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Team:UCSF/Project/Background
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Revision as of 01:26, 28 September 2013
Rarely in nature do bacterial strains exist in isolation; they form complex microbial communities that interact with various organisms. We ourselves contain a major microbial community in our digestive tract that has shown to directly affect our health and well-being. As shown on the left, to improve and maintain healthly living it would be useful to have the ability to change the microbial community. For example, if a large of amount of a certain sugar was present in your gut ("high chemical signal") you might want to slow the growth of a certain bacterial population and have another begin producing a useful toxin. In another scenario ("low chemical signal") it might be useful to upregulate growth of certain bacteria and have others produce a necessary vitamin. But targeting precise bacterial community strains and controlling their growth, activity, and outputs is difficult and requires many new tools.
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
- Selectively target and eliminate harmful bacteria without negatively affecting other bacteria.
- 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 (see diagram below). This tool is comprised of a catalytically dead Cas9 (dCas9) protein that complexes with guide RNAs (gRNA) complementary to the target bacteria’s DNA sequence. This complex binds to DNA complementary to the gRNA and prevents transcription, therefore repressing gene expression.
Solution to Problem 2:
As a means to introduce our CRISPRi system into a microbial community we’ve opted to utilize conjugation - a naturally occurring mechanism bacteria use to transfer DNA. By utilizing this mechanism, we are able to target specific strains of bacteria and affect gene expression. This will have a potential for future applications that require targeted cell death.
As a means to introduce our CRISPRi system into a microbial community we’ve opted to utilize conjugation - a naturally occurring mechanism bacteria use to transfer DNA. By utilizing this mechanism, we are able to target specific strains of bacteria and affect gene expression. This will have a potential for future applications that require targeted cell death.
