University of Arizona 2006
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University of Arizona '''2006''' | University of Arizona '''2006''' | ||
| - | [[Image: | + | [[Image:UA06_cellraiserslogo.jpg]] |
| + | |||
| + | ==Team== | ||
| + | |||
| + | '''The Cell Raisers''' | ||
| - | + | '''"Splice Guys Finish First"''' | |
{| style="border:1px solid #aaaaff" | {| style="border:1px solid #aaaaff" | ||
| Line 32: | Line 36: | ||
!style="border-right:1px solid grey"|[[User:phollinger|Patrick Hollinger]] | !style="border-right:1px solid grey"|[[User:phollinger|Patrick Hollinger]] | ||
!style="border-right:1px solid grey"|dogmod@email.arizona.edu | !style="border-right:1px solid grey"|dogmod@email.arizona.edu | ||
| - | | | + | |Lab Lead / Design |
|- | |- | ||
!style="border-right:1px solid grey"|[[User:jkittles|Josh Kittleson]] | !style="border-right:1px solid grey"|[[User:jkittles|Josh Kittleson]] | ||
!style="border-right:1px solid grey"|jkittles@email.arizona.edu | !style="border-right:1px solid grey"|jkittles@email.arizona.edu | ||
| - | | | + | |Lab work, Design |
|- | |- | ||
| Line 52: | Line 56: | ||
!style="border-right:1px solid grey"|[[User:danman1|Dan Reavis]] | !style="border-right:1px solid grey"|[[User:danman1|Dan Reavis]] | ||
!style="border-right:1px solid grey"|danman1@email.arizona.edu | !style="border-right:1px solid grey"|danman1@email.arizona.edu | ||
| + | | | ||
| + | |||
| + | |- | ||
| + | !style="border-right:1px solid grey"|[[User:KMacDow|Kevin MacDow]] | ||
| + | !style="border-right:1px solid grey"|macdow@email.arizona.edu | ||
| + | | | ||
| + | |||
| + | |- | ||
| + | !style="border-right:1px solid grey"|[[User:heinze|Brian Heinze]] | ||
| + | !style="border-right:1px solid grey"|heinze@email.arizona.edu | ||
|} | |} | ||
| + | |||
| + | ==News== | ||
| + | |||
| + | NEW, we have added a page of pictures of our bacteria, and we have uploaded an almost final draft of our presentation to be given at the Jamboree. To see both of these, scroll down to the bottom. | ||
| + | |||
==Meetings== | ==Meetings== | ||
| - | Lab Work: | + | Lab Work: As needed, various times, various places |
| - | Next Meeting: | + | Next Meeting: No more general meetings, see you in Boston! |
==Resources== | ==Resources== | ||
| Line 71: | Line 90: | ||
=== Articles and References === | === Articles and References === | ||
| + | |||
| + | ''Construction of High-Density Bacterial Colony Arrays and Patterns by the Ink-Jet Method'', Xu et. al | ||
=== Related Projects and Links === | === Related Projects and Links === | ||
| Line 77: | Line 98: | ||
*[[IAP_2004:Attractant-Chemotaxis_Interaction]] | *[[IAP_2004:Attractant-Chemotaxis_Interaction]] | ||
| - | |||
==Projects== | ==Projects== | ||
| - | + | Project ideas that we considered are located at [[University of Arizona 2006/Project Ideas|Project Ideas]]. | |
We also maintain a forum for internal team communication. This is available at our [http://igem.engr.arizona.edu/phpBB2/ Team Forum]. | We also maintain a forum for internal team communication. This is available at our [http://igem.engr.arizona.edu/phpBB2/ Team Forum]. | ||
| - | The "Water Color" | + | The "Water Color" system is the project that we have chosen to build. As of now, we will be focusing our attention on building this design. We want to start with a system that is not as complex and that is somewhat straightforward to build. So that way, we can learn while we build. We wish to add complexity later, time and resources permitting, after we have made what we preliminarily designed. |
==Project Details== | ==Project Details== | ||
| - | The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. | + | The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers. |
| - | The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. A further idea, to be implemented later, is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. | + | The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this. |
| - | All the requisite parts have been identified from the registry, and will | + | All the requisite parts have been identified from the registry, and will have constructed them. Specific part numbers and diagram are shown in the parts construction schedule. A flowchart of the parts construction is located at [[University of Arizona 2006/Parts Schedule|Parts Schedule]] |
| + | |||
| + | We have completed Phase V of the construction (much to our plesant surprise). This means that we have made the final construct. We are currently in the process of sequencing the plasmid, and visualizing the cells with the plasmid. | ||
| + | |||
| + | ==Placing the inducer(s)== | ||
After the challenges of the first aspect of the project are overcome, more mechanical challenges still exist. For example: How to place the inducers?, or What scale should the image be?, or Are any optical techniques needed to fully visualize the image? | After the challenges of the first aspect of the project are overcome, more mechanical challenges still exist. For example: How to place the inducers?, or What scale should the image be?, or Are any optical techniques needed to fully visualize the image? | ||
| + | |||
| + | ===Inkjet Printer=== | ||
The first idea to place the inducers on the media is to use an injet printer. The printer could print solutions of inducers on a thin sheet which can be placed onto the media to put the inducers in contact with the cells. Issues that arrise are: | The first idea to place the inducers on the media is to use an injet printer. The printer could print solutions of inducers on a thin sheet which can be placed onto the media to put the inducers in contact with the cells. Issues that arrise are: | ||
| Line 101: | Line 127: | ||
*The size of molecules and the aperature of the jet | *The size of molecules and the aperature of the jet | ||
| - | *The | + | *The fluid properties of the solution (e.g. viscosity) should match ink |
*The sheet needs to effectively transfer the solutions to the media without mixing of regions | *The sheet needs to effectively transfer the solutions to the media without mixing of regions | ||
| + | |||
| + | ===Rapid Prototyping Mold=== | ||
| + | |||
| + | Digital images could be parsed into its three separate colors. The area were there is color is then cut into a block (not in actuality, it is RP'ed in one step). The block is then used to cast a PDMS mold that will be used as a stamp to place the inducers on the plate of cells. | ||
| + | |||
| + | ===PDMS Mold=== | ||
| + | |||
| + | Similar to the above idea, a PDMS mold with microfluidic channels is made so that a liquid (a solution of inducer) is able to be selectively placed on the plate of cells. | ||
| + | |||
| + | ==Visualization== | ||
| + | |||
| + | One hurdle to overcome is how should we visualize the image. We know that two of the flourescent proteins look very similar by the naked eye, even though they produce light of different wavelengths. Ideas that we have to better visualize the image include: | ||
| + | |||
| + | *Making three plates (each one color) for each image and digitally adding color | ||
| + | |||
| + | *Use light filters to distinguish the proteins | ||
| + | |||
| + | *View under a microscope with filters | ||
| + | |||
| + | ==Characterization== | ||
| + | |||
| + | The bacteria were visualized using fluorescent microscopy and bright field microscopy. | ||
| + | |||
| + | ===Sequencing=== | ||
| + | |||
| + | Parts were sent into the on campus sequencing lab for verification. | ||
| + | |||
| + | ==Last Steps== | ||
| + | |||
| + | ===Issues=== | ||
| + | |||
| + | Currently we are having issues distinguishing the flourescence. Cells with the plasmid alone show up brighter under a flourescent scope than wild type cells. However, once the cells with our plasmid are grown with the inducer, they are only marginally brighter than the cells that were not grown up in inducer. This poses a problem because it is difficult to distinguish between the "on" and "off" states for a certain flourescence. | ||
| + | |||
| + | |||
| + | ===Current Project Version=== | ||
| + | |||
| + | Due to the inability to get the desired response from the inducible fluoresence model of the bacteria we have refocused our project on producing color pictures using multiple strains of bacteria. Each strain will contain a single fluorescent protein which be distributed out seperate nozzles of a printer much as dye is distributed from printer nozzles. We belive this new model will provide higher resolution pictures than the previous model due to the removal of "diffusive fluroesence" as well as providing a basis for future research into fine cell distribution via use of a printer or other apparatus. | ||
| + | |||
| + | ==Presentation Draft== | ||
| + | |||
| + | [[Media:UA06_IGEM_Presentation_Draft_10_30.ppt|Latest Presentation Draft (almost final) 10.30.06]] | ||
==Photos== | ==Photos== | ||
| - | Team | + | NEW, lots of photos of our fluorescing bacteria! |
| + | |||
| + | [[University of Arizona 2006/Photos|Photo page]] | ||
| + | |||
| + | |||
| + | Team Photo: | ||
| + | |||
| + | [[Image:UA_iGEM_2006.JPG]] | ||
| + | |||
| + | Jamboree, here we come! | ||
Latest revision as of 19:02, 31 October 2006
University of Arizona 2006
Contents |
Team
The Cell Raisers
"Splice Guys Finish First"
| Member | Contact | Role | |
|---|---|---|---|
| Joan Curry | curry@ag.arizona.edu | Faculty Advisor | |
| Mark Riley | riley@ag.arizona.edu | Faculty Advisor | |
| Patrick Hollinger | dogmod@email.arizona.edu | Lab Lead / Design | |
| Josh Kittleson | jkittles@email.arizona.edu | Lab work, Design | |
| Tim Spriggs | tims@u.arizona.edu | Project Manager / Documentation | |
| Tyler Brown | tylerb@email.arizona.edu | Documentation | |
| Dan Reavis | danman1@email.arizona.edu | ||
| Kevin MacDow | macdow@email.arizona.edu | ||
| Brian Heinze | heinze@email.arizona.edu |
News
NEW, we have added a page of pictures of our bacteria, and we have uploaded an almost final draft of our presentation to be given at the Jamboree. To see both of these, scroll down to the bottom.
Meetings
Lab Work: As needed, various times, various places
Next Meeting: No more general meetings, see you in Boston!
Resources
Local Resources
- [http://igem.engr.arizona.edu/phpBB2/ Team Forum]
Articles and References
Construction of High-Density Bacterial Colony Arrays and Patterns by the Ink-Jet Method, Xu et. al
Related Projects and Links
Projects
Project ideas that we considered are located at Project Ideas.
We also maintain a forum for internal team communication. This is available at our [http://igem.engr.arizona.edu/phpBB2/ Team Forum].
The "Water Color" system is the project that we have chosen to build. As of now, we will be focusing our attention on building this design. We want to start with a system that is not as complex and that is somewhat straightforward to build. So that way, we can learn while we build. We wish to add complexity later, time and resources permitting, after we have made what we preliminarily designed.
Project Details
The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.
All the requisite parts have been identified from the registry, and will have constructed them. Specific part numbers and diagram are shown in the parts construction schedule. A flowchart of the parts construction is located at Parts Schedule
We have completed Phase V of the construction (much to our plesant surprise). This means that we have made the final construct. We are currently in the process of sequencing the plasmid, and visualizing the cells with the plasmid.
Placing the inducer(s)
After the challenges of the first aspect of the project are overcome, more mechanical challenges still exist. For example: How to place the inducers?, or What scale should the image be?, or Are any optical techniques needed to fully visualize the image?
Inkjet Printer
The first idea to place the inducers on the media is to use an injet printer. The printer could print solutions of inducers on a thin sheet which can be placed onto the media to put the inducers in contact with the cells. Issues that arrise are:
- The size of molecules and the aperature of the jet
- The fluid properties of the solution (e.g. viscosity) should match ink
- The sheet needs to effectively transfer the solutions to the media without mixing of regions
Rapid Prototyping Mold
Digital images could be parsed into its three separate colors. The area were there is color is then cut into a block (not in actuality, it is RP'ed in one step). The block is then used to cast a PDMS mold that will be used as a stamp to place the inducers on the plate of cells.
PDMS Mold
Similar to the above idea, a PDMS mold with microfluidic channels is made so that a liquid (a solution of inducer) is able to be selectively placed on the plate of cells.
Visualization
One hurdle to overcome is how should we visualize the image. We know that two of the flourescent proteins look very similar by the naked eye, even though they produce light of different wavelengths. Ideas that we have to better visualize the image include:
- Making three plates (each one color) for each image and digitally adding color
- Use light filters to distinguish the proteins
- View under a microscope with filters
Characterization
The bacteria were visualized using fluorescent microscopy and bright field microscopy.
Sequencing
Parts were sent into the on campus sequencing lab for verification.
Last Steps
Issues
Currently we are having issues distinguishing the flourescence. Cells with the plasmid alone show up brighter under a flourescent scope than wild type cells. However, once the cells with our plasmid are grown with the inducer, they are only marginally brighter than the cells that were not grown up in inducer. This poses a problem because it is difficult to distinguish between the "on" and "off" states for a certain flourescence.
Current Project Version
Due to the inability to get the desired response from the inducible fluoresence model of the bacteria we have refocused our project on producing color pictures using multiple strains of bacteria. Each strain will contain a single fluorescent protein which be distributed out seperate nozzles of a printer much as dye is distributed from printer nozzles. We belive this new model will provide higher resolution pictures than the previous model due to the removal of "diffusive fluroesence" as well as providing a basis for future research into fine cell distribution via use of a printer or other apparatus.
Presentation Draft
Latest Presentation Draft (almost final) 10.30.06
Photos
NEW, lots of photos of our fluorescing bacteria!
Team Photo:
Jamboree, here we come!
