Difference between revisions of "Team:Marburg/Notebooks"

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         <h2>Projects</h2>
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         <h2>Notebooks</h2>
 
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            <h3 class="text-center">Utilization of artificial endosymbiosis to abolish land grabbing through the production of terpenoid derived chemicals</h3>
 
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             <p>
 
             <p>
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                 The term "land grabbing" describes the acquisition of land, mainly in developing
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                 The team's notebooks. TODO.
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                and newly industrialized countries through foreign investors to plant crops for
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                food production as well as for the production of valuable secondary plant substrates,
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                for example pharmaceuticals or biofuels derived from terpenoids <a href="#ref_1" class="ref">[1]</a>.
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                Although production of secondary plant substrates through microorganisms is possible in general,
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                it is mostly either inefficient or extremely expensive in terms of research <a href="#ref_2" class="ref">[2]</a>.
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                This is mainly due to the different properties of various microorganisms, where some are more
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                suitable than others for the production of a desired substrate. In addition, this often
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                goes beyond the utilization of traditional model organisms in microbiology, such as S.
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                cerevisiae and E. coli. As mentioned before, it requires great effort in terms of engineering
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                one of these organisms to make the production of especially these secondary plant substrates
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                feasible.
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            </p>
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            <p>
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                To make this production through microorganisms more interesting and therefore solve the issue of
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                land grabbing for this purpose, our project "Syndustry – Fuse. Produce. Use" combines the naturally
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                given advantages of various model organism strains. For this, we created an artificial endosymbiosis
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                between different organisms, mainly S. cerevisiae and E. coli. The organisms can be specialized to
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                overcome bottlenecks for improvement of biotechnological productions or can even grant possibilities
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                for productions that have not been established to date. The process to make this possible can mainly be
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                divided into three parts: establishing a dependency between the organisms, implementation of a production
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                pathway and the actual fusion of the organisms.
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            </p>
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            <p>
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                Since the biological safety of our system would be relevant to the recipients and the environment, we
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                also investigated in the behaviour of certain bacterial safety mechanisms, the kill switches. Instead
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                of designing one of our own, we took advantage of the numerous kill switches already implemented in the
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                iGEM database. Using these, we were creating a model describing their escape rate in terms of evolutionary
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                stability seeing them as a genetic network. We did so in collaboration with the iGEM team of Lethbridge,
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                who performed to experimental work for verification of our model.
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            </p>
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            <p>
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                Due to the multiplicity of kill switches designed in the past years of iGEM, we also created a simple and
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                easy overseeable database of all kill switches either described or implemented. It contains all relevant
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                information for the selection of a suitable kill switch, for example a classification regarding the redundancy of crucial compounds, such as inducer and toxin or a topology map.  
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            <h2 class="featurette-heading">
 
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                Dependency.
 
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                <span class="text-muted">
 
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                    Keeps the system together.
 
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            </h2>
 
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            <p class="featurette-text">
 
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                In order to guarantee the fitness of  the host organism as well as the invading cell,
 
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                we established different exchange-based dependencies - a malonate based dependency with
 
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                the invading <i>E. coli</i> cell as the malonate source and a protein based dependency
 
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                complementing essential gene knockout.
 
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            </p>
 
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            <p class="text-center">
 
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                <a class="featurette-button btn btn-default" href="https://2016.igem.org/Team:Marburg/Dependency" role="button">More details &raquo;</a>
 
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            <h2 class="featurette-heading">
 
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                Fusion.
 
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                <span class="text-muted">
 
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                    Brings the system together.
 
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            </h2>
 
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            <p class="featurette-text">
 
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                Since our whole project relies on the utilization of the principles of endosymbiosis for production purposes, we had to decide for a method to bring the organisms together. This was accomplished by modification and optimization of a protocol using <i>polyethylene glycol</i> (PEG).
 
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            </p>
 
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                <a class="featurette-button btn btn-default" href="https://2016.igem.org/Team:Marburg/PEG_Method" role="button">More details &raquo;</a>
 
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                Production Line.
 
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                    Novel system for modular synthesis.
 
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                Design of a production line that starts with limonene production in E. coli and export in S. cerevisiae.                                         
 
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                Limonene gets hydroxylated to the cancer drug perillyl alcohol and exported to the media.
 
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                <a class="featurette-button btn btn-default" href="https://2016.igem.org/Team:Marburg/Production" role="button">More details &raquo;</a>
 
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            <h2 class="featurette-heading">
 
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                Modeling.
 
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                <span class="text-muted">
 
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                    Evolutionary stability analysis of killswitches.
 
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                Quantitative work using mathematical modeling and numerics to study genetical killswitches. Treated as
 
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                genetic regulatory networks, the stability of network topologies against evolution - selection and mutation -
 
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                is studied.
 
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                <a class="featurette-button btn btn-default" href="https://2016.igem.org/Team:Marburg/Modeling" role="button">More details &raquo;</a>
 
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    <h3 class="text-center">Literature</h3>
 
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    <ol class="literature_list">
 
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        <li id="ref_1"><a href="#ref_1" class="ref">[1]</a> Ajikumar, Parayil Kumaran, et al. "Terpenoids: opportunities for biosynthesis of natural product drugs using
 
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        engineered microorganisms." Molecular pharmaceutics 5.2 (2008): 167-190.</li>
 
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        <li id="ref_2"><a href="#ref_2" class="ref">[2]</a> Van Dien, Stephen. "From the first drop to the first truckload: commercialization of microbial processes for
 
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        renewable chemicals." Current opinion in biotechnology 24.6 (2013): 1061-1068.</li>
 
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Revision as of 12:54, 22 November 2016

SynDustry Fuse. Produce. Use.

Notebooks

The team's notebooks. TODO.