Team:Stony Brook/Notebook

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Notebook

January-May

January-May

    January

  • A box of pipette tips could ruin your life.
  • Applications for new iGEM team members are finalized and approved.
  • The new team meets for the first time!

    • Febuary

  • My family is really big on suing
  • Learning about circuit design
  • Attending University lectures on synthetic biology
  • Brainstorming topics for the project

    • March

  • I’m dropping you off on the side of the road on the way home.
  • Planning fundraising events
  • Applying for University sponsored research grants
  • Lab Training
  • Learning about primer design

    • April

  • We’re not poor, we’re environmentally conscious
  • Project Proposal Presentations
  • Choose final project topic
  • Researching Sensing systems in E. coli
  • Researching laboratory protocols
  • Writing to companies to acquire sponsorships

    • May

  • Oh dear, we made it mad
  • Meet with Dr. Balaszi and Dr. Gergen to finalize project topic
  • Making lists of supplies to purchase
  • Literature research
  • May 8th: That’s my life goal...to be an old person.
    • Meet with Dr. Balaszi for help with math modeling and tripeptide expression
    • Sequence tripeptides in a string instead of one at a time
    • Look for a protease to cut tripeptide repeats
  • May 25th: If I could pull a rabbit out of a graduated cylinder...
    • Apply to volunteer and teach synthetic biology at the Long Island Maker Festival
  • May 26th: Avoid breathing in smelly things.
    • First Day in the Laboratory!
    • Setting up the lab equipment
    • Researching a new protease
    • Finding a plasmid backbone
    • Literature research to modify glucose sensing system in E. coli with ompR mutants
    • Setting up controls to test each step of the procedure
    • Literature research to find protein export system
  • May 27th: It’s like a pleasant cup of hot chocolate.
    • Finalizing Circuit constructs
    • Literature research to optimize sensor
    • Use of his tag to track sequences
    • Finding existing BioBricks to use in circuit
    • Working on presentation for Maker festival
  • May 28th: The worst things that humanity has invented are genocide, the atomic bomb and black licorice.
    • Refining shopping list
    • Finalizing circuit
    • Working on presentation for Maker Festival
  • May 29th: It’s kind of redundant having both of you on the team.
    • Learning how to BioBrick Melittin via Add-on-PCR
    • Literature research on rare codons
    • Meeting with Dr. Gergen to talk about how to detect tripeptides
    • Literature research on new protein export system

June

June

  • June 1st: I need an adult
    • Literature research on another new protease
    • Find new plasmid for constructs
    • Literature research on bacteria recombination effects on constructs
    • Email Stony Brook professors for help detecting tripeptides
  • June 2nd: It’s not going to be hard, it’s going to be very difficult
    • Literature research on HlyA secretion tag
    • Literature research on E. coli strains with T7 Polymerase integrated into genome
    • Meeting with Dr. Thanassi to learn about HlyA tag system
  • June 3rd:
    • Decide on plasmid to use from iGEM kit
    • Order E.coli from Yale CGSC
    • Team presented project design at Wantagh High School
    • Video call with Synbiota for sponsorship
    • Emailed director of Humanology project for potential partnership
  • June 4th: Lime green is not for science.
    • Meeting with Dr. Thanassi to discuss secretion system
    • Finalize two plasmid system with secretion system and tripeptides/protease
  • June 5th: duh, diabetes
    • Literature research on linker to get secreted protease to outer membrane
  • June 8th: I don’t trust anything anymore
    • Find new transporter for tripeptides
    • Looking for compatible plasmids in the two plasmid model
  • June 9th: Everyone… drink the peptide (we didn't drink any peptides, safety first!)
    • Research outer membrane fractionation
    • Literature research on plasmid compatibility
  • June 10th: I like dark blue not an azure
    • Find sequence for new protease
    • Found compatible plasmid
    • Ordered E. coli strains and plasmids
  • June 11th: They’ll probably just drop an elephant on it.
    • Meeting with Dr. Gergen to finalize circuit design
    • Meeting with Dr. Karzai to finalize circuit design
    • Working on poster for Maker Festival
  • June 12th: Now address me as the Buddha. Thank you.
    • Ordered IDT Constructs
    • Meet with Dr. Carlson, head of endocrinology at Stony Brook University Hospital, to talk about the medical ethics and applications of our project
  • June 14th: That’s not how cancer works.
    • iGEM presents at the Long Island Maker Festival!
  • June 17th: I’m not stealing his brain, it’s technically mine, he just didn’t die…
    • Making media
  • June 18th: I can fall asleep doing anything, any time…
    • iGEM bake sale
    • E. coli cells arrive!
    • Plated cells to grow
  • June 19th: It’s not like they are going to throw us in science jail…
    • Find Competent Cell Protocol
  • June 22nd: Imagine a doctor giving you a drink that tastes good, but you know it’s actually poop.
    • Making competent cells
    • Literature research: Protease ATP requirements
  • June 23rd: For future reference, I like blue gloves because they are sexier than purple ones.
    • Competent cell test
    • Learn to Measure OD of Liquid Culture
    • Literary Research of Secretion System
  • June 24th: If I die in this lab, I expect one of you to reanimate me.
    • Resuspending IDT constructs
    • Testing Competent cells
    • Literary Research of Secretion System
  • June 25th: You’d probably just vomit everywhere.
    • Digesting constructs
    • Testing Competent cells
  • June 26th: No! Get some oil and light it on fire!
    • Tested Competent cells, learned not enough chloramp was used
  • June 29th: Imagine Greg and I sober…
    • Making Competent cells
    • Testing Competent Cells (chloramp good, experimental not)
    • Learned to Run a Gel
  • June 30th: Smile with your mistake!
    • Digesting constructs with new protocol
    • Competent cells test
    • Meeting with Dr. Czaplinski to troubleshoot competent cell problems
    • Went to molecular cloning facility to order primers

July

July

  • July 1st: So lunch, then cry.
    • Presenting to Green Genes camp at Cold Spring Harbor Laboratory
    • Competent cells test using controls from Dr. Czaplinski
    • Troubleshooting transformation protocol
    • Meeting with Dr. Seeliger to discuss E.coli membrane compositions and sensing ability
  • July 2nd: Oh shoot, he wants to be an oncologist! I’m going to be a fire fighter!
    • Making competent cells again, new protocol
    • Vector digest
    • Competent cells test
  • July 3rd: I’m going to name my kid Kevin… especially if it’s a girl.
    • Competent Cell test success!
  • July 6th: We’re a pretty fertilized species.
    • Start minipreps to extract transformed iGEM vector to use in digestion
    • Vector digest
    • Ligation (test 2 hours and overnight)
    • Gel extraction of Digested Vector
    • Literary Research into Origin Compatibility
  • July 7th: Wow! It wasn’t the right math but it was on forever!
    • Vector Ligation, new protocol
    • Test Rubidium Competent Cells
  • July 8th: They’re gonna die. Don’t get attached.
    • Presenting to Green Genes and DNA Science camp at Cold Spring Harbor Laboratory
    • PCR of Construct 1 (12 cycles- incorrect)
    • Transformations to test Rb competency, plate 4, and ligation product
  • July 9th: You know when you see something hot and you can see the wiggles?
    • New Digestion protocol
    • More vector and construct digestions
    • Meeting with Dr. Gergen to discuss protocols
    • Meeting with Dr. Balaszi to discuss E. coli
  • July 10th:
    • Digest without BSA
  • July 13th: I identify most as a spatula.
    • Testing restriction enzymes
    • Obtaining new Xbal
    • Ordered more IDT constructs
    • More digestions
  • July 14th: I’m no better than a monkey in a lab coat.
    • More digestions of construct
    • Ligation of Constructs
    • Finding a new protease
    • Literature research: diseases that can be treated with tripeptides
  • July 15th:
    • More digestions of construct
    • Successful PCR of constructs
    • Teaching at Cold Spring Harbor
    • Literary research on Diabetes Insipidous
  • July 16th: If Greg doesn’t eat before 1 he must feast on the blood of humans.
    • More construct digestions
    • New ligation protocol
    • Troubleshooting vector digestion
  • July 17th: Manslaughter? Manslaughter.
    • More digestions and ligations
  • July 20th: The shapes add a little bit of fun to it.
    • More digestion and ligation
    • Exploring ways to make gels of a higher resolution
  • July 21st: Can we practice flicking?
    • More digestions and ligations
  • July 22nd: Cells are so stupid.
    • More digestions and ligations
    • Meeting with Dr. Czaplinski to troubleshoot ligation protocol
  • July 24th: He needs to know how heavily he’s vomiting.
    • Finding concentration of DNA using a gel
    • More digestion and ligations
    • Making Competent cells
  • July 27th: He’s bald
    • More digestions and ligations
    • Troubleshooting gel extraction protocol
    • Successful ligation and transformation of construct 3!
  • July 28th: Motherhood made me soft.
    • More digestions and ligations
    • Working on URECA poster
    • Modifying Melittin BioBrick sequence
    • Wiki content writing
  • July 29th: One thing goes wrong and they’re my children, not our children
    • More PCR
    • More digestions and ligations
    • Register for URECA summer research symposium
    • Working on URECA poster
  • July 30th: Either you succeed in life or you’re worthless to me.
    • Successful transformation of construct 3
    • Sequence construct 3
    • Archaea collaboration with UGA
    • Refining project application
    • Working on project abstract
    • Looking at alternative protesases
  • July 31th: If I make a hole big enough for bread to go through, that doesn’t mean that people can.
    • Successful PCR

August-September

August-September

  • August 3rd: I could never wear pants in lab
    • More digestions and ligations
    • Research potential applications of project in microflora and microcapsules
  • August 4th: Why is this our problem? -Because we have so many, we like to focus on the little ones
    • More digestions and ligations
  • August 5th: It’s like giving birth to words.
    • More digestions and ligations
    • Testing tripeptide production in construct 3 via SDS page gel
    • Testing inducibility of tripeptide production
  • August 7th: I’m the least arrogant at 11:50pm because I’ve used it all up
    • More digestions and ligations
    • Presenting at URECA summer research symposium
    • Finalize project title and submit abstract
  • August 10th: Or, depending on your view of life, best case scenario: we all die
    • Troubleshoot oligo resuspension
    • Resuspend oligos
    • More digestions and ligations
  • August 11th: I like it when it’s wet outside, it’s like an extra shower
    • Troubleshooting ligation protocol
    • More digestions and ligations
    • SDS page gel to test tripeptide production
  • August 12th: My mood gets so good when I look at myself
    • Presenting to DNA Science at Cold Spring Harbor Laboratory
    • Troubleshooting transformation
    • Successful PCR of constructs
    • More digestions and ligations
  • August 13th: You have to pay extra for the bathroom
    • Successful transformation of melittin mCherry optimus
    • More digestions and ligations
  • August 14th: I’m like that transformed E. coli cell that actually transformed.
    • More digestions and ligations
    • Successful transformation of Construct 5 and melittin, melittin optimus and melittin mCherry
    • Meeting with the Dean of the College of Arts and Sciences
  • August 15th: Hold your pants
    • More digestions and ligations
  • August 17th: Is it sketchy? Cuz’ I’ll get mugged or something
    • Sequencing constructs
  • August 19th: It’s animated -Yes, because the real dinosaurs are hard to book
    • Presenting to Green Genes camp at Cold Spring Harbor Laboratory
    • Attending training session at New York Hall of Science
  • August 23th: We can put diabetes medicine in your eye
    • Presenting at the New York Hall of Sciences synthetic biology event

September

    What if we get arrested in Boston?
  • Back to school
  • More digestions and ligations
  • BioBricking
  • Testing constructs
  • Working on team poster and presentation
  • Writing wiki content