Team:UCL/Labbook

From 2013.igem.org

(Difference between revisions)
Line 3,273: Line 3,273:
<p class="body_text">
<p class="body_text">
CMV digested and purified conc = 25 ng/ul
CMV digested and purified conc = 25 ng/ul
 +
 +
</p>
 +
<p class="body_text">
 +
<table>
 +
<tr>
 +
<th>CMV (25 ng/ul)</th>
 +
<th>1 c (3:1 molar ratio)</th>
 +
<th>2 c (2:1 molar ratio)</th>
 +
<th>3 c (1:1 molar ratio)</th>
 +
<th>4 c (3:1 molar ratio)</th>
 +
</tr>
 +
<tr>
 +
<td>Water (ul)</td>
 +
<td>1.8</td>
 +
<td>3.2</td>
 +
<td>8</td>
 +
<td>6</td>
 +
</tr>
 +
<tr>
 +
<td>Quick ligase buffer (ul)</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
</tr>
 +
<tr>
 +
<td>Backbone (ul)</td>
 +
<td>4</td>
 +
<td>4</td>
 +
<td>1</td>
 +
<td>1</td>
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</tr>
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<tr>
 +
<td>*Insert (ul)</td>
 +
<td>4.2</td>
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<td>2.8</td>
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<td>1</td>
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<td>3</td>
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</tr>
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<tr>
 +
<td>Ligase (ul)</td>
 +
<td>1</td>
 +
<td>1</td>
 +
<td>1</td>
 +
<td>1</td>
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</tr>
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<tr>
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<td>Total</td>
 +
<td>21</td>
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<td>21</td>
 +
<td>21</td>
 +
<td>21</td>
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</tr>
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<tr>
 +
<td>water (ul)</td>
 +
<td>1.8</td>
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<td>3.2</td>
 +
<td>8</td>
 +
<td>6</td>
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</tr>
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<tr>
 +
<td>Colony count</td>
 +
<td>50</td>
 +
<td>100+</td>
 +
<td>100+</td>
 +
<td>150+</td>
 +
</tr>
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</table>
 +
 +
</p>
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<p class="body_text">
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<table>
 +
<tr>
 +
<th>Zeocin (77 ng/ul)</th>
 +
<th>5 z (3:1 molar ratio)</th>
 +
<th>6 z (2:1 molar ratio)</th>
 +
<th>7 z (1:1 molar ratio)</th>
 +
<th>8 z (3:1 molar ratio)</th>
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</tr>
 +
<tr>
 +
<td>Water (ul)</td>
 +
<td>2.1</td>
 +
<td>3.3</td>
 +
<td>8</td>
 +
<td>8</td>
 +
</tr>
 +
<tr>
 +
<td>Quick ligase buffer (ul)</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
</tr>
 +
<tr>
 +
<td>Backbone (ul)</td>
 +
<td>4</td>
 +
<td>4</td>
 +
<td>1</td>
 +
<td>1</td>
 +
</tr>
 +
<tr>
 +
<td>*Insert (ul)</td>
 +
<td>3.9 from *</td>
 +
<td>2.6 from *</td>
 +
<td>1 from *</td>
 +
<td>1</td>
 +
</tr>
 +
<tr>
 +
<td>Ligase (ul)</td>
 +
<td>1</td>
 +
<td>1</td>
 +
<td>1</td>
 +
<td>1</td>
 +
</tr>
 +
<tr>
 +
<td>Total</td>
 +
<td>21</td>
 +
<td>21</td>
 +
<td>21</td>
 +
<td>21</td>
 +
</tr>
 +
<tr>
 +
<td>water (ul)</td>
 +
<td>1.8</td>
 +
<td>3.2</td>
 +
<td>8</td>
 +
<td>6</td>
 +
</tr>
 +
<tr>
 +
<td>Colony count</td>
 +
<td>30</td>
 +
<td>0</td>
 +
<td>1</td>
 +
<td>0+</td>
 +
</tr>
 +
</table>
 +
 +
* we prepared a tube of concentration 25 ng/ul
<!-- END CONTENT ------------------------------------------------------------------------------------------------------>
<!-- END CONTENT ------------------------------------------------------------------------------------------------------>

Revision as of 22:19, 2 October 2013

Bacterial

Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 14 | Week 15 | Week 16 | Week 17 | Week 18 | Week 19 | Week 20

Mammalian

Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 14 | Week 15 | Week 16 | Week 17 | Week 18 | Week 19 | Week 20

June

Week 1-3

No lab work

Week 4

26th June - We are given safety training in the Advanced Centre for Biochemical Engineering in all relevant laboratories, as well as general procedures in case of emergency.

July

Week 5-6

No lab work

Week 7

Bacterial Lab

15th July - The team is introduced to the laboratories which will be used during the summer for both bacterial and mammalian experiments.

16th July - 5X M9 salts, minimal agar, 1.4% molten agar solution and 0.1M CaCl2/15% glycerol were prepared for the generation of competent cells. Minimal agar plates were poured and streaked with W3110 Escherichia coli cells and left overnight to incubate at 37C.

17th July - Very little colony growth was observed from W3110 ''E.coli'' streaked plates. Plates were therefore left to incubate for a further 17 hours.

18th July - Sufficient colony growth allowed for the selection of a single colony from each plate. This was then inoculated in 5ul LB media + 100ul 1M MgSO4 and left to incu-shake overnight at 37C.

19th July - Cultures re-suspended in new LB media and 100µl aliquots placed into individual eppendorf tubes for placement at -80C.

Mammalian Lab

17th July - Mammalian cell culture and maintenance training by Mrs. Ludmilla Ruban. Passaged primary MEF (mouse embryonic fibroblast) cells. Passage 3.

18th July - MEF passage 4

19th July - MEF passage 5

Week 8

Bacterial Lab

22nd July - Transformation of our competent cells with plasmid YB3110 was carried out.

23rd July - No colony growth was observed on Ampicillin plates indicating no plasmid uptake. transformation was repeated with YB3110.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 0
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 0

24th July - No colony growth from main experiment indicating no plasmid uptake. Transformation was repeated.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 0
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 0

25th July - No colony growth and hence no plasmid uptake. Transformation was repeated.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 0
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 0

26th July - Once again our cells were unsuccessful in taking up the YB3110 plasmid. We concluded that our batch of competent cells were not competent and so these will not be used in any further experiments. A new batch of competent cells are to be generated.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 0
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 0

Mammalian Lab

22nd July - MEF passage 6. Training ends.

Week 9

Bacterial Lab

29th July - A glycerol stock of pSecTag2A from 2009 was restored. This was streaked onto 3 plates (2x LB Amp and 1x No drug), additionally four Falcons with 2ul LB were inoculated with the glycerol stock (2x LB No drug, 2X LB Amp). These were left to incubate overnight.

30th July - pSecTag2A Amp and No drug cultures were centrifuged (5 minutes at 4000rpm) and the pellet frozen to be used later in a miniprep. pSecTag2A plates displayed good colony growth. Colonies were picked from non-competent W3110 streaked plates and inoculated in LB ->incu-shake 37C o/n.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 100+
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 0

31st July - A new stock of competent cells were generated and stored, these were tested for competence via transformation using pSecTag2A and streaking onto amp plates -> incubate 37C o/n.

Ampicillin was produced and stored. Following miniprep of pSecTag2A a gel was prepared for analytical digest with HindIII [link to HindIII conditions] [insert gel image HindIII analytical digest of pSecTag2A]. 50X TAE diluted to 1X.

Item Volume (ul)
DNA pSecTag2A 5
HindIII 1
Buffer 1
BSA 0.5
dH20 2.5
Total 10

Results displayed uncut bands at expected lengths. However HindIII cut pSecTag2A wells displayed too many bands, indicating possible contamination or uncut DNA.

August

1st August - Results from newly generated competent cells transformed with pSecTag2A:

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 100+
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 10

This indicated that the cells are more competent than the last batch, although growth on the negative control was a cause for concern. Therefore the transformation protocol from yesterday was repeated to see whether the ampicilin was working -> plates left for incubation 37C o/n.

Transformation of competent cells with pSecTag2A. 100µl was then spread onto 6 plates (4x Amp, 2x No drug). Left to incubate o/n 37C.

2nd August - Plates displayed significant colony growth on amp plates indicating successful transformation. Negative control however displayed slight colony growth - ampicillin not working effectively, new ampicillin was therefore prepared. End of week inventory was recorded and stocks were topped up.

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 100+
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 15

Mammalian Lab

29th July - Thawed and revived HeLa cells, grown in two T25 flasks in DMEM + 10% FBS + 2 mM L-Glu

30th July - HeLa cells are not looking very happy, with many floating cells. Cells are left to grow over the weekend

Week 10

Bacterial Lab

5th August - The new batch of ampicillin was tested via transformation of competent cells with pSecTag2A. Plates were spread and incubated 37C o/n.

6th August - Results from yesterday’s transformation:

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 (Main) Yes Yes 100+
2 (Positive Control) No Yes 100+
3 (Negative Control) Yes No 15

This indicates that there is still an issue with the ampicillin, possibly a problem with the stock powder used. A final test with both old and new ampicillin was carried out and compared without plasmid insertion.

7th August -

Vial Ampicillin Plate Plasmid Insertion Colony Count
1 Old Ampicillin Yes Yes 100+
2 New Ampicillin v2 No Yes 100+
3 Positive Control Yes No 15

Results indicated that the ampicillin source may not have been fully functional, therefore a new source of amp powder was located and amp was remade.

8th August - Preparation of 4x Amp plates and 4x no drug plates for storage in the fridge.

9th August - Meeting with Darren Nesbeth, requirements for upcoming weeks: create glycerol stocks of both pSecTag2A and pSB1C3, purify and extract pure DNA for pSecTag2A and pSB1C3.

Mammalian Lab

6th August - Checked HeLa cells. Cells are growing slow, left to grow for a few more days

8th August - HeLa cells are about 30% confluent. Changed media.

Week 11

Bacterial Lab

12th August - Chloramphenicol was produced and stored at -20C. In order to produce glycerol stocks, pSecTag2A and pSB1C3 were inoculated with LB media in two falcon tubes each (1x drug, 1x no drug), two plates for each plasmid were also streaked (1x drug, 1x no drug). All were left to incubate at 37C o/n.

13th August - Results from the following plates:

Vial Ampicillin Plate Plasmid Insertion Colony Count
pSecTag2A Cells Yes Yes 100+
W3110 Cells Amp Yes No 0
pSecTag +ve control No Yes 100+
PSB1C3 Cells Yes Yes 0
W3110 Cells Chlor Yes No 25
PSB1C3 +ve control No Yes 0

This indicated that the pSecTag2A cells are acceptable to use for glycerol stock generation and also for plasmid purification. Miniprep was performed on the two incubated Falcon tubes from yesterday.

The results concerning pSB1C3 indicated that the chloramphenicol did not work, and the glycerol stock is dead. Therefore a new glycerol stock was sought after and chloramphenicol was remade. Amp & Cmp were remade and pSB1C3 was located in the 2012 distribution kit. Amp & Cmp were both tested by producing 1x positive and 1x negative plate for each antibiotic streaked with W3110 cells ->left to incubate o/n at 37C. glycerol stocks of pSecTag2A was grown, and a miniprep was carried out. PCR could not be carried out as the primers for pSecTag2A had not arrived.

14th August - Two analytical digests of pSecTag2A with EcoR1-HF and Dpn1 were carried out.

Item A Volume A (ul) Item B Volume B (ul)
pSecTag2A 5 pSecTag2A 5
EcoR1-HF 1 Dpn1 1
Buffer 4 1 Buffer 4 1
BSA 0.5 BSA 0.5
dH20 2.5 dH20 2.5
Total 10 Total 10

[insert image of gel]

[link to enzyme conditions]

The pSB1C3 glyc stock (from HQ) was from the 2012 iGEM box in MMP -20C

Told to use a ratio of 3:1 inoculum:80% glycerol when making glyc stocks

Darren's instructions:

pSB1C3

Transfer entire glycerol tube contents to 10mL LB ND in a 50mL Falcon & measure OD. Place in 37C shakee overnight. Measure OD next morning. If there is growth in the inoculum use a loop to streak onto cmp and ND plates again.

pSecTag2A

50ul of 2013 pSecTag2A glyc stock to inoculate 10mL LB Amp in a 50mL Falcon. Grow overnight and the next day generate 15x glyc stocks sing 1.5mL eppendorfs -> store in MMP -20C.

15th August - OD results for pSB1C3 LB ND inoculum

Plasmid OD Before OD After
PSB1C3 (LB ND) 0.052 0.5

15x eppendorfs of pSecTag2A Amp glycerol stock and 4x eppendorfs of pSB1C3 ND glycerol stock was prepared. pSB1C3 LB ND was streaked onto two plates (1x Cmp, 1xND) ->incubate o/n @37C Remaining 2ml of pSB1C3 LB ND (from falcon) is used to purify and conduct an analytical digest (16th August).

Restriction digest of pSecTag2A:

ul EcoR1 single digest Spe1 single digest Double digest Uncut
pSecTag2A 5 5 5 5
EcoR1 1 0 1 0
Spe1 0 1 1 0
BSA 0.5 0.5 0.5 0.5
Buffer 4 1 1 1 1
dH20 2.5 2.5 1.5 3.5
Total 10 10 10 10

[insert image of gel]

iRRE+PC+RBS and PC+RBS (containing pSB1C3, taken from 2012 iGEM boxes) were plated onto cmp plates -> incubated o/n @37C

Two falcons for each stocks, one containing 5ul and the other 15ul, both were inoculated in 2ml LB+2ml cmp -> incushaker o/n

16th August - Falcons were retrieved:

RESULTS

Inoculum:

Falcon contents (+LB+Amp) ul Colony growth Absorbance
IRRE+PC+RBS (15ul) Yes 0.8
IRRE+PC+RBS (5ul) Yes 0.7
PC+RBS (15ul)/td> No 0.06
PC+RBS (5ul) No 0.08

Plates

Plate contents (+LB+Amp) ul Colony growth Absorbance
IRRE+PC+RBS Yes 100+
IRRE+PC+RBS No 100+
PC+RBS/td> Yes 0
PC+RBS No 20

The PC+RBS plates & falcons were discarded

IRRE+PC+RBS (15ul inoculum) -> underwent miniprep

IRRE+PC+RBS (5ul inoculum) -> 4x glycerols were made: 500ul culture + 166ul 80% glycerol, stored in MMP -20C iGEM 2013 box.

pSB1C3 Gel sd: EcoR1 & Pst1 + dd

Item (ul) EcoR1 Pst1 Double digest Uncut
pSB1C3 5 5 5 5
EcoR1 1 0 1 0
Pst1 0 1 1 0
Buffer 3 1 1 1 1
BSA 0.5 0.5 0.5 0.5
dH20 2.5 2.5 1.5 4.5
Total 10 10 10 10

3ul loading dye to each solution

Lanes:

2 - Hyperladder, 4 - EcoRI, 5 - PstI, 6 - dd, 7 - Uncut

Results from gel: 1kb DNA ladder showed on gel. No bands for EcoR1, Pst1, DD and Uncut plasmid were seen - indicating that no DNA was present -> possibly due to problems with the miniprep.

Therefore from the iGEM 2012 plate 5 (distribution kit) well 23.O, DNA containing BBa_j04450 (colonies are clearly red in colour - RFP) in pSB1C3 was located. The dried DNA was resuspended in 10ul dH2O, left to sit for 5 minutes, then transformed into competent cells -> streaked onto plates and left to incubate o/n @30C over the weekend.

Mammalian Lab

12th August - HeLa cells have confluency of about 60%. Passaged the HeLa cells and ‘backup’ HeLa cells. We set up two 6-well plates at 0.25 x 10^6 cells/ml in preparation for Zeocin kill curve. Cell count involved (0.45 cells/ml).

13th August -

Prepared media with various concentrations of zeocin for each of 6 wells.

Concentration of zeocin (µg/ml) Volume of zeocin (ml) Volume of DMEM + 10% FBS + 2 mM L-Glu (ml)
0 0 30.0
50 15 30.0
100 30 30.0
250 75 29.9
500 150 29.9
1000 300 29.7

T75 flasks: - 90% confluency T25 flasks - 30% confluency 6-well plates - 30% confluency

14th August - T25 flasks 90% confluency

Disc 1 Disc 2

Disc 1 Disc 2
Concentration of zeocin (µg/ml) Confluency (%) Cell Appearance Comment Confluency (%) Cell Appearance Comment
0 65 Healthy Healthy, few swell 65 Healthy minimal floaters
50 40 Healthy, few swell few floaters 65 occasional swell moderate floaters
100 40 Half/moderate swell Moderate floaters, minor infection 50 40% swelling minimal floaters
250 25 most/moderate swell many floaters 60 moderate/severe swelling many floaters
500 40 most clumps dead/ swell many floaters, possibly infection 65 severe swelling all over large number of floaters
1000 45 very severe death/ swell many floaters, minor infection 60 severe swelling all over moderate number of floaters

The two T25 flasks with revived HeLa have confluency of about 90%; T75 flask with ‘backup’ cells 70% confluent. The T25 flasks are discarded.

16th August -

Disc 1 Disc 2
Concentration of zeocin (µg/ml) Confluency (%) Cell Appearance Floaters Confluency (%) Cell Appearance Floaters
0 90 Healthy Minimal 95 Healthy minimal
50 80 minor swell moderate 90 minor swell moderate
100 65 Minor swell, minor death Many 75 Minor swell, minor death moderate
250 50 severe swelling, death many 50 severe swelling, death many
500 60 severe swelling, death many 50 severe swelling, death many
1000 40 severe swelling, death many 50 severe swelling, death many

Split and passaged stock HeLa into 2 flasks

17th August - Passaged HeLa cells

Week 12

Bacterial Lab

19th August - pSB1C3 streaked plates (well 23.O) were retrieved from 30C incubator. Colony growth visible indicating successful transformation. Colonies were expected to be red in colour, however this was not observed.

Plate (competent cell vial) Colony Count
10 50+
20 50+

A single colony from each plate was then inoculated in LB in order to later prepare glycerol stocks.

iGEM 2012 boxes were searched for pSB1C3. Transformation was carried out and then selective plates were spread, incubated o/n @37C.

Innoculations of the following were carried out in 2mL LB:

· IRRE+PC+RBS (pSB1C3) (2x in 2mL LB) -> 2ul and 5ul -> incu-shaker

· RFP+pSB1C3 (scooped from plates) (2x in 2mL LB) -> incu-shaker

^ 1.5mL miniprep, 0.5mL glycerol stock for following day (20th)

20th August - Plates taken from incubation:

Competent cells transformed with plasmid: Colony growth -> cells have successfully taken up plamid.

Negative control (only competent cells): Colony growth -> Most likely problems with Chloramphenicol.

Will therefore re-make chloramphenicol

Plate (pSB1C3+) Colony Count
NUC 5
LAC 20
LAC 15
LAC2 10
CURL1 30
Control 50

take from incu-shaker:

IRRE+PC+RBS ( pSB1C3) -> 4x 200ul glycerols -> glycerol box -20C mmp

RFP+PSB1C3 -> 4x 200ul glycerols/a> ->glycerol box -20C mmp

Minipreped all 4 falcons and a gel was run -> no bands were seen indicating no DNA present.

Item (ul) IrreAcut IrreAuc IrreBcut IrreBuc RFPcut RFPuc Uncut Uncut
pSB1C3 5 5 5 5 5 5 5 5
EcoR1 1 0 1 0 1 0 1 0
Pst1 1 0 1 0 1 0 1 0
Buffer 3 1 0 1 0 1 0 1 0
BSA 0.5 0 0.5 0 0.5 0 0.5 0
dH20 1.5 5 1.5 5 1.5 5 1.5 5
Total 10 10 10 10 10 10 10 10

21st August - Nanodrop of pDNA

Sample Concentration (ng/ul) 260/280
Irre A pDNA -33.0 1.74
Irre b pDNA 123.0 0.94
GFP pDNA -52.1 1.63
LB pDNA -28.4 1.34

10x cmp plates were made using Yanika's chloramphenicol

Meeting with Darren:

The following Biobricks ordered were brought by our supervisor to be streaked onto the relevant antibiotic plates and inoculated in antibiotic+2mL LB -> Incubate o/n @ 37C.

Biobrick Plate (+ND) Inoculation (+ 2mL LB)
J63008 1X AMP, 1X CMP 2 mL AMP + 2 mL CMP
K105028 1X AMP 2 mL AMP
I712004 1X AMP, 1X CMP 2 mL AMP + 2 mL CMP
K105030 1X AMP 2 mL AMP
J63008/9 1X AMP 2 mL AMP
K105027 1X AMP 2 mL AMP
K812014 1X AMP, 1X CMP 2 mL AMP + 2 mL CMP

A PCR of Zeocin was performed and a gel was subsequently ran. PCR tube:

1 - PCR zec bb F, R, 2ul template

2 - PCR zec bb F, R, 1ul template

3 - PCR zec F, R, 2ul template

4 - PCR zec F, R, 1ul template

5 - PCR negative control zec bb F, R,

6 - PCR negative control zec F, R

PCR was unsuccessful

22nd August -

Results from Biobrick streaking and inoculation:

Biobrick Positive Control (ND) Cmp plate Amp plate Falcon
J63008 Growth Growth No Growth No Growth
K105028 Growth Growth Growth
K105027 Growth Growth Growth
K105030 Growth Growth Growth
K812014 Growth Growth Growth
J63008/9 Growth Growth Growth
I712004 No Growth No Growth No Growth No Growth

Glycerol stocks were therefore made from the plates that displayed colony growth.

A second attempt at zeocin PCR was performed using Phusion DNA Polymerase

1 - Zec bb F, R 2ul

2 - Zec bb F, R 1ul

3 - Zec F, R 2ul

4 - Zec F, R 1ul

5 - Negative control zec bb F, R

6 - Negative control zec F, R

A gel was run with 8ul of each of the 6 reactions. PCR was successful.

Restriction digest of the following samples:

A - K105028

B - K105027

C - K105030

D - K812014

E - J63009/8

Double Digest Uncut
Sample 5 5
EcoR1 1 0
Pst1 1 0
Buffer 3 1 0
BSA 0.5 0
dH2O 1.5 5
Total 10 10
Nanodrop of samples:

Sample 260/280 ng/ul
K105028 2.12 39.0
K105027 1.99 47.1
K105030 2.07 48.8
K812014 1.96 113.3
J63008/9 1.95 59.7

PCR Purification

1 - zeo bb F, R 2ul template

2 - zeo bb F, R 1ul template

^ stored in iGEM 2013 box

Preparative digest of K812014 (pSB1C3)

Sample 5ug
E 7
P 7
B3 10
BSA 2
dH2O 30
Total 100

5ug sample = 44ul of 113.3 ng/ul

CMV PCR

Primers used: 2s + 6FW, 2s + bbRE

23rd August -

Gel was ran with (lane):

(3) PCR purified zeo bb FR + 2ul template

(4) PCR purified zeo bb FR + 1ul template

(6) bwf + bb RE + 1ul template

(7) bwf + bb RE + 2ul template

(8) bwf + bb RE

Samples in lanes 3 & 4 failed, therefore a nanodrop was recorded:

Sample 260/280 ng/ul
PCR purified zeo bb FR + 2ul template 1.66 55.6
PCR purified zeo bb FR + 1ul template 1.82 17.2

Mammalian Lab

19th August - Viable cell count data for HeLa growth curve, Day 1 : 0.1 x 10^-6 viable cells per mL

Disc 1 Disc 2

Disc 1 Disc 2
Concentration of zeocin (µg/ml) Confluency (%) Cell Appearance Floaters Confluency (%) Cell Appearance Floaters
0 100 Over confluent Moderate 100 Over confluent moderate
50 50 Moderate swelling and death Many 80 Moderate swelling and death Many
100 20 severe swelling, death Many 20 severe swelling, death many
250 0 - many 0 - many
500 0 - many 0 - many
1000 0 - many 0 - many

Split stock HeLa cells

20th August - Viable cell count data for HeLa growth curve, Day 1 : [0.17, 0.068 (anomaly), 0.23] x 10^-6 viable cells per ml

Disc 1 Disc 2

Disc 1 Disc 2
Concentration of zeocin (µg/ml) Confluency (%) Cell Appearance Floaters Confluency (%) Cell Appearance Floaters
0 100 Over confluent and death Moderate 90 Over confluent moderate
50 80 Over confluent, swelling and death Many 20 Moderate swelling and death Many
100 20 severe swelling and death Many 0 severe swelling, death many
250 0 - many 0 - many
500 0 - many 0 - many
1000 0 - many 0 - many

21st August - Viable cell count data for HeLa growth curve, Day 1 : [0.496, 0.244 (anomaly), 0.356] x 10^-6 viable cells per ml

22nd August - Viable cell count data for HeLa growth curve, Day 1 : [0.79, 1.12, 1.19] x 10^-6 viable cells per ml

Week 13

Bacterial Lab

27th August -

Purify zeocin CMV from zeo FB primers

Zeocin and CMV purification

Tube:

1 - CMV 1ul template bb F, R

2 - CMV 2ul template bb F, R

3 - Zeocin 2ul template zecF, R

4 - Zeocin 1ul template zecF, R

5 - Zeocin 2ul template zecbbF, R

6 - Zeocin 1ul template zecbbF, R

28th August - 3x glycerol stocks of K812014 were prepared from inoculum. 1.5mL of culture was used for miniprep.

Nanodrop of Zec and CMV was recorded:

260/280 ng/ul
ZEC 1.68 21.1
CMV 1.96 82.1

A gel was run on 100ul of prep digest K812014 + 20ul dye. 2000bp was scooped in gel extraction.

Chloramphenicol was tested at x2 and x4 concentration with 50ul cells spread on each plate, results from the next day still showed significant colony growth (100+).

29th August - Nanodrop of pSB1C3 purified from gel extract, 260/280: -25/21, ng/ul: 13.5

5ul was run on a gel, however extract of pSB1C3 was unsuccessful as no bands were visible.

PCR:

3 PCR reactions of zeocin using zec BB F, R primers were performed. First reaction: 1 ul pSecTag2A template, second 2 ul pSecTag2A and third reaction - negative control - no template.

3 PCR reactions for cmv promoter were prepared using the same variation of template volume as above. These were tested the next day and were successful. Gel photo (30/08).

Prep digest+gel+extract+purify+nanodrop+5ul gel of zeocin and CMV were carried out

Prep digest:

Sample (ul) Zeo CMV Cyc100 Cyc100 Cyc70 Cyc70 Cyc28 Cyc28
V. Sample 48 45 17.5 17.5 23 23 23.5 23.5
B3 10 10 5 5 5 5 5 5
E 7 7 5 5 5
P 7 7 5 5 5 5 5 5
X 5 5
BSA 2 2 1 1 1 1 1 1
H2O 26 29 16.5 16.5 11 11 10.5 10.5
Total 100 100 50 50 50 50 50 50

Glycerol stocks (x15) of J63009, K105027, K105028 and K105030 were made.

Additionally, nanodrops were recorded:

Sample 260/280 Absorbance ng/ul
J63009 2.10 0.774 88.7
K105030 209.00 0.653 60
K105028 2.14 0.408 50
K105029 2.18 0.585 77.0
K218014 2.12 0.946 104.9

A prep digest was conducted on K812014 to extract pSB1C3.

Chloramphenicol was tested again but this time with x8 cmp (80ul cmp to 10mL LB agar). Overgrad, undergrad and Yanika chloramphenicol stocks were used and 50ul competent cells were spread -> incubate o/n @37C.

Zec and CMV nanodrops were recorded:

Sample 260/280 Absorbance ng/ul
ZEC 1.87 9.538 2.5
CMV 2.06 11.048 25.4

30th August

Chloramphenicol test - plate colony growth observation and count: all 3 plates prepared using the chloramphenicol from postgrads, us and Yanika had 30+ very small colonies.

After overnight incubation, from each of the the 10 ml inoculations of K812014 (I), pSecTag2A and second (different) sample of K812014 (II), 2.5 ml were minipreped while the rest of 7.5 ml from each was used to make glycerol stocks.

Nanodrop of these minipreps:

Sample ng/ul 260/280 260/230 Absorbance
K812014 (I) 117.8 2.10 2.49 0.944
pSecTag2A 35.9 1.81 1.44 0.496
K812014 (II) 10.7 1.71 2.55 0.084

Prep digest of K812014 (I) - miniprep sample prepared by Andy. Contents of reaction:

Sample K812014 (I) 30 ul
EcoRI (E) 5 ul
PstI (P) 5 ul
BSA 1 ul
Buffer 3 5 ul
Total 4 ul
Total Volume of Reaction 50 ul

A gel was run with the E, P cut K812014 (Gel photo?) and the corresponding band of liniarised pSB1C3 (backbone of K812014) was extracted for purification.

Nanodrop of the purified pSB1C3 DNA showed a concentration of 8.4 ng/ul (260/290 = 2.91; 260/230 = 0.02, Absorbance = 7.379) while the nanodrop of the pSB1C3 DNA offered by the postgrads showed 13.01 ng/ul (260/280=1.34).

PCR:

8 new reactions were prepared for zeocin - same primers bb F,R as used previously.

A checking (analytical) gel was performed revealing no bands for reaction tubes 6 and 7 (each of these with 1 ul template)- PCR unsuccessful.

These amplified zeocin together with the 2 reaction tubes of amplified zeocin f aacmv from a day before and a were loaded onto the gel and the bands corresponding to 2 kb were extracted for purification.

31 August -

Gel extraction purification of zeocin and cmv. We are expecting that through this procedure the Phusion polymerase, DMSO, buffer, template DNA will be washed away, thus achieving purification of zeocin and cmv DNA (which are to be digested hence, prepared for ligation in the pSB1C3 backbone).

PCR:

Zeocin was amplified again, in 9 tubes (same reaction) -> a total volume of 50 ul x 9 = 450 ul.

Prep digest of zeocin and cmv straight after PCR.

Components Prep digest Cmv Prep digest Zeocin
DNA sample 60 ul 60 ul
EcoRI 7 ul 7 ul
PstI 7 ul 7 ul
Buffer 3 10 ul 10 ul
BSA 2 ul 2 ul
Water 14 ul 14 ul
Total 100 ul 100 ul

These digests were used for LIGATION 1

LIGATION 1: using

pSB1C3 digested and purified 10 ng/ul
Zeocin digested and purified 55 ng/ul
Cmv digested and purified 20 ng/ul

Ligation of zeocin to pSB1C3:

Zeocin (55 ng/ul) 3 to 1 6 to 1
Water (ul) 2.1 0
Quick ligase buffer (ul) 10 10
Backbone (ul) 5 5
Insert (ul) 2.7 5.5
Ligase (ul) 1 ul 1 ul
Total (ul) 21 21.5

Ligation of cmv to pSB1C3:

(20 ng/ul) 3 to 1 6 to 1
Water (ul) 2.4 0
Quick ligase buffer (ul) 10 10
Backbone (ul) 5 5
Insert (ul) 2.6 5.3
Ligase (ul) 1 ul 1 ul
Total (ul) 21 21.3

Controls used:

Controls 1 check no circular backbone 2 check no digestion process 3 control (uncut backbone)
Water (ul) 5 6 9
Quick ligase buffer (ul) 10 10 10
Backbone (ul) 5 5 2 of uncut backbone
Insert (ul) 0 0 0
Ligase (ul) 1 0 0
Total (ul) 21 21 21

5 ul of each of each ligation reaction were used to transform our home-made competent cells (4 vials - all ligations apart from the 3 controls) as well as Yanika’s top 10 cells (7 vials - all ligations).

T10 - Top 10 cells

HM - home made competent cells

T10 T10 T10 T10 T10 T10 T10 HM HM HM HM
Cell vial no. 1 2 3 4 5 6 7 28 45 51 52
Vol. ligation plated (ul) 90 & 10 90 & 10 100 100 100 90 & 10 90 & 10 100 90 & 10 100 100
Ligation containing zeo 3:1 zeo 6:1 control 1 control 2 control 3 zeo 3:1 zeo 6:1 zeo 3:1 zeo 6:1 zeo 3:1 zeo 6:1
Cell counts 0 0 0 0 0 0 0 15 0 & 10* 15 15

* 0 colonies in plate with 10 ul inoculum spread and 10 colonies for the 90 ul inoculum spread.

After the transformation protocol we spread the transformed cells on 4x cmp (?) agar plates using both 90 ul and 10 ul cell inoculum in the case of cell vials 1,2,6,7 (Yanika’s) and 45 (ours).

We picked 5 colonies from each plated cell vials 28, 45, 51 and 52 (2 ml and 2 ul cmp) and incubated for 10 hours. These inoculations were then used to make glycerol stocks and minipreps.

Gel extraction purification

The 9 tubes of amplified zeocin performed were loaded on a gel and the 2 kb bands were subsequently extracted (6.2 g of gel). This zeocin DNA was purified using gel extraction purification kit and 3 tubes of each 60 ul purified zeocin resulted (labelling zeo g.e.p.).

Miniprep of K812014 cell-containing-biobrick: in order to make stocks of pSB1C3, the backbone into which this biobrick is inserted.

Nanodrop of purified zeocin (from above):

Zeo g.e.p. tube ng/ul 260/280
1 36.1 1.95
2 38.9 1.90
3 42.9 1.90

Nanodrop of miniprep of K812014: 197 ng/ul (260/280 = 1.94) Mammalian Lab

31 August - HeLa cells confluency: 100% and 40%. Split 100% confluency dish in 1:4, 40% confluency dish in 1:2

September

Week 14

Bacterial Lab

1st September

The 20 inoculations were retrieved from the incu-shaker. All falcons showed growth apart from one inoculation from cell vial 28 (ligation 3:1 zeo).

1.5 ml of each tube was used for miniprep while the other 0.5 ml was used to make glycerol stocks.

Prep digest of K812014 (miniprep prepared on the 31 of August)

Component Volume added (ul)
K812014 DNA 25
EcoRI 5
PstI 5
Buffer 3 5
BSA 1
dH2O 9
Total 50
Nanodrop result of the miniprep of transformations:

Cell vial/colony no. ng/ul 260/280
28/1 84.2 1.65
28/2 58.5 1.77
28/3 49.6 1.83
28/4 14.6 1.97
45/1 130.9 1.72
45/2 18.7 2.34
45/3 49.6 1.73
45/4 111.3 1.64
45/5 23.9 1.96
51/1 69.5 1.70
51/2 60.9 1.78
51/3 41.2 1.85
51/4 50.9 1.79
51/5 23.9 1.96
52/1 40.4 1.83
52/2 40.2 1.87
52/3 78.1 1.94
52/4 127.2 1.62
52/5 16.5 2.11
Analytical digest of the above minipreps - incubated at 37 degrees C for 1 hour

Volume (ul) Single Digest (PstI) Double Digest (EcoRI + PstI)
Miniprep 5 5
EcoRI 0 1
PstI 1 1
Buffer 3 1 1
BSA 0.5 0.5
dH2O 2.5 1.5
Total 10 10

These digests were loaded into a gel in the following order: single digest, double digest, uncut. The result of this gel was negative, there were no bands for the loaded DNAs (the 1 kb DNA ladder was on the gel), the procedures of achieving recombinant zeocin and cmv plasmid were unsuccessful.

We suspect that the water was contaminated with nuclease.

2nd September

Bacterial Lab

We re-autoclaved water due to our suspicion it was nuclease contaminated.

New inoculations (in 3 ml LB) of the transformations were prepared: 5 using cmv ligation and 5 using the zeocin ligation. These were left over night into the incushaker.

The falcons were removed from the incu-shaker. Glycerol stocks were prepared using 0.5 ml while the rest was kept for minipreping.

Preparative digest of zeocin and K812014 plasmid

Components (ul) Prep digest of Zeocin Prep digest of K812014
Zeo/K812014 80+ 20+
EcoRI 10 5
PstI 10 5
Buffer 3 15 5
BSA 3 1
dH2O 22 14
Total 150 50

These were incubated for 1 hour at 37º C and for 20 min heat inactivated.

Nanodrop of the minipreps from the new inoculations

pDNA new ng/ul 260/280
51/1 9.5 2.2
51/2 9.9 1.91
51/3 8.9 1.93
51/4 8.6 2.31
51/5 13.2 2.49
45/1 8.2 1.89
45/2 8.7 2.65
45/3 10.7 2.13
45/4 9.1 2.00
45/5 9.7 2.34
28 glycerol stock 40.4 2.23
45 glycerol stock 36.7 2.24
51 glycerol stock 45.4 2.18
52 glycerol stock 28.4 1.98

These samples of minipreps and from glycerol stocks were run on a gel in order to check if the circularised potentially recombinant plasmid is present. Again, there were no bands for any of these samples, hence we tend to believe the ligations were not successful OR/AND the transformation was faulty.

Gel extraction of digested E and P - K812014 biobrick plasmid: After gel extraction purification of the corresponding 2 kb band, the concentration showed up to around 6.6 ng/ul and 260/280 = 1.73. Given the very small concentration, a second attempt of obtaining pure pSB1C3 was performed, not successful though, only 4.9 ng/ul concentration.

Gel extraction of PCR purified zeocin, 2 kb band. This was purified and the nanodrop showed a concentation of 77.6 ng/ul and 260/280 = 1.82.

Nanodrop of E, P digested cmv (from 30 of August) gave a concentration of 25.1 ng/ul, 260/280 = 1.86.

New inoculations of K812014 biobrick were prepared and left for incubation over night in the incu-shaker (37 degrees Celsius, at 200 rpm). 4th September Miniprep of the K812014 biobrick inoculations showed the following concentrations:

Mammalian lab

2nd September - All 6 dishes have 100% confluency. Split 3 dishes 3:1 obtaining a total of 9 dishes. Discarded 3 dishes.

pDNA new ng/ul 260/280
1 151 1.93
2 80.8 1.93
3 111.5 1.82
4 219.1 1.94
Samples 1 and 2 went through a preparative digest.

Component Volume added (ul)
pDNA 50
EcoRI 7
PstI 7
Buffer 3 10
BSA 2
dH2O 24
Total 100

Ligation 2:

pSB1C3 digested and purified, concentration = 25 ng/ul

Zeo digested and purified conc = 77 ng/ul

CMV digested and purified conc = 25 ng/ul

CMV (25 ng/ul) 1 c (3:1 molar ratio) 2 c (2:1 molar ratio) 3 c (1:1 molar ratio) 4 c (3:1 molar ratio)
Water (ul) 1.8 3.2 8 6
Quick ligase buffer (ul) 10 10 10 10
Backbone (ul) 4 4 1 1
*Insert (ul) 4.2 2.8 1 3
Ligase (ul) 1 1 1 1
Total 21 21 21 21
water (ul) 1.8 3.2 8 6
Colony count 50 100+ 100+ 150+

Zeocin (77 ng/ul) 5 z (3:1 molar ratio) 6 z (2:1 molar ratio) 7 z (1:1 molar ratio) 8 z (3:1 molar ratio)
Water (ul) 2.1 3.3 8 8
Quick ligase buffer (ul) 10 10 10 10
Backbone (ul) 4 4 1 1
*Insert (ul) 3.9 from * 2.6 from * 1 from * 1
Ligase (ul) 1 1 1 1
Total 21 21 21 21
water (ul) 1.8 3.2 8 6
Colony count 30 0 1 0+
* we prepared a tube of concentration 25 ng/ul