Team:Stony Brook/Notebook

Notebook
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Notebook

Our team was divided into a total of 4 subteams: Design, Modeling, Outreach, and Web Development. In order to keep each other updated on the different aspects of our project, we held weekly meetings every Tuesday afternoons on Zoom. Here is a rundown of what we completed every week as we worked on LightSwitch!



WEEK ONE

Area Description
Design and Research
  • Familiarizing ourselves with Bax, HR, and PCD through articles
Outreach and Fundraising
  • Reaching out to farmers, highschool teachers
  • Prepping for iGEM collabs and challenges
  • Setting up Molecular cloud account
  • Submitting Revive and Restore Grant

WEEK TWO

Area Description
Design and Research
  • Finalizing Design and Construct document
  • Meeting with Dr. Balázsi to review our new approach
Outreach and Fundraising
  • Reaching out to OSU and Oneonta for collaboration opportunities
  • Emailing more farmers
  • Begin prepping an outreach presentation for high schools
  • Working on GMO attitude survey
  • Introducing our project in Social Media
  • Organizing #introGEM challenge
Website Development
  • Familiarizing ourselves with Github, HTML & CSS

WEEK THREE

Area Description
Design and Research
  • Reviewing more articles
Modeling
  • Coming up with ideas for potential modeling for our project
Outreach and Fundraising
  • Contacted CSTEP to set up a date for an iGEM presentation
  • Emailing farmers that have not replied back
  • Finalizing meetings with OSU and Oneonta
  • Updating Social Media
  • Reaching out to more high schools we can present to
Website Development
  • Finishing up skeleton pages for the wiki (no content)

WEEK FOUR

Area Description
Design and Research
  • Familiarizing ourselves with Benchling, writing more notes on articles
  • Attempting to finalize BphP1 and Bax constructs
Modeling
  • Reviewing MATLAB and Python
  • Writing notes on Boolean logic, phylogenetic analysis, fluorescnece microscopy, and import/export ODEs
Outreach and Fundraising
  • Met with Jen from HeartBeet farms
  • Established scripts for scientists
  • Continuation of #introGEM challenge
Website Development
  • Establishing a timeline for the Wiki
  • Beginning profile cards for team members

WEEK FIVE

Area Description
Design and Research
  • Establishing a flowchart of our current design and reading more papers
  • Updating Design and Construct document
Modeling
  • Writing up questions for Dr. B meeting
  • Reviewing differential equations
Outreach and Fundraising
  • Began thinking about possible Human Practice ideas, such as a series of educational YouTube video or a GMO handbook for farmers
  • Considering reaching out to SBU BioEthics Club and Philosophy department
Website Development
  • Continuing further page development
  • Writing up content for Wiki
  • Researching past teams' Wikis

WEEK SIX

Area Description
Design and Research
  • Looking into tissue specific promoter for activation of our switch
  • Worked on improving our project after discussing the points made in the meeting with Dr. Hughes
Modeling
  • Reviewing meeting with Dr. Balázsi and reading modeling papers
Outreach and Fundraising
  • Preparing for meeting with Babylon Micro-Farms
  • Established collaboration ideas with OSU and Oneonta. Reaching out to Dr. Kate Creasey
Website Development
  • Further research into other Wikis and writing up more content

WEEK SEVEN

Area Description
Design and Research
  • Looking into locus to insert our construct into, continuing work on gene circuit
  • Meeting with Dr. Verkhusha
Modeling
  • Preliminary flowchart is done
  • Continuing work on BphP1 shuttling, Bax mRNA and protein production, and formation of the MAC
Outreach and Fundraising
  • Preparing for CSTEP presentation
  • Reaching out to more farmers
  • Continuing collabs with OSU and Oneonta
  • Beginning new collab with MSP
Website Development
  • Beginning styling on the website and looking into Bootstrap

WEEK EIGHT

Area Description
Design and Research
  • Looking into the UVR8 optogenetic system, designing siRNA, and working to have our system target CLV/WUS
Modeling
  • Looking into new modeling approaches given the improved design
Outreach and Fundraising
  • Working further into our posters for our collaboration with Oneonta
  • Meeting with David from Babylon Micro-Farms
  • Further collaboration work
Website Development
  • Looking more into Boostrap, website content, and general styling

WEEK NINE

Area Description
Design and Research
  • Moving forward with UVR8
  • Weighing advantages and disadvantages of siRNA, miRNA, and CRISPRi
  • Beginning early stages of establshing an experimental protocol
Modeling
  • More Python tutorials with Justin
  • Looking into prospective modeling approaches
Outreach and Fundraising
  • Working on expanding our Education initiative by looking into pre-freshman/freshman clubs and organizations at Stony Brook University to present to
  • Reaching out to Square Roots Farms
  • More work with OSU, Oneonta, and MSP
  • Beginning to post facts about vertical farming to engage our social media followers
Website Development
  • Wiki styling and preliminary Bootstrap implementation

WEEK TEN

Area Description
Design and Research
  • Looking into complications associated with expressing homologous UVR8, if any
  • Working on a light-inducible promoter for our xiRNA construct
  • Organizing a schedule for the Dr. Creasey presentation
  • Working on the Dr. Creasey Experimental Protocol and Strategy presentation
Modeling
  • Running Tinkercell on GEMini within CoCalc
  • Looking into a way to use GROMACS to stimulate protein protein interactions and determine a few kinetics of our system
Outreach and Fundraising
  • Contacting more organizations and schools like the Educational Opportunity Program (EOP) to ask if we can present to them and further our educational initiative
  • Looking into contacting the USDA
  • Organizing meeting with Maxwell from Square Root Farms
  • Tweaking OSU video collaboration, brainstorming poster ideas for the Oneonta collaboration, and setting up a timeline to finish the MSP collab
Website Development
  • Flushing out features for our Wiki, such as a dark vs. light theme and logos
  • Beginning to finalize design decisions

WEEK ELEVEN

Area Description
Design and Research
  • Finalizing experimental protocols
  • Presenting to Dr. Creasey
  • Looking into transient transformation
  • Looking into possible real-life applications for our project
Modeling
  • Simulating UVR8 dimer in water
  • Going through GROMACS tutorials to become more familiar with the program
Outreach and Fundraising
  • Beginning Instagram Takeover series to increase engagement with our followers
  • Tweaking our GMO survey and reaching out to faculty that can potentially help us distribute it
  • Reaching out to faculty to see where we can put our GMO poster for the Oneonta collaboration
Website Development
  • Starting to finalize styling for the Wiki
  • Updating Wiki content
  • Looking into possible logo ideas

WEEK TWELVE

Area Description
Design and Research
  • Switching our model organism from A. thalina to N. benthamiana
  • Finalizing protocols
  • Starting up MSP Journal Collaboration
  • Revising constructs for N. benthamiana
Modeling
  • Looking into I-TASSER, a server hub that allows us to process protein structure and templates
  • Continuing work on BagelBot
Outreach and Fundraising
  • Organizing meeting with Dr. Dickson Despommier, the founder of modern day Vertical Farming
  • Reaching out to Tony from Freight Farms
  • Beginning video production for the OSU video collaboration
  • Starting up Instagram takeovers
Website Development
  • Reviewing and updating Wiki content
  • Revising schedule to accomodate the new iGEM deadlines

WEEK THIRTEEN

Area Description
Design and Research
  • Finalizing experimental protocols in terms of genotyping and phenotyping
  • Looking into the CLAVATA-WUSCHEL pathway in other organisms
  • Continuing article for the MSP collaboration
  • Continuing to revise constructs for N. benthamiana
Modeling
  • Working with MEGAx, a phylogeny software
  • Debugging BagelBot
Outreach and Fundraising
  • Writing up questions for the meeting with Dr. Despommier
  • Reaching out to Mike Axelrod, Instructional Support Specialist and Greenhouse Curator at Stony Brook University
  • Finalizing voiceovers for the OSU video collaboration
  • Continuing to write stuff up for the MSP journal collaboration
  • Brainstorming ideas for the Oneonta poster collaboration
Website Development
  • Reviewing Wiki content
  • Updating more Wiki content

WEEK FOURTEEN

Area Description
Design and Research
  • Finalizing plant constructs
  • Reaching out to Stony Brook professors for advice on our constructs
Modeling
  • Continuing to upgrade BagelBot
  • Looking into gaining SeaWulf access
Outreach and Fundraising
  • Looking into hosting an event for freshman by reaching out to Stony Brook undergraduate college adviors
  • Making additional changes to our GMO attitude survey
  • Finalizing voiceovers for the OSU video collaboration
  • Committing final changes to the MSP journal collaboration
  • Brainstorming ideas for the Oneonta poster collaboration
  • Editing OSU collaboration video

WEEK FIFTEEN

Area Description
Modeling
  • Conducting even more BagelBot updates and looking into possible future features such as advanced plotting functions and conducting BLAST search on a DNA sequence
Outreach and Fundraising
  • Meeting with Molecular Cloud to reflect on our work and our resilience against COVID-19
  • Continuing poster collaboration with Oneonta
  • Continuing work for iGEM Promotional and Presentation videos

WEEK SIXTEEN

Area Description
Outreach and Fundraising
  • Setting up meeting with Mike Axelrod
  • Organizing presentation for Freshman Symposium
  • Finalizing poster and brochure ideas for Oneonta
  • Continuing to film and do voiceovers for iGEM video deliverables

WEEK SEVENTEEN

Area Description
Modeling
  • Obtaining access to SeaWulf
  • Updating BagelBot
Outreach and Fundraising
  • Working on Presentation and Promotion Videos
  • Continuing collaborations

WEEK EIGHTEEN

Area Description
Modeling
  • Testing SeaWulf
Outreach and Fundraising
  • Working on iGEM Deliverables
Website Development
  • Continuing to update the Wiki before it goes live

WEEK NINETEEN

Area Description
Design and Research
  • Completing iGEM Deliverables
Outreach and Fundraising
  • Completing iGEM Deliverables
Website Development
  • Making further Wiki edits

WEEK TWENTY

Area Description
Design and Research
  • Completing iGEM Deliverables
Modeling
  • Conducting even more BagelBot updates
  • Continuing GROMACS simulations
Outreach and Fundraising
  • Completing iGEM Deliverables
Website Development
  • Making further Wiki edits

WEEK TWENTY ONE

Area Description
Design and Research
  • Completing iGEM Deliverables
Modeling
  • Continuing GROMACS simulations
Outreach and Fundraising
  • Completing iGEM Deliverables
Website Development
  • Making final Wiki edits