Human Practices
Human Practices
We are the first team from the Jagiellonian University in the history of the competition and the only team from Poland participating in this year's iGEM edition. The idea for our project emerged from a deep concern for the environment and serves as a response to an ecological problem that has persisted not only in various regions of our country but also globally.
We have made every effort to delve into the literature and reports on golden algae, methods for its detection, and neutralisation techniques. However, the most enriching aspect of developing PrymDetect has been the conversations, consultations, and collaborations with specialists from diverse fields of science and technology, as well as discussions with individuals directly affected by this issue who have witnessed recurring ecological disasters firsthand.
During our iGEM journey, we wanted to create a sensitive tool – PrymDetect – that allows for field detection of Prymnesium parvum (golden algae) in environmental samples. We aimed for our project to be multifaceted, ensuring that the tools we develop are user-friendly, accessible, cost-effective to produce, and inclusive of all voices. Our team comprises individuals who are deeply concerned about the environment, and each of us has actively participated in integrated human practices to gather feedback and insights on every aspect of our project.
Find out more about what've done to advance our project!
Who we contacted:
Why:
What we learned:
What we adapted to our project:
Who we contacted:
Why:
What we learned:
What we adapted to our project:
Who we contacted:
Adrian Kania, Dr Łukasz Szydłowski
Why:
What we learned:
What we adapted to our project:
Who we contacted:
Audience (students, engineers and scientists)
Why:
What we learned:
What we adapted to our project:
We decided not to pursue the idea of creating a mobile application.
We planned to conduct a control experiment on other algal species and perform bioinformatics analyses to confirm that the targeted sequences are absent in non-target organisms.
The size of the PrymChip remained unchanged.
Who we contacted:
Audience (students, engineers and scientists)
Why:
We gave a presentation on the project topic and gathered feedback.
Additionally, we shared our experiences in iGEM.
What we learned:
What we adapted to our project:
We deepened our understanding of golden algal blooms, including their prevalence, evolution, and strains. We believe that developing our tool can help address this global problem.
Who we contacted:
Dariusz Gurtowski from the company BIOTON at SYMBIOZA Symposium (workshop on problem-solving in biotechnology)
Why:
We encountered issues with PCR results in our various laboratories.
What we learned:
What we adapted to our project:
We created a fishbone diagram to identify areas to investigate for solving our problems. As a result, we were later able to successfully carry out the problematic PCR reactions, fully understanding why they had failed previously.
Who we contacted:
Prof. Jakub Mielczarek, Dr Katarzyna Dziedzic-Kocurek, Dr Grzegorz Bereta
Why:
We aimed to gain insights and practical advice on the design and functionality of the PrymChip device.
What we learned:
What we adapted to our project:
We switched from PLA to PETG for better durability and added LED holders to stabilize the light source in the detection chamber. Additionally, we implemented suggestions to enhance device stability and usability, including a sliding drawer mechanism and improved phone stabilization supports.
Who we contacted:
Dr Paweł Jedynak
Why:
We recognized the need to establish safety guidelines for working with golden algae.
What we learned:
What we adapted to our project:
We created a set of rules for working with Prymnesium parvum which we have documented in our Safety Form.
Who we contacted:
Dr Ewa Górecka
Why:
We encountered some problems with stabilising the culture of Prymnesium parvum.
What we learned:
What we adapted to our project:
We adjusted the culture conditions, including the medium salt composition and lighting. As a result, we stabilized our cultures and were able to conduct further tests.
Who we contacted:
Dr Paweł Brzezowski
Why:
We encountered some problems with stabilising the culture of Prymnesium parvum.
What we learned:
What we adapted to our project:
Thanks to his recommendations, we adjusted the pH of the medium from 5.5 to 7.3.
Who we contacted:
Konrad Uściło, Dr Paweł Jedynak
Why:
Concerns related to the social acceptance of testing water bodies for the presence of golden algae.
What we learned:
What we adapted to our project:
We began comparing our test to widely recognized tests, such as pregnancy tests, to soften its image and highlight similarities in methodology and appearance.
We decided to participate in educational events to spread scientifically proven information about algal blooms and reduce the risk of misinformation and public panic.
Who we contacted:
Prof. Bogdan Wziątek
Why:
We had an in-depth conversation about the suitability of the current monitoring methods for the Oder River, testing methods, the utility of PrymDetect, and potential areas for project development.
What we learned:
We confirmed our suspicions about insufficient water body monitoring and the limitations of current monitoring methods – microscopic counting and PCR results.
The professor suggested that PrymDetect could be highly useful for assessing algae presence in field conditions and for conducting LFA screening of multiple water bodies in a short time.
We also learned that testing for both algae and toxins is crucial for a comprehensive assessment, as high algal cell counts do not always correlate with toxin release. This complex information is necessary for making informed management decisions.
What we adapted to our project:
In the future, the project should focus on correlating golden algae blooms with the presence of other microorganisms and testing for toxins.
However, the immediate priority is to develop a tool for efficiently screening and assessing the number of Prymnesium parvum cells in water bodies.
Who we contacted:
Prof. Jolanta Jura
Why:
Dean of our Faculty was provided with a general overview of the project and highlighted its weak points.
What we learned:
It is essential to develop and test in-field methods for isolating DNA from environmental samples.
What we adapted to our project:
We conducted preliminary analyses and created a protocol for in-field DNA isolation.
Who we contacted:
Vinoo Selvarajah
Why:
We wanted to consult an expert to evaluate the utility and standardization of our part designs, with the goal of maximizing their usefulness for future iGEM teams.
What we learned:
We learned that the initially selected plasmid backbone was not ideal for the SynLOCK Cassette.
Vinoo suggested more suitable options that facilitate easier cassette transfer and compatibility with the BioBrick standard.
We learned best practices for documenting parts as basic and composite.
Integrating a reporter into the cassette would enhance user-friendliness by allowing for easy visual screening of correct colonies.
What we adapted to our project:
We incorporated both a reporter and a new plasmid backbone into our system based on Vinoo's feedback.
During the follow-up call, we presented our lab achievements and gathered data, receiving advice that helped us properly document parts for future iGEM team use.
Who we contacted:
ValleyDAO company – Albert Anis and the DealFlow Team
Why:
We aimed to present our project findings, receive feedback, and seek guidance on addressing unresolved lab challenges, such as issues with in-field DNA isolation.
What we learned:
We gathered useful tips for presenting our results, including what to focus on during the judging session at the Jamboree and how to highlight key accomplishments in our project.
We received guidance on addressing challenges with in-field DNA isolation and learned about options for in-field sample concentration that require minimal equipment, enhancing the applicability of our test.
What we adapted to our project:
We will try to incorporate all of this advice into our presentation at the Grand Jamboree.
Who we contacted:
Prof. Dariusz Dziga
Why:
Exploring future perspectives for the project.
What we learned:
Prof. Dziga sees significant potential and a strong need for the type of test we developed.
What we adapted to our project:
Prof. Dariusz Dziga will consider forming a dedicated team at the university to focus on optimizing our detection test.
The idea for the project began in the minds of our Team Leaders in a small attic apartment eight months before we started our first laboratory work. It all started with a comprehensive report published in March 2023 by the government's Team for the Situation on the Oder River [1]. A year after the first ecological disaster, which resulted in the death of 1,650 tons of fish (a 60% decline in the fish population) [2], we officially learned about the main culprit – Prymnesium parvum (golden algae). However, this algae's blooms and toxins’ release were influenced by many factors, including high water salinity, oxygen levels, and temperature increases. It was impossible to overlook the headlines of online portals that attempted to translate the scientific language of the report into more accessible content for the public.
This report was also crucial for another reason. Initially, we had planned to develop a method for neutralising the algae and restoring balance to the ecosystems. However, the report showed us that there are many techniques for neutralising phytoplankton; it just needed to be tested which one would be most suitable in the context of golden algae. A government source indicated that such actions had already been planned and were partially underway; searching for a means of neutralisation was no longer sensible, especially since it would involve testing in the environment, which would require numerous permits and interventions in nature.
Thus, we continued our search. As articles piled up, we finally came across one that ultimately gave our project its focus. Professor Bogdan Wziątek, in a conversation with journalist Katarzyna Kojzar, admitted that the monitoring of the Oder River and its adjacent bodies of water is insufficient [3]. We also found literature indicating that the method used in Poland for identifying this algal species under a microscope is challenging and requires highly trained specialists [4]. Everything pointed to the fact that to address the problem of algal blooms, we needed to start with an effective detection method.
To witness the scale of the problem firsthand, we visited the Czernica Reservoir on the Oder River, where dead aquatic organisms had been reported. Upon arrival, it turned out that the dead fish had already been removed. The fishermen we encountered explained that the red elements protruding above the water were nets designed to prevent dead fish from drifting further into the reservoir. The area was also surrounded by signs warning of the danger and prohibiting the use of the reservoir, along with instructions for disinfecting anything that had come into contact with the water.
Sign Translation: Prymnesium parvum, known as "golden algae," has been detected in the water reservoir. Do not use the water to avoid spreading the algae to other bodies of water. REMEMBER: If you notice a change in water colour, foam, or dead fish, report it to the Voivodeship Inspectorate for Environmental Protection in Wrocław. IMPORTANT: Objects that have come into contact with the reservoir's water must be thoroughly disinfected before reuse.
After our project idea was approved by the professors and the Dean of the Faculty of Biochemistry, Biophysics, and Biotechnology at Jagiellonian University, Professor Jolanta Jura, we began consultations to seek better solutions. We divided the project's development history into sections to describe it more effectively.
Before and during the purification of the Cas13 protein for our SHERLOCK assays, we consulted with our instructors and university researchers, who had extensive knowledge in protein production and purification.
We decided to base our protein purification protocol on the methodology outlined by Kellner et al.[5], modifying the StrepTag affinity chromatography approach in favour of Immobilized Metal Affinity Chromatography (IMAC) with a HisTag. This adjustment was aimed at enhancing the cost-effectiveness of our purification process. Prof. Andrzej Górecki from the Department of Physical Biochemistry at Jagiellonian University suggested that if the IMAC yields insufficient protein concentrations, we could return to the chromatography utilising StrepTag. Moreover, we decided not to change the steps of Ion Exchange Chromatography (IEC) and Size Exclusion Chromatography (SEC), as these techniques would remove contaminants and allow us to concentrate the protein in the fractions.
Additionally, Professor Górecki recommended performing a Western Blot analysis post-IMAC using anti-HisTag antibodies to verify the presence of the protein in the fractions selected for further purification. However, we ultimately decided against this, as the SDS-PAGE gel results indicated Cas protein production, evidenced by a new band corresponding to the Cas13a protein in the post-IPTG induction fraction, along with eluted fractions demonstrating concentrated protein at the expected molecular weight. We revisited Professor Górecki with our findings, and he agreed with our approach.
We examined the necessity of the SUMO protease cleavage step. Professor Górecki raised questions regarding its essentiality, leading us to digest half of the IMAC fractions with SUMO protease while leaving the other half untreated. We later compared the protein activity in the SHERLOCK assay, as well as assessed structure via circular dichroism and thermal stability using NanoDSF. Following this experimental approach and the insightful suggestion from Professor Górecki, we concluded that the SUMO protease cleavage step is unnecessary and can be omitted from the protocol.
We also discussed the potential for lyophilisation to enhance the protein's (and consequently the SHERLOCK test) applicability for field use. Professor Górecki indicated that it would be worthwhile to evaluate the protein's activity at intervals post-lyophilization (e.g., after 1, 2, 3 months) to determine the longevity of Cas13 protein activity. Ultimately, we decided against lyophilizing the protein as our focus shifted to advancing other components of the project. However, we consider this a potential direction for future exploration.
The decision to produce the Cas13b protein was a significant breakthrough as well, influenced by Professor Górecki's experience in experimental design and his foresight regarding potential issues. The additional protein from the Cas13 family was supposed to be a backup in case the protocol did not work for LwaCas13a (e.g., no protein was observed in the fractions, the protein was not active). Referring to Box 1 in the Kellner et al. publication [3], we selected the CcaCas13b ortholog due to its relatively high sensitivity among the tested Cas13 orthologs, second only to LwaCas13a.
Prof. Górecki noted that producing and purifying both huLwCas13a and CcaCas13b would allow for comparative analysis in the SHERLOCK test, facilitating the identification of the more specific and sensitive option for detecting Prymnesium parvum. Furthermore, both proteins could potentially be employed in a multiplexed detection assay for two organisms in water samples or identifying the presence of algae and algae toxins (prymnesins). Due to time constraints and the need to prioritise other aspects of the project, we were unable to conduct these experiments. Nevertheless, this remains a promising avenue for future investigation.
While working in the Protein Lab, our main advisor was Dr Małgorzata Figiel from the Department of Physical Biochemistry at Jagiellonian University. Her extensive experience and our multiple consultations guided us in making the protocol as practical as possible. Our main goal was to ensure that it was both effective and easy to implement.
Prymnesium parvum genome – creative troubleshooting
The initial version of our project proposed that the crRNA we designed to detect Prymnesium parvum would be created based on the genome sequenced at the University of Gdańsk. This approach would ensure the specificity of the designed construct for the strain found in the Oder River.
Based on the report published in March 2023 by the government's Team for the Situation on the Oder River [1] we learned that a team of scientists from the University of Gdańsk, led by Professor Grzegorz Węgrzyn, successfully sequenced the entire genome of Prymnesium parvum. Thanks to their kindness, we were provided with the complete genomic sequence for analysis by Michał Grabski, a PhD student at the University of Gdańsk. After acquiring the genome as contigs, we searched for the presence of the ITS1-5.8S-ITS2 sequences, which proved to be quite challenging. Lacking extensive experience in genomic analysis, we collaborated with Adrian Kania from our department’s Computational Biophysics and Bioinformatics Lab, who emphasised the need to focus on assessing the quality of the genome and the methods used for its acquisition, as well as the quality of the sample being sequenced. At the same time, we also reached out to Dr Łukasz Szydłowski. After several meetings and collaborative attempts to analyse the genome, we concluded that it may be contaminated with sequences from organisms other than Prymnesium parvum. This could be due to the sequencing being conducted on a sample that was not derived from a pure culture. Another possibility is that the databases used for our analyses were contaminated, which is relatively common given that Prymnesium is a widely understudied organism.
The inability to work with the obtained genome jeopardised the entire project concept. We were reluctant to give up easily and spent several weeks brainstorming solutions. We reached out to foreign institutions that were also reported to have the complete genetic sequence of the algae at that time, but we didn’t get any responses.
We diligently searched available literature and found primers described in a 2008 publication [6], which focused on optimising primers for detecting Prymnesium using PCR techniques. However, these primers only allowed us to amplify a part of the ITS sequences that we needed for designing our crRNA. Nevertheless, we decided to proceed with sequencing using these primers. After analysing the obtained sequence with BLAST, we discovered that the only match was Prymnesium parvum. A light at the end of the tunnel appeared.
Upon compiling all results that showed 100% identity, we found that all sequences within the fragment of interest were identical. Therefore, we selected one sequence from strain KAC39 as the basis for designing our crRNA and optimised RPA primers.
To advance our test and explore various field applications, we decided to develop the 3D-printed PrymChip, designed for semi-qualitative assessments. The primary function of the PrymChip device is to facilitate the SHERLOCK reaction within its reaction chamber and enable fluorescence intensity measurements via a smartphone. Additionally, we have developed a program for analyzing and quantifying the fluorescence signals from the PrymChip.
We first met with Professor Jakub Mielczarek from the Faculty of Physics, Astronomy, and Applied Computer Science at Jagiellonian University, who holds a patent for the 3D-printed device PE3DISH. We received practical tips on spatial printing, as well as instructions for operating Prusa printers, designing software, and preparing models in G-code for printing. We presented our ideas for the PrymChip, and thanks to Professor Mielczarek's experience, we gained insights into the costs associated with developing such a biosensor and the materials we would need to use.
The original PrymChip project proposed using filaments made from polylactic acid (PLA), which is biodegradable. However, this characteristic also makes it more prone to degradation and potentially less durable. Therefore, after consultations, we decided to use polyethylene terephthalate glycol (PETG), which is more suitable for environmental applications.
A graph detailing the principles behind the PrymChip.
One of the challenges we faced while designing the PrymChip was selecting and stabilising the light source for fluorescence excitation. We decided to consult with Dr Katarzyna Dziedzic-Kocurek from the Faculty of Physics, Astronomy, and Applied Computer Science at Jagiellonian University, who suggested incorporating LED holders into the model to stabilise the light source in the correct position. Heeding her recommendation enabled us to achieve consistent lighting across all the photographs.
She also recommended conducting a comparative analysis of the results obtained from LED diodes versus LED lasers and finally, we decided to use LED diodes.
PrymChip was tested by an independent researcher not involved in the project to assess its ease of use and identify potential improvements for future development. The process of detecting fluorescein fluorescence was carried out by Dr Grzegorz Bereta, a postdoctoral fellow at Jagiellonian University with extensive experience in proteins and enzymatic reactions. He worked with fluorescein concentrations ranging from 0.78 µM to 100 µM, which were prepared by a member of our team.
Dr Grzegorz Bereta capturing an image of the detection chamber containing a fluorescein solution with a smartphone.
General Feedback:
Proposed Improvements:
Additional Drawer for the Black Detection Box
The detection chamber occasionally slips while being placed inside the box, leading to liquid spillage. A sliding drawer mechanism could resolve this issue. The detection chamber itself does not require modifications.
Phone Stabilisation Issues
When using a smartphone without a case, the protruding camera made it difficult to stabilise the phone properly. Additional support to elevate the phone would help. While the issue was partially resolved using newly printed black supports, increasing the height of these supports and adding symbols to the box lids for alignment would be beneficial.
External Camera Alternative
Given the various settings and parameters of phone cameras, an alternative solution is proposed. Instead of using a smartphone camera, an external camera connected via USB could be employed. Designing a dedicated space in the lid for this camera would ensure consistent photo results and speed up the photo-taking process. This would also eliminate the need to adjust the Python script for different smartphone models, adding to our design’s standardisation.
Differences in photos of the same fluorescein concentration taken by two different smartphones: a) Samsung Galaxy S23, b) Google Pixel
Scientific conferences proved to be the ideal venue for consultations and gathering opinions. Numerous discussions and sharing experiences allowed us to identify weaknesses in our project, new directions for development, and aspects that still needed consideration. We aimed to present both the overall project and its components thoughtfully, choosing poster and presentation topics that resonated with the focus of each conference.
During this conference, students from our team presented posters and presentations on four different topics. They covered the overall goal and methodology of the project, as well as detection using PrymChip. The large audience was very engaged and asked plenty of questions. The following questions and opinions were particularly significant in shaping our project:
“A mobile application seems to be quite impractical”
After a joint discussion and reevaluating the rapid notification app's usefulness, we concluded that the existing government notification system seems sufficient. It is managed by experts, and alerts about threats are issued when algal quantity thresholds are exceeded, or when fish die-offs occur. Government organisations then send text messages and regularly publish reports on their official website [7]. Our app aimed to facilitate collaboration between state services, scientists, and the fishing community. However, we realised that making it available for public use could lead to social panic. Allowing inexperienced individuals to input data from our test could result in tracking false positive results. Considering the safety and practical aspects, we decided to abandon this idea.
“What other algae do we intend to test in our tests? How do we want to prove the specificity of our test?”
At the outset of designing our test, we researched the conservative yet unique sequences in the genome of the golden algae. According to the literature [8,9], the best sequences for this type of analysis are the ITS sequences, which should possess these characteristics. However, the preceding question prompted us to verify the thesis presented in the articles. We designed a control experiment involving the SHERLOCK test conducted on algal species other than Prymnesium, specifically the commonly found Chlorella sorokiniana and Chlamydomonas reinhardtii. We will carry it out as soon as we receive approval for the Check-In Form to use these species of algae. Additionally, we performed bioinformatics analyses and searched available databases for the sequences targeted in our test. As a result, these sequences were not found in the genomes of other organisms.
“The PrymChip is of an appropriate size; there is no need to reduce its size”
It was a very valuable observation that came after we addressed this concern. As a result, we focused on the next stages of device development, including selecting a light source to excite the fluorescence and searching for materials for the reaction chamber.
At the “Genomica” Conference, we presented a poster showing our project's progress. We felt a bit out of place among the other highly scientific posters during the session, as we didn't yet have much data gathered, and our poster mainly focused on our vision and design. However, the visual appeal of our poster and the easy-to-understand infographics drew the attention of many people – students and visiting professors alike. They approached us to learn more about the project and, most importantly, to ask questions and provide valuable feedback.
We found that the biology of Prymnesium parvum garnered significant interest from scientists, even at a conference primarily focused on genetics. Their questions inspired us to delve deeper into the life cycle of Prymnesium and to refine our culturing techniques, aiming to make studies on this non-model organism more widespread. After consultations with some experts in the field (Dr Ewa Górecka, Dr Paweł Brzezowski) we polished our Prymnesium parvum culture protocols.
Together with the 2023 IFB-Gdansk iGEM team, represented by Mateusz Rudnicki, and Dr Anna Puławska-Czub and Dr Marcin Ziemniak, who were part of the University of Warsaw's iGEM teams from 2009-2011 and 2013, and with the iGEM Ambassador for Europe, Marta Marcheluk, we introduced the participants of the conference to the principles of the iGEM competition, its vision and synthetic biology as a way to shape the future.
How to run a project and never run out of ideas: Lessons from iGEM worldwide synthetic biology competition panel. From the left: IFB-Gdansk team: Maks Dalecki, Adam Gackowski, Marta Sobolewska, Aniela Kosobucka, Mateusz Rudnicki; JU-Krakow team leaders: Nina Kurowska, Marta Luterek; Dr Anna Puławska-Czub; iGEM Ambassador Marta Marcheluk, Dr Marcin Ziemniak.
Participating in iGEM is not just about developing a project; it's also about being bold, brave, and persistent when presenting your ideas to the world. This is especially true when you're working to establish the very first iGEM team at your university, as we did.
At the conference, we aimed not only to spark interest in iGEM and synthetic biology among Polish students but also to gain tips and feedback from our predecessors to help improve our project. They noted that a strong aspect of our project is not only the local nature of golden algae blooms but also its global significance. Our analyses indicate that Prymnesium parvum has been responsible for ecological disasters in at least 13 countries worldwide. We also analysed the evolution of the golden algae and observed a division of strains based on the type of toxin produced (A, B, C).
A map showing in purple the countries where Prymnesium parvum blooms were recorded
During the Symbioza Conference, we had the pleasure of attending a workshop on problem-solving in biotechnology organised by BIOTON. BIOTON is a Polish state-of-the-art biotechnology company that provides patients with safe and comprehensive solutions to treat diabetes.
Dariusz Gurtowski, Bioton’s Science & Technology Director, advised us on problems we were facing in the lab regarding PCRs. Namely, different team members successfully carried out the reaction, while others in different laboratories didn’t, despite all conditions seemingly being the same. Mr Gurtowski shared his expertise in problem-solving techniques, and walked us through the fishbone diagram, which allowed us to identify areas that could be investigated to solve our problems. As a result, we were later able to carry out these ‘problematic’ PCR reactions successfully.
Due to our inability to obtain the expected results from the PCR reaction based on the publication [6], we decided to reach out to its author, Dr Luca Galluzzi. We considered two likely scenarios:
The reaction conditions we were using were not optimal.
The isolation of genomic DNA from Prymnesium parvum was contaminating the genetic material and preventing the reaction from occurring.
Thanks to this correspondence, we were able to get answers to our questions, and by applying the advice we received, we successfully resolved the issue.
None of our team members had any prior experience working with algae, making this aspect of the project particularly challenging. We had to start from scratch, learning about algae biology, culturing techniques, and the specific conditions required for their growth and maintenance. This part of our project wouldn't have been successful without the guidance of other scientists we consulted along the way. Their expertise and advice were indispensable in shaping our approach, helping us navigate this new research focus.
A scientist from the Department of Biochemistry and Plant Physiology at JU, who introduced us to the foundational principles of working with algae cultures, was Dr Paweł Jedynak. After collecting environmental samples, we had to learn how to work with Prymnesium parvum. He guided us through the basics, including the safety rules, the composition of F/2 medium, and the essential techniques for maintaining sterile conditions when handling algae cultures. His expertise and guidance were invaluable, particularly during identifying Prymnesium parvum through microscopic observations. Additionally, his insights inspired several experiments to optimise the culture, such as testing high-volume liquid cultures and exploring various lighting conditions.
During our algae cultivation, we noticed a decline in their numbers and changes in their morphology. This concerned us greatly, so we decided to reach out to other research teams in Poland and Germany that, according to reports, were also working with this organism. The only person who responded to our messages was Dr Ewa Górecka. A scientist from the University of Szczecin shared valuable insights into the culture conditions she uses and the ingredients of F/2 medium in stock solutions. Dr Górecka also shared with us the stocks of her reagents from which she composes the culture medium, which allowed us to check whether one of the reagents we used could cause our failures. Our consultations with her deepened our understanding of Prymnesium parvum requirements in a laboratory setting (mainly lightning) and allowed us to improve the condition of the algae we are cultivating.
We also requested a consultation with another scientist, Dr Paweł Brzezowski, from the Department of Biochemistry and Plant Physiology at JU, who drew our attention to the importance of maintaining the proper pH and composition of F/2 medium. Following our consultation with him, we initiated the process of optimising the medium and changed it from 5,5 to 7,3 (as he recommended). He guided us through working with algae in the lab to ensure a pure culture. By sharing his expertise, he introduced us to the technique of serial dilutions on culture plates and provided valuable advice on identifying Prymnesium parvum through microscopic observations. His dedication and support greatly enhanced our algae harvesting skills and inspired the design of further experiments.
During the Symbioza conference, one of last year's iGEM members from the DTU-Denmark team – Konrad Uściło, raised our awareness of the potential risk of causing public panic by introducing a Lateral Flow test for self-testing of environmental samples. This valuable insight and significant concern prompted us to consult our supervisors. Dr Paweł Jedynak, who has extensive experience in science outreach and science communication, advised us to compare our test to something the general public is familiar with (e.g., a thermometer) when speaking with them. For this reason, we chose to liken our test to a pregnancy test, as it is a well-known item with a similar function and appearance. We also decided to be very cautious when considering the potential distribution of our test in the future. It would require a well-organised educational campaign to minimise the risk of causing panic.
We received a response to our emails from Professor Bogdan Wziątek, who works in the Department of Tourism, Recreation, and Ecology at the University of Warmia and Mazury in Olsztyn. He is also the Vice-Chairman of the State Water Economy Council, the Chair of the Scientific Council at the Polish Angling Association, and an expert on the parliamentary team for the renaturalisation of the Oder River.
During our phone call, he once again emphasised the inadequate monitoring being conducted in water bodies. He noted that counting the algal cells under a microscope is labour-intensive and requires experience, while PCR reactions often yield "strange" results, which makes our solution seem quite useful. To him, a significant advantage of PrymDetect is that it allows for assessing the presence of algae in samples under field conditions.
He also pointed out an aspect we hadn't previously considered: sometimes, toxins are not released despite high concentrations of Prymnesium parvum in water bodies. A "stressor" is necessary for this to occur, such as a sudden change in salinity due to water discharges from mines. An example of this was the situation in the summer of 2023 when high concentrations of algae were recorded, but no ecological disasters occurred. Therefore, the most informative approach for taking action would involve testing for both the presence of the algae and the toxins they produce. His suggestion was a potential application for the second protein we synthesised – Cas13b. However, since our project had already branched out in many directions and our time until the finale was limited, we decided to leave this for future iGEM teams to explore.
We inquired about the usefulness of Lateral Flow testing. Professor Wziątek immediately responded that it is a tool that would provide a real picture of the scale of the situation. This method could be used to test water in reservoirs near mines and identify whether algal growth has already occurred at that stage. Such mass testing would help manage discharges and enable quicker responses. His enthusiasm for the Lateral Flow test led us to double down on our PrymFlow development.
During our conversation, we also identified additional future development opportunities for the project. As an expert in aquatic ecosystems, Professor Wziątek pointed out that blooms of golden algae may be correlated with the presence of other algae or microorganisms due to the complexity of ecosystems and food chains. Therefore, it would be essential to delve deeper into this topic and plan testing for the potential presence of additional organisms.
Throughout our project, we had the pleasure of working with and drawing from the experiences of many knowledgeable scientists from various fields.
Given that our cause united so many voices, we also decided to bring them together in one room!
We organised a meeting with our supervisors, advisors, and consultants to open a discussion about our project and its potential directions. What transpired was truly exceptional: we brought together scientists from three different institutions, with expertise in molecular genetics, bioinformatics, 3D printing, and algal culturing. This diverse mix of experiences and knowledge could rarely be combined under other circumstances, providing a unique opportunity for interdisciplinary collaboration.
During these discussions, we carefully listened as ideas clashed and came together to shape our project – from talks about algal morphology to the mathematical modelling of our solution. We had the chance to both listen to and actively participate in the incredible exchange of ideas about the cause we are passionate about.
One of the most valuable comments we received was from Professor Jolanta Jura, the Dean of the Faculty of Biochemistry, Biophysics and Biotechnology at the Jagiellonian University, who observed that the genetic material used for all previous SHERLOCK tests was isolated under laboratory conditions using specialistic kits. However, we did not propose any method for field isolation of DNA from algae. We immediately delved into the literature and began testing various in-field isolation methods, including isolation using Whatman paper dipsticks and steel ball bearings [10]. Based on our results we created a protocol for in-field DNA isolation.
To ensure that our SynLOCK system would be as useful as possible to the synthetic biology community and future iGEM teams, we consulted its initial design with an expert: Vinoo Selvarajah, a leader in iGEM Technology with extensive experience in part design. His feedback was invaluable in optimising our system for maximum utility.
In the first call with Vinoo we learned the following:
that the plasmid backbone we initially selected for our system was designed to hold basic CDS parts, but it wasn’t ideal for a device like our SynLOCK Cassette. Vinoo pointed us to more suitable backbone options that allowed for easier Cassette transfer and made our system compatible with the BioBrick standard;
how to best document parts as basic and composite;
that our system would benefit significantly and become more user-friendly if we integrated a reporter into the Cassette, allowing for easy visual screening of the correct colonies.
After considering Vinoo's input, we incorporated both the reporter and a new plasmid backbone into our system. We wanted to follow up after our last call and share our final designs in SnapGene to get expert feedback and see if the system makes sense or if any further tweaks could improve the design.
During the call, we discussed our SynLOCK system design in detail and demonstrated how it works using SnapGene simulations. We received feedback that the design was well-thought-out, which gave us the confidence to move forward with the lab work.
After completing the entire iteration of the DBTL cycle with our improved Cassette design and having lab data ready to showcase, we decided to reconnect and schedule another call with Vinoo. In this conversation, we:
Presented our lab achievements and the data we gathered
Received advice on how to best document the parts on the registry for future use by iGEM teams
Learned how to manage twin parts that appear on the registry
Got valuable feedback on the parts we plan to propose for Best New Composite Part and Best Part Collection awards.
ValleyDAO is a global non-profit organisation that provides funding and translational support for synthetic biology research. Its founder, Albert Anis, invited our team to present our project findings and receive feedback.
During the call, our team leader, Nina, presented the project's vision, the problem we aim to solve, our proposed solution, and the achievements we’ve made so far. We received valuable tips on presenting our research to a broader audience, what to focus on during the judging session, and which accomplishments to highlight.
Most importantly, we received advice on addressing some unresolved lab challenges, such as issues with in-field DNA isolation. We also learned about available options for in-field sample concentration requiring minimal equipment, making our test even more applicable in field settings.
During our iGEM journey, we ran into several legal considerations. We needed to figure out whether we should legally protect the PrymChip and whether we might be infringing on any existing patents. Piotr Widerski, the chief specialist and director of administrative affairs at the Faculty of Biochemistry, Biophysics, and Biotechnology at Jagiellonian University, helped clarify our doubts.
As our iGEM project for this year’s competition nears completion, we have started making plans to ensure its continuation in the future. We believe in the significance of early detection of Prymnesium parvum which is why we arranged a meeting with Prof. Dariusz Dziga, an expert from the Faculty of Biochemistry, Biophysics, and Biotechnology at Jagiellonian University, to discuss potential collaborations and pathways for further development of our project.
During the meeting, we presented our findings and the project's key achievements, focusing on the data we gathered and the aspects that still require further optimisation.
Professor Dziga expressed that he sees great potential and a strong need for this type of test. He mentioned being open to forming a dedicated group at our university to focus on optimising the test and advancing it toward becoming a widely used tool. He also shared his hope that our test could play a critical role in ensuring the safety of aquatic ecosystems affected by Prymnesium parvum blooms, highlighting its importance in protecting these environments.
Our project resulted in a collection of tools designed to address the recurring ecological disasters caused by blooms of Prymnesium parvum, as well as tools to enable the easy creation of similar SHERLOCK tests. Its development was inspired by media reports, government documents, and conversations with fishermen who witnessed these catastrophes firsthand. The project's progress was made possible through collaboration with experts from biotechnology companies, scientists, consultations with government institutions, and critical public feedback.
We are incredibly grateful to everyone who contributed to shaping and advancing this initiative.
It’s also worth noting that our entire team demonstrated remarkable creativity and worked with tremendous dedication. Despite pouring our hearts and free time into the project, we thoroughly enjoyed the experience, knowing that we were making a positive impact on the world around us.
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