Human Practices

Choosing The Project

During the spring of 2025 the team met for weekly evening meetings where potential project ideas were being brainstormed. Before the final project was chosen in May. During these weeks all of the discussions were narrowed to four different project ideas. The team was divided into four groups that each carefully researched the topics and presented them to the rest of the team. And finally, the Algalith project was chosen via a final group vote.

To help the team during this process a lot of teachers and experienced mentors showed interest and guidance. When the project ideas were being presented they gave their input and feedback on the different aspects of the projects, both verbally and written. All this feedback was taken into consideration before and during the final vote, as well as the further planning of the project.

Motivation

Our climate is currently changing at an unprecedented speed and we have to do our best to halt the progression in order to minimize damage. The entire team, as well as Uppsala University, is very environmentally aware, therefore choosing this type of project was only natural as it is one of the solutions to halting climate change. Climate change and environmental awareness is a hot topic in Sweden which pushes us to always try to contribute to work as environmentally aware as possible and spread more awareness with our work. Cultivating and harvesting algae is a way to minimize the CO₂ that usually is emitted into the atmosphere during production of fossil fuel. Not only that, but algae can be utilized for bioremediation, to create fertilizers, and they can be eaten! Currently, they are approved as a generally safe food in the US as well as in China (Cao et al., 2024). Discussion with Professor Anthony Forster, professor in synthetic biology, showed us that there was a need for improvement of the algal industry as it is very versatile. His expertise in synthetic biology was very valuable through the project.

The current solutions rely heavily on harsh chemicals to flocculate the algae. Furthermore, the current harvesting process requires a lot of energy since the algae need to be filtered and centrifuged to remove water from them.

Our vision is to biologically engineer Chlamydomonas reinhardtii to express the membrane proteins Z17 and Z18 proteins. These two proteins would then associate to each other and facilitate the flocculation of algae in the growth media. Another idea would be to attach Z17 or Z18 to a membrane and grow the counterpart in algae, and then use the membrane to simply “scoop up” the algae. This gives a system which allows for continuous harvesting, ideally without the need for centrifugation as well.

Advice From Gentekniknämnden

Gentekniknämnden is a Swedish government authority that works to promote ethically justifiable and safe use of genetic engineering while protecting human/animal health and the environment. We came in contact with Annelie Carlsbecker who is an office manager and has a background of lecturing at Uppsala University in genetics, molecular biology and plant physiology, as well as developmental biology and her own research. She told us they were in the planning phase of starting a project related to GMO and micro algae. When asked about ethical research regarding the subject she advised us to contact Arbetsmiljöverket and Madeleine Haienhjelm (also from Genetiknämned). She also shared that she would happily keep contact with our team during the project and keep an open dialog.

Visit to Testa Center

We visited Testa Center in June as part of our exploration of how we could develop our project. The center is a part of Cytiva, a global life science company that provides technologies and services to develop and manufacture biopharmaceutical products. Testa Center's main focus is helping companies and labs to upscale their experiments from small-scale laboratory settings to larger industrial environments, guide them towards choosing the most efficient methods for upscaling and feasibility to industrialize the project. It is a collaboration between the Swedish government and Cytiva which is unique in Europe.

They were of particular interest to us in the sense that our project is meant to be used in large-scale industries. We learned that there are a wide range of bioreactors and there is a lot one has to think about when picking one as this affects the yield and efficiency. This is highly relevant for us as our project aims to be used industrially. Overall, this was a very educational visit and we are happy to have seen such advanced equipment.

Petroutsos Lab

Meeting 23/5/2025

Through the summer we were mentored by the Petroutsos lab at Uppsala University. This was partially helpful since they also work with Chlamydomonas reinhardtii as their model organism. It started off as general advice on how to work with Chlamydomonas, such as using introns for the gene of interest. Asking questions on how to measure sedimentation rate. They told us that if we want to work with open pond systems to try and keep our system and goal method as simple as possible and how it is better for us to find a system/harvesting technique that is not in need of pumping water in and out. Same with heat and heat shock dependent systems. Then they gave us suggestions on how to tweak the system, for example overexpressing lipids or for the algae to use proton pumps, similar to the Petroutsos lab's research, so it doesn't get too acidic and toxic when cultivating. We took this information and suggestion into consideration and continued our research on how to optimize our project idea.

Anthony Forster

Anthony Forster is a professor in Synthetic Biology at the Department of Cell-and Molecular Biology at Uppsala University. He has lent his expertise to iGEM teams from Uppsala for several years, as such, we consulted him regarding several aspects of our project. He talked about biofuels, their impact, and how they are produced today. The lecture showed us that there was a clear need for biofuel for the sake of our climate and by trying to make the harvesting process of algae more efficient with our project, we help promote fossil free fuel.

Meeting with Anthony 07/01/2025

We discussed our plasmid and primers that we wanted to design with Prof. Forster. The biggest challenge we faced were the multiple repeats that prevented the companies from synthesizing the gene. Prof. Forster recommended searching for other, alternative anchor proteins that might be easier to synthesize. Another idea that we discussed was using synonymous codons, however, the gene is too large to make the process feasible. Therefore, we changed our trajectory and decided to focus on Z17/Z18 as well as FLO1.

Other than that, we talked about our alphafold models of the Z17/Z18 interaction which he was positive about. However, he urged us to try the electroporation to make sure it works, as well as look into using a cell wall deficient strain of C.reinhardtii as electroporation of those are more effective and have higher yields of successful transformants. We took this into consideration and decided to work with the cell wall deficient strain CC-3403. This would lower the desirability of our project as a cell wall intact strain is less sensitive to environmental stress, however, time constraints as well as difficulties to synthesize the genes, forced us to compromise.

Samuel Coulbourn Flores

Samuel Coulborn Flores is an associate professor in bioinformatics at Sveriges lantbruksuniversitet (SLU) and he gave us a presentation regarding his current research modeling viral DNA and structure. With his expertise in modeling, we could ask him about our modeling of the Z17-Z18 interactions. He agreed that the modeling looked good but advised us to look at the genetic sequence and see if it follows the model. Furthermore, we discussed the use of disassociating the interaction and the modeling of FLO1, something which had not worked out very well with Alphafold. With Prof. Flores' help, we arrived at the conclusion that we have to try it in the algae despite the modeling troubles.

Visit to SLU Campus

We paid a visit to Sveriges lantbruksuniversitet (SLU) to check out their facilities and share knowledge between us. We started off the visit by having Samuel Flores give us a lecture on his research on protein-protein interactions, such as growth hormone derivatives interactions with growth hormone receptors. We discussed having a workshop where he could teach us more in depth about modelling interactions, relevant for our project.

Afterwards, postdoctoral researcher at the institution for molecular sciences; Yashaswini Nagaraj showed us around the laboratory facilities at SLU. We got to see equipment such as bioreactors which are used by their laboratory group to do research on yeast cells. The group focuses on upscailing production and extraction of carotenoids and lipids from Rhodotorula toruloides, mainly to be used in food but it has potential to be used in other areas such as biofuel, comparable to our research and our project. They also showed us techniques and methodology that could be incorporated to our project, such as utilizing a french press to lyse our Chlamydomonas reinhardtii for certain experiments. Disclosing the possibilities of different types of exchanges possible for our two different and at the same time similar projects.

Kulturnatten (The Culture Night)

Kulturnatten is an annual event held in Uppsala, Sweden. During this day many different museums, galleries, libraries and other venues organize activities, workshops and exhibitions for the public. We therefore believed that this would be an excellent opportunity to spread knowledge about synthetic biology and our project to the public as well as having an information exchange with them! Find out what the public's perception of GMO and the genetic engineering that we had done with our project. During Kulturnatten, on Saturday the 13th of September we therefore organized a laboratory workshop for anyone above the age of 8 to participate. The event was held in both Swedish and English to attract visitors with different backgrounds and experiences. For this workshop we borrowed one of the student laboratories of the university.

Before the start of the event we first held a safety demonstration of dos and don'ts in laboratory settings. Moreover, we held a presentation about our iGEM project with discussions about synthetic biology such as its pros, cons and applications.

We had set up two different experiments for the public to try. The first experiment involved extracting chlorophyll from spinach and analyzing it under UV light. We thought that this would be an easy experiment introducing and reflecting on some properties of our project, such as Chlamydomonas also having chloroplasts with chlorophyll. We encouraged the visitors to set up an hypothesis with possible explanations to what and why they think may happen. They were also given a simple protocol to follow themselves, but with our support and help if needed. The second experiment involved learning how to manoeuvre a microscope and looking at samples of our C. reinhardtii.

At the end of the event we asked the participants to fill out a questionnaire of their thoughts about synthetic biology. Some answers (translated from Swedish to English) are listed below:

Discussion with Sylvia Martin

Sylvia Martin is a clinical psychologist with a PhD in Clinical Psychology and Psychopathology. She works at Uppsala university, department of public health and caring sciences; Centre for Research Ethics and Bioethics. We had the pleasure of having a discussion about ethics in research with her!

What We Learned

Ethics is an important aspect of every research project and it is not very straightforward. After our discussion with Sylvia Martin, we gained insights into aspects that we previously had not thought about. For example, thinking of our project, not only for the purpose that we had intended, but in a more global context. The bioethical principles (benefit, non-malevolence, autonomy, and justice) are applied in clinical studies, however, these ethical principles are applicable to synthetic biology projects, and we believe that it is something all iGEM teams should have in mind when designing their project.

Our main goals were to make the algal harvesting more energy efficient and environment friendly, not geared towards a specific community. However, Sylvia Martin mentioned that our project may be very beneficial in low-income countries, which adds to the justice aspect of the 4 bioethical principles. One thing she mentioned was the importance of transparency. Ethics is a subject where there is no right or wrong which makes it incredibly important that one is transparent about their work so that people may make their own judgements. She drew parallels from her own experiences, where an important question is whether their patients want to know about underlying diseases, and how that would apply to children. In these cases, being transparent about what it could mean for them is important.

Working With NTI Students

As part of our Human Practices, we had the chance to collaborate with students from NTI Gymnasiet, a high school with a strong focus on science and technology. We invited them into our lab, showed them how we work, and let them take part in a few experiments under our supervision. Our aim was to spark curiosity about synthetic biology or at least to nurture it, and at the same time give them experiences that they could use later, for example in their high school final projects (examensarbete in Sweden, a thesis-like project that students complete in their final year of highschool). The collaboration did not stop at the lab bench; they also contributed to our Wiki, which added another dimension to their involvement.

At first, we thought of this as mainly an opportunity for us to share our knowledge, but it quickly became clear that we were also learning from them. They brought a fresh perspective on how to communicate synthetic biology to people outside the field, and they reminded us that science can be explained in simple and engaging ways without losing its depth. Their input also helped us reflect on our own teamwork. For example, when one of us worked alone on the Wiki without the rest of the team being aware of what was happening, it created problems later on. The students' involvement showed us how important it is to talk openly about what we are doing, test things together, and make teamwork an active part of the process.

We also learned from their determination and motivation. Choosing to spend part of their summer joining our project showed us how much energy and commitment they brought into the collaboration. Their enthusiasm inspired us to approach our own work with renewed dedication and reminded us why sharing science beyond the university setting matters so much.

In this way, our collaboration turned into a symbiotic relationship. The students got the chance to explore synthetic biology in a hands-on way and contribute to a real iGEM project, while we gained valuable lessons on teamwork, communication, and motivation. It reminded us that learning does not just flow from the more experienced to the less experienced, It can also move the other way creating growth on both sides.