BioWire Progress Report Week Nine Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Danny...
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Transcript of BioWire Progress Report Week Nine Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Danny...
BioWire Progress ReportWeek Nine
Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Danny Popper, Sasha Rush
Last Week
Rebuilt parts with new YFP reporters Experiments
– Constitutive senders + AHL receivers– AHL + cotransformed receivers
Sent parts in for sequencing Photolithography
Building the Circuits
Rebuilt all major Lux parts with new YFP reporters
Cotransformed AHL receiver with propagation constructs
Nearly complete with major Las constructs
Building the Circuits
Started building new circuit (thanks to Ira)– Based off of “repressilator” – transcriptional
cascade of repressors– Puts a time delay between AHL induction and CI
repression, thus ensuring a pulse– Parts were ordered from MIT; within two cycles of
completion
Building the Circuits
Current Design
– CI, LuxI, and reporter induced at same time New Design
– Cascade causes CI to be induced later than LuxI and reporter, eliminating “competition” between propagation and repression
Experiments
Constitutive Senders to Receivers– Does the LuxI sender part work?– How much LuxI is needed to activate the
receivers?
AHL to Cotransformed Receiver Constructs– Can the contransformed constructs be induced by
AHL?
Experiments: Constitutive Senders
Does the Receiver Test Construct fluoresce when combined with constitutive LuxI senders?– Input: Combining LuxI senders with receiver cells
in varying ratios LuxI produces AHL, which binds with LuxR to activate
LuxPR promoter
– Output: Fluorescence
Constitutive promoter is Plambda, thanks Biosketch
Experiments: Constitutive Senders
Experimental Design– Overnight cultures were backdiluted to 0.1 OD600
Sender cells were backdiluted, IPTG induced for 2 hours, then backdiluted again
– Sender and receiver cells were combined in varying ratios by volume
1:1 (sender:receiver), 2:1, 4:1 Controls
– Positive: AHL + Receiver– Negative: Receivers alone
– Cells were imaged after 40 minutes of incubation
Experiments: Constitutive Senders
Results– Positive control worked as expected– Negative control showed a significant amount of
background fluorescence observed under YFP and GFP filters
– Fluorescence was observed at all sender:receiver ratios under YFP and GFP filters
Experiments: Constitutive Senders
Conclusions– Fluorescence seems qualitatively stronger with
addition of senders, but still unsure if it is caused by senders or background
LuxPR promoter (controls YFP) has weak constitutive expression – noise problems with construct
Complicated because senders and receivers are mixed – unsure what percent of receivers are actually fluorescing
– Solid media may be better way of experimenting Using stamp, can separate senders and receivers while
allowing for induction
Experiments: Cotransformants
Can LuxR producers cotransformed with receiver constructs respond to addition of AHL?– Input: AHL– Output: YFP fluorescence
On KAN plasmid On AMP plasmid
Degradation tags on YFP and LuxI variedCotransformed in
MC4100 cells (LacI-)
Experiments: Cotransformants
Experimental Design– Positive Control: Receiver Construct + AHL– Negative Control: Cells without YFP + AHL– Negative Control: No AHL added to cotransformants– Experimental Strains:
J06007.4A: LuxI (LVA+), strong RBS, YFP (AAV-) J06007.4B: LuxI (LVA+), strong RBS, YFP (AAV+) J06008.4A: LuxI (LVA-), strong RBS, YFP (AAV-) J06008.4B: LuxI (LVA-), strong RBS, YFP (AAV+)
Experiments: Cotransformants
Experimental Design– Overnight cultures were backdiluted to 0.1 OD600– 500 nM AHL was added to each culture– Cells were imaged after 40 minute incubation
Experiments: Cotransformants
Results– Positive Control worked as expected– Negative Control: No YFP cells did not fluoresce– Cells with YFP (AAV-) fluoresced even without
AHL addition– Cells with YFP (AAV+) did not fluoresce even with
AHL addition
Experiments: Cotransformants
Conclusions– AAV tag on YFP is too strong to visualize fluorescence– LVA tag on LuxI (produces more AHL to propagate
signal) significantly reduces efficacy of AHL propagation; LVA+ strain had significantly weaker fluorescence
– Weak constitutive activity of LuxPR is problematic Will test constructs with weaker RBS to reduce amount of
noise Also test constructs with repressor
Planned Experiments
Testing cotransformants with varying RBS strengths Testing receivers cotransformed with repressors
(aka pulse generator) Testing senders with receivers on solid media Using the FACS for more accurate, quantitative
measurements Using the wicked cool stamps
Photolithography
Made 4 rounds of masters– 90 micron; really good uniformity (+/- 10 um)– Unknown, practice at 1mm protocol– 4 wafers, 600 – 900 microns– 1 mm
Really good uniformity All features stayed on!
PDMS and agarose– Stamped from 100 micron and most recent 1mm.
150 micron master8/2 – “150 micron”, second round
85-110 micron range100 um 85 um
90 um90 um
90 um
90 um
85 um90 um
90 um
85 um90 um
110 um
90 um85 um
90 um85 um
90 um
90 um
90 um
85 um
1mm master8/5 – 1 ”millimeter”, second round, 90 sec. exposure
715-975 micron range910 um 870 um
875 um945 um
905 um
955 um
970 um
715 um
725 um725 um
715 um
715 um780 um
790 um
775 um
795 um
890 um
Photolithography
Issues in the cleanroom:– Still not getting perfectly level surfaces.– Wafer still sticks to mask.– Haven’t been able to spin a final coat for
uniformity as the spinners have been down.
Only other step requiring work is actual stamping– Still not very precise; can we blot?
Photolithography
Practice stamping for precise cell growth A few more cleanroom cycles to increase
stamp depth, fix final uniformity issues
This Week
Building parts– Continue cotransforming Lux test constructs– Build revised circuit design– Finish building Las parts with new reporters
Experiments– Test cotransformants with different RBS, repressor
component– FACS– Solid media experiments
Photolithography– STAMP STAMP STAMP STAMP STAMP
Updated Schedule
Week 1 (6/6): Project Choice and Design Week 2 (6/13): Got parts and set up tests Week 3 (6/20): Began building test constructs, finished sender Week 4 (6/27): Finish receiver, receiver w/repressor; CAD a mask Week 5 (7/4): Continued building parts, received mask Week 6 (7/11): Finished Lux, Tested senders, made PDMS molds Week 7 (7/18): More experiments, finish Las, make first
master/PDMS/stamp, eating pizza courtesy of Alain Week 8 (7/25): More experiments, Meeting Their Master Week 9 (8/1): More experiments, construction with new reporters Week 10 (8/8): More experiments, STAMP STAMP STAMP Week 11 (8/15): “ Week 12 (8/22): “ Week 13 (8/29): “