Team:University College London/LabBook/Week14

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== Monday 10.09.12 ==

'''Aim:''' Day 2 of Generating competent cells. The aim is to incubate cells in the presence of CaCl<sub>2</sub> to prepare the cell wall, allowing it to become permeable to DNA for transformation. 


'''Method:''' 


<html><div class="protocol protocol-Generic">Day 2 of making competent cells </div><div class="protocolContent"></html>{{:Team:University_College_London/Protocols/Competency2}}<html></div></html>


== Tuesday 11.09.12 == 
'''Aim: ''' Day 3 of  Generating competent cells


'''Method:'''  

<html><div class="protocol protocol-Generic">Day 3 of making competent cells</div><div class="protocolContent"></html>{{:Team:University_College_London/Protocols/Competency3 }}<html></div></html>

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==Wednesday 12.09.12==


'''Aim:'''  To carry out a transformation using the 3A ligation products in order to be able to analyse whether ligation was successful. 


'''Method:''' 


<html><div class="protocol protocol-Generic">Transformation</div><div class="protocolContent"></html>{{:Team:University_College_London/Protocols/Transformation1}}<html></div></html>

== Thursday 13.09.12 ==


'''Aim:'''


Picking of colonies from the ligation transformation plates


'''Methods:''' https://2012.igem.org/Team:University_College_London/Protocols/ColonyDNAExtraction#DNA_Extraction_from_Colonies


== Friday 14.09.12 ==


'''Aim:''' 


To check whether the 3A assembly ligation has been successful by purifying the overnight culture from the previous day, carrying out an analytical digest and analysing results on a gel. 


'''Methods:''' 


A mini-prep was carried out as per the following protocol:


https://2012.igem.org/Team:University_College_London/Protocols/Miniprep2 


This was followed by a 10ul analytical digest as per the following: 


https://2012.igem.org/Team:University_College_London/Protocols/EnzDig2 


Finally, results of the figest were run on a gel as follows:


https://2012.igem.org/Team:University_College_London/Protocols/Electrophoresis 


'''Results:''' 


The following digram shows results of the analytical digest, with each purified DNA being cut once and twice in order to confirm identity:

{| class ="bigtable"
|-
! BioBricks	!! BioBrick Size (bp) !! Ligation size (bp)  !! Plasmid Backbone !! Plasmid Expected Size (bp) !! Combined Size 
|-
|BBa_K729001 & BBA_J23100 || 933 & 35 || 968 ||	pSB1C3 || 2070 || 3038 
|-
|BBa_K729001 & BBa_J23119 & BBa_B0034 || 933 & 35 & 12 || 980 || pSB1C3 || 2070 || 3050 
|-
|BBa_K729002 & BBa_J23119 & BBa_B0034 || 484 & 35 & 12 || 531 || pSB1C3 || 2070 ||2601 
|}



'''Conclusion:''' 


The bands on the gel indicate are not as expected. Hence, it is concluded that the ligation was unsuccessful.





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==Tuesday 11.09.12==


'''Step 1 - Aim:'''


To generate enough plasmid backbone (pSB1C3) to be used in a 3A ligation. This is followed by a PCR clean-up.


'''Methods:''' 


https://2012.igem.org/Team:University_College_London/LabBook/Protocols/PCR#Transformation_Protocol_2


'''Step 2 - Aim:'''


To check whether PCR is successful. After the PCR reaction, we can detect the presence of the correct products by running a 1% gel electrophoresis.


'''Methods:'''


https://2012.igem.org/Team:University_College_London/Protocols/Electrophoresis 


'''Results:'''


The following gel results indicate whether PCR was successful. 
 

[[File:UCL2012Week14B.png]]


'''Conclusion:'''

Since band sizes were as expected, the PCR was considered to be successful. Hence, the backbone was purified and used in the 3A ligation. 


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== Thursday 13.09.12 ==

'''Aim:'''

To generate enough linker (BBa_J23119 + BBa_B0034) to be used in a 3A ligation.  This is followed by a PCR clean-up.


'''Methods:'''  https://2012.igem.org/Team:University_College_London/LabBook/Protocols/PCR#Transformation_Protocol_2


'''Step 2 - Aim:''' 

To check whether PCR is successful. After the PCR reaction, we can detect the presence of the correct products by running a 1% gel electrophoresis.


'''Methods:'''


https://2012.igem.org/Team:University_College_London/Protocols/Electrophoresis 


'''Results:'''


The following gel results indicate whether PCR was successful. 


[[File:UCL2012Week14A.png]]

 

'''Conclusion:'''


Since we obtained the expected bands in the gel, the PCR was considered successful and the purified DNA used in the 3A ligation. 



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==Friday 14.09.13==


'''Aim:''' To characterise nuclease activity BL21 cells


'''Method:'''
To add protocol


'''Results:''' 


The following table shows readings of the diameters and OD at different time points:


{| class ="bigtable"
|-
! Date	!! Time !! Colony diameter/mm !! Halo diameter/mm !! Absorbance at 600 OD
|-
|Friday || 12.30 ||	0	|| 0	|| 0
|-
|Friday || 16.30 ||	0	||0	||0
|-
|Friday || 19.30 ||	0	||0	||0
|-
|Friday ||22.30	||0	||0	||0
|-
|Saturday ||01.30	||0.5	||1.5	||0.068
|-
|Saturday ||04.30	||1	||2	||0.098
|-
|Saturday ||07.30	||1.5	||3	||0.159
|-
|Saturday ||10.30	||1.5	||3.5	||0.192
|-
|Saturday ||12.30pm	||2	||4	||0.203
|-
|Saturday ||14.30	||2	||4	||0.209
|-
|Saturday || 16.30	||2.5	||5	||0.215
|}
		
	
The average depth of the colonies was noted to be  0.5 - 1mm


'''Conclusion:''' 


It can be seen that nuclease works as expected in BL21 cells. However, nuclease activity is less efficient when compared to nuclease activity in WNu cells. This is in line with expectations, since nuclease is found naturally in WNu cells but not in BL21 cells.



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