iGEM 2015 — Team Stony_Brook

# Team:Stony Brook/Notebook

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## Notebook

# **[January-May](#text1)**

# **[June](#text2)**

# **[July](#text3)**

# **[August-September](#text4)**

![](https://static.igem.org/mediawiki/2015/c/cc/SBU_Side_Pic_1.jpg)

### 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

![](https://static.igem.org/mediawiki/2015/d/db/SBU_Side_Pic_2.jpg)

### 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:** "Ya know, Simon is a really charismatic person!"
  + 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

![](https://static.igem.org/mediawiki/2015/6/68/SBU_Side_Pic_3.jpg)

### 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

![](https://static.igem.org/mediawiki/2015/4/46/SBU_Side_Pic_5.jpg)

### 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

[* Home](https://2015.igem.org/Team%3AStony_Brook)
[* Team](https://2015.igem.org/Team%3AStony_Brook/Team)
[* Project Description](https://2015.igem.org/Team%3AStony_Brook/Description)

[* Project Results](https://2015.igem.org/Team%3AStony_Brook/Results)

[* Team Parts](https://2015.igem.org/Team%3AStony_Brook/Parts)

[* Modeling](https://2015.igem.org/Team%3AStony_Brook/Modeling)
[* Notebook](https://2015.igem.org/Team%3AStony_Brook/Notebook)
[* Collaborations](https://2015.igem.org/Team%3AStony_Brook/Collaborations)
[* Human Practices](https://2015.igem.org/Team%3AStony_Brook/Practices)
[* Attributions](https://2015.igem.org/Team%3AStony_Brook/Attributions)

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