Team:UCSF/Project/Background

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Here we take advantage of conjugation, a natural horizontal gene transfer mechanism to target specific strains of bacteria and affect gene expression, which will have a potential for future applications that require targeted cell death.
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At the beginning of this summer, we asked ourselves a question: “What could we introduce to a microbiome which would allow specific targeting and eventual elimination of harmful bacteria?”  The difficulty faced with eliminating only one strain of bacteria in a microbiome is being able to
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<li>Selectively target and eliminate harmful bacteria without negatively affecting other bacteria. </li>
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<li>Introduce a targeting system into a defined mixture of bacteria</li>
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Rather than using indiscriminate antibiotics and pesticides, we’ve designed a system that will solve these two problems.
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Our project incorporates bacterial conjugation and CRISPRi (Clustered Regularly Interspaced Short Palindromic Repeats inhibition), a tool repurposed from a natural adaptive immunity system in bacteria, comprised of a catalytically dead Cas9 (dCas9) protein that complexes with guide RNAs (gRNA) complementary to the target bacteria’s DNA sequence. The dCas9 complexes with the gRNA and binds to DNA complimentary to the gRNA and prevents transcription, therefore repressing gene expression.
 
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<u>Solution to Problem 1:</u><br>
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To selectively target and eliminate harmful bacteria, we are utilizing the CRISPRi system, a tool repurposed from a natural adaptive immunity system in bacteria.
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<u>Solution to Problem 2:</u><br>
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As a means to introduce our CRISPRi system into a microbiome we’ve opted to utilize a naturally occurring mechanism bacteria use to transfer DNA, which contains the CRISPRi system.
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The combination of conjugation and CRISPRi allows us to create a system capable of both transferring genetic instructions from one cell to another and targeting unique species in a microbial community through a specific gene. </font></center>
 
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Revision as of 15:20, 23 September 2013


Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome
Rarely in nature do bacterial strains exist in isolation; they form complex microbial communities that interact with various organisms. In these communities, there are few ways to target specific strains effectively. The way people control bacteria is through antibiotics, which for the most part act indiscriminately. But often, problems stem from a single species that has invaded the microbial community; normal balanced microbiomes are not only harmless, but are often crucial and positively contribute to an environment. Because most therapies disrupt this balance, there is an obvious need for specific targeting of species in microbial communities.


At the beginning of this summer, we asked ourselves a question: “What could we introduce to a microbiome which would allow specific targeting and eventual elimination of harmful bacteria?” The difficulty faced with eliminating only one strain of bacteria in a microbiome is being able to
  1. Selectively target and eliminate harmful bacteria without negatively affecting other bacteria.
  2. Introduce a targeting system into a defined mixture of bacteria

Rather than using indiscriminate antibiotics and pesticides, we’ve designed a system that will solve these two problems.


Solution to Problem 1:
To selectively target and eliminate harmful bacteria, we are utilizing the CRISPRi system, a tool repurposed from a natural adaptive immunity system in bacteria.

Solution to Problem 2:
As a means to introduce our CRISPRi system into a microbiome we’ve opted to utilize a naturally occurring mechanism bacteria use to transfer DNA, which contains the CRISPRi system.

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