Team:NC School of Sci Math/Lab Notebook

From 2013hs.igem.org

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<b> Update on Proposal </b>
* Proposal is coming along well
* Proposal is coming along well
* Need to finish the methods, but otherwise complete
* Need to finish the methods, but otherwise complete
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* Proposal is done!
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<b>Proposal is completed </b>
* Will submit soon
* Will submit soon
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<b> Tinkercell Model </b>
* Danny has a working Tinkercell model for the copper detector!
* Danny has a working Tinkercell model for the copper detector!
**Outputs increased levels of TagRFP as ion concentration increases
**Outputs increased levels of TagRFP as ion concentration increases
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<b> Preliminary testing with the ADK </b>
* We want to work with the ADK for the next couple of weeks
* 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
* Jack will attempt to code the ADK so it outputs to a text file
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<b> Upcoming ADK Testing </b>
* The ADK has been coded
* The ADK has been coded
* We have glow sticks, E. coli expressing GFP, and dim LEDs to test
* We have glow sticks, E. coli expressing GFP, and dim LEDs to test
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<b> Data from the ADK preliminary experiment </b>
* Tested the sensing ability of the ADK today
* Tested the sensing ability of the ADK today
* Data is output in the form of the file below
* Data is output in the form of the file below
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<b> Completed Biobrick </b>
* Everyone should begin working to finish their individual parts before the wiki freeze
* Everyone should begin working to finish their individual parts before the wiki freeze
* Jack and Danny will take results from the Tinkercell model
* Jack and Danny will take results from the Tinkercell model
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<b> Experimentation Data </b>
* Poster abstract, introduction, and methods are completed
* 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
* The Tinkercell data shows our part effectively responds to the influx of the ions for which we are testing
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<b> Poster Update </b>
* Draft poster is complete!
* Draft poster is complete!
[[File:Poster.jpg]]
[[File:Poster.jpg]]

Revision as of 15:12, 20 June 2013

Name.png
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2013

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 should be done

  • 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
    • Environmental factors and unknown variables

Multibiosensor chosen

02/15/2013

A few members met 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 the 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
Design.jpg

03/25/2013

Everyone began editing the proposal on a Google Doc today

  • Want to be finished by March 29th
  • Tinkercells 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

Time to 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

Screenshot.jpg

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

PGLOGraphs.png

  • 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 freeze
  • 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

Results.jpg

  • We will write up the results in the coming week


06/15/2013

Poster Update

  • Draft poster is complete!

Poster.jpg

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