Team:William and Mary/Notebook

Page Title

Notebook

Week 1: 190528 - 190602

  • Set-up lab books and Google File Stream.
  • Transformed quorum sensing parts into NEB-5a.
  • 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

Week 4: 190617 - 190623

  • Plate reader experiment on circuit WM19_001.
  • Gibsoned and transformed circuits WM19_003-006.
  • Plate reader experiment confirmed circuit WM19_002 functionality.
  • 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.
    • Fine tuning variables in blue-light experiments.
    • Completed iGEM safety form, inspiration form, IBC protocol, project description.
    • Tested pDAWN + AG43 control circuits.
    • Gibsoned and transformed circuits WM19_007-012.
    • Continued testing of quorum sensing systems.
    • 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

    Week 14: 190924-191009

    • Tested circuit WM19_023 with congo red assay
    • Assembled stronger IPTG-inducible curli operon circuit and cI-repressed curli operon circuit
    • Co-transformed circuit WM19_023 with pDAWN + AG43
    • Made competent mycobacteria cells and successfully transformed with shuttle vector
    • Designed geneblocks and primers for mycobacteria parts
    • Blue-light experiment for pDAWN + AG43 + WM19_023
    • Ladies in the Lab event
    • Gibsoned and transformed WM19_027
    • Plate reader experiment with WM19_026-036, WM19_027 with congo red assay
    • Imaged WM19_026 in JS006 under fluorescence microscope
    • Researched mycobacteria parts
    • Ordered parts for collaboration with University of Pittsburgh
    • Worked on OpenStax supplement
    • Tested EL222/pBlind system
    • Tested circuits WM19_033, WM19_037, WM19_040
    • Gibsoned circuits WM19_029
    • Shared the finished curriculum with Virginia teams

    Week 15: 191010-191017

    • Assembled circuits WM19_043-046, tested with congo red assay
    • Worked on Judging form
    • Ran statistical tests on experimental data
    • Tested WM19_033, WM19_037, WM19_040-041 with congo red assay
    • Gibsoned and transformed mycobacteria parts
    • Used electroporation to transform competent mycobacterial cells
    • Imaged plates of mycobacteria under fluorescent microscope

    Week 16: 191016-191021

    • WIKI WORK!!!!