Team:William and Mary/Notebook

Spring Semester 2021 Summer 2021 Fall Semester 2021


Notebook

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Spring Semester 2021:

2/14 - 2/20:

  • First meeting: discussed basic tenets and principles of synthetic biology
  • Discussed past iGEM projects that included wetlab and modelling

2/21 - 2/27:

  • Discussed what makes a great iGEM project
  • Discussed basic tenets and principles of synthetic biology
  • Reviewed medal criteria
  • Presented on past iGEM projects that stood out to us

2/28 - 3/06:

  • Read papers on bioremediation and synthetic biology applications
  • Continued discussion on synthetic biology fundamentals

3/07 - 3/13:

  • Started brainstorming project ideas
  • Started literature search for topics
  • Discussed many applications of synthetic biology: bioremediation for aquatic systems and pharmaceutical waste

3/14 - 3/20:

  • Compiled ideas from project brainstorming
  • Continued idea research
  • Continued discussion of synthetic biology fundamentals

3/21 - 3/27:

  • Discussed oyster parasitic infection ideas
  • Continued idea research - discussion of orthogonality

3/28 - 4/03:

  • Continued oyster discussion
  • Continued orthogonality discussion
  • Continued marine bioremediation discussion
  • Continued idea research

4/04 - 4/10:

  • Continued idea research: orthogonality
  • Arranged for summer housing
  • Prepared for outreach BioEngineering presentation to students

4/11 - 4/17:

  • Discussed bacterial plastic remediating
  • Continued idea research

4/18 - 4/24:

  • Conducted BioEngineering presentation
  • Discussed orthogonality
  • Continued discussing plastic and microplastic remediation

4/25 - 5/01

  • Read and searched for literature on orthogonality
  • Continued discussing microplastic remediation

5/02 - 5/08

  • Discussed diatoms for microplastic remediation
  • Continued discussing orthogonality

5/09 - 5/15

  • Made individual iGEM accounts under team name
  • Decided on orthogonality focus

5/16 - 5/22

  • Searched Addgene for interesting circuits in E. coli
    • Reviewed details and decided on favorites
  • Ordered Addgene circuits in E. coli for testing over the summer

5/23 - 5/29

  • Assigned circuits to people and working groups for testing
    • Reviewed strains and feasibility of testing
  • Researched literature on orthogonality in Synthetic Biology
  • Completed CITI research training modules online

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Summer 2021:

5/30 - 6/05

  • Completed basic laboratory training
  • Conducted a series of minipreps to confirm plasmids
  • Finished institutional research training
  • Developed protocols for equipment in the lab
  • Reviewed papers concerning orthogonality
  • Created Powerpoint presentation for outside our lab

6/06 - 6/12

  • Performed restriction digests on minipreps to confirm plasmids
  • Conducted team wide discussions on orthogonality papers
  • Looked into previous iGEM projects involving orthogonality
  • Reached out to the Second Sundays organization to present at their festival
  • Wrote our Meet the Team Page
  • Formed Wiki work groups

6/13 - 6/19

  • Performed restriction digests on minipreps to confirm presence of plasmids
  • Wrote protocols to confirm functionality of plasmids
  • Filled out safety form
  • Designed primers to confirm plasmids
  • Searched the literature for RNA-sequencing of circuits

6/20 - 6/26

  • Began working on confirming plasmid functionality
  • Conducted team discussion on papers related to orthogonality that used RNA-seq
  • Started brainstorming larger picture ideas of how to apply our orthogonality model
  • Miniprepped and made official glycerol stocks from AddGene colonies
  • Submitted our Safety Form
  • Finished Powerpoint for outside lab
  • Worked on Impact Grant application

6/27 - 7/03

  • Continued working on confirming plasmid functionality
  • Completed surveys posted by other iGEM teams
  • Began looking for RNA extraction protocols suited for our experiments
  • Began working on the script for the Promotional Video
  • Started planning for the Mid-Atlantic Meetup
  • Reached out to retirement homes
  • Worked on identifying circuit backbones
  • Started discussing design ideas for the diagnostic circuit

6/27 - 7/03

  • Continued working on confirming plasmid functionality
  • Completed surveys posted by other iGEM teams
  • Began looking for RNA extraction protocols suited for our experiments
  • Began working on the script for the Promotional Video
  • Started planning for the Mid-Atlantic Meetup
  • Reached out to retirement homes
  • Worked on identifying circuit backbones
  • Started discussing design ideas for the diagnostic circuit

7/04 - 7/10

  • Worked on animations for Promotional Video
  • Worked on the script for the Promotional Video
  • Began looking for speakers for the Mid-Atlantic Meetup
  • Decided which circuits to continue working with for RNA extraction

7/11 - 7/17

  • Worked on animations for Promotional Video
  • Started creating databases for papers/projects mentioning orthogonality
  • Continued protocol for circuits whose RNA we planned to sequence
  • Began drafting IHP emails
  • Started planning for this year’s Mid-Atlantic Meetup

7/18 - 7/24

  • Planned for this year’s Mid-Atlantic Meetup
  • Finalized editing for Promotional Video
  • Analyzed DE genes from genetic circuits in the literature
  • Froze cell samples for RNA extraction from pDawn-Ag43 in E. coli JS006
  • Continued work on databases for papers/projects mentioning orthogonality

7/25 - 7/31

  • Designed schematic for sensor circuit, looked into individual parts
  • Added marker genes to host model, found parameters, started working on PTM model
  • Researched PTMs with regard to metabolism and heat shock response
  • Drafted IHP emails to researchers and stakeholders with updates to reflect circuit design
  • Finished database for ACS SynBio papers published in 2020

8/01 - 8/07

  • Continued search for the individual parts of our circuit
  • Hosted the Mid-Atlantic Meetup
    • Prepared for animation and data science seminar
    • Prepared for team presentation
  • Continued analysis of DE genes from genetic circuits, considering potential environmental interactions
  • Researched population models including colony formation

8/08 - 8/14

  • Started reviewing ACS SynBio database and 2019 iGEM project database
  • Wrote team Attributions page for Wiki
  • Assigned responsibilities for Wiki pages and started drafting
  • Started drafting Review
  • Inoculated samples of untransformed DH5-alpha and JS006
    • Spun down samples for RNA extraction
  • John Marken IHP Interview
  • Aptamer literature search
    • Searched for new aptamer for in vivo transcription sensor circuit
    • Searched for optimal promoter
  • Began transcription, translation, and post translational modification literature search for in vitro system
  • Began genome integration literature search
  • Had IHP meeting with John Marken

8/15 - 8/21

  • Edited and revised Wiki drafts
  • Aqib Hasnain IHP interview
  • Continued ACS SynBio and 2019 iGEM database reviews
  • Updated transcriptional sensor circuit parts
  • Dr. Barrick IHP interview
  • Ordered transcriptional sensor circuits from IDT
  • Continued translational sensor circuit literature review
  • Worked on differential gene Venn Diagram
  • Presented at WindsorMeade retirement home

8/22 - 8/28

  • Dr. Barrick follow up interview
  • Researched Beyond Central Dogma differential genes
  • Continued ACS SynBio and 2019 iGEM database reviews
  • Ordered translational sensor circuits from IDT
  • Designed Gibson primers for sensor circuit assembly
  • Made protocol for transcriptional circuit testing

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Fall Semester 2021:

8/29 - 9/04

  • Designed Beyond Central Dogma circuits to detect differential gene expression
  • Finished review of ACS SynBio article spreadsheet
  • Finished full drafts of Wiki pages
  • Reviewed education pamphlet
  • Ran double digest on pSB1C3 vector to confirm sequence
  • Received translation and posttranslational modification circuits
  • Made protocols for resuspension of gBlocks and oligonucleotides
  • Performed PCR purification of pSB1C3 vector
  • Performed Gibson assembly of circuits 11, 12, 13, and 16 and transformed into DH5-alpha
  • Installed GENOCad

9/05 - 9/11

  • Designed circuits to detect expression from lon promoter and hslUV promoter
  • Reviewed education pamphlet
  • Worked on designing in vitro sensor
  • Transformed PTM circuit
  • Recorded video for promotion of iGEM team
  • Performed colony PCR on Gibsoned and transformed circuits
  • Transformed circuit 15 into NEB 5-alpha for cloning
  • Tested fluorescence of translational circuits in plate reader
  • Performed primer resuspension of primers 702 and 703
  • Sent out circuits 11, 12, and 16 for sequencing with primers 1, 16, 17, and 18
  • Tested fluorescence of translational circuits using the plate reader
  • Transformed circuits 13 and 16 into BL21(DE3)
  • Edited wiki page drafts
  • Created presentation for SDG Conference
  • Learned and wrote code and instructions for differential gene expression analysis
  • Calculated figures from spreadsheet of iGEM projects addressing orthogonality
  • Continued genome integration research

9/12 - 9/18

  • Continued in vitro sensor circuit design
    • Decided on in vitro aptamer
  • Miniprepped transcriptional and translational circuits
  • Finalized sensor circuit testing protocol
  • Dr. Smith IHP interview
  • Colony PCR on colonies 13, 15, and 16
  • Finalized and ordered lon, hslUV, and clpB circuits
  • Conducted NovaVax interview

9/19 - 9/25

  • Began fluorescence testing of designed sensor circuits
  • Gibsoned, transformed, and colony PCRed remaining circuits from IDT
  • Sent out IHP emails

9/26 - 10/02

  • Previewed Wiki pages and coding on site
  • Continued testing designed sensor circuits
  • Transformed translational circuits into BL21(DE3)
  • Finalized project abstract

10/03 - 10/09

  • Transformed Ceroni circuits into NEB 5-alpha and cotransformed with pBbB8k curli fiber circuit
  • Began fluorescence testing Ceroni sensor circuits
  • Dr. Renda IHP interview
  • Started analyzing fluorescence data

10/10 - 10/16

  • Continued and finished circuit fluorescence testing
  • Continued data analysis
  • Luis Ortiz IHP interview
  • Transcriptional circuit functionality testing
  • Converted fluorescence measurements to number of molecules
    • Input collected data into model

10/17 - 10/21

  • Finalized Wiki
  • Paul Maschoff IHP Interview

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