class="element" style="height:350px; width:120px; text-align:center">
+                      <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/b/b3/Bielefeld-CeBiTec_2014-10-14_Knockout_deletion-cassette_PCR_08_09.png" height="230px"></a><br><font size="1">Agarose gel from colony PCR. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font>
+                    </div>
 </ul>
+</ul>
+</ul>
+</ul>
 <br>
 <ul>
 	<li><b><i>Fum A</i></b></li>
 	<ul>
-<li>This week we assembled the T7-Promotor as well als several Anderson-Promotor with <i>FumA</i> using Biobrick-Assembly</li>
+<li>This week we assembled <i>FumA</i> it with the T7-Promotor as well as with several Anderson-Promotor using Biobrick-Assembly</li>
-<ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of <i>Fum A</i> </li>
-</ul>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#BioBrick" target="_blank">BioBrick Assembly</a> (Suffix)</li>
@@ Line 91: / Line 104: @@
 	</ul>
 </ul>
-<ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Transformationviaelectroporation" target="_blank">Transformation</a> of <i>pSB1C3_T7_Fum A</i> with electrocompotetent cells</li>
-</ul>
-<ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VF-Primer" target="_blank">VF-Primer</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VR-Primer" target="_blank">VR-Primer</a>)
-            </li>
-	<ul>
-		<li>Annealing temperature: 55 °C</li>
-		<li>Bands as expected (~2130 bp)</li>
-	</ul>
-</ul>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#BioBrick" target="_blank">BioBrick Assembly</a> (Suffix)</li>
@@ Line 116: / Line 119: @@
 		</ul>
 	</ul>
+</ul>
+</ul>
+</ul>
+<br>
+<ul>
+<li><b>Cultivation of <i>E.coli</i> with neutral red and bromphenol blue</b></li>
+<ul><li>This week we tested if neutral red and bromphenol blue have an influence on the growth of <i>E. coli</i>. Therefore we cultivated <i>E.coli</i> wildtype in <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#M9medium" target="_blank">M9 medium</a> with glucose supplemented with 100 µM of neutral red or bromphenol blue. Samples were taken for OD<sub>600</sub> measurement to document the growth curve.</li>
+</ul>
+</ul>
           </div>
        </div>
@@ Line 135: / Line 146: @@
 <ul>
 <li><b>Deletion of <i>dcuB</i> and integration of <i>oprF</i> into chromosome</b></li>
 <ul>
+<li>This week we checked our first colonies to verify the deletion of <i>dcuB</i></li>
+<ul>
 <li><i>pR6K</i></li>
 <ul>
@@ Line 167: / Line 180: @@
 <ul>
 	<li><b><i>Fum A</i></b></li>
+<ul>
+<li> This week we assembled <i>FumA</i> with different promotor</li>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Transformationviaelectroporation" target="_blank">Transformation</a> of
@@ Line 194: / Line 209: @@
 <li><a href="http://parts.igem.org/Part:BBa_J23104" target="_blank">BBa_J23104</a>_<i>FumA</i></li>
 <li>pSB1A2_T7_<i>FumA</i> showed different mutations
+</ul>
 </ul>
 </ul>
@@ Line 199: / Line 215: @@
 <ul>
 	<li><b><i>Fum BCD</i></b></li>
+<ul>
+<li>This week wie amplified <i>FumBCD</i> and its backbone </li>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> of <i>Fum BCD</i>-backbone (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_pre_Fum_BCD" target="_blank">pSB1C3_pre_Fum_BCD </a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_suf_Fum_BCD " target="_blank">pSB1C3_pre_Fum_BCD</a>)</li>
@@ Line 215: / Line 233: @@
 		<li>Bands not as expected (1579 bp)</li>
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 220: / Line 239: @@
 <ul>
 	<li><b><i>ccm</i></b></li>
+<ul>
+<li>This week we amplified the <i>ccm</i>-cassette and its backbone</li>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> of the ccm-backbone (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_suf_ccm" target="_blank">pSB1C3_suf_ccm</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_pre_ccm" target="_blank">pSB1C3_pre_ccm</a>)</li>
@@ Line 244: / Line 265: @@
 	</ul>
+</ul>
+<div class="element" style="height:350px; width:120px; text-align:center">
+                      <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/f/f8/Bielefeld-CeBiTec_2014-10-14_Ccm_cassette_PCR_08_16.png" height="230px"></a><br><font size="1">Agarose gel from colony PCR. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font>
+                    </div>
 </ul>
 </ul>
@@ Line 250: / Line 276: @@
 	<li><b><i>GSU 3274</i></b></li>
 <ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification of <i>GSU 3274</i>-backbone</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_pre_pccH" target="_blank">pSB1C3_pre_pccH</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_suf_pccH" target="_blank">pSB1C3_suf_pccH</a>)</li>
+<li> This week we amplified the <i>GSU 3274</i> cytochrome and its backbone</li>
+<ul>
+	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification </a> of <i>GSU 3274</i>-backbone (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_pre_pccH" target="_blank">pSB1C3_pre_pccH</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pSB1C3_suf_pccH" target="_blank">pSB1C3_suf_pccH</a>)</li>
 	<ul>
 		<li>Annealing temperature: 65 &deg;C</li>
@@ Line 261: / Line 289: @@
 </ul>
 <ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a>of <i>GSU 3274</i> using a gradient (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_fwd" target="_blank">pccH_fwd</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_rev" target="_blank">pccH_rev</a>)</li>
+	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> of <i>GSU 3274</i> using a gradient (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_fwd" target="_blank">pccH_fwd</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_rev" target="_blank">pccH_rev</a>)</li>
 	<ul>
 		<li>Annealing temperature: 55 &deg;C appeared as the optimum</li>
@@ Line 268: / Line 296: @@
 </ul>
 <ul>
-<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a>of <i>GSU 3274 </i> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_fwd" target="_blank">pccH_fwd</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_rev" target="_blank">pccH_rev</a>)</li>
+<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> of <i>GSU 3274 </i> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_fwd" target="_blank">pccH_fwd</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#pccH_rev" target="_blank">pccH_rev</a>)</li>
 	<ul>
 		<li>Annealing temperature: 55 &deg;C</li>
@@ Line 278: / Line 306: @@
 </ul>
 </ul>
+<div class="element" style="height:350px; width:120px; text-align:center">
+                      <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/3/3d/Bielefeld-CeBiTec_2014-10-14_PccH_PCR_08_17.png" height="230px"></a><br><font size="1">Agarose gel from colony PCR. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font>
+                    </div>
          </div>
        </div>
@@ Line 296: / Line 328: @@
 <ul>
 	<li><b>Deletion of <i>dcuB</i> and integration of <i>oprF</i> into chromosome</b></li>
+<ul>
+<li> This week we contninued to test colonies for the verification of the deletion if <i>dcuB</i>
 <ul>
 <li>Connection of <i>pR6K</i>-cassette and <i>oprF</i>
@@ Line 306: / Line 340: @@
 </ul>
 <ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#dcuB_del_kon1" target="_blank">dcuB_del_kon1</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#dcuB_del_kon2" target="_blank">dcuB_del_kon2</a>)
+	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> to verify the deletion of <i>dcuB</i> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#dcuB_del_kon1" target="_blank">dcuB_del_kon1</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#dcuB_del_kon2" target="_blank">dcuB_del_kon2</a>)
              </li>
 	<ul>
@@ Line 312: / Line 346: @@
 		<li>Bands not as expected (~4046 bp)</li>
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 318: / Line 353: @@
 <ul>
 	<li><b><i>Fum A</i></b></li>
+<ul><li> This week wie tested some colonies for <i>FumA</i></li>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VF-Primer" target="_blank">VF-Primer</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VR-Primer" target="_blank">VR-Primer</a>)
@@ Line 325: / Line 361: @@
 		<li>Bands as expected (1843 bp)</li>
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 330: / Line 367: @@
 <ul>
 	<li><b><i>frd (E. coli)</i></b></li>
+<ul>
+<li> This week we amplified and transformed <i>frd (E. coli)</i></li>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#T7_frd_Ec_fwd" target="_blank">T7_frd_Ec_fwd</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#T7_frd_Ec_rev" target="_blank">T7_frd_Ec_rev</a>)</li>
@@ Line 352: / Line 391: @@
 		<li>Bands not as expected (~3600 bp)</li>
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 357: / Line 397: @@
 <ul>
 	<li><b><i>ccm</i></b></li>
+<ul>
+<li> This week we transformed the <i>ccm</i>-cassette and tested colonies for it</li>
 <ul>
 <li>DpnI-digest of <i>ccm</i>-backbone</li>
@@ Line 387: / Line 429: @@
 	<li><b><i>GSU 3274</i></b></li>
 <ul>
+<li>This week we transformed the <i>GSU 3274</i> and tested colonies for it</li>
+<ul>
 <li>DpnI-digest of <i>GSU 3274</i>-backbone</li>
 </ul>
@@ Line 433: / Line 477: @@
 <ul>
 <li><b>Deletion of <i>dcuB</i> and integration of <i>oprF</i> into chromosome</b></li>
+<ul>
+<li>This week we tested the next colonies for the deletion of <i>dcuB</i> and performed the NPN-assay to verify the integration of <i>oprF</i> into chromosome
 <ul>
 	<li><i>oprF</i></li>
@@ Line 449: / Line 495: @@
 <li> another <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> to verify the positive colony
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 456: / Line 503: @@
 	<li><b><i>FumA</i></b></li>
 <ul>
-	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#BioBrick" target="_blank">BioBrick Assembly</a> (Suffix</li>
+<li>This week we assembled <i>FumA</i> with different promotor</li>
+<ul>
+	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#BioBrick" target="_blank">BioBrick Assembly</a> (Suffix)</li>
 	<ul>
 		<li>Backbone (digested with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionDigestion" target="_blank"><i>Spe</i>I</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionDigestion" target="_blank"><i>Pst</i>I</a>)</li>
@@ Line 481: / Line 530: @@
 		<li>Bands as expected (~2100 bp) for <a href="http://parts.igem.org/Part:BBa_J23101" target="_blank"> BBa_J23101</a>_<i>FumA</i> and pSB1A2_T7_<i>FumA</i>
 	</ul>
+</ul>
 </ul>
 </ul>
@@ Line 486: / Line 536: @@
 <ul>
 	<li><b><i>frd (E. coli)</i></b></li>
+<ul>
+<li> This week we transformed <i>frd</i> and checked several colonies for it
 <ul>
 <li> DpnI digest of Gibson-Assembly of <i>frd (E. coli)</i> to remove the template</li>
@@ Line 548: / Line 600: @@
 <ul>
 <li>next the illegal restriction sites had to be removed</li>
+</ul>
 </ul>
 </ul>
@@ Line 554: / Line 607: @@
 <ul><li><b><i>ccm</i></b></li>
 <ul>
+<li> This week we performed Eckhardt gels as a new method besides <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> to identify positiv colonies
+<ul>
 <li>Eckhardt gel of <i>ccm</i> was performed two times</li>
 <ul>
 <li> Bands not impeccable to identify (~6230 bp) and therefore a <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">restriction digestion</a> was done</li>
 <ul><li>Bands not as expected (~2070 bp and ~6239 bp) </li>
+</ul>
 </ul>
 </ul>
@@ Line 564: / Line 620: @@
 <br>
 <ul><li><b><i>GSU 3274</i></b></li>
+<ul>
+<li> This week we tested colonies for <i>GSU 3274</i>
 <ul>
 	<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> of <i>GSU 3274</i> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VF-Primer" target="_blank">VF-Primer</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VR-Primer" target="_blank">VR-Primer</a>)

Team:Bielefeld-CeBiTec/Notebook/Journal/rMFC/Aug

From 2014.igem.org

Latest revision as of 19:52, 16 October 2014

August

Week 1 08/04 - 08/10

Week 2 08/11 - 08/17

Week 3 08/18 - 08/24

Week 4 08/25 - 08/31