Difference between revisions of "Team:UNOTT"

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==University of Nottingham==
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{{UNOTT}}
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<html>
  
  
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<h2>Keycoli</h2>
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<div class="column full_size" >
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'''The first biological password that changes over time!
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<img src="http://placehold.it/2000x300/d3d3d3/f2f2f2">
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*Microorganism is transformed using BioBricks to produce secondary metabolites, initially the metabolites will be a simpler product such as fluorescent proteins. The secondary metabolites will be produced in a unique and random configuration and as as our "key". In order to produce this randomness, shuffling of metabolite expression levels via transposons or error prone RNase will be applied. To produce a unique configuration of the metabolite varying promoter expression levels will produce unique metabolites. This key will be used to open locked mechanism such as safes and secure doors.
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</div>
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*For the key to be practical it would need to be portable, this is where our key transport device comes in. It will consist of a similar design to a chemostat. Our Key colony metabolites will degrade a desired amount of time before they must be renewed from the Lock colony, when this occurs the configuration of the key is shuffled once again to ensure the key and lock are changing.
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*Once the key has been transported to the locked object a juxtaposition of a detection technique such as gas chromotography or mass spectrometry and data comparison software will compare the secondary metabolites of the "key" microorganism to the "reference/lock" colony. If the metabolies of both colonies exceeds a threshold of similarity the locked object will become unlocked.
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<h2>Project Overview</h2>
 
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'''
 
  
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<h3>Radiation altered plasmid</h3>
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<div class="column full_size" >
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<h1> Welcome to iGEM 2017! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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</div>  
  
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[[Image:Nottsplasmidr.png|600px|]]
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<div class="clear"></div>
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[[Image:Nottsplasmidt.png|600px|]]
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<h2>Plan</h2>
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<div class="column half_size" >
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Plan here
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<h5>Keycoli</h5>
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<h2>Bacterial Chassis type</h2>
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<p>The first biological password that changes over time!</p>
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[[Image:Nottsadvdis.png]]
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<ul>
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<h2>Transposon selection</h2>
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<li>Microorganism is transformed using BioBricks to produce secondary metabolites, initially the metabolites will be a simpler product such as fluorescent proteins. The secondary metabolites will be produced in a unique and random configuration and as as our "key". In order to produce this randomness, shuffling of metabolite expression levels via transposons or error prone RNase will be applied. To produce a unique configuration of the metabolite varying promoter expression levels will produce unique metabolites. This key will be used to open locked mechanism such as safes and secure doors. </li>
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Tn7 Transposon used due to specific target site selection for its transposition, which is impossible in other transposon species, without this modular increases in promoter activity could not be achieved as random insertions would create a gradient rather than step wise expression pattern of proteins.
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<li> For the key to be practical it would need to be portable, this is where our key transport device comes in. It will consist of a similar design to a chemostat. Our Key colony metabolites will degrade a desired amount of time before they must be renewed from the Lock colony, when this occurs the configuration of the key is shuffled once again to ensure the key and lock are changing. </li>
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[[Image:Nottstranspose.png|300px|thumb|right|]]
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<li>Once the key has been transported to the locked object a juxtaposition of a detection technique such as gas chromotography or mass spectrometry and data comparison software will compare the secondary metabolites of the "key" microorganism to the "reference/lock" colony. If the metabolies of both colonies exceeds a threshold of similarity the locked object will become unlocked.</li>
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<h2>Promoter selection</h2>
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</ul>
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Promoters are selected to have a greatly varied production of products. These will then allow easy recognition of each level 0-3
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</div>
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<h2>Bacterial Key Transport</h2>
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There is a need for a transport mechanism for the key. This presents problems depennding on the bacteria used.
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<div class="column half_size" >
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*In Ecoli Our key transport system would need to:
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<div class="highlight">
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Keep our colonies alive for a few days  
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<h5> Project Overview </h5>
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Potentially could freeze. Freezing is one of the best ways to store bacteria.
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<p>PUT SOMETHING HERE</p>
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The lower the temperature the longer the culture will retain viable cells
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<p></p>
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PROBLEM: Ice can damage cells due to localised accumulation of salt, it can also rupture membranes.
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</div>
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SOLUTION: Use glycerol as a cryoprotectant  
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</div>
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Inhibit conjugation/recombination/genome shuffling
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Synthetic fatty acids prevents plasmid-mediated horizontal gene transfer (M.Getino, Et al,. 2015)
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<div class="column full_size" >
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Act against the induction of mutations
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<h5> PLAN OF ACTION </h5>
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*In Clostridium, spore storage could be used, however this presents the problem of spore awakening and time taken for product synthesis
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<p>We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the <a href="https://2017.igem.org/Judging/Pages_for_Awards">Pages for awards</a> link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!</p>
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<h2>Key comparison Environment</h2>
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A method by which the comparative environment for mother and daughter key colonies can be compared in alternative environments
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</div>
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<div class="column half_size" >
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<h5> Transposon selection </h5>
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<p>Tn7 Transposon used due to specific target site selection for its transposition, which is impossible in other transposon species, without this modular increases in promoter activity could not be achieved as random insertions would create a gradient rather than step wise expression pattern of proteins.</p>
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<h5> Promoter selection </h5>
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<p>Promoters are selected to have a greatly varied production of products. These will then allow easy recognition of each level 0-3</p>
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 +
</div>
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 +
 
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<div class="column half_size" >
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<h5>Bacterial Key Transport</h5>
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<p>There is a need for a transport mechanism for the key. This presents problems depending on the bacteria used.</p>
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<p> In Ecoli Our key transport system would need to: </p>
 +
<ul>
 +
<li>Keep our colonies alive for a few days. </li>
 +
<li>Potentially could freeze. Freezing is one of the best ways to store bacteria. </li>
 +
<li>The lower the temperature the longer the culture will retain viable cells.</li>
 +
<li>PROBLEM: Ice can damage cells due to localised accumulation of salt, it can also rupture membranes. </li>
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<li>SOLUTION: Use glycerol as a cryoprotectant </li>
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</ul>
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</div>
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<div class="column half_size" >
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<h5>Sponsors</h5>
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<p>Here are our sponsors. FEEL FREE TO EXPAND</p>
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<ul>
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<li>Prince of Nigeria</li>
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</ul>
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</div>
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<div class="column half_size" >
 
<h2>Possible Metabolites</h2>
 
<h2>Possible Metabolites</h2>
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<h4>LIMS1</h4>
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<h4>INSERT LATER</h4>
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*Limonene synthase 1 from Citrus limon (accession AF514287). Synthesised by Geneart. Limonene synthase converts farnesyl-diphosphate to (+)-limonene, which is a component of lemon scent. Note: several codons were altered silently to remove several forbidden restriction sites. The N-terminal region (plastid targeting sequence) was removed, removing the first 51 amino acids and replacing codon 52 with the start codon ATG.
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For a diagram of limonene synthesis, and the synthesis of other lemon flavour compounds see Edinburgh Yoghurt Wiki
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</div>
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<h4>SAM:benzoic acid carboxyl methyltransferase</h4> converts benzoic acid to methyl benzoate (floral odor)
 
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BBa_J45002 encodes SAM benzoic acid carboxyl methyltransferase I derived from BAMT from Antirrhinus majus (snapdragon). BAMT catalyzes the conversion of benzoic acid to methyl benzoate. Methyl benzoate has a floral smell.
 
  
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*Enzyme is active as a dimer.
 
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There are two methionine codons at the begnning of the BAMT cDNA. The BAMT resulting from amplification from the second methionine shows a 2.4 times higher specific activity than from the first methionine in protein purified from cell lysate; on the other hand, BAMT purified from E. coli shows no difference in specific activity (from both Met codons). The Km and kcat are the same from both codons in E. coli.
 
  
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*Inhibition by SAH was competitive with respect to SAM and noncompetitive with respect to benzoic acid. SAM appears to be the first substrate to bind to the enzyme. Methyl benzoate is released first and SAH last.
 
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BAMT activity may be regulated by the intracellular SAM/SAH concentration ratio rather than benzoic acid availability.
 
  
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<h4>alcohol acetyltransferase I</h4>
 
  
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*BBa_J45014 encodes alcohol acetyltransferase I derived from ATF1 from Saccharomyces cerevisiae. ATF1 catalyzes the conversion of isoamyl alcohol to isoamyl acetate. Isoamyl acetate has a banana smell. converts isoamyl alcohol to isoamyl acetate (banana odor)
 
  
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*[Note that this is not aspartate amino transferase (also called "AATase"), and that "ATF1" also refers to "Activating Transcription Factor 1" in humans (an entirely different protein that is homologous to "Atf1" in mouse).]
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</html>
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Sequence and Features
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Revision as of 17:17, 28 June 2017

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JUDGING FORM

UNOTT

Welcome to iGEM 2017!

Your team has been approved and you are ready to start the iGEM season!

Keycoli

The first biological password that changes over time!

  • Microorganism is transformed using BioBricks to produce secondary metabolites, initially the metabolites will be a simpler product such as fluorescent proteins. The secondary metabolites will be produced in a unique and random configuration and as as our "key". In order to produce this randomness, shuffling of metabolite expression levels via transposons or error prone RNase will be applied. To produce a unique configuration of the metabolite varying promoter expression levels will produce unique metabolites. This key will be used to open locked mechanism such as safes and secure doors.
  • For the key to be practical it would need to be portable, this is where our key transport device comes in. It will consist of a similar design to a chemostat. Our Key colony metabolites will degrade a desired amount of time before they must be renewed from the Lock colony, when this occurs the configuration of the key is shuffled once again to ensure the key and lock are changing.
  • Once the key has been transported to the locked object a juxtaposition of a detection technique such as gas chromotography or mass spectrometry and data comparison software will compare the secondary metabolites of the "key" microorganism to the "reference/lock" colony. If the metabolies of both colonies exceeds a threshold of similarity the locked object will become unlocked.
Project Overview

PUT SOMETHING HERE

PLAN OF ACTION

We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the Pages for awards link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!

Transposon selection

Tn7 Transposon used due to specific target site selection for its transposition, which is impossible in other transposon species, without this modular increases in promoter activity could not be achieved as random insertions would create a gradient rather than step wise expression pattern of proteins.

Promoter selection

Promoters are selected to have a greatly varied production of products. These will then allow easy recognition of each level 0-3

Bacterial Key Transport

There is a need for a transport mechanism for the key. This presents problems depending on the bacteria used.

In Ecoli Our key transport system would need to:

  • Keep our colonies alive for a few days.
  • Potentially could freeze. Freezing is one of the best ways to store bacteria.
  • The lower the temperature the longer the culture will retain viable cells.
  • PROBLEM: Ice can damage cells due to localised accumulation of salt, it can also rupture membranes.
  • SOLUTION: Use glycerol as a cryoprotectant
Sponsors

Here are our sponsors. FEEL FREE TO EXPAND

  • Prince of Nigeria

Possible Metabolites

INSERT LATER