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Team:Wageningen UR/Journal/week4
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== office work == | == office work == | ||
| - | + | <p align="justify"> | |
| - | This week | + | This week felt a bit of a slow week. Two of our team members were a day sick. After the great success with the phyre2 program, we searched for a program that uses the output of the phyre2 program to predict the quaternary structure of the VLPs. In other words can a VLP be formed if we apply certain . We found out that there aren't many programs that can accurately predict the quaternary structure and the programs that are available aren't really compatible with phyre2.<br> |
| - | Besides getting stuck with the prediction model Mark is investigating further for a new methodology to determine if VLPs were formed. He found two methods that can be used: | + | Besides getting stuck with the prediction model Mark is investigating further for a new methodology to determine if VLPs were formed. He found two methods that can be used: asymmetric flow field-flow fractionation (AFFFF) followed by multi angle light scaterring (MALS) and dynamic light scatering (DLS).<br> |
Thijs and Jasper continued further with the development of The Constructor and they hope to have he program ready for bet testing after the weekend | Thijs and Jasper continued further with the development of The Constructor and they hope to have he program ready for bet testing after the weekend | ||
| - | + | </p> | |
[meeting] | [meeting] | ||
| Line 19: | Line 19: | ||
Monday: | Monday: | ||
| - | * | + | *Sonification of cells grown last week |
| - | * | + | * specifications: 6 x 30 seconds, output 3-4, amplitude around 20 on ice! cool as much possible, 50 seconds on ice between 30 second steps. |
| + | *Lysate dissolved in 50 ml disassembly buffer. | ||
*Centrifuged at 15000 RPM, 3 minute | *Centrifuged at 15000 RPM, 3 minute | ||
| - | *Start dialysis | + | *Start of dialysis |
Tuesday: | Tuesday: | ||
| - | *Took negative control for SDS, non induced BL21 CCMV, | + | *Took a negative control for SDS, non induced BL21 ''E.coli'' with CCMV wt, |
| - | * | + | *Grown overnight in liquid LB+Kanamycin |
| Line 37: | Line 38: | ||
Thursday: | Thursday: | ||
| - | *BL21 | + | *BL21 plated and grown in Greiner tube 10 ml tube |
<ol> | <ol> | ||
<li>BL21 2 plates freezer</li> | <li>BL21 2 plates freezer</li> | ||
| Line 43: | Line 44: | ||
</ol> | </ol> | ||
*SDS-PAGE to check for the abundance of CCMV wt capsid proteins | *SDS-PAGE to check for the abundance of CCMV wt capsid proteins | ||
| - | **10% SDS gel | + | **6 different samples |
| - | **staining for 15 min with Coomassie blue following 15 min of destaining | + | **10% SDS gel for proteins of 10 to 100 kDa size |
| + | **staining for 15 min with Coomassie blue following rinsing with MQ water and 15 min of destaining | ||
---- | ---- | ||
[[https://2012.igem.org/Team:Wageningen_UR/Journal/week3 previous week]] [[https://2012.igem.org/Team:Wageningen_UR/Journal/week5 next week]] | [[https://2012.igem.org/Team:Wageningen_UR/Journal/week3 previous week]] [[https://2012.igem.org/Team:Wageningen_UR/Journal/week5 next week]] | ||
Latest revision as of 22:40, 26 September 2012
week 4: 21 may - 27 may
office work
This week felt a bit of a slow week. Two of our team members were a day sick. After the great success with the phyre2 program, we searched for a program that uses the output of the phyre2 program to predict the quaternary structure of the VLPs. In other words can a VLP be formed if we apply certain . We found out that there aren't many programs that can accurately predict the quaternary structure and the programs that are available aren't really compatible with phyre2.
Besides getting stuck with the prediction model Mark is investigating further for a new methodology to determine if VLPs were formed. He found two methods that can be used: asymmetric flow field-flow fractionation (AFFFF) followed by multi angle light scaterring (MALS) and dynamic light scatering (DLS).
Thijs and Jasper continued further with the development of The Constructor and they hope to have he program ready for bet testing after the weekend
[meeting]
written by: Mark
lab work
Testing CCMV protocol
Monday:
- Sonification of cells grown last week
- specifications: 6 x 30 seconds, output 3-4, amplitude around 20 on ice! cool as much possible, 50 seconds on ice between 30 second steps.
- Lysate dissolved in 50 ml disassembly buffer.
- Centrifuged at 15000 RPM, 3 minute
- Start of dialysis
Tuesday:
- Took a negative control for SDS, non induced BL21 E.coli with CCMV wt,
- Grown overnight in liquid LB+Kanamycin
- Sample transferred to new tube
- Stored in -20 degree Celcius
Thursday:
- BL21 plated and grown in Greiner tube 10 ml tube
- BL21 2 plates freezer
- BL21 2 Greiner tubes 30 degree Celcius stove
- SDS-PAGE to check for the abundance of CCMV wt capsid proteins
- 6 different samples
- 10% SDS gel for proteins of 10 to 100 kDa size
- staining for 15 min with Coomassie blue following rinsing with MQ water and 15 min of destaining
