Difference between revisions of "Team:Edinburgh OG/Human Practices"

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<p style="text-align: justify;">The team has not only focused on how to contribute to solving the plastic problem, but it also has thought of the potential use of Synthetic Biology in other fields. Accordingly, we collaborated with other iGEM teams and organised different presentations to promote Synthetic Biology and the iGEM competition in our local community as well as with young students in Macao. As a result, we are happy to have spread the wonder of this world and work with the future first iGEM team in Macao.&nbsp;&nbsp;</p>
 
<p style="text-align: justify;">The team has not only focused on how to contribute to solving the plastic problem, but it also has thought of the potential use of Synthetic Biology in other fields. Accordingly, we collaborated with other iGEM teams and organised different presentations to promote Synthetic Biology and the iGEM competition in our local community as well as with young students in Macao. As a result, we are happy to have spread the wonder of this world and work with the future first iGEM team in Macao.&nbsp;&nbsp;</p>
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<a class="cd-faq-trigger" href="#0">How often do you see evidence of antibiotic resistance in livestock?</a>
 
<a class="cd-faq-trigger" href="#0">How often do you see evidence of antibiotic resistance in livestock?</a>
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<p>We often don&rsquo;t test for resistance in farm vet practice as farmers don&rsquo;t have a lot of money to spare, so it isn&rsquo;t that common you would go round culturing for resistances. Therefore there could well be a lot of antibiotic resistant
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bacteria - hard to know without looking for them! Farms have bacteria everywhere (just like on your skin) so there is always a risk of disease.</p>
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<p>It is reported by vets that &lsquo;bad&rsquo; farmers exist where they might try to save money by halving the dosage or sharing it between two animals, increasing the chance of selecting resistant bacteria. There are plenty of fantastic farmers
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out there that our very diligent with their antimicrobial usage.</p>
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<p>The phrase &lsquo;that drug doesn&rsquo;t work on our farm&rsquo; often raises levels of suspicion of resistant bacteria on farm. However, without culture and sensitivity we simply can&rsquo;t make any assumptions. It could be something as simple
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as not giving the correct dose for the weight of the animal, not following the instructions (different frequency of administration) or not administering the drug properly.</p>
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Revision as of 21:37, 17 October 2018

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

 

 

 

 

 

Integrated Human Practices

The University of Edinburgh OG iGEM team 2018 worried about the plastic problem; consequently, we choose to focus our efforts on bioplastic production, specifically the co-polymer PHBV. As a group, we firmly believe that in order to approach the plastic issue it is necessary to design environmentally responsible products. For that reason, it was essential to engage in conversation with experts in the field from consultants to bioplastic and plastic producers. As a result of the discussions with various stakeholders, the OG iGEM team designed genetically modified parts and integrated a sustainability analysis to Valeris.Ed. Moreover, for our Integrated Human Practices, we wanted to show how the dialogue with multiple sources shaped our project and how it evolved from the initial idea to the final project we are presenting. Following this, in the left-side section, we summarised how stakeholders’ interaction lead to changes in the design of the project. On the other hand, in the right section and organised in chronological order, we listed the consulted stakeholders and the valuable insights they provided to the project.

The team has not only focused on how to contribute to solving the plastic problem, but it also has thought of the potential use of Synthetic Biology in other fields. Accordingly, we collaborated with other iGEM teams and organised different presentations to promote Synthetic Biology and the iGEM competition in our local community as well as with young students in Macao. As a result, we are happy to have spread the wonder of this world and work with the future first iGEM team in Macao.  

  • How often do you see evidence of antibiotic resistance in livestock?

    We often don’t test for resistance in farm vet practice as farmers don’t have a lot of money to spare, so it isn’t that common you would go round culturing for resistances. Therefore there could well be a lot of antibiotic resistant bacteria - hard to know without looking for them! Farms have bacteria everywhere (just like on your skin) so there is always a risk of disease.

    It is reported by vets that ‘bad’ farmers exist where they might try to save money by halving the dosage or sharing it between two animals, increasing the chance of selecting resistant bacteria. There are plenty of fantastic farmers out there that our very diligent with their antimicrobial usage.

    The phrase ‘that drug doesn’t work on our farm’ often raises levels of suspicion of resistant bacteria on farm. However, without culture and sensitivity we simply can’t make any assumptions. It could be something as simple as not giving the correct dose for the weight of the animal, not following the instructions (different frequency of administration) or not administering the drug properly.

    • Dialogue with

           

     

     

     

         

    Dialogue with

       

     

     

     

    Dialogue with

       

     

     

     

     

     

    Dialogue with

           

     

     

     

     

     

     

     

     

    During the last lecture for the course Tools of Synthetic Biology the team explained to our classmates about the iGEM competition through an introduction of the iGEM history and principles. We also presented our idea of producing bioplastics from local materials with the purpose of delivering a sustainable process.

     

    Feedback

    Our classmates pointed out the importance of bioplastics and challenged us of to understand how synthetic biology could improve a process that has been done using biotechnology. They also suggested to look into the whisky industry or wastewater as potential raw materials. 

     

     

     

     

     

    Dr Lorraine Kerr - Commercial Relations Manager at School of Biological Sciences, University of Edinburgh

    Dr. Kerr was our principal contact between stakeholders and experts in the bioplastic field. During meetings we discussed our project, objectives and approach to work out the story and how to talk to stakeholders. She advised us to use the expert's experience and point of view to get more specific information, define targets and to set goals prior to interviewing.

     

     

     

     

     

    Dr Adrian Higson - Director and Lead Consultant for Biobased Products, NNFFCC The Bioeconomy Consultants

    Plastics are one of the most versatile materials that are immensely beneficial to our society (e.g. food packaging which helps in reducing food wastage). However, their life cycle constitutes a big challenge. Current proposals to confront this issue include recycling, the reduction of plastic consumption, and a change from plastic to bioplastic. Nonetheless, it is necessary to consider the type of bioplastic and its life cycle. On top that, it is not recommended to consider bioplastics as carbon sink, instead we should look into the circular economy where plastic is use multiple times instead of one, in addition to the design of products where recycling could be possible. The major barrier in bioplastic production is the economy of scale – the increase in innovation can only happen with the increase in production, however the current condition does not permit that due to low sales.

    Assessing the sustainability

    Dr Adrian Higson discussed the necessity of plastics and the problems of their current life cycle. We expressed our major concerns; the feedstock materials and the sustainability of the process. As a result, the project gained great insight from the experience of Dr. Higson. He commented that in terms of feedstock, the use of agriculture materials is simple not feasible. The use of side products however is more sustainable and by using them we are making a good choice of raw material. We need to look at the energy efficiency, water efficiency, and conversion process. The GHG emissions and water footprint are not the only impacts to look at, we have to consider the social and economic sustainability of the production.

    We also discussed the possible end-of-life scenarios, according to him the recycling of bioplastics and the final break of the polymer into monomers constitute a splendid way of tackling the waste problem. This also increases the chain value of the bioplastic as the monomers can be sold as chemicals for another industry.

    Implementation

    Dr Adrian Higson supported our idea of using by-products from other industry (whisky to be exact) due to its sustainability features. However, he pointed the necessity of looking in detail to some other impacts. This conversation was followed by a team discussion, where, with the advice of our supervisors we started to research the incorporation of the Life Cycle Assessment model to look into the life cycle of our bioplastic.

     

     

     

     

     

    After of our talks with experts and stakeholders we incorporated the LCA tool to measure the impacts of each aspect of our product life.

    Life Cycle Assessment is a systematic way of quantifying the environmental sustainability of a product and helps to identify aspects for improvement. It is a vital tool for sustainability studies and if implemented correctly can act as the basis to evaluate different scenarios and facilitate decisions.

    Implementations

    The LCA resulted in an iterative tool that began as the repercussion of the dialogues with experts and ended as a decision making instrument. The LCA supported the idea of using the in-situ secretion system and showed us that the recycling scenario modelled for our process contributed to decrease the environmental impacts up to 70%. To read more about our LCA results please click here.

     

     

     

     

     

    Dr. James Hallinan, Dr. Steve Thomas & Dr. James Brown,– Experts in Synthetic Biology and Material Sciences, Cambridge Consultants

    The interviewed experts endorsed our project and explained that PHAs represent an innovating example of the delivery of sustainable products through cutting edge technology. They suggested the group to focus on the properties, design and potential applications of PHAs instead of tackling the production price. Furthermore, they emphasised the manufacturing challenges of producing PHAs, which are the major hurdle preventing their wide scale adoption: the scalability.

    Assessing Feedstock and Downstream Processing

    It was also discussed the topic relating to the present obstacles in bioplastic production, according to them feedstock resources and downstream processing are the key problems that must be addressed immediately. Feedstock is an environmentally sustainable way to sequester carbon source. Additionally, the interviews added the attractiveness of using underutilised products from industries as raw materials, because they are more budget friendly since they are usually under-priced, however, it needs to be built on an effective logistics strategy in terms of the usage as well as the consistency of the components in the by-product itself. The downstream processing is one of the biggest bottlenecks in the process, for this reason having a method for delivering the bioplastic without the necessity of disrupting the cells would increase the efficiency of the overall production and potentially can lead to the implementation of continuous-batch fermentation which could run for more hours and the carbon source and the product can be simultaneously added and removed, respectively.

    Implementation and Impacts in our project

    First, the use of whisky by-products as raw material is supported by the consistency of their elements. Second, the logistics of using them can be more achievable as they are the product of a local industry. The in-situ secretion system constitutes a potential method for reducing the use of hazardous chemicals in the process hence reduces the environmental impact of the PHBV production. Moreover, the potential use of continuous-batch fermentation can contribute to the overall efficiency of the manufacture. The cost of the bioplastic production is not the most important factor, due to the necessity of shift from oil to bio-based raw material. We took their advice of looking more into the properties and we decided to only focus on PHBV production because PHBV is a PHA copolymer with a larger thermal processing window, thus less brittle than PHB.

     

     

     

     

     

    We were invited to the  iGEM Northern Meet-up organised by the St Andrews iGEM team. This event was intended for the cooperation between teams as a space to share ideas, experiences and feedback for the projects. During the event we got feedback from professors and previews generations of iGEMers.

    Implementation

    They gave us advice of how to construct our narrative and to shape our objectives. Regarding the design of the process, they suggested to look into the use of fed-batch or continuous fermentation in order to increase the yield of PHBV. Furthermore, they also suggested alternatives for our in silico model.

     

     

     

     

     

    Morag Garden - Head of Sustainability & Innovation, Scotch Whisky Association

    Morag facilitated the group a lot of information about the local situation of the whisky market and their by-products. She highlighted the increasing global demand for Scotch and the now 128 distillers operating across Scotland's five different whisky  regions. In addition, she gave us suggestions for alternative community members looking at valorising the distillery materials, as they would be a useful source of information.  Additionally, she also mentioned their interest in the outcomes of the research.

    Some notes from the Whisky by-products study case

    The whisky sector remains high with a growth rate estimated at 2.1% over the period to 2018. This would result in an approximate increase in by-products in the region of: Draff – 52,800 tonnes and Pot ale – 88,800 tonnes. By-products from Scotch Whisky distillery (draff and pot ale for example), have long been reused by the agriculture sector as a valuable animal feed and fertiliser for agricultural land (Figure 1). However, suitable routes would be need to be found for these by-products, as existing are near their natural capacity. New developments have recently opened up new markets for the use of by-products as feedstock for renewable heat or its use to make protein feed for salmon farming and biofuel. 

    Figure 1 Availability of by-product feedstocks by local authorities in Scotland. Taken from Ricardo Energy & Environment for Zero Waste Scotland (2017). Biorefining Potential for Scotland. 

    Figure 2. The current uses for whisky by-products in Scotland. Taken from Zero Waste Scotland (2015). Sector Study on Beer, Whisky and Fish. Final Report

    A circular economy approach is to use resources more efficiently, keep resources in use for as long a time as possible and to minimise waste. Identifying opportunities to improve circular approaches, for example keeping by-product materials within Scotland for further processing. There are many potential products that could feasibly be made from by-products, adding further value to a business.

    References

     

     

     

     

     

    Through this visit, we learnt about the whisky production and collected whisky production by-products samples (i.e. pot ale and draff) to be used as carbon source in our experiments. 

    We were introduced to the whisky production through the tour throughout the distillery. We learnt that the whisky industry managed their resources locally and sustainably and ensured that minimum waste is generated in every batch of the production. The information obtained was very helpful in conducting the Life Cycle Assessment.  

     
      
    Figure 1 (from top to bottom) Tour guide explained about the kiln. Samples of malt before separated into husk, grist, and flour. Our team collected samples. 

     

     

     

     

     

    Dr. Guo-Qiang Chen - Director of Center for Synthetic and Systems Biology, Tsinghua University and Chief Scientist at BLUEPHA

    Jin Yin - Technique Manager at BLUEPHA

    They endorsed our project explaining that our work is conducive to the long-term development of the world. As global environmental awareness increases, the market for biodegradable plastics will certainly develop. This includes the PHA market and research is needed to achieve this shift from plastics to bioplastics, especially in Europe where composting action is encouraged by the government. PHAs certainly has this unique advantage over other bioplastics. 

    Over the interviews with Jin Yin and Dr. Chen, it was discussed the ways of solving the plastic pollution. In their point of view, one of them is promoting the use of bio-based plastics for containers and bags. However, they emphasised the necessity of research institutes and industry to work in the optimisation of the manufacturing processes and strain properties. For them, the bottlenecks in the PHA production are the strain properties, as the ability of using different raw materials, and the downstream process which is limiting the efficiency and purity of the product. As SynBio practitioners, they believe that the answer is in the use of this discipline to help solving these problems.

    Bluepha Co., Ltd. is a synthetic biology and biomaterial company established in Beijing, China. The company was the first SynBio Startup Founded by iGEMers, and they were the winner of the Future Planet Award for Sustainable Growth. Moreover, they are pioneering a revolutionary cost-effective method for producing bioplastics.

    Jin Yin and Dr. Chen:

    “Over 20 companies from different countries are focusing on the optimisation of PHA production, all of us are trying hard on solving many practical problems and we truly believe that the answer of some of these problems is in the use of Synthetic Biology. However, it is also important to focus on the discovery of medical applications of PHAs. The biocompatibility of PHAs enclose the potential for using it as artificial cartilage and nerve conducts. For example, US has permit the usage of P(4HB) in surgery. They believe that PHAs is a new thing deserving further studies with surprising properties that can be a potential answer for diseases such like osteoporosis. Despite of the current drawbacks, we believe in a more optimistic future for PHAs“

     

    Implementations

    We confirmed that our in-situ secretion system is a good approach to tackle the downstream processing problem. As further directions, they recommended us to look for improvements to the strain for being able to use whisky by-products more efficiently. However, it is important to note, that solving technical issues of PHA production is as important as it is related to the biomedical research. As a result, a new focus for our future research is to look into new biomedical applications of PHAs and specifically PHBV.

     

     

     

     

     

    Paul Tan – Officer SINOPEC Guangzhou, China

    Sinopec Guangzhou Petrochemical Company (“Guangzhou Company” for short) is one of the leading petrochemical enterprises in South China. The core business of Guangzhou Company covers refining products including solid plastics, such as polyethylene, polypropylene and polystyrene.

    Jianfeng and Paul endorsed our project explaining that they welcome the technology development of bioplastic, even as a competitor to them. The mass convenience of plastic in food, clothes, car industry, etc. are too important and so far there is no other material that can replace plastic. And, currently the degradation of plastic is still too expensive for its price and its environmental impact. As a result, bioplastics constitute a possible solution to the growing demand of plastics.

    Understanding the recycling market of plastics

    Jianfeng and Paul have experience in the petroleum-based industry and knowledge of how the plastic market has change. We were aiming to understand the importance of different disposable scenarios and they gave us an insight of the recycling industry. They explained that after the reduction of oil prices in 2014, the recycling industry had retreated as making new plastic became much cheaper than recycling it. In addition, they mentioned that recycled plastics are slightly different and the manufacturers need to add other materials to improve the physical properties. These additives tend not be in the labels of the plastics making the recycling process more difficult in a further stage.

    Implementations

    The recycling scenario would not be the best end-of-life for our plastics, in conjugation with the comments of Dr. Higson from NNFCC we believe that a combination of recycling and composting could be helpful in terms of the sustainability of our bioplastics. The results of the research in PHBV degradation and composability should be incorporated to the design of PHBV products.

     

     

     

     

     

    Paul Mines– CEO at Biome Technologies

    “Plastics: wonder materials or existential threat”

    Paul Mines began the lecture at The University of St Andrews by disclosing the issue of plastic pollution and the ubiquity of plastic due to its cheap and useful properties. Plastics have been around since 70 years ago, replacing other materials and expanding the plastic market. Then he continued discussing how bioplastic products can help to solve plastic pollution by offering plant-based and biodegradable alternatives to petroleum-derived plastics.

    Understanding the impacts of the process

    Regarding the carbon sequestration in bioplastics, the net carbon footprint is less and bioplastic can function as CO2 storage, but however, it cannot help with the GHG problem in the world. Furthermore, he talked about the possible disposal scenarios such as composting, anaerobic digestion and incineration. Finally, he ended his presentation by emphasising on what needs to be developed to achieve the wide use of bioplastic. Some of his examples were: Plant science, biomass production, pre-treatment of the biomass, monomer treatment, and tests and scale up. Nevertheless, the market cannot go forward if the impact of bioplastics products to the environment and society is not understood.

    The lecture reaffierded that ‘Human Practices’ aspect is crucial in every project design and not just iGEM. Through our Human Practices journey, we found LCA tool which assessed the environmental impacts of a product and/or process, which is in line with what Paul Mines mentioned.