Difference between revisions of "Team:ITB Indonesia/Description"

 
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Plastic pollution, especially in the ocean, has always been a very concerning environmental issue, both globally and regionally. PET (polyethylene glycol)-based plastics polluting our ocean are very difficult to degrade (takes 450-1000 for a single plastic bottle to be naturally degraded). Moreover, harsh ocean environment (waves and sunlight) cuts these plastics into very small fragments called microplastics, which size is only several milimeters in diameter. These microplastics make plastic pollution even more hazardous and harder to deal with. Microplastics are commonly unintentionally consumed by marine organisms causing poisoning which leads to deaths. And while normal sized plastics are easy for humans to collect and recycle, in microplastic form, these plastics are impossible to collect, making them an untreatable pollution.
 
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Realizing those facts, and seeing that treating plastic pollution is currently one of Indonesia’s main concerns, iGEM ITB 2017 team decides to step in and try to address this seemingly impossible-to-treat issue from synthetic biological perspective.
 
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The core of our project is to create a bacterial machine which will be able to 1.) detect the presence of microplastics, 2.) attach and colonize around the microplastics fragments, and 3.) degrades microplastics efficiently. Aside from that, our team plans to also ensure that our bacterial machine will also be able to 4.) utilize microplastics as its nutrition source, further enhancing its efficiency, 5.) grow and survive well in harsh marine environments, and 6.) prevent DNA leaks to nature.
 
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<div style="background-color:black;color:white;padding:20px;class="ITB_p"> Application and Implication
 
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This project can be applied to treat microplastic pollutions in bodies of water. Especially because treating plastic pollution is a very dire need for Indonesia and also internationally. Its implication includes the reduction of microplastics in treated areas. In case of the oceans, the reduction of microplastics will save million lives of marine organisms which in turn protects biodiversity.
 
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Although the grand idea of this project is the degradation of plastics in the ocean. This project can also be applied in plastic degradation projects in reactors. Due to the fact that our bacteria will be able to create a biofilm formation prior to degradation, the degradation action of the enzymes will be more focused around the substrate (PET) thus increasing its degradation effectivity. We predict that our bacterial machine will have a higher effectivity in PET degradation in dry fermentation bioreactors compared to convetional plastic degrading bacteria.
 
  
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<h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 50px; font-size: 36pt; border-bottom: 2px solid #e8e6d1 !important; padding-left: 30px; text-align: center;">Project Description</h1>
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<p style="font-style: italic;"><strong><a href="#problems" style="color:white">The Problems </a>
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</strong> /<a href="#solution" style="color:white"> The proposed solution </a></p>
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<h1 class="ITB_h1" id="problems">Ocean Plastic Pollution </h1>
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<p>Plastic pollution is recently become the major problem in the waste management, since there are around 275 million metric tons of them generated around the world in 2010. Indonesia itself is the second biggest source contributor of plastic waste in the ocean, with an estimation of 0.48 – 1.29 million metric tons in 2010[1].
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Why does the plastic waste end up in the ocean? Mismanagement of the plastic waste in the landfill is one of the major cause. The plastics can be carried by wind and rain into rivers, then flow into the sea. Many rivers around the world carry about 1.15-2.41 million tons of plastic waste, transporting them into the ocean [2].
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One of the real-world examples happen around our city, Bandung, in the landfill of Sarimukti. The majority of the waste is plastics, stacked into mountains of dirt and trash. When the rainy season is coming, the rain washed out the plastics left behind by the treatment facility into the river nearby. Eventually, these are the plastics that will reach the ocean.
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<img src="https://static.igem.org/mediawiki/2017/f/fd/Gambarsampah.png" style="width: 900px; height: auto;"/>
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<h1 class="ITB_h1">Microplastics  </h1>
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<p></p>
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                        <p style="text-align:justify">After reaching the ocean, the plastic waste is available in many forms. It can be found at the surface, in the depths, even in the sediment. Plastic bags need up to 20 years to break down completely, while plastic bottles need a hefty 450 years to break down. But actually, one of the pressing concerns is the microplastics.
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Microplastics formation is caused by combination of physical, chemical, and biological processes. Using modelling approach, it has been estimated that around 15-51 trillion microplastic particles have accumulated in the ocean [3].
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</p>
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                        <img src="https://static.igem.org/mediawiki/2017/thumb/9/9c/Microplastic_pollution.jpg/800px-Microplastic_pollution.jpg" style="width: 900px; height: auto;"/>
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                        <h1 class="ITB_h1">Impacts  </h1>
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<p style="text-align:justify">A number of studies have revealed the harmful impacts of microplastics on the marine biota. Those covers the physical-chemical effects of microplastics ingestion, and the transport of invasive species. Direct effects of ingestion of microplastics is the blockage of intestinal tract which impedes the organisms from taking in more resources. Microplastics also contain harmful chemical such as Bisphenol-A (BPA) which is originated from parent plastics during manufacturing process. They also provide raft substrates for various fauna and microbes, and transporting them to regions where they were not existing before.</p>
  
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<h1 class="ITB_h1" id="solution">The Degradation </h1>
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<p></p>
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<p style="text-align:justify">There are many ways to control plastic waste from going in to the ocean. Better recycling system and waste treatment are handful of solution to be implemented. But how about the plastic that is already being in the ocean? How about the microplastics which is already broken down and difficult to find, yet still threatening the ocean ecosystem?
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We present DewaRuci, engineered Escherichia coli which have ability to locate the microplastic and degrade them effectively through biofilm-based degradation.
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DewaRuci is based on based on the Indonesian Navy barquentine ship which was used as a sail training vessel for naval cadets and is the largest tall ship in the Indonesian fleet. Dewaruci also serves as a goodwill ambassador for Indonesia to the rest of the world.
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<h1 class="ITB_h1">The System</h1>
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<figure><img src="
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                    https://static.igem.org/mediawiki/2017/5/53/Skema_desain.jpg" style="height: 75%; width: 75%;"/>
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                                          <figcaption><i><b>Figure 4:</b> The Main System of the Project</i></figcaption></figure>
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<figure><img src="
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                    https://static.igem.org/mediawiki/2017/f/f5/Skema_desain_support.jpg" style="height: 75%; width: 75%;"/>
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                                          <figcaption><i><b>Figure 5:</b> The Support System of the Project</i></figcaption></figure>
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<strong> <font-size=15pt>The detection module</f> </strong> <br>
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This module uses indirect detection of organic pollutants in the plastic surface, with pSal inducible promoter.<br>
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<strong>The degradation module</strong><br>
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Approach that we’re using is PET-plastic degradation using PETase enzyme from Ideonella sakaiensis.<br>
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<strong>The biofilm-enhancing module</strong><br>
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We want to see if increased expression of biofilm will enhance the degradation efficiency. The gene used is transcriptional activator NhaR, which will affect the expression of pgaABCD operon required for production of biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamine.<br>
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<strong>The salt-tolerance module</strong><br>
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Because we need our E. coli to be resistant to extreme environment, we also used irrE gene from Deinococcus radiodurans to protect them from salt, oxidative, and thermal shock.<br>
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<strong>The converter module</strong><br>
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One of the byproduct of PET-degradation is ethylene glycol, which is toxic to bacteria at certain concentration. We tackle this problem by expressing glycolaldehyde reductase and glycolaldehyde dehydrogenase, which will convert ethylene glycol into nontoxic glycolate – metabolite found in the Krebs cycle.<br>
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<strong>The genetic containment module</strong><br>
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If we release the engineered organism to nature, there are possibilities of genetic makeup contamination of natural ecosystem. We use EndA endonuclease from Vibrio fischeri that will cleave extracellular DNA going outside of the cell.<br>
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Latest revision as of 19:45, 1 November 2017

Team Attributions
Collaborations Overview Design Notebook Contribution Results Improve
Basic Parts Composite Part Part Collection
Silver HP Integrated and Gold Public Engagement


Project Description

The Problems / The proposed solution

Ocean Plastic Pollution

Plastic pollution is recently become the major problem in the waste management, since there are around 275 million metric tons of them generated around the world in 2010. Indonesia itself is the second biggest source contributor of plastic waste in the ocean, with an estimation of 0.48 – 1.29 million metric tons in 2010[1]. Why does the plastic waste end up in the ocean? Mismanagement of the plastic waste in the landfill is one of the major cause. The plastics can be carried by wind and rain into rivers, then flow into the sea. Many rivers around the world carry about 1.15-2.41 million tons of plastic waste, transporting them into the ocean [2]. One of the real-world examples happen around our city, Bandung, in the landfill of Sarimukti. The majority of the waste is plastics, stacked into mountains of dirt and trash. When the rainy season is coming, the rain washed out the plastics left behind by the treatment facility into the river nearby. Eventually, these are the plastics that will reach the ocean.

Microplastics

After reaching the ocean, the plastic waste is available in many forms. It can be found at the surface, in the depths, even in the sediment. Plastic bags need up to 20 years to break down completely, while plastic bottles need a hefty 450 years to break down. But actually, one of the pressing concerns is the microplastics. Microplastics formation is caused by combination of physical, chemical, and biological processes. Using modelling approach, it has been estimated that around 15-51 trillion microplastic particles have accumulated in the ocean [3].

Impacts

A number of studies have revealed the harmful impacts of microplastics on the marine biota. Those covers the physical-chemical effects of microplastics ingestion, and the transport of invasive species. Direct effects of ingestion of microplastics is the blockage of intestinal tract which impedes the organisms from taking in more resources. Microplastics also contain harmful chemical such as Bisphenol-A (BPA) which is originated from parent plastics during manufacturing process. They also provide raft substrates for various fauna and microbes, and transporting them to regions where they were not existing before.

The Degradation

There are many ways to control plastic waste from going in to the ocean. Better recycling system and waste treatment are handful of solution to be implemented. But how about the plastic that is already being in the ocean? How about the microplastics which is already broken down and difficult to find, yet still threatening the ocean ecosystem? We present DewaRuci, engineered Escherichia coli which have ability to locate the microplastic and degrade them effectively through biofilm-based degradation. DewaRuci is based on based on the Indonesian Navy barquentine ship which was used as a sail training vessel for naval cadets and is the largest tall ship in the Indonesian fleet. Dewaruci also serves as a goodwill ambassador for Indonesia to the rest of the world.

The System

Figure 4: The Main System of the Project

Figure 5: The Support System of the Project

The detection module
This module uses indirect detection of organic pollutants in the plastic surface, with pSal inducible promoter.
The degradation module
Approach that we’re using is PET-plastic degradation using PETase enzyme from Ideonella sakaiensis.
The biofilm-enhancing module
We want to see if increased expression of biofilm will enhance the degradation efficiency. The gene used is transcriptional activator NhaR, which will affect the expression of pgaABCD operon required for production of biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamine.
The salt-tolerance module
Because we need our E. coli to be resistant to extreme environment, we also used irrE gene from Deinococcus radiodurans to protect them from salt, oxidative, and thermal shock.
The converter module
One of the byproduct of PET-degradation is ethylene glycol, which is toxic to bacteria at certain concentration. We tackle this problem by expressing glycolaldehyde reductase and glycolaldehyde dehydrogenase, which will convert ethylene glycol into nontoxic glycolate – metabolite found in the Krebs cycle.
The genetic containment module
If we release the engineered organism to nature, there are possibilities of genetic makeup contamination of natural ecosystem. We use EndA endonuclease from Vibrio fischeri that will cleave extracellular DNA going outside of the cell.