editors highlights
ENERGY STORED IN CELLULOSE • LIGHT-SENSING DORMANCY SYSTEM • OPTIMISED NANOWIRES Abstract The PowerLeaf introduces a novel solution, for long-term storage of solar energy, thus becoming an alternative to solar cells. This is accomplished without the use of environmentally harmful resources. 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 collaboration. The bacterial solar battery is composed of an energy storing unit (1), and an energy converting unit (2). The energy storing unit (1) is defined by a genetically engineered Escherichia Coli, which fixates carbon dioxide into the chemically stable polymer cellulose. A light sensing system activates dormancy during nighttime, to reduce energy lost by metabolism. The energy converting unit (2) uses genetically engineered Geobacter Sulfurreducens to consume the stored cellulose. Retrieved electrons are transferred by optimised nanowires to an anode resulting in an electrical current. About Our Wiki Functionality on the Wiki Hi there, and welcome to our iGEM experience. I’m the creator of this wiki, and this year I decided to make it a one-page wiki - to make it stand out from the crowd. All you have to do is keep scrolling, and you will be guided through the project. You will always be able to follow your process through the wiki, by looking at the navigation bar. Whenever you want, you can click on one of the tabs, to get an overview of the sections associated with it. If you know where you want to go, you can click the section-links in each of the tab menus, and they will get you there immediately.
A Green Wiki Our project is all about ensuring a greener and more sustainable future for ourselves and the coming generations. This of course meant, that our wiki had to to follow this pursue. CO2NeutralWebsite sponsored our wiki with a CO2 quota equal to the amount of CO2 produced, by having the wiki running until 31-Oct-2018. This does not mean the wiki is CO2 neutral, but that the quote equal to its pollution is bought. Buying a quota means, that other companies won’t be able to buy this CO2 quota, thus, forcing them to improve their environmental policies if they wish to become CO2 neutral.
Introduction Welcome to our wiki! We are the IGEM team from the University of Southern Denmark. We have been waiting with great anticipation, for the chance to introduce you to our project, and to tell you our story.
Bronze Requirements 4/4 Register and attend - Our team applied 2017-03-30 and got accepted 2017-05-04. We had an amazing summer and are looking very much forward to attending the Giant Jamboree! Silver Requirements 3/3 Validated part/contribution - pending Gold Requirements 4/4 Integrated Human Practices - We have been in close relationship with city planners from our hometown on the development and implementation of the device (link). This regards anything from size, shape, color, plastic types and locations to implement it. A Global Problem The planet’s ecosystem is currently on a path out of balance, caused by our extreme abuse of its natural habitat and valuable resources, for the advancement of our society. An ecosystem in imbalance can have a severe impact on our everyday lives. The unique diversity of the Earth’s inhabitants, will not be the only consequence of such an imbalance. As a more extreme example; scientists believe that humankind, could go extinct, as our fervor drives us to further better our ways of life. Restoring this balance should be the highest priority, in the advancement of our civilization.
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. We are also a generation that appreciates 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 eventual energy crisis, would be to seek out experts, the general public, even children, in order to rethink the current notion; That the only way to save our planet, is to compromise our living standards.
Inspiration Our early ideas were reviewed after attending the Danish Science Festival, where we met several young minds with creative and inspiring ideas. The children 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. See a selection of their amazing drawings here. Through this, we felt inspired and decided to revise our ideas. At this point, our project was starting to take shape. They even inspired the physical design for our final product; the PowerLeaf.
Our Solution 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, which essentially is the 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 optimised nanowires to an anode, resulting in an electrical current. The complete system will be combined into a single device containing a compartment for each of the two units. Details about the construction and device will be discussed in the Integrated Practices section.
It will then be up to prospective iGEM teams to continue on the development of the PowerLeaf. 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 the project.
Project & Results The outline for the project design is very concise. We have 2 units for our system - an energy storing and an energy converting. Each of the unit’s systems has been given a symbol to help you navigate throughout the wiki: Light-sensing dormancy CO2 fixation Cellulose production and secretion Energy converting (G. Sulfurreducens) Breakdown of cellulose Optimised nanowires Once you reach each of the 5 systems, you will first be given a short introduction to the underlying theory, which you will be able to expand on, by pressing “read more”. Which in turn will open a pop-up window. After the theory, you will be given the approach used in the respective parts of the project, before moving on to the next system. Once you reach the next sections of the wiki, you will be able to find the Experiments followed by Results & Demonstration. To make things easier on you, we have continued to use the above symbols throughout the wiki.
lets gooo lets goo lets gooo lets goo lets gooo lets goo lets gooo lets goo Parts & Procedures Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam consequat sodales nisl at blandit. Suspendisse nisl tortor, dignissim vel ultricies ut, tincidunt eget nisi. Proin nec viverra erat. Vivamus commodo metus neque, non feugiat dolor viverra vel. Nullam sit amet elit luctus, interdum nisl fringilla, vestibulum libero. Nullam iaculis, purus non imperdiet vulputate, mi augue gravida lacus, eu sollicitudin lacus orci a ipsum. Aenean maximus porttitor viverra. Praesent sed fringilla mauris. Duis eu molestie orci, id pellentesque lorem. Interdum et malesuada fames ac ante ipsum primis in faucibus. Sed orci elit, sodales vel nibh sed, rhoncus ultrices dolor.
BBa_K2449000
BBa_K2449002 Notebook
Week 8 SOPs Protocols SOP01 - LA plats with antibiotic SOP02 - ONC E. Coli SOP03 - Gel purification SOP04 - Colony PCR with MyTaq SOP05 - Plasmid MiniPrep SOP06 - TSB transformation SOP07 - Fast digest SOP08 - M9 minimal medium SOP09 - Ligation SOP10 - Phusion PCR SOP11 - Bacterial freeze stock SOP12 - Making LB and LA media SOP13 - Agarose gel DNA SOP14 - Table Autoclave SOP15 - Preparing Primers SOP16 - PCR Protocol USER Cloning SOP17 - Excision and Ligation of PCR Product in USER Cloning SOP18 - Speedy Vac SOP19 - Preparing Eurofins sequencing samples SOP20 - Antibiotic stock production SOP21 - Electroporation SOP22 - P1 phage transduction SOP23 - Genome extraction SOP24 - Plasmid miniprep without kit SOP25 - NBAFYE Geobacter SOP26 - Electroporation Geobacter Jonas is cheering on Neergaard to try DMSO next Proper Risk Management
Biosafety and proper risk assessment are important aspects to consider before any handling of genetically modified organisms (GMOs). There are several concerns that must be properly addressed. The safety of the public as well as of the environment, is of the utmost importance, but the safety of the person in direct contact with the GMOs shouldn’t be compromised either. The risk associated with laboratorial work can be evaluated using the statement “Risk = Hazard x Probability” (link). To responsibly assess this inquiry, the entire team was given a mandatory lab safety course held by Lab Technician Simon Rose. In addition, we received a detailed handbook regarding lab safety. This ensured that all our team members were well equipped to work safely in the lab at all times. Throughout the project we have continuously been evaluating the safety of our work. These assessments can be found in the safety form (link).
Public and Environmental Risk Assessment
The chassis organisms containing the system is meant to be contained within a container, which should be incorporated into an urban environment. While this device would be a safely enclosed container, it still possess the risk of physical breakage from violent acts or environmental disturbances. It is for this reason, that we consulted a plastics expert, who advised us to use the plastic known as Polycarbonate. This plastic is remarkably durable, with the ability to ward off most physical traumas. As such the plastics expert believe that the container would last in an urban environment for at least 20 years, and most likely more than that. To illustrate the durability of the plastics, he notified us of several devices from the 1970ies made of the same plastic, that still stand strong today.
List of Assessed Items Chassis Organisms Practices Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam consequat sodales nisl at blandit. Suspendisse nisl tortor, dignissim vel ultricies ut, tincidunt eget nisi. Proin nec viverra erat. Vivamus commodo metus neque, non feugiat dolor viverra vel. Nullam sit amet elit luctus, interdum nisl fringilla, vestibulum libero. Nullam iaculis, purus non imperdiet vulputate, mi augue gravida lacus, eu sollicitudin lacus orci a ipsum. Aenean maximus porttitor viverra. Praesent sed fringilla mauris. Duis eu molestie orci, id pellentesque lorem. Interdum et malesuada fames ac ante ipsum primis in faucibus. Sed orci elit, sodales vel nibh sed, rhoncus ultrices dolor.
lets gooo lets goo lets gooo lets goo lets gooo lets goo Prospects Our prospects section is aimed to expand on our visions regarding the PowerLeaf. A vision we would very much love to see become a reality. For this reason, we have concentrated on creating an overview of the project, for the benefit of future iGEM teams. Hopefully it can assist prospective teams on how to take the PowerLeaf to the next level. Lastly, we decided to list some of our project ideas to the teams wishing to create a completely new project. Perhaps some of these ideas can be used by prospective iGEM teams, or just help to kickstart their creative thinking.
Building a Product for a Better Future
The purpose of the PowerLeaf, is to provide a greener alternative to the currently available energy sources. An important aspect of such an undertaking, is to limit the use of depleting resources, such as silicon, in the construction of the device itself. This is accomplished through the use of the most common resources available. This will contribute to our dream of building a better future, where fear of reaching a critical shortage of natural resources has been eliminated. The production of the PowerLeaf itself is made easier too, as the device benefits from the bacteria's ability to self-replicate, if provided with essential nutrients.
Genetic Code Expansions for Biological Engineering Expanding beyond those technologies used in today's Synthetic Biology, many research groups are working on genetic code expansion. We had an interesting talk from post.doc Julius Fredens, about his work on genetic code expansion. Once a technology like this advances, it will completely revolutionize biological engineering, including that of the PowerLeaf. Genetic code expansion could be used for optimization of the systems in the PowerLeaf; optimization of nanowires, improvement of the light-sensing system and making the breakdown of cellulose inducible.
Hello future iGEM’er and welcome to the section where you are the center of attention. First of all, congratulations on starting your iGEM journey, you are going to have a amazing summer with plenty of wonderful experiences and new friendships. In this section, there will be two main topics, improvement and further development of our project, the PowerLeaf, and some of our project ideas generated in the startup phase to use for your project or start your creative thinking. Further Development of Our Project For those of you, that found interest in our project this year and would like to continue on improving it; this is the section you were looking for. We have listed the systems and the related information on theses needed for the device we envisioned, however you should not be limited to those. You are more than welcome to contact any of us regarding questions to the project, you can find our email addresses to each of us in the Team section of the Credits. Systems that didn’t work: Systems we didn’t work on, but should be implemented in the device: Ideas from Our Idea Generation List of ideas from our idea generation Credits Just like in movies, you get to meet the brilliant minds behind the project in the credits. Some might leave the cinema without reading the credits, but we hope you will continue to read ours, as it’s just as important and you will get to know us on a more personal level through this. We probably have more in common than you think. Behind every great team is a great amount of external attributions. The contributors have supported and inspired us, especially when things have been rough and deadlines near. Afterwards you can turn your attention to our collaborations, which was an amazing experience, this really shows of the true iGEM spirit.
Welcome to the team page, here you get to know us on a more personal level. As a team, we are 12 students from 8 different majors. As friends, we experienced the most amazing summer together, filled with various fun activities, both in- and outside the lab. To mention a few; we had road trips, dinners, Game of Thrones night and we even celebrated Christmas in July! We shared all of this with our amazing supervisors, for which we are truly greatful.
Emil Bøgh Hansen Study: Biology Emil Søndergaard Study: History Emil Vyff Jørgensen Study: Physics Ellen Gammelmark Study: Biochemistry and Molecular Biology Felix Boel Pedersen Study: Biochemistry and Molecular Biology Frederik Bartholdy Flensmark Neergaard Study: Biochemistry and Molecular Biology Frederik Mark Højsager Study: Medicine Jonas Borregaard Eriksen Study: Pharmacy Lene Vest Munk Thomsen Study: Philosophy Malte Skovsager Andersen Study: Biochemistry and Molecular Biology Sarah Hyllekvist Jørgensen Study: Biochemistry and Molecular Biology Sofie Mozart Mortensen Study: Biomedicine Nothing can be done alone, so please scroll further to read about all the people contributing to our project, they help us greatly and without them our project would not have become what it is now. Nothing can be done alone, so please scroll further to read about the contributors, who helped make this project a reality. Laboratory, Technical and General support We would like to give a special thanks to our supervisors: We would also like to thank: Sponsors Thanks to: Litterature Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Vestergaard P, Rejnmark L, Mosekilde L. Osteoporosis is markedly underdiagnosed: a nationwide study from Denmark. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA. 2005;16(2):134-41. Project Synergism We have all been working together in every aspect of our project. Nevertheless, some people have had to focus on some areas more than others. The main groups are listed as follows; ‘Alone we can do so little; together we can do so much.’ The American author Helen Keller had it right! As an iGEM team, you can reach many goals, but as an entire community, we can aspire to achieve so much more. Thanks to all the people that made this iGEM experience so memorable, we truly enjoyed your companionship! 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 teams: 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 memorable. We decided to take advantage of our interdisciplinary team roster, and designed a wiki and ethics workshop to aid our fellow Danish teams.
Attending meetups Besides 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 Biobricks, but also worked as a foundation for friendships across the teams.
Further collaboration In our project, we have been in contact with the iGEM teams from Bielefeld and Imperial College, who helped us by sending crucial parts relevant to the execution of our project.
‘Thank you for your time, we hope you enjoyed our wiki and project’. Now you can sit back, relax, and be proud of your hard work. While you do so, feel free to enjoy some of the less serious pictures and snippets of stories from our amazing iGEM summer.
lots of fun stories and pictures
All the best,PowerLeaf - a bacterial solar battery
Abstract
About Our Wiki
Since it’s a one page wiki, all of our text will be displayed on this page, which might seem overwhelming at first. Don’t worry though, to avoid unnecessary time consumption, the front page of the wiki will only contain the strictly necessary information. Whenever you need this additional information, you can always click a ‘read more’-link, which will display the information as a pop-up window. Once you have finished reading the in-depth details, you simply close the pop-up window, and continue right where you left off. We have prepared an example for you right here. Throughout the wiki, you might stumble upon this icon (book icon), which if you hover over it with the mouse, will show the references used for the associated statements.
I am fully aware of our readers being in a constant race against time, and I definitely identify with those who just want to read the essentials of the wiki as fast as possible. So, I went ahead and highlighted some of the important segments, making the entire wiki easy to quickly skim-read. Whenever you need my highlights, just go ahead and enable them in the top right corner. Go ahead and give it a try, it makes this wiki-nonsense so much easier to read. ;-)
It all began with a meeting between a group of strangers, each with their own disciplinary origin. Despite our differences, we had one thing in common; a shared interest in synthetic biology. Soon after our first meeting, we were herded off to a weekend in a cottage - far away from our regular lives. It was a place to bond, and to discuss project ideas. It immediately became apparent, that being an interdisciplinary team, was going to be our strength. Each member had unique qualities, that enabled them to efficiently tackle different aspects of the iGEM competition. So we made it our goal to take advantage of these qualities.
We decided to make a proof-of-concept project. Specifically, we wanted to use bacteria as a novel and greener solution for solar energy storage. This project was later dubbed the PowerLeaf – a bacterial solar battery. There is so much to tell you about our bacterial solar battery and its’ amazing features.
Since it’s a one-page wiki, you will be taken on a journey, and introduced to our story throughout the wiki-page. Just keep scrolling, and we will gently guide you through our project.
Achievements
Meet all the deliverables requirements - You’re reading the team wiki now, so that’s one down. You can find all attributions made to the project in the credits section of the wiki, here. The team poster and team presentation is all ready to go for the Giant Jamboree. We also filled the safety form(link), the judging form (link) and all our parts were registered and submitted (link) in time.
Clearly state the Attributions - All attributions made to our project has been clearly credited in our credits section at the end of the wiki.
Improve and/or characterize an existing Biobrick Part or Device - pending
Collaboration - We have collaborated with several teams through project discussions, meetups, answering questionnaires and even hosted our first meetup ever, for our fellow Danish teams. You will get to read all about it in the credits section of our wiki.
Human Practices - Our philosopher, historian and biologist have discussed the bioethical (link) aspect of our project in great detail. In extension to their work, we have been working extensively with public engagement and education (link).
Improve a previous part or project - pending
Model your project - There has been made extensive modelling of our light sensing system, which proved to be highly informative. Through this we learned that it was possible to control the bacterial dormancy, by insertion of both the toxin and the anti-toxin where only the anti-toxin is regulated. You can read all about the project modelling here.
Demonstrate your work - pending
World Situation
One of the most recognized approaches to restore this balance, is the advancement and implementation of technologies for renewable energy. However, there are currently certain limitations on the existing solutions for renewable energy; the intermittency- and the 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.
Thankfully, through interaction with local experts, we learned that a great deal of people share our belief; that we ought to pursue the advancement of low energy cities with a high quality of life. In fact, we even discovered that our own 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 pursue this goal, by taking on the challenge to create a truly green solution, which will provide both an environmentally friendly source of energy, as well as green aesthetics 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.
Our Solution
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:
Energy storing (E. Coli)
Project Design
Modelling
Experiments
Demonstration and Results
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Parts
Basic Parts
Contain the genes for pilA-N found in G. Metallireducens.
BBa_K2449001
Contain the sequence for the PilA-C genes of G. Metallireducens.
BBa_K2449003
Contain the sequence for the Cep94A gene, an enzyme that breaks down cellobiose.
BBa_K2449008
Contain the sequence for the antitoxin RelB.
BBa_K2449010
Codes for a Ptac promoter regulating csoS2.
BBa_K2449011
Contain the sequence for CenA (Endoglucanase), encoding a cellulose degrading enzyme. It was optimised for E. coli.
BBa_K2449012
Contain the sequence for Cex (Exoglucanase), encoding a cellulose degrading enzyme. It was codon optimised for E. Coli.
BBa_K2449013
Contain the sequence for CenA (Endoglucanase) fusioned with HlyA using a G-Linker. Optimised for E. Coli.
BBa_K2449014
Contain the sequence for Cex (Exoglucanase) codon, together with G-Linker and HlyA.
BBa_K2449015
Contain the sequence for HlyB + HlyD, a system used for secretion of HlyA.
Composite Parts
Contain a LacI promoter, RBS, pilA-C from G. Metallireducens, RBS, PilA-N from G. Metallireducens and a double terminator.
BBa_K2449004
Contain a LacI promoter, RBS, Cep94A and a double terminator.
BBa_K2449005
Contain a LacI promoter, RBS, BglX and a double terminator.
BBa_K2449006
Contain a promoter, RBS, BglX and a double terminator.
BBa_K2449009
Contain a LacI promoter, RBS, the gene sequence for RelB, controlled by a Lacl regulated lambda pL hybrid promoter and a double terminator.
BBa_K2449016
Contain a PenI promoter, HlyA tagged CenA.
BBa_K2449017
Contain PenI promoter, HlyA tagged Cex and a double terminator.
BBa_K2449018
Contain PenI promoter, HlyB, and HlyD.
BBa_K2449019
Contain HlyA tagged Cex, PenI promoter, HlyB, and HlyD.
BBa_K2449020
Contain a PenI promoter, HlyA tagged CenA, PenI promoter, HlyB, and HlyD.
BBa_K2449021
Contain a PenI promoter, HlyA tagged Cex, PenI promoter, double terminator, HlyB and HlyD.
BBa_K2449022
Contain a promoter, HlyA tagged Cex, HlyA tagged CenA, a double terminator, a promoter, HlyB and HlyD.
BBa_K2449023
Contain a PenI promoter, HlyB and HylD.
Notebook
Notebook
The team meets for the first time on 22nd of february. As a team building excercise the team cooks and eats together.
Week 9
For the sake of future cooporation the team makes a cooperation contract. Thus the team has an agreement on time spent, what to expect from eachother, and what to do in case of conflict.
SOPs and Protocols
SOPs
Safety
Furthermore, our team participated in the 5th annual BioBrick workshop hosted by DTU BioBuilders. Here we engaged in a lab safety course before entering their lab. Both of these lab safety courses gave us the necessary knowledge to work safely with GMO, proper handling of waste and the according procedures in case of an emergency.
In the lab, we worked with several potentially harmful chemical agents such as DMSO (dimethyl sulfoxide), ethidium bromide, chloroform, phenol, Congo red, antibiotics and autoclaved glycerol. These chemical agents were handled using gloves at all times, and, whenever deemed necessary, handled in a fume hood. We used a UV board to visualize bands in agarose gels. UV rays are carcinogenic when exposed frequently and for longer periods of time. To reduce the amount of exposure, several precautions were made; gloves, long sleeves and a facial screen were worn at all times and the time spend at the UV board was no longer than the necessary. GMOs were always handled wearing gloves, and all team members wore clean lab coats restricted to the laboratorial areas.
One of the biggest concerns would be the release of GMOs into nature. While the GMOs used aren’t pathogenetic, they would be able to share the plasmids containing antibiotic resistance selectors to other pathogenic bacteria. Antibiotic resistance in pathogenic bacteria, complicates the treatment of an infected individual, and could in tragic cases be the line between life and death. However small this scenario is, it should be addressed properly. Furthermore, antibiotic resistant E. Coli strains could outmatch some of their fellow E. Coli strains through natural selection. This could negatively affect the natural balance, that we are aiming to restore with the development of the PowerLeaf.
To safely avoid these risks, there should be implemented several kill switch mechanisms into the final device. This could be performed by implementation of a light sensing system into the energy converting unit, which would turn on the kill switch if exposed to light. This would of course mean, that the energy converting unit’s container, would need to block all sunlight. A task that could easily be carried out by adding Carbon Black to the required areas of the container. The energy storing unit, which requires light to actively function, could then have a kill switch which makes it completely dependant on presence of the container. This could be accomplished by having harmless molecules not naturally found in nature circulate in the system. Which should be required for the survival of the energy converting unit. A similar effect could be accomplished by making the energy converting and the energy storing units codependent on each other for their survival. The implementation of such kill switch mechanisms, would tremendously improve the biosafety of the device, by opposing hazards related to any kind of physical breakage.
Escherichia coli strains: K12, TOP10, MG1655, KG22, BW25113, DF25663127
Geobacter Sulfurreducens strain: PCA
Vectors
pSB1A3: An iGEM plasmid backbone carrying an ampicillin resistance gene
pSB1C3: An iGEM plasmid backbone carrying a chloramphenicol resistance gene
pSB1K3: An iGEM plasmid backbone carrying a kanamycin resistance gene
Bacteriophages
P1 phage, using its site-specific recombinase for transduction of E. Coli
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Bioethics
Integrated Practices
Education & Public Engagement
Perspectives
As tools for genomic editing improves, the advancement of biological devices will conceivably become even more complex and independant. They will do so by introducing new metabolic pathways inspired from other organisms using genetic engineering. This could potentially allow the PowerLeaf to become completely independent through its self-replication, by producing their own essential nutrients directly from unwanted pollution in the environment. A process that would lead to cleaner cities, along with providing a natural solution to sustainable energy.
The PowerLeaf will be representing a natural leaf design, thus leading to a nature-in-city ambiance, which can have a soothing effect in the ever so stressful cities. 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.
To Future iGEM Teams
Systems that did work:
Last but not least, don’t miss out on the ‘after-the-credits-clip’, which summarizes the fun we had during this wonderful iGEM experience. This is especially important, since you get the words ‘thank you for listening, we hope you enjoyed our wiki and project’ - we know you have been waiting impatiently to reach that part of the wiki.
Team
E-mail: ehans15@student.sdu.dk
Howdy! I’m the first of many Emil’s, and the team's only biologist! I am a huge wolf enthusiast! This summer I put my boots in the closet, in order to put on a proper lab coat doing iGEM. Besides my time in the lab I’ve also looked into how GMOs can influence the environment.
E-mail: emsoe09@student.sdu.dk
Ahoy thar! My name is Emil, and I want to be the next Indiana Jones. But before I can raid any tombs, I’ve decided to raid iGEM trophies. When I’m not cooking or travelling, I’m drawing on my background in history for communications and human practices.
E-mail: ejoer15@student.sdu.dk
Mojn! I am yet another Emil! I might not be a model biochemist, so instead I am modelling biochemistry! My iGEM existence is a stochastic binary function between naps and extreme bursts of energy.
E-mail: elgam15@student.sdu.dk
Why, hello there! My name is Ellen, and I spend most of my waking hours either in the lab with a pipette in my hand, or just outside it with a computer on my lap. You know.. Learn iGEM, live iGEM, love iGEM!
E-mail: feped15@student.sdu.dk
Aloha. My name is Felix and I bring joy to others by eating my daily ryebread with paté and wearing my magical red racer rain coat. Speaking of magic, I’m the team’s wiki lizard (get it?). I also do dry-lab and when the other miss me too much, I join them in the wet lab.
E-mail: frnee15@student.sdu.dk
Hey yo! I’m Frederik and I have worked day and night on iGEM, mostly drinking beers at night time, but that should count as well. When I’m not working in lab or on the PC, I make fun with the other teammates and tell bad dad jokes. Also I make crazy ideas come true, like celebrating christmas in July.
E-mail: frhoe14@student.sdu.dk
Heyah! I’m the other Frederik. I’m a green, lean, coffee-machine. I’ve been the steady supplier, and consumer of coffee on the team. My main focus has been on how to build a sustainable iGEM-project. I’ve been planting trees, eating green and lowering our team's carbon-footprint. Oh, and did I also mention I starred in our commercial? You can get autographs later.
E-mail: jerik15@student.sdu.dk
Hey sup? I’m Jonas and used to like sports, partying, eating cake, hanging out with friends and such things most people like to do. During iGEM these interest has changed… I have been enslaved into the lab, and has realised that the only purpose of my life is to be in the lab.
E-mail: letho11@student.sdu.dk
Hey, is it solipsistic in here, or is it just me? When not wondering whether or not there is an external world, I’ve been busy working out how to implement our solar battery into our local community and what to gain from doing so. Oh, and imposing metaethics on my team members, but I Kant go into detail with this just yet.
E-mail: malta14@student.sdu.dk
Ey what up pimps, I’m Malte. I’ve mostly been working in the lab wrapped in the dankest of lab coats, doing the most exciting of experiments. All in the name of why the hell not. In the lab the utmost highest level of patience is needed, especially when tasked with testing if biobricks function as intended. This has, as seen in the image, caused me to pull out most of my hair.
E-mail: sajo415@student.sdu.dk
Despite my favorite occupation being going into depth with theory, my main attribution to our project has primarily been running around in the lab. Luckily, there is a clear link between wet- and dry-lab. I am the smallest member of the SDU iGEM team, but I have definitely risen to the occasion.
E-mail: sofmo15@student.sdu.dk
Hi there! My name is Sofie, and I am the team mama! I am the one who makes sure everyone gets their fair share of cake. When I’m not in the kitchen, busy making cakes for my teammates, you can find me in the lab, where I’m working on enhancing our systems cellulose production.Attributions
Articles
Websites
Books
Collaboration
We utilised the broad interdisciplinary profile of our team, to have Emil S. and Lene present the perception of science throughout the history and the bioethical aspects of GMO, respectively. Emil S. has a Bachelor of Arts in History, and Lene has a Bachelor of Arts in Philosophy. The ethical presentation was purposely turned into an ethical debate, where viewpoints of ethical conduct were exchanged and discussed. After the presentations and discussions on bioethics, it was time for the wiki workshop.
The SDU-Denmark 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. To facilitate this exchange of knowledge on wiki development, we recruited our current supervisor Thøger Jensen Krogh, to hold 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 team wikis, which won the special prize on both occasions. During the presentation, Thøger had arranged several exercises where the attendees got to mingle, discuss and evaluate their wikis. This resulted in a steady flow of information and constructive feedback between all three teams.
After a long day of learning and discussing, we went for a tour around campus under the summer sun, which concluded in a visit to the roof terrace of the campus dormitory, followed by dinner. It was requested, by our fellow Danish teams, to make the SDU meetup a tradition. They suggested for all of us to meet again closer to the wiki deadline, to evaluate each team’s progress.
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. Participating in this gave us useful feedback from the judges, as well as from our fellow iGEM teams. This helped us greatly shape and develop our project for the better.
To celebrate the beginning of our iGEM summer, we went on a road trip to attend 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 projects, and made new friends from all over Europe.
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, our wiki became CO2 neutral and we made an effort to sort our waste. The full report can be scrutinized here.
We sought expertise from the Macquarie iGEM team, who has worked with the implementation of photosynthesis in E. coli since 2013. We had an interesting Skype call with their team, where we discussed the particular challenges the previous teams had experienced throughout their projects. During the skype conversation, we realised, that they could benefit from our knowledge on the electron transport pathways, that we used for our project.
We were also 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 an email from the Cologne-Düsseldorf iGEM team regarding a postcard campaign, which we gave some feedback on.
During our project we received several questionnaires from fellow teams. We were delighted to help the teams by answering their questionnaires. The questionnaires were from:
Final Words
SDU-Denmark 2017