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Team:Todai-Tokyo/Notebook/bread
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| + | <title>the notebook</title> | ||
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=='''Plan'''== | =='''Plan'''== | ||
'''Aim:'''Create yeast that can be used to make sweet and low energy bread<BR> | '''Aim:'''Create yeast that can be used to make sweet and low energy bread<BR> | ||
| Line 6: | Line 31: | ||
1.Clone the glu1 (glucoamylase) from Saccharomycopsis fibuligera and insert it in the yeast chromosome by homologous recombination.<BR> | 1.Clone the glu1 (glucoamylase) from Saccharomycopsis fibuligera and insert it in the yeast chromosome by homologous recombination.<BR> | ||
2-a Clone mtlD (mannitol synthase) from E.coli and insert it in the yeast chromosome by homologous recombination<BR> | 2-a Clone mtlD (mannitol synthase) from E.coli and insert it in the yeast chromosome by homologous recombination<BR> | ||
| - | + | |<BR> | |
| + | v<BR> | ||
| + | Replace gpd1 gene by mtlD and gpd2 gene by glu1<BR> | ||
2-b Clone xylose isomerase gene and D-tagatose 3-epimerase gene from Mesorhizobium loti.<BR> | 2-b Clone xylose isomerase gene and D-tagatose 3-epimerase gene from Mesorhizobium loti.<BR> | ||
| - | + | |<BR> | |
| + | v<BR> | ||
| + | Replace gpd1 gene by D-tagatose 3-epimerase gene and gpd2 gene by glu1. Transform a plasmid coding xylose isomerase gene. | ||
| + | ='''September'''= | ||
=='''~9/20'''== | =='''~9/20'''== | ||
| Line 17: | Line 47: | ||
=='''9/21'''== | =='''9/21'''== | ||
| - | *Miniprep of mtlD<BR> | + | *[[Team:Todai-Tokyo/Protocols/Miniprep|Miniprep]] of mtlD<BR> |
=='''9/22'''== | =='''9/22'''== | ||
| - | *read the | + | *read the [[Team:Todai-Tokyo/Protocols/Sequencing|Sequencing]] of mtlD→successful<BR> |
*mtlD primers with HAtag come<BR> | *mtlD primers with HAtag come<BR> | ||
| Line 32: | Line 62: | ||
*PCR of gpd1 promoter with Pfu Ultra<BR> | *PCR of gpd1 promoter with Pfu Ultra<BR> | ||
| - | + | ='''October'''= | |
| + | =='''10/1~11'''== | ||
*PCR of Glu1<BR> | *PCR of Glu1<BR> | ||
*TA cloning of Glu1<BR> | *TA cloning of Glu1<BR> | ||
*PCR of gpd1 promoter with ExTaq<BR> | *PCR of gpd1 promoter with ExTaq<BR> | ||
| + | |||
| + | == '''10/12''' == | ||
| + | *PCR of glu1 and gpd1<BR> | ||
| + | *colony PCR of gal1 | ||
| + | *ligation of glu1 and pMD20-T vector | ||
| + | *Cut mtlD with X and P | ||
| + | |||
| + | == '''10/13''' == | ||
| + | *[[Team:Todai-Tokyo/Protocols/Sequencing|Sequencing]] of mtlD<BR> | ||
=='''10/14'''== | =='''10/14'''== | ||
| Line 46: | Line 86: | ||
*colony PCR of mtlD+plate1-7D<BR> | *colony PCR of mtlD+plate1-7D<BR> | ||
=='''10/18'''== | =='''10/18'''== | ||
| - | *Miniprep of mtlD+plate1-7D<BR> | + | *[[Team:Todai-Tokyo/Protocols/Miniprep|Miniprep]] of mtlD+plate1-7D<BR> |
| - | *MtlD made a debut as an iGEM part!<BR> | + | *MtlD made a debut as an iGEM part!<BR> |
| + | |||
| + | =='''10/19'''== | ||
| + | *read the sequence of mtlD | ||
| + | *PCR of mtlD and gpdI | ||
| + | =='''10/20,21'''== | ||
| + | * Amplification of liner DNA (gpd1 deletion and mtlD expression) by Pfu Ultra II PCR<BR> | ||
| + | (1) gpd1_5'_mtlD_5' primer<BR> | ||
| + | T(ADH)_mtlD_3' primer<BR> | ||
| + | Amplify mtlD gene(1149bp) by using the above 2 primers<BR><BR> | ||
| + | mtlD plasmid（25 ng） 0.1 ul<BR> | ||
| + | each primer（100 uM） 0.1 ul<BR> | ||
| + | 2.5mM dNTPs 2.0 ul<BR> | ||
| + | 10×PfuUltra II buffer 2.0 ul<BR> | ||
| + | PfuUltra II 0.4 ul<BR> | ||
| + | MilliQ 15.3 ul<BR> | ||
| + | <BR> | ||
| + | Program<BR> | ||
| + | 1 : 95 oC, 2min<BR> | ||
| + | 2 : 95 oC, 30sec<BR> | ||
| + | 3 : 55 oC, 30sec<BR> | ||
| + | 4 : 72 oC, 30sec<BR> | ||
| + | 5 : go to 2, 24times<BR> | ||
| + | 6 : 25 oC, for ever<BR> | ||
| + | 7 : End<BR> | ||
| + | <BR> | ||
| + | (2) T(ADH) primer<BR> | ||
| + | gpd1_3'_T(TEF1) primer<BR> | ||
| + | Amplify GFPKan4MX6 gene (1715bp) by using the above 2 primers<BR> | ||
| + | <BR> | ||
| + | pYM27 plasmid（30 ng） 0.1 ul<BR> | ||
| + | each primer（100 uM） 0.1 ul<BR> | ||
| + | 2.5mM dNTPs 2.0 ul<BR> | ||
| + | 10×PfuUltra II buffer 2.0 ul<BR> | ||
| + | PfuUltra II 0.4 ul<BR> | ||
| + | MilliQ 15.3 ul<BR> | ||
| + | <BR> | ||
| + | Program<BR> | ||
| + | 1 : 95 oC, 2min<BR> | ||
| + | 2 : 95 oC, 30sec<BR> | ||
| + | 3 : 55 oC, 30sec<BR> | ||
| + | 4 : 72 oC, 30sec<BR> | ||
| + | 5 : go to 2, 24times<BR> | ||
| + | 6 : 25 oC, for ever<BR> | ||
| + | 7 : End<BR> | ||
| + | <BR> | ||
| + | Confirm those 2 PCR products by 1% agarose gel electrophoresis and purify them by Promega Gel Extract Kit.(Elute 30 ul MilliQ)<BR> | ||
| + | <BR> | ||
| + | (3)Overlap PCR<BR> | ||
| + | (i) Amplify the full-length fragment by using 2 PCR products<BR> | ||
| + | <BR> | ||
| + | Overlap extension PCR<BR> | ||
| + | 5’ Fragment (99 ng) 3.3 ul<BR> | ||
| + | 3’ Fragment (100 ng) 10 ul<BR> | ||
| + | 2.5mM dNTPs 2.0 ul<BR> | ||
| + | 10×PfuUltra II buffer 2.0 ul<BR> | ||
| + | PfuUltra II 0.4 ul<BR> | ||
| + | MilliQ 2.3 ul<BR> | ||
| + | <BR> | ||
| + | Program<BR> | ||
| + | 1 : 95 oC, 2min<BR> | ||
| + | 2 : 95 oC, 30sec<BR> | ||
| + | 3 : 55 oC, 30sec<BR> | ||
| + | 4 : 72 oC, 45sec<BR> | ||
| + | 5 : go to 2, 10times<BR> | ||
| + | 6 : 25 oC, for ever<BR> | ||
| + | 7 : End<BR> | ||
| + | <BR> | ||
| + | (ii) Amplify the full-length fragment by using 2 primers<BR> | ||
| + | gpd1_5'_mtlD_5' primer<BR> | ||
| + | gpd1_3'_T(TEF1) primer<BR> | ||
| + | <BR> | ||
| + | gpd1_5'_mtlD_5' primer（100 uM） 0.2 ul<BR> | ||
| + | gpd1_3'_T(TEF1) primer（100 uM） 0.2 ul<BR> | ||
| + | 2.5mM dNTPs 2.0 ul<BR> | ||
| + | 10×PfuUltra II buffer 2.0 ul<BR> | ||
| + | PfuUltra II 0.5 ul<BR> | ||
| + | MilliQ 15.1 ul<BR> | ||
| + | <BR> | ||
| + | Add the above mixture to the former PCR reaction mixture<BR> | ||
| + | <BR> | ||
| + | Program<BR> | ||
| + | 1 : 95 oC, 2min<BR> | ||
| + | 2 : 95 oC, 30sec<BR> | ||
| + | 3 : 55 oC, 30sec<BR> | ||
| + | 4 : 72 oC, 45sec<BR> | ||
| + | 5 : go to 2, 24times<BR> | ||
| + | 6 : 25 oC, for ever<BR> | ||
| + | 7 : End<BR> | ||
| + | <BR> | ||
| + | <BR> | ||
| + | * Amplification of liner DNA (gpd2 deletion and glu1 expression) by Pfu Ultra II PCR<BR> | ||
| + | (1) F2 primer<BR> | ||
| + | gpd2_3'_R1 primer<BR> | ||
| + | Amplify GFPHis3MX6 gene (約2500bp) by using the above 2 primers<BR> | ||
| + | <BR> | ||
| + | pFA6-GFP-His3MX6 plasmid 1 ul<BR> | ||
| + | each primer（100 uM） 0.1 ul<BR> | ||
| + | 2.5mM dNTPs 2.0 ul<BR> | ||
| + | 10×PfuUltra II buffer 2.0 ul<BR> | ||
| + | PfuUltra II 0.4 ul<BR> | ||
| + | MilliQ 15.3 ul<BR> | ||
| + | <BR> | ||
| + | Program<BR> | ||
| + | 1 : 95 oC, 2min<BR> | ||
| + | 2 : 95 oC, 30sec<BR> | ||
| + | 3 : 55 oC, 30sec<BR> | ||
| + | 4 : 72 oC, 45sec<BR> | ||
| + | 5 : go to 2, 24times<BR> | ||
| + | 6 : 25 oC, for ever<BR> | ||
| + | 7 : End<BR> | ||
| + | <BR> | ||
| + | <BR> | ||
| + | *made PYD plate<BR> | ||
Latest revision as of 03:49, 22 October 2009
| Home | The Team | The Project | Parts Submitted to the Registry | Modeling | Notebook | Protocols | Ethics |
|---|
Contents |
Plan
Aim:Create yeast that can be used to make sweet and low energy bread
Methods:
1.Clone the glu1 (glucoamylase) from Saccharomycopsis fibuligera and insert it in the yeast chromosome by homologous recombination.
2-a Clone mtlD (mannitol synthase) from E.coli and insert it in the yeast chromosome by homologous recombination
|
v
Replace gpd1 gene by mtlD and gpd2 gene by glu1
2-b Clone xylose isomerase gene and D-tagatose 3-epimerase gene from Mesorhizobium loti.
|
v
Replace gpd1 gene by D-tagatose 3-epimerase gene and gpd2 gene by glu1. Transform a plasmid coding xylose isomerase gene.
September
~9/20
- PCR of mtlD
- PCR of gpd1 promoter
- TA cloning of mtlD
9/21
- Miniprep of mtlD
9/22
- read the Sequencing of mtlD→successful
- mtlD primers with HAtag come
9/25
- PCR of mtlD with new primer→failed
9/26
- PCR of mtlD with new primer→successful
9/27
- PCR of gpd1 promoter with Pfu Ultra
October
10/1~11
- PCR of Glu1
- TA cloning of Glu1
- PCR of gpd1 promoter with ExTaq
10/12
- PCR of glu1 and gpd1
- colony PCR of gal1
- ligation of glu1 and pMD20-T vector
- Cut mtlD with X and P
10/13
- Sequencing of mtlD
10/14
- cut mtlD and plate1 7D both by EcoRI and PstI
- colony PCR of Glu1
10/15
- ligate mtlD and plate1 7D
10/17
- colony PCR of mtlD+plate1-7D
10/18
- Miniprep of mtlD+plate1-7D
- MtlD made a debut as an iGEM part!
10/19
- read the sequence of mtlD
- PCR of mtlD and gpdI
10/20,21
- Amplification of liner DNA (gpd1 deletion and mtlD expression) by Pfu Ultra II PCR
(1) gpd1_5'_mtlD_5' primer
T(ADH)_mtlD_3' primer
Amplify mtlD gene(1149bp) by using the above 2 primers
mtlD plasmid（25 ng） 0.1 ul
each primer（100 uM） 0.1 ul
2.5mM dNTPs 2.0 ul
10×PfuUltra II buffer 2.0 ul
PfuUltra II 0.4 ul
MilliQ 15.3 ul
Program
1 : 95 oC, 2min
2 : 95 oC, 30sec
3 : 55 oC, 30sec
4 : 72 oC, 30sec
5 : go to 2, 24times
6 : 25 oC, for ever
7 : End
(2) T(ADH) primer
gpd1_3'_T(TEF1) primer
Amplify GFPKan4MX6 gene (1715bp) by using the above 2 primers
pYM27 plasmid（30 ng） 0.1 ul
each primer（100 uM） 0.1 ul
2.5mM dNTPs 2.0 ul
10×PfuUltra II buffer 2.0 ul
PfuUltra II 0.4 ul
MilliQ 15.3 ul
Program
1 : 95 oC, 2min
2 : 95 oC, 30sec
3 : 55 oC, 30sec
4 : 72 oC, 30sec
5 : go to 2, 24times
6 : 25 oC, for ever
7 : End
Confirm those 2 PCR products by 1% agarose gel electrophoresis and purify them by Promega Gel Extract Kit.(Elute 30 ul MilliQ)
(3)Overlap PCR
(i) Amplify the full-length fragment by using 2 PCR products
Overlap extension PCR
5’ Fragment (99 ng) 3.3 ul
3’ Fragment (100 ng) 10 ul
2.5mM dNTPs 2.0 ul
10×PfuUltra II buffer 2.0 ul
PfuUltra II 0.4 ul
MilliQ 2.3 ul
Program
1 : 95 oC, 2min
2 : 95 oC, 30sec
3 : 55 oC, 30sec
4 : 72 oC, 45sec
5 : go to 2, 10times
6 : 25 oC, for ever
7 : End
(ii) Amplify the full-length fragment by using 2 primers
gpd1_5'_mtlD_5' primer
gpd1_3'_T(TEF1) primer
gpd1_5'_mtlD_5' primer（100 uM） 0.2 ul
gpd1_3'_T(TEF1) primer（100 uM） 0.2 ul
2.5mM dNTPs 2.0 ul
10×PfuUltra II buffer 2.0 ul
PfuUltra II 0.5 ul
MilliQ 15.1 ul
Add the above mixture to the former PCR reaction mixture
Program
1 : 95 oC, 2min
2 : 95 oC, 30sec
3 : 55 oC, 30sec
4 : 72 oC, 45sec
5 : go to 2, 24times
6 : 25 oC, for ever
7 : End
- Amplification of liner DNA (gpd2 deletion and glu1 expression) by Pfu Ultra II PCR
(1) F2 primer
gpd2_3'_R1 primer
Amplify GFPHis3MX6 gene (約2500bp) by using the above 2 primers
pFA6-GFP-His3MX6 plasmid 1 ul
each primer（100 uM） 0.1 ul
2.5mM dNTPs 2.0 ul
10×PfuUltra II buffer 2.0 ul
PfuUltra II 0.4 ul
MilliQ 15.3 ul
Program
1 : 95 oC, 2min
2 : 95 oC, 30sec
3 : 55 oC, 30sec
4 : 72 oC, 45sec
5 : go to 2, 24times
6 : 25 oC, for ever
7 : End
- made PYD plate
| Home | The Team | The Project | Parts Submitted to the Registry | Modeling | Notebook | Protocols | Ethics |
|---|
