Team:University College London/Research

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Latest revision as of 23:15, 26 October 2012

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- 1: Detection
- 2: Aggregation
- 3: Degradation
- 4: Buoyancy
- 5: Salt Tolerance
- 6: Containment
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Project Overview

In many of the world's oceans, currents carry debris and pollution originating from coastlines. This waste accumulates in regional gyres - where ocean currents meet, and can reach extremely high concentrations. Plastic is estimated to account for 60-80% of this debris, and is known to be gradually broken down by solar energy and the mechanical action of the sea. This means the majority of the plastic waste are several millimetres in diameter or less, which has made efforts to clean them from the ocean largely unsuccessful. These tiny plastic fragments - microplastics - enter the digestive systems of resident organisms, which are affected either by the physical size of the plastic or its toxicity from adsorbing organic pollutants.

UCL iGEM proposes a synthetic biology approach for the bioremediation of micro-plastic pollutants within the marine environment, with emphasis on regions of excessive debris accumulation, such as the 'Great pacific garbage patch’ in the North Pacific gyre.

We intend to engineer Escherichia coli and marine bacteria Roseobacter denitrificans & Oceanibulbus indolifex to degrade plastic, or aggregate it for collection.

Detection Module

Detection of plastics as a trigger for the Aggregation module

Our Detection module will allow our bacteria to detect the presence of plastic. This serves to control the production of our adhesive – curli fibrins – which binds non-specifically to an extraordinary array of surfaces. By producing adhesive only when plastic is present, we prevent our bacteria binding to non-plastic materials.

Aggregation Module

Curli expression for the aggregation of plastic and production of biofilm

The Aggregation Module confers onto our bacteria the means of plastic adhesion. To implement this we have decided to transform our bacteria with a genetic circuit to produce adhesive proteins called curlis. As curlis are non-specific in the surfaces they bind to, the Detection module will limit their production, unless they are in the presence of plastics.

Plastic Degradation

Multi-copper oxidase/Laccase for the degradation of polyethylene

As an alternative to the Aggregation system, we are also developing an alternative solution – the degradation of plastic. This will investigate enzymes expressed by numerous organisms that have been demonstrated to degrade plastics.

Buoyancy Module

Glucose concentration dependent buoyancy for localisation of engineered bacteria within the water column

The Buoyancy module is key to both the Degradation and the Aggregation systems. Buoyancy is required to position our bacteria in the water column, alongside the plastic fragments, and also to enable them to buoy the plastic aggregates.

Salt Tolerance

IrrE a global regulator from Deinococcus radiodurans for increased salinity tolerance in E. coli

A core module for our project is enabling E. coli to tolerate the salt content of the ocean; without this ability E. coli could not survive in a marine environment. Due to the widespread use of E. coli as a chassis for synthetic biology, this module is being developed to demonstrate that E. coli, as well as marine bacteria, could be used as the chassis for this project.

Containment Components

A novel threefold active biological containment system

UCL iGEM 2012 addresses fundamental barriers to the implementation of traditional biological containment systems. As our project proposes the release of genetically modified bacterium into the environment, we feel it is necessary to contain the risk of spreading genetic information by horizontal gene transfer. To do so we are suggesting a periplasmic nuclease system in order to degrade genetic material in the surrounding area.

A multi-containment system, consisting of three toxin/anti-toxin pairs - Holin / Anti-Holin Endolysin, Colicin-E3 / Colicin Immunity E3, and Endunuclease EcoRI / Methyltransferase EcoRI will also be considered in our containment system.

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-{{:Team:University_College_London/templates/head|coverpicture=training}}
+{{:Team:University_College_London/templates/headnocover}}<html><img src="http://www.plasticrepublic.org/wikifiles/overview-research.png" /></html>
-= Research =
 == Project Overview ==
+In many of the world's oceans, currents carry debris and pollution originating from coastlines. This waste accumulates in  regional gyres - where ocean currents meet, and can reach extremely high concentrations. Plastic is estimated to account for 60-80% of this debris, and is known to be gradually broken down by solar energy and the mechanical action of the sea. This means the majority of the plastic waste are several millimetres in diameter or less, which has made efforts to clean them from the ocean largely unsuccessful. These tiny plastic fragments - microplastics - enter the digestive systems of resident organisms, which are affected either by the physical size of the plastic or its toxicity from adsorbing organic pollutants.
-UCL iGEM proposes a synthetic biology approach for the bioremediation of micro-plastic pollutants within the marine environment, with emphasis on regions of excessive debris accumulation, such as the North Pacific ‘garbage patch’.
+UCL iGEM proposes a synthetic biology approach for the bioremediation of micro-plastic pollutants within the marine environment, with emphasis on regions of excessive debris accumulation, such as the 'Great pacific garbage patch’ in the North Pacific gyre.
-We intend to engineer enhanced adhesive properties in ''Escherichia coli'' and marine bacteria ''Roseobacter denitrifican''s & ''Oceanibulbus indolifex'', of the ''Roseobacter'' clade. To alter the composition and dynamics of resultant biofilms for the adhesion of micro-plastic pollutants, with an extended vision of creating mass aggregates, or ‘Plastic Islands’.
+We intend to engineer ''Escherichia coli'' and marine bacteria ''Roseobacter denitrifican''s & ''Oceanibulbus indolifex'' to degrade plastic, or aggregate it for collection.
-We will attempt to demonstrate micro-plastic particle aggregation and several additional genetic components, including plastic degradation, salinity/osmotic tolerance in ''E. coli'', bacterial buoyancy and novel active biological containment strategies, for an integrative approach to marine bioremediation.
+== Detection Module ==
+'''Detection of plastics as a trigger for the Aggregation module'''
+Our Detection module will allow our bacteria to detect the presence of plastic. This serves to control the production of our adhesive – curli fibrins – which binds non-specifically to an extraordinary array of surfaces.  By producing adhesive only when plastic is present, we prevent our bacteria binding to non-plastic materials.
-In many of the worlds oceans, currents carry debris and pollution originating from coastlines. This waste accumulates in  regional gyres, where the worlds ocean currents meet, and can reach extremely high concentrations. Plastic is estimated to account for 60-80% of this debris, and is known to be gradually broken down by solar energy and the mechanic action of the sea. This means the majority of the plastic waste are several millimetres in size or less, which has made efforts to clean them from the ocean largely unsuccessful. These tiny plastic fragments - microplastics - enter the digestive systems of resident organism, which are affected either by the physical size of the plastic or its toxicity from adsorbing organic pollutants.
-== Aim ==
-We aim to genetically engineer a bacterial machine capable of constructing 'islands' from microplastics. Using  Roseobacter denitrificans, a marine bacterium, we will insert genes that allow it to adhere to, aggregate and buoy fragments. While relatively small, these ‘Plastic Islands’ could be collected and recycled, or alternatively clumped into large artificial ‘islands’. Our vision is to reclaim waste by ‘terraforming’ it into a habitable island – dubbed by our team as the ‘Plastic Republic’.
-We are pursuing this project as several separate modules which we will assemble once we have tested their competence.
-== Plastic specificity ==
-Hydrophobicity and surface properties of plastic surfaces are such that they significantly adsorb synthetic organic compounds compared to ambient seawater. The accumulation of organic pollutants forms the basis of our detection system, whereby expression of adhesive components are induced by the presence of such compounds, these include PCBs, PAHs, DTTs and a wide range of hydrophobic organic compounds.
 == Aggregation Module ==
-'''Curli expression for the aggregation of plastic particulates and alteration of biofilm properties
+'''Curli expression for the aggregation of plastic and production of biofilm'''
-BBa_K729003'''
-We intend to aggregate microplastic particulates through expression of highly adhesive curli amyloid appendages, subsequent adhesive and shear properties of biofilms and ability to accumulate nano-plastic/micro-plastic debris will be investigated in the context of marine systems.
+The Aggregation Module confers onto our bacteria the means of plastic adhesion. To implement this we have decided to transform our bacteria with a genetic circuit to produce adhesive proteins called curlis. As curlis are non-specific in the surfaces they bind to, the Detection module will limit their production, unless they are in the presence of plastics.
 == Plastic Degradation ==
-'''Multi-copper oxidase/Laccase for the degradation of polyethylene and other plastics BBa_K729002'''
+'''Multi-copper oxidase/Laccase for the degradation of polyethylene'''
-Recent evidence has implicated the role of laccase/multi-copper oxidase in the degradation of polyethylene (Santo et al. 2012). We will investigate the potential of a laccase based BioBrick for the degradation of microplastic debris, with focus on polyethylene and polypropylene.
+As an alternative to the Aggregation system, we are also developing an alternative solution – the degradation of plastic. This will investigate enzymes expressed by numerous organisms that have been demonstrated to degrade plastics.
 ==Buoyancy Module==
-'''Temperature dependent buoyancy for localisation of engineered bacteria within the water column BBa_K729000'''
+'''Glucose concentration dependent buoyancy for localisation of engineered bacteria within the water column '''
-For optimal aggregation and sustained buoyancy, we propose a method for the localisation of engineered bacteria within the water column, dependent on ambient temperature for the synthesis of the gas vesicle polycistronic cluster(Melbourne 2007).
+The Buoyancy module is key to both the Degradation and the Aggregation systems. Buoyancy is required to position our bacteria in the water column, alongside the plastic fragments, and also to enable them to buoy the plastic aggregates.
 ==Salt Tolerance==
-'''irrE a global regulator from ''Deinococcus radiodurans'' for increased salinity tolerance in E. coli BBa_K729001'''
+'''IrrE a global regulator from ''Deinococcus radiodurans'' for increased salinity tolerance in ''E. coli'''''
-irrE, a global regulator of radiation resistance confers resistance to various abiotic stresses through regulation of numerous  effectors, including DNA recombination protein recA (Earl et al. 2002). We will specifically investigate the ability of irrE to confer salinity tolerance in ''E. coli'', as previously demonstrated by (Pan et al. 2009).
+A core module for our project is enabling ''E. coli'' to tolerate the salt content of the ocean; without this ability ''E. coli'' could not survive in a marine environment. Due to the widespread use of ''E. coli'' as a chassis for synthetic biology, this module is being developed to demonstrate that ''E. coli'', as well as marine bacteria, could be used as the chassis for this project.
 ==Containment Components==
-UCL iGEM 2012 addresses fundamental barriers to the implementation of traditional biological containment systems.
+'''A novel threefold active biological containment system'''
-'''A novel threefold active biological containment system
-BBa_K729010, BBa_K729009'''
-In view of inactivating mutations and consideration for multiple targets for the induction of cell death, we have devised a robust three fold active biological containment system to address horizontal gene transfer. Consisting of toxin anti-toxin pairs Colicin-E3/Colicin Immunity E3 and EcoRI/methyltransferase EcoRI, in addition to the Holin/Anti-Holin endolysin pair described by Berkley 2008.
-'''Nuclease from Staphylococcus aureus for genomic deletion
+UCL iGEM 2012 addresses fundamental barriers to the implementation of traditional biological containment systems. As our project proposes the release of genetically modified bacterium into the environment, we feel it is necessary to contain the risk of spreading genetic information by horizontal gene transfer. To do so we are suggesting a periplasmic nuclease system in order to degrade genetic material in the surrounding area.
-BBa_K7290011'''
+A multi-containment system, consisting of three toxin/anti-toxin pairs - Holin / Anti-Holin Endolysin, Colicin-E3 / Colicin Immunity E3, and Endunuclease EcoRI / Methyltransferase EcoRI will also be considered in our containment system.
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