Difference between revisions of "Team:Amsterdam/Collaborations"

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        <header class="major"><h1>Collaboration: imagining the future together</h1></header>           
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In the world of iGEM, teams from different universities usually work on distinct projects tackling separate issues. Sometimes, however, the combination of two projects can give rise to novel solutions that could not be achieved by either project alone. As it turns out, the iGEM projects of team Amsterdam and team TU Delft give rise to such combination. In this essay we wrote together, we explore how our projects could be combined and describe a potential application of combining Amsterdam’s synthetic consortium with Delft’s nanowires and 3D-biofilm printer.
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<header class = "major"><h1>3D-printing biofilm-based consortia</h1></header>
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<h4 style = "text-align:center;"><i>Creating a new generation of affordable biorefineries</i></h4>
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  <h4 style = "text-align:center;"><i>An exploration of combined projects and visions<br />iGEM Amsterdam & Synenergene</i></h4>
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<header class = "major"><h3>Delft</h3></header>
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The TU Delft iGEM team designed constructs that give bacteria the ability to form nanowires between each other, creating an extracellular matrix which forms a structure, and form a biofilm. In the project of Amsterdam, the E.coli and cyanobacteria will form the biofilms. The E.coli bacteria are producing the nanowires. The cyanobacteria will be trapped by these nanowires in such a way that specific structures of both E.coli and cyanobacteria are formed. These specific structures can increase the production rate as the  ratio of cyanobacteria to E.coli can be engineered to ideally match the steady state conversion rates, while at the same time reducing diffusion limitations between both partners.
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<header class = "major"><h3>Amsterdam</h3></header>
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The iGEM team of Amsterdam is creating a self-sustaining bio-factory of cyanobacteria and chemotrophs. The cyanobacteria produce sugars and oxygen from CO2 , water and light; known as photosynthesis. In their prototype consortium the sugars are used as a carbon source for, E.coli, which uses it to create a desired end-product. In their proof-of-concept bio-factory this product will be isobutanol, a potential biofuel. That said, their cyanobacterial carbon fixation module can be coupled to a multitude of biotechnological production processes to make these processes more sustainable. Using TU Delft’s 3D printer could improve both the reproducibility and specificity of a biofilm-based consortium. The 3D printer would, for example, be able to print a layer of cyanobacteria in between two layers of E.coli to create specific patterns that optimize carbon sharing and product formation in Amsterdam’s consortium.
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<header class = "major"><h3>The Bio-composite Leaf,</h3></header>
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Besides potentially optimizing the productivity of  Amsterdam’s consortium in a bioreactor, accurately printing biofilms allows for a whole range of novel consortia applications. One of these is the so-called ‘bio-composite leaf’, an approach described by Bernal et al. as ‘[an] approach to improve solar energy harvesting capacity [by] fabricating inexpensive water- based ‘‘cellular biocomposite’’ materials that mimic or exceed the function and stability of natural plant leaves by ordering layers of closely packed living photosynthetic cells on a surface with a non-toxic adhesive polymer binder’ (2014). Such multilayered composites of densely packed cells could significantly improve the low light harvesting capacity of cyanobacteria commonly observed in photobioreactors.
  
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<h2> Collaborations</h2>
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<header class = "major"><h3>Re-invented  </h3></header>
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Packing cyanobacterial cells together without losing photosynthetic capacity poses a scientific challenge. The most successful method used to date exploits adhesive colloidal polymer particles that bind the cyanobacteria to a leaf that consists of porous paper, which hydrates the cell coating via the fluid in the paper pores below the coating [figure 1]. Although this approach generates high photosynthetic rates, creating the latex coating is a time-consuming, complex process that has not been optimised for uniformity of the coating. A standardised, relatively simple process for creating such coatings could not only overcome these problems, but could ultimately enable the mass-production of bio-composite leaves for high-yield sustainable bioproduction.
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<header class = "major"><h3>A new approach</h3></header>
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That’s where TU Delft’s 3D-printer for biofilms comes in. By using their biobricks that enable rapid immobilization of organisms via nanowires, together with the ability to accurately print these in the form of biofilms, one could create coatings that would be easy to produce and ideally suited for bio-composite leaves. A coating of cyanobacteria could simply be printed on a piece of porous paper and placed in the gas-phase of a photobioreactor for a steady supply of CO2, where it would function much in the way as described by Bernal et al. [2014]. Further leveraging Amsterdam’s consortium design, a layer of cyanobacteria would be printed on top of a layer of chemotrophic cell-factories like E. coli, who would use the constant supply of carbon provided by the cyanobacteria to produce end-products like biofuels, which would be transported to an extraction chamber where the product would be isolated.
  
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Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
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  <img src="https://static.igem.org/mediawiki/2015/8/87/Bionic_leaf.png" alt="Lactate Qp and growth">
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  <figcaption>Previous method based on extrusive coating method described by Bernal et al. (2014). .</figcaption>
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Together, the work of team Amsterdam and TU Delft shows how combining separate iGEM projects can unlock new solutions to existing problems that could lead to new innovations. Indeed, the sustainable product formation enabled by Amsterdam’s consortium and the ease of printing biofilms with immobilizing nanowires developed by TU Delft could turn the type of biocomposite devices described by Bernal et al. into the cheap, versatile biofactory of the future.
  
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<h4> Which other teams can we work with? </h4>
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You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the <a hreef="https://2015.igem.org/Judging/Awards#Medals">iGEM team collaboration gold medal criterion</a>.
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In order to meet the gold medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.
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Here are some suggestions for projects you could work on with other teams:
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<li> Improve the function of another team's BioBrick Part or Device</li>
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Latest revision as of 01:32, 19 September 2015

iGEM Amsterdam 2015

Collaboration: imagining the future together

In the world of iGEM, teams from different universities usually work on distinct projects tackling separate issues. Sometimes, however, the combination of two projects can give rise to novel solutions that could not be achieved by either project alone. As it turns out, the iGEM projects of team Amsterdam and team TU Delft give rise to such combination. In this essay we wrote together, we explore how our projects could be combined and describe a potential application of combining Amsterdam’s synthetic consortium with Delft’s nanowires and 3D-biofilm printer.

3D-printing biofilm-based consortia

Creating a new generation of affordable biorefineries

An exploration of combined projects and visions
iGEM Amsterdam & Synenergene

Delft

The TU Delft iGEM team designed constructs that give bacteria the ability to form nanowires between each other, creating an extracellular matrix which forms a structure, and form a biofilm. In the project of Amsterdam, the E.coli and cyanobacteria will form the biofilms. The E.coli bacteria are producing the nanowires. The cyanobacteria will be trapped by these nanowires in such a way that specific structures of both E.coli and cyanobacteria are formed. These specific structures can increase the production rate as the ratio of cyanobacteria to E.coli can be engineered to ideally match the steady state conversion rates, while at the same time reducing diffusion limitations between both partners.

Amsterdam

The iGEM team of Amsterdam is creating a self-sustaining bio-factory of cyanobacteria and chemotrophs. The cyanobacteria produce sugars and oxygen from CO2 , water and light; known as photosynthesis. In their prototype consortium the sugars are used as a carbon source for, E.coli, which uses it to create a desired end-product. In their proof-of-concept bio-factory this product will be isobutanol, a potential biofuel. That said, their cyanobacterial carbon fixation module can be coupled to a multitude of biotechnological production processes to make these processes more sustainable. Using TU Delft’s 3D printer could improve both the reproducibility and specificity of a biofilm-based consortium. The 3D printer would, for example, be able to print a layer of cyanobacteria in between two layers of E.coli to create specific patterns that optimize carbon sharing and product formation in Amsterdam’s consortium.

The Bio-composite Leaf,

Besides potentially optimizing the productivity of Amsterdam’s consortium in a bioreactor, accurately printing biofilms allows for a whole range of novel consortia applications. One of these is the so-called ‘bio-composite leaf’, an approach described by Bernal et al. as ‘[an] approach to improve solar energy harvesting capacity [by] fabricating inexpensive water- based ‘‘cellular biocomposite’’ materials that mimic or exceed the function and stability of natural plant leaves by ordering layers of closely packed living photosynthetic cells on a surface with a non-toxic adhesive polymer binder’ (2014). Such multilayered composites of densely packed cells could significantly improve the low light harvesting capacity of cyanobacteria commonly observed in photobioreactors.

Re-invented

Packing cyanobacterial cells together without losing photosynthetic capacity poses a scientific challenge. The most successful method used to date exploits adhesive colloidal polymer particles that bind the cyanobacteria to a leaf that consists of porous paper, which hydrates the cell coating via the fluid in the paper pores below the coating [figure 1]. Although this approach generates high photosynthetic rates, creating the latex coating is a time-consuming, complex process that has not been optimised for uniformity of the coating. A standardised, relatively simple process for creating such coatings could not only overcome these problems, but could ultimately enable the mass-production of bio-composite leaves for high-yield sustainable bioproduction.

A new approach

That’s where TU Delft’s 3D-printer for biofilms comes in. By using their biobricks that enable rapid immobilization of organisms via nanowires, together with the ability to accurately print these in the form of biofilms, one could create coatings that would be easy to produce and ideally suited for bio-composite leaves. A coating of cyanobacteria could simply be printed on a piece of porous paper and placed in the gas-phase of a photobioreactor for a steady supply of CO2, where it would function much in the way as described by Bernal et al. [2014]. Further leveraging Amsterdam’s consortium design, a layer of cyanobacteria would be printed on top of a layer of chemotrophic cell-factories like E. coli, who would use the constant supply of carbon provided by the cyanobacteria to produce end-products like biofuels, which would be transported to an extraction chamber where the product would be isolated.

Lactate Qp and growth
Previous method based on extrusive coating method described by Bernal et al. (2014). .

Together, the work of team Amsterdam and TU Delft shows how combining separate iGEM projects can unlock new solutions to existing problems that could lead to new innovations. Indeed, the sustainable product formation enabled by Amsterdam’s consortium and the ease of printing biofilms with immobilizing nanowires developed by TU Delft could turn the type of biocomposite devices described by Bernal et al. into the cheap, versatile biofactory of the future.