Difference between revisions of "Team:Alverno CA"

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                         Reducing Noise in Multi-Gene Synthetic Biology Circuits
 
                         Reducing Noise in Multi-Gene Synthetic Biology Circuits
 
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             <p>Building complex biological systems with many
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             <h5>Building complex biological systems with many
 
             genes requires isolating genes. Active genes can cause nearby DNA
 
             genes requires isolating genes. Active genes can cause nearby DNA
 
             to become supercoiled, leading to unpredictable behavior of
 
             to become supercoiled, leading to unpredictable behavior of
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             DNA-binding proteins) placed between genes can stop this
 
             DNA-binding proteins) placed between genes can stop this
 
             interference. If this project succeeds, it will allow bioengineers
 
             interference. If this project succeeds, it will allow bioengineers
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             to build more predictable genetic circuits.</p>
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             to build more predictable genetic circuits.</h5>
 
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                     <h4>Watch our introduction video here.</h4>
 
                     <h4>Watch our introduction video here.</h4>
 
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         <p>Programming cells often requires building
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         <h5>Programming cells often requires building
 
         "circuits" of several genes together on the same piece of DNA.
 
         "circuits" of several genes together on the same piece of DNA.
 
         Bioengineers have observed that when two genes are placed next to each
 
         Bioengineers have observed that when two genes are placed next to each
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         tightly-wound phone cord. Supercoils directly affect the expression of
 
         tightly-wound phone cord. Supercoils directly affect the expression of
 
         genes, turning them on or off depending on the direction of the
 
         genes, turning them on or off depending on the direction of the
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         supercoil.</h5>
  
  
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         <p>If successful, a DNA-binding, gene- isolating clamp
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         <h5>If successful, a DNA-binding, gene- isolating clamp
 
         could be used in any multi-gene circuit assembly, making multi-gene
 
         could be used in any multi-gene circuit assembly, making multi-gene
 
         assemblies more predictable and their assembly much more efficient.
 
         assemblies more predictable and their assembly much more efficient.
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         screened for activity. By making gene expression more predictable, our
 
         screened for activity. By making gene expression more predictable, our
 
         results could greatly improve the predictability (and, therefore,
 
         results could greatly improve the predictability (and, therefore,
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         designability) of large gene circuits for metabolic engineering</p>
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         designability) of large gene circuits for metabolic engineering</h5>
  
  
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         <p>We will first build several plasmids (circular
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         <h5>We will first build several plasmids (circular
 
         pieces of DNA) that demonstrate cross-talk between genes. These
 
         pieces of DNA) that demonstrate cross-talk between genes. These
 
         plasmids will consist of genes for two different fluorescent proteins
 
         plasmids will consist of genes for two different fluorescent proteins
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         "clamps" made from DNA-binding repressor proteins between the two
 
         "clamps" made from DNA-binding repressor proteins between the two
 
         genes. We will again quantify the effects of cross-talk between genes,
 
         genes. We will again quantify the effects of cross-talk between genes,
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         which will hopefully be ameliorated by our additions.</p>
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         which will hopefully be ameliorated by our additions.</h5>
  
  
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         <p>We created a variety of social media accounts
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         <h5>We created a variety of social media accounts
 
         (Twitter, YouTube, Facebook, and Instagram) as a means to reach out to
 
         (Twitter, YouTube, Facebook, and Instagram) as a means to reach out to
 
         other teams, and to keep interested people informed about our
 
         other teams, and to keep interested people informed about our
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         progress.</p>
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         progress.</h5>
  
  
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Revision as of 06:59, 18 October 2016


Clamp Down on Crosstalk
Alverno_CA

Reducing Noise in Multi-Gene Synthetic Biology Circuits
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Clamping Down on Crosstalk:
How can we keep genes from interfering with each other in synthetic DNA circuits?

About this Project

Building complex biological systems with many genes requires isolating genes. Active genes can cause nearby DNA to become supercoiled, leading to unpredictable behavior of synthetic biology systems. We will test if DNA clamps (made from DNA-binding proteins) placed between genes can stop this interference. If this project succeeds, it will allow bioengineers to build more predictable genetic circuits.

Watch our introduction video here.

What is the context of this research?

Programming cells often requires building "circuits" of several genes together on the same piece of DNA. Bioengineers have observed that when two genes are placed next to each other, they often unexpectedly interfere with each other's expression in an unexpectedly orientation-dependent manner. Nobody knows with certainty what causes this genetic crosstalk, but one promising theory involves DNA supercoiling. The transcription of DNA into RNA, the transcription process introduces supercoils, similar to kinks in a tightly-wound phone cord. Supercoils directly affect the expression of genes, turning them on or off depending on the direction of the supercoil.

What is the significance of this project?

If successful, a DNA-binding, gene- isolating clamp could be used in any multi-gene circuit assembly, making multi-gene assemblies more predictable and their assembly much more efficient. This is particularly relevant when engineering metabolic pathways to produce chemicals like methanol, insulin, or antibiotics, where circuits of many genes are routinely constructed. The physical layout of these circuits can unpredictably affect production of the desired output by several orders of magnitude, so large engineered metabolic pathways must typically be hand-tuned or have many configurations screened for activity. By making gene expression more predictable, our results could greatly improve the predictability (and, therefore, designability) of large gene circuits for metabolic engineering

What are the goals of the project?

We will first build several plasmids (circular pieces of DNA) that demonstrate cross-talk between genes. These plasmids will consist of genes for two different fluorescent proteins (green fluorescent protein and red fluorescent protein) next to each other, in different orientations. We expect to see differences in the relative expression of the two genes depending on how they are arranged and oriented, and we will quantify this effect. Next, we will try several strategies for removing these differences, including adding extra base pairs of spacing between the two genes and adding DNA "clamps" made from DNA-binding repressor proteins between the two genes. We will again quantify the effects of cross-talk between genes, which will hopefully be ameliorated by our additions.

Social Media

We created a variety of social media accounts (Twitter, YouTube, Facebook, and Instagram) as a means to reach out to other teams, and to keep interested people informed about our progress.


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