Team:William and Mary/Notebook



Notebook

Week 1: 200601-200605

  • Researched factors that affect recombination
  • Completed literature review of viral recombination
  • Considered using Flexbooks for an education project
  • Compared the benefits and drawbacks of using the nasal microbiome or the gut microbiome for probiotic delivery
  • Looked into programs to use to analyze recombination within viral genomes and to predict future locations of recombination

Week 2: 200608-200612

  • Discovered that Arachidonic Acid (AA) and Linoleic Acid (LA) have the potential to halt viral replication
  • Looked into inhibiting cPLA2 to prevent membrane rearrangement by viruses
  • Researched the antiinflammatory role of Docosahexaenoic acid (DHA)
  • Worked on potential project of creating an iGEM Modeling Guide (eventually decided to not continue with this project)
  • Learned that AA can be incorporated into the phospholipid bilayer
  • Started to look into RDPv4

Week 3: 200615-200519

  • Created a discord account and GroupMe to facilitate group discussion
  • Considered what organisms would be able to produce PUFAs at human body temperature
  • Combed through papers in which RDP was used to learn more about program
  • Researched programs that can predict RNA structure from genome sequences
  • Discovered potential alignment problem with RDP

Week 4: 200622- 200626

  • Drafted emails to invite teams to our Meetup
  • Started correspondence with Dr. Shelhammer
  • Team completed human subjects protocol training
  • Looked into various alignment programs: MUSCLE, MAUVE, MAFFT, and MUMMER
  • Started to look into accuracy of RDP

Week 5:200629- 200703

  • Considered the possibility of using gram negative bacteria instead of gram positive bacteria
  • Conducted interview with Dr. Shelhammer
  • Researched ways to compare accuracy of genomic alignments
  • Looked into potential speakers for Meetup
  • Continued to examine papers that used RDP
  • Searched for ways to compare RDP outputs that used different alignments to analyze large genomes

Week 6:200706- 200710

  • Decided to develop circuit that initially secretes AA then switches to DHA
  • Researched using an Omp-sensor to determine TNF-α or IFN-γ concentrations
  • Started preparing Camp Launch Presentation
  • Started to model circuit
  • Looked into methods to vet the accuracy of RDP
  • Reached out to Dr. Rothschild concerning presenting at our Meetup
  • Continued to develop TikTok Scripts and searched for images

Week 7: 200713-200717

  • Prepared for and hosted Meetup
  • Camp Launch Presentation

Week 8: 200720- 200724

  • Reached out to people concerning IHP
  • Corresponded with Pittusburg about participating in their podcast project
  • Wrote promoter script for Purdue collaboration
  • Started looking for parameters for the model
  • PLUS-S presentation

Week 9: 200727- 200731

  • Considered how to export fatty acids across the cell membrane
  • Created plan for gram positive export of DHA
  • Continued writing TikTok scripts
  • Looked into using a band-pass filter for controlling AA and DHA production
  • Ran RDP with different parameters to determine effect
  • Researched possible simulation methods for assessing RDP
  • Looked into ways to develop datasets for RDP analysis

Week 10: 200803-200807

  • Conducted additional IHP interviews
  • Worked on developing simulated data set

Week 11: 200810-200814

  • Continued looking into using a band-pass filter for controlling AA and DHA production
  • Started to write parts page summaries for the following parts: OmpA, FabH, FadD, OprF, FadE, FadL
  • Researched RDPv4 and alignment
  • Continued to write scripts for TikTok Videos
  • Considered using IGTV as a possible alternative to TikTok if it became banned

Week 12: 200817- 200821

  • Started to create equations for model
  • Looked into possible ways to induce band-pass filter
  • Wrote script outline for Modeling for the Masses Video
  • Hosted Pandemic Preparedness Panel for the iGEM 2020 Global Meetup

Week 13: 200824-200828

  • Continued parameter hunting
  • Recorded voice overs for TikTok videos
  • Looked into possible RNA toehold switch to control production of DHA and AA

Week 14: 200831- 200904

  • Posted first round of TikTok videos
  • Looked into functions for production and decay of TNF-α and IFN-γ
  • Parameter hunting

Week 15: 200907-200911

  • Developed presentation for Biomath portion of our biology program for feedback on our work
  • Reached out to various popular science accounts on TikTok to try and have them promote our videos

Week 16: 200914- 200918

  • Posted additional installation of TikTok videos
  • Started to write protocols
  • Parameter search continued

Week 17: 200921-200925

  • Additional parameter hunting
  • Worked on writing script for Promotional Video
  • Filmed and edited promotional video

Week 18: 200928- 201002

  • Tried to promote TikTok videos within our own community: reached out to public health club, William and Mary Facebook pages, and neuroscience club
  • Continued parameter search
  • Worked on model development

Week 19: 201005- 201009

  • Wrote team abstract
  • Parameter search
  • Worked on developing model

Week 20: 201012-201016

  • Continued searching for parameters

Week 21: 201019- 201023

  • Started to work on coding the wiki
  • Worked on finalizing protocols for wiki
  • Developed Modeling for the Masses script
  • Developed summary of RDPv4 research
  • Wrote individual Meet the Team sections
  • Continued working on the model

Week 22: 201026- 2010-27

  • Finalizing the wiki