Difference between revisions of "Team:Vilnius-Lithuania/Description"

 
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{{Vilnius-Lithuania project description}}
 
 
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                    <h1>Description</h1>
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                    <div class="category"></div>
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                    <p>Find out why plasmid copy number control and multiple plasmid systems are so important, what is SynORI, how does it work, and where you can apply it.</p>
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                    <div class="readmore" data-modal="1">Read more</div>
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                </div>
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                    <h1>Overview of the project</h1>
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                    <div class="category">Students</div>
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
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                        copy plasmids tend to be lost in next generations.</p>
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                    <div class="readmore" data-modal="2">read more</div>
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                </div>
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                <div class="slide-right-content slide-right-content-3 hidden">
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                    <h1>Trumpas title, per dvi eilutes</h1>
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                    <div class="category">Students</div>
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 +
                        copy plasmids tend to be lost in next generations.</p>
 +
                    <div class="readmore" data-modal="3">read more</div>
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                </div>
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                <div class="slide-right-content slide-right-content-4 hidden">
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                    <h1>Trumpas title, per dvi eilutes</h1>
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                    <div class="category">Students</div>
 +
                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 +
                        copy plasmids tend to be lost in next generations.</p>
 +
                    <div class="readmore" data-modal="4">read more</div>
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                </div>
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                <div class="slide-right-content slide-right-content-5 hidden">
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                    <h1>Trumpas title, per dvi eilutes</h1>
 +
                    <div class="category">Students</div>
 +
                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 +
                        copy plasmids tend to be lost in next generations.</p>
 +
                    <div class="readmore" data-modal="5">read more</div>
 +
                </div>
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                <div class="slide-right-content slide-right-content-6 hidden">
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                    <h1>Trumpas title, per dvi eilutes</h1>
 +
                    <div class="category">Students</div>
 +
                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 +
                        copy plasmids tend to be lost in next generations.</p>
 +
                    <div class="readmore" data-modal="6">read more</div>
 +
                </div>
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            <li><a href="/Team:Vilnius-Lithuania/Description" class="active">Description</a></li>
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                <a href="/Team:Vilnius-Lithuania/Design">Design and Results</a>
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            <li><a href="/Team:Vilnius-Lithuania/Model">Modelling</a></li>
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<h1> Controllable and flexible multi-plasmid system </h1>
 
  
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<p>In the field of synthetic biology there is a need for a standardized, stable and quickly expandable <b>multi-plasmid system</b> (A system in which we have different, unique plasmid groups in cell culture, and no plasmid group is lost during cell replication). Due to plasmid incompatibility<b>*</b>, current commercially available systems offer up to 5 different plasmids in cell using different origin of replication (ori) sequences that do not interfere with each other. Yet these systems are often unstable and unpredictable, also limited due to the fact that ori sequences are taken from plasmids that originate from different organisms. It is hard to expand the compatible ORI sequence list because, at the moment, we would need to discover the new sequences in nature, which would require a considerable amount of effort and time. Also, mentioned systems do not offer <b>any</b> way to control plasmid copy number of each plasmid group separately. </p>
 
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<p>With that in mind we have set ourselves <b>several goals we want to reach in our project</b>: </p>
 
  
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<ul>
 
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<p><li> Development of synthetic plasmid origin of replication (ori) site, based on ColE1 replicon, which would <b>tackle the problem of incompatibility by using uniquely barcoded RNA I/RNA II gene pairs</b> for each group of plasmid and show that we are able to stably co-maintain at least six of our newly made plasmids in E. coli. Using this strategy we also gain an opportunity to control the copy number of each plasmid group separately by adjusting RNA I gene expression of each group separately.</li></p>
 
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<p><li>Construction of a <b> discrete, recombinase based multi-level synthetic switch system </b> that would allow scientists to precisely control the copy number and ratio between different groups of plasmids, also eliminating the need of periodical addition of inducers to the growth medium.</li></p>
 
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<p><li>Because our system will contain different plasmids, we are doing research to develop <b>alternatives to antibiotics</b> (for purposes of biosafety) in order to apply external selection pressure,to ensure that any cell that loses a single group of plasmid would not survive.</li></p>
 
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        <h1>Description</h1>
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        <p></p>
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      <p></p>
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        <h2>What is SynORI?</h2>
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        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single and multi-plasmid systems precise, easy and on top of that - more functional.</p>
 +
<p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
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<ol>
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                      <li>Selecting the number of plasmid groups</li>
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                        <li>Choosing the copy number of each group</li>
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                        <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
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                    </ol></p>
  
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<p>In parallel with wet-lab experiments we plan to and currently began <b>writing a mathematical model to describe various aspects of our system</b>. Our dynamical plasmid replication models will allow us to predict theoretical outcomes of the system with various different parameters. We also aim to predict the probabilities of plasmid loss during the cell division and parameters that may influence that loss in order to minimize the depletion.</p>
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      <p></p>
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      <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low copy number plasmid groups are not lost during the division.
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</p>
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  <p></p>
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        <h2>Applications</h2>
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        <p>
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                        <h5>Everyday lab work</h5><p>
 +
A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your research to a particular plasmid copy number just because there are not enough right replicons to choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that suits your needs.</li></p>
 +
                        <h5>Biological computing</h5><p>
 +
The ability to choose a wide range of copy number options and their control types will make the synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number regulation is equivalent to adding a global parameter to a computer system. It enables the coordination of multiple gene group expression.
 +
</p>
 +
                        <h5>Smart assembly of large protein complexes</h5><p>
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The co-expression of multi-subunit complexes using different replicons brings incoherency to an already chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses the same type of control, and in addition can act in a group-specific manner.</p>
  
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<p>Our system would open the door to various new applications, such as larger synthetic metabolic pathways, drug synthesis, biological computing and much more!</p>
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<h5>Metabolic engineering</h5><p>
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A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in transcriptional control and synthetic ribosome binding sites in translational control are already widely used to maintain expression levels. In addition to current approaches, our framework allows a simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the search for perfect conditions a lot easier.
  
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<p><b>*</b>Plasmid incompatibility is defined as the failure of two different co-resident plasmids to be stably inherited together. It mainly arises because of fact that some plasmids share and compete for replication factors. For example, plasmids that replicate faster due to their small size would outgrow other plasmids really fast in a culture of cells, and the plasmid group with lesser copy number would have a much higher chance to be lost during cell division compared to the dominating group of plasmids.</p>
 
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<h2>Follow and support us at facebook &rarr; <a href="https://www.facebook.com/VilniusiGEM/"><img src="http://i.imgur.com/JF7xQDq.png" alt="Vilnius-Lithuania iGEM facebook" width="29" height=“29"> </a> </h2>
 
  
  
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Latest revision as of 13:28, 15 December 2017

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Description

Find out why plasmid copy number control and multiple plasmid systems are so important, what is SynORI, how does it work, and where you can apply it.

Read more

Description

What is SynORI?

SynORI stands for synthetic origin of replication. It is a framework designed to make working with single and multi-plasmid systems precise, easy and on top of that - more functional.

The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:

  1. Selecting the number of plasmid groups
  2. Choosing the copy number of each group
  3. Picking the type of copy number control (specific to one group or regulating all of them at once).

The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low copy number plasmid groups are not lost during the division.

img

Applications

Everyday lab work

A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your research to a particular plasmid copy number just because there are not enough right replicons to choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that suits your needs.

Biological computing

The ability to choose a wide range of copy number options and their control types will make the synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number regulation is equivalent to adding a global parameter to a computer system. It enables the coordination of multiple gene group expression.

Smart assembly of large protein complexes

The co-expression of multi-subunit complexes using different replicons brings incoherency to an already chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses the same type of control, and in addition can act in a group-specific manner.

Metabolic engineering

A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in transcriptional control and synthetic ribosome binding sites in translational control are already widely used to maintain expression levels. In addition to current approaches, our framework allows a simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the search for perfect conditions a lot easier.