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Team:Cornell/Week 11
From 2011.igem.org
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::*RFP being expressed in such little quantity that it cannot be confirmed by the naked eye | ::*RFP being expressed in such little quantity that it cannot be confirmed by the naked eye | ||
:::- Instead, RFP expression can be confirmed with a western blot on the cell lysate using an antibody for Avi-Tag | :::- Instead, RFP expression can be confirmed with a western blot on the cell lysate using an antibody for Avi-Tag | ||
| - | ::*Distance between the ribosomal binding site (RBS) and the AUG start codon | + | ::*Distance between the ribosomal binding site (RBS) and the AUG start codon of the RFP mRNA may be too long |
:::- Redesign primers for the sake of cloning and expressing RFP | :::- Redesign primers for the sake of cloning and expressing RFP | ||
:'''What We Did''' | :'''What We Did''' | ||
::- Picked a culture sample from the pellet formed after the centrifuge step | ::- Picked a culture sample from the pellet formed after the centrifuge step | ||
| - | ::- Incubated in the | + | ::- Incubated in the 37°C shaker of Room 304 for Miniprep and sequencing tomorrow |
:::'''p.s. -- Submit Didi's sequencing samples along with RFP sample!''' | :::'''p.s. -- Submit Didi's sequencing samples along with RFP sample!''' | ||
Revision as of 23:18, 16 August 2011
Week 1 | Week 2 - 5 | Week 6 | 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 | Week 21 |
August 14th - August 20th
Sunday, August 14
Afternoon lab work done by: Charlie Chung
- Picked three colonies from the two (GFP + Avi-Tagged pZE12 backbone) plates
- - GFP + Avi + BB (1) #1, 2, 3
- - GFP + Avi + BB (2) #1, 2, 3
- Incubating overnight in 37°C shaker of Room 304
- Re-picked three colonies from the (RFP + Avi-Tagged pZE12 backbone) plate in order to retry subculturing, induction, and cell lysis
- - RFP + Avi + BB #7, 8, 9
- Incubating overnight in 37°C shaker of Room 304
Monday, August 15
Afternoon lab work done by: Youjin Cho, Maneesh Gupta
- Objective
- Miniprep GFP samples that were cultured overnight and send them off for sequencing.
- Set-up the PCR for vioB using vio operon.
- Miniprep & Sequencing
- Miniprepped the GFP samples using standard Qiagen Miniprep protocol.
- GFP+Avi-Tag+pZE12 backbone (1)- 1,2,3
- GFP+Avi-Tag+pZE12 backbone (2)- 1,2,3
- Set-up the samples for sequencing using the reverse primer.
- Order number: 10254977
- PCR Reaction
- Set-up the vioB PCR using the vio operon (= 20.3ng/μL).
- As Didi suggested, used the melting temperature of 53°C and annealing time for 3:30 minutes.
Evening lab work done by: Maneesh Gupta, Charlie Chung
- Preparing a Subculture
- Set up two cuvettes for preliminary optical density (OD) reading: (1) control (2) RFP sample from Sunday evening
- - Purpose of preliminary OD reading is to determine how much RFP sample you need to add to a new 25mL culture
- - Use a 1:10 dilution of sample to minimize error when running the spectrophotometer
- Control: 1000µL LB
- RFP Sample: 900µL LB + 100µL (RFP + Avi-Tagged pZE12) Colony #9
- RFP Sample OD = 0.329 (treat as [bacteria with RFP]), which translates to actual OD of 3.29 in Sunday's 3mL culture tube (after undoing the 1:10 dilution)
- Use dilution equation to determine how much RFP bacteria culture is needed for the 25mL culture
- (3.29)(? µL) = (desired beginning [RFP bacteria] = 0.05)(25mL = 25000µL)
- ? = 380µL Sunday's RFP bacteria culture to 25mL LB + 25µL ampicillin
- Incubate new 25mL RFP bacteria subculture in 37°C shaker for ~2 hours and 45 minutes (6:30pm start)
- At end of incubation time, check OD. Target OD = 0.6-0.8, which means ready for induction of RFP production via IPTG
- OD was 0.49 at 9pm. Let culture grow until 11pm for induction (IPTG addition).
- Induce 25mL RFP bacteria culture with 25µL 1M IPTG for desired 1mM addition (completed at 11pm)
- Incubate induced 25mL culture flask on room temperature shaker
Tuesday, August 16
Afternoon lab work done by: Maneesh Gupta, Charlie Chung
- Repeated cell lysis protocol (see Saturday, August 13) on 25mL culture from Monday.
- - However, after centrifuging, the pellet was not red.
- Troubleshooting Possibilities
- RFP being expressed in such little quantity that it cannot be confirmed by the naked eye
- - Instead, RFP expression can be confirmed with a western blot on the cell lysate using an antibody for Avi-Tag
- Distance between the ribosomal binding site (RBS) and the AUG start codon of the RFP mRNA may be too long
- - Redesign primers for the sake of cloning and expressing RFP
- What We Did
- - Picked a culture sample from the pellet formed after the centrifuge step
- - Incubated in the 37°C shaker of Room 304 for Miniprep and sequencing tomorrow
- p.s. -- Submit Didi's sequencing samples along with RFP sample!
