Team:KIT-Kyoto/c6h12o6

From 2012.igem.org

(Difference between revisions)
Line 6: Line 6:
<h2>August 1st</h2>
<h2>August 1st</h2>
-
<br>
 
-
<strong>*TNFAIP3</strong>
 
<br>
<br>
<br>
<br>
-
Since it takes at least one month to establish transgenic flies, we decided to first construct the P-element plasmid for microinjection into Drosophia embryos.
+
Since it takes at least one month to establish transgenic flies, we decided to first construct the P-element plasmid for microinjection into Drosophia embryos.<br>
-
<br>
+
<br>
<br>
① We performed PCR in the following conditions.<br>
① We performed PCR in the following conditions.<br>
<br>
<br>
-
<strong>primer</strong><br>
+
 
-
<br>
+
(ⅰ)TNFAIP3<br>
(ⅰ)TNFAIP3<br>
Composition for reaction
Composition for reaction
Line 45: Line 41:
</Table>
</Table>
<br>
<br>
-
 
+
<br>
<h2>August 2nd</h2>
<h2>August 2nd</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
① PCR product check<br>
① PCR product check<br>
Line 69: Line 64:
Left : 1kb marker(5uL)<br>
Left : 1kb marker(5uL)<br>
Right: attB TNFAIP3<br>
Right: attB TNFAIP3<br>
 +
<br>
<strong>Results</strong>
<strong>Results</strong>
Line 97: Line 93:
We purifed DNA from the gel by QIA Quick Gel Extraction Kit.<br>
We purifed DNA from the gel by QIA Quick Gel Extraction Kit.<br>
-
<br>
+
<br><br>
・Eatimation of the amount of attB TNFAIP3 DNA fragments by electrophoresis.<br>
・Eatimation of the amount of attB TNFAIP3 DNA fragments by electrophoresis.<br>
-
<br>
 
Order of samples applied to the agarose gel<br>
Order of samples applied to the agarose gel<br>
The samples were electrophoresed in 0.7% agarose gel in following order.<br>
The samples were electrophoresed in 0.7% agarose gel in following order.<br>
-
<br>
 
Right to left:3uL of 1kb marker 1uL of 5 fold dilution of attB TNFAIP3 DNA fragments,1uL of 10 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 20 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 1kb marker.<br>
Right to left:3uL of 1kb marker 1uL of 5 fold dilution of attB TNFAIP3 DNA fragments,1uL of 10 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 20 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 1kb marker.<br>
<br>
<br>
Line 110: Line 104:
<img src="https://static.igem.org/mediawiki/2012/0/0e/0802-3.png" width="500" height="300">
<img src="https://static.igem.org/mediawiki/2012/0/0e/0802-3.png" width="500" height="300">
<br>
<br>
-
We have estimated amount of the attB TNFAIP3 DNA to be 80ng/uL.<br><br>
+
We have estimated amount of the attB TNFAIP3 DNA to be 80ng/uL.<br>
-
 
+
<br>
<br>
<br>
-
 
-
 
-
 
-
 
-
<strong>Result</strong>
 
-
<br><br>
 
<h2>August 3rd</h2>
<h2>August 3rd</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
①BP reaction<br>
①BP reaction<br>
<br>
<br>
Line 148: Line 135:
<h2>August 4th</h2>
<h2>August 4th</h2>
-
<br>
 
-
<strong>*TNFA and API2</strong>
 
<br><br>
<br><br>
-
Four independent 4 colonies were picked up from the plate incubated from 8/3 as described in ②,then cultured in 2.5mL of LB Kanamycin(+) liquid culture medium for 16 hours.<br><br>
+
Four independent 4 colonies were picked up from the plate incubated from 8/3 as described in ②,then cultured in 2.5mL of LB Kanamycin(+) liquid culture medium for 16 hours.<br>
 +
<br>
 +
<br>
<h2>August 5th</h2>
<h2>August 5th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
Plasmid DNAs were isolated from E.coli cultured in 4 of LB liquid culture medium which we made on 8/4 by the alkaline-lysis method, we added the DNA to 20uL TE and added 10uL of the solution to 2uL of 6×Dye. Then we electrophoresed it with marker, 2uL of pDONR+ 2uL of 6×Dye+ 8uL of TE,in 0.7% agarose gel in following order (from left to right)<br>
Plasmid DNAs were isolated from E.coli cultured in 4 of LB liquid culture medium which we made on 8/4 by the alkaline-lysis method, we added the DNA to 20uL TE and added 10uL of the solution to 2uL of 6×Dye. Then we electrophoresed it with marker, 2uL of pDONR+ 2uL of 6×Dye+ 8uL of TE,in 0.7% agarose gel in following order (from left to right)<br>
Line 165: Line 151:
<br>
<br>
-
<strong>Results</strong>
+
<strong>Results</strong><br>
-
<img src="https://static.igem.org/mediawiki/2012/3/31/0805.png" width="500" height="300">
+
<img src="https://static.igem.org/mediawiki/2012/3/31/0805.png" width="500" height="300"><br>
-
<br><br>
+
<br>
 +
<br>
<h2>August 6th</h2>
<h2>August 6th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
E.coli carrying the plasmid sample -1 and -2 in LB Kanamycin(+)liquid culture medium for 16 hours.<br>
-
 
+
<br>
-
 
+
<br>
<h2>August 7th</h2>
<h2>August 7th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
①Purification of candidate pENTR-TNFAIP3<br>
 +
We purified candidate plasmid-1 and -2 by QIA Prep Spin Miniprep Kit, dissolved  it in 30uL of Buffer EB.<br>
 +
Then,the samples were electrophoresed in 0.7% agarose gel.<br>
 +
<br>
 +
We made samples as follows.
<Table Border Cellspacing="0">
<Table Border Cellspacing="0">
<Tr><Td>  </Td><Td> pDONR </Td><Td> BP TNFA-1 </Td><Td> BP TNFA-2 </Td></Tr>
<Tr><Td>  </Td><Td> pDONR </Td><Td> BP TNFA-1 </Td><Td> BP TNFA-2 </Td></Tr>
Line 189: Line 180:
</Table>
</Table>
<br>
<br>
-
 
+
<br>
-
 
+
We electrophoresed them in following order.<br>
-
<br><br>
+
Left marker 5uL control pDONR DNA ,pENTR-TNFAIP3-1 DNA,pENTR-TNFAIP3 -2 DNA marker 4uL marker 3uL Wright.<br>
 +
<br>
 +
<strong>Results</strong><br>
<img src="https://static.igem.org/mediawiki/2012/2/2e/0807.png" width="500" height="300">
<img src="https://static.igem.org/mediawiki/2012/2/2e/0807.png" width="500" height="300">
-
<br><br>
+
<br>
-
 
+
Concentration of pENTR-TNFAIP3-2 DNA was estimated at around 100ng/uL.<br>
-
 
+
<br>
-
 
+
<br>
 +
② LR reaction<br>
 +
We made following solution(vials)in 1.5mL tube.<br>
<Table Border Cellspacing="0">
<Table Border Cellspacing="0">
Line 204: Line 199:
<Tr><Td> total </Td><Td> 9μL </Td></Tr>
<Tr><Td> total </Td><Td> 9μL </Td></Tr>
</Table>
</Table>
 +
<br>
 +
we added 1uL of LR clonaseⅡ enzyme mix to this solution and incubate it for 2.5 hours.<br>
 +
<br>
 +
③ Transformation of E.coli with LR reaction products.<br>
 +
Transformation of E.coli was carried out by adding 2uL of LR reaction products to 100uL of XL1-Blue and plated on the LB ampicillin(+)plate and cultured at 37°C.<br>
 +
<br>
<br>
<br>
 +
 +
WEEK1終わり
WEEK1終わり
 +
 +
 +
 +
<br>
<br>
Line 217: Line 224:
<h2>August 8th</h2>
<h2>August 8th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
We isolated 5 colonies from the LB plate, and cultured.<br>
-
 
+
<br>
 +
<br>
<h2>August 9th</h2>
<h2>August 9th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
 
 +
①Purification of the candidate pUAS-flag-TNFAIP3 DNA<br>
 +
<br>
 +
The candidate pUAS-flag-TNFAIP3 DNAs from five independent sample -1,-2,-3,-4 and -5 were purified by the alkaline-lysis method.<br>
 +
We added 0.2uL of 10ng/uL RNase A to them and incubate them for 1 hour.<br>
 +
<br>
 +
<br>
 +
②Characterization of the candidate pUAS-flag-TNFAIP3 DNA<br>
 +
<br>
 +
The candidate pUAS-flag-TNFAIP3 DNA was digested wit EcoRⅠ as follows.<br>
 +
<br>  
<Table Border Cellspacing="0">
<Table Border Cellspacing="0">
-
<Tr><Td> DNA sample </Td><Td> 1μL </Td></Tr>
+
<Tr><Td> Each diluted DNA sample </Td><Td> 1μL </Td></Tr>
<Tr><Td> 10×H buffer </Td><Td> 0.5μL </Td></Tr>
<Tr><Td> 10×H buffer </Td><Td> 0.5μL </Td></Tr>
<Tr><Td> EcoRⅠ </Td><Td> 0.2μL </Td></Tr>
<Tr><Td> EcoRⅠ </Td><Td> 0.2μL </Td></Tr>
Line 236: Line 254:
<br>
<br>
<br>
<br>
 +
 +
After incubation of these samples for 1hour, we added 1uL of 6×Dye to each of them and electrophoresed in 0.7% agarose gel in following order.<br>
 +
Left, 10fold dilution, 2uL marker, 20fold dilution, 30fold dilution, 1uL marker, 40fold dilution, 0.5uL marker right.<br>
 +
<br>
 +
<br>
 +
 +
 +
<strong>Results</strong><br>
<img src="https://static.igem.org/mediawiki/2012/9/9b/0809.png" width="500" height="300">
<img src="https://static.igem.org/mediawiki/2012/9/9b/0809.png" width="500" height="300">
<br><br>
<br><br>
 +
The concerntration of the candidate pUAS-flag-TNFAIP3 DNA was estimated as 200ng/uL.<br>
 +
<br>
 +
<br>
 +
③ PCR amplification of the insert DNA<br>
 +
<br>
 +
The four 5'primers were designed for PCR as follows.<br>
 +
<br>
 +
 +
・GW3r<br>
 +
5’-ATCGAGGCCTGTCTAGAGAAGC<br>
 +
・TNFA-1<br>
 +
5’-GGCTTTGCTATGATACTCGGAACTG<br>
 +
・TNFA-2<br>
 +
5’-GTAAAATGTGAAACGCCCAACTGC<br>
 +
・TNFA-3<br>
 +
5’-GGACTCCAGAAAACAAGGGCTTT<br>
 +
<br>
 +
<br>
 +
 +
 +
The 3’ primer was designed as follows.<br>
 +
・SVr<br>
 +
5’-GGCATTCCACCACTGCTCCC<br>
 +
<br>
 +
<br>
 +
 +
 +
PCR reactions with the following combinations of primers were carried out.<br>
 +
sample1→GW3r―SVr<br>
 +
sample2→TNFA-1―SVr<br>
 +
sample3→TNFA-2―SVr<br>
 +
sample4→TNFA-3―SVr<br>
 +
 +
<br>
 +
<br>
 +
 +
PCR was carried out in the following reactions.
<Table Border Cellspacing="0">
<Table Border Cellspacing="0">
-
<Tr><Td>  </Td><Td> 1-2 </Td></Tr>
+
<Tr><Td>  </Td><Td> Each sample </Td></Tr>
<Tr><Td> 50ng/μL LR TNFA-1 </Td><Td> 1μL </Td></Tr>
<Tr><Td> 50ng/μL LR TNFA-1 </Td><Td> 1μL </Td></Tr>
<Tr><Td> 10×rTaq buffer </Td><Td> 2μL </Td></Tr>
<Tr><Td> 10×rTaq buffer </Td><Td> 2μL </Td></Tr>
Line 251: Line 314:
<Tr><Td> total </Td><Td> 20μL </Td></Tr>
<Tr><Td> total </Td><Td> 20μL </Td></Tr>
</Table>
</Table>
-
<br>
+
<br><br>
-
 
+
 +
Reaction conditions of PCR
<Table Border Cellspacing="0">
<Table Border Cellspacing="0">
<Tr><Td> temperature </Td><Td> time </Td><Td> cycle </Td></Tr>
<Tr><Td> temperature </Td><Td> time </Td><Td> cycle </Td></Tr>
Line 270: Line 333:
<h2>August 10th</h2>
<h2>August 10th</h2>
<br>
<br>
-
<strong>*TNFA and API2</strong>
+
<br>
-
<br><br>
+
 
-
<br><br>
+
Electrophoresis of PCR products was carried out.<br>
 +
After adding 2uL of 6×Dye to each 10uL of sample, we electrophoresed them in 0.7% agarose gel in following order.<br>
 +
<br>
 +
Left marker5uL sample1 sample2 sample3 sample4 Wright<br>
 +
<br>
 +
 
 +
<strong>Results</strong><br>
 +
 
<img src="https://static.igem.org/mediawiki/2012/8/84/0810.png" width="500" height="300">
<img src="https://static.igem.org/mediawiki/2012/8/84/0810.png" width="500" height="300">
-
<br><br>
+
<br>
 +
The sizes of the PCR products were unexpected ones. We therefore concluded the construction of pUAS-flag-TNFAIP3 DNA was not successful.<br>
 +
<br>
 +
<br>
 +
 
 +
 
 +
 
 +
 
 +
 

Revision as of 12:54, 25 September 2012

August 1st



Since it takes at least one month to establish transgenic flies, we decided to first construct the P-element plasmid for microinjection into Drosophia embryos.

① We performed PCR in the following conditions.

(ⅰ)TNFAIP3
Composition for reaction
   sample1 
 10ng/μL TNFAIP3  6μL 
 10× KOD plus buffer  10μL 
 2mM dNTPs  10μL 
 25mM MgSO4  3.2μL 
 10P 5'primer  3μL 
 10P 3'primer  3μL 
 KOD plus  2μL 
 dH2O  62.8μL 
 Total  100μL 

Reaction conditions
 temperature  time  cycle 
 95°C  2min.   
 95°C  15sec  25cycle 
 60°C  30sec  25cycle 
 68°C  2min30sec  25cycle 
 68°C  2min30sec   
 14°C  ∞   


August 2nd



① PCR product check

We run 0.7% agarose gel electorophoresis in the following conditions. Composition
   8/1 the attB TNFAIP3 PCR products 
 DNA sample  10μL 
 6×Dye  2μL 
 total  12μL 


The order of sample application
Left : 1kb marker(5uL)
Right: attB TNFAIP3

Results


② DNA purification from gel
We electrophoresed in 0.7% agarose gel in the following conditions.

Composition
   8/1 attB TNFAIP3 PCRproduct 
 DNA sample  90μL 
 6×Dye  18μL 
 total  108μL 


We applied half of 108 uL of sample to each of two lanes of Agaroe gel with 5uL of 1kb marker.Then we detected the DNA band in the gel.

Results

We purifed DNA from the gel by QIA Quick Gel Extraction Kit.


・Eatimation of the amount of attB TNFAIP3 DNA fragments by electrophoresis.
Order of samples applied to the agarose gel
The samples were electrophoresed in 0.7% agarose gel in following order.
Right to left:3uL of 1kb marker 1uL of 5 fold dilution of attB TNFAIP3 DNA fragments,1uL of 10 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 20 fold dilution of attB TNFAIP3 DNA fragments, 1uL of 1kb marker.

Results

We have estimated amount of the attB TNFAIP3 DNA to be 80ng/uL.


August 3rd



①BP reaction

BP reaction was carried out in the following conditions.
 attB TNFAIP3(80ng/μL)  1μL 
 pDONR(455ng/μL)  0.35μL 
 TE buffer  7.65 
 total  9μL 


One uL of BP Clonase Ⅱ enzyme mix was added to this solution and incubated for 2.5 hours.


② Transformation of E.coli by BP reaction products
2uL of BP TNFA reaction product was added to 100uL of E.coli XL1-Blue to do transform ation.
At last, cells were divided into 10,40,100,and 200 uL,and spreaded on LB Kanamycin(+)plate,Plats wera incubated for 16 hours at 37°C.


August 4th



Four independent 4 colonies were picked up from the plate incubated from 8/3 as described in ②,then cultured in 2.5mL of LB Kanamycin(+) liquid culture medium for 16 hours.


August 5th



Plasmid DNAs were isolated from E.coli cultured in 4 of LB liquid culture medium which we made on 8/4 by the alkaline-lysis method, we added the DNA to 20uL TE and added 10uL of the solution to 2uL of 6×Dye. Then we electrophoresed it with marker, 2uL of pDONR+ 2uL of 6×Dye+ 8uL of TE,in 0.7% agarose gel in following order (from left to right)

Left control pDONR DNA, BP TNFA-1,-2,-3,-4

Results



August 6th



E.coli carrying the plasmid sample -1 and -2 in LB Kanamycin(+)liquid culture medium for 16 hours.


August 7th



①Purification of candidate pENTR-TNFAIP3
We purified candidate plasmid-1 and -2 by QIA Prep Spin Miniprep Kit, dissolved it in 30uL of Buffer EB.
Then,the samples were electrophoresed in 0.7% agarose gel.

We made samples as follows.
   pDONR  BP TNFA-1  BP TNFA-2 
 DNA sample  1μL  1μL  1μL 
 6×Dye  1μL  1μL  1μL 
 dH2O  4μL  4μL  4μL 
 total  6μL  6μL  6μL 


We electrophoresed them in following order.
Left marker 5uL control pDONR DNA ,pENTR-TNFAIP3-1 DNA,pENTR-TNFAIP3 -2 DNA marker 4uL marker 3uL Wright.

Results

Concentration of pENTR-TNFAIP3-2 DNA was estimated at around 100ng/uL.


② LR reaction
We made following solution(vials)in 1.5mL tube.
 BP TNFA-2  2μL 
 pTFW(Destination vector)  0.5μL 
 TE buffer  6.5μL 
 total  9μL 

we added 1uL of LR clonaseⅡ enzyme mix to this solution and incubate it for 2.5 hours.

③ Transformation of E.coli with LR reaction products.
Transformation of E.coli was carried out by adding 2uL of LR reaction products to 100uL of XL1-Blue and plated on the LB ampicillin(+)plate and cultured at 37°C.


WEEK1終わり

August 8th



We isolated 5 colonies from the LB plate, and cultured.


August 9th



①Purification of the candidate pUAS-flag-TNFAIP3 DNA

The candidate pUAS-flag-TNFAIP3 DNAs from five independent sample -1,-2,-3,-4 and -5 were purified by the alkaline-lysis method.
We added 0.2uL of 10ng/uL RNase A to them and incubate them for 1 hour.


②Characterization of the candidate pUAS-flag-TNFAIP3 DNA

The candidate pUAS-flag-TNFAIP3 DNA was digested wit EcoRⅠ as follows.

 Each diluted DNA sample  1μL 
 10×H buffer  0.5μL 
 EcoRⅠ  0.2μL 
 dH2O  3.3μL 
 total  5μL 


After incubation of these samples for 1hour, we added 1uL of 6×Dye to each of them and electrophoresed in 0.7% agarose gel in following order.
Left, 10fold dilution, 2uL marker, 20fold dilution, 30fold dilution, 1uL marker, 40fold dilution, 0.5uL marker right.


Results


The concerntration of the candidate pUAS-flag-TNFAIP3 DNA was estimated as 200ng/uL.


③ PCR amplification of the insert DNA

The four 5'primers were designed for PCR as follows.

・GW3r
5’-ATCGAGGCCTGTCTAGAGAAGC
・TNFA-1
5’-GGCTTTGCTATGATACTCGGAACTG
・TNFA-2
5’-GTAAAATGTGAAACGCCCAACTGC
・TNFA-3
5’-GGACTCCAGAAAACAAGGGCTTT


The 3’ primer was designed as follows.
・SVr
5’-GGCATTCCACCACTGCTCCC


PCR reactions with the following combinations of primers were carried out.
sample1→GW3r―SVr
sample2→TNFA-1―SVr
sample3→TNFA-2―SVr
sample4→TNFA-3―SVr


PCR was carried out in the following reactions.
   Each sample 
 50ng/μL LR TNFA-1  1μL 
 10×rTaq buffer  2μL 
 2mM dNTPs  2μL 
 25mM MgCl2  0.8μL 
 10P 5'primer  0.6μL 
 10P 3'primer  0.6μL 
 rTaq  0.4μL 
 dH2O  12.6μL 
 total  20μL 


Reaction conditions of PCR
 temperature  time  cycle 
 95°C  2min   
 95°C  15sec  25cycle 
 55°C  30sec  25cycle 
 68°C  2min30sec  25cycle 
 68°C  2min30sec   
 14°C  ∞   

August 10th



Electrophoresis of PCR products was carried out.
After adding 2uL of 6×Dye to each 10uL of sample, we electrophoresed them in 0.7% agarose gel in following order.

Left marker5uL sample1 sample2 sample3 sample4 Wright

Results

The sizes of the PCR products were unexpected ones. We therefore concluded the construction of pUAS-flag-TNFAIP3 DNA was not successful.


August 13th


*TNFA and API2

 1-1  1μL 
 10×M buffer  0.5μL 
 Hind Ⅲ  0.2μL 
 dH2O  3.3μL 
 total  5μL 




August 14th


*TNFA and API2

 1-1  sample1 
 10ng/μL TNFAIP3  6μL 
 10×KOD plus buffer  10μL 
 2mM dNTPs  10μL 
 25mM MgSO4  3.2μL 
 10P 5'primer  3μL 
 10P 3'primer  3μL 
 KOD plus  2μL 
 dH2O  62.8μL 
 total  100μL 

 temperature  time  cycle 
 95°C  2min   
 95°C  15sec  25cycle 
 60°C  30sec  25cycle 
 68°C  2min30sec  25cycle 
 68°C  2min30sec   
 14°C  ∞   




WEEK2終わり

August 20th


TNFA and API2

1. Reproduction of DNA from gel
We did agarose gel electrophoresis (0.7% gel).

Composition
   a product of PCR attB TNFAIP3(8/1) 
 DNA sample  90μL 
 6×Dye  18μL 
 Total  108μL 

We separated 54uL×2 from 108uL (sample) and we did electrophoresis (54uL sample and 1kb marker 5uL).We separated gel containing DNA.

Results
We isolated DNA from these gels by QIA quick Gel Extraction Kit.
Finally we melt DNA to TE Buffer(40uL)

August 21st


TNFA and API2

1. Density measurement of attB TNFAIP3
We did agarose gel electrophoresis (0.7% gel). (1kb marker-3uL, 5times dilution attB TNFAIP3-1uL (make August 20 ), 10times dilution-1uL, 1kb marker-2uL, 15times dilution-1uL, 20times dilution-1uL, 1kb marker-1uL )

Results
We estimated attB TNFAIP3(we make this time) is 35ng/uL



2. BP reaction
We adjusted solution (vials) on 1.5mL tube to next composition.
 attB TNFAIP3(35ng/μL)  2μL 
 pDONR(150ng/μL)  1μL 
 TE buffer  5μL 
 Total  8μL 

We added BP Clonase Ⅱ enzyme mix-2uL to this vials.
We incubated these vials for 2hour at 25˚C. Next we did BP reaction

3. Transformation
We added BP TNFAIP3-2uL to XL1-Blue-100uL and we did Transformation.
Finally we spread 10uL, 40uL and 100uL on plate of LB Kanamycin(+) and we keep 37℃ overnight.

August 22nd


TNFA and API2

We separated six colonies from 40uL spread plate of BP TNFAIP3 (make August 21 ) .
We cultivated these colonies on 2.5mL Kanamycin(+) LB culture medium and we kept shaking this medium overnight.