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BioSketch The bacterial sketch pad. Chris Doucette, Thomas Noriega, Hing Eng Yves Wang, Jennifer Gao, Yin Li Group Meeting 2005-08-15. BioBricks Team. LacI Switch. Constructed J06961 – LacI (mut 241) switch with EYFP Failed to make J06962 – LacI (mut 265) switch with EYFP.
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BioSketchThe bacterial sketch pad. Chris Doucette, Thomas Noriega, Hing Eng Yves Wang, Jennifer Gao, Yin Li Group Meeting 2005-08-15
LacI Switch • Constructed J06961 – LacI (mut 241) switch with EYFP • Failed to make J06962 – LacI (mut 265) switch with EYFP
LacI (mut241) Switch • After overnight Growth:
LacI (mut241) Switch • After 4 h in 40°C:
LacI (mut241) Switch • Suspect that the ligation actually failed = • No cI production, no LacI gene • Supported by an analytical digest • Redid digestion and ligation • Analytical digest shows appropriate bands • Microscope lamp broken • Sending out for sequencing
A Cautionary Tale • What I was trying to do: Use miniprep isolated from a ligation mixture to transform JM2.300 cells for experiments. • Mini Prep: Decided to use J06961 mini 4 J06962 mini 2
When I transformed the JM2.300 cells with the minis they did not act as expected under the microscope. Confused, hurt, and betrayed I picked ten colonies from the transformation and looked at their plasmids: Minis 1, 2, 3, 5, 8, and 9 were CONTAMINATED Minis 4, 6, 7, and 10 Were GOOD
Sadly, the other plasmid transformation did not yield any good results…
MORAL • Beware of contaminated minis, especially if you plan on using them to transform bacteria that you are going to experiment on directly.
What has been done: CollinsMod • Experimenting with UV irradiation of cells on plastic substrate • Replicating last week’s results with Collins Switch • Finding temperature at which ThermoSwitches are bistable • Examining apparent mutations in CI-repressed P(L*)
Irradiating Cells on Plastic Substrate • Logic: • Eliminate the agar bits that might be mistaken for cells • Substrate: • 3-cm polysterene petri plates • Cells: • JM 2.300 cells with amp resistance • Experiment (UV killing curve): • Dilute OD600 = 0.5 cells 1:107. • Pipet 50 or 100ul cells into 3-cm dish; spread evenly. • Irradiate. • Pipet another 100ul LB into dish. • Resuspend cells and pipet onto standard selective LB plates; spread. • Grow overnight.
JM 2.300 GFP reporter Collins – 6 J/m2 Collins – 0 J/m2 Collins – 12 J/m2 Collins – 48 J/m2 Collins – 24 J/m2 UV Induces Signal in Collins Switch Day 1: 37C Day 2: 2mM IPTG Day 3: UV irradiation, o.n. @ 37C Day 4: Assay
Finding Thermo-Bistability • Experimental design: • Expected results: • If cells are incubated (Day 3) at a temperature that permits bistability (Tb), then • Cells previously incubated @ 30C would remain ON. • Cells previously incubated @ 40C would remain OFF. • In other words: the state of the cell at Tb should be history-dependent. Day 1 30C Day 2 30C (ON) 40C (OFF) Day 3 30, 32, 35, 37, 40C (stay ON?) 30, 32, 35, 37, 40C (stay OFF?)
JM 2.300 GFP reporter 40C switch 37C switch 30C Tb 30C Tb 40C Tb 30C Tb 40C Tb 30C 30C 40C Tb ThermoSwitches Exhibit Bistability at 30°C 30C 32C 35-38C 37C 40C
M1 M1 M1 M1 A Closer Look at Behavior at 30°C A Closer Look at Behavior at 30°C 40C Switch 30C Switch 23.7% 76.3% 23.0% 77.0% 30C 30C 37.5% 62.5% 42.1% 57.9% 40C 30C
Mutations in CI-repressible PL* Promoter • pWG (GFP reporter) • "Correct" sequence w.r.t. file sent from Collins lab • Canonical polymerase-binding regions (-10, -35) • Noncanonical CI-binding site OL1 • pTS (Collins switch) • Mutations are in -10 TATA box and OL1 binding site. • Should make LacI expression weaker and CI repression stronger. P(L*) from pWG 5’-GCGTCCTGCTGATGTGCTCATTATAACCGCCAGTGGTATTTATGTCAACACCGCCAGAGATAATTTATCACCGCAGATGGTTATCTGT-3’ 3’-CGCAGGACGACTACACGAGTAATATTGGCGGTCACCATAAATACAGTTGTGGCGGTCTCTATTAAATAGTGGCGTCTACCAATAGACA-5’ P(L*) from pTS/241/265 TATCACCGCCAGTGGTA:OL1 OL3: TATCACCGCAGATGGTT 5’-GCGTCCTGCTGATGTGCTCAGTATCACCGCCAGTGGTATTTATGTCAACACCGCCAGAGATAATTTATCACCGCAGATGGTTATCTGT-3’ 3’-CGCAGGACGACTACACGAGTCATAGTGGCGGTCACCATAAATACAGTTGTGGCGGTCTCTATTAAATAGTGGCGTCTACCAATAGACA-5’ GTTGTGGCGGTCTCTAT :OL2 lacI -10: TAATAT -35: ACAGTT
ThermoSwitches: Results and Implications • Turning ON: Weak • Basal level of reporter expression at 30C is weakly elevated (compared to OFF state). • Would a lower temperature further increase GFP inductin? • Does UV irradiation increase GFP induction above baseline? • Turning OFF: Strong • Reporter expression is well-suppressed by temp > 37C. • Maintaining state: Weak • Reporter expression is moderately history-dependent at 30C, with tendency to be ON. • Reporter expression is history-independent at 32C, with weak suppression of signal. • Are the promoters leaky? • Is CI activity reduced at 30C? • In a previous experiment, IPTG-based repression at 30C did not work well. Was this due to decreased LacIts sensitivity to IPTG or decreased CI activity at 30C?
Achieving Better ON State o.n. @ 40C (OFF) Day 1: 0, 12, 24, 48 J/m2 Day 2: 4h @ 25C (ON?) 4h @ 30C (ON?)
Achieving More Robust Bistability • Continue playing with environmental parameters? • Try 31C? …. • If a more complete ON state is achieved, perhaps we will see a difference between maintaining the OFF state and maintaining the ON state. • Alter the parameters of the underlying circuit? • Put the switch circuit on a medium copy plasmid? • Make sure that both the LacIts promoter and the CI promoter have canonical polymerase binding regions or stronger RBSs. • Is CI activity weak at 30C? • Is state maintained in the Collins switch at 30C?
T-Shirt Design Orr & Yin
BBa_RTeKN0 BBa_B2WTF! Promoter Pizza-Inducible RBS Reference NA; could possibly work … maybe BBa_C(rand # of choice) BBa_B6D1N0 CDS BioWiredSketch-a-Lator Terminator Strength 5.5; units NA Front + = …
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