Difference between revisions of "Team:London Biohackspace/Design"

 
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                <h2>making better beer</h2>
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<h2>The Motivation</h2>
  
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                <h3>What is the SYNBIO Brewery DIY-Brewkit</h3>
+
<p>We want to introduce a whole new group of people to the DIYBio community using the exciting products of synthetic biology. The DIYBio community is still a nascent one, and we believe it has the potential to become a big thing (hopefully a really big thing). The SynBio Brewery DIY Brew Kit is therefore designed to get members of the home-brewing and micro-brewing community interested in DIYBio and synthetic biology - who better to get involved, than people that are already familiar with manipulating biology to do their bidding?</p>
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<p><img src="https://static.igem.org/mediawiki/2015/0/08/LONBIO-BrewKit-box.jpg" style="margin-right:20px;" align="left"/>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 commercially 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>
+
                  <p>Our project is not about increasing crop yield or increasing shelf life of crops. We are trying to make synthetic biology and genetic modification easy to understand by making the changes "easy to see" in the product. We believe that without given the opportunity to learn what synbio is all about - the public wouldn't be able to decide whether they want to use this technology in the future or not. We aimed to involve the public in synthetic biology in a fun and engaging in way!</p>                
  
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<br/>
 
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  <h3>How we created the SYNBIO Brewery DIY-Brewkit <br/>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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<div>
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<h2>What is the Synbio Brewery DIY-Brewkit</h2>
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<img src="https://static.igem.org/mediawiki/2015/1/13/LONBIO-extracting-yeast-from-beer-bottles.png" style="border:solid 1px black;margin-top:5px;"/><p><b>Capturing wild yeast from beer bottles</b><br/>  Yeast sediment from unfiltered craft beer was grown on YEPD agar plates to provide the source strains for the SYNBIO Brewery DIY-BrewKit.  We also cultured a number of yeast strains purchased from home brew equipment suppliers.</p>
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</div>
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<h3>How we created the SYNBIO Brewery DIY-Brewkit <br/>The BrewKit gene library</h3>
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<p><img src="https://static.igem.org/mediawiki/2015/0/08/LONBIO-BrewKit-box.jpg" style="margin-right:20px;" align="left" height="207" width="135"/>The SynBio Brewery DIY-Brewkit is a package containing everything an established home-brewer or micro-brewer needs to start making beer with a synbio twist. Each basic package contains six GM brewing yeast strains - each of which adds one novel property to the beer brewed with it. We hope brewers will start to experiment with different combinations and quantities of our yeast strains to produce truly unique beers. Each kit also contains a simple explanation of what each strain does and the science behind it as well as resources to help the brewers dig deeper into how to go about making new strains themselves as DIY-biologists. <a href="/Team:London_Biohackspace/product-design">More about the design of the kit.</a>
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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 genetically 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 makes for a healthier alternative to natural sugars found in most products.  A number of other naturally occuring flavour enhancing compounds such as beta-ionone 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 as an antioxidant and therefore has a number of health benefits when consumed as part of a balanced diet.</p>
+
  
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<p>The SYNBIO DIY-Brewkit also includes a mechanism for regulating the expression of each protein inserted into a yeast strain via RNA interference in order to produce high, medium and low levels of expression without the need to use different transcriptional promoters. This is achieved through the use of a set of paired termini anti-sense RNA interference parts designed to target each gene in the Brewkit which act to reduce mRNA transcription to a desired level. To create a medium expression level RNA knockdown we added a number of mismatched bases into the H-stem of the paired termini antisense RNA in order to reduce overall stability of the RNAi and subsequently inhibit its ability to bind to the target mRNA sequence. This has the effect of reducing the level of target mRNA as well as its subsequent translation into the final protein product. These RNAi knockdown parts can therefore be used by home brewers in conjunction with the genes from the DIY-Brewkit library to refine the final product of their engineered yeast strains</p>
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                  <div><img src="https://static.igem.org/mediawiki/2015/d/d8/LONBIO-MANUAL-pg1.jpg" width="100px" height="490px" /></div>
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                  </div>
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                <h3>scroll through the pages to check out the booklet</h3>
 +
            </p>
 +
<h2 style="clear: both;">The Strains</h2>
 +
 
 +
<p>We have designed a number of strains as a starting point for the yeast library that brewers can use to easily enhance the flavour, smell, colour and nutritional content of their beer:</p>
 +
 
 +
<h3>Miraculin expression</h3>
 +
<p>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 artificial sweetener and makes for a healthier alternative to natural sugars found in most products. We have designed a yeast strain expressing the miraculin protein which will create a beer with this interesting flavour additive.
 +
</br>
 +
Related part: <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1845002">BBa_K1845002</a></p>
 +
 
 +
<h3>Lycopene biosynthesis</h3>
 +
<p>Lycopene is a carotenoid compound that can be found in tomatoes and many other red fruits. We have designed a yeast strain expressing the three enzymes (CrtE, CrtB, CrtI) responsible for the biosynthesis of lycopene which will create red pigmented beer. Research into the nutritional value of lycopene also suggests that it acts as an antioxidant and therefore has a number of health benefits when consumed as part of a balanced diet. Additionally, this strain provides a basis for producing a yeast strain that synthesises beta-ionone, a woody flavour compund, as lycopene is a precursor in beta-ionone's synthesis.</p>
 +
 
 +
<h3>ATF1 overexpression</h3>
 +
<p>The yeast alcohol acetyltransferase gene ATF1 is responsible for regulating the production of a broad range of volatile compounds by yeast during fermentation. We have designed a yeast strain with an overexpressed copy of ATF1 derived from Saccharomyces carlsbergensis which will create a beer with boosted fruity notes.</br>
 +
Related part: <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1845003">BBa_K1845003</a></p>
 +
 
 +
<h3>OneProt2 expression</h3>
 +
<p>OneProt2 is a synthetic protein based on the principle of <a href="https://2014.igem.org/Team:SDU-Denmark/Tour23">Team SDU-Denmark 2014</a>'s OneProt protein. It contains all the essential amino acids (in the WHO recommended ratio) required in human diet. We have designed a yeast strain expressing the OneProt2 protein which will create a beer with improved nutritional element.</br>
 +
Related part: <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1845004">BBa_K1845004</a></p>
 +
 
 +
 
 +
<h2>Community resources for growing the brew kit yeast library</h2>
 +
 
 +
<p>We have great hope that brewers and already established members of the DIYBio community will want to create new strains of yeast and add to our open source strain library. TO facilitate this, we have designed a set of genetic parts and protocols to enable the community to more easily produce new and interesting yeast strains from existing commercially available brewing strains. Additionally, these open-source tools for working with yeast are primarily designed to work in a community lab setting, thus 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 resources.</p>
 +
 
 +
<h3>Filtration method for competent cells preparation</h3>
 +
<p>An easy, cheap and automated (convenient) method for preparing competent cells in a community lab without a -80 freezer. <a href="/Team:London_Biohackspace/protocols/filtercomp">More...</a></p>
 +
 
 +
<h3><span style="text-transform: none">SPliCE</span> vector assembly</h3>
 +
<p>We have developed an easy and cheap method for assembling vectors without the need for expensive purified restriction enzymes and ligases. A great method for community labs to lower the cost of constructing vectors. <a href="/Team:London_Biohackspace/protocols/egassembly">More...</a></p>
 +
 
 +
<h3>RNA interference based regulation</h3>
 +
<p>We have developed a set of genetic parts that will allow users to modify the expression levels of genes inserted into yeast via RNA interference so that the novel brewing strains can be tuned. <a href="/Team:London_Biohackspace/experiments/rna-based-regulation">More...</a></p>
 +
 
 +
<h3>Creating Leucine auxotrophic S. cerevisiae strains</h3>
 +
<p>We have developed protocols for producing auxotroph mutants of existing brewing 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.  We have designed a set of genes parts that enable the user to create 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>
  
 
</div>
 
</div>

Latest revision as of 03:43, 19 September 2015

BEER.CO - Royal quality

  • The DIY-BrewKit

The Motivation

We want to introduce a whole new group of people to the DIYBio community using the exciting products of synthetic biology. The DIYBio community is still a nascent one, and we believe it has the potential to become a big thing (hopefully a really big thing). The SynBio Brewery DIY Brew Kit is therefore designed to get members of the home-brewing and micro-brewing community interested in DIYBio and synthetic biology - who better to get involved, than people that are already familiar with manipulating biology to do their bidding?

Our project is not about increasing crop yield or increasing shelf life of crops. We are trying to make synthetic biology and genetic modification easy to understand by making the changes "easy to see" in the product. We believe that without given the opportunity to learn what synbio is all about - the public wouldn't be able to decide whether they want to use this technology in the future or not. We aimed to involve the public in synthetic biology in a fun and engaging in way!

What is the Synbio Brewery DIY-Brewkit

The SynBio Brewery DIY-Brewkit is a package containing everything an established home-brewer or micro-brewer needs to start making beer with a synbio twist. Each basic package contains six GM brewing yeast strains - each of which adds one novel property to the beer brewed with it. We hope brewers will start to experiment with different combinations and quantities of our yeast strains to produce truly unique beers. Each kit also contains a simple explanation of what each strain does and the science behind it as well as resources to help the brewers dig deeper into how to go about making new strains themselves as DIY-biologists. More about the design of the kit.

scroll through the pages to check out the booklet

The Strains

We have designed a number of strains as a starting point for the yeast library that brewers can use to easily enhance the flavour, smell, colour and nutritional content of their beer:

Miraculin expression

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 artificial sweetener and makes for a healthier alternative to natural sugars found in most products. We have designed a yeast strain expressing the miraculin protein which will create a beer with this interesting flavour additive.
Related part: BBa_K1845002

Lycopene biosynthesis

Lycopene is a carotenoid compound that can be found in tomatoes and many other red fruits. We have designed a yeast strain expressing the three enzymes (CrtE, CrtB, CrtI) responsible for the biosynthesis of lycopene which will create red pigmented beer. Research into the nutritional value of lycopene also suggests that it acts as an antioxidant and therefore has a number of health benefits when consumed as part of a balanced diet. Additionally, this strain provides a basis for producing a yeast strain that synthesises beta-ionone, a woody flavour compund, as lycopene is a precursor in beta-ionone's synthesis.

ATF1 overexpression

The yeast alcohol acetyltransferase gene ATF1 is responsible for regulating the production of a broad range of volatile compounds by yeast during fermentation. We have designed a yeast strain with an overexpressed copy of ATF1 derived from Saccharomyces carlsbergensis which will create a beer with boosted fruity notes.
Related part: BBa_K1845003

OneProt2 expression

OneProt2 is a synthetic protein based on the principle of Team SDU-Denmark 2014's OneProt protein. It contains all the essential amino acids (in the WHO recommended ratio) required in human diet. We have designed a yeast strain expressing the OneProt2 protein which will create a beer with improved nutritional element.
Related part: BBa_K1845004

Community resources for growing the brew kit yeast library

We have great hope that brewers and already established members of the DIYBio community will want to create new strains of yeast and add to our open source strain library. TO facilitate this, we have designed a set of genetic parts and protocols to enable the community to more easily produce new and interesting yeast strains from existing commercially available brewing strains. Additionally, these open-source tools for working with yeast are primarily designed to work in a community lab setting, thus 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 resources.

Filtration method for competent cells preparation

An easy, cheap and automated (convenient) method for preparing competent cells in a community lab without a -80 freezer. More...

SPliCE vector assembly

We have developed an easy and cheap method for assembling vectors without the need for expensive purified restriction enzymes and ligases. A great method for community labs to lower the cost of constructing vectors. More...

RNA interference based regulation

We have developed a set of genetic parts that will allow users to modify the expression levels of genes inserted into yeast via RNA interference so that the novel brewing strains can be tuned. More...

Creating Leucine auxotrophic S. cerevisiae strains

We have developed protocols for producing auxotroph mutants of existing brewing 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. We have designed a set of genes parts that enable the user to create 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.

Read more