Notebook

We kept a notebook so that you can find a brief overview of our team's activities from week to week.






Project Brainstorming



February 3

  • First meeting as a team, selected the brainstorming leader

February 6-12

  • Established the ground rules for team meetings

  • Team members presented information on a past iGEM project that succeeded in the competition 

  • We critiqued each project and evaluated what allowed each project to succeed

February 13-19

  • Attended a workshop on reading scientific papers with Dr. Moriana Garcia from the University of Rochester Libraries

  • Reviewed the iGEM safety policies to ensure our project ideas were viable

  • Presented interesting current scientific research articles that inspired project ideas

February 20-26

  • Continued brainstorming project ideas

    • Thought of problems local to the Rochester area

    • Thought of problems in multiple iGEM project tracks to ensure variety in our project ideas

  • Presented our 27 ideas to each other and began to eliminate project ideas for our top 10 project ideas. For those interested in our brainstorming process please look here [link to the brainstorming write up]

February 27-March 5

  • Finished narrowing down the list of project ideas to the top 10 ideas

  • Presented our top 10 ideas for feedback to the advisors

March 6-12

  • Spring break, no meetings, but we individually continued to research and develop our top 10 ideas

March 13-19

  • Met with the 2021 University of Rochester iGEM team for advice

  • Narrowed down the top 10 project ideas to the top 5 project ideas

March 20-26

  • Researched and developed the top 5 project ideas

March27-April 2

  • Narrowed down the top 5 project ideas to the top 3 project ideas

April 3-9

  • Presented our top 3 ideas for feedback to the advisors

  • Picked our project

  • Selected team roles

Getting Started



April 10-16

  • Signed up for subteam roles (Wet lab, Hardware, Modeling, Policy and Practice)

  • Finalized biobrick candidates and split the project up into two modules, the buddy sap module and the ropy syrup module

  • Began reaching out to maple farmers

April 17-23

  • Presented biobrick ideas to the advisors and received feedback

  • Continued refining the ideas for the biobricks and hardware associated with each module of the project

April 24-30

  • Continued refining the ideas for the biobricks

  • Started making the lab safety protocol

May 1-7

  • Finals week, no meetings

Beginning of Summer



May 8-14

  • Wrote protocols to be used for experiments in the summer

  • Presentation on basic lab safety/techniques by the wet lab teaching assistants

May 15-21

  • Wet lab bootcamp run by the teaching assistants

    • Learned basic lab protocols such as pipetting, PCR, gel electrophoresis, and aseptic techniques for bacteria

  • Started reaching out to companies for donations of needed chemicals or funding

May 22-28

  • Introduced the invert sugar module after discussions with maple farmers

  • Chose to use ropy syrup to make hydrogels

  • Continued putting together sequences for the biobricks

  • Began planning for the Disability Justice in STEM Webinar Series

May 29-June 4

  • Ordered the biobricks

  • Continued working on protocols

  • Continued soliciting donations from companies

June 5-11

  • Continued working on protocols

  • Continued soliciting donations from companies

June 12-18

  • Continued working on protocols

    • Eliminated hazardous reagents from our protocols and edited them accordingly

  • Continued soliciting donations from companies

June 19-25

  • Made chemically competent E. coli TOP10 and BL21 cells

  • Biobricks arrived

  • Ordered aptamer biobricks 

June 26-July 2

  • Began attempts to join the halves of the dextran biobrick using stitch PCR and overhang PCR procedures

End of Summer



July 3-9

  • Biobricks were amplified and digested in preparation for 3A assembly

  • Continued to attempt to join the halves of the dextran biobrick using stitch PCR and overhang PCR procedures

July 10-16

  • Performed 3A assembly on all complete biobricks

  • Began attempts to transform E. coli cells with the biobricks

  • Used NEBuilder procedure to join the halves of the dextran biobrick

July 17-23

  • Continued attempts to assemble and transform E. coli cells with the biobricks

  • Began chemically reducing graphene oxide

July 24-30

  • Continued attempts to assemble and transform E. coli cells with the biobricks

July 31-August 6

  • Continued attempts to assemble and transform E. coli cells with the biobricks

  • Synthesized BSA beads

  • Made chemically competent BL21 cells

August 7-13

  • Continued attempts to assemble and transform E. coli cells with the biobricks

August 14-20

  • Made electrochemically competent BL21 cells

  • Retried the NEBuilder kit of the two halves of the dextran biobrick

  • Synthesized BSA beads

August 21-27

  • Miniprepped all of the biobricks

Wrapping Up



August 28-September 3

  • Created dextran hydrogels

  • Assessed the quality of the synthesized BSA beads

September 4-10

  • Performed small scale induction tests of EibA, EibD, choline oxidase, and all of the glucose oxidase variants in E. coli BL21 strains

  • Performed a colony PCR of the dextran biobrick

  • Performed a pH test of the dextran hydrogels

  • Microscopic examination of the BL21 cells expressing EibA/EibD

September 11-17

  • Reattempted to PCR the dextran biobrick

  • Continued purifying the glucose oxidase an choline oxidase enzymes

  • Transformed the glucose oxidase enzymes with two and seven mutations into E. coli shuffle strains

  • Tested the effect of induction concentrations on EibD expression and autoagglutination

  • Fluorescence microscopy of EibD-expressing cells bound to anti-GFP antibody and GFP

September 18-24

  • Performed small scale induction tests of the glucose oxidase enzymes with two and seven mutations in E. coli shuffle strains

  • Continued purifying the glucose oxidase and choline oxidase enzymes

  • Tested GFP biosensor on GFP samples of different concentrations

September 25-October 1

  • Continued purifying the glucose oxidase and choline oxidase enzymes

  • Prepared and harvested more EibD-expressing bacteria

  • Repeated testing on the effect of addition of antibody on EibD-expressing bacteria

  • Tested asparagine biosensor on asparagine samples of different concentrations

  • Repeated testing of GFP biosensor on GFP samples of different concentrations

October 2-8

  • Continued purifying the glucose oxidase and choline oxidase enzymes

  • Performed activity testing on the glucose oxidase variants and the choline oxidase

  • Reperformed the growth test on the dextran hydrogels

  • Continued performing the sedimentation assay on EibD

October 9-15

  • Wiki freeze