Team:DTU-Denmark/Practices


Human Practices

Scroll down for more

Achievements

Our Human Practice managed to change the educational platform for 200 high schools in Denmark!

Our Human Practice pushes Danish high school students a major step towards making their first BioBrick! The project design circumvent controversial rules issued by the Danish Ministry of Education, limiting high school students not to modify plasmids. In collaboration with an elite student organization Biotech Academy, our solution allows ordinary high schools to perform restriction based cloning. The project is already funded for the early development, and the plan is to ship complete experimental kits to 200 high schools in Denmark in early 2016.

Our Human Practice consists of many activities, all with a purpose in relation to the Human Practice Strategy. The “Biosensor” is our main achievement as a strong education tool, and the other activities complemented its maturation. Other aspects of our Human Practice concern also communication, safety and ethics. All of our activities are presented beneath, and we invite to explore our practices.

 

As a part of the DTU iGEM 2015 outreach, three eager highschool students followed the joined journey of hard work! By taking part in the meetings, working in the lab and participating in the Giant Jamboree they were given the possibility to experience working on a scientific project and to follow their interest in biotechnology. 

Our iGEM team is highly diverse in terms of age, interests and scientific experience. To push these norms and the element of teaching, we adopted three elite high school students onto our team. They all study at Bagsværd Kostskole og Gymnasium, being a collaborating partner with the DTU Systems Biology. With a background of biotechnology, they became an active part of the team. Importantly for their development, they got involved in diverse activities, such as brainstorming sessions, workshops, and technical- and practical tasks in the laboratory. Moreover, they shared their experience and knowledge about the DTU iGEM project by giving a lecture to broader audience at their school. 

 

Contributions, experiences and thought of reflections

The best way to understand the extent of their participation is to read their own personal accounts so we asked them before joining our team, and after a maturation period of months of intense work. They were asked: What do you want to learn by taking part in iGEM? Why do you want to participate?

"I hope to get some academic knowledge, which primarily is the reason why I want to participate. But I’m also looking forward to following the process from idea to product and to experience the atmosphere in a group of passionate people. MAJA (format this to quote). I would love to see how a research project goes from all the way from being just an idea to being realised and presented. I would also like to become much more comfortable in a lab." Thea

“As a high school student, being a part of the DTU iGEM project has been a challenging, educational, and worthwhile experience. It has given me the opportunity to become acquainted with a new field within science - synthetic biology - which is rarely given attention in school. But this project has not only taught me scientific things; it has given me a lesson that I can use in other contexts as well. I have learned that Google isn’t the answer to everything – using your brain, analysing and discussing your mistakes with team mates sometimes provides greater results. Furthermore, this project has made me even more aware of the importance of patience and perseverance while doing research – piecing pieces of knowledge together takes time and so does lab work. It has been a fun process which I’m looking forward to seeing the result of in Boston!” Maja

“Being a part of the DTU iGEM 2015 has given me insight into the field of synthetic biology from both a theoretical and practical point of view. I had a good introduction to the lab work and the methods used such as PCR, gel electrophoresis, DNA purification... After a week of practice, I followed some protocols and did experiments by myself and independently, from which I experienced the way of thinking while in the lab. In dry lab I have practised reading scientific articles and learned how to design optimized oligos for the MAGE-protocol.

Besides the biological part of iGEM I have also been introduced to fund-raising and wiki-design, which were also instructive.

Although it was tough some days, meeting early in the morning and going to the lab, I think we had a good team-working ethic and were also able to do other things and enjoy each other’s company though we are all not the same age.” Nicolai 

“For me, working with the DTU iGEM team has been a great opportunity to experience the inner workings of a research project. It has been incredibly inspiring to be able to follow the entire journey, from the original idea, through hours of work, and ending up at the finished project. Through working in the lab I've discovered new methods and gained a feeling of independence in applying them. The team have all been immensely warm, welcoming and willing to answer my many, many questions.” Thea

 

They shared also their reflections about the project after summer holidays and experience while giving a lecture to their friends and other school mates at their high school. 

"When we came back to school after the summer holidays, some of our stories fit the ones of our classmates. We, too, had spent time on beaches and with friends. But one part of our vacation stood out; the time we’d used in the lab, feverishly pipetting. We decided to do a presentation and defend our decision to spend a few weeks away from the sun.
Instead of trying to explain the larger strokes of the project to a classroom of tired high-school students, we chose to focus on a couple of smaller steps that we have been involved in. Firstly, the knockout of the mutS gene. Even though it had proved to be horribly difficult in the lab, merely explaining it was no problem. Especially since our audience were no usual high school students. They had been working closely with biotechnology since they, way back in the seventh grade, chose that as their focus. While the concepts of antibiotics and resistance markers hardly needed explaining, the method of homologous recombination was new to most. Then we turned to the more concrete of what actually goes on, in and out of the lab. Once again some methods, PCR and gel electrophoresis, were very familiar to the class, while methods like NanoDrop, MiniPREP and MAGE warranted longer explanation. The latter of which was even new to our, otherwise seasoned, teachers. Next were the dry-lab activities such as oligo modelling for optimization of MAGE protocol. We showed some of the models and explained how they could be used. To finish off our presentation, we took a second to divert our attention from the many hours in the lab and behind the computer, and showed some pictures from back when we went canoeing on Bagsværd Lake." Thea, Maja and Nicolai

 

“Biosensor” is a product of our dedicated passion to teach synthetic biology to all high school students in Denmark. We designed an interdisciplinary laboratory and theoretical project for high school students. The goal is to teach them, how to design and make a biosensor by combining two biobricks from the parts registry.

We tested the project with three highschool students. Together, they made three biosensors that could detect the active compound in aspirin, acetylsalicylic acid. The three biosensors produced different signals which they selected themselves. We tested GFT, YFP, and a blue chromodomain protein.

The biosensor was created in three easy steps:

  1. Digestion of the two Biobricks BBa_J61051 and BBa_K592009 with different restriction enzymes generating overhangs that are makes them non-compatible for with re-ligation without the other part. (~1 hour)
  2. Heat-inactivation step of restriction enzymes. (20 minutes)
  3. Ligation of two biobricks  (15 minutes)
  4. Transformation of chemical competent E. coli K12 strain..
  5. Selection on LB agar plates containing chloramphenicol and optional acetylsalicylic acid.

 

Challenges

There were three main challenges with designing an iGEM project for 200 highschools in Denmark:

  • The Danish Ministry of Education must pre-approve all GMO projects for high schools. According to their regulations (Danish version here), highschool students are not allowed to modify plasmids. They are allowed to work with E. coli K12 strains and transform them with antibiotic resistance plasmids and test there transformants, but they are not allowed to purify the plasmid for the purpose on re-introducing it into E. coli or modify it. This means that while Danish high schools would be allowed to receive the iGEM Parts Distribution and transform the parts into E. coli, they are not allowed to modify the plasmid.
  • In addition to the regulations, materials propose a problem as not all high schools have access to standard molecular biology lab equipment such as: PCR machine, gel electrophoresis, and centrifuge.
  • Last the cost of restriction enzymes, ligases, competent cells, and other reagents is a limiting factor for the possibility of high schools to engage in iGEM.

Solutions

In order to achive these solutions, we teamed up with Biotech Academy, which is a student-run non-profit organisation that provides free learning materials in biotechnology for high schools and middle schools.

  • The goal is to send up to a 100 purified plasmids from the BioBrick Registry in quantities that can be used for cloning out to up to 200 highschools. By sending out selected BioBricks in enough quantities to do restriction based cloning, we would make it possible for high school students to make their own BioBrick for the first time. In addition, we ensure that the biobricks they would receive and work with are in compliance with the rules from the Ministry of Education.
  • In addition, the shipment of BioBricks would also include the standard iGEM restriction enzymes (EcoRI, PstI, XbaI, and SpeI) and DNA ligase. Biotech Academy received so far 70,000 DKK from the Lundbeck Foundation for costs associated with development of the project.
  • It was our goal that high schools would not be limited by lack of equipment. The project was designed so that it can be done without any special equipment. By using 3A assembly and digesting the two BioBricks with different restriction enzymes, it is possible to achieve this omitting the need to do PCR or gel extraction. Since antibiotic resistance is a concern to the Danish Ministry of Education, we designed the experiment to only contain two plasmids and one antibiotic resistance marker. We tested it and saw that in 1/2 the cases the two BioBricks were ligated correctly, when they were digested for 15 minutes at 37C.
  • By prodividng the reagents for the cloning, the high schools only have to provide sterile media/agar plates. Incubation of transformants can be done at room temperature and the short duration of the heat shock can be achieved easily. For detection of BioBricks, we included chromodomain proteins which can be seen directly on the plates. Aspirin can be bought at drug stores or even synthesized by the high school students as a part of their chemistry lab. If the high schools have more advanced equipment, they can use other detection options such as enzymes or fluorescence proteins.

We submitted our blue biosensor to the registry and included on the parts page a detailed protocol for the experiment, so that other teams and high school students can make their own BioBricks. Find it here. 

Information about the project and timeline:

This project is designed in part with Biotech Academy with Pernille Myers as project developer. Biotech Academy have so fair raised 70,000 DKK (more than $10,000 to fund the project) from the Lundbeck Foundation. The project will be sent to the Ministry of Education for pre-approval and is predicted to be launched and distributed to the approx. 200 high schools in the first half of 2016.

 

Elements of communication to the general public has been used to educate and inspire in Synthetic Biology. Several channels of communication was set up including social media and public science papers. A key purpose by the use of social media is to demystify the team as “scary scientists” and elaborate details about the project. Postings of science and team updates attracted the attention of over 150 followers on both media outlets indicating strong interest in our progress and synthetic biology in general. Links to our Facebook and twitter page can be found on the "home" page as well as here and here respectively. In addition, the team got contacted by the Technologist and the DTU paper for a piece about the iGEM participation. The DTU paper is printed to the Technical University of Denmark and reaches out to employees, university students and high school students. The article was printed the 7th of September and can be found here. The Technologist is a website and a magazine of the EuroTech Universities Alliance, bringing together the best and most exciting research and innovation from Europe and beyond. Our article will be printed in November and we look forward to contributing to the Pan-European promotion of iGEM!

Life Science and Beyond is an annual conference organized by the Society for Biological Engineering (SBE) at Technical University of Denmark. The aim of the conference is to promote different life science activities, helping in the organisation of reasonable study plans and sharing a variety of experience between students.

The program of the event attracted over 100 curious students from Bachelor as well as Master degree programs with different biological and biotechnological backgrounds. As the event was held in the main library of the university, many other students got involved in discussions on different stands and during the final dinner.

One of the most popular stands was our iGEM stand, where our team was able to share knowledge on synthetic biology and its applications. We familiarised others with the idea of iGEM, focusing on open-sourcing, collaboration between people with different backgrounds and creating Biobricks. To increase the attraction of our stand, make people read our posters and talk to us, we prepared a quiz about the iGEM competition as well as synthetic biology with some awards! After a few hours our hands were full of correctly filled-in questionnaires!

We can say with certainty that this event was a success, as many of the participants showed great enthusiasm and interest in joining the next iGEM 2016 competition as well as focusing on topics related to synthetic biology during their studies.

After a lot of work our team has been accepted as an official Blue Dot Project at the Technical University of Denmark. This gesture infers that our university recognize the efforts, we, students put into the iGEM competition. This benefit the outreach potential of the iGEM idea to fellow students and raise awareness in the academic landscape. The increased focus on the iGEM competition promote the interest in participation increasing the academic level of selected participants of future teams.

“The name ’Blue Dot’ refers to the Earth, which - although it is huge - looks like a small blue dot when viewed from space. While big ideas can appear simple and tangible when seen from the outside, from the inside they are often rather intricate and complex. The name ’Blue Dot’ thus also refers to an engineer’s ability to remain focues and see the big picture while simultaneously delving into the details in order to solve problems and challenges.” DTU official site

Our titel can be found on the official Blue Dot Project website under the name DTU Biobuilders.

 

 

Human Practice Strategy

Dissemination of knowledge to future researchers

Our human practices strategy is defined by our team’s desire to inspire high school students to pursue a study line in synthetic biology. The aim is to push the boundaries of traditional high school education by increasing awareness and integrating students in the scientific process of the iGEM competition.

 

Outline of our visions - What did we want to accomplish?

Our goal was to interact with bright high school students focusing on a future career in scientific research, university students who could become the next iGEM participants, and in general to extend the exposure of iGEM to the general public. To that end, we intended to invite three high school students onto our team as contributing members with the purpose of creating a “ripple effect” of learning and teaching. This did happen and we taught them how to work in the lab and then asked them to present their mini-project to their classmates to inspire them. We also participated in campus events to engage the university students and invite them to join our team. Public outreach was achieved through social media, conferences, and articles in the university paper.

 

Considerations in strategy design

The primary focus of the Human Practice strategy was involvement, education and safety (see Figure 1).

Involvement is an essential step towards getting people interested in the world of synthetic biology. We wanted to address critical questions about genetic modification in biological organisms, and involve peers in related discussions. This was a vital element as discussions bring new thoughts, encourage the exchange of ideas and raise the level of learning. Advanced knowledge about particular topics in synthetic biology could contribute a solid foundation to young students along with promoting innovative futuristic ideas and perspectives to the iGEM community.

Figure 1. Visual representation of the three core elements in the human practice strategy.

Education was our second agenda and we sought to inspire high school students to explore and utilize synthetic biology tools. Familiarizing the next generation with synthetic biology techniques has the potential to inform and inspire young scientists to work towards a bio-sustainable environment in-line with the iGEM philosophy. We believe that education is key to generate new hypotheses and experiment with the creation of new concepts in synthetic biology. Ethics, a topic of great importance within the field of synthetic biology, was discussed to address concerns about ‘playing God’ with nature, and the potential risk of GMOs.

 

Safety was our third focus, as we believe young scientists should be responsible with the workflow of their project and its output. We believe it is crucial to ensure the safety of the environment and personal health. Many of the techniques used in the laboratory and the handling of a variety of organisms have the potential to be dangerous. Therefore, risk assessment of planned projects is essential, see the Safety section. Safety was also one of the elements in our outreach work with the high school students. We examined the potential consequences of the work, and encouraged the students to raise concerns about laboratory work, project design and the implementation of innovative ideas into real life. This is elaborated upon in detail in Ethic implications on society.

Ethical implications on society

Introduction

During outreaching activities such as the BioBusiness Summer School 2015, important questions were raised about the ethics in relation to field of biotechnology. This sparked an inspiration in our iGEM team to raise the questions ourselves and analyze our project and educational elements in a bigger perspective. According to guidelines from the “European Commission, research proposals towards the Horizon 2020 funding” we contacted a local expert for guidance. A session was established with Bioethics specialist Martin Mose Bentzen from the Technical University of Denmark, to have a talk about ethical concerns of relevance in relation to our project. He highlighted numerous important aspects to consider and the team left the session with a clear direction to make an ethic self-assessment. From these considerations, our team identified the following aspects to be essential in the assessment of how our project may affect society:

 

  • Bioethics
  • Environmental ethics
  • Ethical dilemmas in teaching of high schoolers

 

What have we created!?

The Synthesizer-project has many delicate elements, which could be analyzed for bioethical concerns. Our final product is a tool that allows any individual to design a synthesis of a desired product and help fellow scientists all around the world. With this in mind and the method being accessible for everyone, many crucial questions should be addressed - how do we as the creators make sure, our tool is not being used with a bad purpose? What would happen if the tool would be used to make disastrous findings? As inventors, are we directly related to someone's bad intentions or are we rather providing the tool? Ethically, would we be held accountable for any individual radical agenda? We have approached the subject by this assessment and believe in the importance of this initial precaution by raising thoughts of the precautionary principle - do we dare to release our product and how can we prevent its misuse? An obvious suggestion would be introduction of limitations in the presented features, limiting the use of the tool for products that are known toxic and the use with a bad intention. This could be implemented by an input blacklisting of NPRS complexes associated with toxin products. Still, these limitations could be insufficient in prevention of uncharacterized toxic products due to lack of prediction. However, engaging this topic by utilitarianism, we should not limit ourselves by these precautions before applying a risk-benefit analysis of individual usage. The outcome of the combined achievement of medical, social and financial gain should by default strongly overweight the risk at hand.

 

But… you work with GMO?!

Yes, as we work with GMO, biosafety is important to address the protection of the environment. Biosafety entails environment, health and safety, and ethical considerations would concern the correct handling of microorganisms. This ensures a safe lab environment and the prevention of microorganisms contamination or being released into nature with a negative influence. As distributers of the synthesizer tool, we cannot ensure certified safety standards when users apply our tool. As a preventive measure, out team has highlighted the importance of basic lab safety measures in the wiki safety page one should always be prepared for any safety-compromised situation. In addition, our team facilitated the BioBrick workshop with an extensive safety introduction ensuring a basic understanding of safety to follow iGEM team of Denmark.

 

The element of teaching

While teaching high school students about synthetic biology – questions can be raised about the ethics and safety in the passing of mentioned knowledge. As these students are unfamiliar with in-depth knowledge about the particular scientific development in this field, they may not be aware of the unspoken ethic consensus. This adds layers of complexity and considerations to the teaching, as material, teaching methods and especially lab exercises should be under proper supervision.

An obvious concern is the element of biosecurity as our project facilitates the knowhow to manipulate GMO that potentially could be dangerous for human health. Ethical gray-area experiments could become a Trivial Trap as the line between “wrong” and “no harm, no foul” may blur out leaving the susceptible students prone to “the ends justify the means” in order to gain the respect from their supervisors. A transparency must be kept in the knowledge transition from teacher to student if utilitarianism is the prevailing mindset. This highlights the importance of open discussions on the particular topic as an integrated part of the teaching procedure and an encouragement for the students, that no question or concern is too little to be addressed.

 

Conclusion

The Synthesizer-project has many elements, which have been assessed ethically. In this context of synthetic biology, we have briefly touched upon ethics in relation to safety and teaching. The tool does have the potential to compromise safety, and in terms of ethical conduct of research, our team is aware of possible usage not intended by us designers. We have also addressed ethical elements in our teaching and highlighted preventive measures. As the project is fairly young, we expect additional ethic problems to surface and as a consequence, we are prepared to continually assess the project for ethic dilemmas.

Safety Concerns

Initial thoughts of project safety 

When experimenting in synthetic biology, we should be aware of the consequences, our actions can have. It is our responsibility to ensure the safety of the environment and the health of involved parties. A direct consequence is the need to assess potential risks, our project could inflict. Elements of relevance could be handling of chemicals and organisms, laboratory techniques, waste collection, shipping methods and even the level of expertise of individual iGEM team members.

Our team has been in close contact with safety officers management representative: Jan Martinussen and work environmental representative: Marzanna Pulka-Amin. They gave us the compulsory guided safety tour at the Center for Systems Microbiology. Highlights were the guidelines on conducting research with genetically modified organisms (GMO) and handling of hazardous materials. In complement, this section elaborates insights and suggestions of safety in project design, safety in the lab and the projects possible influence on society.

 

Safety in Project Design  - One should consider safety from the beginning!

At the initial stage of the project brainstorm, one should consider potential risks related to involved organism. The choice of organism largely affects the potential risk along with the type of protocols. Also, science departments are usually limited in their ability to house unfamiliar organisms. Lastly and important, the iGEM rules prohibit organisms from Risk Group 3 and 4 to ensure safety.

We tackled this concern by deciding on a non-pathogenic chassis (Risk Group 1) and choose methods and protocols using non life-threatening substances, minimizing potential risks. As these were well established, they were ideal for our proof-of-concept of experiments. In line with the educational agenda, this ensured a safe laboratory environment for our Outreach Initiatives such as the high school students, elite student interaction and the BioBrick workshop. Moreover, a mandatory safety introduction encouraged safe and proper execution of experiments.

 

Safety in the lab

When working with GMO it is important to have proper clearance what to do. The Technical University of Denmark has special_permissions from the Danish authorities covering a broad range of GMO projects including the iGEM project. Before entering the lab, our iGEM team had an introduction to the safety rules in the lab. Importantly, our safety advisor presented how to work with GMO in the lab. In order to ensure a safe workflow in the lab, we identified the most prominent risks that was present in our designed experiments. As an inspiration, we will list a few of our identified risk factors in relation to the lab:

  • Chemicals
    • Floueouracil was used in production of minimal media plates for our experiment. It is toxic when ingested, inhaled or in a contact with skin.
    • Ethidium bromide was used for pre-staining gels for gel electrophoresis analysis. Ethidium bromide (EtBr) is lethal when inhaled and suspected to be mutagenic.
  • Genetic material
    • Antibiotic resistance genes are a necessity in the lab. We utilized a wide range in our experiments: Neomycin, Erythromycin, Ampicillin, Chloramphenicol, Kanamycin, and Zeocin.
    • The toxic gene mazF is considered to be toxic for mammal cells, but has low-risk when integrated into a plasmid in laboratory conditions. 

Importantly,  involved  chemicals should be handled appropriately. They should be used in designated areas: at separate benches for gels, where gloves should be worn. The used chemicals in our project were found in our laboratory building, and registered at www.kemibrug.dk.

 

A product safe for society?

In iGEM projects, final products and biobricks may have toxic or hazzardous features. The impilcations on society can be hard to assess but in many cases it comes down to common sense. In doubt the iGEM wiki safety page suggest question sessions with  local laboratory supervisors. Another assessment approach is to raise questions about ethics. As open questions could identify concerns, they also cause discussions about safety of differnet aspects of final product.

Our team followed official guidelines and raised discussions about the safety of the Synthesizer-project and its impact on society. We considering unintended adverse effects of our tool and possible bioterrorism. The most prominent risk was the ability for users could design toxins peptide products for potential of bioterrorism. This raised a discussion about an implementation of a special blockade in the software to avoid the synthesis suggestions of harmful products. Still, the Synthetizer tool is intented to have positive influence on people's health by improving production of pharmaceuticals and reducing side-effects.

 

 

 

Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
P: +45 45 25 25 25
M: dtu-igem-2015@googlegroups.com