Team:NC School of Sci Math/Lab Notebook

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===Lab Notebook===
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<html><h2><a name="Planning" style="color:#00008B;">Planning and Development</a></h2>
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<h4><a style="color:#00008B; float:right;" name="01/11/2013">01/11/2013</a></h4></html>
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<h2><a name="Planning" style="color:#00008B;">Planning and Development</a></h2>
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<h4><a style="color:#00008B;" name="01/11/2013">01/11/2013</a></h4>
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<b>Brainstorming for project ideas </b>
<b>Brainstorming for project ideas </b>
<br />
<br />
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*Ocean salinity regulator (especially for coral reefs)
*Ocean salinity regulator (especially for coral reefs)
*Water contaminant multibiosensor
*Water contaminant multibiosensor
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<br />
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<b>More research should be done</b>
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<b style="margin-top:2px;">More research</b>
*Find related projects that have been completed
*Find related projects that have been completed
*Obstacles?
*Obstacles?
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*Presentations in 3-4 weeks
*Presentations in 3-4 weeks
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<html><h4><a style="color:#00008B; float:right;" name="01/18/2013">01/18/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="01/18/2013">01/18/2013</a></h4>
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<b>Discussions of each project</b>
<b>Discussions of each project</b>
<br />
<br />
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**Will look up data on promoter/FP expression
**Will look up data on promoter/FP expression
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<html><h4><a style="color:#00008B; float:right;" name="02/01/2013">02/01/2013</a></h4></html>
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<b>Presentations</b>
<b>Presentations</b>
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*Meet next week to decide which idea to pursue
*Meet next week to decide which idea to pursue
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<html><h4><a style="color:#00008B; float:right;" name="02/08/2013">02/08/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="02/08/2013">02/08/2013</a></h4>
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<b>Decision on project</b>
<b>Decision on project</b>
*LDL-cholesterol idea won't work
*LDL-cholesterol idea won't work
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**Expandable with many different FPs
**Expandable with many different FPs
**Could bring in new technology
**Could bring in new technology
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*Ocean salinity regulator is difficult because of the ocean
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*Ocean salinity regulator is difficult because of the ocean environment
**Environmental factors and unknown variables
**Environmental factors and unknown variables
<b>Multibiosensor chosen</b>
<b>Multibiosensor chosen</b>
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<html><h4><a style="color:#00008B; float:right;" name="02/15/2013">02/15/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="02/15/2013">02/15/2013</a></h4>
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<b> A few members met with Mr. Jon Davis to discuss potential technology </b>
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<b>Meeting with Mr. Jon Davis to discuss potential technology</b>
*Suggested a Google device called ADK
*Suggested a Google device called ADK
**Comes with a colorimeter
**Comes with a colorimeter
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**School has a few we could try out
**School has a few we could try out
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<html><h4><a style="color:#00008B; float:right;" name="02/22/2013">02/22/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="02/22/2013">02/22/2013</a></h4>
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<b>Goals for the immediate future</b>
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<b>Goals for immediate future</b>
*Find Biobricks
*Find Biobricks
*Set up schedule for lab work
*Set up schedule for lab work
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*Preliminary lab experiments
*Preliminary lab experiments
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<html><h2><a name="Proposal" style="color:#00008B;">Project Proposal</a></h2>
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<h4><a style="color:#00008B; float:right;" name="03/01/2013">03/01/2013</a></h4></html>
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<b>Discussion of upcoming project proposal</b>:
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<h2><a name="Proposal" style="color:#00008B;">Project Proposal</a></h2>
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<br />
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<h4><a style="color:#00008B;" name="03/01/2013">03/01/2013</a></h4>
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<p><b> Discussion of upcoming project proposal</b>:</p>
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* Introduction, Solution Statement, and Methods
* Introduction, Solution Statement, and Methods
* Need to find out some background information
* Need to find out some background information
* Should make use of Tinkercell modeling
* Should make use of Tinkercell modeling
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<html><h4><a style="color:#00008B; float:right;" name="03/04/2013">03/04/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="03/04/2013">03/04/2013</a></h4>
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</html>
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<p><b> Assignments of roles for the upcoming project proposal</b>:</p>
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<b>Assignments of roles for the upcoming project proposal</b>:
* Madeline will investigate background information
* Madeline will investigate background information
* Danny will work on Tinkercell models
* Danny will work on Tinkercell models
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* Try to have individual parts done in about 2 weeks
* Try to have individual parts done in about 2 weeks
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<html><h4><a style="color:#00008B; float:right;" name="03/18/2013">03/18/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="03/18/2013">03/18/2013</a></h4>
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<b>The following models have been created</b>
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<p><b> The following models have been created</b></p>
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* We should use these in the proposal, but continue to work on the Tinkercell model
* We should use these in the proposal, but continue to work on the Tinkercell model
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[[File:Design.jpg|700px]]
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<div style="margin-top:7px;">[[Image:Design.jpg|center]]</div>
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<html><h4><a style="color:#00008B; float:right;" name="03/25/2013">03/25/2013</a></h4></html>
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<b>Editing poster on Google Doc</b>
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<h4><a style="color:#00008B;" name="03/25/2013">03/25/2013</a></h4>
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</html>
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<p><b>Everyone began editing the proposal on a Google Doc today</b></p>
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*Want to be finished by March 29th
*Want to be finished by March 29th
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*Tinkercells will probably not be ready in time
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*Tinkercell model will probably not be ready in time
**Having a lot of trouble getting fluorescent protein levels to zero when they should be
**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
**Danny will talk to Morgan to see if he can help
*Edit Edit Edit!
*Edit Edit Edit!
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<html><h4><a style="color:#00008B; float:right;" name="03/27/2013">03/27/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="03/27/2013">03/27/2013</a></h4>
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</html>
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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
* Take pictures of the ADK and lab work
* Take pictures of the ADK and lab work
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<h4><a style="color:#00008B;" name="03/29/2013">03/29/2013</a></h4>
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<html><h4><a style="color:#00008B; float:right;" name="03/29/2013">03/29/2013</a></h4></html>
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</html>
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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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<html>
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<h4><a style="color:#00008B;" name="04/06/2013">04/06/2013</a></h4>
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<html><h4><a style="color:#00008B; float:right;" name="04/06/2013">04/06/2013</a></h4></html>
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</html>
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<p><b>Time to focus on creating the plasmid</b></p>
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<b>Focus on creating the plasmid</b>
* Finished Tinkercell model will help a bunch
* Finished Tinkercell model will help a bunch
* Do we want to think about ordering de novo from a gene synthesis company?
* Do we want to think about ordering de novo from a gene synthesis company?
* Computer modeling is the best approach for now
* Computer modeling is the best approach for now
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<html>
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<html><h4><a style="color:#00008B; float:right;" name="04/17/2013">04/17/2013</a></h4></html>
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<h4><a style="color:#00008B;" name="04/17/2013">04/17/2013</a></h4>
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</html>
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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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* The lead detector may be especially difficult because the ion binds to a promoter to create a transcription factor
* The lead detector may be especially difficult because the ion binds to a promoter to create a transcription factor
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<html>
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<html><h2><a name="Experimentation" style="color:#00008B;">Experimentation</a></h2>
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<h2><a name="Experimentation" style="color:#0008B;">Experimentation</a></h2>
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<h4><a style="color:#00008B; float:right;" name="04/27/2013">04/27/2013</a></h4></html>
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<br />
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<h4><a name="04/27/2013">04/27/2013</a></h4>
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<b>Preliminary testing with the ADK </b>
-
</html>
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* 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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** Dimmed LED lights
** Dimmed LED lights
** pGLO E. coli
** pGLO E. coli
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<br />
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<html><h4><a style="color:#00008B; float:right;" name="05/04/2013">05/04/2013</a></h4></html>
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<h4><a name="05/04/2013">05/04/2013</a></h4>
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</html>
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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
* Testing this Tuesday
* Testing this Tuesday
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<br />
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<html><h4><a style="color:#00008B; float:right;" name="05/07/2013">05/07/2013</a></h4></html>
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<h4><a name="05/07/2013">05/07/2013</a></h4>
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</html>
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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
-
[[File:Screenshot.jpg|400px]]
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<div style="margin:10px 0px;">[[Image:Screenshot.jpg|700px|center]]</div>
* The pGLO E. coli is the most closely related to our project and data is shown below
* The pGLO E. coli is the most closely related to our project and data is shown below
-
[[File:pGLOGraphs.png|800px]]
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<div style="margin:10px 0px;">[[Image:pGLOGraphs.png|center]]</div>
* Data from LED lights is very similar but allowed us to understand the sensing "logic" of the ADK
* 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 red, green, or blue light increases only the color being shown
** Showing yellow light increases both red and green light
** Showing yellow light increases both red and green light
-
** Can identify which color is being shown only from the data
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** Can identify which color is being shown from the data
 +
 
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<html><h4><a style="color:#00008B; float:right;" name="05/17/2013">05/17/2013</a></h4></html>
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<b>Completed Biobrick</b>
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* 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
 +
 
 +
<html><h4><a style="color:#00008B; float:right;" name="06/06/2013">06/06/2013</a></h4></html>
 +
 
 +
<b>Experimentation Data</b>
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* 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
 +
[[Image:Results.jpg|575|center]]
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* We will write up the results in the coming week
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{{clear}}
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<html><h4><a style="color:#00008B; float:right;" name="06/15/2013">06/15/2013</a></h4></html>
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<b>Poster Update</b>
 +
* Draft poster is complete!
 +
[[Image:Poster.jpg|475|center]]
 +
* Will continue to edit
 +
* Need to start adding all of our stuff to the wiki
}}
}}

Latest revision as of 03:49, 22 June 2013

Name.png
[[ |  ]]
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

  • 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
Design.jpg

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
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 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
575
  • We will write up the results in the coming week

06/15/2013

Poster Update

  • Draft poster is complete!
475
  • Will continue to edit
  • Need to start adding all of our stuff to the wiki
Retrieved from "http://2013hs.igem.org/Team:NC_School_of_Sci_Math/Lab_Notebook"