With the PowerLeaf, iGEM SDU is introducing a novel solution for long-term storage of solar energy, thus 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 plant leaf, thereby 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 Escherichia 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 a great performance in the iGEM Goes Green initiative! Green just got greener.
Determination of Noise Levels
For these experiments, the promoters controlling an RFP reporter system were cloned into E. coli strain MG1655 on pSB1A2. The cultures were grown in LB medium containing 50 µg/mL ampicillin and examined by fluorescence microscopy, using an Olympus IX83 with a photometrics prime camera and 200 ms exposure time, when cultures were at OD600=0.3-0.5. For flow cytometry, both LB medium with 50 µg/mL ampicillin and M9 medium with 100 µg/mL ampicillin were used. Excitation of RFP was at 561 nm, and emission was measured around 580 nm.
The images obtained by fluorescence microscopy, which are given in Figure 1, revealed that the weak promoter, BBa_J23114, presented high variability in the expression of RFP between cells, indicating a high level of noise. Contrarily, RFP expression was more uniform in the bacterial cells containing the medium promoter Bba_J23106. Similarly, another medium strength promoter BBa_J23110, showed uniform level of RFP expression, although less consistent than the observed for BBa_J23106. Expectedly, the strong promoter, BBa_J23102 exhibited high RFP expression in cells and a low level of noise was observed.
Figure 1. Fluorescence microscopy of RFP under the regulation of four members of the Anderson promoter collection, (BBa_J23114, BBa_J23110, BBa_J23106 and BBa_J23102) on pSB1A2 in E. coli MG1655 at OD600=0.3-0.5. BBa_J23114 displayed a low and noisy expression of RFP, whereas both BBa_J23106 and BBa_J23110 showed a more uniform expression of medium intensity. The strongest promoter, BBa_J23102, exhibited a high level of consistent RFP expression
The noise levels observed by fluorescence microscopy led to the design of an experiment, by which the cell population could be quantitatively studied. The change in expression levels and noise during growth of cell populations were tested for the weak and strong constitutive promoters, for which flow cytometry was used to assess the expression of the RFP reporter system. First, the cell populations were studied in LB media with 50 µg/mL ampicillin, thereby maintaining similar conditions as for the fluorescence microscopy experiment. All cultures were prepared from overnight cultures, obtaining a starting OD600=0.005.
Figure 2. Flow cytometric fluorescence measurements in arbitrary units as a function of time. Left: Cultures were grown in LB medium. Right: Cultures were grown in M9 minimal medium supplemented with 0.2% glycerol. Fluorescence of RFP expressed by the weak and strong constitutive promoters were measured relative to the negative control WT E. coli MG1655. Samples where measured in technical replicates and standard error of mean is shown, but are in several cases indistinguishable from the graph.
The data obtained in this experiment revealed that the strong promoter displayed a higher basal level of RFP expression than the weak promoter. Moreover, both promoters exhibited similar decrease in fluorescence over time, as seen in Figure 2, indicating that a considerable portion of the cell populations for both promoters lost their ability to fluoresce during growth, with one population containing around 60% non-fluorescent bacteria, clearly divided from the fluorescent portion. As expected, the strong promoter displayed a high level of RFP expression, roughly 500-fold of the non-fluorescent MG1655 control at 1 hour. A 10-fold decrease in fluorescence was observed from 1 hour to 4 hours. The RFP expression mediated by the weak promoter exhibited a similar decrease in fluorescence over time, though with measured fluorescence levels 5 times lower than for the strong promoter.
Comparing these findings to the fluorescence microscopy data, it was hypothesised, that the increasing noise could be caused by bacterial plasmid loss. This could be ascribed to degradation of ampicillin in the medium, since the mechanism behind ampicillin resistance relies on the β-lactamase mediated cleavage of the antibiotic, thereby relieving the selective pressure. Consequently, the bacteria, which have lost their plasmid could be able to compete with the bacteria still containing their plasmid.
The fluorescence microscopy for the strong promoter did not exhibit a considerable level of noise, however, this does not reject the hypothesis. The increase in noise was revealed by flow cytometry, as measurements were carried out at several times throughout growth. However, the fluorescence microscopy measurements were only carried out once in the exponential phase, where the noise was not prevalent yet.
To substantiate the hypothesis, the experiment was performed anew using M9 minimal medium supplemented with 0.2 % glycerol and 100 µg/mL ampicillin, in an attempt to decrease the plasmid loss rate and optimise the selection.
The resulting data revealed, that the decrease in fluorescence levels had a lower rate for both promoters when the bacteria were cultured in M9 minimal medium, seen in the right graph in Figure 2, than in LB medium, seen in the left graph in Figure 2. Furthermore, when the bacteria were grown in M9 minimal medium with double amount of antibiotics compared to the LB medium, they displayed a higher level of fluorescence. Some of these observations could potentially be ascribed to the increased selection, that was strived after in this experiment. Moreover, the difference between the measured fluorescence levels for the two reporter systems was notably lower. This could indicate, that the reason behind the difference in expression levels between the weak and strong constitutive promoters, is due to the fact that bacteria cloned with the weak constitutive promoter are more prone to plasmid loss. However, it was observed that the bacteria expressing RFP under control of the weak promoter, did in fact fluoresce with a lower intensity.
To verify the hypothesis regarding the plasmid loss, the cultures were plated on 50 µg/mL ampicillin LA selection plates as well as LA plates without antibiotic, 12 hours after incubation start. For comparison, cultures containing either chloramphenicol and kanamycin resistance cassettes, were likewise plated out after similar treatment. The average plasmid loss measured as non-resistant CFU as a percentage of the total population is seen Figure 3.
Figure 3. The average plasmid loss measured as non-resistant CFU as a percentage counts for the ampicillin resistance of the weak and strong promoter, as well as for chloramphenicol and kanamycin resistance controls. Samples were obtained for spread-plating at 12 hours after incubation start.
From this test, it is evident that antibiotic resistance is reduced for the ampicillin-resistance carrying bacteria, compared to chloramphenicol and kanamycin resistant cultures.
This consolidates the hypothesis, that the bacteria transformed with the weak and strong promoter controlling RFP expression lose their plasmids throughout growth. However, it was further observed, that the plasmid loss in bacteria carrying the strong constitutive promoter was markedly higher than for bacteria carrying the weak constitutive promoter. This could be due to the fact that RFP in high concentrations is toxic for the cells, resulting in an increased pressure to lose the plasmid.
The photocontrol device genes were, on the basis of the above mentioned promoter experiments, placed under control of the strong promoter BBa_J23102. However, the observed plasmid loss should be taken into account, and compensated for, e.g. by continuous supply of antibiotic or substitution of the ampicillin resistance cassette.
Furthermore, as a result of the irregular expression levels controlled by the constitutive promoters, it was decided to place the relB gene under control of a tightly regulated uniform promoter, as the modelling had established the necessity of this.
To verify the correct assembly of the strong constitutive promoter, BBa_J23102, the part was sequenced using the iGEM primer VF2 and a self designed reverse primer , located in the ho1 gene of the photocontrol device. Through this, it was discovered that a plasmid fragment coinciding with the length of the promoter and the BioBrick prefix, had been removed from the plasmid, as illustrated on Figure 1.
Figure 1. A fragment containing the strong constitutive promoter and the BioBrick prefix with the EcoRI (E) and XbaI (X) restriction sites had been removed from the plasmid containing the photocontrol device.
The original sequencing data can be found here
In the light of this finding, it was investigated whether the Mnt-regulated or PenI-regulated promoter was suitable to control the expression of the photocontrol device.
During the cloning of GFP, BBa_I13504 under control of the LacI-regulated lambda pL hybrid promoter, BBa_R0011, it was observed that the part yielded three bands when digested with EcoRI and PstI, see Figure 1. One band was observed at 2000 bp, corresponding to the pSB1C3 backbone, one band at around 950 bp, correlating with the expected length for the part, and a third band with a length around 1200 bp.
Figure 1. Agarose gel showing the digestion of the composite part by EcoRI and PstI. Three bands where observed. The bands at 2000 bp and 950 bp corresponded to the backbone and inserted part respectively. The third band at 1200 bp was unexpected.
To ascertain the reason for the band with the unaccountable length, the part was sequenced using the iGEM primers VF2 and VR. The sequencing revealed a repeated sequence inserted between the LacI-regulated, lambda pL hybrid promoter and the GFP reporter, encoding a transposable element. The cloning was repeated, with a similar result. Given that a similar part , differing only in the RBS sequence, had been successfully assembled and tested before by the Kyoto iGEM team from 2010. It was hypothesised, that this particular assembly could cause the formation of a transposon hotspot.
Our project is all about ensuring a greener and more sustainable future for ourselves and the coming generations. This of course meant, that our wiki had to to follow this purpose as well.CO2 Neutral Website sponsored our wiki with a CO2 offset equal to the amount of CO2 produced by having the wiki running until October 31 2018. This does not mean the wiki is CO2 neutral in itself, but that the offset, equal to its pollution, is compensated. Compensating an offset could for example be global initiatives like replacing stoves in Africa with energy efficient stoves and building new, renewable energy sources. Also companies will be instructed in reducing their CO2 offset.
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
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 treesGlobal warming and lawnsCarbon 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.
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.
Welcome to our wiki! We are the iGEM team from the University of Southern Denmark and 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 as 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.
Bronze Medal Requirements
Register and Attend – Our team applied on the 30th of March 2017 and got accepted the 4th 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. 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 Escherichia coli to survive on cellobiose, which we validated by growth experiments. The data obtained in these experiments are presented in the Demonstration & 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 education and public engagement .
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, would also require tight regulation of the antitoxin RelB. This information was used to shape the entire approach of the light-dependent dormancy system.
A Global Challenge
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 some of 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 we 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.
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.
“Well, if it can be thought, it can be done, a problem can be overcome”
E.A. Bucchianeri, Brushstrokes of a Gadfly
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 (E. 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
Our device is composed of two units, an energy storing unit and an energy converting unit, each divided into systems, all of which have been given a symbol to help you navigate throughout the wiki.
Energy Storing Unit
Energy Converting Unit
Breakdown of Cellulose
Extracellular Electron Transfer
In the Project Design section, you will first be given a short introduction to the background, followed by the approach of that system, before you move on to the next system. Once you reach the next section of the wiki, Demonstration & Results, you will be guided through the performed experiments and the derived conclusions. To make things easier for you, we have continued to use the above symbols throughout our wiki.
Figure 1. 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.
Dormancy Optimises the Efficiency of the Bacterial Solar Battery
Photosynthetic bacteria draw energy from sunlight to drive the fixation of carbon, implying that the bacteria are not able to carry out carbon fixation in absence of light. However, the bacteria constantly metabolise and the carbon fixed during time of exposure to light, will be used as an energy source for the cells. To circumvent this, a photocontrol system created by the UT Austin iGEM 2004 team was used in combination with the RelE-RelB toxin-antitoxin system native to E. coli. In this way, a light-dependent dormancy system was implemented in E. coli.
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 2. 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 2, 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 modelling of the dormancy system, read the full results here.
The Gillespie algorithm is a way to calculate the evolution of stochastic functions; in this case cell concentrations. To use the algorithm, two things are required:
Reaction rates of the system at a given configuration.
A random number generator.
For each time step, two things are calculated using the random number generator:
The time before next reaction.
Which reaction occurs.
The time before next step is given by:
Where S is the sum of the reaction rates and r1 is a random number between 0 and 1. This gives the time, as if the system was one reaction with reaction rate S, using the random number to give an exponential distribution.
The reaction is chosen proportionally to each individual reaction rate using another random number, where reactions with high rates will occur most frequently.
As each reaction is carried out, the new time is the sum of the previous and added reaction times.
These calculations are carried out until the time reaches the wanted limit, or a specific number of reactions has occurred. It is necessary to have a limit on the number of reactions, as it elsewise is possible for the calculations to continue indefinitely.
Figure 2. 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.
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
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 1. The increase of free RelE molecules in E. coli cells, after activation of the artificial RelE production, shown logarithmically. 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 2. The logarithmic plots shows that 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 3. 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 4. 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
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 RelEtot=RelEfree+RelEbound, because of the short simulated timespan. Thus, in activation runs, where the number of free RelE molecules reaches a high level, the amount of RelEbound 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.
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 system is essential. The impact of different RelE-RelB expression levels was simulated by modelling. Using the results obtained by this 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-dependent dormancy system in E. coli has been optimised, and the final approach shaped. Ultimately, the light-dependent dormancy system, which is illustrated in Figure 3, 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 3. 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 vector.
Light Sensing System
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 1.
Figure 1. 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 2.
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.
Figure 3. 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 4, 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 4. 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.
Figure 5. 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 carbon fixation, read here.
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.
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 1. 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 1. 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 1. 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.
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 1. With a plasmid with a total length over 9000 bp, the cloning emerged difficult. After several unsuccessful attempts, a different approach was sought.
Figure 1. 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.
Figure 9. Phosphorylation of the β-1,4-linkages in cellobiose by the enzyme cellobiose phosphorylase, thereby producing D-glucose and α-D-glucose-1-phosphate.
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-glucanases, 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 in Figure 10.
Figure 10. BioBrick, containing the genes cenA, cex, hlyB, and hlyD controlled by PenI-regulated promoters.
Cellobiose to Glucose
The Edinburgh 2011 iGEM team team created a BioBrick with the bglX gene, which is endogenous to E. coli, in the endeavour to increase the efficiency of the degradation of cellobiose to glucose. However, it seems that the enzymatic activity of the periplasmic β-glucosidase has faded as a result of evolution, rendering E. coli incapable of surviving solely on cellobiose. Thus, even though E. coli can absorp cellobiose, it is not able to survive with this as it’s only carbon source.
As a solution to this, a part containing the cep94A gene was synthesised, with the intend to enable E. coli to survive solely on cellobiose. Thus, a construct containing cep94A controlled by a LacI-regulated promoter, was composed, as illustrated in Figure 11.
Figure 11.BioBrick comprising cep94A controlled by a LacI-regulated promoter. This part was cloned into both a high and low copy vector.
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, which are separated by a proton exchange membrane, as illustrated in Figure 12. Both the anode and the cathode in an MFC can use various forms of graphite as base material and in the anode chamber, microbes are utilised as catalysts to convert organic matter into metabolic products, protons, and electrons Khanal YLaSK. Microbial Fuel Cells, Capter 19. In: Khanal. EbYLaSK, editor. Bioenergy: Principles and Applications. First Edition ed: Published 2017 by John Wiley & Sons, Inc.; 2016.. This is carried out through metabolic pathways such as glycolysis, thereby generating ATP needed to maintain cellular life. This metabolic pathway also releases electrons, which are carried by NAD+ in its reduced form, NADH.
Figure 12. A microbial fuel cell utilising glucose as substrate. The glucose is consumed to protons, electrons, and CO2. The electrons are transferred to the anode while the protons diffuse over the proton exchange membrane. A gradient causes the electrons to flow through an external load to the cathode, which generates an electrical current.
Figure 13. Three different ways to transfer electrons from microorganisms to an anode. a) Transfer of electrons to the anode using a redox shuttle.Two different types of redox shuttles exit: One going through the membrane and another receiving electrons from membrane proteins. b) Transfer of electrons to the anode by direct contact. c) Electrons are carried from the inside the cell, directly to the anode through nanowires.
The redox shuttles use extracellular electron mediators, which hold the advantage of not being limited by the surface area of the anode, although it is restricted by the slow diffusion of the extracellular mediators. The direct contact electron transfer is, in contrast to the redox shuttles, strongly limited by the surface area of the anode, but the membrane bound cytochromes that are in direct contact with the anode, rapidly deliver the electrons. Bacterial nanowires are known to efficiently transfer electrons, as for 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. This is due to the ability of bacterial nanowires to form complex networks of interacting nanowires in biofilm, thereby efficiently transferring electrons from distant microbes to the anodeKhanal YLaSK. Microbial Fuel Cells, Capter 19. In: Khanal. EbYLaSK, editor. Bioenergy: Principles and Applications. First Edition ed: Published 2017 by John Wiley & Sons, Inc.; 2016..
Originally, it was intended to implement bacterial nanowires from G. sulfurreducens into E. coli. Through research, it was found that the Bielefeld iGEM team from 2013 had come to the conclusion, that this task was too comprehensive to undertake in the limited time of an iGEM project. However, a different approach was deviced, as postdoc Oona Snoeyenbos-West suggested us to use G. sulfurreducens as the model organism for our MFC.
It was then decided to work on optimisation of the G. sulfurreducens by increasing the electrical conductivity of its endogenous nanowires. To achieve this, synthesis of the pilA genes from G. metallireducens was ordered, which was used to create a BioBrick. Using the same approach for homologous recombination as in the dormancy system, a DNA fragment containing the chloramphenicol resistance cassette of the pSB1C3 backbone, was made for later selection of recombinant G. sulfurreducens. The PCR product was ligated with fragments retrieved from the 500 bp upstream and downstream regions of the chromosomal pilA genes of the G. sulfurreducens PCA strain, creating the fragment seen in Figure 15.
Figure 15. The linear DNA fragment intended for homologous recombination into G. sulfurreducens.
Determination of Noise Levels in Constitutive Promoter Family Members
Fluorescence microscopy and flow cytometry revealed that a strong constitutive promoter was suitable for the expression of the photocontrol device.
To assess which of the constitutive promoters would be suitable for a uniform expression of the photocontrol device, BBa_K519030, and the antitoxin RelB, BBa_K2449028, the expression levels and the noise of four different members of the Anderson promoter collection and their RFP reporter systems, were studied by fluorescence microscopy. These were, in increasing promoter strength, BBa_J23114, BBa_J23110, BBa_J23106, and BBa_J23102.
Additionally, the change in RFP expression levels and noise during growth were tested for the promoters with the highest and lowest relative promoter strength by flow cytometry and qualitative analysis by fluorescence microscopy. Combining these two techniques, the expression and noise levels for the promoters were determined as follows:
The weak promoter, BBa_J23114, exhibited a relatively low expression of RFP, indicating low gene expression and an increasing high level of noise throughout growth.
Both medium strength promoters, BBa_J23110 and BBa_J23106, displayed a moderate level of both noise and protein expression of the RFP reporter.
The strong promoter, BBa_J23102, exhibited a comparatively high expression of the reporter RFP and an increasing high level of noise throughout growth.
For further information about the experiments and a proposed cause for the increasing noise level, read here. As the strong constitutive promoter exhibited the most uniform expression, this was chosen to regulate the expression of the photocontrol device genes. With the modelling results in mind, it was decided that the relB gene should be regulated by a tightly controllable uniform promoter, thereby ruling out the constitutive promoter family members as a possibility.
Expression Level of the Mnt- and Penl-Regulated Promoters
The PenI-regulated promoter was chosen to control the expression of the photocontrol device, as it mediated a stronger expression than the Mnt-regulated promoter.
The cloning of the strong constitutive promoter, BBa_J23102, and the photocontrol device, BBa_K519030, emerged problematic. For further information about these difficulties, read here.
Consequently, the applicability of two different promoters was studied. These were the PenI-regulated, BBa_R0074, and the Mnt-regulated promoters, BBa_R0073, whose repressors are not found in E. coli, making the gene expression constitutive in this organism.
The relative expression and noise levels were quantitatively assessed using fluorescence microscopy of a YFP reporter system expressed on pSB1C3 in MG1655 at OD600=0.3-0.5. For this purpose an Olympus IX83 with a photometrics prime camera was used with exposure time for YFP at 200 ms.
Figure 16. Fluorescence microscopy of YFP under the control of PenI-regulated and Mnt-regulated promoters on pSB1C3 in E. coli MG1655 at OD600=0.3-0.5.
From the data obtained, it was evident that the PenI-regulated promoter mediated a substantially higher level of YFP expression than the Mnt-regulated promoter, as seen in Figure 16. Furthermore, the PenI-regulated promoter displayed a notably lower level of noise. On the basis of these results, the PenI-regulated promoter was chosen to control the expression of the photocontrol device.
Leaky Expression by the OmpR-Regulated Promoter on Different Vectors
The leaky expression by the OmpR-regulated promoter is reduced when cloned into a low copy vector compared to a high copy vector.
Proper regulation of the OmpR-dependent promoter, BBa_R0082, is necessary for the implementation of a functional dormancy system, as the balance between RelE and RelB is imperative. To verify that the OmpR-regulated promoter is up to the task, a reporter system containing RFP under control of the OmpR-regulated promoter, BBa_M30011, was cloned into E. coli strain SØ928 ΔOmpR, lacking the OmpR transcription factor, on a high copy vector. By using a ΔOmpR strain, the background generated by stimulation of the intrinsic OmpR system is removed, and the strain functions as a negative control.
RFP expression was assessed by fluorescence microscopy using an Olympus IX83 with a photometrics prime camera, with exposure time for RFP at 200 ms.
Assessing the RFP expression by fluorescence microscopy, it was discovered that the OmpR-regulated promoter mediated gene expression even in the absence of its transcription factor, see Figure 17. This observation was confirmed by going through the literatureLevskaya 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..
Figure 17. Fluorescence microscopy of RFP controlled by the OmpR-regulated promoter on a high copy vector in E. coli strain SØ928 ΔOmpR.
On the basis of this finding, the relE gene controlled by the OmpR-regulated promoter required a low copy plasmid or insertion into the chromosome. Protein expression of RFP in pSB1C3 with a copy number of 100-300 plasmids per cell, and pSB3K3 with a copy number of 10-12 plasmids per cell, was studied by flow cytometry. As for the determination of noise levels in the weak, BBa_J23114, and strong BBa_J23102 constitutive promoters, , the experiment was carried out in both LB medium and M9 minimal medium, the latter supplemented with 0.2% glycerol. In the LB medium, selection was carried out by the addition of 30 µg/mL chloramphenicol, 30 µg/mL kanamycin, or 50 µg/mL ampicillin, depending on the resistance, and for M9 minimal medium, the concentrations used were 60 µg/mL chloramphenicol, 60 µg/mL kanamycin, and 100 µg/mL ampicillin. Excitation of RFP was at 561 nm, and emission was measured around 580 nm. Expression levels in both E. coli MG1655 and E. coli MG1655 ΔOmpR were studied to determine the baseline of the leaky expression not influenced by intrinsic pathways including the OmpR transcription factor.
Figure 18. Flow cytometric fluorescence measurements in arbitrary units as a function of time. Left: Cultures were grown in LB medium. Right: Cultures were grown in M9 minimal medium supplemented with 0.2% glycerol. Fluorescence of RFP expressed by the the OmpR-regulated promoter on the high copy vector, pSB1C3, and the low copy vector, pSB3K3, in MG1655 WT and ΔOmpR MG1655 strain. All fluorescence levels were measured relative to the negative control WT E. coli MG1655, and the weak and strong constitutive promoters are included as references. Standard error of mean is shown, but are in several cases indistinguishable from the graph.
Fluorescence levels in the two different media display similar behavior, as seen in Figure 18. The main difference observed, was that the decrease in fluorescence over time was faster in LB medium than in M9 minimal medium, in concordance with the observations made in previous experiments. On a general level, the data revealed, that MG1655 cloned with the POmpR-RFP reporter system on the high copy vector exhibited a fluorescence level, equivalent to that mediated by the strong constitutive promoter. On the low copy vector, the POmpR-RFP reporter system yielded a fluorescence level comparable to the gene expression mediated by the weak constitutive promoter. On the other hand, expression levels in the MG1655 ΔOmpR strain were markedly reduced compared to MG1655, indicating that pathways including the transcription factor OmpR interfere with RFP expression under these conditions. Again, the fluorescence levels observed for the POmpR-RFP reporter system on the low copy vector were distinctly lower than for the high copy vector.
All things considered, the OmpR-regulated promoter was found to exhibit leaky expression comparable to the expression levels mediated by the constitutive promoters. When cloned into a low copy vector, the leaky expression was reduced prominently. Thus, to obtain proper regulation of RelE expression by the OmpR-dependent promoter, a low copy vector is required.
Transposon Hotspot Formation in LacI-Regulated lambda pL Hybrid Promoter Reporter System
During cloning, formation of a transposon hotspot between the LacI-regulated lambda pL hybrid promoter and a reporter system was observed, making this promoter inapt for the dormancy system
To control the gene expression of RelB, the LacI-regulated lambda pL hybrid promoter, BBa_R0011, was chosen. Due to a putative formation of a transposon hotspot between the promoter sequence and the GFP reporter, which is described further here, another inducible promoter was chosen to regulate the expression of RelB.
Induction and Subsequent Inhibition of the pBAD Promoter
Expression by the pBAD promoter can be regulated tightly by induction and subsequent inhibition.
The pBAD promoter holds great potential to regulate the expression of the relB gene in our system, as it is capable of both an induction and repression. The HKUST-Rice iGEM team from 2015 found that the pBAD promoter exhibits an almost all-or-none behaviour upon induction with arabinose when located on a high copy vector, but allows for gradual induction when cloned into a low copy vector. Thus, it was evident that this promoter on a high copy vector would be inappropriate for the regulation of RelB expression. Based on these findings, a low copy vector was used to investigate the ability to inhibit gene expression subsequent to induction of pBAD.
RelB expression was simulated by fluorescence microscopy using a pBAD-YFP reporter system, BBa_I6058.
For this purpose, an Olympus IX83 with a photometrics prime camera was used with an exposure time for YFP at 200 ms. Transformed E. coli MG1655 cells were cultured in M9 minimal medium supplemented with 0.2% glycerol and 30 µg/mL chloramphenicol, to avoid catabolite repression from glucose residues present in LB medium. Two cultures were incubated, of which one was induced with 0.2 % arabinose from the beginning. At OD600=0.1, designated time 0, the cultures were split in two and 0.2 % glucose was added to one of each pair. Samples were obtained at time 0, before division of the cultures, and at 30 min, 60 min, and 120 min.
The resulting images revealed, that the inducer arabinose was required to stimulate expression of YFP, and that the addition of the repressor glucose to a uninduced culture had no effect. Furthermore, it was evident that addition of arabinose induced expression of YFP, and that subsequent addition of glucose terminated the pBAD regulated gene expression on a low copy vector, resulting in a reduced fluorescence level. 30 minutes after inhibition this reduction was already evident, and after 120 minutes the gene expression controlled by pBAD was even further decreased, as seen in Figure 19.
Figure 19. YFP fluorescence levels in E. coli MG1655 transformed with the pBAD-YFP reporter system on pSB3K3. Left: Cultures with the inducer arabinose added. Right: Cultures not induced with arabinose. Both cultures were split up at OD600=0.1, designated time 0, and the inhibitor glucose was added to one half of each culture. Images were obtained at 0, 30, 60, and 120 minutes.
This experiment made it clear, that gene expression controlled by the pBAD promoter is both inducible and repressible as required when cloned into the low copy vector pSB3K3. Consequently, the pBAD promoter was found to be suitable for controlling gene expression of the antitoxin RelB in the implemented dormancy system.
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.
As 12 strangers we met for the first time on the 22nd of February. We cooked and ate a lovely meal together, and hereby had our first team building experience.
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.
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.
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.
Through an iterative process, the list of project ideas was cut down. Ultimately, the PowerLeaf - A Bacterial Solar Battery was chosen as our project.
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!
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.
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.
We got the first look at promoter reporter systems in the fluorescence microscope.
The team started their collaboration with Odense Municipality. The main focus in this collaboration was to integrate our project into an urban setting.
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.
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.
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.
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.
The genes encoding RelE and RelB, which comprise a toxin-antitoxin system, were purified from E. coli.
We cracked the code of modelling and our modelling system stabilised. Furthermore, the secretion system was created.
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.
Our lab workers analysed the properties of the LacI-regulated, lambda pL hybrid promoter for the energy storing unit.
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.
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.
The abstract for the iGEM Jamboree was finished. In this week we also decided that we should enter the energy track.
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.
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.
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.
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.
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.
The final promoter for the RelB expression, pBAD, was chosen and cloned.
We ceased trying to perform the recombination in Geobacter after several difficulties.
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.
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.
With the wiki freeze around the corner, we worked day and night, caffeine concentrations in our blood running high. We shall make it!
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 5th 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.
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
P1 phage, using its site-specific recombinase for transduction of E. Coli
“Change is the law of life; and those who look only to the past or present are certain to miss the future”
John F. Kennedy
Welcome to our Human Practices! Now, when it comes to the particulars of our Human Practices, you will find that it has been separated into three main parts. This is all strictly for narrative purposes, as every single aspect of our project and Human Practices, are deeply intertwined through a shared philosophy: If you want change, look to the future!
1. A Philosopher’s Guide to the Future
To ensure an ethically sound iGEM product and experience, we have discussed the ethical considerations that ought to be taken into account. As luck would have it, one of our team members is a philosopher with an interest in bioethics. Thus a guidebook was created, a guide that amongst other things includes an overview of some of the bioethical arguments iGEM participants are likely to encounter, when discussing synthetic biology. You can find these considerations in our section on Bioethics.
2. An Implementation of the Future
We reached out to our local Municipality of Odense along with various experts, for their advice on the development and implementation of our device in an urban environment. You can read more about this in our section on Integrated Human Practice.
3. A Trip to the Future and Beyond!
Considering how our main philosophy was: If you want change, look to the future! It seemed prudent to bring our message on sustainability to the next generation. You can read more about our efforts in the section on Education and Public Engagement.
- A Philosopher’s Guide to the Future
“The facts of life... to make an alteration in the evolvement of an organic life system is fatal. A coding sequence cannot be revised once it's been established.”
Synthetic biology and the iGEM competition are aimed to help solve societal issues, issues such as agriculture, medical research, and environmental resource management, the last of which has been our motivation throughout our project. However, while synthetic biology offers many new exciting possibilities, several concerns have to be met when dealing with living organisms. Against, the excitement of the iGEM community, skeptics have pointed to the uncertainty and potentiality for unwanted consequences that might arise from working with synthetic biology. We as a team decided to give these concerns some serious thought! We have had several conversations on topics such as meta ethics, applied ethics, sustainability, GMO, and so on. Furthermore, we established an open and honest mode of discourse to use when engaging with other teams and the public. We held a workshop in bioethics in relation to our Danish Meetup. This workshop consisted of a historical insight into the history of GMO provided by our very own historian, as well as a hefty, kind-hearted debate, supervised by our own philosopher.
All of these considerations, debates, and results led our philosopher Lene to write a longer guidebook entailing an overview of the various bioethical arguments often made for and against the use of synthetic biology. The guidebook is mainly an insight into the most important ethical considerations made by our team, e.g. how they shaped our product, but it also offers a personal and clear overview of arguments and principles meant to help future teams to get a conversation on ethics started!
Make sure to give this guidebook a read, it is definitely worth it!
- An Implementation of the Future
“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. Nonetheless, we do agree that to create the future we all hope for, we must contribute to find a sustainable solution for a greener future. Before we can tackle the task of providing a sustainable future for the entire world, we must first look to our own local environment. 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. Hopefully, this approach will help future iGEM teams find a connection between global issues and local ones. This approach has helped us elucidate specific issues and find sustainable solutions, which can be implemented into our society with the help and endorsement of local agents.
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.
“We face a series of challenges that we have to recognise, in the chase of the 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 dependent 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 that solves global issues, while contributing to local city growth”
The core philosophy of our Integrated Human Practices has been to incorporate local experts in the development of our project. We wanted to examine how results produced in the laboratory, could be used to shape a product that corresponds with the green values of Odense.
We sought the advice of experts in other fields, e.g. expert in plastics to design the best possible exterior of our device. Furthermore, we met with business developer Ann Zahle Andersen to investigate the core value of our product from a business perspective. We believe that Human Practices have played an essential role in our iGEM project. Everything from the design of our prototype to ethical considerations have been influenced by the people we engaged with.
Interviewing Smart City Odense
For the possible implementation of the PowerLeaf in the local environment of Odense, we decided to reach out to Kristina Dienhart, project manager of Smart City Odense. Smart City Odense is a project within Odense Municipality, that seeks to combine urban planning with new technologies and open-data toward creating a smarter, more sustainable city.
This made us aware of necessities essential to Odense and its citizens. She gave us feedback that we integrated into numerous areas of our overall project.
Changeability - From Mrs. Dienhart’s point of view, one of the most advantageous attributes of our device is the potential for changeability in the size and shape of the design. We had yet to consider the PowerLeaf as a device not limited by physical dimensions. This has been the most significant element we took with us from the interview. Changeability is a necessity to a city planner, as various laws and aesthetic considerations need to be taken into account, when altering or creating an urban environment.
Accessibility - She also discussed accessibility with us. The citizen will not use our device unless it is easily accessible. This means that the overall design of the PowerLeaf, regardless of its aesthetics, always needs to be designed with a user in mind. Reflecting on the advice of Mrs. Dienhart, we decided to reevaluate the means of implementation of the PowerLeaf to ensure that the need for accessibility and user-comfort is met.
Essentiality - She supported our notion if the needs for accessibility and changeability are met, the PowerLeaf could help ensure that citizens of Odense use and remain 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.
Mrs. Dienhart introduced us to several considerations that shaped large parts of our project. We do not know the needs of every urban area in Odense and consequently, we have aimed to create a device that is changeable to a city in movement such as Odense.
Furthermore, this interview was also a source of inspiration for our ethical and safety thoughts. While we ought to strive for a sustainable tomorrow, we do not necessarily have to provide an exhaustive description of what the future should look like.
Interviewing the City Renewal Project My Bolbro
Rikke Falgreen Mortensen is the manager of the Bolbro’s city renewal project called Mit Bolbro i.e. My Bolbro. We arranged a meeting with her with the intent of further investigating how the PowerLeaf could and should be integrated in an urban area of Odense, in this case the neighbourhood of Bolbro.
Bolbro is an old neighbourhood in Odense historically known to be the home of the working class. 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 approximately 1.6 million US dollars to renew its city space and to 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 also argued that a changeable design would be the optimal solution to fit the challenges one faces in creating a vibrant, green city ambience. Such a task depends on different preferences, laws and needs. A technology needs to be both flexible and accessible to successfully contribute to the process of creating an engaging city environment. She showed great interest in our device and even offered to implement it in the parks of Bolbro, should the product become a reality.
We had a discussion with Mrs. Mortensen about the creation of a prototype based on the wishes of Bolbro’s local citizens. Following this conversation, she provided us with a pitch that aimed to help us develop this prototype.
“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. Your solution should be able to contribute to help citizens recharge their phones, e.g. a solution could be implanting the PowerLeaf into a interactive furniture, but where the demand an aesthetic pleasing 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. 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 playground is to be developed especially for the young audience, which is a major consumer of power for phones. The playground must be a place where youngsters hang out after school, while maintaining its status as a green space.”
The making of the furniture as a prototype called for a revisit of our safety concerns. We now knew that children would be climbing and playing on the furniture, making it crucial that the material of the PowerLeaf will not break. This is a concern we discussed with Flemming Christiansen, which you can read all about next.
Finding the Proper Material
Criteria to the Prototype
The system itself will consist of two different compartments, an outer and an inner chamber. The first will be facing the sun, while the other will be facing the building or furniture. Since one culture of the bacteria depends on solar energy to produce its product, the outer compartment must allow for sunlight to pass. It should here be noted that the prototype is purely hypothetical, as the membrane, between the two compartments, should exclusively be permeable to cellulose. For that reason, we wanted to find a material, that fulfilled our established criteria, so that we could illustrate the technology.
The device itself will be made entirely from plastic, a material that is thought to be undesirable due to the difficulties in its disposal. This is due to plastic being of a xenobiotic nature, making it generally recalcitrant to microbial degradation Fewson CA. Biodegradation of xenobiotic and other persistent compounds: the causes of recalcitrance. Cell. 1988.. Following these concepts, we can identify the following set of criteria for the desired material:
Solar exposure. The material covering the solar cell, must allow sunlight to pass through to reach the bacteria.
UV resistance.As the material will be exposed to the sun, it must be resistant to the UV radiation.
Bacterial growth The material must neither be growth inhibitory, nor toxic to the bacteria.
Easy to mold. The outside of the device could be molded depending on the circumstances, as the device only relies on the bacterial technology.
Durability. The device will be located outside, meaning that the material must be able to withstand hard conditions and heavy weight.
Temperature. The material must allow for an appropriate constant temperature for the bacteria, despite the variations in sun exposure.
Longevity. We would like for the material to have as long a durability as possible, since replacing the device could prove cumbersome. We are aiming for at least twenty years of durability.
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 green 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. A meeting was quickly arranged for the purpose of confirming our 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 Polycarbonate. Unfortunately, the material cannot fulfil the criteria on its own. He therefore suggested that we take a few liberties with it. In order to prevent UV degradation to the exposed parts, we will be adding certain additives to the surface. This increases the UV resistance of the device, without hindering the sunlight from reaching the bacteria.
During our conversations 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 environment will be exposed to the GMO inside. The solution we came up with was the possible implementation of a kill-switch in the inner compartment, making it vulnerable to sunlight. Should the bacteria of said unit be exposed to sunlight, they would perish. As the outer compartment would be dependent on the continued coexistence of the two units, the entire GMO system would be purged in case of a breach . To implement this feature, the inner chamber 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. The material is expensive at 4-5.5 USD per kg at orders above 1 metric ton, according to Mr. Christiansen, but its longevity and durability means it would not need to be replaced for a long time. Lastly, we discussed the reusability of Polycarbonate, which he assured us was of no concern, as the material could be reused and recycled with ease.
Workshop with Business Developer Ann Zahle Andersen
For the purpose of getting a business perspective on our project, we met with Business Developer Ann Zahle Andersen. She arranged two workshops for us based on a business model canvas. She encouraged us to view our project, as if we meant to make startup business. These workshops gave us a better comprehension of society’s pull and pushes on a project like ours. This forced us as a team to get to the bottom of what we found important about our project.
Upcoming Meeting with Borgernes Hus
Borgernes Hus i.e. House of the Citizens is a new initiative offered by the City Central Library. The initiative aims to offer guidance and advice to projects such as ours. It is meant to aid Odense in its journey towards the status of becoming a modern Danish city. Unfortunately, the building remains under construction until after our trip to Boston, meaning that they have been busy with the construction while our project was underway. It is for this reason that we, along with director Jens Winther Bang Petersen, agreed 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 teams from SDU as well as other students from Odense.
Education & Public Engagement
- A Trip to the Future and Beyond!
If you want change, look to the future! Such was the wording of our core philosophy. A philosophy that was carried out, by reaching out to the people of our society to ensure the engagement of the next generation, within the world of synthetic biology.
Ever since World War II, the West has seen an expansion and intensification of anti-scientific sentiment, which today primarily concern Genetically Modified Organisms (GMO). We will for that reason explore GMO’s role in history, to see if a historical perspective will allow us reach a new understanding of these sentiments. You can read all about it here.
A Historical Perspective on GMO
From Food Concerns to Sustainable Energy
When talking about the history of GMO, we have the rare privilege of choice, as depending on how you define GMO, One could potentially choose any historical period as their starting point. For instance, we could be examining the breeding of wolves to dogs, or simple agriculture, where the bad seeds are destroyed in favour of higher quality cropsRangel G. From Corgis to Corn: A Brief Look at the Long History of GMO Technology. Genetically Modified Organisms and Our Food. August 2015.
For the purpose of narrative, we will be starting our examination with the dawn of the 20th century. A time in which stale and rotten food lead to health concerns. Through several years, the public was continuously made aware of health problems regarding food in the United States. This culminated in the 1906 statute:, which allowed the inspection and ban of products JP S. The 1906 Food and Drugs Act and Its Enforcement. FDA History - Part I US Food and Drug Administration. 2013.. During the time leading up to this act, the public grew to appreciate items labeled as pure. A trend we can observe in most journalistic material from the time period O’Keefe TJ. The Alliance herald. : (Alliance, Box Butte County, Neb.) 1902-1922. T.J. O'Keefe; 1902.
This need for pure food naturally originated partly from several years of unsatisfactory food and health concerns JP S. The 1906 Food and Drugs Act and Its Enforcement. FDA History - Part I US Food and Drug Administration. 2013., and partly from a political fiction: The Jungle, by Upton Sinclair Sinclair U. The Jungle. New York: Grosset & Dunlap,; 1906 1906..
The readers became aware of unsanitary practices in the American food industry. Sinclair was considered a whistleblower, having exposed the practices of the food industry. After the act of 1906, we can observe a rise in concerns over the purity of food, which in turn lead to a focus on maintaining a certain standard in foods. Over time, this concern became the driving force behind the development of pesticides, and to a certain extent, GMO. With the introduction of these solutions to food purity, a new and opposite response could quickly be observed in the public. With pesticides and GMO, the public quickly grew concerned that food would be unnatural, and thus we can observe what is known as a reverse halo effect Konnikova M. The Psychology of Distrusting G.M.O.s. THE NEW YORKER. 2013.. A reverse halo effect is defined by the unconscious creation of a negative assumption based on a positive evaluation. In this case, the positive evaluation, would be the ensured purity and health benefits of GMO foods, where the negative assumption would be the concerns for unnaturalness.
So we detect a tendency in the public to follow a reverse halo effect, which is most often associated with GMO foods. The problem we face today, is the continuation of this reverse halo effect, where the public would receive any GMO device negatively, simply by association to the word GMO. So how do we change this dynamic between GMO and the public?
The conclusion we reached was that in order to change a tendency in public opinion, it was important to educate the coming generations on the possibilities of GMO. Another important aspect seemed to be a general perception of GMO as an unnatural element that would harm both humans and nature alike. As such, we wanted to illustrate how GMO could be used, not to harm nature, but to help lead it towards a more sustainable future. So, we set out to teach children of all ages about GMO in general, as well as about our own PowerLeaf, to show them that this concept, which is considered to be unnatural, could actually be used to help nature.
At the Danish Science Festival we hosted a workshop for kindergarteners, during which we taught them about synthetic biology, sustainability, the history of GMO, and bioethics. The children would in turn teach us as well, as they showed us the endless possibilities for bacteria designs, through the “Draw-a-Bacteria”-contest. This inspired us to reevaluate our initial idea.
School Project Interview with 6th Graders
Following the Danish Science Festival, we were contacted by two enthusiastic 6th graders, Bastian and Magnus. The two boys wanted to learn more about iGEM and GMO, which they intended to write about in a school project. They were curious to what range GMO could be used, and how we utilised it in our project, the PowerLeaf.
UNF Summer Camp
The UNF Summer Camp is an opportunity for high school students to show extra dedication towards science. We talked to some of the brightest young minds imaginable, all of whom aim to work in different fields of science in the future. At the summer camp, we held a presentation about our project, the iGEM competition, as well as how to handle and work with genes. We taught them how to assemble BioBricks and provided them with BioBricks for DNA assembly experiments, creating a ‘hands-on’ experience for these enthusiastic teenagers.
One of the high school students suggested that the Powerleaf should be able to rotate according to the sun, to ensure maximum exposure and outcome. We took this brilliant advice into consideration and contacted Robot Systems Engineer student, Oliver Klinggaard, who helped us with the potential implementation of a pan/tilt system. He provided us with his recent project report on the subject, as well as a description of the adjustments required for the implementation in our system, which you can find here.
Two students from the UNF Summer Camp thought the PowerLeaf was an interesting approach to sustainable energy, and they wanted to hear even more! So, they contacted us in late October, as they were interested to work on a project about green technology.
The Academy for Talented Youth
We hosted a workshop for the Academy for Talented Youth, an association for some of the most talented high school students in Denmark. During the workshop we invited the students into our laboratories, where they conducted a miniprep and a gel electrophoresis on bacteria containing our BioBricks. Additionally, we held a presentation and discussion about our project, with the dedicated students. We strongly believe in mutual communication and made sure to compile feedback, all of which was positive!
Presentations for the Local Schools
The local high schools, Mulernes Legatskole and Odense Tekniske Gymnasium, invited us to present our project, in addition to starting discussions with the students about GMO. An 8th grade class from the local public school, Odense Friskole, were invited to see our laboratory workspace. It was a challenge to successfully convey our project and the concept of synthetic biology in a way that would be easily understandable by 8th graders, who have only recently been introduced to science. A challenge that we accepted and solved, by relaying the fundamentals in synthetic biology, e.g. the basics of a cell, DNA, and GMO.
From all of these presentations and interactions with younger individuals, we had a strong intuition that it had made an influence on their awareness of synthetic biology. This intuition was supported by the positive feedback provided by teachers and students. An awareness of how new scientific technologies can be a feasible solution to a possible energy crisis. Technologies such as synthetic biology, with endless capabilities to achieve efficacy, since no one knows what tomorrow brings. For more information about this read To Future iGEM Teams
Final Presentation at SDU-Denmark
The day before we travelled to Boston, we booked one of the big auditoriums at the University of Southern Denmark, for the final rehearsal of our jamboree presentation. We made sure to take note of all the feedback and tips we received, while also implementing these into our final presentation. This event was promoted on all the information screens at our university in order to attract a broad audience and increase the interest for iGEM. Thus, making it possible to reach a substantial amount of future applications for the SDU-iGEM team and ensure that the iGEM spirit will continue to prosper in the future!
Social media is an easy way to impact a high number of people, so a strategy was concocted with the intention of reaching as many people as possible with our outreach.
Our strategy yielded marvellous results, amongst which was a video on our project, that reached viewers equal to 16% of our hometown’s population, along with becoming the second most seen bulletin of the year from University of Southern Denmark. They have also asked us to film our experiences at the Jamboree, which will feature on the homepage of the student’ initiative BetonTV.
Several articles were written about our project in local newspapers, one was even featured in the saturday special. You can read all about our social media strategy and results here. The commercial can be seen right here:
Social Media Report
"I hate social media. I have Twitter, just so I can tell people what to buy.”
The design of our logo consisting of a light font and a picture of a leaf combined with an electrical plug, was determined in the start of April. We sought to make a simple logo that showed the essence of our project, The PowerLeaf, not only in name but in brand as well.
During spring we narrowed down the relevant hashtags of our Twitter and Instagram to #science, #igem, #sdu, #gmo, and #forsksdu. These hashtags were used at relevant occasions and generally helped expanding our reach on social media. A few times we even used a couple of silly hashtags like #adventuretime and #lifechoices when we found it appropriate.
A complete relaunch of our social media platforms was made in the start of April. One of the changes we made was the setup of the Facebook page and Twitter account, that we changed to resemble an enterprise.
Looking at Figure 1 we see the number of followers on our Facebook page throughout the year. There is a sharp increase around the start of April, this correlate nicely with the relaunch of our social media. Since we started using the Facebook page on March 1st, we have seen an increase of followers on 44%.
Figure 2 shows the number of unique interactions with our Facebook posts each day. Some posts gained around 200 interactions per day, while the highest amount of interactions per day was seen at end of April. This high amount of interactions correlates with us being at the Danish Science Festival, where we inoculated bacteria from the fingers of the attendants on agar plates. The photo gallery of these plates was widely shared on our Facebook page, and it probably was the reason for the rise in amounts of interactions.
During the summer, we realised that an increasing fraction of our followers on Facebook were non-Danish speakers. Therefore, we set out to analyse the distribution of first languages among our followers seen in Figure 3, which showed that one in three of our followers were not speaking Danish as their first language. This data led to us switching the language used in our Facebook posts from Danish to English.
Figure 1. Number of followers on our Facebook page throughout the year.
Figure 2. Unique interactions per day on our Facebook page.
Figure 3. Distribution of first language among our followers
On the 8th of September a commercial about our project aired on the website and Facebook page of the University of Southern Denmark. We made this commercial in collaboration with the communications department of the University of Southern Denmark, specifically a producer named Anders Boe. It was seen 27,526 times, which is equivalent to 16% of our hometowns population. The click-through rate was around 10%, which is much greater than the average rate of videos on their Facebook page. The commercial led to random people, including doctors on the hospital of Odense, asking team members about the project and about GMO in general. With all this in mind it seems fair to state that the commercial was a smash hit of our human outreach and our engagement in the social media. In combination with our easily recognisable logo and our human outreach initiatives, we have been using our social media as a platform to show interest in synthetic biology and for sharing our work.
After seeing the commercial a local newspaper reached out to us to bring an interview in their Saturday special Newspaper article from Fyens.dk (Danish). In collaboration with the student media RUST and Beton TV we have been featured in their magazine and a video of our attendance in Boston will be shown on their Facebook page briefly after our return. This is done to ensure an awareness of the iGEM competition among the students on the University of Southern Denmark. We hope this will inspire a lot of students to apply for the iGEM team next year, since it is a hallmark of the SDU-Denmark team to be interdisciplinary.
The effort put into our social media strategy and our goal of following it has paid off. Social media has shaped our outreach and made it possible for us to talk about iGEM and our project to people we did not know. Several times our outreach has led us to public discussion of GMO and solar panels due to persons contacting us, wanting to know more.
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.
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
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.
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.
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.
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.
“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’.
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.
Study: Biochemistry and Molecular Biology
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
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.
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
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
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
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
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
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
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
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
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
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.
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.
"Alone we can do so little; together we can do so much"
The American author Helen Keller had it right! As an iGEM team, you can reach many goals, but as an entire community, we can aspire to achieve so much more. 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.
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.
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
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 11th 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 5th 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 8th 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.
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.
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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.