Team:NC School of Sci Math/Lab Notebook

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Lab Notebook

Planning and Development

01/11/2013

Brainstorming for project ideas

• LDL-cholesterol biosensor
• Ocean salinity regulator (especially for coral reefs)
• Water contaminant multibiosensor

More research

• Find related projects that have been completed
• Obstacles?
• BioBricks?
• Presentations in 3-4 weeks

01/18/2013

Discussions of each project

• LDL-cholesterol biosensor
  • Could be used as a blood test
  • Blood sugar monitor-like device
  • Hard to measure any color change in blood
• Ocean salinity regulator (especially for coral reefs)
  • Need a lot of bacteria
  • Environmental concerns
  • Bacteria can do well in coral reefs
• Water contaminant multibiosensor
  • Several Biobrick promoters for common contaminants
  • Usage in sewer tanks
  • Many different colors of fluorescent proteins
  • Could incorporate newer technology for better color-sensing
  • Will look up data on promoter/FP expression

02/01/2013

Presentations

• All ideas sound promising
• Meet next week to decide which idea to pursue

02/08/2013

Decision on project

• LDL-cholesterol idea won't work
  • Costly and hard to detect FPs in blood
• Multibiosensor is appealing
  • Many applications
  • Expandable with many different FPs
  • Could bring in new technology
• Ocean salinity regulator is difficult because of the ocean environment
  • Environmental factors and unknown variables

Multibiosensor chosen

02/15/2013

Meeting with Mr. Jon Davis to discuss potential technology

• Suggested a Google device called ADK
  • Comes with a colorimeter
  • Can be programmed for many functions
  • School has a few we could try out

02/22/2013

Goals for immediate future

• Find Biobricks
• Set up schedule for lab work
• Further research into possible uses
• Preliminary lab experiments

Project Proposal

03/01/2013

Discussion of upcoming project proposal:

• Introduction, Solution Statement, and Methods
• Need to find out some background information
• Should make use of Tinkercell modeling

03/04/2013

Assignments of roles for the upcoming project proposal:

• Madeline will investigate background information
• Danny will work on Tinkercell models
• Jack will write the solution statement and methods sections
• Synthesize our writing on a Google Doc
• Try to have individual parts done in about 2 weeks

03/18/2013

The following models have been created

• We should use these in the proposal, but continue to work on the Tinkercell model

03/25/2013

Editing poster on Google Doc

• Want to be finished by March 29th
• Tinkercell model will probably not be ready in time
  • Having a lot of trouble getting fluorescent protein levels to zero when they should be
  • Danny will talk to Morgan to see if he can help
• Edit Edit Edit!

03/27/2013

Update on Proposal

• Proposal is coming along well
• Need to finish the methods, but otherwise complete
• Take pictures of the ADK and lab work

03/29/2013

Proposal is completed

• Will submit soon

04/06/2013

Focus on creating the plasmid

• Finished Tinkercell model will help a bunch
• Do we want to think about ordering de novo from a gene synthesis company?
• Computer modeling is the best approach for now

04/17/2013

Tinkercell Model

• Danny has a working Tinkercell model for the copper detector!
  • Outputs increased levels of TagRFP as ion concentration increases
• We should be able to figure out the others soon
• The lead detector may be especially difficult because the ion binds to a promoter to create a transcription factor

Experimentation

04/27/2013

Preliminary testing with the ADK

• We want to work with the ADK for the next couple of weeks
• Jack will attempt to code the ADK so it outputs to a text file
• Potential preliminary tests
  • Diluted glow sticks
  • Dimmed LED lights
  • pGLO E. coli

05/04/2013

Upcoming ADK Testing

• The ADK has been coded
• We have glow sticks, E. coli expressing GFP, and dim LEDs to test
• Testing this Tuesday

05/07/2013

Data from the ADK preliminary experiment

• Tested the sensing ability of the ADK today
• Data is output in the form of the file below

• The pGLO E. coli is the most closely related to our project and data is shown below

• Data from LED lights is very similar but allowed us to understand the sensing "logic" of the ADK
  • Showing red, green, or blue light increases only the color being shown
  • Showing yellow light increases both red and green light
  • Can identify which color is being shown from the data

05/17/2013

Completed Biobrick

• Everyone should begin working to finish their individual parts before the wiki freezes
• Jack and Danny will take results from the Tinkercell model
• Sequences for all parts have been found and the Biobrick as a whole is "completed"
• Meet next week to start uploading everything to the wiki and start to design the poster

06/06/2013

Experimentation Data

• Poster abstract, introduction, and methods are completed
• The Tinkercell data shows our part effectively responds to the influx of the ions for which we are testing

• We will write up the results in the coming week

06/15/2013

Poster Update

• Draft poster is complete!

• Will continue to edit
• Need to start adding all of our stuff to the wiki