Revision as of 23:45, 19 October 2016

IGEM-IIT Kharagpur- Notebook

NOTEBOOK

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WEEK ONE - ( 20th July - 22th July )

20th july, Wednesday

DH5 alpha competent cells were prepared for transformation experiments.

21st July, Thursday

Transformation of the prepared competent cells was carried out. The plasmids used for transformation were YFP (BBa_K592101), HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013)

22nd July, Friday

Replication plating for above transformed parts was done. This including the three sets of transformed cells containing the plasmids YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013).

WEEK TWO - ( 25th July - 30th July )

25th july, Monday

1 litre of LB media was prepared and duly autoclaved. 5 plates each of the antibiotics chloramphenicol, ampicillin and ampicillin+Kanamycin were prepared.

26th July, Tuesday

20ml Cultures were prepared for the plasmid extraction of each of YFP (BBa_K592101), the HIV cleavage site (BBa_I712015) and the protease construct (BBa_K743013).

27th July, Wednesday

Plasmid extraction was done for YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013) using mini-prep plasmid DNA extraction kit.

28th July, Thursday

DNA quantification was done using Nano Drop. YFP: 250 ng/ul
Protease: 170 ng/ul
Cleavage Site: 120 ng/ul
1% agarose gel was prepared for screening of the plasmids extracted by the mini prep kit.
The FRET construct was kept for overnight digestion at the restriction sites E and P.
Digestions with E and P for YFP, Protease and Cleavage Site

	YFP	Protease	Cleavage Site
Component	Volume(ul)	Volume(ul)	Volume(ul)
DNA	2	3	3.5
2.1 Buffer	2	2	2
ECoRI	0.5	0.5	0.5
Psti	0.5	0.5	-
Nf H2O	15	14	14

WEEK THREE - ( 1st August - 7th August )

1st August, Monday

3ml cultures made for the preparation of competent cells of DH5 alpha cells. 20ml culture prepared for the construct BBa_K844004. (MaSP without ATG)

2nd August, Tuesday

11 vials of DH5 alpha competent cells were prepared. Plasmid extraction done for the construct BBa_K844004 (MaSP without ATG).

3rd August, Wednesday

As a part of the iGEM 2016 interlab study, transformations were done for the following:
Test device1
Test device2
Test device3
Positive control
Negative control
Also, transformed cells were prepared with the part BBa_K844008 (MaSP with ATG)

4th August, Thursday

Colonies were seen for all six of the transformed plates. The transformation procedure was hence successful.

7th August, Sunday

20ml Culture was prepared for the screening of BBa_K844008 (MaSP with ATG). Also, 20ml cultures were prepared for each of test device 1, test device 2, and test device 3 for the interlab study.

WEEK FOUR - ( 8th August - 12th August )

8th August, Monday

PPlasmid extraction performed for the screening of the parts BBa_K844008 (MaSP with ATG); and test device 1, test device 2, test device 3 for the interlab study.

9th August, Tuesday

Gel Electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 for screening. The run was not successful due to gel over flow.

10th August, Wednesday

20ml Culture was prepared for screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.

11th August, Thursday

Plasmid extraction for the screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 was done.

12th August, Friday

Gel electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.

WEEK FIVE - ( 15th August - 18th August )

16th August, Tuesday

Plasmid extraction of BBa_K844008 (MaSP with ATG), test device 1, test device 2, and test device 3 was done with mini-prep kit. Digestion of above obtained plasmids with E And P was carried out.

17th August, Wednesday

1% agarose gel was prepared for digested plasmids PCR of protease construct for HIV site primers was done PCR parameters:
{95 degree 2 minutes
[95 degree 30 seconds
60 degrees 30 sec
68 degree 2 min] X35 cycles
68 degree 10 min}
PCR products run in 1% agarose gel.
Amplification not upto expectation.
Repetition of the experiment, with different conditions suggested.
Note: Too many non specific products were observed that is why the same was repeated next week.

18th August, Thursday

PCR of protease construct for HIV site primers was done.
PCR products were run in 1% agarose gel.
PCR Parameters:
{95 degree 2 minutes
[95 degree 20 seconds
62 degrees 30 sec
68 degree 2 min 15 sec] X35 cycles
68 degree 10 min}
Amplification not upto expectation.
Repetition of the experiment, with different conditions suggested.

WEEK SIX - ( 22nd August - 26th August )

22th August, Monday

PCR for both fret and silk constructs at two conditions was done.

Condition 1
{95 degree 5 minutes
Taq DNA polymerase is added.
[95 degree 30 seconds
57.5 degrees 40 sec
68 degree 40 sec] X35 cycles
68 degree 10 min}
Condition 2
{95 degree 2 minutes
[95 degree 30 seconds
58 degrees 1 min
68 degree 2 min] X35 cycles
68 degree 10 min}

23rd August, Tuesday

PCR for FRET construct was done. PCR Parameters:
{95 degree 2 minutes
[95 degree 30 seconds
57 degrees 40 sec
68 degree 2 min] X35 cycles
68 degree 10 min}

24th August, Wednesday

Gel run for FRET construct was performed.

25th August, Thursday

PCR for silk construct was done with the following parameters:
{95 degree 2 minutes
[95 degree 30 seconds
57 degrees 40 sec
68 degree 2 min] X35 cycles
68 degree 10 min}

26th August, Friday

PCR for FRET construct was done.
PCR Parameters:
{95 degree 2 minutes
[95 degree 30 seconds
58 degrees 1 min
68 degree 2 min] X35 cycles
68 degree 10 min}

WEEK SEVEN - ( 29th August - 2nd September )

29th August, Monday

Nano drop analysis for pSB1K3( Kanamycin backbone) was done. Result:Obtained concentration was 192.6mg/ul.

31st August, Wednesday

Digestion for Kanamycin backbone and FRET PCR with E And P

	K backbone	FRET PCR
Component	Volume(ul)	Volume(ul)
DNA	6	2.3
2.1 Buffer	2	2
ECoRI	1	1
Psti	1	1
Nf H2O	10	13.7

1st September, Thursday

Ligation for Kanamycin backbone and FRET PCR with E and P was done Vector:Insert=1:3

2nd September, Friday

Transformation for Kanamycin backbone and FRET PCR with E and P failed.
Note: Reason was determined to be inadequate amount of the PCR product

WEEK EIGHT - ( 8th September - 10th September )

8th September, Thursday

2 ml culture of CFP and YFP was prepared.
PCR done for FRET construct and silk construct
Digestion with E and P of FRET PCR product was done.

	FRET PCR
Component	Volume(ul)
DNA	19
2.1 Buffer	2.5
ECoRI	1
PstI	1
NF H2O	1.5

9th September, Friday

PCR purification of digested FRET PCR product was done. Plasmid isolation of YFP and CFP was performed.
YFP: 250 ng/ul
CFP: 218 ng/ul
Glycerol stock for CFP and YFP was prepared.
Restriction digestion(overnight) of YFP and cleavage site was done.

	YFP
Component	Volume(ul)
DNA	5
ECoR buffer	2
ECoRI	1
NF H2O	12

	Cleavage Site
Component	Volume(ul)
DNA	10
3.1 Buffer	2
ECoRI	1
Xbal	1
NF H2O	6

10th September, Saturday

PCR purification of YFP digested with E was done. Digestion of purified YFP was done with S for 4 hrs at 37 degrees.

	YFP
Component	Volume(ul)
DNA	20
Cutsmart Buffer	2.5
Spel	1
NF H2O	1.5

WEEK NINE - ( 12th September - 13th September )

12th September, Monday

22 ml cultures of CFP, YFP, HIV site, MASP with ATG and MASP without ATG was prepared.

13th September, Tuesday

Glycerol stock and plasmid extraction of CFP, YFP, HIV site, MASP with ATG and MASP without ATG was performed.
CFP:437.5 ng/ul
YFP: 286.7 ng/ul
HIV Cleavage Site: 357.1 ng/ul
MaSP with ATG: 268.2 ng/ul
MaSP w/o ATG: 123ng/ul

WEEK TEN - ( 19th September - 24th September )

19th September, Monday

PCR for FRET (2 sets) Digestion with E and X for HIV site and E for CFP was successfully done.

	CFP
Component	Volume(ul)
DNA	20
ECoR buffer	2
ECoRI	1
NF H2O	14.7

	Cleavage Site
Component	Volume(ul)
DNA	2.8
3.1 Buffer	2
ECoRI	1
Xbal	1
NF H2O	13.2

20th September, Tuesday

PCR purification of CFP digested with E was done. Digestion with S of purified product was done for 6 hours at 37 degrees.

	CFP
Component	Volume(ul)
DNA	20
Cutsmart Buffer	2.5
Spel	1
NF H2O	1.5

Gel extraction of digested CFP and HIV site was successfully performed. The gel pieces stored at 4 degrees

21st September, Wednesday

Gel extraction of stored gel pieces Amount of extracted DNA too low to proceed to ligation step

22nd September, Thursday

S digestion of CFP and X digestion of HIV

23rd September, Friday

PCR purification of above digested followed by E digestion of both for 6 hrs at 37 degrees Gel extraction after completion of digestion followed by ligation of E and X digested HIV site and E and S digested CFP at 16 degrees overnight

24th September, Saturday

Transformed DH5 alpha cells with ligation mix and plating on A+K plates

WEEK ELEVEN - ( 25th September - 2nd October )

25th September, Sunday

Colonies observed on incubated plates

26th September, Mondayy

18 colonies from the 1:3 plate were put into 1 ml media overnight for screening
14 colonies from the 1:5 plate were put into 1 ml media overnight for screening
Digestion of YFP with X and P
Digestion of HIV site with S and P

27th September, Tuesday

PCR for FRET (2 sets)
Gel extraction for PCR products and digestion with P
Digestion of K backbone with P
Screening for 18 colonies from the 1:3 plate and 14 colonies from the 1:5 plate
Colonies 1, 4, 7, 10 from 1:3 plate showed a shift
Colonies 1, 5, 11 from 1:5 plate showed a shift
Ligation of YFP digested with X and P with HIV site digested with S and P

28th September, Wednesday

PCR purification of P digested K backbone and FRET PCR followed by E digestion Gel Extraction of the digested products followed by ligation Colonies observed of ligated YFP and HIV site observed

29th September, Thursday

25 colonies from the ligated YFP and HIV site plate picked for screening X and P digestion for CFP+ HIV

30th September, Friday

Screening of YFP + HIV
Gel run X and P digested CFP + HIV
20 ml cultures for plasmid extraction of K-backbone, CFP+HIV and HIV Site, YFP+HIV (colony 7) and YFP+HIV (colony 13)

1st October, Saturday

Plasmid extractions for the above cultures
Digestion with X and P for YFP+HIV (colony 7) and CFP+HIV
Gel run for the digested YFP+HIV (colony 7) and CFP+HIV
Digestion with X of YFP+HIV
Digestion with S of CFP

2nd October, Sunday

PCR purification of the digested products
Digestion with E of S digested CFP and X digested YFP+HIV
Gel extraction of the digested product
Ligation of E and S digested CFP and E and X digested YFP+HIV

WEEK TWELVE - ( 3rd October - 9th October )

3rd October, Monday

Transformation of the Ligated product onto A+K plates.

4th October, Tuesday

Growth was observed on both the plates.
1 ml culture was given for 14 colonies of each of the plates, for the purpose of screening.

5th October, Wednesday

1% Agarose gel was run for the plasmids extracted from the overnight cultures.
Sufficient number show the desired shift.
20 ml culture was given for miniprep extraction of CFP+HIV+YFP form colony 10 and 15 of the 1:3 ligation plate

5th October, Thursday

PCR was run (2 sets)
The PCR product was run on 1% agarose gel for extraction.
Amount too low to continue.
Miniprep for CFP+HIV+YFP
Colony 10: 187.5 ng/ul
Colony 15: 185 ng/ul
Digestion with X and P for the isolated plasmid (overnight)

	CFP+HIV+YFP
Components	Volume(µl)
DNA	6
3.1 Buffer	2
Xbal	1
Pstl	1
NF H2O	10

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 					Digestion with X and P for the isolated plasmid (overnight)<br>
 					<table>
-						<tr><th></th></tr>
+						<tr><th></th><th>CFP+HIV+YFP</th></tr>
+						<tr><td>Components</td><td>Volume(&micro;l)</td></tr>
+						<tr><td>DNA</td><td>6</td></tr>
+						<tr><td>3.1 Buffer</td><td>2</td></tr>
+						<tr><td>Xbal</td><td>1</td></tr>
+						<tr><td>Pstl</td><td>1</td></tr>
+						<tr><td>NF H2O</td><td>10</td></tr>
 					</table>

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