Team:UC Davis

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<p class="indent"> Welcome to our page!  Our team is comprised of 8 dedicated individuals: 6 undergraduates and 2 advisors. This will be the second year that iGEM @ UC Davis participates in the competition.  We are hard at work and are looking forward towards the completion of our project. Stay tuned for the results!<p>
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<p class="indent"> Welcome to our page!  Our team is comprised of 8 dedicated individuals: 6 undergraduates and 2 advisors. This will be the second year that iGEM @ UC Davis participates in the competition.  We are hard at work and are looking forward towards the completion of our project. Stay tuned for the upcoming results!<p>
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<p class="header"><b>Updates</b></a><p>8.25.10 We are successfully piecing numerous parts together. After a couple more ligations and sequencing to confirm the parts, we will be entering testing phase!<p>7.19.10 The team has had a run-in with some major issues cutting parts out. We have traced the source of the problem and have been getting more positive results ever since.<p>7.8.10 We have our model and simulation completed!<p>6.30.10 We have developed a workplan for physically assembling and testing our devices. <p>6.28.10  We have finalized our project and have extracted our parts. </td></tr></table></td>
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<p class="header"><b>Characterizing and Improving Registry Part BBa_C0051: cI-Lambda, the Promoter in Disguise</b></a><p>
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<img src="https://static.igem.org/mediawiki/2010/1/17/Uhoh1.jpg"><br />
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<p class="indent">This summer, we started with the goal of building a novel circuit encoding the function of spatial oscillator that would push the bounds of what had been done before, both scientifically and in the context of device complexity. Our device required the assembly of >30 individual parts and had 7 promoters - both on the very high end of what has been demonstrated in most projects. Clearly, this was ambitious and was going to test how robust the immature technologies we use in synthetic really are. We anticipated challenges and got them in spades. . . One of the most interesting, in which we invested a lot of effort tracking down, was the discovery that the commonly used part BBa_C0051 (the cI lambda phage repressor) could, in the right context have promoter activity. We have spent some time tracking the source of this activity and generated a construct that corrects this error . . .for more, <a href="https://2010.igem.org/Team:UC_Davis/notebook/c0051debug.html">click here!</a>
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               <td class="kirby"><p class="indent">Throughout evolutionary history, spatial pattern formation has played a vital role in developmental biology. This is seen clearly in nature throughout the eukaryotic domain; examples include coat patterns (think zebras) and body segmentation (differentiated stem cells). We want to bring this sort of spatial pattern creation to the prokaryotic world. Previous iGEM projects have created patterns that require a projection of some sort of image before the cells react. We are engineering a strain that will create a pattern with no input from outside the system except an inducer.
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               <td class="kirby"><p class="header"><b>Spatial Oscillation! It Makes Stripes!</b></p>Repeating patterns are an overwhelmingly common sight in nature, whether it comes in the form of a zebra's stripes or a centipede's repeated segmented body.  And although it may seem a simple task to replicate this behavior, in reality, cells that undertake transformations into specific states to express a certain phenotype undergo very complicated biological processes. These biological processes often involve a cell to know where it is spatially (spatial awareness), and given the information it receives from the state of its environment, a cell may choose to perform one action over others. Our iGEM project involves building a device that when implanted in a cell allows the cell to choose from one of two states given a stimulus (in our case, the absence of light), in a project we have named "<a href='https://2010.igem.org/Team:UC_Davis/Projects'>Spatial Oscillation</a>".<br/><br/><p class="header"><b>CPOTATo: The Weapon Against Crosstalk</b></p><p class="indent">A second challenge we've tried to overcome that grew from our main project, the cI Lambda problem and the pH sensor project is the realization that our intermediate devices were causing slow growth phenotypes in our cells.  This, and other observations, led us to conclude that we were witnessing the unintended interaction between our device and the host. This is not only bad, but it is also a critical challenge in general in synthetic biology.  To attempt to remedy this issue in the future, we have designed CPOTATo (Crosstalk Predictive Organism Targeted Analysis Tool), a computational tool that attempts to predict potential cross-talk between a synthetic circuit and its host so that the engineer might know before starting a project what the likelihood of potentially disruptive interactions between the host and the device is. For more, <a href="https://2010.igem.org/Team:UC_Davis/Projects?3">click here!</a><p>
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      <p class="indent">This genetic circuit allows us to create biological systems with spatially varying genetic expression profiles. This has applications in a variety of fields such as nanofabrication, tissue engineering, environmental engineering, and of course, synthetic biology.  
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      <p align="right">Read more...</a></td></tr></table></td>
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               <td class="kirby"><p class="indent"> A good scientist always keeps a lab notebook at hand in order to keep track of what they do. This ensures that they have a written record of their data, allows others to retrace their steps, and most importantly of all, back up their research findings. Sift through our notebook pages to see how this project was built!<td></tr>
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               <td class="kirby"><p class="indent"> A good scientist always keeps a lab notebook at hand in order to keep track of what they do. This ensures that they have a written record of their data, allows others to retrace their steps, and most importantly of all, back up their research findings. Sift through our notebook pages to see how this project was built! </td></tr>
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                   <table><tr><td class="kirby" width="200px"><p class="header"><b>Overall Workplan</b></a><p> Get the big picture of what we are trying to build!</td> <td class="kirby" width="200px"><p class="header"><b>Assembly Workplan</b></a><p> Our parts didn't just come together magically.  Learn about how we assembled our parts piece by piece!  Also, stay tuned for possible protocols that may save you hours on your experiment.</td> <td class="kirby" width="200px"><p class="header"><b>Testing & Validation</b></a><p> Building our parts also include  testing our parts and ensuring that they work, since we cannot see what is actually going on with the naked eye. Learn how we identified problems, validated our experiments, and how we overcame various issues.</td></table></td></tr>
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                   <table><tr><td class="kirby" width="200px"><p class="header"><b>Overall Workplan</b></a><p>
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<center><a href="https://2010.igem.org/Team:UC_Davis/notebook/overallworkplan.html"><img src="https://static.igem.org/mediawiki/2010/0/03/Overallbutton.jpg"></a></center><br />
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Get the big picture of what we are trying to build! Learn the logistics behind our circuit and how we implemented biological concepts to create a robust system.
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<td class="kirby" width="200px"><p class="header"><b>Assembly Workplan</b></a><p>
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<center><a href="https://2010.igem.org/Team:UC_Davis/notebook/assembly.html"><img src="https://static.igem.org/mediawiki/2010/3/32/Assemblymethod1.jpg"></a></center><br />
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Our parts didn't just come together magically.  Learn about how we assembled our parts piece by piece!  Also, stay tuned for possible protocols that may save you hours on your experiment.  
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<td class="kirby" width="200px"><p class="header"><b>Testing & Validation</b></a><p>  
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<center><a href="https://2010.igem.org/Team:UC_Davis/notebook/c0051debug.html"><img src="https://static.igem.org/mediawiki/2010/d/d1/Sequencingbutton.jpg"></a></center><br />
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Building our parts also include  testing our parts and ensuring that they work, since we cannot see what is actually going on with the naked eye. Learn how we identified problems, validated our experiments, and how we overcame various issues. </td></tr></table></td></tr>
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     <p class="indent">Using mathematical modeling, we were able create a computer simulation of how our lawn of E. Coli will look like.  The red plane in the center is the original stimulus that triggered the striping. <p align="right">Read more...</a> </td>
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     <p class="indent">Using mathematical modeling, we were able create a computer simulation of how our lawn of E. Coli will look like.  The red plane in the center is the original stimulus that triggered the striping. <p align="right"><a href="https://2010.igem.org/Team:UC_Davis/Modeling" class="help">Read more...</a></a> </td>
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                     <td class="kirby" align="center">We would like to take a moment to thank all of our sponsors for their very generous donations, as we could not have done this without your help! <p>
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                     <td class="kirby" align="center"><a name="credits"></a></html>{{Team:UC_Davis/sponsors}}<html>
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Want to sponsor us?  Send an email to <a href="mailto:mtfacciotti@ucdavis.edu">mtfacciotti@ucdavis.edu</a> to discuss various ways you can help! :)
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                   <tr><td class="kirby">Criteria</td></tr></table>
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                   <tr><td class="kirby"><p class="indent">Over the course of putting together our iGEM project, we have kept all goals in mind that may qualify us for a Gold Award Medal. In this section, we would like to directly address all the medal requirements listed on the iGEM Judging Criteria list.<p>
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<p align="right"><a href="https://2010.igem.org/Team:UC_Davis/Judging" class="help">Read more..</a></a></td></tr></table>
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Latest revision as of 03:39, 28 October 2010

Welcome to our page! Our team is comprised of 8 dedicated individuals: 6 undergraduates and 2 advisors. This will be the second year that iGEM @ UC Davis participates in the competition. We are hard at work and are looking forward towards the completion of our project. Stay tuned for the upcoming results!

Characterizing and Improving Registry Part BBa_C0051: cI-Lambda, the Promoter in Disguise


This summer, we started with the goal of building a novel circuit encoding the function of spatial oscillator that would push the bounds of what had been done before, both scientifically and in the context of device complexity. Our device required the assembly of >30 individual parts and had 7 promoters - both on the very high end of what has been demonstrated in most projects. Clearly, this was ambitious and was going to test how robust the immature technologies we use in synthetic really are. We anticipated challenges and got them in spades. . . One of the most interesting, in which we invested a lot of effort tracking down, was the discovery that the commonly used part BBa_C0051 (the cI lambda phage repressor) could, in the right context have promoter activity. We have spent some time tracking the source of this activity and generated a construct that corrects this error . . .for more, click here!

Spatial Oscillation! It Makes Stripes!

Repeating patterns are an overwhelmingly common sight in nature, whether it comes in the form of a zebra's stripes or a centipede's repeated segmented body. And although it may seem a simple task to replicate this behavior, in reality, cells that undertake transformations into specific states to express a certain phenotype undergo very complicated biological processes. These biological processes often involve a cell to know where it is spatially (spatial awareness), and given the information it receives from the state of its environment, a cell may choose to perform one action over others. Our iGEM project involves building a device that when implanted in a cell allows the cell to choose from one of two states given a stimulus (in our case, the absence of light), in a project we have named "Spatial Oscillation".

CPOTATo: The Weapon Against Crosstalk

A second challenge we've tried to overcome that grew from our main project, the cI Lambda problem and the pH sensor project is the realization that our intermediate devices were causing slow growth phenotypes in our cells. This, and other observations, led us to conclude that we were witnessing the unintended interaction between our device and the host. This is not only bad, but it is also a critical challenge in general in synthetic biology. To attempt to remedy this issue in the future, we have designed CPOTATo (Crosstalk Predictive Organism Targeted Analysis Tool), a computational tool that attempts to predict potential cross-talk between a synthetic circuit and its host so that the engineer might know before starting a project what the likelihood of potentially disruptive interactions between the host and the device is. For more, click here!

A good scientist always keeps a lab notebook at hand in order to keep track of what they do. This ensures that they have a written record of their data, allows others to retrace their steps, and most importantly of all, back up their research findings. Sift through our notebook pages to see how this project was built!

Overall Workplan


Get the big picture of what we are trying to build! Learn the logistics behind our circuit and how we implemented biological concepts to create a robust system.

Assembly Workplan


Our parts didn't just come together magically. Learn about how we assembled our parts piece by piece! Also, stay tuned for possible protocols that may save you hours on your experiment.

Testing & Validation


Building our parts also include testing our parts and ensuring that they work, since we cannot see what is actually going on with the naked eye. Learn how we identified problems, validated our experiments, and how we overcame various issues.

Using mathematical modeling, we were able create a computer simulation of how our lawn of E. Coli will look like. The red plane in the center is the original stimulus that triggered the striping.

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We would like to take a moment to thank all of our sponsors for their very generous donations, as we could not have done this without your help!

We would also like to thank and acknowledge:
Our Advisors
Marc Facciotti
Ilias Tagkopoulos
Technical Guidance
David Larsen
Andrew Yao
Visiting iGEMer
Jia Li of Zhejiang University (TEAM ZJU-China)
cI Promoter Screen
Drew Endy - Stanford
Thomas Schneider - NIH
Want to sponsor us? Send an email to mtfacciotti@ucdavis.edu to discuss various ways you can help! :)

No synthetic biology team should go without considering the potential dangers that their project(s) may cause! Because science can be prone to error, we ensured that our project is safe on many different levels.

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Over the course of putting together our iGEM project, we have kept all goals in mind that may qualify us for a Gold Award Medal. In this section, we would like to directly address all the medal requirements listed on the iGEM Judging Criteria list.

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