Difference between revisions of "Team:London Biohackspace/the-diy-brewkit"

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                 <h3>WHO ARE WE</h3>
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                 <h3>What is the SYNBIO Brewery DIY-Brewkit</h3>
<p>The London Biohackspace is a UK open biolab, run entirely by its volunteer members, based at the London Hackspace. We are the first community lab in the UK approved for carrying out genetic techniques and we are the only community lab taking part in iGEM from Europe. Our lab is grounded on open-source principles and community development, which allows the freedom for anyone to pursue collaborative or individual projects. The strength of the biohacking and DIYbio community is the diversity of its members. London Biohackspace hopes to encourage enthusiastic amateurs and professionals with backgrounds in a broad mix of professions such as artists, engineers, biologists and programmers to carry out innovative bioscience projects. Anybody can join us and become a Biohacker!</p>
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<p>The SYNBIO Brewery DIY-Brewkit is an all-in-one open-source toolbox designed to allow home brew enthusiasts to create novel brewing yeast strains and become involved in the burgeoning DIY-bio community.  The DIY-Brewkit will comprise a set of sample yeast strains as well as a library of genetic parts that allow users to genetically modify existing commerially available brewing strains in order to produce new and interesting types of beer.  The DIY-Brewkit gene library consists of a variety of genes from different organisms that when expressed in brewing yeast strains will alter the taste, smell, colour and nutritional content of the beer produced. Additional genes will also be included that allow users to modify the expression levels of these genes via RNA interference so that a wide range of unique beers can be created and perfected.  Finally, by providing an open-source set of components for working with yeast we hope to lower the entry barrier for new and existing community labs looking to participate in iGEM as well as making it easier for community labs to share resouces.</p>
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  <h3>How we created the SYNBIO Brewery DIY-Brewkit -  Creating Auxotophic strains</h3>
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<p>The first step in creating novel brewing yeast strains is to modify an existing strain that has either been purchased from a home brew supplier or isolated from a bottle of beer so that it becomes auxotrophic for a particular key nutrient. This is an essential step as it provides a means to select subsequent strains that have been further genetically modified.  The SYNBIO Brewery DIY-Brewkit will contain genes part that creates auxotrophic mutants lacking the ability to synthesize uracil and leucine that are key amino acids required for protein synthesis.  These mutant strains will therefore only grow on a media containing uracil or leucine or via further genetic modification which restores the strains ability to synthesize these amino acids.</p>
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<p>We aim to create auxotropic strains using two approaches.  The first approach will use homologous recombination to knockout a key amino acid biosynthesis gene such as LEU2.  Subsequent transformations with a plasmid capable of expressing the LEU2 gene along with any gene of interest will restore uracil biosynthesis and allow for selection of transformants containing this plasmid. The second approach will use RNA interference to down regulate the LEU2 gene to a sufficient level to make the strain auxotrophic without altering the leucine biosynthesis pathway itself.  A further transformation and homologous recombination event using a DNA sequence designed to replace the LEU2 RNA knockout will therefore restore the strains capacity for leucine biosynthesis as well as incorporate a gene of interest into the chromosomal DNA.  This approach can be expanded by incorporating an additional RNA-based knockdown for another amino acid such as Uracil (URA3) therefore creating an additional homologous recombination target site for further chromosomal insertion and subsequent strain selection.  Using this approach it will be possible to alternate between uracil and leucine auxotrophy and allow for multiple chromosomal insertion events via these synthetic homolgous recombination/RNA interference sequences.</p>
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  <h3>How we created the SYNBIO Brewery DIY-Brewkit -  The BrewKit gene library</h3>
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<p>The SYNBIO Brewery DIY-Brewkit has been designed as an open-source resource for home brew enthusiasts looking to modify brewing yeast in order to enhance the flavour, smell, colour and nutritional content of the beer that the yeast produces.   To demonstrate these capabilities we have included several genes which can be used to modify the flavour of any beer created by a gentically engineered yeast strain.  Miraculin is a protein found naturally in the fruits of the Miracle Berry plant <i>Synsepalum dulcificum</i> and has been found to make sour foods taste sweeter.  The taste altering property of Miraculin therefore means it has potential use as an artficial sweetener and is therefore a healthier alternative to natural sugars found in most products.  A number of other naturally occuring flavour enhancing compounds such as X which originates in raspberry plants derive from the precursor carotenoid compound lycopene.  We have therefore chosen to include a genetic part encoding the three enzymes responsible for the biosynthesis of lycopene.  Research into the nutritional value of lycopene also suggests that it acts has an antioxidant and therefore has a number of health benefits when consumed as part of a balanced diet.</p>
  
  <h3>PROJECT OUTLINE</h3>
 
<p>Our project aims to develop an all-in-one toolbox for creating designer brewing yeast strains that can be modified to produce beers with novel flavours, scents, colours, nutrients and bioluminescence.  We will also hope to enhance the use of yeast as a suitable chassis for community labs involved in synthetic biology.  This will be achieved by developing new genetic parts which when combined will function as a platform to allow multiple genes to be integrated into chromosomal DNA of existing brewing strains.  Additional parts will be created that allow designers to regulate the level of expression of inserted proteins thus giving users the ability to create novel brewing strains.  The project will also explore how effective such organisms are in producing genuinely novel drink products that can challenge what beer can be, the project will produce an example product for the future of home brewing: a variety pack / kit for home brewers to experiment with different varieties of engineered yeast in their home brewing endeavours.</p>
 
 
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Revision as of 13:21, 23 August 2015

a few words about us

What is the SYNBIO Brewery DIY-Brewkit

The SYNBIO Brewery DIY-Brewkit is an all-in-one open-source toolbox designed to allow home brew enthusiasts to create novel brewing yeast strains and become involved in the burgeoning DIY-bio community. The DIY-Brewkit will comprise a set of sample yeast strains as well as a library of genetic parts that allow users to genetically modify existing commerially available brewing strains in order to produce new and interesting types of beer. The DIY-Brewkit gene library consists of a variety of genes from different organisms that when expressed in brewing yeast strains will alter the taste, smell, colour and nutritional content of the beer produced. Additional genes will also be included that allow users to modify the expression levels of these genes via RNA interference so that a wide range of unique beers can be created and perfected. Finally, by providing an open-source set of components for working with yeast we hope to lower the entry barrier for new and existing community labs looking to participate in iGEM as well as making it easier for community labs to share resouces.

How we created the SYNBIO Brewery DIY-Brewkit - Creating Auxotophic strains

The first step in creating novel brewing yeast strains is to modify an existing strain that has either been purchased from a home brew supplier or isolated from a bottle of beer so that it becomes auxotrophic for a particular key nutrient. This is an essential step as it provides a means to select subsequent strains that have been further genetically modified. The SYNBIO Brewery DIY-Brewkit will contain genes part that creates auxotrophic mutants lacking the ability to synthesize uracil and leucine that are key amino acids required for protein synthesis. These mutant strains will therefore only grow on a media containing uracil or leucine or via further genetic modification which restores the strains ability to synthesize these amino acids.

We aim to create auxotropic strains using two approaches. The first approach will use homologous recombination to knockout a key amino acid biosynthesis gene such as LEU2. Subsequent transformations with a plasmid capable of expressing the LEU2 gene along with any gene of interest will restore uracil biosynthesis and allow for selection of transformants containing this plasmid. The second approach will use RNA interference to down regulate the LEU2 gene to a sufficient level to make the strain auxotrophic without altering the leucine biosynthesis pathway itself. A further transformation and homologous recombination event using a DNA sequence designed to replace the LEU2 RNA knockout will therefore restore the strains capacity for leucine biosynthesis as well as incorporate a gene of interest into the chromosomal DNA. This approach can be expanded by incorporating an additional RNA-based knockdown for another amino acid such as Uracil (URA3) therefore creating an additional homologous recombination target site for further chromosomal insertion and subsequent strain selection. Using this approach it will be possible to alternate between uracil and leucine auxotrophy and allow for multiple chromosomal insertion events via these synthetic homolgous recombination/RNA interference sequences.

How we created the SYNBIO Brewery DIY-Brewkit - The BrewKit gene library

The SYNBIO Brewery DIY-Brewkit has been designed as an open-source resource for home brew enthusiasts looking to modify brewing yeast in order to enhance the flavour, smell, colour and nutritional content of the beer that the yeast produces. To demonstrate these capabilities we have included several genes which can be used to modify the flavour of any beer created by a gentically engineered yeast strain. Miraculin is a protein found naturally in the fruits of the Miracle Berry plant Synsepalum dulcificum and has been found to make sour foods taste sweeter. The taste altering property of Miraculin therefore means it has potential use as an artficial sweetener and is therefore a healthier alternative to natural sugars found in most products. A number of other naturally occuring flavour enhancing compounds such as X which originates in raspberry plants derive from the precursor carotenoid compound lycopene. We have therefore chosen to include a genetic part encoding the three enzymes responsible for the biosynthesis of lycopene. Research into the nutritional value of lycopene also suggests that it acts has an antioxidant and therefore has a number of health benefits when consumed as part of a balanced diet.