Designed primers for quorum sensing parts to make them 3G compatible.
Cloned pSB1C3.
Starting to take deep learning course online, get some basics laid down before starting to clean up the database.
STEM Community Day.
Week 2: 190603 - 190609
Cloned quorum sensing parts with W&M PAD.
Tested projector set-up for pDAWN experiments.
Designed primers to isolate and make pDAWN subunits 3G compatible (including AG43)
Assembled and tested circuit WM19_001 (tests Las QS system).
Continue with deep learning course, starting to look for a python web crawler that could help us get all the information from other team’s outreach website
Created outreach poster to present at Mid-Atlantic Synthetic Biology Symposium
Presented past projects and outreach at Mid-Atlantic Synthetic Biology Symposium
Week 3: 190610 - 190616
Miniprepped pDAWN + AG43 control circuits.
Designed and 3G assembled circuit WM19_002.
Plate reader experiment with circuit WM19_002.
PCRed and cloned now 3G compatible pDAWN subparts.
Finished the modeling for Stanford Paper, tested their hypothesis and confirmed the validity of their conclusion.
Starting to use their biofilm lithography method to form our own double ring experiment but dimension keeps getting dimensions wrong
Blue-light optogenetic experiment on pDAWN + AG43, visualized with crystal violet.
Transformed pDAWN + AG43 control circuits.
Was able to get the double ring experiment dimensions correctly, but was not able to get the diffusion matrix to work as we expected, the number kept going higher and higher to infinity.
Discussed with professor Patel, resolved this problem by changing the way that we convolve matrix while counting HSL concentration on one grid.
Met with W&M admissions on ways to expand our outreach through their resources
Week 5: 190624 - 1900630
Designed and 3G Assembled Tet-inducible AG43 circuit.
Co-transformed WM17_399 and pDAWN AG43 for fluorescent biofilms.
Focused on utilizing machine learning method to clean up previous year’s outreach data, tried different types of RNNs, language mode, different scales of parameters. Without much luck because the best accuracy that we can get is 42% for project tags.
Presented to PLUS students at Navigating W&M event
Week 6: 190701 - 190707
Designed primers to create quorum quenching parts based on HSL-binding domains of quorum sensing system.
Continued pDAWN + AG43 experiments.
Diagnostics of problematic circuits WM19_007-008, WM19_010-012.
Determined no reasonable way to do ultrasound induction as is inextricably linked to heat or oxygen stress.
3G Assembled and miniprepped circuits WM19_013-016.
Transformed circuits WM19_13-16 into pDAWN + AG43 JS006.
Encountered some problems with our diffusion model: because of the way that we convolve the matrix, the run time is very long. But we are getting results for the double ring experiment, concentration of HSL does not meet our expectations.
Week 7: 190708 - 190714
Plate reader experiment for quorum sensing systems.
Transformated quorum sensing systems WM19_003, WM19_005-006 into pDAWN+AG43 JS006.
Created of QUBES conference materials.
PCRed quorum quenching parts.
Plate reader ring-forming experiment with circuits WM19_003-004.
Research for adhesin library.
Tested ATC-inducible AG43 circuits.
Gibsoned and transformed circuits WM19_017-021.
Blue-light experiment with circuits WM19_013-015.
Completed IBC protocol.
Prepped for PLUSS outreach event.
Blue-light experiment with media on agar.
Kept adjusting the parameters for the double ring experiment.
Week 8: 190715 - 190721
Reviewed curli fibers; continued research on other adhesins.
Gibsoned and transformed circuit WM19_022.
Reviewed curli and fap primers and geneblocks.
Blue-light experiment with circuit WM19_022.
Exploring word2vec embedding method within scikit learn for our database
Read the turing paper, brainstorming ways of modeling the fast diffusing inhibitor and slow diffusing activator.
Participated in PLUS-S as teaching assistants and hosted 3 PLUS-S students for daily lab work
Presented our “Integrating Synthetic Biology and Big Data” poster and materials at the QUBES conference
Presented to Camp Launch students at Focusing on the Future
Week 9: 190722 - 190728
Prepped for Mid-Atlantic Meet-up and presented there.
Plate reader experiment for quorum quenching.
Skype call with Dr. Joshi.
Prepped for outreach activity.
Colony PCRed off of Pseudomonas aeruginosa, Eschichriae coli, and Staphylococcus aureus for adhesins.
Distance-dependent quorum sensing experiment.
3G assembled and transformed curli operon (divergent).
Designed and 3G assembled of arabinose-inducible AG43.
Gibsoned and transformed circuits WM19_023-024.
Wrapping up with the turing model, looking through microbacteria paper and looking for ways to model microbacteria.
Hosted 30 Camp Launch for a day in the lab
Week 10: 190729 - 190804
Troubleshooting fap, need to do site-directed mutagenesis.
Continued distance-dependent quorum sensing experiment.
3G assembly of SaSuhB circuits.
Designed circuits WM19_026-027.
Designed fap site-directed mutagenesis (SDM) primers (KLD).
Designed Turing pattern parts.
Outlined mycobacteria work.
Final adjustments for parameters according to some rough experimental data.
Summer Break: 190805-190828
Wrote iGEM Summer Report (Project Description and Literature Review, Methodology)
Worked on OpenStax supplements
Reviewed and ordered SDM primers to remove illegal cutsite from fap from IDT
Reviewed and ordered Turing pattern parts from Twist and IDT
Ordered parts for alternative optogenetics circuit
Finalized curriculum
Week 11: 190829-190910
Gibsoned and transformed circuits WM19_030-035
Gibsoned and transformed Turing parts included in distribution kit
Made Turing parts from distribution kit 3G compatible
Gibsoned and transformed csgBAC and csgEFG geneblocks
Skype conference with University of Pittsburgh iGEM team
Diagnostics on circuits WM19_030-035
Inoculated circuits WM19_032-WM19_034 for testing
Implemented cell collision, cell division, cell death in all models to increase their accuracy
Combined machine learning with web scraping database
Began advertising for Ladies in the Lab event
Week 12: 190911-190914
Miniprepped csgBAC geneblock in Pad1C3
Retransformed circuits WM19_030 and WM19_031
Electrocompetent cell preparation
Ordered primers to add new sticky ends to some of the Turing pattern parts
Ring (quorum sensing) experiment by using blue light to place circuit WM19_005 around circuit WM19_006
Completed Safety Form
Week 13: 190915-190923
Transformed circuits WM19_023-024, WM19_030-031
Transformed Dr. Joshi’s plasmid
Plate reader experiment with WM19_023-024, WM19_030-031, Joshi plasmid using congo red assay
Transformed circuits WM19_023 and WM19_031
Gibsoned transformed YF1/FixJ
Induced and imaged quorum sensing experiment under fluorescence microscope
Tested circuit WM19_033 with congo red assay
Transformed circuits WM19_032-WM19_034
Skype call with Cornell iGEM team
Cloned fap operon
Site directed mutagenesis (SDM) with KLD and Gibson Assembly to remove the illegal cutsite in the fap operon and allow for 3G assembly
Assembled circuits WM19_026 and WM19_036
Gibsoned and transformed all Turing pattern parts
Changed sticky ends of WM19_CD_114, WM19_CD_116, WM19_CD_117 using designer primers
