Team:RHIT/Notebook

From 2012.igem.org

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Members: Bobby, Adam, Dr. A
Members: Bobby, Adam, Dr. A
<h3>August 29, 2012</h3>
<h3>August 29, 2012</h3>
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Digested and isolated Red Construct and pRS413 from gel, Innoculated liquid media with BBa_E0422 reporter<br />
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Digested and isolated Red Construct and pRS413 from gel, Inoculated liquid media with BBa_E0422 reporter<br />
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Members: Adam
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<h3>August 31, 2012</h3>
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Digested pRS413 and Red Construct, Isolated from gel and Ligated, Transformed E. Coli.<br />
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Members: Adam
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<h3>August 30, 2012</h3>
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Digested pRS413 and Red Construct<br />
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Members: Bobby, Adam, Dr. A
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<h3>September 1, 2012</h3>
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Started cultures of pRS413 and the Red construct form frozen cultures<br />
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Members: Adam
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<h3>September 2, 2012</h3>
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Inoculated liquid media with colonies from plates of pRS413 and Red Construct strains<br />
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Members: Adam
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<h3>August 29, 2012</h3>
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Ran mini-preps of liquid colonies<br />
Members: Adam
Members: Adam
</div>
</div>
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<div class="rhit-fourthSheet" id="rhit-fourthSheet">
<div class="rhit-fourthSheet" id="rhit-fourthSheet">
<h2>Researcher, Public, and Environmental Safety</h2>
<h2>Researcher, Public, and Environmental Safety</h2>
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<p>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 some biohazard signs. The lab is a school lab that is shared by many professors and students during the school year. These safety practices are rarely in use, and are more of a precaution. Some of the lab methods require using potentially hazardous chemicals that could cause injury to any one of the researchers. Another potential safety risk for researchers results from dealing with microbial agents. While it is unlikely that a researcher would develop an infection from the strains he or she is working with, contagion is still a possible safety concern. To combat these risks, the team was sure to follow all safety protocols, from aseptic techniques to complete labeling. Proper lab attire was worn at all times in the lab. Procedures such as these were taught by the team’s advisor while in the lab.
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<p>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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When considering public safety, it is important to consider every aspect and intermediate step of the project. In Checkmate, the strains of yeast used contain a knockout for an essential amino acid. As a result of this knockout, it is highly unlikely that this yeast could ever escape the lab and be released into the public. However, not all the species involved in the project are so easily controlled. The selection scheme for maintaining the plasmid in E. Coli involved providing the bacteria with antibiotic resistance. In an age where multiple drug resistant bacteria are on the rise and responsible for killing several thousand people a year, the potential of this bacteria escaping and passing this plasmid on to another bacteria cannot be ignored. When handling E. Coli, the team used aseptic techniques and sterilized their equipment.
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Similar to the public safety concerns, most of the environmental safety concerns stem from chemicals or biological agents leaving the lab and being exposed to the environment outside the lab. Improper disposal or contamination of the environment by a couple of Checkmate’s chemicals could prove deleterious to outside environments. Once again, sterilization and aseptic techniques prevented any calamity.</p>
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<h2>BioBrick Safety</h2>
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<p>To ensure the safety of our BioBricks, we consulted the BioBrick standard for regulation of restriction sites when designed the DNA sequence. In addition, *SENTENCE TALKING ABOUT VECTOR KNOCKOUT OF KEY AMINO ACID.  By characterizing the BioBricks to their fullest potential, it will allow other participates of iGEM to use our BioBricks in their intended way, optimizing the efficiency of their projects.</p>
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<h2>Biosafety Group</h2>
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<p>Rose-Hulman Institute of Technology, due to a small applied biology program, does not have a biosafety group. Instead, safety procedures are integrated into classes by professors. The United States of America has many biosafety rules about working with human cells, but projects that work without human cells, such as Checkmate, are not regulated by these rules because they do not pose the same threat as projects that use human cells.</p>
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<h2>Future Safety</h2>
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<p>Future iGEM teams can be safe by following appropriate lab safety procedures. When considering their project, future iGEM teams need to be aware that they are creating something new, and should proceed with caution, always keeping safety at the forefront. Specifically, one way to be sure that iGEM projects cannot be a danger to the public or the environment is to include some form of self-destruct. This would make the cells unable to live in a non-lab environment. The DNA could be degenerative over time, or a strain could be dependent on a vital nutrient only found in a laboratory setting.</p>
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Revision as of 23:27, 3 September 2012

Home
Team
Project
BioBricks
Modeling
Notebook
Outreach
Daily Log
Lab Notebook
Lab Protocols
Safety

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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