A Global Problem

Our planet is currently facing a human caused energy crisis, due to increased demands for limited resources. This demand has caused severe damage to the ecosystem (see analysis by Bøgh), the consequences of which could be catastrophic. To prevent this, balance must be restored (needs to explain balance).
One of the most recognized methods to restore this balance, is the implementation and advancement of technologies for renewable energy. However, there are currently certain limitations on the existing solutions for renewable energy; the intermittency- and diluteness problem. The intermittency problem describes the discontinuous energy production, with inefficient storage. Whereas the diluteness problem is described as the resource demanding production of technical devices, such as solar cells and batteries.
To face these problems, we took on the challenge of creating a truly green solution!

In a Local Environment

We are a team of young adults, raised to be aware of climate changes and the potential limitations to the continuation of our way of life. However, we are also a generation of open source and shared information. A generation, that has been encouraged to constantly challenge the ideas of our peers. With this in mind, we decided the best solution to the future energy crisis, would be to seek out experts, the general public, even kids, in order to rethink the current notion; where the only way to save our planet, is to reduce our standard of living.
Thankfully, through our interaction with local experts, we quickly learned that a great deal of people share our philosophy – the belief that we ought to pursue the creation of low energy cities with a high quality of life. In fact we even discovered that our very own city(hometown) – Odense – wants to be the greenest, most renewable city in Denmark by 2050 https://www.odense.dk/borger/miljoe-og-affald/klima.
We decided to partake in this goal, by taking on the challenge to create a truly green solution, which will offer not only a source of energy, but also a green aesthetic and naturalistic ambience to compliment a high quality of city-life.
Please keep scrolling if you wish to read more about our solution, or go straight to bioethics, if you wish to read about why we not only could, but ought to do something about the current energy crisis.

Inspiration

Our early ideas were reviewed after attending the Danish Science Festival, where we met several young minds with very creative ideas. The kids would come to our booth with their parents to learn about bacteria, GMO, ethics and iGEM. After which, they would attend our “Draw-a-bacteria”-competition. While drawing their own unique bacteria, they would present us with detailed stories about their design.
(picture of some drawings)
Through this, we felt inspired and decided to revise our ideas. At this point, our project was starting to take its final shape. They even inspired the physical design for our final product; the PowerLeaf.

Our Solution

this section needs a really great illustration about the system
The bacterial solar battery we envision, is composed of an energy storing- and an energy converting unit. The energy storing unit is defined by a genetically engineered Escherichia Coli (E. Coli). The E. Coli uses solar energy for ATP production, to fixate carbon dioxide into the chemically stable polymer, cellulose, essentially making it a battery. A light sensing system activates dormancy during nighttime, in order to reduce energy lost by metabolism. The energy converting unit uses genetically engineered Geobacter Sulfurreducens to consume the stored cellulose, using an inducible switch. Retrieved electrons are transferred by optimized nanowires to an anode, resulting in an electrical current.
The device is designed to resemble a plant leaf, which is meant to provide a nature-in-city ambience. This hypothetical implementation of the PowerLeaf in an urban environment, was developed through public engagement and collaborations. We even worked together with local city planners from our hometown, Odense.
Our vision was clear and ambitions were high, probably too high, considering the limited timeframe. So, at an early stage, we decided to focus on the following features:

• Converting CO2 to glucose
• Producing and secreting cellulose from glucose
• Light-sensing system to regulate dormancy
• Converting cellulose to glucose
• Optimizing the nanowires

It will then be up to prospective iGEM teams to finish our vision, and take the PowerLeaf all the way. We would love to see our project become a reality one day, and have therefore created a special page for future iGEM teams. This page includes suggestions for further development of our/the project.
this section needs a little more text and an illustration of the system

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Building a Product for a Better Future

How will our product affect the future? First and foremost, it will be able to provide an even greener alternative to already sustainable energy sources like solar. It will do so, by building complex technological energy solution, using the most common resource on our planet. This will contribute to a future without a critical shortage in natural resources like silica for technological devices. Not only will programming of biological systems like the PowerLeaf be complex, it will be self-replicating for easy expansion and integration into an urban environment.
As the technology of the PowerLeaf develops, it will not only be self-replicating, it will also be able to replicate using CO2 from its environment. This will make it able to clean the cities from pollution. The PowerLeaf even has the potential to become even less dependent on inputs to the device, as biological editing tools become better and more complex. The device might become completely independent, when it comes to the metabolic pathways that produce essential amino acids and vitamins required for its functionality.
Sociologically the PowerLeaf will, by representing a natural leaf design, lead to a nature-in-city ambiance. Not only will the design represent a plant leaf, but some of the key functionality aspects of the device are inspired from those of a plant leaf. Hereby, we refer to photo synthesis and building cellulose as a biological product.

Genetic Code Expansions for Biological Engineering

Expanding beyond those technologies used today in Synthetic Biology, many research groups are working on genetic code expansion. We had an interesting talk with post.doc Julius Fredens, working at the Jason Chin Lab, about his work on genetic code expansion. Once this technology is fully working, it could completely revolutionize biological engineering, including that of the PowerLeaf. Genetic code expansion could potentially be used for optimization of all the biological systems used in the PowerLeaf; optimization of nanowires, improvement of the light-sensing system and making the breakdown of cellulose inducible.

So what worked? Nothing. Nothing worked. And that’s the first lesson you should remember when you start your own iGEM journey, be prepared that most things that you plan in the lab will probably go wrong at some point. Just kidding of course, a few things did work, and the things that didn’t work, we will tell you about as well, so you can learn from that as well.
Systems that did work:

• Light-sensing system, this was used to reduce metabolism when there was no solar energy (night time) for the energy storing unit to store. This system has been modelled and many experiences were made. You can read more about this system here.
• Cellulose consumption, this was used by the energy converting unit to degrade cellulose to glucose from which electrons could be retrieved. This system has also been worked on thoroughly, and you can read more about it here.
• Optimization of the nanowires. This was built from an existing article and implemented for the BioBrick standard. You can read more about the nanowires here.

Systems that didn’t work:

• CO2 fixation, we retrieved the parts from the Bielefeld 2014 iGEM team and worked on assembling their system into one model organism. However, we had trouble assembling it, and it seems that Bielefeld 2014 didn’t succeed in combining all the components needed for CO2 fixation, so be aware of this. It seems like a simple assembly, but has caused lots of problems, some BioBricks tend to do that when they reach a certain size. You can give it a go anyways, but have a backup-plan, or maybe even try to redo the CO2 fixation by using a system from a different organism than theirs. We essentially decided to let go of that part of the project, and focus on some of the other components used for the PowerLeaf.
• Cellulose production and secretion from the fixated CO2. These parts were retrieved from the Imperial College London 2014 project, this, much like the CO2 fixation, gave us trouble, when it came to the assembly of the large BioBricks. After a lot of struggle with this, we had to give up on this part of our project as well. It did seem that Imperial College London 2014 made the system work, but in the end, they proved it to be very inefficient of producing cellulose. So, this part could be the very thing to improve. There is a 2017 team which has been working on improving the activity of algae, which are great at producing cellulose. Essentially, if the metabolic rate is increased enough, this could become the chassis organism instead of E. coli.

System we didn’t work on but should be implemented in the device:

• ATP production from solar energy comes to mind as the first and most important element, needed for the PowerLeaf to work. This is an essential part of the project, but since we already had a lot of different components to work with, we decided to remove this part from our project, and leave it for future iGEM teams to develop on. However we did have a great Skype call with the Australia Macquarie iGEM team, whom has been working with photosynthesis in E. coli for the past many years. You could always contact them, they are very nice, just be aware that they assemble their team a little later than most of other teams.
• Making the activation/transcription of the genes encoding the cellulose degrading enzymes controllable, so it could become a switch. This is also a very important aspect of the PowerLeaf, since it will otherwise be converting cellulose into an electrical current non-stop, even when it isn’t needed. Being able to turn this on and off is crucial.
• Last but not least, there is a large hardware portion for the device, making it possible to convert CO2 to cellulose, which will be happening aerobically. And then the energy converting unit will have to degrade stored cellulose in an anaerobic chamber. This will most likely need to implement a completely different option to overcome this obstacle. Engineering of the hardware required is very important for the final product, e.g. anode, chamber, circulation of important nutrients and use of the correct plastic. We already worked on the plastic part, you can read about this here.

Tips and Tricks from our Experiences

Something about tips and tricks we learned

Ideas from Our Idea Generation

List of ideas from our idea generation

Laboratory, Technical and General support

We would like to give special thanks to our supervisors:

• Assistant professor Mikkel Girke Jørgensen, for his general support and advice on development of the project, the laboratory, fundraising and team synergy.
• Ph.D. student and former iGEM participant Patrick Rosendahl Andreassen, for his guidance and technical assistance in the laboratory.
• Ph.D student and former iGEM participant Thøger Jensen Krogh, for his help in developing the wiki, as well as his laboratory guidance.
• Cand.phil student and former iGEM participant Tim Munk, for his focus on team dynamics and advice for our human practices.

Thanks to:

• Academic assistant Tina Kronborg for guidance in the lab and for providing us with lab equipment.
• Medical Laboratory Technician, Simon Rose, for giving us a course in security and lab safety.
• Postdoc Oona Sneoyenbos-West provided us with Geobacter sulfurreducens PCA and knowledge, on growing this bacterial strain. As well as lending, us her laboratory for culturing of the Geobacter sulfurreducens PCA.
• Business scout and PhD Ann Zahle Andersen presented tools to us for the development of innovative business ideas.
• Stud.scient Kristian Severin Rasmussen helped us using the oCelleScope for testing.
• Stud.scient and former iGEM participant Brian Baltzar for hosting a workshop about graphical representation in Adobe Illustrator.
• Title Jonas Hartwig for helping with some JQuery functionality on the wiki.
• Stud.scient Birka Jensen, for advice on how to build an iGEM wiki.
• Stud.med Ida Charlotte Hvam for helpful discussions on development of the wiki.
• Ph.D student and current iGEM advisor of the team from Bielefeld, Boas Pucker has provided us with BioBricks created by former iGEM teams from Bielefeld.
• Dem fra Imperial?
• Stud.polyt Oliver Klinggaard, for helpful discussions on the implementation of a pan-tilt system and for providing os with his project report on the subject.
• DTU BioBuilders hosted their 5th Annual Biobrick Workshop.
• The UNIK Copenhagen iGEM team hosted the Nordic Meetup.
• The TU-Delft iGEM team for hosting the European Meetup.
• The Danish Science Festival for having us at their annual event.
• Mimo Antabi for adding our adverts to the university screens preceding the Danish Research Festival.
• Allan Haurballe Madsen for the practical help associated with our appearance at the Danish Science Festival.
• Lise Junker Nielsen for practical help associated with the Danish Science Festival and visit from the Academy for Talented Youth. As well as lending us iPads for laboratory use.
• The Danish Science Festival for having us and to all the visitors attending our booth.
• Dem der hjælper os med SDU-Meetup hvis nogen
• Colombia til modelling
• The high schools that we visited and presented our iGEM project at. These include Odense Technical gymnasium, Mulernes Legatskole and Academy for Talented Youth.
• The UNF Camp for having us present our project to the students attending.
• The elementary schools:
• All former iGEM participants from SDU, attending our preliminary presentation and giving us feedback before the Giant Jamboree.
• The following groups and associations, for helping us develop our human practices: (SP-Moulding, Borgernes Hus, Kommunens bygninger, Bolbro - områdefornyelse, Odense Byudvikling)
• Matlab user Nezar for an easy implementation of the gillespie algorithm into matlab.
• empty spot

Sponsors

Thanks to:

• The Faculty of Science at University Southern Denmark for providing us with fundamental funds which have been required to make our project possible, and for providing lab benches and equipment.
• The Faculty of Health Sciences at University of Southern Denmark for providing us with important funds to our project.
• Integrated DNA Technologies for providing us with 20 kilobases of gBlock gene fragments.
• SnapGene for providing our team with memberships to their software during the competition.
• PentaBase for sponsoring us with 10.000 DKK worth of oligos and a further 10% discount.
• Eurofins Genomics for providing us with an 80% discount on a Mix2Seq kit.

Litterature

Lots of nice articles and booksAkimov V, Henningsen J, Hallenborg P, Rigbolt KT, Jensen SS, Nielsen MM, Kratchmarova I, Blagoev B. StUbEx: Stable tagged ubiquitin exchange system for the global inves tigation of cellular ubiquitination. Journal of proteome res earch. 2014;13(9):4192-204..

Project Synergism

We have all been working together in every aspect of our project. Nevertheless, some people has had their focus on some areas more than others. The main groups are listed as follows;

• The group focusing on fixation of CO2, production and secretion of cellulose and light-sensing dormancy consisted of Sarah Hyllekvist Jørgensen, Ellen Gammelmark, Sofie Mozart Mortensen and Emil Bøgh Hansen
• The group focusing on the breakdown of cellulose to create an electrical current and optimization of nanowires consisted of Felix Boel Pedersen, Frederik Bartholdy Flensmark Neergaard, Jonas Borregaard Eriksen and Malte Skovsager Andersen.
• The group focusing on implementation of the device into an urban environment, as well as our outreach consisted of Emil Søndergaard, Frederik Mark Højsager and Lene Vest Munk Thomsen.
• The mathematical modelling of our project was single-handedly performed by Emil Vyff Jørgensen.
• Coding and design of the wiki was performed by Felix Boel Pedersen and Frederik Mark Højsager.

Danish ethics and wiki workshop at SDU

In the spirit of the iGEM community, we hosted a meetup in august for our fellow Danish iGEM team: InCell from the University of Copenhagen (KU), and the Snakebite Detectives from the Technical University of Denmark (DTU). A total of seven members from these two teams joined us for breakfast and attended our meetup. This was the first ever iGEM meetup hosted by our university, so we decided to make it something special. For this purpose we took advantage of our interdisciplinary team roster, and designed a workshop that focused on aiding our fellow Danish teams with their wiki and project related ethics. An undertaking that was, to our knowledge, the first time in the history of iGEM, that these two subjects were combined into a single workshop. We utilised the broad interdisciplinary profile of our team by having Emil S., who has a Bachelor of Arts in History, and Lene, who has a Bachelor of Arts in Philosophy, hold presentations. These concerned respectively the perception of science throughout history and the bioethical aspects surrounding GMO. The ethical presentation was purposely turned into an ethical debate, where the different facets and viewpoints of ethical conduct were exchanged and discussed. After the presentations and discussions on ethical conduct, it was time for the second topic on the agenda: the wiki workshop. The SDU iGEM teams have won the Best Wiki prize several times in the past. As such we wanted to share the knowledge gained from our university's past experiences, with our fellow Danish teams. To facilitate this exchange of knowledge on wiki development, we recruited our current supervisor Thøger Jensen Krogh, to hold several presentations on how to design a good wiki. He was qualified for this task through his role as the designer of the SDU iGEM 2013 and 2014 teams wikis, which won the special prize on both occasions. During the presentation, Thøger had arranged for several workshop segments. All three teams were to mingle, discuss and evaluate the wikis, which resulted in a steady flow of information and constructive feedback between all three teams. After the a long day of learning and discussing, we went for a tour under the summer sun around our campus, which concluded in a visit to the roof terrace of the campus dormitory, followed by dinner.
As part of the evaluation of the meetup, it was suggested, that we should make the SDU meetup a tradition for future teams. Another suggestion was that the teams ought to get together later in the process, where they could once again evaluate each other's progress on the wikis.

Attending meetups

Additionally to hosting our own meetup, we also attended several ones during our iGEM experience. The first of which, was the 5th Annual Biobrick Workshop in March, hosted by the Technical University of Denmark. This meetup not only gave us our first experience with the Biobrick Standard, but also worked as a foundation for friendships across the team.
Our second meetup, the Nordic iGEM Conference, was hosted by the University of Copenhagen in june. The main focus of this meetup, was the traditional mini Jamboree. The outcome of participating in which was useful feedback from the judges, as well as the other iGEM teams - which helped us further shape and develop our project.
To celebrate the beginning of our iGEM summer, we went on a road trip to attend at the European Meetup, hosted by the Delft University of Technology in the Netherlands. Here we discussed ideas regarding our project at a poster session, learned from all the other great iGEM team’s projects and made new friends from all over Europe.

Further collaboration

In our project, we have been in contact with the iGEM teams from Bielefeld and Imperial College, who have helped us by sending us crucial parts for our project.
As our project revolves around global warming and green sustainable energy, we were thrilled to hear about the iGEM Goes Green initiative from the TU Dresden iGEM team. Following their guidelines, we have calculated the carbon footprint of our laboratory work and travelling. We have, in part, tried to make up for our carbon footprint, by changing our travelling and eating habits in our everyday lives. Furthermore we have reduced our daily electricity consumption and made an effort of sorting waste. The full report can be scrutinized here **det skal så være link til en model, hvori der er meget mere tekst*
As the iGEM team from Macquarie has worked with the implementation of photosynthesis in E. coli since 2013, we sought their expertise. Which we achieved through a Skype call. Here we discussed what particular challenges the current and previous teams have experienced in their projects. Furthermore, we found that their team could equally benefit from our team, as they were interested in the electron transport pathways that we used.
Additionally, we were able to help the Stony Brook iGEM team by facilitating communication with members of the SDU iGEM team from 2016. Shortly after the European meetup, we received a mail from the Cologne-Düsseldorf iGEM team regarding a postcard campaign idea, which we gave some feedback.
During our project we have received several questionnaires from fellow teams, which we have been happy to fill out. These included questionnaires from the following iGEM teams:

• Waterloo - regarding 3D printing of lab equipment
• Dalhousie - regarding the common conception of science literature
• University of Washington - regarding communication platforms used by teams
• Vilnius-Lithuania - regarding cotransformation
• Nanjing-China - regarding whole-cell sensor for formaldehyde
• University of Sydney - regarding the use and accessibility of insulin

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