Difference between revisions of "Team:Stony Brook/Notebook"

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                           <h1>July</h1>
 
                           <h1>July</h1>
 
                               <ul>
 
                               <ul>
−
                                 <!--<h5 id=cow>Topic 1</h5>-->
+
                                 <li><b>July 1st:</b> <q>So lunch, then cry.</q>
 +
                                  <ul>
 +
                                    <li>Presenting to Green Genes camp at Cold Spring Harbor Laboratory</li>
 +
                                    <li>Competent cells test using controls from Dr. Czaplinski</li>
 +
                                    <li>Troubleshooting transformation protocol</li>
 +
                                    <li>Meeting with Dr. Seeliger to discuss E.coli membrane compositions and sensing ability</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 2nd:</b> <q>Oh shoot, he wants to be an oncologist! I’m going to be a fire fighter!</q>
 +
                                  <ul>
 +
                                    <li>Making competent cells again, new protocol</li>
 +
                                    <li>Vector digest</li>
 +
                                    <li>Competent cells test</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 3rd:</b> <q>I’m going to name my kid Kevin… especially if it’s a girl.</q>
 +
                                  <ul>
 +
                                    <li>Competent Cell test success!</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 6th:</b> <q>We’re a pretty fertilized species.</q>
 +
                                  <ul>
 +
                                    <li>Start minipreps to extract transformed iGEM vector to use in digestion</li>
 +
                                    <li>Vector digest</li>
 +
                                    <li>Ligation (test 2 hours and overnight)</li>
 +
                                    <li>Gel extraction of Digested Vector</li>
 +
                                    <li>Literary Research into Origin Compatibility</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 7th:</b> <q>Wow! It wasn’t the right math but it was on forever!</q>
 +
                                  <ul>
 +
                                    <li>Vector Ligation, new protocol</li>
 +
                                    <li>Test Rubidium Competent Cells</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 8th:</b> <q>They’re gonna die. Don’t get attached.</q>
 +
                                  <ul>
 +
                                    <li>Presenting to Green Genes and DNA Science camp at Cold Spring Harbor Laboratory</li>
 +
                                    <li>PCR of Construct 1 (12 cycles- incorrect) </li>
 +
                                    <li>Transformations to test Rb competency, plate 4, and ligation product</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 9th:</b> <q>You know when you see something hot and you can see the wiggles?</q>
 +
                                  <ul>
 +
                                    <li>New Digestion protocol</li>
 +
                                    <li>More vector and construct digestions</li>
 +
                                    <li>Meeting with Dr. Gergen to discuss protocols</li>
 +
                                    <li>Meeting with Dr. Balaszi to discuss E. coli</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 10th:</b>
 +
                                  <ul>
 +
                                    <li>Digest without BSA</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 13th:</b> <q>I identify most as a spatula.</q>
 +
                                  <ul>
 +
                                    <li>Testing restriction enzymes</li>
 +
                                    <li>Obtaining new Xbal</li>
 +
                                    <li>Ordered more IDT constructs</li>
 +
                                    <li>More digestions</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 14th:</b> <q>I’m no better than a monkey in a lab coat.</q>
 +
                                  <ul>
 +
                                    <li>More digestions of construct</li>
 +
                                    <li>Ligation of Constructs</li>
 +
                                    <li>Finding a new protease</li>
 +
                                    <li>Literature research: diseases that can be treated with tripeptides</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 15th:</b> <q>I never understood family.</q>
 +
                                  <ul>
 +
                                    <li>More digestions of construct</li>
 +
                                    <li>Successful PCR of constructs</li>
 +
                                    <li>Teaching at Cold Spring Harbor</li>
 +
                                    <li>Literary research on Diabetes Insipidous</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 16th:</b> <q>If Greg doesn’t eat before 1 he must feast on the blood of humans.</q>
 +
                                  <ul>
 +
                                    <li>More construct digestions</li>
 +
                                    <li>New ligation protocol</li>
 +
                                    <li>Troubleshooting vector digestion</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 17th:</b> <q>Manslaughter? Manslaughter.</q>
 +
                                  <ul>
 +
                                    <li>More digestions and ligations</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 20th:</b> <q>The shapes add a little bit of fun to it.</q>
 +
                                  <ul>
 +
                                    <li>More digestion and ligation</li>
 +
                                    <li>Exploring ways to make gels of a higher resolution</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 21st:</b> <q>Can we practice flicking?</q>
 +
                                  <ul>
 +
                                    <li>More digestions and ligations</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 22nd:</b> <q>Cells are so stupid.</q>
 +
                                  <ul>
 +
                                    <li>More digestions and ligations</li>
 +
                                    <li>Meeting with Dr. Czaplinski to troubleshoot ligation protocol</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 24th:</b> <q>He needs to know how heavily he’s vomiting.</q>
 +
                                  <ul>
 +
                                    <li>Finding concentration of DNA using a gel</li>
 +
                                    <li>More digestion and ligations</li>
 +
                                    <li>Making Competent cells</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 27th:</b> <q>He’s bald</q>
 +
                                  <ul>
 +
                                    <li>More digestions and ligations</li>
 +
                                    <li>Troubleshooting gel extraction protocol</li>
 +
                                    <li>Successful ligation and transformation of construct 3!</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 28th:</b> <q>Motherhood made me soft.</q>
 +
                                  <ul>
 +
                                    <li>More digestions and ligations</li>
 +
                                    <li>Working on URECA poster</li>
 +
                                    <li>Modifying Melittin BioBrick sequence</li>
 +
                                    <li>Wiki content writing</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 29th:</b> <q>One thing goes wrong and they’re my children, not our children</q>
 +
                                  <ul>
 +
                                    <li>More PCR</li>
 +
                                    <li>More digestions and ligations</li>
 +
                                    <li>Register for URECA summer research symposium</li>
 +
                                    <li>Working on URECA poster</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 30th:</b> <q>Either you succeed in life or you’re worthless to me.</q>
 +
                                  <ul>
 +
                                    <li>Successful transformation of construct 3</li>
 +
                                    <li>Sequence construct 3</li>
 +
                                    <li>Archea collaboration with UGA</li>
 +
                                    <li>Refining project application</li>
 +
                                    <li>Working on project abstract</li>
 +
                                    <li>Looking at alternative protesases</li>
 +
                                  </ul>
 +
                                </li>
 +
                                <li><b>July 31th:</b> <q>If I make a hole big enough for bread to go through, that doesn’t mean that people can.</q>
 +
                                  <ul>
 +
                                    <li>Successful PCR</li>
 +
                                  </ul>
 +
                                </li>
 +
 
 
                                   </ul>
 
                                   </ul>
 
                           </div>
 
                           </div>

Revision as of 05:21, 18 September 2015

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Notebook

The Problem

January-April

    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 sueing
  • 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

The Idea

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

Sensor

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: I never understood family.
    • 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
    • Archea 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

Effector

August-September