Team:UESTC Life/Notebook

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== ''' ''' ==
== ''' ''' ==
'''Jun 20th~Jul 1st,'''<br/>
'''Jun 20th~Jul 1st,'''<br/>
-
We met with our mentors and got an overview of the basics of synthetic biology, namely characterization, which will be the focus of our works during the summer. We did a survey of previous iGEM teams that got the Best Experimental Measurements award, then presented the findings to our mentors.Then we did some experiment technologies trainings, such as making gel, gel electrophoresis.<br/>
+
After having a meeting with our instructors and got an overview of the basics of synthetic biology. We did a survey of previous iGEM teams that got the Best Experimental Measurements award and read many papers. Base on the condition of our college and our expectation, we decided our project and create a schedule. Then we did some experiment technologies trainings, such as making gel, gel electrophoresis. <br/>
'''Jul 1st~Jul 8th ,'''<br/>
'''Jul 1st~Jul 8th ,'''<br/>
-
We construct our single enzyme carriers<br/>
+
1.The construction of single enzyme carries.<br/>
-
LinA https://static.igem.org/mediawiki/igem.org/5/5a/Uestclifenote1.png    LinB https://static.igem.org/mediawiki/igem.org/f/fc/Uestclifenote2.png<br/>
+
:To facilitate the overexpression of target genes, the four genes ''LinA'', ''LinB'', ''DhaA'', and ''HheC'' were optimized, synthesized and cloned into the vector of PUC51 by Gene script Corporation. The resulting vector S1 contains gene fragments of ''LinA'' and ''LinB'', while vector S2 contains gene fragments of ''DhaA'' and ''HheC''.(Fig.1) After digestion using Xbal and Xhol, the four genes were cloned into a modified pBAD expression vector pOHC_00, respectively, resulting in the following four vectors, POHC_01 (''LinA''), POHC_02 (''LinB''), POHC_03 (''DhaA''), POHC_04 (''HheC''). ''E. coli'' strain ''DH5α'' was used as a host cell. (Fig.2) The isolated positive colonies were further confirmed by restriction digestion analysis.(Fig.3) Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).<br/>
-
DhaA https://static.igem.org/mediawiki/igem.org/9/9c/Uestclifenote3.png    HheC https://static.igem.org/mediawiki/igem.org/1/1a/Uestclifenote4.png<br/>
+
''LinA'' https://static.igem.org/mediawiki/igem.org/5/5a/Uestclifenote1.png    ''LinB'' https://static.igem.org/mediawiki/igem.org/f/fc/Uestclifenote2.png<br/>
 +
''DhaA'' https://static.igem.org/mediawiki/igem.org/9/9c/Uestclifenote3.png    ''HheC'' https://static.igem.org/mediawiki/igem.org/1/1a/Uestclifenote4.png<br/>
-
 
-
Gels analysis <br/>
 
https://static.igem.org/mediawiki/igem.org/5/5b/Uestclifenote5.png<br/>
https://static.igem.org/mediawiki/igem.org/5/5b/Uestclifenote5.png<br/>
-
PCR colonies ,and keep them in refrigerator.
+
Fig. 1 Amplification of gene fragments by PCR. pOHC_00 (empty modified pBAD vector )<br/><br/>
 +
https://static.igem.org/mediawiki/igem.org/2/2d/Uestclife1.2.png<br/>
 +
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR. <br/> <br/>
 +
https://static.igem.org/mediawiki/igem.org/0/07/Uestclife1.3.png <br/>
 +
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.<br/>
-
'''Jul 9th~Jul 14th,''' <br/>
 
 +
'''Jul 9th~Jul 14th,''' <br/>
Construct co-expression system.<br/>
Construct co-expression system.<br/>
-
LinA-F2A-LinB https://static.igem.org/mediawiki/igem.org/a/ae/Uestclifenote6.png    DhaA-P2A-HheC https://static.igem.org/mediawiki/igem.org/b/bc/Uestclifenote7.png<br/>
+
:To facilitate the overexpression of target genes, the two genes ''LinA+F2A+LinB'', ''DhaA+P2A+HheC'' were optimized, synthesized and cloned into the vector of PUC51 by Gene script Corporation. The resulting vector S1 contains gene fragments of ''LinA+F2A+LinB'', while vector S2 contains gene fragments of ''DhaA+P2A+HheC''.After digestion using Xbal and Xhol, the four genes were cloned into a modified pBAD expression vector pOHC_00, respectively, resulting in the following two vectors, POHC_05 (''LinA+F2A+LinB''), POHC_06 (''DhaA+P2A+HheC''). ''E. coli'' strain ''DH5α'' was used as a host cell.The isolated positive colonies were further confirmed by restriction diges-tion analysis. Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).<br/>
 +
 
 +
''LinA+F2A+LinB'' https://static.igem.org/mediawiki/igem.org/a/ae/Uestclifenote6.png    ''DhaA+P2A+HheC'' https://static.igem.org/mediawiki/igem.org/b/bc/Uestclifenote7.png<br/>
gel electrophoresis.<br/>
gel electrophoresis.<br/>
-
https://static.igem.org/mediawiki/igem.org/6/64/Uestclifenote8.png
+
https://static.igem.org/mediawiki/igem.org/6/64/Uestclifenote8.png<br/>
 +
Fig. 1 Amplification of gene fragments by PCR. pOHC_00 (empty modified pBAD vector )<br/><br/>
 +
 
 +
https://static.igem.org/mediawiki/igem.org/e/e8/Uestclife2.2.png <br/>
 +
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR.<br/>
 +
<br/>
 +
https://static.igem.org/mediawiki/2013/8/88/Uestclife2.3.jpg <br/>
 +
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.<br/>
 +
 
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Transformed those genes into ''MC1061'' , and growth of of strain ''MC1061'' transformed  pOHC_05, pOHC_06 in LB medium with inducer and 5mM  substrate in batch culture .As the growing of the E.coli ,the substrate disappears .So new clones show the activity predicted and our co-expression system worked .<br/>
Transformed those genes into ''MC1061'' , and growth of of strain ''MC1061'' transformed  pOHC_05, pOHC_06 in LB medium with inducer and 5mM  substrate in batch culture .As the growing of the E.coli ,the substrate disappears .So new clones show the activity predicted and our co-expression system worked .<br/>
https://static.igem.org/mediawiki/igem.org/d/df/Uestclifenote9.png https://static.igem.org/mediawiki/igem.org/0/0d/Uestclifenote10.png<br/>
https://static.igem.org/mediawiki/igem.org/d/df/Uestclifenote9.png https://static.igem.org/mediawiki/igem.org/0/0d/Uestclifenote10.png<br/>
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https://static.igem.org/mediawiki/igem.org/0/05/Uestclifenote11.jpg<br/>
 
-
 
'''Jul 22nd~Jul 27th '''<br/>
'''Jul 22nd~Jul 27th '''<br/>
 +
 +
https://static.igem.org/mediawiki/igem.org/0/05/Uestclifenote11.jpg<br/>
https://static.igem.org/mediawiki/igem.org/6/65/Uestclifenote12.jpg<br/>
https://static.igem.org/mediawiki/igem.org/6/65/Uestclifenote12.jpg<br/>
From the gel ,we can see that F2A can cleave LinA and LinB,however ,P2A can’t work like that.<br/>
From the gel ,we can see that F2A can cleave LinA and LinB,however ,P2A can’t work like that.<br/>
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'''Jul 29th~Aug 7th '''<br/>
'''Jul 29th~Aug 7th '''<br/>
-
We did GC analysis , Growth of E.coli strain ''MC1061'' transformed ''LinA+F2A+LinB'' and ''LinA'' gene in LB medium with inducer and 5mM γ-HCH respectively, and Growth of ''E.coli'' strain ''MC1061'' transformed ''DhaA+P2A+HheC'' and ''DhaA'' gene in LB medium with inducer and 5mM TCP respectively.<br/>https://static.igem.org/mediawiki/igem.org/4/48/Uestclife00.jpg<br/>
+
We did GC analysis , Growth of'' E.coli'' strain ''MC1061'' transformed ''LinA+F2A+LinB'' and ''LinA'' gene in LB medium with inducer and 5mM γ-HCH respectively, and Growth of ''E.coli'' strain ''MC1061'' transformed ''DhaA+P2A+HheC'' and ''DhaA'' gene in LB medium with inducer and 5mM TCP respectively.<br/>https://static.igem.org/mediawiki/igem.org/4/48/Uestclife00.jpg<br/>
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'''Aug 13th~Aug 19th'''<br/>
'''Aug 13th~Aug 19th'''<br/>
-
We purified HheC and DhaA+P2A+HheC by AKTA FPLC and assayed the activity of them using 1,3-DCP. Special activity of HheC was 6.72(U/mg) and the chimeric protein was 5.28(U/mg).  
+
We purified ''HheC'' and'' DhaA+P2A+HheC '' by AKTA FPLC and assayed the activity of them using 1,3-DCP. Special activity of ''HheC'' was 6.72(U/mg) and the chimeric protein was 5.28(U/mg).  
'''Aug 20th~Aug 24th '''<br/>
'''Aug 20th~Aug 24th '''<br/>
RBS co-expression system constructed.<br/>
RBS co-expression system constructed.<br/>
-
LinA-RBS-LinB https://static.igem.org/mediawiki/igem.org/9/92/Uestclifenote18.png  DhaA-RBS-HheC https://static.igem.org/mediawiki/igem.org/3/37/Uestclifenote19pOHC.png
+
:Add XhoI and PstI restriction digest sites in the opposite terminate of ''LinB'' and'' HheC'' gene.After digestion using Xbal and PstI, the two genes were cloned into pOHC_01, pOHC_03 respectively, resulting in the following two vectors, POHC_07 (''LinA+RBS+LinB''), POHC_08 (''DhaA+RBS+HheC''). ''E. coli'' strain ''DH5α'' was used as a host cell.The isolated positive colonies were further confirmed by restriction digestion analysis. Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).
 +
 
 +
 
 +
''LinA-RBS-LinB'' https://static.igem.org/mediawiki/igem.org/9/92/Uestclifenote18.png  ''DhaA-RBS-HheC''      https://static.igem.org/mediawiki/igem.org/3/37/Uestclifenote19pOHC.png
 +
<br/>
 +
https://static.igem.org/mediawiki/igem.org/1/15/Uestclifenote20.png <br/>
 +
Fig. 1 Amplification of gene fragments by PCR. <br/><br/>
 +
<br/> https://static.igem.org/mediawiki/igem.org/f/f3/Uestclife3.2.png <br/>
 +
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR.<br/> <br/>
 +
<br/> https://static.igem.org/mediawiki/igem.org/0/01/Uestclifenote3.3.png <br/>
 +
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.
 +
 
-
https://static.igem.org/mediawiki/igem.org/1/15/Uestclifenote20.png gel electrophoresis.
 
'''Aug 24th~Aug 27th'''gel  <br/>
'''Aug 24th~Aug 27th'''gel  <br/>
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Latest revision as of 16:02, 27 September 2013

Notebook

Jun 20th~Jul 1st,
After having a meeting with our instructors and got an overview of the basics of synthetic biology. We did a survey of previous iGEM teams that got the Best Experimental Measurements award and read many papers. Base on the condition of our college and our expectation, we decided our project and create a schedule. Then we did some experiment technologies trainings, such as making gel, gel electrophoresis.


Jul 1st~Jul 8th ,
1.The construction of single enzyme carries.

To facilitate the overexpression of target genes, the four genes LinA, LinB, DhaA, and HheC were optimized, synthesized and cloned into the vector of PUC51 by Gene script Corporation. The resulting vector S1 contains gene fragments of LinA and LinB, while vector S2 contains gene fragments of DhaA and HheC.(Fig.1) After digestion using Xbal and Xhol, the four genes were cloned into a modified pBAD expression vector pOHC_00, respectively, resulting in the following four vectors, POHC_01 (LinA), POHC_02 (LinB), POHC_03 (DhaA), POHC_04 (HheC). E. coli strain DH5α was used as a host cell. (Fig.2) The isolated positive colonies were further confirmed by restriction digestion analysis.(Fig.3) Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).

LinA Uestclifenote1.png LinB Uestclifenote2.png
DhaA Uestclifenote3.png HheC Uestclifenote4.png

Uestclifenote5.png
Fig. 1 Amplification of gene fragments by PCR. pOHC_00 (empty modified pBAD vector )

Uestclife1.2.png
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR.

Uestclife1.3.png
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.


Jul 9th~Jul 14th,
Construct co-expression system.

To facilitate the overexpression of target genes, the two genes LinA+F2A+LinB, DhaA+P2A+HheC were optimized, synthesized and cloned into the vector of PUC51 by Gene script Corporation. The resulting vector S1 contains gene fragments of LinA+F2A+LinB, while vector S2 contains gene fragments of DhaA+P2A+HheC.After digestion using Xbal and Xhol, the four genes were cloned into a modified pBAD expression vector pOHC_00, respectively, resulting in the following two vectors, POHC_05 (LinA+F2A+LinB), POHC_06 (DhaA+P2A+HheC). E. coli strain DH5α was used as a host cell.The isolated positive colonies were further confirmed by restriction diges-tion analysis. Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).

LinA+F2A+LinB Uestclifenote6.png DhaA+P2A+HheC Uestclifenote7.png


gel electrophoresis.
Uestclifenote8.png
Fig. 1 Amplification of gene fragments by PCR. pOHC_00 (empty modified pBAD vector )

Uestclife2.2.png
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR.

Uestclife2.3.jpg
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.


Jul 15th~Jul 21st

Transformed those genes into MC1061 , and growth of of strain MC1061 transformed pOHC_05, pOHC_06 in LB medium with inducer and 5mM substrate in batch culture .As the growing of the E.coli ,the substrate disappears .So new clones show the activity predicted and our co-expression system worked .
Uestclifenote9.png Uestclifenote10.png

Jul 22nd~Jul 27th

Uestclifenote11.jpg
Uestclifenote12.jpg
From the gel ,we can see that F2A can cleave LinA and LinB,however ,P2A can’t work like that.


Jul 27th
Today ,we just put down our assays in the lab ,and went to a senior high school to have fun with them with the goal of promoting IGEM and Synthetic biology .
Uestclifenote13.jpg


Uestclifenote14.jpg


Uestclifenote15.jpg


Jul 29th~Aug 7th

We did GC analysis , Growth of E.coli strain MC1061 transformed LinA+F2A+LinB and LinA gene in LB medium with inducer and 5mM γ-HCH respectively, and Growth of E.coli strain MC1061 transformed DhaA+P2A+HheC and DhaA gene in LB medium with inducer and 5mM TCP respectively.
Uestclife00.jpg


Aug 8th~Aug 12th
Crude activity detecting in supernatant and sediment.
Uestclifenote16.jpg Uestclifenote17.png


Aug 13th~Aug 19th
We purified HheC and DhaA+P2A+HheC by AKTA FPLC and assayed the activity of them using 1,3-DCP. Special activity of HheC was 6.72(U/mg) and the chimeric protein was 5.28(U/mg).

Aug 20th~Aug 24th
RBS co-expression system constructed.

Add XhoI and PstI restriction digest sites in the opposite terminate of LinB and HheC gene.After digestion using Xbal and PstI, the two genes were cloned into pOHC_01, pOHC_03 respectively, resulting in the following two vectors, POHC_07 (LinA+RBS+LinB), POHC_08 (DhaA+RBS+HheC). E. coli strain DH5α was used as a host cell.The isolated positive colonies were further confirmed by restriction digestion analysis. Agarose gel showed cloning confirmation of the four target genes in pOHC plamid. Successful plasmid construction was confirmed by sequence analysis (Invitrogen).


LinA-RBS-LinB Uestclifenote18.png DhaA-RBS-HheC Uestclifenote19pOHC.png
Uestclifenote20.png
Fig. 1 Amplification of gene fragments by PCR.


Uestclife3.2.png
Fig. 2 Positive colonies identification. Positive colonies were confirmed by performing colony PCR.


Uestclifenote3.3.png
Fig. 3 Digestion the obtained plasmids with XbaI and XhoI.


Aug 24th~Aug 27thgel
SDS-PAGE analysis.
Uestclifenote21.png Uestclifenote22.png