PowerLeaf - A Bacterial Solar Battery

ENERGY MADE BEAUTIFUL

Abstract

With the PowerLeaf, iGEM SDU is introducing a novel solution for long-term storage of solar energy, becoming an alternative to solar cells, without using environmentally harmful resources. We aim to accomplish this through the creation of a device visually shaped to resemble a leaf, thus providing a nature-in-city ambience. The team invested heavily in public engagement and collaborations to investigate how the device hypothetically could be implemented into an urban environment. From a technical perspective, the bacterial solar battery is composed of an energy storing unit and an energy converting unit. The energy storing unit is defined by a genetically engineered Escherichia coli, that fixates carbon dioxide into the chemically stable polymer cellulose, while the energy converting unit uses genetically engineered E. coli to consume the stored cellulose. Electrons retrieved from this process, are transferred to an anode by optimised nanowires, thereby creating an electrical current. Last but not least; the energy storing unit has a light-dependent system which activates dormancy during nighttime to reduce energy lost by metabolism.

A green project, a green wiki, and the best performance in the iGEM Goes Green initiative! Green just got greener.

“It’s not easy being green”

Kermit the Frog

The Collaboration

As part of a Human Practices collaboration project the iGEM team of TU Dresden invited us to participate in iGEM Goes Green. The main idea of the collaboration is to calculate and consider the emission of CO₂ related to iGEM.
We are grateful for the opportunity to be play a part in a collaboration which focuses on the green aspects of GMO, as it corresponds with a main focus of our project.

Our Carbon Footprint

Much like the coastline paradox presented by Mandelbrot, our total carbon footprint is hard to measure since we cannot take the following into account: Every single kilometer we have driven, the exact size of our trees and so forth.
The estimated carbon footprint of a flight from Copenhagen, Denmark, to Boston, Massachusetts, USA and back again is 3.430 kg/person Flight emission calculator . With a team of 14 individuals, this culminates in a total of 48.020 kg or roughly 48 tonnes of carbon dioxide for our team - just from flying intercontinental. Added to this is the carbon footprint of the Danish trains at 30 g/km/person DSB environmental report. With the same 14 individuals and 175 km to Copenhagen from Odense this yields a total of 147 kg. We have been on a total of three trips, one to Langeland, Denmark, two to Copenhagen, Denmark, and one to Delft, Holland. We have travelled to these destinations in two Volkswagen Transporter vans. The carbon footprint of these is 188 kg/km/car Volkswagen automobile details. With a total of 2320 km travelled our trips yield a total of 844.5 kg of CO₂.
Thus our total carbon footprint of travelling is roughly 49 tonnes of CO₂.
Regarding our wiki, we have received help from our sponsors CO₂ Neutral Website in calculating the carbon footprint. They estimated roughly 10,000 views during the next year, but sponsored carbon elimination equivalent to 120,000 views. All in all the sponsorship from CO₂ Neutral Website has made our wiki net CO₂ negative.
We received a spreadsheet from TU-Dresden to estimate our carbon footprint from our lab Go Green Guide. The carbon footprint calculated from our lab is estimated at a total of 1 tonne of CO₂.
Thus our total carbon footprint is roughly 50 tonnes CO₂

Our Solution

To reduce our net carbon footprint we have made some local and one global initiative. The local initiatives are planting trees, buying green and travelling green. After thorough systematic research we could conclude that in general planting grass and most trees would increase our net carbon footprint, so we planted a few apple trees Carbon sequestration of trees Global warming and lawns Carbon sequestration in turfgrass.
Acknowledging this is not even cents on the dollar, we had to do more. Therefore some of the team changed their eating habits into a more local, organic and sustainable diet. The main focus of this diet was that a majority of the vegetables had to be local and should be picked up on nearby farms. For this reason one of the teammates signed up for “Odense Food Community” Odense Food Community (translated) .
The last element of the local initiatives was to travel green. In general the team has been travelling by bike or public transport when going to and from the university. For the purpose of travelling to every meetup, we have been driving in vans, leaving very little carbon footprint. Had we been able to go to Boston in a more eco-friendly way, we of course would.
Regarding global initiatives we started a partnership with CO₂ Neutral Website, which ended up in a sponsorship from them. What they have done in our name is

Build energy efficient stoves for families in Africa, reducing CO₂ emissions as less trees are logged. It also creates local jobs and creates a healthier life. Certified and audited through the Gold Standard.
Build boreholes for clean water instead of families boiling water. This also improves quality of life and reduces CO₂ emission. Certified and audited through the Gold Standard.
Build new, renewable energy sources. So far we are involved in several windmill parks.
Help protect rainforest from devastating deforestation. Certified and audited through the Redd+.
Help companies reduce their climate impact through energy efficiency.

Thus we have had a global impact on climate, which cannot be estimated precisely.

Conclusion

In conclusion we would like to highlight the following

Due to flying being a necessity for us when going to Boston we have a massive carbon footprint.
We acknowledge that any local initiative we have made are pennies on the dollar in regards to CO₂ emission and reduction.
The main initiative from us is the partnership with CO₂ Neutral Website, which has had a global impact.

Introduction

Welcome to our wiki! We are the iGEM team from the University of Southern Denmark. We have been waiting in great anticipation for the chance to tell you our story.
Our adventure began with a meeting between strangers from eight different studies. Despite our different backgrounds, we had one thing in common; a shared interest in synthetic biology. Soon after this first meeting, we were herded off to a weekend in a cottage - far away from our regular lives. The cottage was a place to bond and 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.
Since it is a one-page wiki, you can just keep on scrolling, and you will be taken on a journey through our iGEM experience.

Achievements

Bronze Medal Requirements

Register and attend – Our team applied on the 30^th of March 2017 and got accepted the 4^th of May 2017. We had an amazing summer and are looking forward to attend the Giant Jamboree!
Meet all the deliverables requirements – You are reading the team wiki now, so that is one cat in the bag. You can find all attributions made to the project in the credits section of the wiki. The team poster and team presentation are ready to be presented at the Giant Jamboree. We also filled the safety form, the judging form and all our parts were registered and submitted in time.
Clearly state the Attributions – All attributions made to our project have been clearly credited in the credits section.
Improve and/or characterise an existing Biobrick Part or Device – The characterisation of the OmpR-regulated promoter BBa_R0082 was improved, as the level of noise was studied on different vectors.
Induction and inhibition of the pBAD promoter, BBa_I0500, were studied, whereby the characterisation of this part was improved.
Furthermore, we characterized if the periplasmic beta-glucosidase could make E. coli live on cellobiose in fluid medium BBa_K523014, submitted by the 2011 iGEM Edinburgh Team. The data obtained in these experiments are presented in the demonstration and results section.

Silver Medal Requirements

Validated part/contribution – We created the part BBa_K2449004, containing a cellobiose phosphorylase. This enzyme enables E. coli to survive on cellobiose, which we validated by growth experiments. The data obtained in these experiments are presented in the demonstration and results section.
Collaboration – We have collaborated with several teams throughout our project by taking part in discussions, meetups, and answering questionnaires - we even hosted our first meetup for our fellow Danish iGEM teams. You will get to read all about this in the credits section.
Human Practices – Our philosopher, historian, and biologist have discussed the ethical and educational aspects of our project in great detail. In extension to their work, we have been working extensively with public engagement and education.

Gold Medal Requirements

Integrated Human Practices – Regarding the development and implementation of the device, we reached out to and remained in contact with city planners from our hometown throughout our project. This regarded advice and conversations on anything from the possible design, value, safety, use, placement, and plastic type of our device. We also made sure to integrate the findings of said conversations into our overall project. Last but not least, we focused on demonstrating this process on our wiki in order to inspire future iGEM teams.
Model your project – Through extensive modelling, we have learned that it is possible to regulate bacterial dormancy. However, the modelling showed that it would be inadequate to only regulate the toxin RelE, as this would make the bacteria unable to exit dormancy. To regulate dormancy properly, it would also require tight regulation of the antitoxin RelB. This information was used to shape the entire approach of the light-dependent dormancy system.

World Situation

A Global Problem

In the world of today, it is becoming increasingly important to ensure a sustainable future Green Growth Papers (Myriam Linster). Material Resources, Productivity and the Environment. 2013.. Not just for our generation, but especially for the generations to come, as their possibilities should not be limited by our choices. Our solution, is the development of a green and renewable technology, which offers new advantages to the field of sustainable energy. There are currently certain limitations to the existing options for renewable energy, namely the intermittency and the diluteness problem Alexandre Chagnes JS. Global Lithium Resources and Sustainability Issues. Lithium Process Chemistry: Elsevier; June 2015. p. pp.1-40.. The intermittency problem describes the discontinuous energy production, along with inefficient storage. On the other hand, the diluteness problem is characterised as the resource-demanding production of technical devices, such as solar cells and batteries. This means that a lack of resources eventually would eliminate the current forms of green technology. As such, we need to introduce a new and sustainable approach to green energy to ensure the continuation of our beautiful world for the coming generations.

In a Local Environment

We are a team of young adults raised with an awareness of climate changes and the potential limitations to our ways of life. As a generation that appreciates open source and shared information, we have been encouraged to constantly challenge the ideas of yesterday. With this in mind, we decided the best solution to the eventual energy crisis would be to seek out experts and 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.
Fortunately, we learned through interaction with local agents that a great deal of people share our belief; that we ought to pursue the development 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 Odense Municipality’s website, regarding their politics on the current climate changes..
In the pursuit of this goal, rose to the challenge of creating a truly green solution, which would provide an environmental friendly source of energy.
Please keep scrolling if you wish to read more about our solution, or go straight to bioethics if you are curious why we not only could, but ought to do something about the current and forthcoming energy crisis.

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 came to our workshop with their parents to learn about bacteria, the history of GMO, ethics, and iGEM. They attended our “Draw-a-Bacteria”-competition, where they designed their own bacteria, some even with detailed stories. From this the children taught us a thing or two about the endless possibilities of GMO.

See a selection of their amazing drawings here.

Our Solution

Our Solution

The vision for our bacterial solar battery is to combine two aspects: energy storage and energy conversion, by which we will produce a new and improved type of solar battery. We have named this vision The PowerLeaf. The PowerLeaf consist of two chambers that will be referred to as the outer chamber or energy storing unit and the inner chamber or energy converting unit.

The energy storing unit comprises genetically engineered Escherichia coli, which uses solar energy for ATP production to fixate carbon dioxide into the chemically stable polymer cellulose. The cellulose works as the battery in the PowerLeaf, storing the chemical energy. A light sensing system activates dormancy during nighttime, leading to a reduced loss of energy through metabolism.
The energy converting unit uses genetically engineered E. coli to consume the stored cellulose by using an inducible switch. Retrieved electrons are transferred by extracellular electron carriers 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.
The device was originally designed to resemble a plant leaf aimed to provide a nature-in-city ambience. This hypothetical implementation of the PowerLeaf in an urban environment was developed through careful consideration, public engagement, and collaborations. We worked with local city planners from our hometown Odense, along with a plastic specialist from SP Moulding, the purpose of which was to advance our pre-established design, as well as attaining other changeable designs.
Our vision was clear and ambitions were high. As it turned out though, we had aimed too high, considering the limited timeframe, so at an early stage, we decided to focus on the following features:

Light-dependent dormancy system
Converting CO₂ into glucose
Biosynthesis and secretion of cellulose produced from glucose
Converting cellulose to glucose
Extracellular electron transfer

It will then be up to future iGEM teams to continue on the development of the PowerLeaf. We would love to see our project become a reality one day, and so we have created a special page for future iGEM teams, which includes suggestions for a further development of the project.

Project & Results

We have throughout the project worked on the development of 2 units for our device, an energy storing and an energy converting unit. Each of the systems we worked on for the units can be seen here:
Energy storing (E. Coli)

Light-dependent dormancy system
Carbon fixation
Cellulose biosynthesis and secretion

Energy converting (G. Sulfurreducens)

Breakdown of cellulose
Extracellular electron transfer

Once you reach each of the 5 systems in the 'Project Design'-section, you will first be given a short introduction to the underlying theory, which you will be able to expand on, by pressing “read more”. After the theory, you will be given the approach used in each of the respective systems for the project. Before continuing on to the next system. To make things easier on you, we have developed icons to each of the above systems which will be used throughout the rest of the wiki.

Project Design

Dormancy System

Project Overview

Theory

Cyanobacteria contain signal transduction systems, thereby making them capable of sensing and responding to light Bussell AN, Kehoe DM. Control of a four-color sensing photoreceptor by a two-color sensing photoreceptor reveals complex light regulation in cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(31):12834-9.. This ability gives the organisms the opportunity, to adapt and optimize their metabolism to a circadian rhythm. Photoreceptors in the plasma membrane, of which phytochromes are especially abundant and well described, are responsible for this property Vierstra RD, Davis SJ. Bacteriophytochromes: new tools for understanding phytochrome signal transduction. Seminars in cell & developmental biology. 2000;11(6):511-21.. In 2004, the UT Austin iGEM team made a light response system consisting of a photoreceptor combined with an intracellular indigenous regulator system Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, et al. Synthetic biology: engineering Escherichia coli to see light. Nature. 2005;438(7067):441-2.. EnvZ and OmpR makes up the two-component system naturally found in E. coli. The photoreceptor known as Cph1 was isolated from the cyanobacteria Synechocytis PCC6803. Cph1 has functional combination sites, which combined with the kinase EnvZ forms a two-domain receptor, known as Cph8. Activation of Cph8 is mediated by the chromophore phycocyanobilin, PCB that is sensitive to red light with maximal absorbance at 662 nm Lamparter T, Esteban B, Hughes J. Phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803. Purification, assembly, and quaternary structure. European journal of biochemistry. 2001;268(17):4720-30..
When not exposed to light, PCB activates the phytochrome Cph1, thereby promoting kinase activity through the EnvZ kinase. When the transcription factor OmpR is phosphorylated by EnvZ, expression of genes regulated by the OmpR-regulated promoter is initiated. Excitation of PCB by red light results in a situation where the transcription factor OmpR is not regulated. The absence of phosphorylated OmpR leads to no activation of the OmpR-regulated promoter, thereby preventing gene expression.

Figure #. Left: Red light activates PCB, which in turn inactivates the photoreceptor complex Cph8, preventing gene expression from the OmpR-regulated promoter. Right: In absence of light, PCB is inactive, which enables the Cph8 to phosphorylate the transcription factor OmpR. This promotes gene expression from the OmpR-regulated promoter.

Using the photocontrol device to control a toxin-antitoxin system is a system composed of two gene products, of which one specifies a cell toxin and the other an antitoxin, which neutralizes the toxic effect caused by the toxin. In E. coli K-12 the cytotoxin RelE and antitoxin RelB comprise such a system Gotfredsen M, Gerdes K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Molecular microbiology. 1998;29(4):1065-76.. Expression of the cytotoxin RelE inhibits translation in the cells, due to its ability to cleave mRNA found in the A-site of the ribosome. RelB neutralizes the toxic effect of RelE through interaction between the two proteins. Whether the cell lie dormant in response to expression of RelE depends on the ratio of antitoxin RelB and RelE present in the cell. Several studies have shown that RelB and RelE form a complex with RelB:RelE stoichiometry of 2:1 Overgaard M, Borch J, Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. Journal of molecular biology. 2009;394(2):183-96.Overgaard M, Borch J, Jorgensen MG, Gerdes K. Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular microbiology. 2008;69(4):841-57.. When the RelB:RelE stoichiometric-ratio is lowered to 1:1, studies show that RelB is not able to protect the cells against the RelE-caused translational inhibition Overgaard M, Borch J, Jorgensen MG, Gerdes K. Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular microbiology. 2008;69(4):841-57.. For further information about the theory behind the light-dependent dormancy system, read here.

Modelling

Modelling of the RelE-RelB System is Essential to Avoid Irrevocable Dormancy

Controllable dormancy is a feature that holds the potential to be applied in many different situations. However, inducing dormancy and bringing the bacteria back to a metabolic active state is like balancing on a tightrope, and to establish the basis of future implementations, the properties of this system would have to be investigated further. In an endeavour to provide this basic knowledge, stochastic modelling utilising the Gillespie algorithm was performed in an attempt to prognosticate the system and simulate the interactions between the toxin and antitoxin. The toxin RelE is inhibited by the antitoxin RelB through complex formation, and both proteins interact with their promoter in a feedback mechanism. To consolidate the model, the capacity of the toxin-antitoxin system was assessed in an experiment, as the controllability of the dormancy system was studied through manual regulation of RelE and RelB expression.
You can read more about the modelling here.

Figure #. Left: The time required for the bacteria to enter dormancy varies with the expression level of RelB. Right: Only one of the tested configurations, RelB₂:50-RelE:35, causes the bacteria to regain their activity within the modelled time. The data is based on the simulation of 1000 independent bacteria.

The simulated data revealed, that when enhanced RelE production is implemented in order to induce dormancy in E. coli, the effect come easily. However, implementation of RelB expression is also found necessary to ensure that the bacteria are able to enter an active state again.
The model showed that the system is sensitive to the RelE:RelB ratio as well as the total amount of produced toxin. As seen in figure #, implementation with production rates in the vicinity of 50 and 35 molecules per minute for RelB and RelE respectively was found to be suitable for balancing our system; the bacteria lay dormant within the computed time and re-enter an active state within minutes.
The simulated data made it evident, that implementing an optimised dormancy system comprises a challenge, as the individual expression levels of RelE and RelB, as well as their interaction, has a crucial impact on the regulation of dormancy. Thus, controlled gene expression of both RelE and RelB is required to implement a controllable dormancy system in the PowerLeaf. If you want to dig deeper into this crucial part of our system, read the full results here.

RelE and RelB Regulate Dormancy and Influence Their Own Expression

Modelling of the effects of different RelE and RelB expression levels were performed as an important aspect in the implementation of the RelE-RelB toxin-antitoxin system. The toxin RelE constrains bacterial growth by mRNA degradation, thereby inhibiting translation, whereas the antitoxin RelB inhibits this toxic effect by forming complexes with RelE. As seen in figure #a, three different protein complexes are formed, namely RelB₂, RelB₂RelE, and RelB₂RelE₂, containing zero, one, and two RelE molecules respectively Guang-Yao Li, Yonglong Zhang, Masayori Inouye, Mitsuhiko Ikura, Structural Mechanism of Transcriptional Autorepression of the Escherichia coli RelB/RelE Antitoxin/Toxin Module, In Journal of Molecular Biology, Volume 380, Issue 1, 2008, Pages 107-119, ISSN 0022-2836.

Figure #. The three toxin-antitoxin complexes RelB₂, RelB₂RelE, and RelB₂RelE₂.

The expression of both RelE and RelB is regulated by the relBE promoter, which is influenced differently by each of the complexes, as seen in figure #b. When small amounts of RelE is present, RelB₂ and RelB₂RelE repress transcription through relBE by binding to the operator sequence. However, when high amounts of RelE are present, the toxin mitigates this repression by reacting with complexes bound to the operator sequence Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297.

Figure #. The interactions between the toxin-antitoxin complexes and the relBE promoter controlling the expression of RelE and RelB. RelE mediates the degradation of mRNA, thereby inhibiting translation.

During starvation, the half-life of RelB decreases significantly due to a Lon-proteaseOvergaard, M., Borch, J., Jørgensen, M. G. and Gerdes, K. (2008), Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular Microbiology, 69: 841–857. doi:10.1111/j.1365-2958.2008.06313.x, causing a shift in the equilibrium of RelB and RelE to a higher level of RelE. In a non-starvation situation, the interactions with the operator sequence keeps the amount of free RelE at a low level, thereby stabilising the system Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297. In our simulation, the shift in equilibrium is made by introducing additional expression of RelE.
Two different models were used with two different approaches:

How a given configuration of RelB and RelE production increases the RelE concentration and whether it could induce dormancy within 2 hours.
The time required for the bacteria to exit dormancy for each of the configurations, that is, how long it takes the levels of free RelE to decrease again.

Rates and Reactions

Molecule	Initial number of copies
mRNA	7
RelB₂	410
RelE	0
RelB₂RelE	65
RelB₂RelE₂	11
Free operator sites	0
O(RelB₂)	2
O(RelB₂RelE)	0
O(RelB₂RelE)₂	2

All values are integers as the Gillespie algorithm works with discrete numbers of molecules. The values were chosen based on a stable equilibrium found by letting the model run a simulation of the inherent system over 450 minutes with different starting values.
Ranging from 1-350 molecules per minute, the implemented expression rates of RelE and RelB in the model might seem too high, as the rates in the inherit system is effectively around 80-100 for RelB and 2-5 for RelE. However, the possibility of placing the relE and relB genes under regulation of controllable promoters makes the high total production values reasonable.
When the inherent toxin-antitoxin system is activated under starvation, 40-70 molecules of free RelE are found in each cell, making it reasonable to believe that the cells enter dormancy when a few tens of free RelE copies are present. This result obtained from the model is in agreement with literatureCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297.
For the full list of constants, see the attached Table 1 at the bottom of this page.

Running the Model

To give a stochastic view of the system, the Gillespie algorithm was run in the computer programming language MATLAB, utilising an implementation made by MATLAB user Nezar.
For the runs simulating dormancy, deterministic initial values were used and the system was run for 30 minutes without activation of the inserted toxin promoter. This resulted in a stochastic distribution of initial values mimicking variations between cells. Analysis showed, that 30 minutes was enough for the model to find a stable distribution, which is realistic considering the growth cycle of an E. coli cell.
For the runs simulating activation, the data generated at the end of a dormancy run was used as initial value and deactivated expression of RelE. When the concentration of free RelE decreases to below 15 copies, a cell is considered active. This value was probably set too low, but tests displayed marginal difference between 15 and 45 copies, where the lower limit was chosen to decrease uncertainty of the cell state.
All runs simulated 1000 cells, which should be sufficient to get stable averages and the model assumed well-mixed conditions in every cell and considered each cell independently. Furthermore, the model has no cut-off for maximum values of RelE, as the exact relation between RelE concentration and dormancy state is unknown, yet a functional cut-off was found through activation times.
Download of Matlab-scripts

Table 1

Constant	Identifier	Units	Value
mrna transcription rateCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	α₀	1/min	154.665
mrna half-lifeCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	τ_m	min	7.2
RelB half-lifeCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297Overgaard M., Borch J., Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J. Mol. Biol. 2009;394:183–196. doi: 10.1016/j.jmb.2009.09.006	τ_B	min	4.3
RelE half-lifeCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	τ_E	min	43 (growing) 2000 (dormant)
Bound RelB half-lifeCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297Overgaard M., Borch J., Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J. Mol. Biol. 2009;394:183–196. doi: 10.1016/j.jmb.2009.09.006	τ_c	min	17
RelB transcription rateCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	trans_B	1/min	15
RelE transcription rateCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	trans_E	1/min	0.3
Binding rateSneppen K, Zocchi G. Physics in Molecular Biology. Cambridge, UK: Cambridge University Press; 2005.	k _b	1/min	3.8
Dissociation rate B₂EOvergaard, M., Borch, J., Jørgensen, M. G. and Gerdes, K. (2008), Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular Microbiology, 69: 841–857. doi:10.1111/j.1365-2958.2008.06313.x	K_D (B₂E)	molecules	0.3
Dissociation rate B₂E₂Overgaard, M., Borch, J., Jørgensen, M. G. and Gerdes, K. (2008), Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular Microbiology, 69: 841–857. doi:10.1111/j.1365-2958.2008.06313.x	K_D(B₂E₂)	molecules	0.3
Dissociation rate O.B_fGotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.xCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	K_D1	molecules	10
Dissociation rate O.B₂EGotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.xCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	K_D2	molecules	0.04
Dissociation rate O.(B₂E)₂Gotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.xCataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	K_D3	molecules	30
Cleavage ratePedersen K, et al. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell. 2003;112:131–140. doi: 10.1016/S0092-8674(02)01248-5 Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297	k_c	1/min 1/molecules	2.0

Results

As the bacteria only require a few tens of RelE molecules to enter dormancy, the threshold was placed at 40 copies to allow for lag in activation. This is of course an oversimplification, but it is not a problem that activation and dormancy are defined at different levels, since the exact number of RelE molecules required to induce dormancy is unknown.

The Impact of Promoters with Different Production Rates on RelE Expression
During the implementation of RelE, gene expression was simulated for promoters with different strengths, which were chosen through an iterative process. Promoters with production rates of 3.5 and 10.5 molecules per minute, both induce dormancy rather slowly, with the latter inducing dormancy in approximately 50 minutes. In cells cloned with a promoter producing 35 molecules per minute, the cells will enter dormancy in about 10 minutes, while promoters producing 105 and 350 molecules per minute both have a negligible timeframe. In the simulated dormancy system, the three strongest promoters exhibited similar results, indicating that a certain threshold value had been transcended. This means, that not only was the gene expression disproportional to the promoter strength, but the risk of overshooting was also increased tremendously.

Figure #. The increase of free RelE molecules in E. coli cells, after activation of the artificial RelE production. The condition for induced dormancy is an amount of free RelE molecules around tens of copies. The three highest levels of RelE production, correlating with the highest promoter strengths, show little difference in the time at which dormancy occurs. When the RelE production is set to 10.5 molecules per minute, dormancy is induced more slowly and stabilises at lower concentrations. The lowest RelE production value does not trigger dormancy, and has only little effect on the system.

RelB is Required for Activation of Bacteria after Dormant State
If RelB was not expressed, the bacteria remained dormant for hours after RelE production had ceased, making it clear, that production of the antitoxin RelB was necessary for activation. Considering the stability of RelE in non-growing conditions, it was not surprising to find that RelB production would be the primary element in sequestering free RelE.

Figure #. The decrease in free RelE in dormant bacteria is low without artificial expression of RelB. None of the simulated bacteria reentered an active state within the modelled time.

Appropriate Ratio of RelE and RelB Expression is Essential
Different expression rates of RelB were combined with production rates of RelE at 35 and 100 molecules per minute, corresponding to relatively medium and strong expression levels respectively. This revealed that variation in RelB had a higher impact on the time required before the dormant state was reached when the RelE production is lowered. Out of the established configurations, the RelB₂:50-RelE:35 configuration showed promising results. Compared to the RelB₂:35-RelE:35 configuration, where only few bacteria reenter an active state within the modelled time set to 2.5 hours, the RelB₂:50-RelE:35 configuration revealed a high sensitivity to the expression level of RelB. This indicated a need for the expression of RelB to be higher than RelE, but as the best results were achieved at low production rates of RelE, it is important to stringently control the expression of RelB to ensure that the bacteria are able to enter dormancy.

Figure #. The variation in time required for the bacteria to enter an active state for different expression levels of RelB is dependent on the level of RelE expression. All configurations achieve dormancy within the modelled time.

Figure #. RelB₂:50-RelE:35 induces an active state within minutes, whereas RelB:35-RelE:35 only causes few of the bacteria to enter an active state. In the remaining configurations all bacteria remained dormant.

Discussion of Model Regarding the Artificial Dormancy System

Model Limitations
As the model only simulates the dormancy for 2 hours, not all configurations have reached equilibrium, therefore these configurations might attain a higher concentration of free RelE than modelled. This could result in a prolonged phase reentering an active state. The activation model has a rather weak predictability, as the half-life of RelE is quite high. This essentially means, that the model is unable to reduce the total amount of RelE, given by RelE_tot=RelE_free+RelE_bound, because of the short simulated timespan. Thus, in activation runs, where the number of free RelE molecules reaches a high level, the amount of RelE_bound is equally high. The problem arises, since the model works under the assumption that bound RelB is not completely stable, causing RelE-RelB complexes to dissociate, whereby RelE is freed. This causes the induced RelB expression to approach equilibrium, implying that the decrease in free RelE is rather slow. It is therefore not only the amount of free RelE that determines the activation time, but also whether the amount of dissociating complexes is high enough to counter the RelB production. Hence, it has no relevance to further test high RelE production in this model, as a high number of complexes will easily be achieved.
Light Sensitivity
One thing the model does not include, is the actual sensitivity to light. Out in the open, the amount of light is rarely an on/off switch, which means there will be periods with varying degrees of activation. Since the bacteria should be active during overcast days, the system requires a threshold, both in the sensitivity of the light-regulated promoter, but also in the activation of the toxin-antitoxin system. Variation of light is implicitly modelled through variation in promoter strength, for instance a half probability of activation translates roughly to a half production rate in the individual bacteria. Because of this, it is important not only to find functioning configurations, but also to investigate the closely related configurations, so that the bacteria neither lay dormant at overcast days, nor make the dormancy system obsolete in moonlight.

Approach

In 2004 the Austen and UCSF iGEM team created a device sensitive to light, laying the foundation for the Coliroid project. In this project, the system is combined with the RelE-RelB toxin-antitoxin system in the endeavour to mediate light-dependent dormancy in bacteria. As tight regulation is required for the RelE-RelB system Tashiro Y, Kawata K, Taniuchi A, Kakinuma K, May T, Okabe S. RelE-Mediated Dormancy Is Enhanced at High Cell Density in Escherichia coli. J Bacteriol. 2012;194(5):1169-76., modelling of the toxin-antitoxin systemis essential. The impact of different RelE-RelB expression levels was simulated by modelling. Using the results obtained by modelling, a hypothetical working system-design was devised.
On basis of the modulated system, the potential of different vectors and promoters in various combinations was tested. This constitutes the foundation for how the design of the light induced dormancy system in E. coli has been optimized and the final approach shaped. Ultimately, the light-dependent dormancy system, which is illustrated in figure #, was composed of the following parts:

The photocontrol device controlled by the PenI-regulated promoter, BBa_R0074, on a high copy vector.
The antitoxin RelB controlled by pBAD, BBa_K2449031, on a low copy vector.
The toxin RelE controlled by the OmpR-regulated promoter, BBa_R0082, on either a low copy vector or the chromosome.

For further information about our approach, read here.

Figure #. The final design of the light-dependent dormancy system. RelE under control of the OmpR-regulated promoter on the chromosome or a low copy vector, RelB under the control of the pBAD promoter on a low copy vector, and the photocontrol device controlled by the PenI-regulated promoter on a high copy plasmid.

Approach

Balancing Bacterial Dormancy Requires Accurate Regulation of the System
The genes needed for inducing dormancy when the bacteria are not exposed to light, are found in the photocontrol device part, BBa_K519030. This part is composed of three genes named ho1, pcyA, and cph8, all of which are essential to ensure the cells ability to respond to red light. When the photocontrol device is exposed to light, a phosphorylation cascade activates the transcription factor OmpR, which in turn induces transcription through the OmpR-regulated promoter, BBa_R0082. This system is combined with the RelE-RelB toxin-antitoxin system in the endeavour to mediate light-dependent dormancy in bacteria. In the first considered design of the light-dependent dormancy system, the aim was to clone the photocontrol device, BBa_K519030, under control of a constitutive promoter, RelE under control of the OmpR-regulated promoter, BBa_R0082, and RelB under control of a constitutive promoter, all into one high copy BioBrick assembly plasmid pSB1C3, as seen on figure #.

Figure #. All three components of the light-dependent dormancy system cloned into one high copy plasmid.

The Photocontrol Device was Placed under Control of a Constitutive Promoter
From the constitutive promoter family the weak promoter, BBa_J23114, the two medium promoters, BBa_J23106, and BBa_J23110, and the strong promoter, BBa_J23102, were tested by fluorescence microscopy to determine which one to use for expression of the photocontrol device and RelB. Overnight cultures of the submitted parts expressed in E. coli TOP10 illustrated a clear gradient of increasing red fluorescent protein (RFP) expression correlated with the strength of the promoter, as seen on figure #.

Figure #. Cultures of E. coli TOP10. From left to right: WT, the weak promoter, BBa_J23114, the two medium promoters, BBa_J23110, and BBa_J23106, and the strong promoter, BBa_J23102.

On the basis of the data obtained by fluorescence microscopy, the strong constitutive promoter, BBa_J23102, was chosen to control the photocontrol device. For still inexplicable reasons the photocontrol device emerged difficult to clone with the strong constitutive promoter. Although the molecular cloning of these parts was optimised several times very few successful clonings were accomplished, and the few times correct assembly was obtained, the BioBrick was not reproducibly purifiable. By sequencing, it was deduced that a region of the plasmid containing both the promoter and the BioBrick prefix had vanished. To circumvent this inconvenient cloning two other promoters, that are constitutive in E. coli, were examined, namely the PenI-regulated, BBa_R0074, and the Mnt-regulated, BBa_R0073, promoters. By performing fluorescence microscopy on composite parts of the promoters controlling yellow fluorescent protein (YFP), BBa_I6102, and BBa_I6103, respectively, the expression levels were assessed. The obtained results revealed that the PenI-regulated promoter facilitated very strong expression of the marker gene, whereas the expression controlled by the Mnt-regulated promoter was noticeably lower. Based on these findings, the photocontrol device was placed under the control of the PenI-regulated promoter instead of the strong constitutive promoter from the constitutive promoter family. As it turned out, this cloning likewise emerged difficult. After several attempts, it was decided to focus on the other aspects of the dormancy system.

Regulation of the OmpR-dependent Promoter Required a Low Copy Vector
The first construct containing the genes required for the light-induced dormancy was designed as shown in figure #. (Reference to first figure) As the conducted modelling clarified, the necessity for stringent regulation of the RelE and RelB expression, the properties of the OmpR-regulated promoter were studied thoroughly. To assess the functionality of the OmpR-regulated promoter in practice, a reporter system containing the OmpR-regulated promoter controlling RFP was cloned into the E. coli strain MG1655 ΔOmpR. The phenotype of the resulting cultures revealed a dysregulation of the OmpR-regulated promoter. Thorough research lead to the finding that the OmpR-dependent promoter is not controllable when cloned on a high copy vector. As the modelling revealed, and which is evident from figure #, a relatively low expression of RelE is required to induce dormancy, whereas high expression levels quickly result in overshooting. Since the OmpR-regulated promoter is an integrated part of the light sensing system, replacement is not an option. Therefore, the variability of the relE gene copy number was studied, and it was found that the OmpR-regulated promoter should be cloned into the bacterial chromosome or a low copy vector to obtain proper regulation Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, et al. Synthetic biology: engineering Escherichia coli to see light. Nature. 2005;438(7067):441-2.. This intriguing finding let to the aspiration to investigate the controllability of the OmpR-dependent promoter on vectors with different copy numbers compared to the chromosome, thereby improving the characterisation of the promoter for the benefit to future iGEM teams.
To incorporate DNA onto the bacterial chromosome, homologous recombination with the red λ recombinase is a suitable approach Thompson JF, de Vargas LM, Skinner SE, Landy A. Protein-protein interactions in a higher-order structure direct lambda site-specific recombination. Journal of molecular biology. 1987;195(3):481-93.. Using this technique, a short fragment of chromosomal DNA at the bacterial attachment site attB Groth AC, Calos MP. Phage integrases: biology and applications. Journal of molecular biology. 2004;335(3):667-78. can be replaced with a linear DNA fragment encoding the OmpR-dependent promoter, RelE, and an chloramphenicol resistance cassette. Using polymerase chain reaction (PCR), the linear DNA sequence was flanked by sequences, which are homologous to part of the chromosome. The linear DNA fragment was electroporated into bacteria containing the pKD46 plasmid, encoding the red λ recombinase Thompson JF, de Vargas LM, Skinner SE, Landy A. Protein-protein interactions in a higher-order structure direct lambda site-specific recombination. Journal of molecular biology. 1987;195(3):481-93., which mediated the recombination. The fundamental concept of this approach is illustrated in figure #.

Figure #. The principle behind the recombination. By PCR, the two flanking sequences are assembled with the fragment containing the chloramphenicol resistance gene (camR), the OmpR-regulated promoter, and the relE gene. The flanking sequences are homologous to part of the chromosome around the bacterial attachment site (attB), enabling the homologous recombination.

Using this approach, it was attempted to assemble the OmpR-regulated promoter controlling RelE with the flanking regions by PCR. The assembly of the fragment derived from the plasmid with either one of the flanking fragments was achieved. However, the assembly of the complete chromosomal insertion fragment containing all three segments emerged problematic. Several attempts with numerous process optimisations were performed, but unfortunately without success. To circumvent this, another attachment site was chosen. The assembly of the complete fragment by PCR was achieved and chromosomal insertion by electroporation was attempted several times, but in vain. In consideration of the fact that RelE is a bacterial toxin, the cloning of this gene was inconvenient. The model indicated, that overexpression of the antitoxin RelB would bypass this difficulty. As the homologous recombination of this fragment emerged such a challenging task, it was decided to focus on the conduct of the OmpR-regulated promoter on different plasmids, as this was evidently the more convenient approach of the general implementation of the OmpR-regulated promoter.

An Inducible Promoter was Chosen to Regulate the Gene Expression of the Antitoxin RelB
Originally, it was thought to place the antitoxin RelB under a constitutive promoter of appropriate strength. However, as the modelling revealed, strict regulation of RelB is essential to counteract the toxic effect of RelE and enable a functional dormancy system. Thus, it was deduced that it would be more suitable to utilise an inducible promoter for this purpose and it was decided to put RelB under control of the LacI-regulated, lambda pL hybrid promoter, BBa_R0011. The William and Mary team found that the LacI-regulated, lambda pL hybrid promoter had a low level of noise, a measure of the variability in gene expression between cells in the population, when cloned into a low copy vector. Therefore, this regulated promoter was chosen.
To mimic the expression of RelB, a reporter system composed of the LacI-regulated, lambda pL hybrid promoter and GFP was assembled. Hereby, the appropriate concentration of IPTG required to induce the promoter on a low copy vector, was identified. During the cloning, it was discovered that the site between the LacI-regulated, lambda hybrid promoter and this particular construct under the tested conditions had formed a hotspot for transposons. In the light of this finding, another inducible promoter was chosen. The HKUST-Rice iGEM 2015 team demonstrated that induction of the AraC-regulated promoter, pBAD, caused a gradual increase in gene expression when cloned into the low to medium copy plasmid, pSB3K3, in contrast to an all-or-none behavior when cloned into the high copy vector, pSB1K3. Taking these results into consideration, the pBAD promoter was used in combination with the pSB3K3 vector to regulate the expression of the antitoxin RelB. Again, a reporter system was used to mimic the expression of RelB, as the part, BBa_I6058, containing YFP controlled by pBAD, was assessed on different vectors.

The Final Approach for the Three Components Comprised Three Different Vectors
Based on the modelling the system approaches reviewed in the preceding part, the final design, which is illustrated on figure #, was established. Ultimately, the dormancy system was composed of the photocontrol device controlled by the PenI-regulated promoter on a high copy vector, RelB controlled by pBAD, BBa_K2449031, on a low copy vector and RelE controlled by the OmpR-regulated promoter on either a low copy vector or the chromosome.

Figure #. The final design of the light-dependent dormancy system. RelE under control of the OmpR-regulated promoter on the chromosome or a low copy vector, RelB under the control of the pBAD promoter on a low copy vector, and the photocontrol device controlled by the PenI-regulated promoter on a high copy plasmid.

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Carbon Fixation

Theory

Carbon fixation in autotrophic organisms is responsible for the net fixation of 7×10¹⁶ g carbon annually Berg IA. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Applied and Environmental Microbiology. 2011;77(6):1925-36.. Six different pathways related to carbon fixation have been discovered, but the most widespread of these, is the Calvin-Benson-Bassham (CBB) cycle found in photosynthetic eukaryotes, e.g. plants and algae, as well as in photo- and chemosynthetic bacteria B. Bowien MG, R. Klintworth, U. Windhövel. Metabolic and Molecular Regulation of the CO2-assimilating Enzyme System in Aerobic Chemoautotrophs. Microbial Growth on C1 Compounds: Proceedings of the 5th International Symposion. 1st ed. Institute for Microbiology, Georg-August-University Göttingen, Federal Republic of Germany: Martinus Nijhoff Publishers; 1987.. Out of the eleven enzymes needed for the Calvin cycle, only three are heterologous to E. coli, namely; ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), sedoheptulose-1,7-bisphosphatase (SBPase) and phosphoribulokinase (PRK). By the concurrent heterologous expression of the three genes encoding these enzymes, E. coli can be engineered to perform the full Calvin cycle.

Figure #. A simplified illustration of the Calvin cycle, with the enzymes heterologous to E. coli and their respective substrates and products shown.

The carboxysome is a microcompartment utilised by many chemoautotrophic bacteria, including cyanobacteria, as a CO₂ accumulating mechanism to increase carbon fixation efficiency . This organelle-like polyhedral body is able to increase the internal concentrations of inorganic carbon by 4000-fold compared to the external concentration Mangan NM, Brenner MP. Systems analysis of the CO(2) concentrating mechanism in cyanobacteria. eLife. 2014;3.. One type of carboxysome, is the ɑ-carboxysome, which consists of a proteinaceous outer shell composed of six different shell proteins designated CsoS1ABCD and CsoS4AB. This shell encloses RuBisCo, the shell associated protein (CsoS2), and the enzyme carbonic anhydrase (CsoS3). In the proteobacteria Halothiobacillus neapolitanus, these genes are clustered into the cso operon. The carbonic anhydrase converts HCO₃^-, which diffuses passively into the carboxysome, to CO₂, thereby driving the continued diffusion of HCO₃^- into the microcompartment Mangan NM, Brenner MP. Systems analysis of the CO(2) concentrating mechanism in cyanobacteria. eLife. 2014;3.. The increased CO₂ concentration in the vicinity of RuBisCo increases the rate of carbon fixation by saturating the RuBisCo enzyme and increasing the CO₂ to O₂ ratio, enabling carboxylation to dominate over oxygenation Mangan NM, Brenner MP. Systems analysis of the CO(2) concentrating mechanism in cyanobacteria. eLife. 2014;3.. The shell associated protein is essential for the biogenesis of the ɑ-carboxysome Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, et al. Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component. Life (Basel, Switzerland). 2015;5(2):1141-71..

Figure #. An illustration of the ɑ-carboxysome. The shell proteins CsoS1ABC and CsoS4AB enclose the enzymes RuBisCo and carbonic anhydrase.

For the Calvin cycle to proceed, energy in the form of ATP and electrons carried by NADPH are required. The photosystems are complexes in photosynthesising organisms that can supply this by photophosphorylation. To engineer E. coli to do photosynthesis, 13 genes is needed for the assembly of chlorophyll a and 17 genes for the assembly of photosystem II, which needs to be heterogeneously expressed. An alternative process, in which a diverse array of phototrophic bacteria and archaea harvest energy from light, is through a retinal-containing protein called proteorhodopsin, which catalyses the light-activated proton efflux across the cell membrane and thereby drive ATP synthesis. Opposed to the photosystems, the proteorhodopsin is anoxygenic and generates no NADPH, which is crucial for the Calvin cycle to proceed Walter JM, Greenfield D, Bustamante C, Liphardt J. Light-powering Escherichia coli with proteorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 2007;104(7):2408-12.. For further information about the theory behind the carbon fixation, read here.

Approach

In order to engineer E. coli in the outer chamber to turn atmospheric CO₂ into cellulose, the carbon first needs to be fixated by the bacteria. This requires the heterologous expression of the genes encoding the three enzymes RuBisCo, SBPase, and PRK. Furthermore, the implementation of the carboxysome from the cso operon can increase the levels of carbon fixation. The 2014 Bielefeld iGEM team had worked with a similar approach in their project. In an endeavour to optimise the carbon fixation process, our project build upon their experiences. The assembly of the individual parts into a composite part, BBa_K2449030, was achieved, however, the cloning of these parts with a promoter emerged problematic. Consequently, it was decided to prioritise other aspects of the project and therefore keep this part theoretical henceforth. For further information about our approach, read here.

Approach

Engineering E. coli to Perform the Calvin Cycle
In order to engineer E. coli in the outer chamber to turn atmospheric CO₂ into cellulose, the carbon first needs to be fixated by the bacteria. This requires the heterologous expression of the genes encoding the three enzymes RuBisCo, SBPase, and PRK. In correspondence with the 2014 Bielefeld iGEM team, who worked with a similar subpart of their project, we discussed the cloning of these genes and received two crucial parts. The first of this was BBa_K1465214, containing RubisCO from Halothiobacillus neapolitanus and PRK from Synechococcus elongatus under the control of a composite promoter controllable by IPTG. The second was BBa_K1465228, which contained SBPase from Bacillus methanolicus. Through the concurrent expression of these parts in E. coli, all enzymes required to fixate CO₂ through the Calvin cycle were present in the cells.
The first approach was to assemble both parts on one plasmid by molecular cloning, as shown on figure #. In doing this, it was discovered that the BBa_K1465214 part was missing roughly 1 kbp when digested with standard restriction enzymes with recognition sites within the BioBrick prefix and suffix. Sequencing of the part revealed that the part was missing the entire promoter sequence of 1239 bp. Consequently, the assembly of the parts additionally required the cloning of a promoter. For this purpose, the Tac-promoter (Ptac) from the part BBa_K864400 was chosen, as this is commonly used to overexpress genes in E. coli. With the objective to place the two Calvin cycle parts on different vectors, it was attempted to clone Ptac in front of both parts. However, this did not succeed and it was decided to prioritise other aspects of the project and therefore keep this part theoretical henceforth.
Implementing the Carboxysome in E. coli to Increase Carbon Fixation Efficiency
The implementation of the microcompartment carboxysome in the test organism can increase the efficiency of the carbon fixation process substantially. As for the Calvin cycle parts, we corresponded with the 2014 Bielefeld iGEM team on their experience of the implementation of the carboxysome, and received the two parts that together contained the cso operon from Halothiobacillus neapolitanus. These parts were BBa_K1465204, containing csoS2, and BBa_K1465209, containing csoS3, csoS14, and csoS1D. As part of the optimisation, we aimed to combine these parts into one part containing the entire cso operon, as shown on figure #. Furthermore, a promoter was required to drive the gene expression. For this purpose, Ptac was chosen, as for the genes encoding the Calvin cycle enzymes.

Figure #. The envisaged design of the carboxysomal genes, encoded in the composite part, BBa_K2449030, under control of the Tac-promoter.

We succeeded in assembling both carboxysome parts in the composite part, BBa_K2449030, but for some inexplicable reason, this composite part likewise emerged difficult to clone with the Tac-promoter. Therefore, it was decided to focus at other aspects of the project and, as for the Calvin cycle part, keep this part theoretical henceforth.
A fitting approach to verify the expression of the genes involved in carbon fixation, could consist of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and quantitative PCR (qPCR). For this, one could build upon the experience obtained by the 2014 Bielefeld iGEM team.
In order to test the functionality of the parts we had hoped to assemble, we had reached out to Nordcee, which is a major research group within the Department of Biology at SDU. Our hope was to compare the carbon fixation rates for cultures expressing the Calvin cycle enzymes alone and in combination with the carboxysome, whereby the effectivity of the microcompartment also would have been assessed. In cooperation with Nordcee, measurements of CO₂ decrease in an airtight culture would have been carried out with an infrared CO₂analyser. Another test approach would have been using ¹⁴CO₂, and then measure the amount our organism had taken in.

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Cellulose Biosynthesis

Theory

Bacterial cellulose is one of the most abundant biopolymers produced by different species of gram-negative bacteria, especially by Acetobactors. Glucoacetobacter xylinus is a bacterial species, which produces cellulose in large quantities of high quality Lin, SP., Loira Calvar, I., Catchmark, J.M. et al. Cellulose (2013) 20: 2191.. Cellulose is produced from the resource glucose-6-phosphate. This phosphorylated glucose is a key intermediate in the core carbon metabolism of bacteria given its importance in glycolysis, gluconeogenesis and pentose phosphate pathway Joanne Willey LS, Christopher J. Woolverton. Prescott’s Microbiology. 9th edition 2014.. Even though the pathway, where glucose and glucose-6-phosphate is converted into cellulose, only includes few steps, it requires a great amount of energy. Not only does the cell spend energy on forming UDP-glucose for cellulose biosynthesis, it also uses glucose, which otherwise would have contributed to generation of ATP Florea M, Hagemann H, Santosa G, Abbott J, Micklem CN, Spencer-Milnes X, et al. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(24):E3431-40..
The ability for G. xylinus to produce cellulose nanofibers from UDP-glucose, crystallize, and secrete it, is controlled by genes in the Acetobacter cellulose synthase (acs) operon acsABCD. This operon encodes four different proteins: AcsA, AcsB, AcsC and AcsD. A dimer, known as AcsAB, is formed by a catalytic domain, AcsA, and a regulatory domain, AcsB. This dimer is responsible for synthesising the cellulose nanofibers from UDP-glucose, whereas AcsC and AcsD secretes cellulose and forms an interconnected cellulose pellicle around the cells Mehta K, et al. Characterization of an acsD disruption mutant provides additional evidence for the hierarchical cell-directed self-assembly of cellulose in Gluconacetobacter xylinus. Cellulose. 2014;22:119–137., as illustrated in figure #.

Figure #. The AcsAB dimer synthesises cellulose nanofibers. AcsC and AcsD mediate the secretion and formation of an interconnected cellulose pellicle.

Other genera, including some E. coli strains, secrete cellulose as a component of their biofilm. Even though cellulose biosynthesis is intrinsic to E. coli, the quantity of the production is incomparable to cellulose biosynthesis in G. xylinus. Indigenously, E. coli is not capable of degrading cellulose into a metabolisable energy source Gao D, Luan Y, Wang Q, Liang Q, Qi Q. Construction of cellulose-utilizing Escherichia coli based on a secretable cellulase. Microbial Cell Factories. 2015;14:159.. However, if this structural and water-holding polymer is enzymatically degraded, first into cellobiose and then to glucose residues, the cellulose polymer is a potent source of energy Arai T, Matsuoka S, Cho HY, Yukawa H, Inui M, Wong SL, et al. Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proceedings of the National Academy of Sciences of the United States of America. 2007;104(5):1456-60..

Approach

To link the two bacterial compartments of the PowerLeaf, an efficient way to store the harvested energy was required. Research led to the finding that storing the chemical energy in cellulose would be a suitable approach, since this is a polysaccharide that bacteria normally are unable to degrade Gao D, Luan Y, Wang Q, Liang Q, Qi Q. Construction of cellulose-utilizing Escherichia coli based on a secretable cellulase. Microbial Cell Factories. 2015;14:159.. After looking into earlier iGEM projects it was found that the 2014 project Aqualose from Imperial College London, had worked with optimisation of cellulose biosynthesis in E. coli. Our aim was to enhance cellulose biosynthesis in E. coli MG1655, which naturally secretes small amounts of cellulose as a part of its biofilm Gualdi L, Tagliabue L, Bertagnoli S, Ierano T, De Castro C, Landini P. Cellulose modulates biofilm formation by counteracting curli-mediated colonization of solid surfaces in Escherichia coli. Microbiology (Reading, England). 2008;154(Pt 7):2017-24.. This would be achieved by the cloning of plasmids containing the cellulose synthase operon acsABCD, utilising the two parts BBa_K1321334 and BBa_K1321335, constructed by Imperial College London 2014. This would enhance the cellulose biosynthesis and thereby optimise the energy outcome of the entire system in our project. Due to cloning difficulties, it was decided to prioritise other aspects of the project and therefore keep this part theoretical henceforth. For further information about the cellulose biosynthesis approach, read here.

Approach

Optimised Cellulose Biosynthesis in E. coli
To enhance the cellulose biosynthesis, parts containing the coding sequence of the Cellulose Synthase enzyme were cloned into the E. coli strain MG1655. The original idea was to clone the entire cellulose synthase operon acsABCD into one vector under control of the Ptac, as seen in figure #. With a plasmid with a total length over 9000 bp, the cloning emerged difficult. After several unsuccessful attempts, a different approach was sought.

Figure #. The acsABCD operon controlled by Ptac cloned into one high copy vector.

In this design, it was attempted to implement the acsABCD operon into E. coli MG1655 on two separate vectors, with both parts controlled by PtacBBa_K864400, ensuring equal expression levels of the parts. The AcsAB dimer, encoded in the part BBa_K1321334, was attempted to be inserted into the vector pSB1C3. The part BBa_K1321335, containing AcsC and AcsD, was inserted into the vector pSB1A3. Several combinations of the two parts and different vectors carrying different resistance cassettes were attempted, but unfortunately without success. Correspondence with a supervisor from the Imperial College London team, revealed that cloning with these parts had emerged difficult for them as well. Due to time constraints, it was decided to prioritise other aspects of the project and therefore keep this part theoretical henceforth.
If the cloning of the acsABCD operon had been successful, the cellulose biosynthesis would have been tested using fluorescent brightener 28. This is a colourless organic compound that fluoresces with a bright blue color under ultraviolet radiation, and it is used as a fluorescent brightening agent for polyamide and cellulose fabrics. Fluorescent brightener 28 binds non-specifically to polysaccharides with β-1,3 and β-1,4 linkages, of which the latter is present in cellulose Staining of fungal hyphae and propagules with fluorescent brightener.

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Breakdown of Cellulose

Theory

Cellulose is a natural biopolymer used for a huge variety of biological purposes. It is most commonly found in plants, where it serves as the main structural component. Since plants are primary producers, many organisms of the Earth’s ecosystems have adapted accordingly [kilde 4]. One of the key evolutionary features for the primary consumers, was the development of the ability to degrade cellulose into glucose, which could then be used as a cellular fuel. A simple organism, able to efficiently do so, is the Cellumonas fimi, which converts cellulose to glucose in a two-step process, with cellobiose as the intermediate [kilde 7].

Breakdown of Cellulose to Cellobiose
Cellulose is a long polysaccharide consisting of β-1,4 linked D-glucose units. Many organisms, including E. coli, lack the enzymes able to degrade these strong β-linkages. To overcome this, the C. fimi developed two cellulases, namely the endo-β-1,4-glucanase and exo-β-1,4-glucanase, respectively encoded by the cenA and cex genes [kilde 7]. The endoglucanase is able to randomly degrade the amorphous structure of cellulose, thereby allowing the exoglucanase to cleave the β-1,4 linkages at every other D-glucose unit. Thus disaccharides are released in the form of cellobiose [kilde 8], as illustrated in figure #. Cellulose itself is too large to be transported across the bacterial cell membrane. Therefore, the breakdown of cellulose into cellobiose must take place in the extracellular fluid.

The α-Hemolysin Transport System
The ɑ-hemolysin transport system is an ABC transporter complex, consisting of three proteins, namely the outer membrane protein TolC, Hemolysin B (HlyB), and Hemolysin D (HlyD) [kilde 3]. The ABC transporter complex effectively transports intracellular Hemolysin A (HlyA) to the extracellular fluid. Utilising a linker peptide, the protein of interest can be fused with HlyA. Once a protein is HlyA-tagged, it can be recognized by the ATP-binding cassette HlyB, which will initiate transportation of the HlyA-tagged protein to the extracellular fluid, as seen in figure # [kilde 3, kilde 6].

Uptake of Cellobiose
While cellulose is too large to be pass the cell membrane, transportation of cellobiose is a common feature found in many organisms. An example is E. coli, which utilises the membrane protein lactose permease (LacY) [kilde 5]. In the cytosol, cellobiose is enzymatically catabolised.

Breakdown of Cellobiose to Glucose
Through evolutionary events, many organisms have developed the ability to express enzymes, capable of breaking the β-linkage in cellobiose. E. coli expresses the periplasmic β-glucosidase encoded by the bglX gene, which is known to have said feature, by hydrolysing the cellobiose β-linkage[kilde 1]. Saccharophagus degradans expresses a different enzyme, which efficiently cleaves the β-linkage in cellobiose, namely cellobiose phosphorylase encoded by the cep94A gene. This enzyme phosphorylates the cellobiose at its β-linkage, resulting in the degradation of cellobiose to D-glucose and α-D-glucose-1-phosphate [kilde 5], as seen in figure #.

Approach

Cellulose to Cellobiose
In the endeavour to engineer E. coli to utilise cellulose as it’s only carbon source, inspiration was drawn from the Edinburgh 2008 iGEM team project, who developed two BioBricks containing the cenA and cex genes. In this project, the α-hemolysin transport system was utilised by creating HlyA-tagged endo- and exo-β-1,4-glucanase, using a peptide linker. To implement this system in E. coli, heterogeneous expression of hlyB, hlyD, cenA-hlyA and cex-hlyA was required.
To achieve this, DNA synthesis of cenA and cex was ordered, each tagged with HlyA. The genes encoding HlyB and HlyD were retrieved from the part BBa_K1166002 by phusion PCR. Using the resulting PCR product, the following construct was composed for the degradation of cellulose into cellobiose, as illustrated on figure #.

Cellulose to Cellobiose
The Edinburgh 2011 iGEM team team created a BioBrick encoding periplasmic β-glucosidase endogenous to E. coli, proposed to increase its efficiency at degrading cellobiose to glucose. However, it seems that the enzymatic activity of bglX has faded as a result of evolution, rendering E. coli incapable of surviving solely on cellobiose. So even though E. coli can absorp cellobiose, it is not able to survive with this as its only carbon source.
To solve this issue, we decided to synthesise a cep94A Biobrick, intended to make E. coli capable of effectively surviving on cellobiose. To achieve this we composed the following construct:

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Extracellular Electron Transfer

Theory

Microbial Fuel Cell
Electrochemical devices such as batteries and fuel cells are broadly used in electronics to convert chemical energy into electrical energy. A Microbial Fuel Cell (MFC) is an open system electrochemical device, consisting of two chambers, an anode chamber and a cathode chamber, separated by a proton exchange membrane as illustrated in figure y. Both the anode and the cathode in a MFC can use various forms of graphite as the base material. In the anode chamber of a MFC, microbes are utilised as catalysts to convert organic matter into metabolic products, protons and electrons [kilde 8]. This is carried out through metabolic pathways such as glycolysis, to generate needed ATP to maintain cellular life. This metabolic pathway also generates a release of electrons carried by NAD⁺ in its reduced form NADH.

Under aerobic conditions, the generated NADH will deliver its electron as part of the electron transfer chain, to return to its oxidised form NAD⁺. Under anaerobic conditions the electron transport chain will not be able to continue, which will cause the generated NADH to accumulate. As a consequence of accumulated NADH, the concentration of available NAD⁺ for glycolysis will decrease. This will drive the cell to carry out other metabolic pathways, such as fermentation, in order to maintain its ATP levels. Instead the accumulating NADH generated under anaerobic conditions, can be utilised to drive an electrical current by depositing the retrieved electrons to an anode coupled with an appropriate cathode. The cathode catalyst in a MFC will usually catalyse the reaction of 4 H⁺ + 2 O₂ à H₂O. The transfer of electrons from NADH to the anode can be executed in three different ways as shown in figure x; redox shuttles, direct contact electron transfer, and bacterial nanowires [kilde 7][kilde 8].

The redox shuttles use extracellular electron mediators, which hold the advantage of not being limited by the surface area of the anode. However, it is restricted by the slow diffusion of the extracellular mediators. The direct contact electron transfer, in reverse to the redox shuttles, is strongly limited by the surface area of the anode, but the membrane bound cytochromes in direct contact with the anode, rapidly delivers the electrons. Bacterial nanowires are known to efficiently transfer electrons, much like the direct contact electron transfer. However, bacterial nanowires are not as strictly limited by the surface area of the anode as the direct contact electron transfer is. This is due to bacterial nanowires ability to form complex networks of interacting nanowires in biofilm, to efficiently transfer electrons from distant microbes all the way to the anode using this network. [kilde 8]

Bacterial Nanowires
Nanowires are long electrically conductive pili found on the surface of various microorganisms, such as the metal reducing Geobacter sulfurreducens. G. sulfurreducens utilises nanowires to transfer accumulating electrons retrieved from metabolism, to metals in the nearby environment [kilde 3]. G. sulfurreducens is strictly anaerobic, as it would not be able to transfer its electrons to the environment in the presence of the highly reducing oxygen. Nanowires found in G. sulfurreducens is a type IV pilin polymer chain composed of pilA monomers, which can reach nearly 10 mm in length [kilde 4]. The proteins required for the effective transfer of electrons by nanowires is a complex and poorly understood system, which involves a long series of c-type cytochromes [kilde 6].

The electrical conductivity of the nanowires in G. sulfurreducens can be optimised by exchanging endogenous pilA with heterologous pilA rich in aromatic amino acids. Tan Yang et. al [kilde 1] did an exchange like this by heterogeneously expressing pilA from G. metallireducens, which proved to increase the electrical conductivity of the G. sulfurreducens recombinant by a 5000-fold. This optimisation can be helpful in the development of highly efficient bacterial strains for MFCs. With the intention of optimising a MFC, G. sulfurreducens is a lot easier to work with than G. metallireducens [kilde 1].

Approach

Originally, we wanted to implement bacterial nanowires from G. sulfurreducens into E. coli. Through extensive research, we came to a similar conclusion as the Bielefeld 2013 iGEM team did; that this task was too comprehensive to undertake in the limited time of an iGEM project. Postdoc Oona Snoeyenbos-West suggested us to use G. sulfurreducens as the model organism for our MFC.
We then decided to work on optimisation of the G. sulfurreducens by increasing the electrical conductivity of its endogenous nanowires. To achieve this we ordered synthesis of the pilA genes from G. metallireducens, which was used to create a Biobrick. From this Biobrick, a PCR product was made containing the chloramphenicol resistance cassette of the pSB1C3 backbone for later selection of recombinant G. sulfurreducens. The PCR product was ligated with PCR products retrieved from the 500 bp upstream and downstream regions of the chromosomal pilA genes of the G. sulfurreducens PCA strain. This was used to create the following linear DNA fragment, intended for homologous recombination into G. sulfurreducens:

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Demonstration and Results

Parts & Procedures

In this section, you will find all the needed information to replicate our approach and experiments. The constructed parts, notebook, SOPs and protocols will show in a pop-up window , from which you can obtain all the necessary knowledge, should you be interested. An essential part of going to the lab is risk and safety assessments, which you will find at the end of the section.

Parts

Notebook

Week 8
As 12 strangers we met for the first time on the 22^nd of February. We cooked and ate a lovely meal together, and hereby had our first team building experience.

Week 10
We went to the DTU-Denmark BioBrick tutorial event, where we had an unforgettable experience. Here, we met some of the other Scandinavian teams, with whom we had a wonderful time.

Week 11
A group contract was discussed and the first version was written.
As part of the promotion of the team and iGEM, a banner was created for the information screens at our university, the University of Southern Denmark.

Week 12

Excursion to a cabin on Langeland. At this idyllic spot, different ideas for our project were discussed and narrowed down to only a handful of ideas. It was a fun weekend and friendships among the team members began to sprout.

Week 14
Through an iterative process, the list of project ideas was cut down. Ultimately, the PowerLeaf - A Bacterial Solar Battery was chosen as our project.

Week 16
The team had a weekend of lab training with the supervisor Patrick, where we learned about all the basic applications for cloning. The work on the dormancy system had begun!

Week 17
We had a lab safety course with Lab Technician Simon Rose. Thereby, we became qualified for unsupervised laboratory work. Now we were properly equipped to start the work!
During the Danish Science Festival, we presented our iGEM team. Here, we talked to a lot of people about GMO, especially with children. We had prepared several activities for the children to participate in, one being a drawing competition. In this competition, the most innovative and creative idea of a bacteria won. From this activity, the team received a lot of fantastic drawings, with endless creative ideas, that the team took into consideration and used to further shape our project.

Week 18
The team had a course in innovation with Ann Zahle Andersen, from the patent office of the University of Southern Denmark. Here, we gained a better understanding of our project from a business point of view.
Bastian and Magnus, 6. grade students from a local public elementary school, interviewed us on the topic of GMO. After the interview, the boys received a guided tour around the iGEM lab. The boys used the obtained information about GMO to write an assignment at their school.

Week 19
We got the first look at promoter reporter systems in the fluorescence microscope.

Week 21
The team started their collaboration with Odense Municipality. The main focus in this collaboration was to integrate our project into an urban setting.

Week 23
Putting our final touches on the PowerPoint presentation for the Nordic Meetup, held by the KU iGEM team. This was the first time, our project was presented for other teams. At the meetup, the team members met a lot of wonderful people, some for the first time, others were enjoyable reunions.

Week 24
We received parts from the Bielefeld team for the carbon fixation system. There was a breakthrough regarding the secretion system, as we succeeded in the creation of the cex part.

Week 26
The team filled out the first three parts of the safety form. We had a talk with postdoc Oona Snoeyenbos-West, who suggested that we should work with Geobacter sulfurreducens to test the bacterial nanowires.

Week 27
The entire team went to the Netherlands, where we joined the European Meetup at TU Delft. At this meetup, we had the pleasure of meeting new people from several European iGEM teams, alongside meeting old friends from the Nordic teams. The team extended the trip while in the Netherlands, to spend a day in beautiful Amsterdam together.

Week 28
The genes encoding RelE and RelB, which comprise a toxin-antitoxin system, were purified from E. coli.

Week 29
We cracked the code of modelling and our modelling system stabilised. Furthermore, the secretion system was created.

Week 30
A presentation was held at the UNF (Danish Youth Association of Science) high school camp, where we taught them about synthetic biology and how to work with genes.
In the lab, we received parts from the Imperial College team for cellulose biosynthesis. We also began creating the BioBrick for our nanowires. The cenA part was created, and the assembly of the entire secretion system was begun.

Week 31
Our lab workers analysed the properties of the LacI-regulated, lambda pL hybrid promoter for the energy storing unit.

Week 33
The team celebrated an early christmas. Yes, in July! Crazy, we know! There was a christmas tree, a cosy atmosphere and more food, especially gravy, than should be possible to consume. The team had a jolly good time.

We finally made our PCR fragment for Geobacter, which would be used for homologous recombination. Testing on our cellobiose phosphorylase, that we received from IDT, was begun.

Week 34
We held our own SDU meetup with focus on wiki and ethics for KU and DTU. The reunion with the other Danish iGEM teams was a welcoming experience.

Week 35
The abstract for the iGEM Jamboree was finished. In this week we also decided that we should enter the energy track.

Week 36
The team members working on human practices had a really informative meeting with Kristina Dienhart from Smart City Odense. We held a presentation at the local high school OTG (The Technical High School of Odense). SDU communication helped us produce a video about our project, which reached more than 27000 people on Facebook. Furthermore, an article about our project and team was published in the local newspaper Fyens Stiftstidende.
The genes encoding the carboxysome were assembled. Furthermore, the expression levels of the Mnt- and PenI-regulated promoters were compared in the fluorescence microscope.

Week 37
We hosted an event for ATU (Academy for Talented Youths) with transformation and synthetic biology as the main focus. This began with a general presentation, after which we went to our lab, where the aspiring scientists from ATU performed plasmid purification and gel electrophoresis. The team had a marvelous day as it was wonderful to see so many young individuals being engaged in science.

Week 38
We had a human practises meeting with Rikke Falgreen Mortensen about integrating our project in MyBolbro. Furthermore, we held a presentation about GMO and our project for the local public school, Odense Friskole.
We were surprised to discover that a transposon hotspot had formed between the LacI-regulated, lambda pL hybrid promoter and the GFP reporter.

Week 39
We held a presentation at the local high school, Mulernes Gymnasium, where synthetic biology was the main focus.
The lab workers discovered that a region containing the strong constitutive promoter and the BioBrick prefix had vanished from the photocontrol device plasmid. Furthermore, it was decided to keep the cellulose biosynthesis subproject theoretical henceforth.

Week 40
Materials for our prototype were set after a talk with the plastic expert Flemming Christiansen.
Second part of the course in innovation and patents with Ann Zhale Andersen was completed.
The last two part of the safety form part were completed and submitted. Additionally, it was decided to keep the carbon fixation subproject theoretical henceforth.

Week 41
The final promoter for the RelB expression, pBAD, was chosen and cloned.
We ceased trying to perform the recombination in Geobacter after several difficulties.

Week 42
We got together with the old iGEM teams from SDU-Denmark at the Old-iGEM Meetup. Both the project in general and our wiki were presented to them, and we got a lot of useful feedback to improve our project, presentation, and wiki. We shared a lovely meal and had a great night.
We managed to create our secretion system part after several tries and problems.

Week 43
Parts were sent to HQ and the Judging form was filled out.
In the lab, we obtained promising results, as the features of the pBAD and OmpR-regulated promoters were studied in the fluorescence microscope and flow cytometer.
Besides working in the lab to get the last results ready for the wiki freeze, the team spend the weekend going through all of the text.

Week 44
With the wiki freeze around the corner, we worked day and night, caffeine concentrations in our blood running high. We shall make it!

Week 45
Wiki freeze!!!

SOPs and Protocols

SOP01 - LA plates 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

SOP27 - SDS-PAGE

Safety

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 addressed properly. 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 should not be compromised either. The risk associated with laboratorial work can be evaluated using the statement “Risk = Hazard ✕ Probability”. To responsibly address 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. Throughout the project we have continuously been evaluating the safety of our work. These assessments can be found in the safety form. Furthermore, our team participated in the 5^th annual BioBrick workshop hosted by DTU BioBuilders. Here we participated in a lab safety course before entering their laboratories. Both of these lab safety courses gave us the necessary knowledge to work safely with GMO and handle waste appropriate, as well as the according procedures in case of an emergency.
In the lab, we worked with several potentially harmful chemical agents such as dimethylsulfoxide (DMSO), 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. Gloves were worn when necessary, and clean lab coats were worn restrictedly in the laboratorial areas. To visualise bands in agarose gels, we used an UV board. UV rays are carcinogenic when exposure is frequent and prolonged. 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 kept at a minimum.

Public and Environmental Risk Assessment

The chassis organisms containing the system is meant to be contained in a device, which is 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. For this reason, 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. The plastics expert has estimated that such a 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 1980s made of the same plastic, which still stand strong today.
One of the biggest concerns would be the release of GMOs into nature. While the GMOs used are not pathogenetic, they would be able to share the plasmids containing antibiotic resistance selectors to other bacteria, that might be pathogenic. Antibiotic resistance in pathogenic bacteria complicates the treatment of an infected individual and could, in tragic cases, be the difference between life and death. However small the risk of this scenario might be, 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 balance of nature, that we are aiming to restore with the development of the PowerLeaf.
To avoid these risks, several kill switch mechanisms should be implemented into the final device. This could be performed by implementation of a kill switch activated by exposure to light in the energy converting unit. 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 function, could then have a kill switch which makes it dependent on the presence of the energy converting unit. This could be accomplished by having harmless molecules, not naturally found in nature but required for the survival of the energy converting unit, circulating in the system. A similar effect could be accomplished by making the bacteria in the energy converting and 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.

List of Assessed Items

Chassis Organisms
Escherichia coli strains: K12, TOP10, MG1655, KG22, BW25113, DF25663127, SØ928
Geobacter Sulfurreducens strain: PCA

Vectors
pSB1A2: An iGEM plasmid backbone carrying a ampicillin resistance gene
pSB1A3: An iGEM plasmid backbone carrying an ampicillin resistance gene
pSB1C3: An iGEM plasmid backbone carrying a chloramphenicol resistance gene
pSB3C5: An iGEM plasmid backbone carrying a chloramphenicol resistance gene
pSB1K3: An iGEM plasmid backbone carrying a kanamycin resistance gene
pSB4K5: An iGEM plasmid backbone carrying a kanamycin resistance gene
pSB3K3: An iGEM plasmid backbone carrying a kanamycin resistance gene

Bacteriophages
P1 phage, using its site-specific recombinase for transduction of E. Coli

Practices

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Bioethics

ethics is forcing Neergaard drink phenol

Jonas can approve on this

Integrated Practices

“The best way to predict your future, is to create it”

Abraham Lincoln - (former) president of the United States of America

Not that we can claim to be anything like Abraham Lincoln, or even to be vampire hunters, but we do agree that to create the future we all hope for, we must contribute to finding a sustainable solution for a greener future. However, before we can tackle the arduous task of providing a sustainable future for the entire world, we must first look to our own local environment to better understand its vision for the future. Hopefully this approach will help future iGEM teams find a connection between global issues and local ones - as we believe that the best way to gain a better understanding of a global dilemma, is to examine how a local environment is affected by it, and how it could possibly be tackled in such a setting. This approach has helped us elucidate specific issues and to find sustainable solutions that can be implemented into our society with the help and endorsement of local agents.

integrate a pizza here

A Statement from the Mayor of Odense

We first decided to reach out to the mayor of Odense, to investigate the possibilities for iGEM to help in the government's endeavours to make Odense a CO₂ neutral city, with a high quality of life.

“We face a series of challenges that we have to recognize, in the chase of a good and sustainable life in the city of Odense. Some of these concern local circumstances, while others contain national and even global issues. We as the municipality can only go so far on our own. So we are entirely dependehttps://2017.igem.org/Team:SDU-Denmark/testnt on the help of local agents. It makes me so happy, when the students of the city, have taken on the mantle of developing new green technologies, which global issues while also contributing to the city's high quality of life.”

Peter Rahbæk Juel - Mayor of Odense

The core philosophy of our integrated human practices has been to integrate local experts in the development of our project; in order to better comprehend how to use the knowledge gained in the laboratory to shape a product that would compliment Odenses (or beyond) green values. We have also made use of experts in other fields in order to better understand how to shape our project - and so our human practice has influenced everything from the design of our prototype(s), laboratory work to ethical considerations.
We will now walk you through our integrated human practices, so scroll on down to find out more about who we spoke with and how their input and advice came to influence our entire iGEM experience.

Meeting with Kristina Dienhart

For the purpose of a possible implementation of the PowerLeaf into the different areas of Odense city’s renewal, we decided to reach out to Kristina Dienhart. Kristina Dienhart was at this point in time project manager of Smart City Odense – a project within Odense Municipality that seeks to combine urban planning with new technologies and open-data, in order to create a smarter city. We decided to consult mrs. Dienhart, as Smart City Odense shares our core values; working transparently, openly and collaborative, while also sharing know-how. Mrs. Dienhart made us aware of the following necessities for Odense and its citizens - feedback that we have integrated in numerous areas of our overall project. It is important to note that at the time of our meeting with Mrs. Dienhart, our vision of the PowerLeaf was exclusively in the shape of a leaf; a leaf designed to be implemented on various buildings around Odense.

From Mrs. Dienhart’s point of view, one of the most advantageous attributes of our device, is the the potential for changeability in the size and shape of the PowerLeaf - as this means it could be shaped depending on what urban area we wish to integrate the PowerLeaf within. We had yet to consider the PowerLeaf as a device not limited by physical dimensions, and it’s perhaps the most significant element we took away from our meeting with Mrs. Dienhart. Changeability is a necessity to a city planner, as various laws and aesthetic aspects need to be taken into consideration, when altering or creating an urban environment.
Accessibility – the citizen will not use our device if it is not easily accessible. This means that the overall design of PowerLeaf – regardless of its aesthetic – always needs to be designed with a user in mind. Offering a mobile-charger in a city-space is only clever insofar that the citizen using the public space is aware of the device and how to easily access it. Reflecting on the advice of Mrs. Dienhart, we decided to reevaluate the means of implementation of our bacterial solar battery in the prototype, to ensure that the need for accessibility and user-comfort is met.
Mrs. Dienhart supported our notion that offering free and accessible energy within public space could help ensure that the ordinary citizen of Odense uses and stays in the public space for a longer amount of time. Something that is valuable not only to the individual citizen but also to the community as a whole, as it creates a sense of city-cohesion and hence a high quality of city-life.
Overall Mrs. Dienhart confirmed that our PowerLeaf could play a part in Odenses dream of developing into an even greener and more lively city. She also made us aware that not every neighbourhood in Odense will be desiring the same design, and that we ought to focus on the changeability aspect in the development of our prototype’s design.

Overall Mrs. Dienhart introduced us to several considerations that shaped large parts of our project. Her call for ‘the changeability aspect’ of the PowerLeaf has been used to reconsider the construction of the solar battery’s exterior and sustainability. We do not know the needs of every urban area in Odense; and consequently - with Mrs. Dienhart in mind – we have aimed to create a device that is changeable to a city in movement such as Odense. Mrs. Dienhart therefore challenged what we thought we wanted from a prototype - namely a fixed design - into the belief that we ought to create a prototype that can be shaped and reshaped depending on the requested necessities of the customer.
Furthermore the conversation with Mrs. Dienhart was also a source of inspiration in regards to our ethical and safety thoughts. The belief that while we ought to create a better more sustainable tomorrow for ourselves and future generations, we do not necessarily have to provide an exhaustive description of what that future should like, very much evolved from the changeability aspect, which was brought about by our conversation with Mrs. Dienhart.

Meeting with Rikke Falgreen Mortensen

Mrs. Dienhart also helped to establish contact with Rikke Falgreen Mortensen, manager of the Bolbro’s city-renewal project called MyBolbro. We arranged a meeting with Mrs. Mortensen with the intent of further investigating how the PowerLeaf could and should be integrated into an urban area of Odense - in this case the neighbourhood Bolbro.
Bolbro is an old neighbourhood in Odense historically known to be the home of the working-class, and while Bolbro provides a homely atmosphere known to the locals, it has had a hard time attracting new residents. However, this is subject to change as the neighbourhood in 2016 received a reservation of approximately 1,6 million us dollars to renew its city-space and create an even more appealing and vibrant neighbourhood. This will be achieved by including the locals, as Bolbro is characterized by having a strong, engaging civil society. Mrs. Mortensen is not only an expert in urban renewal but also in how to include local citizens in reshaping the public space in which they reside.
Mrs. Mortensen, as Mrs. Dienhart, also argued that a changeable design would be the optimal solution to fit the challenges, One faces in creating a vibrant, green city-ambience. As such a task depends on preferences, laws and needs. Instead a technology needs to be both flexible and accessible in order to successfully contribute to the process of creating a successful city environment. Furthermore we had a discussion with Mrs. Mortens about the creation of a prototype based on the wishes of Bolbro’s local citizens.

“Hauge’s square is a spot in Bolbro, which we aim to make a central place in Bolbro; a place that invites the citizen to meet and dwell. At the same time it must also be an orientations point, from where citizens and visitors can find their way to other places and attractions in Bolbro. Today the possibility for enjoying the outside consists of the space in Hauge’s square, which is made up by a bakery, a small local library, and a parking lot. However, we believe that the space contains better opportunities. In short, the space must be transformed from primarily being a parking spot to a recreational place with a much more aesthetic design. Your solution should be able to contribute to help citizens recharge their phones, ex. A solution could be implanting the PowerLeaf into a ‘living’ furniture, but where demands for the aesthetic design still remains”

“A part of the vision of this project is the concept of making a pop-up park with differently designed multi-furniture, preferably in wood and organic design, which are removable to the various areas where we are going to develop in the district. It is furniture that should be able to be used to relax in and at the same time also motivates children to move - and there should also be platforms that invite to activity ex. table tennis or a more screened seating for lovers, conversation or work. There is also a need for charging devices and it therefore demands that your solution is an integrated but still mobile solution, as the park will move physically over time”

“Finally, the church / playground is to be developed especially for the young audience, which is a major consumer of power for phones. The place must be a place where the youngsters hang out after school, still a green space where the solution should be integrated into the interior and could keep the target audience children and adolescents. The site is in a socially charged area, so it demands a robustness from of the solution, to help when faced with ex. vandalism”

The making of the furniture as a prototype called for a re-visit of our safety concerns, as children will be climbing and playing on the furniture, it is crucial that the material of the PowerLeaf will not break; a concern we discussed with Flemming Christiansen, which you will be able to read more about next. Just keep scrolling!

Flemming Christiansen

Criteria to the Prototype
Having decided that the exterior of the device would be made entirely from plastic, we set out to.
Plastic is thought of as an undesirable material, due to the difficulties in its disposal. This is due to plastic being of a xenobiotic nature, making it generally recalcitrant to microbial degradation. This predicament is complicated further by biodegradable plastics being of a compensatory nature; sacrificing form-stability and strength for biodegradability. Following these concepts, we can identify the following set of criteria for our material:

Solar exposure - The material covering the solar cell, must allow sunlight to pass through it to the bacteria.
UV resistance - As the material will be exposed to the sun, it should be resistant to the UV radiation.
Bacterial growth - The material must support, or not be toxic to the bacteria.
Easy to mold - As the device is only dependent on the insides, the outside could be molded depending on the co
Durability - material must be able to withstand hard conditions and heavy weight.
Temperature -The material must allow for appropriate temperature for the bacteria, despite the constant sun exposure.
Longevity - We would like for the material to have as long a durability as possible, as replacing the leaves often would prove cumbersome. In this regard we are aiming for at least twenty years.
Price - We are looking for a material that is as cheap as possible, without sacrificing the necessary criteria.
Environmentally friendly - Considering the goal of this project being the creation of an environmentally friendly energy source, the ideal material would be as environmentally friendly as possible.

Interview with Flemming Christiansen
For the purpose of finding the necessary materials for our prototype, we contacted one of the leading plastic experts in Denmark, Flemming Christiansen, who acts as the market development manager of SP Moulding. He has been acting as a plastics consultant, since his graduation as a master of science in Engineering with a speciality in plastics in the 1970ies. A meeting was quickly arranged, where we fleshed out the criteria, the technical design, the material and the possible price of creating the PowerLeaf.
In accordance with our established criteria, mr. Christiansen suggested that we use the plastic known as Polycarbonate, specifically Lexon 103R-III (kilde). The material, however, cannot fulfill the criteria on it’s own. Therefore, Mr. Christiansen suggested that we take a few liberties with it. In order to prevent the exposed part of the prototype from degradation by UV radiation, we will be adding certain additives to the surface of the exposed part. This doesn’t hinder the sunlight from entering the device and thus the bacteria, but just increases the UV-resistance of the material. During our consultations with Mr. Christiansen, we reached the topic of what to do in case of a breach. Should the container against all expectations be damaged, the GMOs inside would be exposed to the environment. The solution we came up with was the possible implementation of a kill-switch in the energy storage unit, making it vulnerable to light. Should the bacteria of said unit be exposed to sunlight, they would die, and since it’s counterpart in the solar cell unit would be dependent on the continued coexistence of the two units, the entire GMO system would be purged. With Mr. Christiansen’s help we designed the container for Cell 2 of the same material as Cell 1, albeit with an added compound. The container for Cell 2 would be covered with Carbon Black, which has the ability to absorb sunlight, thus leaving the compartment itself in darkness.
The process of constructing our device would be through an extensive use of Injection Moulding, which is considered pricey equipment. Next, one must purchase the required material, which at above 1 ton would cost around 4-5.5 USD per kg. As such it’s an expensive material compared to others, but it’s longevity and durability means one would not be required to replace the devices for a long time. Lastly, we discussed the reusability of Polycarbonate, which Mr. Christiansen assured us was of no concern, as the material could be reused and recycled with ease.

Meeting with Ann Zahle Andersen

During our iGEM experience we met with Business Developer Ann Zahle Andersen twice. Mrs. Andersen had arranged two workshops for us based on a business canvas. This helped us to understand our project in a larger perspective. She encouraged us to view our project as if it was supposed to be a startup business, and through this perspective we gained a better comprehension of society’s pull and pushes on a project like ours. In a time of crisis she discussed our project’s advantages and disadvantages from a business perspective. A perspective and talk that forced us as a team to get to the bottom of what we found important about our project. And to truly appreciate the advice we have been given throughout our human practice work, as if we were a business trying to understand the needs of a costumer.

Upcoming Meeting with Borgernes Hus

‘Borgernes Hus’ is a new initiative offered by the city’s central library. The name translates to ‘House of the Citizen’s’. The house aims to offer guidance and advice to projects such as our own. It is meant to aid Odense in its journey towards the status of a modern, danish city. Unfortunately, the building remains under construction until after our trip to Boston, meaning that they have been busy finishing said construction while our project was underway. It is for this reason, that we along with director Jens Winther Bang Petersen decided that a future collaboration would be the most suitable solution.
It is our hope, that a collaboration with Borgernes Hus will be of assistance to future iGEM SDU-Denmark teams as well as students from Odense. In extension of this, we hope that such a collaboration will help them see the benefits in collaborating with local agents.

Education & Public Engagement

hello my friend, wanna learn something? the wiki isn't done yet.

lets goo

Prospects

The aim of our prospect section is to expand on the vision of the PowerLeaf; a vision we would love to see realised. An overview of the project, has been created, in the hope that it will benefit future iGEM teams. Additionally, it is aimed to assist iGEM teams-to-be, should they wish to take the PowerLeaf to the next level.

Perspectives

Building a Product for a Better Future

The purpose of the PowerLeaf is to provide a greener alternative to the currently available sources of energy. An important aspect of such an undertaking is to limit the use of depleting resources in the construction of the device itself. This is accomplished through the use of the most common resources available, namely recyclable plastics and bacteria. In turn, this will contribute to our dream of building a better future. A future where fear of reaching a critical shortage of natural resources has been eliminated. Another benefit of the PowerLeaf is the bacteria's ability to self-replicate, if provided with the essential nutrients.
As tools for genomic editing improves, the advancement of biological devices will conceivably become even more complex and independent. They will do so by introducing new metabolic pathways originated from other organisms using genetic engineering. This could potentially allow the PowerLeaf to become completely independent through its self-replication. Independency would occur, when the bacteria are modified to produce their own essential nutrients directly from unwanted pollution in the environment. This trait would lead to cleaner cities, along with providing a natural solution of sustainable energy.

Genetic Code Expansions for Biological Engineering

In an effort to advance the current technologies used in synthetic biology, research groups are working on genetic code expansion. We had an interesting talk from postdoc and former iGEM participant, Julius Fredens, about his work on genetic code expansion. Once a technology like this expands, it will completely revolutionise biological engineering, including that of the PowerLeaf. Genetic code expansion could be used for optimisation of the systems in the PowerLeaf, such as optimisation of nanowires, improvement of the light-sensing system, and making the breakdown of cellulose inducible.

To Future iGEM Teams

Hello future iGEM’er and congratulations on starting your iGEM journey! You are going to have an amazing time with plenty of wonderful experiences, new friendships, and an extensive amounts of obtained knowledge. In this section some ideas for improvement and further development of our project, the PowerLeaf, will be presented.

Further Development of Our Project

For those of you that are interested in our project and would like to improve upon it, this is the section you have been looking for. We have listed the systems and the related information needed for the fulfillment of the device we envisioned. Nonetheless, you should not feel restricted by these suggestions. You shall be more than welcome to contact any of us regarding questions about the project. You can find each of our team members contact informations in the Team section in the credits.

Investigated and Researched Systems

Dormancy System
Utilised by the energy storing unit, the dormancy system can reduce metabolism during times of the day with no solar energy available, e.g. at nighttime. We encountered a few challenges during the assembly and optimisation of the dormancy system. However, through modeling we obtained vital knowledge on how to regulate the system. If you are interested, you can read more about the work performed on the light-dependent dormancy system.

Carbon Fixation
We received the required parts from the Bielefeld 2014 iGEM team and began assembling the parts into one fully functional BioBrick. However, we encountered some trouble cloning these parts. You can give it a go anyways, or maybe even try to redo the carbon fixation by using a system from a different organism. Regrettably, we eventually had to let go of this system, so we could focus on other components of the PowerLeaf. If you are interested, you can read more about the work we did regarding the carbon fixation.

Cellulose Biosynthesis and Secretion
These parts were retrieved from the 2014 Imperial College iGEM team. Assembly of these long BioBricks emerged to be troublesome, which regularly occurs when cloning long sequences of DNA. Thus, this part could be the very thing to improve, as it is a rather central part of the system. If you are interested, you can read more about our work on the cellulose biosynthesis and secretion.

Cellulose Breakdown
Employed by the energy converting unit, this system degrades cellulose to glucose, from which electrons could be retrieved. After extensive work the system showed promising results as our bacteria were able to grow on cellobiose. If you are interested, you can read more about the work we did regarding the cellulases.

Extracellular Electron Transfer
Inspired by a previous study Tan Y, Adhikari RY, Malvankar NS, Ward JE, Woodard TL, Nevin KP, et al. Expressing the Geobacter metallireducens pilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity. mBio. 2017;8(1)., we set out to create the required BioBricks for the system. However, to successfully implement optimized nanowire in G. sulfurreducens, further work would have to be performed. If you are interested, you can find additional information about the work we did regarding the nanowires.

Subjects that Ought to be Implemented in the Device

ATP Production from Solar Energy
Harvest of solar energy comes to mind as one of the most essential systems needed for the PowerLeaf to actually work. We had to select parts of the PowerLeaf to work on, and at the end of the day, we decided to cut this subpart. Instead, we had a great Skype call early on in the process with the Australian Macquarie iGEM team, who has been working for several years with the implementation of the photosynthetic systems in E. coli.

Cellulose and the Cellulases forming an On/Off Switch
This is also a very crucial part of the PowerLeaf, since it would otherwise be generating an electrical current non-stop, even when not needed. Thereby overthrowing the potential for long term-storage of solar energy. We believe this can be solved either through precise gene circuit regulation or by physical compartmentalisation, but there might be even more elegant ways in which to handle this challenge.

Physical Engineering of the Hardware
It should be possible for the energy storing unit to convert CO₂ into cellulose, thereby producing O₂ making its chamber aerobic. For the energy converting unit to effectively transfer retrieved electrons to an anode, it requires anaerobic conditions. Thus the removal of O₂ from the device is an obstacle to overcome. It will require some out-of-the-box thinking to come up with a novel idea without having to require more energy than produced.

To make a workable prototype of the PowerLeaf, proper engineering of the hardware is necessary. This includes elements such as anodes, chambers, circulation of important nutrients, removal of wastes, and the use of appropriate materials. We worked out the optimal type of plastic for the system with the help of a local expert. You can read about our work regarding the plastic here.

Credits

“You'll stay with me?” - “Until the very end”

J.K. Rowling, Harry Potter and the Deathly Hallows

Just like in the movies, you only get to meet the brilliant minds behind the project in the closing credits. Some might leave the cinema without sitting through the credits, but we hope you will sit through ours, as you will get to know us on a more personal level. We probably have more in common than you think. And do not forget that behind every great team is an equally great amount of external attributions. The contributors have supported and inspired us, especially when things have been rough and deadlines closeby. When you finish this section, we kindly ask that you turn your attention to our various collaborations, all of which have been amazing experiences. They truly show of that wonderful iGEM spirit!
Finally, we do not want you to miss out on the ‘after-the-credits-clip’ that summarises the fun we had during this fantastic iGEM adventure. This is will be the moment you will get that long-awaited ‘thank you for listening, we hope you enjoyed our wiki and project’.

Team

Welcome to the team page! Here you will get to know us on a more personal level. Our team is made up by 12 students from 8 very different majors. As friends, we experienced the most amazing summer together, filled with various fun activities, both in- and outside the lab. We would like to mention a few. We had road trips, dinners, Game of Thrones nights, heck, we even celebrated Christmas in July! All of this was shared with our amazing supervisors, to whom we are truly grateful.

Ellen Gammelmark

Study: Biochemistry and Molecular Biology
E-mail: elgam15@student.sdu.dk
Why, hello there! My name is Ellen and I have spend most of my waking hours either in the lab with a pipette in hand, or just outside the lab with a computer on my lap. You know - learn iGEM, live iGEM, love iGEM!

Emil Bøgh Hansen

Study: Biology
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 left my boots in the closet, in order to put on a proper lab coat and suit up for iGEM. In addition to my time in the lab, I have also looked into how GMO can influence the environment and what we need to do to ensure a safe iGEM project.

Emil Søndergaard

Study: History
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.

Emil Vyff Jørgensen

Study: Physics
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.

Felix Boel Pedersen

Study: Biochemistry and Molecular Biology
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 whenever I miss the “sunlight”, I kindly join the others in the wet lab.

Frederik Bartholdy Flensmark Neergaard

Study: Biochemistry and Molecular Biology
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 have fun with my teammates and tell bad dad jokes. I also make crazy ideas come true - like celebrating Christmas in July.

Frederik Damsgaard Højsager

Study: Medicine
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 that I starred in our commercial? You can get autographs later.

Jonas Borregaard Eriksen

Study: Pharmacy
E-mail: jerik15@student.sdu.dk
Hey sup? I’m Jonas and used to like sports, partying, eating cake, hanging out with friends and other such things most people like to do. During iGEM these interests have changed… As I have been enslaved in the lab, I’ve come to realise that the only purpose of my life is to be in the lab.

Lene Vest Munk Thomsen

Study: Philosophy
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 here.

Malte Skovsager Andersen

Study: Biochemistry and Molecular Biology
E-mail: malta14@student.sdu.dk
Eyy, 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 heck 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, sadly caused me to pull out most of my hair.

Sarah Hyllekvist Jørgensen

Study: Biochemistry and Molecular Biology
E-mail: sajo415@student.sdu.dk
Despite my favorite occupation is digging into literature, my main attribution to our project has been to run around in the lab. Luckily, there is a clear link between wet- and dry-lab. Even though I am the smallest member of the SDU iGEM team, I have definitely risen to the occasion. iGEM has been an amazing period of my life!

Sofie Mozart Mortensen

Study: Biomedicine
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 and baked goodies. When I’m not in the kitchen busy making cakes for my teammates, you can find me in the lab with a pipette in my hand.

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;

The group focusing on fixation of CO₂, production of cellulose and light-dependent dormancy system 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 the optimisation of nanowires consisted of Felix Boel Pedersen, Frederik Bartholdy Flensmark Neergaard, Jonas Borregaard Eriksen and Malte Skovsager Andersen.
The group focusing on the implementation of the device in an urban environment as well as our outreach consisted of Emil Søndergaard, Frederik Damsgaard 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 Damsgaard Højsager.

To ensure a good team spirit and dynamic we formulated a cooperation agreement.
Nothing can be done alone, so please scroll further down, to read about all the people who contributed to making our project successful. We are so grateful for all the help and support we have been offered throughout our iGEM experience.

Collaboration

"Alone we can do so little; together we can do so much"

Helen Keller

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. We would like to thank all the people that made our 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 took advantage of our interdisciplinary team roster, and thus designed a wiki and ethics workshop to aid our fellow Danish teams.
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 meta-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 metaethics, 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 experience. To facilitate this exchange of knowledge on wiki development, we recruited our current supervisor Thøger Jensen Krogh, to facilitate presentations on how to design a good wiki page. Thøger was qualified for this task through his role as the designer of the SDU iGEM 2013 and 2014 team wikis, both of 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. This 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 an iGEM tradition.

Attending Meetups

Besides hosting our own meetup, we also attended several meetups during our iGEM experience. The first of which, was the 5th Annual Biobrick Workshop in March, hosted by the Technical University of Denmark, DTU-Denmark. This meetup not only gave us our first experience with Biobricks, but also worked as a foundation for friendships across different teams.
Our second meetup, the Nordic iGEM Conference was hosted by the University of Copenhagen, UCopenhagen, and took place in June. The main focus of this meetup was the traditional mini Jamboree. Participating in this meetup gave us useful feedback from both the judges as well as from our fellow iGEM teams. This helped us greatly to 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, and learned about all the other great iGEM projects. We also made new friends from all over Europe.

Further Collaboration

In regard to 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.
As our project revolves around global warming and green sustainable energy, we were thrilled to hear about the iGEM Goes Green initiative made by 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 scrutinised here. Due to our team being the most green dream team, TU-Dresden asked us to lead the iGEM Goes Green project in year 2018.
We sought expertise from the Macquarie Australia 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 their previous teams had experienced throughout their projects.
We were also able to help the Stony Brook iGEM team by facilitating communication with members of the SDU iGEM team from 2016.
During our project we received several questionnaires from fellow iGEM teams. We were delighted to help the teams by answering their questionnaires. These included from:

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 a whole-cell sensor for formaldehyde
University of Sydney - regarding the use and accessibility of insulin
Georgia State - regarding disabilities
Greece - regarding modular RNAi-based logic circuits

Attributions

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:

Assistant professor, Mikkel Girke Jørgensen, for his general support and advice on the project, the laboratory, the fundraising and our 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.

We would also like to thank:

Academic assistant, Tina Kronborg, for her guidance in the lab, as well as for providing us with laboratory equipment.
Medical Laboratory Technician, Simon Rose, for giving us a course in lab safety, risk assessment and general guidance in the lab.
Postdoc, Oona Sneoyenbos-West, for providing us with Geobacter Sulfurreducens PCA and the necessary knowledge on how to grow this particular bacterial strain. Furthermore, she helped us greatly with helpful discussions regarding the advancement of our project. We would also like to thank her for lending us her laboratory, for the cultivation of G. Sulfurreducens PCA.
Postdoc, Satoshi Kawaichi, for his assistance in measuring the electrical conductivity of our nanowires, as well as providing us with knowledge on the G. Sulfurreducens.
Business scout and PhD, Ann Zahle Andersen, for presenting us with the necessary tools for the development of innovative business ideas.
Stud.scient, Kristian Severin Rasmussen, for helping us use the oCelleScope for testing.
Stud.scient, Brian Baltzar, for hosting a workshop regarding the use of Adobe Illustrator, which has been a great help to the development of graphics for our wiki.
Ph.D student, Richard Xavier Etienne Valli, for helpful discussions in the lab.
Software Developer, Jonas Hartwig, for his help on some JQuery functionality on the wiki.
Stud.scient, Birka Jensen, for general advice and suggestion on how to build an iGEM wiki.
Stud.med, Ida Charlotte Hvam, for helpful discussions on the development of our wiki, helping with last minute figures to the wiki, as well as proofreading its content.
Stud.med, Maria Victoria Mikkelsen, for helpful guidance regarding the composition of experiment pages and proofreading.
Stud.med, Liza Gaardsted Hansen, for proofreading our wiki in the 11^th hour.
Ph.D student and current iGEM advisor for the Bielefeld team, Boas Pucker, for providing us with BioBricks created by former iGEM teams from Bielefeld.
Our iGEM HQ Representative, Traci Haddock-Angelli, for her general guidance and assistance in registering our Danish Ethics and Wiki Workshop to the official iGEM meetup page.
iGEM HQ Representative and Lab Technician, Abigail Sison, for her help in registering our Danish Ethics and Wiki Workshop to the official iGEM meetup page.
Stud.polyt, Oliver Klinggaard, for helpful discussions on the implementation of a pan-tilt system and for providing us with his project report on the subject.
DTU BioBuilders, for hosting their 5^th Annual Biobrick Workshop and for attending our Danish Ethics and Wiki Workshop.
The UNIK Copenhagen iGEM team, for hosting the Nordic Meetup and for attending our Danish Ethics and Wiki Workshop.
The TU-Delft iGEM team, for hosting the European Meetup.
Mimo Antabi, for adding our adverts to the University of Southern Denmark’s info screens preceding the Danish Science Festival.
Anders Boe, for putting an enormous amount of work into the postproduction of our commercial.
Allan Haurballe Madsen, for helping us with our appearance at the Danish Science Festival.
Outreach Coordinator and PhD, Lise Junker Nielsen, for for helping us with the Danish Science Festival as well as with the visit from the Academy for Talented Youth. We would also like to thank her for providing us with iPads for laboratory use.
The Danish Science Festival, for having us at their annual event. We would also like to thank all the visitors who attended our booth, especially the children who participated in our ‘Draw-a-Bacteria’-contest.
The high schools Odense Technical Gymnasium, Mulernes Legatskole and Academy for Talented Youth, for letting us present our project and to engage in rewarding discussions about synthetic biology.
The UNF Biotech Camp, for having us present our project to the attending students.
The elementary school, Odense Friskole, for letting us present our project for their 8^th grade students, thereby forcing us to contemplate how to convey a subject depending on the audience.
All former iGEM participants from SDU, for 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.
Project manager (Smart City Odense), Kristina Dienhart, for wonderful advice on how to involve Odense Municipality in our project. We want to thank her for our conversation on the implementation of The PowerLeaf in Odense. We would also like to thank her for leading us to the ongoing project of Bolbro’s city renewal.
Project Manager Bolbro City Renewal (DitBolbro), Rikke Flagreen Mortensen, for meeting with us to discuss how The PowerLeaf could be implemented in the neighbourhood of Bolbro. We would also like to thank her for providing us with a pitch and reading-materials on Odense’s green goals.
Director of audience - and Central Library Odense (Borgernes Hus), Jens Winther Bang Petersen, for our email correspondence and upcoming meeting with members of our iGEM team.
MATLAB user Nezar, for an easy implementation of the gillespie algorithm into MATLAB.
Flemming Christiansen, for his guidance and expertise in choices regarding materials and prototype.

Sponsors

Thanks to:

The Faculty of Science at University of Southern Denmark, for providing us with the fundamental funds required for our participation in the iGEM competition, and for providing us with laboratory benches and essential equipment.
The Faculty of Health Sciences at University of Southern Denmark, for their much needed funding of 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 duration of the competition.
PentaBase, for sponsoring us with 10,000 DKK worth of oligos and a further 10% discount.
New England Biolabs, for providing our team with a BioBrick® Assembly Kit, a Q5® High-Fidelity 2X Master Mix and a Quick-Load® Purple 2-Log DNA Ladder.
CO₂ Neutral Website, for attributing to green energy in our name, and thereby eliminating the carbon footprint our wiki makes.
Piktochart, for extending their student offer to our mail, and for providing us with easy access to great graphics.

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.

Administration USDoEEI. Method for Calculating Carbon Sequestration by Trees in Urban and Suburban Settings. 1988.
Alper T, Gillies NE. The relationship between growth and survival after irradiation of Escherichia coli strain B and two resistant mutants. Journal of general microbiology. 1960;22:113-28.
Andreas M. Kaplan MH. The Britney Spears universe: Social media and viral marketing at its best. Business Horizons. 2012.
Anna Prusak GR, Jacek Strojny. IS GMO “SUSTAINABLE”? A REVIEW OF THE ENVIRONMENTAL RISKS OF GM PLANTS IN COMPARISON WITH CONVENTIONAL AND ORGANIC CROPS. MODERN MANAGEMENT REVIEW. 2004. Arai TM, S. Cho, H. Y. Yukawa, H. Inui, M. Wong, S. L. Doi, R. Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proceedings of the National Academy of Sciences of the United States of America. 2007;104(5):1456-60.

Final Words

Thank you for your time! We hope you enjoyed our wiki and getting to know our 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 from our amazing iGEM adventure.
Take a look at these telling pictures from our iGEM experience.

Team:SDU-Denmark

PowerLeaf - A Bacterial Solar Battery

Abstract

About Our Green Wiki

iGEM Goes Green

Achievements

World Situation

Our Solution

Project Design

Dormancy System

Light-Dependent Dormancy System

Gillespie Algorithm

Stochastic Modelling of the RelE-RelB Dormancy System

Modelling Results of the RelE-RelB System

Light Sensing System

Carbon Fixation

Carbon Fixation

Carbon Fixation

Cellulose Biosynthesis

Cellulose Biosynthesis

Breakdown of Cellulose

Extracellular Electron Transfer

Demonstration and Results

Parts

Basic Parts

Notebook

Notebook

SOPs and Protocols

SOPs

Protocols

Safety

Bioethics

Integrated Practices

Education & Public Engagement

Perspectives

To Future iGEM Teams

Team

Collaboration

Attributions

Articles

Websites

Books

Final Words