Team:Rochester/Notebook

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Notebook

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Below you can find a brief overview of our team's activities from week to week.

    February 7-13

  • Each team member picked a past project that did well and presented it to the group.
  • We discussed what we liked and disliked about the projects and what made them successful.

    • February 14-20

  • Team brainstorming session: we listed any ideas we came up with.
  • Thought of local problems in Rochester and how we could address them.
  • Team members presented slides on potential projects.
  • Attended a virtual scientific paper workshop with Dr. Moriana Garcia from the University of Rochester Libraries.

    • February 21-27

  • Team members presented more slides on our 23 potential projects.
  • We discussed the modularity of each idea, considering the potential for hardware, policy and practice, lab safety, overall importance, novelty, et. cetera.

    • February 28-March 6

  • Voted on potential projects and narrowed our list down to our Top 20.
  • Worked in Zoom breakout rooms to do more research on the ideas we had.
  • Voted again to determine our Top 10 ideas.

    • March 7-13

  • Worked in small groups to give formal presentations of our Top 10 ideas.

    • March 14-20

  • Received feedback from our TAs and advisors on our Top 10 ideas.
  • Read through the other groups’ ideas and generated questions for each other.

    • March 21-27

  • Researched and discussed medal requirements.
  • Researched and discussed Top 10 project ideas in detail in small groups.
  • Voted to determine our Top 3 ideas.

    • March 28-April 3

  • Toured our lab space.
  • Started reaching out to potential sponsors for funding.
  • Prepared our presentations on the Top 3 ideas.

    • April 4-10

  • Presented our Top 3 ideas and received feedback from TAs and advisors.
  • Team members ran for different positions and gave a short speech on our qualifications.

    • April 11-15

  • Voted on and assigned team roles.
  • Decided on our project: biosensor device for the rapid diagnosis of sepsis using patient sweat!

    April 15-18

  • First meeting after picking team roles.
  • Discussing general logistics and expectations.
  • Everyone joins subteams to begin working on the project.

    • April 19-25

  • Discussing general meeting logistics of every subteam, since collaboration between subteams will be crucial.
  • Every subteam is doing deeper research into their respective focus of the project.
  • Picked a logo, team name and slogan to represent our team.
  • Big focus on policy and practice to find initial professionals to talk to to get background information on sepsis and first feedback on general idea.

    • April 26-May 2

  • Every subteam looked at successful previous iGEM teams in their area (ie wetlab, hardware, wiki, collaboration, etc) to understand what makes a good team and project.
  • Wetlab and hardware started working on proposals for protocols for the individual parts of the project and researching alternatives.
  • Reaching out to the Rochester community and local professionals and organizations to see what we can do to have a local impact.

    • May 3-9

  • No meeting due to Final Exams Season.

    • May 10-16

  • No meeting due to Final Exams Season.

    • May 17-23

  • Wetlab is compiling a final list of biomarkers to look at (CRP, lactoferrin, IL-1B, IL-6, TNF-a) and is working on the protocols for the production of rGO.
  • Get initial prototype sketch/model from hardware combining all individual components.
  • Confirmed participation in Upward Bound and potentially with a local prison education project for education and outreach.
  • Started huge fundraising efforts by reaching out to sponsors.

    • May 24-30

  • Wetlab started working on designing sequences and on a cloning plan, is finalizing the methods for GO reduction, decided to overexpress flavins to produce GO.
  • Policy and Practice keeps reaching out to and meeting with professionals and started thinking about possible inclusivity efforts and target groups.
  • Hardware’s initial efforts focus on microfluidics and understanding the underlying mechanisms.
  • Modeling is working on finding different models to inform the project and trying to find the best models and practices to do these.
  • Started working on initial idea and script for promotional video.

    June 1-7

  • Getting codon optimized sequences ready for sending in orders to IDT.
  • Researching: LATE PCR, RCA.
  • Contacting professionals for policy and practice and hardware.
  • Divided modeling team into teams for different models.
  • Wiki launched.
  • Started meeting different teams for collaboration.

    • June 7-13

  • Aptamer sequences ordered, Biobrick fro TU delft on its way.
  • Made freezer stock for WT S. oneidensis and E coli.
  • Made preliminary design for microfluidic part.
  • Secured sponsorship from Graphanea.

    • June 14-20

  • Applied for Beckman Coulter grant.
  • Secured plasmids from University of Texas, Keitz laboratory.
  • Synthesized GO chemically.
  • Models all started.
  • Postcard made for global collaboration.
  • Promo Video script finalized.

    • June 21-27

  • Still ordering aptamer and rGO sequences.
  • Secured NEB sponsorship.
  • Characterised GO with raman spectra.
  • Began transforming aptamer sequences into E. Coli.
  • Shewanella oneidensis metabolism model coming along.
  • Promo video filmed.

    • June 29-July 6

  • Freeze dried GO, made electrocompetent S. oneidensis.
  • Hardware team learnt COMSOL and onshape.
  • Initial Wiki template done.
  • Hosted regional meet Up for iGEM.

    • July 7-13

  • Chemically reduced GO.
  • All synthetic DNA received.
  • Started designing microfluidics design in COMSOL.
  • Consulting professionals for advice on models.
  • Went to summer camps for outreach.

    July 14-20

  • Successfully transformed aptamers.
  • Started carrying out reduction of rGO with Texas plasmids (cymA, mtrA, mtrC, and two empty vectors).
  • Started looking into different alternatives instead of freeze drying rGO.
  • Finished designing microfluidic device on COMSOL.
  • Started researching which electrodes to use.
  • Finished riboflavin portion of the S. onediasis metabolic modeling.
  • Reached out to OSU about collaborating with them for testing aptamers and creating a children’s book.

    • July 21-27

  • Noticed slower reduction of Texas mtrA and mtrC strains of S. onediasis as compared to wildtype.
  • Used the quantifluor kit on PCR products from last week to see ss versus ds DNA, as well as compared to primers mix. We got significant results for all but IL6.
  • Finalized plan to test aptamer binding.
  • Tourred an ICU at UR Medicine Strong Memorial Hospital to get a better understanding of how our device could be implemented.
  • Worked on analysis of fractals in MATLAB for dissociation/binding of biomarkers.
  • Backbone of wiki page completed.
  • Continuing going to summer camps for outreach, getting feedback from participants and making edits to activities.
  • Submitted promotion video with multilingual narration and subtitles.

    • July 28-August 3

  • Did quantifluor on new PCR products, looked promising for CRP and Lactoferrin.
  • Took Raman spectra of wild type rGO reduction.
  • Wrote two policies for inclusivity: lab course and teaching best practices.
  • Met with the director of University of Rochester’s Greene Center and Disabilities office to discuss inclusivity efforts.
  • Starting to manufacture first microfluidic device.
  • Will use silver conductive ink for testing resistance.
  • Met with Rio-UFRJ Brazil, offered to help figure out drop casted on screen-printed electrode and for any 3D design using Onshape or COMSOL.

    • August 4-August 10

  • Working on removing surface area occupied by oxygen groups on reduction method model.
  • Continued working on children’s book with OSU.

    • August 11-August 17

  • Wetlab team synthesized aptamers via RCA.
  • Policy and Practice planned dates for a sepsis symposium.
  • Collaboration submitted our rough draft of the Maastricht paper.

    • August 18-24

  • Wet lab transformed cymA, ydeH, oprF and ribF into E coli.
  • Policy and Practice finalized the date of our sepsis symposium.
  • Hardware continued to test the resistance of rGO with silver ink.

    August 25-September 5

  • Gold Collaboration with UFRJ Brazil; they advised us on impedance measurements.
  • Aptamer team ran a gel binding assay to test aptamer binding.
  • Wetlab team attached aptamers to rGO.
  • Hardware tested the resistance of rGO with silver ink.
  • Team featured in the Campus Times.

    • September 6-11

  • Collaboration team contacted Amazon about publishing our book on Kindle.
  • Policy and Practice advertised our symposium.
  • Modeling added the last data on blood/sweat ratios for biomarkers.
  • Hardware did their first tests of microfluidics with food dye.

    • September 13-19

  • Collaboration team sent Peer Review for Maastricht journal project.
  • Software team began developing our readout.
  • Hardware worked out some bugs in our potentiostat code.
  • Policy and Practice ran our sepsis symposium.

    • September 20-26

  • Policy and Practice discussed ideas for inclusivity with a professor at the University of Rochester.
  • Modeling worked on code documentation.
  • Hardware finished testing the resistance of bacterially reduced rGO.

    • September 27-October 2

  • Wetlab continued to test the binding of aptamers to rGO.
  • Public Relations raised over $200 for Sepsis Alliance.
  • Hardware connected our circuit to Arduino.

    • October 3-10

  • Collaboration’s children’s book was published on Kindle.
  • Software finished their code and sent it to UFRJ Brazil for testing.
  • Hardware tested the sensitivity of our potentiostat.