Team:NCTU Formosa/notes

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Notes

The experimental log that records down the purpose, method, result and date of each experiment that we have conducted.

About the notes

Our notes are the abbreviations of the experimental process, including titles, genes we transformed, plasmids we used, and resistances on the plasmids. We categorized these notes by date. Moreover, team members followed the iGEM protocol in each experimental step in order to get better experimental efficiency and the results we had expected.

March 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

11

12

13

mini-prep of cultivated AlsS, pSB1K3, pSB1A3, and pSB1C3 E.coli (G2)

14

digestion : [Zif268] ES & [AlsS] XP & [pSB1C3] EP (G2)
ligation : insert[Zif268] ES & [AlsS] XP/Vector[pSB1C3] EP (G2)

15

16

Transformation of B0034
Cultivation of transformed E.coli on LBA plate

17

18

19

Transformation of Zif268+AlsS+pSB1C3 in DH5-alpha (G2)
Point mutation HivC (PCR, DPN1 digest, TA cloning, transform) (G2)

20

PCR of point mutation HivC (G2)
PCR of insert fragment [Zif268+AlsS] (G2)

21

electrophoresis of insert fragment [Zif268+AlsS]----NOT OK (G2)

22

Single colony isolation from pLac LBA plate, and cultivation of pLac E.coli in liquid LBA
Single colony isolation from pSB1K3 LBK plate, and cultivation of pSB1K3 E.coli in liquid LBK

23

mini-prep of cultivated pLac & pSB1K3 E.coli

24

digestion : [pSB1K3] EP

25

26

27

28

29

Single colony isolation from Zif268 LBA plate, and cultivation of Zif268 E.coli in liquid LBA
Single colony isolation from AlsS LBA plate, and cultivation of AlsS E.coli in liquid LBA

30

mini-prep of cultivated Zif268 Ecoli & AlsS Ecoli
digestion :[Zif268] ES/[AlsS] XP

31

April 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

1

ligation : insert Zif268 [ES] & AlsS [XP]/Vector pSB1K3 [EP]

2

transformation of Zif268+AlsS+pSB1K3 and cultivation on LB-K plate

3

4

digestion : [pSB1K3] EP
digestion : [pSB1K3] EP

5

6

7

PCR of insert fragment [Zif268+AlsS] OK
DNA Sequencing OK
ligation : point mutation HivC
TA cloning : point mutation HivC

8

9

Single colony isolation from Zif268+AlsS LB-K plate, and cultivation of in liquid LB-K

10

mini-prep of cultivated Zif268+ AlsS E. coli
transformation of point mutation HivC and cultivation on LB-A plate
transformation of B0034 and cultivation on LB-A plate

11

12

Single colony isolation from HivC LB-A plate, and in liquid LB-A
Single colony isolation from B0034 LB-A plate, and in liquid LB-A

13

mini-prep of cultivated point mutation HivC E. coli & B0034 E. coli

14

digestion : Zif268+AlsS [XP]

15

16

17

Single colony isolation from ilvD LB-A plate, and cultivation in liquid LB-A

18

mini-prep of cultivated ilvD E. coli
digestion : ilvD [EP] & pSB1K3 [EP]
transformation of 37℃ RBS and cultivation on LB-C plate

19

Single colony isolation from HivC LB-A plate, and cultivation in liquid LB-A

20

digestion : B0034 [SP]
gel extraction
ligation :insert Zif268+AlsS [XP]/Vector B0034 [SP]
mini-prep of cultivated Hivc E. coli

21

transformation of B0034+Zif268+AlsS and cultivation on LB-A plate
transformation of HivC and cultivation on LB-A plate

22

PCR of insert fragment [B0034+Zif268+AlsS] OK
DNA Sequencing NOT OK
digestion : B0034 [SP] & Zif268+AlsS [XP]
gel extraction
ligation :insert Zif268+AlsS [XP]/Vector B0034+pSB1A3 [SP]
transformation of B0034+Zif268+AlsS and cultivation on LB-A plate
Single colony isolation from B0034 LB-A plate, and cultivation in liquid LB-A
SCI from ilvD LB-K plate, and cultivation in liquid LB-K

23

PCR of insert fragment [B0034+Zif268+AlsS] NOT OK
transformation of B0034+Zif268+AlsS and cultivation on LB-A plate
mini-prep of cultivated B0034 and ilvD E. coli
Single colony isolation from HivC LB-A plate, and cultivation in liquid LB-A

24

mini-prep of cultivated HivC E. coli
digestion : B0034 [SP] & ilvD [XP]

25

digestion : pSB1C3 [EP] & HivC [ES] & HivC [SP]
ligation :insert HivC [ES] & ilvD [XP]/Vector pSB1C3 [EP]
ligation :insert ilvD [XP]/Vector HivC+pSB1A3 [SP]

26

transformation of HivC+ilvD and cultivation on LB-A & LB-C plate

27

PCR of insert fragment [B0034+Zif268+AlsS] NOT OK

28

transformation of pSB1A3 & pSB1C3 and cultivation on LB-A & LB-C plate
PCR of insert fragment [HivC+ilvD] OK
DNA sequencing NOT OK

29

Single colony isolation from pSB1C3 LB-C plate, and cultivation in liquid LB-C

30

mini-prep of cultivated & pSB1C3 E. coli

May 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

1

digestion : pLac [EP] & pSB1K3 [EP]
ligation :insert pLac [EP]/Vector pSB1K3 [EP]
transformation of pLac+pSB1K3 and cultivation on LB-K plate

2

PCR of insert fragment [pLac+pSB1K3] OK
DNA Sequencing OK
transformation of B0034_new and cultivation on LB-A plate
Single colony isolation from B0034 LB-A plate, and cultivation in liquid LB-A

3

mini-prep of cultivated B0034 E. coli
digestion : B0034 [SP]
ligation :insert Zif268+AlsS [XP]/Vector B0034+pSB1A3 [SP]
transformation of B0034+Zif268+AlsS
cultivation on LB-A plate

4

PCR of insert fragment [B0034+Zif268+AlsS]-----self ligation
transformation of 37℃ RBS and cultivation on LB-C plate

5

6

7

8

transformation of 37℃ RBS and cultivation on LB-Kplate

9

Single colony isolation from 37℃ RBS LB-K plate, and cultivation in liquid LB-K

10

digestion : B0034 [ES] & pSB1C3 [EP]
mini-prep of cultivated 37℃ RBS E. coli

11

ligation :insert B0034 [ES] & pSB1C3 [EP]/Vector pSB1C3 [EP]
transformation of B0034+Zif268+AlsS and cultivation on LB-C plate

12

digestion : pLac [ES] & pLac [SP]
digestion : B0034 [SP] Kr (gel extraction) , B0034 [SP] Ar (gel extraction) , 37℃ RBS [XP] & HivC [XP]
ligation : (1. 2 parts) insert HivC [XP], Vector B0034+pSB1K3 [SP]
ligation : (2. 3 parts) insert HivC [XP], Vector B0034+pSB1A3 [SP]

13

14

15

PCR of insert fragment [B0034+Zif268+AlsS] OK
DNA Sequencing OK
transformation of B0034+ HivC and cultivation on LB-A & LB-K plate

16

17

18

Single colony isolation from pSB1A3 LB-A plate, and cultivation in liquid LB-A
Single colony isolation from B0034+Zif268+AlsS LB-C plate, and cultivation in liquid LB-C
Single colony isolation from B0034+HivC LB-A & K plate, and cultivation in liquid LB-A & K

19

mini-prep of cultivated pSB1A3 E. coli & B0034+Zif268+AlsS
digestion: pSB1A3 [EP] & B0034+Zif268+AlsS [XP]
ligation: (1.3 parts)insert pLac [ES] & B0034+Zif268+AlsS [XP], Vector pSB1A3 [EP]
ligation: (2.2 parts)insert B0034+Zif268+AlsS [XP], Vector pLac+pSB1K3 [SP]
transformation of pLac+B0034+Zif268+AlsS and cultivation on LB-A plate & LB-K plate
mini-prep of cultivated B0034+HivC (Ar & Kr)

20

PCR of insert fragment [pLac+B0034+Zif268+AlsS] OK
DNA Sequencing 3 parts OK

21

digestion : 37℃ RBS [XP] , ilvD [ES] & pSB1C3 [EP]

22

23

digestion : HivC+ilvD-3,18 [EP]
ligation :insert ilvD[ES] & 37℃ RBS [XP], Vector pSB1C3 [EP]

24

Single colony isolation from pLac+B0034+Zif268+AlsS LB-A plate, and cultivation in liquid LB-A

25

mini-prep of cultivated pLac+B0034+Zif268+AlsS E. coli
transformation of ilvD+37℃ RBS and cultivation on LB-C plate

26

PCR of insert fragment [ilvD+37℃]-----OK
DNA Sequencing OK

27

28

29

30

Single colony isolation from PBSII+ilvC LB-K plate, and cultivation in liquid LB-K
ligation : insert HivC [XP], vector B0034+pSB1A3 [SP]

31

mini-prep of cultivated PBSII+ilvC E. coli
digestion : pSB1C3 [EP] & PBSII+ilvC [XP]
ligation : insert B0034 [ES] & PBSII+ilvC [XP], vector pSB1C3 [EP]
transformation of B0034+PBSII+ilvC and cultivation on LB-C plate
transformation of B0034+HivC and cultivation on LB-A plate

June 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

1

PCR of insert fragment [B0034+PBSII+ilvC] OK!
DNA Sequencing OK!

2

3

mini-prep of cultivated B0034+PBSII+ilvC E. coli & pLac+B0034+Zif268+AlsS E. coli

mini-prep of cultivated HivC+ilvD-12,20 E. coli

4

digestion : HivC+ilvD-12,20 [XP]

5

Design the primer for pLac+B0034+Zif268+AlsS point mutation (pm)

6

digestion : B0034 [ES] & HivC [XP] & pSB1C3 [EP] & HivC [EP]
ligation : insert B0034 [ES] & HivC [XP]/vector pSB1C3 [EP]
ligation : insert HivC [EP]/vector pSB1C3 [EP]
transformation of B0034+ HivC & HivC ,and cultivation on LB-C plate

7

PCR of insert fragment [B0034+ HivC] & [HivC] OK

8

Design the primer for B0034+PBSII+ilvC point mutation (pm)
Single colony isolation from HivC, B0034+HivC & ilvD+37℃ RBS LB-C plate, and cultivation in liquid LB-C

9

mini-prep of cultivated HivC & B0034+HivC & ilvD+37℃ RBS E. coli
Testing the temperature of the point mutation between of HivC & ilvD by the m.p 50℃ of PCR
ligation: insert B0034+HivC [ES] & ilvD [XP]/vector pSB1A3 [EP];insert B0034+HivC [ES] & ilvD+37℃ RBS [XP]/vector pSB1A3 [EP]

10

transformation of B0034+ HivC+ ilvD & B0034+ HivC+ ilvD+37℃ RBS ,and cultivation on LB-A plate
Testing the temperature of the point mutation between of pLac+B0034+Zif268 & AlsS by the m.p 55℃ of PCR failed

11

DNA Sequencing B0034+HivC & HivC OK
PCR of insert fragment [B0034+ HivC+ilvD] & [B0034+ HivC+ilvD+37℃ RBS] OK

12

Single colony isolation from B0034+ HivC+ilvD+37℃ RBS & B0034+ HivC+ ilvD LB-A plate, and cultivation in liquid LB-A
Single colony isolation from HivC(TA) LB-A plate, and cultivation in liquid LB-A

13

mini-prep of cultivated B0034+ HivC+ilvD+37℃ RBS , B0034+ HivC+ ilvD & HivC(TA) E. coli
Testing the temperature of the point mutation between of pLac+B0034+Zif268 & AlsS by the m.p 50 & 52℃ of PCR----50℃ is better

14

PCR of insert fragment [pLac+B0034+Zif268+AlsS] with designed primer for point mutation -----NOT OK

15

DNA Sequencing B0034+ HivC+ilvD+37℃ RBS & B0034+ HivC+ ilvD OK

16

17

18

19

PCR of insert fragment [pLac+B0034+Zif268+AlsS] with designed primer for point mutation OK
digestion: pLac+B0034+Zif268+AlsS [DPn1]

20

transformation of pLac+B0034+Zif268+AlsS (point mutation), and cultivation on LB-A plate

21

Single colony isolation from pLac+B0034+Zif268+AlsS (pm) LB-A plate, and cultivation in liquid LB-A

22

mini-prep of cultivated pLac+B0034+Zif268+AlsS (pm) E. coli
digestion : pLac+B0034+Zif268+AlsS (pm) [EP]

23

DNA sequencing OK

24

25

PCR of insert fragment [B0034+ PBSII+ilvC] with designed primer for point mutation OK
digestion : B0034+ PBSII+ilvC [DPn1]

26

transformation of B0034+ PBSII+ilvC (pm), and cultivation on LB-C plate------Fail

27

PCR of insert fragment [B0034+ PBSII+ilvC] with designed primer for point mutation OK

28

digestion : B0034+ PBSII+ilvC [DPn1]

29

transformation of B0034+ PBSII+ilvC (pm), and cultivation on LB-C plate

30

PCR of insert fragment [B0034+ PBSII+ilvC] (pm) OK
Single colony isolation from B0034+ PBSII+ilvC (pm) LB-C plate, and cultivation in liquid LB-C

July 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

1

mini-prep of cultivated B0034+ PBSII+ilvC (pm) E. coli
digestion : B0034+ PBSII+ilvC (pm) [EP]

2

DNA sequencing OK

3

4

5

6

7

digestion : pLac+B0034+zif268+AlsS (pm) [ES] & B0034+ PBSII+ilvC (pm) [XP]

8

9

Testing the temperature of the point mutation between of HivC & ilvD by the m.p 50℃ of PCR
digestion : pSB1K3 [EP]
ligation : insert pLac+B0034+zif268+AlsS (pm) [ES] & B0034+ PBSII+ilvC (pm) [XP]/vector pSB1K3 [EP]
transformation of pLac+B0034+zif268+AlsS+ B0034+ PBSII+ilvC (pm) and cultivation on LB-K plate

10

Testing the temperature of the point mutation between of HivC & ilvD by the m.p 48℃ of PCR
Digestion : B0034+ HivC+ilvD+37℃ RBS [DPn1]
PCR of insert fragment [pLac+B0034+zif268+AlsS+ B0034+ PBSII+ilvC] (pm) OK
SCI from pLac+B0034+zif268+AlsS+ B0034+ PBSII+ilvC (pm) LB-K plate, and cultivation in liquid LB-K

11

mini-prep of cultivated pLac+B0034+zif268+AlsS+ B0034+ PBSII+ilvC (pm) E. coli
DNA sequencing OK
culture condition test: activation DH5αovernight

12

transfer to new medium(1/100), OD0.2 start counting culture time
transfer to 30゜C and 27゜C

13

transfer to 30゜C and 27゜C

14

15

transformation of B0034+ HivC+ ilvD+37℃ RBS (pm),and cultivation on LB-A plate

16

PCR of insert fragment [B0034+ HivC+ilvD+37℃ RBS](pm)-----NOT OK

17

Point mutation by PCR of insert fragment [B0034+ HivC+ilvD+37℃ RBS]
Digestion: B0034+ HivC+ilvD+37℃ RBS [DPn1]

18

19

transformation of B0034+ HivC+ ilvD+37℃ RBS (pm),and cultivation on LB-A,K,C plate (A sucessful)

20

PCR of insert fragment [B0034+ HivC+ilvD+37℃ RBS](pm) ---- OK
Single colony isolation from B0034+ HivC+ilvD+37℃ RBS (pm) LB-A plate, and cultivation in liquid LB-A

21

mini-prep of cultivated B0034+ HivC+ilvD+37℃ RBS (pm) E. coli
Digestion: pLac+B0034+zif268+AlsS+ B0034+ PBSII+ilvC (pm)(G1) [ES] & B0034+ HivC+ilvD+37℃ RBS (pm)(G2) [XP]
ligation : insert G1[ES] & G2[XP] vector pSB1C3[EP]

22

transformation of G1+G2,and cultivation on LB- C plate failed

23

ligation : insert G1[ES] & G2[XP]/vector pSB1C3[EP]

24

transformation of G1+G2,and cultivation on LB- C plate
Digestion: G2’(B0034+HIVC+ilvD) [XP]
ligation : insert G1[ES] & G2‘[XP]/vector pSB1C3[EP]

25

PCR of insert fragment [kivD+B0015]
transformation of G1+G2’, and cultivation on LB- C plate failed

26

Single colony isolation from kivD+B0015 LB-C plate, and cultivation in liquid LB-C
sample and do GC

27

mini-prep of cultivated kivD+B0015 E. coli

28

29

Point mutation by PCR of insert fragment [B0034+ HivC+ilvD(G2’)]
Digestion: G2’ [DPn1]

30

transformation of G2’, and cultivation on LB- A plate

31

Digestion: kivD+B0015 [EP] (checking bp----failed)
Single colony isolation from G2’ (pm) LB-A plate, and cultivation in liquid LB-A

August 2013

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

1

mini-prep of cultivated G2’ E. coli

2

3

4

5

6

7

8

9

Digestion: G1 [ES] & G2‘ [XP] & pSB1C3 [EP]
ligation : insert G1[ES] & G2‘[XP]/vector pSB1C3[EP]

10

strain test: activation of different strains overnight

11

transfer to new medium, OD0.2 IPTGinduction, culture in 37゜C

12

Single colony isolation from G1+G2’ LB-C plate, and cultivation in liquid LB-C
transfer to 27゜C

13

mini-prep of cultivated G1+G2’ E. coli

14

15

Digestion: Ptet+B0032[ES] & GliI+KivD[XP]
sample and do GC

16

ligation : insert Ptet+B0032[ES] & GliI+KivD[XP]/vector pSB1K3[EP]
Single colony isolation from G1+G2 LB-C plate, and cultivation in liquid LB-C

17

transformation of Ptet+B0032+ GliI+KivD, and cultivation on LB- K plate
mini-prep of cultivated G1+G2 E. coli

18

PCR of insert fragment [Ptet+B0032+ GliI+KivD]-----OK
DNA sequencing------NOT OK

19

20

21

22

23

24

carbon source test: activation DH5α overnight

25

transfer to new medium(1/100), OD0.2 start counting culture time

26

culturing for 72hours, inject feeding solution per 24hours

27

culturing for 72hours, inject feeding solution per 24hours

28

transformation of DNA program, and cultivation on LB- A plate
culturing for 72hours, inject feeding solution per 24hours

29

ligation : insert Ptet+B0032[ES] & GliI+KivD[XP]/vector pSB1K3[EP]
Single colony isolation from DNA program LB-C plate, and cultivation in liquid LB-C
sample & do GC

30

transformation of Ptet+B0032+ GliI+KivD, and cultivation on LB- K plate
mini-prep of cultivated DNA program E. coli
Do GC

31

PCR of insert fragment [Ptet+B0032+ GliI+KivD] OK
DNA sequencing NOT OK