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| | |{{#calendar: title=Imperial_College |year=2008 | month=08}} | | |{{#calendar: title=Imperial_College |year=2008 | month=08}} |
| | |{{#calendar: title=Imperial_College |year=2008 | month=09}} | | |{{#calendar: title=Imperial_College |year=2008 | month=09}} |
| - | | rowspan="2" bgcolor=#fff width="100%" | | + | | rowspan="2" bgcolor=#ffffff width="100%" | |
| | |} | | |} |
| | = 21 August 2008 = | | = 21 August 2008 = |
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| | * Continued work on modelling the growth curve of bacteria using ODEs | | * Continued work on modelling the growth curve of bacteria using ODEs |
| | | | |
| - | == Wet Lab== | + | == Wet Lab== |
| - | * Some parts of the registry ( notably GFP terminator) were double digested | + | |
| | + | ===Cloning=== |
| | + | |
| | + | * Double digest (''EcoRI'' and ''SpeI'') of all registry sequences performed and insert sizes checked on gel |
| | + | [[Image:21-8.PNG|center|frame| Lanes : M = Marker, 1 = Terminator Undigested, 2 = Terminator Digested, 3 = mRFP - Terminator Undigested, 4 = mRFP - Terminator Digested, 5 = AK3 Undigested, 6 = AK3 Digested, 7 = GFP-mut3b Undigested, 8 = GFP-mut3b Digested, 9 = CAT Undigested, 10 = CAT digested]] |
| | + | |
| | + | No insert can be observed for the terminator, this insert is too small to be visualised but a short run on a gel will be used to check for the presence of this insert tomorrow. The mRFP - terminator insert is approximately 1kb and can be seen, similarily GFP - Terminator is approximately 1kb (also shown). AK3 does not appear to have an insert (which would be correct as the nromal insert is lethal to ''E.coli'' and there is a 600bp insert clearly visible from the CAT digest. All registry sequences appear to be the correct size, indicating that they are probably what they are meant to be. |
| | + | |
| | ===''B.subtilis''=== | | ===''B.subtilis''=== |
| | * The ''B.subtilis'' was successfully transformed using transformation of protocol 2, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_4#Transformation_Protocol_2| Click link here for protocol]. However, colonies were seen on the plates were no DNA was used for transformation. The most likely cayse of this is contamination whilst carrying out the electroporation. To check that the LB agar plates contained streptinomycin we picked a transformed colony and streaked it out on a freshly made LB agar plate containing streptinmycin. | | * The ''B.subtilis'' was successfully transformed using transformation of protocol 2, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_4#Transformation_Protocol_2| Click link here for protocol]. However, colonies were seen on the plates were no DNA was used for transformation. The most likely cayse of this is contamination whilst carrying out the electroporation. To check that the LB agar plates contained streptinomycin we picked a transformed colony and streaked it out on a freshly made LB agar plate containing streptinmycin. |
| - | *In addition the transformation protocol 1 was carried out, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_2| click here for a link to the protocol]. The principle of this protocol is that a culture is grown to a high O.D.<sub>600</sub>, this induces the stress pathways in ''B.subtilis'' and induces natural competence. These high cultures are diluted and then incubated with suitable concentrations of DNA. Transformed ''B.subtilis'' can then be plated out and grown on antibiotic resistant plates. | + | *In addition the transformation protocol 1 was carried out, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_2| click here for a link to the protocol]. The principle of this protocol is that a culture is grown to a high O.D.<sub>600</sub>, this induces the stress pathways in ''B.subtilis'' and induces natural competence. These high cultures are diluted and then incubated with suitable concentrations of DNA. Transformed ''B.subtilis'' can then be plated out and grown on antibiotic resistant plates. Today ''B.subtilis'' were grown to an O.D.<sub>600</sub> of 2.0 and incubated with 40ng to 400ng of pDR110 DNA. |
| | + | <br> |
| | + | {{Imperial/EndPage|Notebook|Notebook}} |
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| July
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| M | T | W | T | F | S | S
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| [http://2008.igem.org/wiki/index.php?title=Imperial_College/1_July_2008&action=edit 1]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/2_July_2008&action=edit 2]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/3_July_2008&action=edit 3]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/4_July_2008&action=edit 4]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/5_July_2008&action=edit 5]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_July_2008&action=edit 6]
|
| [http://2008.igem.org/Imperial_College/7_July_2008 7]
| [http://2008.igem.org/Imperial_College/8_July_2008 8]
| [http://2008.igem.org/Imperial_College/9_July_2008 9]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/10_July_2008&action=edit 10]
| [http://2008.igem.org/Imperial_College/11_July_2008 11]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/12_July_2008&action=edit 12]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/13_July_2008&action=edit 13]
|
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/14_July_2008&action=edit 14]
| [http://2008.igem.org/Imperial_College/15_July_2008 15]
| [http://2008.igem.org/Imperial_College/16_July_2008 16]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/17_July_2008&action=edit 17]
| [http://2008.igem.org/Imperial_College/18_July_2008 18]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/19_July_2008&action=edit 19]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/20_July_2008&action=edit 20]
|
| [http://2008.igem.org/Imperial_College/21_July_2008 21]
| [http://2008.igem.org/Imperial_College/22_July_2008 22]
| [http://2008.igem.org/Imperial_College/23_July_2008 23]
| [http://2008.igem.org/Imperial_College/24_July_2008 24]
| [http://2008.igem.org/Imperial_College/25_July_2008 25]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/26_July_2008&action=edit 26]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/27_July_2008&action=edit 27]
|
| [http://2008.igem.org/Imperial_College/28_July_2008 28]
| [http://2008.igem.org/Imperial_College/29_July_2008 29]
| [http://2008.igem.org/Imperial_College/30_July_2008 30]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/31_July_2008&action=edit 31]
|
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| August
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| M | T | W | T | F | S | S
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| [http://2008.igem.org/Imperial_College/1_August_2008 1]
| [http://2008.igem.org/Imperial_College/2_August_2008 2]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/3_August_2008&action=edit 3]
|
| [http://2008.igem.org/Imperial_College/4_August_2008 4]
| [http://2008.igem.org/Imperial_College/5_August_2008 5]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_August_2008&action=edit 6]
| [http://2008.igem.org/Imperial_College/7_August_2008 7]
| [http://2008.igem.org/Imperial_College/8_August_2008 8]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/9_August_2008&action=edit 9]
| [http://2008.igem.org/Imperial_College/10_August_2008 10]
|
| [http://2008.igem.org/Imperial_College/11_August_2008 11]
| [http://2008.igem.org/Imperial_College/12_August_2008 12]
| [http://2008.igem.org/Imperial_College/13_August_2008 13]
| [http://2008.igem.org/Imperial_College/14_August_2008 14]
| [http://2008.igem.org/Imperial_College/15_August_2008 15]
| [http://2008.igem.org/Imperial_College/16_August_2008 16]
| [http://2008.igem.org/Imperial_College/17_August_2008 17]
|
| [http://2008.igem.org/Imperial_College/18_August_2008 18]
| [http://2008.igem.org/Imperial_College/19_August_2008 19]
| [http://2008.igem.org/Imperial_College/20_August_2008 20]
| [http://2008.igem.org/Imperial_College/21_August_2008 21]
| [http://2008.igem.org/Imperial_College/22_August_2008 22]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/23_August_2008&action=edit 23]
| [http://2008.igem.org/Imperial_College/24_August_2008 24]
|
| [http://2008.igem.org/Imperial_College/25_August_2008 25]
| [http://2008.igem.org/Imperial_College/26_August_2008 26]
| [http://2008.igem.org/Imperial_College/27_August_2008 27]
| [http://2008.igem.org/Imperial_College/28_August_2008 28]
| [http://2008.igem.org/Imperial_College/29_August_2008 29]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/30_August_2008&action=edit 30]
| [http://2008.igem.org/Imperial_College/31_August_2008 31]
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| September
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| M | T | W | T | F | S | S
|
| [http://2008.igem.org/Imperial_College/1_September_2008 1]
| [http://2008.igem.org/Imperial_College/2_September_2008 2]
| [http://2008.igem.org/Imperial_College/3_September_2008 3]
| [http://2008.igem.org/Imperial_College/4_September_2008 4]
| [http://2008.igem.org/Imperial_College/5_September_2008 5]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_September_2008&action=edit 6]
| [http://2008.igem.org/Imperial_College/7_September_2008 7]
|
| [http://2008.igem.org/Imperial_College/8_September_2008 8]
| [http://2008.igem.org/Imperial_College/9_September_2008 9]
| [http://2008.igem.org/Imperial_College/10_September_2008 10]
| [http://2008.igem.org/Imperial_College/11_September_2008 11]
| [http://2008.igem.org/Imperial_College/12_September_2008 12]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/13_September_2008&action=edit 13]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/14_September_2008&action=edit 14]
|
| [http://2008.igem.org/Imperial_College/15_September_2008 15]
| [http://2008.igem.org/Imperial_College/16_September_2008 16]
| [http://2008.igem.org/Imperial_College/17_September_2008 17]
| [http://2008.igem.org/Imperial_College/18_September_2008 18]
| [http://2008.igem.org/Imperial_College/19_September_2008 19]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/20_September_2008&action=edit 20]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/21_September_2008&action=edit 21]
|
| [http://2008.igem.org/Imperial_College/22_September_2008 22]
| [http://2008.igem.org/Imperial_College/23_September_2008 23]
| [http://2008.igem.org/Imperial_College/24_September_2008 24]
| [http://2008.igem.org/Imperial_College/25_September_2008 25]
| [http://2008.igem.org/Imperial_College/26_September_2008 26]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/27_September_2008&action=edit 27]
| [http://2008.igem.org/wiki/index.php?title=Imperial_College/28_September_2008&action=edit 28]
|
| [http://2008.igem.org/Imperial_College/29_September_2008 29]
| [http://2008.igem.org/Imperial_College/30_September_2008 30]
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21 August 2008
Dry Lab
- Generated a synthetic video of a bacterium swimming as it would be seen from the microscope, i.e with a noisy background, with realistic cell and background intensities
- Tested the synthetic video with the SpotTracker pluggin for ImageJ: results were unconvincing
- Continued work on modelling the growth curve of bacteria using ODEs
Wet Lab
Cloning
- Double digest (EcoRI and SpeI) of all registry sequences performed and insert sizes checked on gel
 Lanes : M = Marker, 1 = Terminator Undigested, 2 = Terminator Digested, 3 = mRFP - Terminator Undigested, 4 = mRFP - Terminator Digested, 5 = AK3 Undigested, 6 = AK3 Digested, 7 = GFP-mut3b Undigested, 8 = GFP-mut3b Digested, 9 = CAT Undigested, 10 = CAT digested No insert can be observed for the terminator, this insert is too small to be visualised but a short run on a gel will be used to check for the presence of this insert tomorrow. The mRFP - terminator insert is approximately 1kb and can be seen, similarily GFP - Terminator is approximately 1kb (also shown). AK3 does not appear to have an insert (which would be correct as the nromal insert is lethal to E.coli and there is a 600bp insert clearly visible from the CAT digest. All registry sequences appear to be the correct size, indicating that they are probably what they are meant to be.
B.subtilis
- The B.subtilis was successfully transformed using transformation of protocol 2, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_4#Transformation_Protocol_2| Click link here for protocol]. However, colonies were seen on the plates were no DNA was used for transformation. The most likely cayse of this is contamination whilst carrying out the electroporation. To check that the LB agar plates contained streptinomycin we picked a transformed colony and streaked it out on a freshly made LB agar plate containing streptinmycin.
- In addition the transformation protocol 1 was carried out, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_2| click here for a link to the protocol]. The principle of this protocol is that a culture is grown to a high O.D.600, this induces the stress pathways in B.subtilis and induces natural competence. These high cultures are diluted and then incubated with suitable concentrations of DNA. Transformed B.subtilis can then be plated out and grown on antibiotic resistant plates. Today B.subtilis were grown to an O.D.600 of 2.0 and incubated with 40ng to 400ng of pDR110 DNA.
|
"
