Team:TU Eindhoven/Collaborations
Collaborations
Collaborations
Throughout the year we have talked to a lot of other iGEM teams. This has resulted in multiple collaborations. The collaborations ranged from participating in others collaboration and discussing each other’s projects, to organizing our own, very successful, BeNeLux Mini Jamboree.
BeNeLux Mini Jamboree
On Friday October 25, the TU Eindhoven iGEM team will organize the BeNeLux Mini Jamboree. 6 Dutch teams will attend this event as a final rehearsal before the real deal in Boston a week later. Unfortunately the teams from KU Leuven and Groningen are unable to attend. The attending teams are:
During this meet-up at the Eindhoven University of Technology, the teams will present their project and show their poster as a final practice session before leaving for Boston. The presentations are performed in front of four judges who all have, in some way, experience with the iGEM competition. This year the jury will consist of: Niek Savelkoel (European iGEM Ambassador), Pieter van Boheemen (Rathenau Institute), Lilian van Hove (Rathenau Institute), and Korienke Smit (RIVM). They will provide the teams with detailed feedback to finalize their presentation and posters.
Next to the presentations of the iGEM teams, a guest speaker is invited from the Queen Astrid Military Hospital in Brussels, Dr. Jean-Paul Pirnay. He will give a lecture about phage therapy, a subject our team discusses for Human Practices.
At the end, the winner of the BeNeLux Mini Jamboree will receive a prize. And the day will be concluded with dinner, drinks, and discussion at the Hubble café on the TU/e campus.
An impression of last year's Mini Jamboree.
For a first impression of the BeNeLux Mini Jamboree of 2019, take a look at our program booklet.
After the iGEM competition we will give an update about the meet-up and the winning team.
Other collaborations
iGEM Stockholm: Phages collaboration and troubleshooting
Like our team, iGEM Stockholm is also fighting antimicrobial resistance. They want to achieve this by improving the delivery system of bacteriophages in phage therapy by using a harmless carrier bacteria. This was achieved by taking over the control of the molecular switch that puts bacteriophages in their active lytic state. This would combine well with our detection method, and will add the possibility to use non lytic phages in our system. In our collaboration we described how our systems would work together in the future.
Furthermore, Stockholm also had some cloning troubles at first. However, they successfully ligated multiple DNA fragments by using the NEB Hi-Fi DNA assembly master mix. We still had some trouble with the ligation of our DNA fragments with the NEB Hi-Fi DNA assembly master mix. Together we discussed our protocols and troubleshoot the cause of the failed experiments.
iGEM Stockholm: Phages collaboration
Working towards a common need
According to experts in Global Health and recent reports from the World Health Organization (WHO), antimicrobial resistance (AMR) presents a worldwide threat to our health. Data show that AMR continues to grow, which would mean that in 2050, 10 million people across Europe and the US alone will die because of AMR [1]. Hence, the need for a quick detection system and effective treatment becomes crucial.
Diagnosis, right on the spot – iGEM TU Eindhoven
Most infections go undiagnosed or miss-diagnosed, the most common form of diagnosis is the treatment itself. In other words, in many countries, broad-spectrum antibiotics are given to the patient during their first visit to the clinic, because a proper diagnosis can take days and economic resources. The miss-use of antibiotics contributes enormously to the increase of AMR. The importance of a fast diagnosis system that can be easily used by physicians right on the spot is therefore highlighted. Our team, iGEM TU Eindhoven, talked to physicians about the introduction of a fast diagnosis system. We confirmed the usefulness of such a system at our Human Practices page.
Bacteria are present in very low concentrations and therefore very difficult to detect without having to culture them, which takes several days. Our team uses lytic phages to indirectly detect which bacteria is present. The temperate phages from iGEM Stockholm can also be used. As long as they have been genetically engineered to deprive them of the repressor protein – this is, deleting the protein that keeps phages on their lysogenic cycle, making them obligated lytic.
Based on the suspicion on the origin of the infection by the general practitioner, specific lytic phages are selected and added to the device in separate compartments. Thereafter the sample of the patient is added from which we can detect whether the suspected bacteria are present. For example, if there is a urinary tract infection, there are five different bacteria that can cause this infection. The sample of the patient is then divided over five aliquots (Figure 1). To each aliquot, a specific lytic phage will be added. When the target bacteria of the phage are present, the phage amplifies itself, which creates an increase in phage DNA. The increase in phage DNA is measured by using one of the sensors of TU Eindhoven which sends out a light signal. The sample that lights up red indicates which phage has amplified, so indirectly the bacteria causing the infection is identified. At the same time, it is also confirmed which phage will kill the bacteria, so this diagnosis system is perfect to combine with Phage Therapy. However, when the phages do not find the specific bacteria in the sample, there is no amplification of phages, and therefore no red light signal.
Figure 1: Schematic representation of the detection device. The mechanism of one of our detection proteins is represented on the right.
Treating bacterial infections using Esther – iGEM Stockholm
Considering the swift decrease in the discovery of new antibiotics and the rather rapid increase in AMR, an alternative treatment to bacterial infections is required. Phage Therapy has been gaining more attention over the last years, as it utilizes the natural capacity of bacteriophages to kill harmful bacteria. It involves the administration of phages through inhalation, oral intake or directly into the bloodstream. However, once inside the body, phages encounter many barriers, such as the immune system, that can inactivate them; or the secretory system, which causes their accumulation in the liver and kidneys. [2][3]
The iGEM Stockholm team has developed a method to deliver phages directly to the site of the infection, by using a non-pathogenic bacterium as a vehicle, which will keep the temperate phage dormant until it reaches the site of infection. Once the bacteria sense the immune response at the infected site, it will switch the phage from its lysogenic (dormant) state to an active (lytic) state, bursting out of the carrier bacteria and infecting surrounding pathogens. For more information, please visit the wiki of iGEM Stockholm.
This method increases the overall efficiency of Phage Therapy, as it increases the concentration of active phages directly in the site of infection; avoiding barriers that phages would find otherwise. It also decreases the chances of phage accumulation in non-targeted organs, as they will remain encapsulated until the target has been reached.
Figure 2: General method of iGEM Stockholm.
Integration: from diagnosis to treatment
iGEM TU Eindhoven and iGEM Stockholm have united forces to work towards a common goal. The detection system designed by iGEM TU Eindhoven will allow us to identify the strain of the bacterial infection in a matter of hours. Not only that, but it will also allow performing a fast screen to identify the phage that will kill the pathogen. With Esther, the system by iGEM Stockholm, we will be able to deliver this exact phage to the site of infection, providing a reliable treatment to the patient without the need for antibiotics. To facilitate the combination of both systems and to ensure a fast action, a library of phages ready to be used in the detection system and in the delivery system would be developed.
We believe our systems will have an important role in the future market, as AMR becomes more persistent and antibiotics don’t work any longer. By joining forces, we are able to provide a solution from the very beginning to the very end, from diagnosis to treatment; providing a health service where bacterial infections are no longer a threat.
References
- O’Neill, J. Review on Antimicrobial Resistance. Antimicrobial Resistan(1) O’Neill, J. Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations, 2014. 2014, 4 (December).Ce: Tackling a Crisis for the Health A. 2014, 4 (December).
- Kakasis A, Panitsa G. Bacteriophage therapy as an alternative treatment for human infections. A comprehensive review. Int J Antimicrob Agents [Internet]. 2019;53(1):16–21. Available from: https://doi.org/10.1016/j.ijantimicag.2018.09.004
- Otero J, García-rodríguez A, Cano-sarabia M, Maspoch D, Marcos R, Cortés P. Biodistribution of Bacteriophages and Their Transcytosis During Oral Phage Therapy. 2019;10(April):1–12.
VIT_Vellore iGEM team: AMR collaboration
The VIT Vellore team from India Vellore is also working on the problem of AMR. They achieve this by engineering a bacteriophage. Their phage will only lyse the bacteria when the antibiotic resistance gene is present. For this collaboration we have exchanged information about both our project and concluded that our systems could benefit from each other. This because with their system we would be able to only detect bacteria which have resistance. Therefore, a report is written about how both our projects would perfectly fit together into one project.
VIT_Vellore iGEM team: AMR collaboration
AMR will become one of the biggest threats to global health. And in 2050, 10 million people across Europe and the US alone will die because of AMR [1]. To reduce the threat of AMR, iGEM VIT Vellore and iGEM TU Eindhoven will join forces by developing a point-of-care detection system to detect the presence of resistant bacteria.
One of the biggest problems of AMR development is the unspecific use of antibiotics. Antibiotics are used unspecific because the general detection time of bacteria takes more than 48 hours. In the meantime, broad-spectrum antibiotics are given to the patient as a precaution. The use of broad-spectrum antibiotics increases the chance of developing AMR. To decrease this unspecific administration of antibiotics, our team, the TU Eindhoven team, has developed a point of care detection system that can detect the presence of a certain bacteria within the time scale of 1 hour. This will help reduce the infection diagnosis time and improve the efficiency of the treatment.
The detection system works as follows: Bacterial cultures are obtained by taking a fluid sample from the patient. This sample is added to the device (Figure 1) and based on the suspicion on the origin of the infection by the general practitioner, specific lytic bacteriophages are selected and added to the device in separate compartments. If present, the lytic phages infect the bacteria, replicate themselves and eventually lyse the bacteria. Thereafter the phages are denatured by using a heat shock, that releases the phage DNA for detection. The increase in phage DNA is then measured using one of the dCas9 based sensors, that can bind to specific DNA sequences and display a light signal after binding. The specificity of the sensor is determined by altering the gRNA of the dCas9 protein.
Figure 1: Schematic representation of the detection device. The mechanism of one of our detection proteins is represented on the right.
However, no resistance is measured with the detection system of our team, that’s where iGEM VIT Vellore comes in. To detect the presence of resistant bacteria, the machinery of team VIT Vellore is utilized in tandem with the system of TU Eindhoven. The nature of ARMD’UP of detecting and lysing only resistant bacteria would result in luminescence occurring only in the samples where resistant bacteria are present. This is achieved by using an antisense detection mechanism (Figure 2). If present, the phage infects the bacteria and injects its DNA into it. The DNA is then incorporated into the bacterial genome. After transcription, the antisense mRNA complementarily attaches to the gene responsible for antibiotic resistance (eg. the β-lactamase mRNA responsible for producing the enzyme which degrades B-lactam antibiotics). Once the antisense attaches, the mRNA responsible for the translation of Cro protein is released and translated. This Cro protein inhibits the cI promotor and leads to the activation of the viral lytic cycle and consequent cell death by lysis. If the resistance gene is not present, Antisense forms a complementary loop with itself and is inactivated by RNaseIII. For more information about their device, check their description page.
Figure 2: Schematic representation of the anti-sense detection mechanism.
So by combining the machinery of VIT Vellore and the detection system of TU Eindhoven, only resistant bacteria are detected due to using the dCas9 based sensors and the antisense mechanism of VIT Vellore.
References
- O’Neill, J. Review on Antimicrobial Resistance. Antimicrobial Resistan(1) O’Neill, J. Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations, 2014. 2014, 4 (December).Ce: Tackling a Crisis for the Health A. 2014, 4 (December).
iGEM Wageningen: Collaboration about phages, lab work, detection and troubleshooting
Like us, iGEM Wageningen university is also using phages in their project. And because we are both Dutch teams we started collaborating right away. We troubleshooted a lot together and discussed the opportunity of working together in the lab.
iGEM TU Dresden: CRISPR collaboration
We met the TU Dresden team at the iGEM Europe meetup in The Hague and discovered some similarities between our projects. We are both working with dCas9. When we started the expression of our construct, we had some problems because we were unable to express our protein. We had contact with Dresden about our expression problems and troubleshooted our project together. They gave us insight into their expression protocols and their dCas9 sequence. Based on their protocol and the literature we tested different expression conditions. However, this did not solve our expression problem. When we compared our sequences for dCas9, we found out that there was a difference in the codons. We changed the sequence of our dCas9, and this solved our expression problem. We thank the TU Dresden team for sharing information and helping to solve our problem.
Claire Michielsen from TU Eindhoven and Sebastian Eguiguren from TU Dresden at the iGEM Europe meetup in The Hague.
iGEM Duesseldorf: Postcard project
Like every year, iGEM team Duesseldorf organized the postcard project. The goal of this collaboration was to design a postcard regarding synthetic biology. We as TU Eindhoven team designed a postcard with a 4-picture strip about our project. We really enjoyed receiving all the postcard from teams all over the world!
Our postcard for the collaboration.
Washington iGEM team: Testing and/or Translating Outreach Booklet Activities
iGEM team Washington had written a 2019 outreach booklet meant to introduce schoolchildren to the field of synthetic biology through fun and interactive activities. They sent us an email and asked for our help in translating them to Dutch. We have provided translations of 3 of the outreach PDFs and shared the contact details of the other Dutch teams for the other translations.
Translation of booklet cover from the Washington iGEM team.
iGEMxSGDs challenge: participating in their challenge on Instagram about SGD
The teams of Costa Rica, Tuebingen, and TAS Taipei started the iGEMxSDGs instagram challenge. This challenge aims to promote the Sustainable Development Goals (SDGs) proposed by the United Nations. After being tagged by a team that had already completed the challenge you were asked to post your own 3 to 4 SDGs. We posted this on June 27, 2019.
Our Instagram post for the iGEMxSGDs challenge.
US AFRL Carroll HS iGEM team (iGEM Lab Pats): #MiketheMicrobe
For this collaboration of US_AFRL_CarrollHS, we had to post a picture with Mike the Microbe and Chia the Chitinase while they were visiting our lab. Thereafter we posted the picture on Instagram with the hashtag #MiketheMicrobe and #ChiatheChitinase together with mentioning iGEM Lab Pats @igemlabpats. Mike and Chia were a really good help in the lab and helped us well in performing our experiments!
Eva Hanckmann in the lab with Mike the Microbe and Chia the Chitinase.
