Team:RHIT/Notebook

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Week 1

  • 6/4/2012: First round of project planning, lab clean-up, general outline for summer.

  • 6/5/2012: Second round of project planning, lab clean-up, research into Johns Hopkins 2008 summer project.

  • 6/6/2012: Third and final round of project planning, final lab clean-up, research into the pigment pathways and reporter genes, analysis of Cambridge project.

  • 6/7/2012: Broke down Johns Hopkins 2008 project, results in wiki, found pigments for A and a, found possible fluorescence colors, found possible proteins.

  • 6/8/2012: Research on Promoters, updated Next Actions.

Week 2

  • 6/11/2012: Identified a positive feedback loop that's been done in yeast before and a possible selection scheme, started plasmid mapping, set up server for wiki, began wiki design and looked at color schemes, block-diagrammed positive feedback loop, ate a whole tray of brownies.

  • 6/12/2012: Found gene sequences, continued work on graphic for top of Wiki, looked for selection schemes, shot down selection schemes.

  • 6/13/2012: Fluorescence construct, research on Gibson assembly and gateway vectors, updated wiki to make it more functional, talked about selection schemes, obtained 2 posters, tooks some pics.

  • 6/14/2012: Preparation for Journal Club, lunch with IRC and Math REU people, checked for sequences for plasmid construction.

  • 6/15/2012: Used Gene Designer to do primilary sequencing of plasmid, research on spacing of plasmid.

Week 3

  • 6/18/2012: Optimized DNA sequences, found all of the filler DNA.

  • 6/19/2012: Talked with Dr. Almaas, started web design, took pictures with storm troopers, team movie night.

  • 6/20/2012: Web design, learned HTML.

  • 6/21/2012: Web design, preliminary website up, team lunch, IRC meeting.

  • 6/22/2012: Individual work day.

Week 4

  • 6/25/2012: Group discussion, work on school website, organization of collected information.

  • 6/26/2012: Obtained shirts, found and organized all sequences, started to verify sequences, school page is 85% done.

  • 6/27/2012: Changes to DNA sequences, worked on finalization of sequence, looked at a 3D modeling program, contacted original DNA company about sequencing.

  • 6/28/2012: Worked on finalizing the sequence, identified materials needed for Gibson assembly, went to IRC presentation on grad. school/UC from Rose Undergraduate.

  • 6/29/2012: Individual work day.

Team Break Week

Week 5

  • 7/9/2012: Got back from break. Learned DNA had not shipped yet. :( Worked on wiki.

  • 7/10/2012: Worked on wiki.

  • 7/11/2012: Received edited version of what original DNA company will do to our DNA sequences. We compared them to the originals and prepared questions for original DNA company.

  • 7/12/2012: Talked to original DNA company about questions.

  • 7/13/2012: Individual work day.

Week 6

  • 7/16/2012: Decided to use GeneArt for sequences instead of original DNA company.

  • 7/18/2012: Brainstormed ideas for side projects while waiting for DNA shipment.

  • 7/19/2012: Continued brainstorm, expanding into Human Practices.

  • 7/20/2012: Created teams: Wiki, Presentation, Poster, and Maya.

  • 7/21/2012: Met in teams to plan and brainstorm. Added Team Board Game.

Week 7

  • 7/23/2012: Devon and Kristen began planning the THCM exhibit.

  • 7/24/2012: Continued work in Teams. Began intial research into pathway for modeling.

  • 7/25/2012: Continued work in Teams; added Team Modeling.

  • 7/26/2012: Continued work in Teams.

  • 7/27/2012: Continued work in Teams, lunch with IRC people

Week 8

  • 7/30/2012: Ironed out wiki formatting, began adding content, continued Maya animation.

  • 7/31/2012: Lab work, continued adding content to wiki.

  • 8/1/2012: Lab work, added more content to wiki, got update on additional computer for Maya animation, made significant progress on math model, Rose-Hulman team page went live.

  • 8/2/2012: Lab work, continued work in Teams.

  • 8/3/2012: Lab work, continued work in Teams.

Week 9

  • 8/6/2012: Canoe trip with IRC members, lab work.

  • 8/7/2012: Lab work, focus on modeling information for NTNU, continued work in Teams.

  • 8/8/2012: Second Skype meeting with NTNU, continued work in teams, conclusion and review of Maya animation, lab work.

July 31, 2012

Made media: YPD, L-AMP, CSM, and CSM-His


Members: Ben, Bobby, Alex, Kristen, Devon, Dr. A.

August 1, 2012

Streaked out plasmid-bearing E. coli strains (pRS416 & pRS413) and yeast strains
Members: Ben, Bobby, Alex, Kristen, Devon, Dr. A.

August 2, 2012

Checked for E. coli colonies: success. Made liquid L-AMP media, innoculated small cultures.
Members: Ben, Bobby, Alex, Kristen, Devon, Dr. A.

August 3, 2012

Qiagen minipreps
Members: Ben, Bobby, Alex, Kristen, Devon, Dr. Dave.

August 6, 2012

Made stock solutions for transformation procedures
Members: Adam, Kristen, Dr. A

August 7, 2012

Transformed E. coli with our red construct
Members: Bobby, Adam, Devon, Kristen, Ben, Dr. A

August 8, 2012

Inoculated liquid media with transformed E.Coli
Members: Bobby, Adam

August 9, 2012

Ran Mini-Preps of pRS413, pRS416, and Red construct bearing E. Coli, stored extracted DNA
Members: Bobby, Adam

August 10, 2012

Ran quick gel of extracted DNA
Members: Bobby, Adam

August 11, 2012

Digested extracted DNA, isolated pRS413 & pRS416 fragments from gel
Members: Bobby, Adam

August 12, 2012

Isolated red construct fragments on gel, poured chloramphenicol plates
Members: Bobby, Adam

August 13, 2012

Digested extracted DNA, isolated pRS413, pRS416, and Red Construct from gel, Transformed E. Coli with NTNU construct
Members: Bobby, Adam, Dr. A

August 14, 2012

Ligated pRS413 and red construct, transformed E. Coli with ligated plasmid, inoculated liquid media with NTNU E. Coli
Members: Bobby, Adam

August 15, 2012

Mini-Preps of NTNU construct, confirmed presence on gel, Digested pRS413, pRS416, and Red Construct, poured ampicillin plates
Members: Bobby, Adam

August 16, 2012

Isolated pRS413, pRS416, and Red Construct from gel, began storing strains, DNA, and equipment
Members: Bobby, Adam

August 17, 2012

Ran digestion of pRS413, pRS416, and Red Construct, stored remaining strains, DNA, and equipment
Members: Bobby, Adam, Dr. A

August 28, 2012

Transformed E.Coli with BBa_E0422 reporter
Members: Bobby, Adam, Dr. A

August 29, 2012

Digested and isolated Red Construct and pRS413 from gel, Inoculated liquid media with BBa_E0422 reporter
Members: Adam

August 31, 2012

Digested pRS413 and Red Construct, Isolated from gel and Ligated, Transformed E. Coli.
Members: Adam

August 30, 2012

Digested pRS413 and Red Construct
Members: Bobby, Adam, Dr. A

September 1, 2012

Started cultures of pRS413 and the Red construct form frozen cultures
Members: Adam

September 2, 2012

Inoculated liquid media with colonies from plates of pRS413 and Red Construct strains
Members: Adam

August 29, 2012

Ran mini-preps of liquid colonies
Members: Adam
Protocol text

Researcher, Public, and Environmental Safety

The Rose-Hulman iGEM team has kept safety a top priority since the very early stages of the project. As a result, any project that might have posed as a significant threat to safety was quickly dismissed. During the planning phase of Checkmate, team members brainstormed lab procedures as well as guidelines for plasmid construction to provide a safe and effective workplace. The team used yeast and E.coli in their project, which are both considered Risk Group 1 microorganisms according to the Laboratory Biosafety Manual by the World Health Organization. A Risk Group 1 organism is defined as “(no or low individual and community risk) A microorganism that is unlikely to cause human or animal disease.” The team’s lab is a Basic-Biosafety Level 1 lab, but contains a few aspects from the other categories. The lab does have controlled access, special waste disposal bins, and som

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