Team:Shenzhen/Result/YAO.Suicider
From 2012.igem.org
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S
BioBricks
- Summary
- YAO.Genome
- YAO.Channel
- YAO.Sensor
- YAO.Suicider
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p
Notebook
- Team History
- YAO.Genome
- YAO.Channel
- YAO.Sensor
- YAO.Suicider
- YAO.Factory
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e
Practices
- I. Construction of Vector
- March 12th, 2012
- March 15th – April 13th, 2012
- II. Construction of Yeast Expression Vector
- III. Yeast Transformation Experiment:
- I. Construction of Vector (GAL promoter+Holin) in PSB1C3
- II. Construction of vector(GAL promoter+holing) in PSB1C3
- III. Construction of Yeast Expression Vector
- IV. Yeast transformation experiment:
Preview for Whole Experiments
GAL1 promoter + signal peptide to mitochondria + T7 RNAP + ADH terminator (backbone:YEP325)
T7 promoter + DNase + terminator for mitochondria (under consideration)
DLD3 promoter + Holin +ADH terminator
Identification of T7 RNAP Function in Nucleus
1. Bacterial culture (BBa_I712074(T7 poromter,Amp resistant or Kana resistant),E0840(GFP generator,Amp resistant)
2. Plasmid extraction for BBa_I712074,E0840( Tiangen normal plasmid extraction kits
3. Measure the concentration of plasmid by NANODROP 2000(Thermo)
4. Digestion: (enzymes are all from Takara
BBa_I712074 2-3ug
PstI 2ul
SpeI 2ul
10 x H Buffer 5ul
ddH2O 50ul
E0840 2-3ug
XbaI 2ul
PstI 2ul
10 x H Buffer 5ul
ddH2O 50ul
37oC 3h
80 oC 20min
5. Electrophoresis:
1% agarose gel, 120V, after 45min,EB dye.
6. Gel recovery of GAL(EcoRI/SpeI), Holin(XbaI/PstI) (QIAquick Gel recovery kits)
7. Measure the concentration of fragment of interest by NANODROP 2000(Thermo)
8. Linage:
BBa_I712074 ((stI/SpeI) 2ul
E0840 (PstI/XbaI) 6ul
T4 ligase 1ul
T4 ligase Buffer 1ul
16 oC 3 hours
9. Transduction:
1. UV sterilization half an hour before, get DH5a (competent yeast) out of fridge, thawing in water bath.
2. 10μlinkage production with 50μl competent yeast cells, ice-bath for 30mins.
3. 42oC ice-bath heat shock for 50s.
4. Stewing on ice for 2mins.
5. Add 500μl LB medium without antibiotic, 37℃ shaking(225rpm/min), recover it for culturing it for 1 hour.
6. 3000rpm/min for 5mins, abandon the supermate, mixing the left.
7. 60μl broth spread the Amp anti-LB soli
<P>Events:</P> <P>March 12th. The first iGEM meeting was a very serious one, and there were only 5 members: Kang Chen Zhang Ou and Gong ,respectively.</P> <P>We decided to build a list about the whole previous iGEM projects and divided it into five parts: America for Kang and Chen, Europe for Zhang and Ou, Asia for Gong. All of us were in charge of scanning the projects, summarized them and gave the other members a brief description. Each one for one minute.</P>
<P>Events:</P> <P>Though a recruitment talk with the other classmate in BGI, nearly 20 students and two instructors became members of us. We established a team consisted of eight schools—SCUT, SCNU, SCU, UESTC, WHU, HUST, SEU, UST.</P> <P>We continued to sum up the projects from 2008 to 2011, and in the meanwhile, we separated the whole into more parts and assigned to the other members.</P> <P>Finally, we finished the summary. </P> <P>And we also discussed what we should do, we originally put up with 4 schemes: Schrodinger’s cat—randomly producing 0 and 1; Density sensing application--based on the result of JIandong Wang’s research; Christmas tree—sparks different colors ceaselessly; Yeast artificial organelle—transform mitochondria into a biofactory. The former 3 projects were gave up due to the similarity to the previous iGEM projects. We lay down our consideration on Yeast artificial organelle.</P> <P>Chen Yu search more articles about mitochondria transgene and mitochondrial signaling pathways he can and pack it as a file of endnote.</P> <P>We clarify our projects as a combination of five modules: NAD+/NADH Sensor, self-killer, post-invader, sel-control transporter and artemisinin producer.</P> <P>We divided our group into five parts according to the modules and select two members of each modules to make up two new squads—modeling construction and lab experiments.</P>
2012/3/7 MISSION START 1. TEAM BUILDING: OICQ GROUP; 2. ARRANGEMENTS FOR THE FIRST SEMINAR. 2012/3/8 noon THE FIRST SEMINAR: 1. Discussion about our project; 2. Registration for iGEM 2012 and self-introduce. 2012/3/14 THE SECOND SEMINAR: 1. Discussion about our project; 2. Task assignment for latter seminar mainly about previous teams’ projects; 3. New member’s introduction. 2012/3/15 Group email application succeeded. 2012/3/17 Quan ZHOU withdrew from the team. 2012/3/18 Jianhui GONG made a list of all projects of iGEM 2008-2011 and assigned each one’s seminar task. 2012/3/19 THE THIRD SEMINAR: 1. Introduction of new members; 2. Rearrangements for everyone’s task. 2012/3/22 THE FOURTH SEMINAR: Introduction of a few projects of iGEM 2008-2011. 2012/3/26 THE FIFTH SEMINAR: Introduction of a few projects of iGEM 2008-2011. 2012/3/29 THE SIXTH SEMINAR: 1. Introduction of a few projects of iGEM 2008-2011; 2. Introduction of new members; 3. Rearrangements for everyone’s task again. 2012/4/5 THE SEVENTH SEMINAR: Introduction of a few projects of iGEM 2008-2011. 2012/4/7 TEAM BUILDING ACTIVITY: KTV and dine outside together. 2012/4/10
THE EIGTHTH SEMINAR: Each modules and logo designed.</ul></div>d plat, 37℃ inversed culture in incubation overnight.10. Colony PCR:
dNTPmix(2.5mM) 1μl
PCR 10×buffer2μl
VF 0.5μl
VR 0.5μl
Ex Taq 0.5μl
H2O 15.5μl
Primer
VF: TGCCACCTGACGTCTAAGAA
VR: ATTACCGCCTTTGAGTGAGC
94℃ 3min
94℃ 30s
55℃ 30s
72℃ 1min
72℃ 10min
12℃ ∞
30 cycles
11. 1%~1.5% agarose gel electrophoresis, <130V, 40mins.
12. Sequencing:
Pick the positive colony(colony PCR verification), marking lines and culture(Cmr resistant), sequencing. Name the right vector PSB1AK3-T7 poromter+GFP+T7 terminater
1. Culture of PSB1AK3-T7 poromter+GFP+T7 terminater (Cmr resistant)gz-YEP352(AmpResistant, we have replaced the URA mark with trp mark)
2. Plasmid extraction: PSB1AK3-T7 poromter+GFP+T7 terminater,gz-YEP352
3. Digestion:
Gz-YEP352 2ug
XbaI 2ul
PstI 2ul
10 x H Buffer 5ul
ddH2O 50ul
PSB1AK3-T7 poromter+GFP+T7 terminater 2ug
XbaI 2ul
Pst 2ul
10 x H Buffer 5ul
ddH2 50ul
4. Electrophoresis:
1% agarose gel, 120V, after 45min,EB dye.
5. Gel recovery of gz-YEP352 (XbaI /PstI)PSB1AK3-T7 poromter+GFP+T7 terminater (XbaI / PstI) (Qiagen Gel recovery kits)
6. Lingake:
Gz-YEP352 (XbaI /PstI) 100ng
PSB1AK3-T7 poromter+GFP+T7 terminater 100ng
T4 buffer 1ul
T4 ligase 1ul
ddH2O 10ul
16oC overnight
7. Transduction:
1. UV sterilization half an hour before, get DH5a (competent yeast) out of fridge, thawing in water bath.
2. 10μlinkage production with 50μl competent yeast cells, ice-bath for 30mins.
3. 42oC ice-bath heat shock for 50s.
4. Stewing on ice for 2mins.
5. Add 500μl LB medium without antibiotic, 37℃ shaking(225rpm/min), recover it for culturing it for 1 hour.
6. 3000rpm/min for 5mins, abandon the supermate, mixing the left.
7. 60μl broth spread the Amp anti-LB solid plat, 37℃ inversed culture in incubation overnight.
8. Clony PCR: <p> dNTPmix(2.5mM) 1μl
PCR 10×buffer 2μl
M13_pUC_fwd_primer 0.5μl
M13_reverse_primer 0.5μl
Ex Taq 0.5μl
H2O 15.5μl
94℃ 3min
94℃ 30s
55℃ 30s
72℃ 1.5min
72℃ 10min
12℃ ∞
30 cycles
9. 1.5% agarose gel electrophoresis, <130V, 40mins.
10. Sequencing:
Pick the positive colony(colony PCR verification), marking lines and culture(Cmr resistant), sequencing. Name the right vector:EP352-GAL1,Holin-ADH1
1. plasmid extraction.
2. Preparation of Competent Yeast Cells - LiAc Method
1.treak a YPDA agar plate with a small portion of AH109 or Y187. Incubate the plate upside down at 30°C until colonies appear(~3days). Yeast strains can be stored for up to 1 month at 4°C on YPDA medium in culture plates.
2.Prepare 1.1X TE/LiAc Solution
3.Prepare YPDA liquid medium (Yeast Protocols Handbook)
4.Inoculate one colony(<4 weeks old, 2–3mm in diameter) into 3ml of YPDA medium in a sterile, 15-ml centrifuge tube.
5.Incubate at 30°C with shaking for 8hr.
6.Transfer 5µl of the culture to a 250-ml flask containing 50ml of YPDA.
7.Incubate at 30°C with shaking at 230–250 rpm for 16–20hr.The OD600 should reach 0.15–0.3.
8.Centrifuge the cells at 700 x g for 5min at room temperature.
9.Discard the supernatant and resuspend the cell pellet in 100 ml of YPDA.
10.Incubate at 30°C for 3–5hr (OD600= 0.4–0.5).
11.Centrifuge the cells at 700 x g for 5min at room temperature.
12.Discard the supernatant and resuspend the cell pellet in 60ml of sterile, deionized H2O.
13.Centrifuge the cells at 700 x g for 5min at room temperature.
14.Discard the supernatant and resuspend the cells in 3 ml of 1.1 X TE/LiAc Solution.
15.Split the resuspension between two 1.5-ml microcentrifuge tubes (1.5 ml per tube).
16.Centrifuge each tube at high speed for 15 sec.
17.Discard the supernatant and resuspend each pellet in 600 µl of 1.1 X TE/LiAc Solution.
3.Transformation:
1. Gz-YEP352-T7poromter+GFP+T7terminater 0.2ug
Sperm DNA*(10 mg/ml) 0.1mg
Sperm DNA :when prepared, water-bath boiling for 20mins, then ice-bath, -20°C preservation.
2. 100 ul dense medium of yeast competent cell by 1×TE/LiAc. Whirlpool oscillation.
3. 600 ulPEG/LiAc, oscillation strongly, 30°C,200rpm, culture oscillating for 30mins.
4. Add 70ul DMSO, mixing it slightly and 42oC heat shock by water-bath for 15mins, ice-bath for 1-2mins
5. Centrifuging for 14,000rpm for 5sec, abandon the supermate, 0.1ml 1x TE suspense the cell precipitation, spread it to SD/ -Ura-trp solid plat, 30°C culture reversely for 3 days.
6. Holin function identification:
Pick a SD/ -Ura-trp-cultured colony and inoculate it to 50ml YPDA medium, 30°C,220rpm culture reelingly to OD-0.1, transfer 20ml to 50ml sterile medium (alpha-galactose), versus is added by equivalent water. Measuring the OD value one time for one hour and drawing the curve.
Result analyzation:
If the bacteria in alpha-galactose show flurorescence, that shows T7 RNAP/T7 promoter can work.
Protocol: Test of Holin Function
1. Plasmid extraction for T-Gal, T-holin
2. PCR amplification of linear vector PSB1C3, purification(Qiagen PCR purification kits)
3. Digestion:
T-GAL1 2ug
ECoRI2ul
SpeI 2ul
10 x H Buffer 5ul
ddH2O50ul
T-holin 2ug
XbaI 2ul
PstI 2ul
10 x H 5ul
ddH2O 50ul
purified backbone PSB1C3 1ug
ECoRI 2ul
PstI 2ul
10 x H Buffer 5ul
ddH2O 50ul
37oC 1h
80oC 20min
4. Electrophoresis:
1% agarose gel, 120V, after 45min,EB dye.
5. Gel recovery of GAL(EcoRI/SpeI), Holin(XbaI/PstI) (Qiagen Gel recovery kits)
6. Linage:
PSB1C3 2ul
GAL1( ECoRI / SpeI) 100ng
Holin( XbaI/PstI) 100ng
T4 buffer 1ul
T4 ligase 1ul
ddH2O 10ul
16 oC overnight
7. Transduction:
1. UV sterilization half an hour before, get DH5a (competent yeast) out of fridge, thawing in water bath.
2. 10μlinkage production with 50μl competent yeast cells, ice-bath for 30mins.
3. 42oC ice-bath heat shock for 50s.
4. Stewing on ice for 2mins.
5. Add 500μl LB medium without antibiotic, 37℃ shaking(225rpm/min), recover it for culturing it for 1 hour.
6. 3000rpm/min for 5mins, abandon the supermate, mixing the left.
7. 60μl broth spread the Amp anti-LB solid plat, 37℃ inversed culture in incubation overnight.
8.Colony PCR:
dNTPmix(2.5mM) 1μl
PCR 10×buffer 2μl
VF 0.5μl
VR 0.5μl
Ex Taq 0.5μl
H2O 15.5μl
Primer
VF: TGCCACCTGACGTCTAAGAA
VR:ATTACCGCCTTTGAGTGAGC
94℃ 3min
94℃ 30s
55℃ 30s
72℃ 1min
72℃ 10min
12℃ ∞
30 cycles
9. 1%~1.5% agarose gel electrophoresis, <130V, 40mins.
10. Sequencing:
Pick the positive colony(colony PCR verification), marking lines and culture(Cmr resistant), sequencing. Name the right vector PSB1C3-GAL
1. Plasmid extraction: BBa-J63002(ADH terminator), PSB1C3-GAL1-Holin.
2. Digestion:
BBa-J63002 2ug
XbaI 2ul
PstI 2ul
10 x H Buffer 5ul
ddH2O 50ul
37oC 1h
PSB1C3-GAL1-Holin 2ug
SpeI 2ul
PstI 2ul
10 x H Buffer 5ul <p> ddH2O 50ul
80oC 20min
3. Electrophoresis:
1% agarose gel, 120V, after 45min,EB dye.
4. Gel recovery of BBa-J63002 (XbaI /PstI),PSB1C3-GAL1-Holin(SpeI/ PstI) (Qiagen Gel recovery kits)
5. Linkage:
PSB1C3-GAL1-Holin(SpeI/ PstI) 100ng
BBa-J63002 (XbaI /PstI) 100ng
T4 buffer 1ul
T4 ligase 1ul
ddH2O 10ul
16 oC overnight
6. Transduction:
1. UV sterilization half an hour before, get DH5a (competent yeast) out of fridge, thawing in water bath.
2. 10μlinkage production with 50μl competent yeast cells, ice-bath for 30mins.
3. 42oC ice-bath heat shock for 50s.
4. Stewing on ice for 2mins.
5. Add 500μl LB medium without antibiotic, 37℃ shaking(225rpm/min), recover it for culturing it for 1 hour.
6. 3000rpm/min for 5mins, abandon the supermate, mixing the left.
7. 60μl broth spread the Amp anti-LB solid plat, 37℃ inversed culture in incubation overnight.
7. Colony PCR:
dNTPmix(2.5mM)v1μl
PCR 10×buffer 2μl
VF 0.5μl
VR 0.5μl
Ex Taq 0.5μl
H2O 15.5μl
Primer
VF: TGCCACCTGACGTCTAAGAA
VR: ATTACCGCCTTTGAGTGAGC
94℃ 3min
94℃ 30s
55℃ 30s
72℃ 1.5min
72℃ 10min
12℃ ∞
30 cycles
8. 1%~1.5% agarose gel electrophoresis, $lt;130V, 40mins.
9. Sequencing:
Pick the positive colony(colony PCR verification), marking lines and culture(Cmr resistant), sequencing. Name the right vector PSB1C3-GAL1, Holin-ADH1
1. Culture of PSB1C3-GAL1-Holin-ADH1 (Cmr resistant) YEP352 (AmpResistant)
2. Plasmid extraction: PSB1C3-GAL1-Holin-ADH1,YEP352
3. Digestion:
YEP352 2ug
XbaI 2ul
PstI 2ul
10 x H 5ul
ddH2O 50ul
PSB1C3-GAL1-Holin-ADH1 2ug
XbaI 2ul
PstI 2ul
10 x H Buffer 5ul
ddH2O 50ul
4. Electrophoresis:
1% agarose gel, 120V, after 45min,EB dye.
5. Gel recovery of YEP352 (XbaI /PstI),PSB1C3-GAL1-Holin-ADH1(XbaI / PstI) (Qiagen Gel recovery kits)
6. Lingake:
YEP352 (XbaI /PstI) 100ng
PSB1C3-GAL1-Holin-ADH1(XbaI / PstI) 100ng
T4 buffer 1ul
T4 ligase 1ul
ddH2O 10ul
16oC overnight
7. Transduction:
1. UV sterilization half an hour before, get DH5a (competent yeast) out of fridge, thawing in water bath.
2. 10μlinkage production with 50μl competent yeast cells, ice-bath for 30mins.
3. 42oC ice-bath heat shock for 50s.
4. Stewing on ice for 2mins.
5. Add 500μl LB medium without antibiotic, 37℃ shaking(225rpm/min), recover it for culturing it for 1 hour.
6. 3000rpm/min for 5mins, abandon the supermate, mixing the left.
7. 60μl broth spread the Amp anti-LB solid plat, 37℃ inversed culture in incubation overnight.
8. Clony PCR: <p> dNTPmix(2.5mM) 1μl
PCR 10×buffer 2μl
M13_pUC_fwd_primer 0.5μl
M13_reverse_primer 0.5μl
Ex Taq 0.5μl
H2O 15.5μl
94℃ 3min
94℃ 30s
55℃ 30s
72℃ 1.5min
72℃ 10min
12℃ ∞
30 cycles
9. 1.5% agarose gel electrophoresis, <130V, 40mins.
10. Sequencing:
Pick the positive colony(colony PCR verification), marking lines and culture(Cmr resistant), sequencing. Name the right vector:EP352-GAL1, Holin-ADH1
1. plasmid extraction.
2. Preparation of Competent Yeast Cells—LiAc Method
1.treak a YPDA agar plate with a small portion of AH109 or Y187. Incubate the plate upside down at 30°C until colonies appear(~3days). Yeast strains can be stored for up to 1 month at 4°C on YPDA medium in culture plates
2.Prepare 1.1X TE/LiAc Solution
3.Prepare YPDA liquid medium (Yeast Protocols Handbook)
4.Inoculate one colony (<4 weeks old, 2–3mm in diameter) into 3ml of YPDA medium in a sterile, 15-ml centrifuge tube.
5.Incubate at 30°C with shaking
6.Transfer 5µl of the culture to a 250-ml flask containing 50ml of YPDA.
7.Incubate at 30°C with shaking at 230–250 rpm for 16–20hr.The OD600 should reach 0.15–0.3.
8.Centrifuge the cells at 700 x g for 5min at room temperature.
9.Discard the supernatant and resuspend the cell pellet in 100 ml of YPDA.
10.Incubate at 30°C for 3–5hr (OD600= 0.4–0.5).
11.Centrifuge the cells at 700 x g for 5min at room temperature.
12.Discard the supernatant and resuspend the cell pellet in 60ml of sterile, deionized H2O.
13.Centrifuge the cells at 700 x g for 5min at room temperature.
14.Discard the supernatant and resuspend the cells in 3ml of 1.1 X TE/LiAc Solution.
15.Split the resuspension between two 1.5-ml microcentrifuge tubes (1.5 ml per tube).
16.Centrifuge each tube at high speed for 15 sec.
17.Discard the supernatant and resuspend each pellet in 600µl of 1.1 X TE/LiAc Solution.
3.Transformation:
1. plasmid 0.2ug
Sperm DNA*(10 mg/ml) 0.1mg
*Sperm DNA: when prepared, water-bath boiling for 20mins, then ice-bath, -20°C preservation.
2. 100 ul dense medium of yeast competent cell by 1×TE/LiAc. Whirlpool oscillation.
3. 600 ulPEG/LiAc, oscillation strongly, 30°C,200rpm, culture oscillating for 30mins.
5. Centrifuging for 14,000rpm for 5sec, abandon the supermate, 0.1ml 1x TE suspense the cell precipitation, spread it to SD/Ura solid plat, 30°C culture reversely for 3 days.
6. Holin function identification:
Pick a better-cultured colony and inoculate it to 50ml YPDA medium, 30°C,220rpm culture reelingly to OD-0.1, transfer 20ml to 50ml sterile medium (alpha-galactose), versus is added by equivalent water. Measuring the OD value one time for one hour and drawing the curve.
Result analyzation:
If the bacteria in alpha-galactose grow slower that in water, that shows holing can work.