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Team:NC School of Sci Math/Lab Notebook
From 2013hs.igem.org
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*Water contaminant multibiosensor | *Water contaminant multibiosensor | ||
| - | <b style="margin-top:2px;">More research | + | <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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**Expandable with many different FPs | **Expandable with many different FPs | ||
**Could bring in new technology | **Could bring in new technology | ||
| - | *Ocean salinity regulator is difficult because of the ocean | + | *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> | <html><h4><a style="color:#00008B; float:right;" name="02/15/2013">02/15/2013</a></h4></html> | ||
| - | <b> | + | <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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<html><h4><a style="color:#00008B; float:right;" name="02/22/2013">02/22/2013</a></h4></html> | <html><h4><a style="color:#00008B; float:right;" name="02/22/2013">02/22/2013</a></h4></html> | ||
| - | <b>Goals for | + | <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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<html><h4><a style="color:#00008B; float:right;" name="03/04/2013">03/04/2013</a></h4></html> | <html><h4><a style="color:#00008B; float:right;" name="03/04/2013">03/04/2013</a></h4></html> | ||
| - | <b> Assignments of roles for the upcoming project proposal</b>: | + | <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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<html><h4><a style="color:#00008B; float:right;" name="03/18/2013">03/18/2013</a></h4></html> | <html><h4><a style="color:#00008B; float:right;" name="03/18/2013">03/18/2013</a></h4></html> | ||
| - | <b> The following models have been created</b> | + | <b>The following models have been created</b> |
* 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 | ||
<div style="margin-top:7px;">[[Image:Design.jpg|center]]</div> | <div style="margin-top:7px;">[[Image:Design.jpg|center]]</div> | ||
| - | <html> | + | <html><h4><a style="color:#00008B; float:right;" name="03/25/2013">03/25/2013</a></h4></html> |
| - | <h4><a style="color:#00008B; float:right;" name="03/25/2013">03/25/2013</a></h4> | + | |
| - | </html> | + | <b>Editing poster on Google Doc</b> |
| - | + | ||
*Want to be finished by March 29th | *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 | **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! | ||
| - | <html> | + | <html><h4><a style="color:#00008B; float:right;" name="03/27/2013">03/27/2013</a></h4></html> |
| - | <h4><a style="color:#00008B; float:right;" name="03/27/2013">03/27/2013</a></h4> | + | |
| - | </html> | + | <b>Update on Proposal </b> |
| - | <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 | ||
| - | <html> | + | |
| - | <h4><a style="color:#00008B; float:right;" name="03/29/2013">03/29/2013</a></h4> | + | <html><h4><a style="color:#00008B; float:right;" name="03/29/2013">03/29/2013</a></h4></html> |
| - | </html> | + | |
<b>Proposal is completed </b> | <b>Proposal is completed </b> | ||
* Will submit soon | * Will submit soon | ||
| - | <html> | + | |
| - | <h4><a style="color:#00008B; float:right;" name="04/06/2013">04/06/2013</a></h4> | + | <html><h4><a style="color:#00008B; float:right;" name="04/06/2013">04/06/2013</a></h4></html> |
| - | </html> | + | |
| - | + | <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 | ||
| - | <html> | + | <html><h4><a style="color:#00008B; float:right;" name="04/17/2013">04/17/2013</a></h4></html> |
| - | <h4><a style="color:#00008B; float:right;" name="04/17/2013">04/17/2013</a></h4> | + | |
| - | </html> | + | <b>Tinkercell Model </b> |
| - | <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 | ||
| - | <html> | + | <html><h2><a name="Experimentation" style="color:#00008B;">Experimentation</a></h2> |
| - | <h2><a name="Experimentation" style="color:# | + | <h4><a style="color:#00008B; float:right;" name="04/27/2013">04/27/2013</a></h4></html> |
| - | + | ||
| - | <h4><a name="04/27/2013">04/27/2013</a></h4> | + | <b>Preliminary testing with the ADK </b> |
| - | </html> | + | |
| - | <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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** Dimmed LED lights | ** Dimmed LED lights | ||
** pGLO E. coli | ** pGLO E. coli | ||
| - | <html> | + | |
| - | + | <html><h4><a style="color:#00008B; float:right;" name="05/04/2013">05/04/2013</a></h4></html> | |
| - | <h4><a name="05/04/2013">05/04/2013</a></h4> | + | |
| - | </html> | + | <b>Upcoming ADK Testing</b> |
| - | <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 | ||
| - | <html> | + | |
| - | + | <html><h4><a style="color:#00008B; float:right;" name="05/07/2013">05/07/2013</a></h4></html> | |
| - | <h4><a name="05/07/2013">05/07/2013</a></h4> | + | |
| - | </html> | + | <b>Data from the ADK preliminary experiment </b> |
| - | <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 | ||
| - | [[ | + | <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 | ||
| - | [[ | + | <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 from the data | ** Can identify which color is being shown from the data | ||
| - | <html> | + | |
| - | + | <html><h4><a style="color:#00008B; float:right;" name="05/17/2013">05/17/2013</a></h4></html> | |
| - | <h4><a name="05/17/2013">05/17/2013</a></h4> | + | |
| - | </html> | + | <b>Completed Biobrick</b> |
| - | <b> Completed Biobrick </b> | + | * Everyone should begin working to finish their individual parts before the wiki freezes |
| - | * Everyone should begin working to finish their individual parts before the wiki | + | |
* Jack and Danny will take results from the Tinkercell model | * 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" | * 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 | * Meet next week to start uploading everything to the wiki and start to design the poster | ||
| - | <html> | + | |
| - | + | <html><h4><a style="color:#00008B; float:right;" name="06/06/2013">06/06/2013</a></h4></html> | |
| - | <h4><a name="06/06/2013">06/06/2013</a></h4> | + | |
| - | </html> | + | <b>Experimentation Data</b> |
| - | <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 | ||
| - | [[ | + | [[Image:Results.jpg|575|center]] |
* We will write up the results in the coming week | * We will write up the results in the coming week | ||
| - | <html> | + | |
| - | + | <html><h4><a style="color:#00008B; float:right;" name="06/15/2013">06/15/2013</a></h4></html> | |
| - | <h4><a name="06/15/2013">06/15/2013</a></h4> | + | |
| - | </html> | + | <b>Poster Update</b> |
| - | <b> Poster Update </b> | + | |
* Draft poster is complete! | * Draft poster is complete! | ||
| - | [[ | + | [[Image:Poster.jpg|475|center]] |
* Will continue to edit | * Will continue to edit | ||
* Need to start adding all of our stuff to the wiki | * Need to start adding all of our stuff to the wiki | ||
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}} | }} | ||
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Latest revision as of 03:49, 22 June 2013
2013
Home Team Project Details Lab Notebook Results Human Impact Biosafety Acknowledgments Official Team Profile
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
