Team:Vilnius-Lithuania/Human Practices
Human practices
iGEM provides a wide range of possibilities for aspiring young scientists aiming to develop and implement their ideas. iGEM involves different stakeholders, such as students, academia/scientists, public authorities, and private businesses, who exchange ideas in developing solutions for the same issues.
Our project development includes three most important stages: 1) forming a team, 2) shaping the idea, 3) implementing and improving the processes according to received feedback. The outcomes of each stage, such as conversations, discussions and received feedback, shaped our project and were crucial for pushing forward our final product -"Colight".
The focal point of the forming stage was the meeting with our long-term sponsor Thermo Fisher Scientific Baltic, which has significantly contributed to the development and achievements of our team goals by supporting the preparation of the strategic plan. The plan outlined the main team rules and indicators on how to measure our progress in order to succeed as a team.
During the implementation of the project, we were aiming to receive as much different feedback as possible. We were consulting the representatives of various fields, including but not limited to, academia, business, public authorities, and the general public.
Based on the discussions with bioinformatics specialists, we established the idea of necessary analytical tools for in silico metagenomic mining. The development of the software was one of the most fundamental parts of our project, which was remarkably refined during our organized event-BioHackathon'19.
The aforementioned debate led to the evolution of our project from a transcriptional light-inducible system to a framework for multilevel light-control in bacteria that we are proud to introduce – "Colight".
Please follow our interactive timeline by clicking on each of the icons to learn more.
Team-building
We started our journey to Boston in mid-January when the new team of Vilnius-Lithuania iGEM gathered. The first team forming activity under informal direction umbrella took place in mid-February when the whole team had a workshop on team dynamics and conflict management. The workshop was led by a professional facilitator and consultant on strategy management Mrs. Eglė Daunienė, an Associate Professor of Vilnius University, and was mainly focused on the formation of the team at different stages of its development.
Everyone was asked to name 'my why' – the purpose of joining the team and expectations for the following year. This exercise is designed to make everyone feel the freedom to express their ideas and accept positive and negative feedback.
Another focus point of the workshop was team roles. Each team member was provided with the theoretical descriptions of four role areas: 1) interpersonal roles; 2) informational roles; 3) analytical roles; 4) acting roles.
Finally, we were told what problems may arise and what are the ordinary stages of a winning team. Team members were introduced to Tuckman's stages of group development: Forming, storming, norming, and performing.
Read more in our Team Building Handbook
Implementations:
- Understanding of Tuckman's model at the very beginning of our team forming stages helped a lot in the future. One of the most important aspects was realizing that storming is a normal and even crucial stage of successful team development. However, if solved right, each conflict leads to an improvement in working. It is essential to understand that the storming stage comes to each team, and the worst choice is to ignore it. In our group, we had a rather long storming phase, understanding principles of team development helped us not to avoid conflicts but form healthy team relationships from the early beginning.
- The mapping of our team interpersonal role matrix showed that we have all types of people in our team, which turns out to be the best possible composition of the team, aiming to achieve common goals.
- Therefore, Vilnius-Lithuania 2019 iGEM team was able to reach the peak of performing during autumn. We now know how to use everyone's potential, and this has lead to completing our project the best way we could.
Photos from team building workshop
Strategic plan preparation
One of our first meetings in iGEM was with members of our long-term sponsors – Thermo Fisher Scientific Baltics. During the session, we were encouraged to make a strategic plan for a year, as it would help us to better coordinate work and follow our progress.
After the meeting, we were introduced to Senior Business Excellence Manager Evelina Markauskė, who told us about the methods and philosophy implemented in Thermo Fisher Scientific. She also taught us about the X-Matrix, Lean Tools, Lean Management, and A3 Management.
Read more in our Strategic Plan Handbook
Implementations:
- After the meeting, our team prepared this year's plan.
- We have structurized our weekly meetings.
- We started filling a weekly plan and a progress table.
Photos from meeting with Senior Business Excellence Manager Evelina Markauskė
Forming Vilnius-Lithuania iGEM 2019 team
At the beginning of 2019, a group of students was selected by Vilnius-Lithuania 2018 iGEM team. This happens every year – the last year's team prepares a questionnaire and runs an interview session to choose new members from various disciplines, including math, computer science, politics, medicine, and, of course, biology and biochemistry. This is because every Vilnius-Lithuania iGEM team was, is, and will be entirely student-run and diverse, and we consider this our biggest strength. The PI, instructors, advisors, and anything else the team needs are selected during the year and depend on the project's main idea and the help needed.
Photos from interview session
Receiving good practices from previous Vilnius-Lithuania iGEM teams
The first month of the newly assembled students was dedicated mostly to meeting with the participants of the previous year's competition and learning from them as much as possible about iGEM in general, idea development, marketing strategies, PR, and other smaller, but crucial, things. Without these talks, we would not have been able to navigate during the first few months.
Implementations:
- The team decided to spend January gathering knowledge about synthetic biology and other iGEM projects, only then progressively move on to generating the idea. This meant studying from the edX course "Principles of Synthetic biology" and reading the most recent articles in the field of synthetic biology.
- During our weekly meetings, we presented the best iGEM projects to each other and discussed them to learn about the types of projects and what can be done in a year.
- The new team agreed to organize Biohackathon for the second time.
- We were recommended to do team-building with the help of professionals.
- Members with no previous experience got accustomed to the working discipline and tempo that a competitive iGEM team requires.
Photos from meetings with the participants of the previous year's competition
Prof. Rolandas Meškys
Because we wanted to work with metagenomics and create systems that would help in various areas of biology, including biocatalysis, our team reached out to Professor Rolandas Meškys, the head of the Department of Molecular Microbiology and Biotechnology in Life Sciences Center.
Prof. Meškys encouraged us to follow through with this idea as it is a growing field with huge potential. He asked about the applications of optogenetics in bacteria, and while discussing it, we came up with a way to apply light-inducible bacterial systems in cancer therapy. We postulated that this would allow treatment to be surgically non-invasive by allowing highly precise therapeutic protein release inside the tumor.
The professor also suggested not to limit ourselves with the search of new possible tools, but also, by applying rational design, develop optogenetic tools from known proteins.
Since Prof. Meškys had such great insight, we asked him to take the role of our Principal Investigator, and he gladly accepted. Vilnius-Lithuania 2019 iGEM team feels very proud to have such an established member of the academia as our PI.
Implementations:
- Together we came up with the Idea of application - light inducible bacterial systems in cancer therapy.
- Decided not only rely on in silico metagenomic mining but try rational design for creating novel optogenetic tools.
- We welcomed our new PI.
Photos from meeting with Prof. Rolandas Meškys
Dr. Darius Kazlauskas
We had a meeting with Dr. Darius Kazlauskas, who is a scientist working with in silico metagenomics. In one of his projects, he tried to assemble viral genomes from various metagenomic datasets. He worked with Ebi-metagenomics, IMG/M, iMicrobe.us. However, he had problems with the biggest metagenomic database MG-RAST, which stores more than ten times more information than all the other databases together.
According to him, there are massive problems with some databases, especially MG-RAST, as the data is not structured. Moreover, data storage and analysis requires enormous amounts of system resources and advanced expertise in the field. Therefore, we decided to work further with the MG-RAST database for gene mining of novel optogenetic tools. We made an aim to open up this metagenomic database for scientists with no prior IT knowledge and to provide a means to develop new parts in synthetic biology.
Implementations:
- Decided to work with MG-RAST
Photos from meeting with Dr. Darius Kazlauskas
Thermo Fisher Scientific Baltic
It is essential to gather as many different opinions as possible, and what can be more different than business and academia. Our team wanted to find out about the potential applications and marketability of our project from the business point of view. So we organized a meeting with Dr. Remigijus Skirgaila, a scientist from Thermo Fisher Scientific, and his colleague Dainius Tautvaišas, an iGEM judge, who helped to organize this meeting and often provided our team with general consulting.
Team members were pleased to hear that optogenetics might be the key to make the regulation of bacteria easier. Dr. Skirgaila saw our project as being technically implementable, as well. We also learned that as far as they know, bacterial control is only possible at the transcriptional level.
Moreover, they were very interested in our metagenomic sequences mining software. They told us that we should seek the development of this software thoroughly as it would open up a possibility to access a considerable amount of data. They also suggested to do a cloud-based system and to contact with cloud offering companies such as Google.
Implementations after a meeting:
- We understood that in silico metagenomic mining has considerable potential.
- Our team contacted Google to receive a cloud for performing computations.
- We started to discuss the possibility of control not only at the transcriptional but also at the translational level.
- The team started to think of ways to make our project more marketable.
Photo from meeting with Dr. Remigijus Skirgaila from Thermo Fisher Scientific Baltic
Lithuanian School Student Union
Vilnius-Lithuania 2019 iGEM team had a chance to participate in the Lithuanian School Student Union (LMS) organized event – Student Organization Fair in Memory of the 30th Anniversary of The Baltic Way.
I fear that even if I were able to create the most nonsense idea for my book, scientists would find a way to say – well, that is already possible!
In the event, we created a quiz inspired by famous Lithuanian public figures - publisher Tomas Ramanauskas and philosopher Kristupas Sabolius who run an online channel to foster pupil creativity. They took synthetic biology as an example of a source of inspiration for writing a science fiction novel. One of their concerns took our attention. “I fear that even if I were able to create the most nonsense idea for my book, ” T. Ramanauskas explained, “scientists would find a way to say – well, that is already possible!”. Inspired by this idea, we wanted to see whether people could distinguish real synthetic biology projects from futuristic ideas and science fiction, while also having a meaningful conversation with them. This way, we were aiming to introduce the possibilities of science through some examples of applications.
During the event, we gave participants six synthetic biology projects, including a description of our iGEM project. Their task was to select two projects that have already been completed, two which are currently being developed, and two ideas that fall under the science fiction or futurism tab.
For the already completed projects, we introduced digital information coding in bacteria genome and synthesis of spider’s silk in yeast.
We talked about how information coding in the bacterial genome will prevail in the future since we will be short of data storage resources soon. Another presented project was spider’s silk that is produced by yeast – researches have created new material that mimics spider silk’s strength, stretchiness, and energy-absorbing capacity. Surprisingly, the majority of participants had already heard of these inventions and were able to distinguish them quickly.
The second part included projects that are being developed. We described our iGEM project (light-controlled bacteria). Interestingly, some people described it as futuristic, as we described it more as a fundamental project and didn’t mention application fields. The project that captured the participant's attention the most was bioluminescent plants and algae. Explaining the main steps of gene cloning and giving some examples of inserting fluorescent protein-coding genes to plant genome, we were seeking to introduce people to applications of synthetic biology in everyday life. Plants that could work as night lamps brought immense attention not only from young people but also from the elders, who thought that would be suitable for home decoration.
To represent futuristic projects, we chose the Designer Baby project, which would enable parents to choose their desired characteristics for their future children. Most of the participants immediately distinguished it as not yet possible. However, when discussing the possibility of altering a baby's genetic make-up, people found themselves in a moral quandary. Some would like to use this application to avoid hereditary illnesses. Still, the majority of people saw it as an unethical and unsafe procedure. The last project we presented was about synthetic cells that could be designed and programmed over a personal computer and then created from scratch. Most of the time, participants choose this project as already developed. People mostly thought it was the same as genetically modified organisms. Although some of them were not familiar with the method of GM organism's creation and after our explanation, they were enthusiastic to know more.
Implementations:
- We noticed that people happen to distinguish synthetic biology projects as futuristic when everyday life application is not provided. Therefore, in our future presentations, we included more examples of synthetic biology's practical use.
- Even though participants knew some facts of biotechnology and synthetic biology, the majority still lacked some background knowledge about biotechnology methods and principles of biology. Thus, we decided to include more practical activities in our future events.
Photos from Lithuanian School Student Union (LMS) organized event – Student Organization Fair
Student for one day
Vilnius-Lithuania 2019 iGEM team participated in the Vilnius University event Student for One Day. During this event, we not only presented our project and synthetic biology in general but also included some practical tasks.
High school students were given a chance to do some laboratory work and at the same time, learn about the methods and principles of biotechnology. They performed an experiment to incorporate urease into alginate capsules and then used these capsules to detect urea. This way, they learned that urease hydrolyzed urea to ammonia and carbon dioxide and were able to gain an understanding of indirect measuring methods (in this case, change in pH to detect urea). This was applied to estimate water pollution in various samples.
After the practical tasks, the students split into groups to participate in a synthetic biology quiz, which further deepened their understanding of possible biotechnology applications. Their final exercise was to think of a real-world implementation of our light controlled bacterial system (as our team members were explaining the mechanism of the system before, they skipped this part on purpose). Real iGEM participants blended with the student teams to act out a brainstorming and idea pitching session. And even though students regarded the task as challenging, they were able to create genuinely original ideas. The most imaginative idea was about a bacterial strain that could be used for repairing buildings. As light penetrated slits in a ruptured brick, it would activate a response in bacteria for secreting appropriate substances, thus fixing the break.
Implementations:
- Simple, practical exercises attracted the pupil’s attention when explaining biotechnology methods and presenting synthetic biology. Therefore, we included more practical experiments to explain theoretical principles in our future presentations.
Photos from the event Student for one day
International Conference The COINS 2019
Both 2018 and 2019, Vilnius-Lithuania iGEM teams participated in an international conference of life sciences The COINS. Here we attended company fair and made both oral and poster presentations of the 2018 Vilnius-Lithuania iGEM team project.
More than 300 students attended the presentation to hear about iGEM competition and synthetic biology. This presentation was the very first from Vilnius-Lithuania iGEM 2018 to our local community after they had come back from Boston.
The attention of participants was captured not only by the last year's but also by the current team. New iGEM participants were reaching out to potential sponsors, mentors, communicating with interested members of the academia.
Most importantly, our team had an exclusive opportunity to talk with the Nobel prize laureate in Physiology or Medicine in 2014, Prof. John O'Keefe, and hear the story of his life, research, as well as the path of becoming such an esteemed member of the scientific community. He talked passionately about the importance of interdisciplinary thinking, especially philosophy, and not giving up when it seems rough.
Because Prof. O'Keefe is a neuroscientist with a background in engineering, he was able to point out the benefits of implementing engineering principles while working with biological systems. This was important to us, as we were already thinking of working with optogenetics, the start of which is also closely related to neuroscience.
Also, we took the professor's advice on interdisciplinarity, therefore later on we tried to discuss our project with mathematicians, physicists. Moreover, every time organizing an event, we tried to invite as intellectually diverse people as possible (for example, we asked the philosopher Dr. Jonas Čiurlionis, to participate in our discussion on the future of humanity and technology).
Photos from International Conference The COINS 2019
International Biology Olympiad
Vilnius-Lithuania 2019 iGEM team did not miss a chance to help students preparing for the International Biology Olympiad. We organized a practical work activity based on Practical Paper 2 from the 2015 International Biology Olympiad.
During the practice, students performed standard lab procedures, such as PCR, restriction analysis, and gel electrophoresis. The experimental work required critical thinking and previous knowledge as the participants had to choose the required temperature, restriction enzymes, and primers. When they finally got the results, they learned how to interpret them and make the right conclusions.
After the experiments, we examined the main mistakes. Then we showed tips and tricks preparing reaction mixtures for PCR and restriction analysis and together discussed the results. Afterward, the students were introduced to iGEM competition, synthetic biology, explained to why and how the principles of engineering and Boolean logic are used in the process of creating a genetically modified organism. Moreover, we invited them to join the competition during their studies at Vilnius University!
Photos from International Biology Olympiad
Kotryna Kvederavičiūtė
In March, the team had a meeting with Ph.D. candidate Kotryna Kvederavičiūtė who works in the field of bioinformatics to discuss our approach to in silico metagenomic mining.
Firstly, Kotryna suggested finding access to enough computer memory and computational power to store all the necessary data and run the algorithms needed for our software. Together we found a way how to solve this problem. Our team members asked Prof. Juozas Rimantas Lazutka if we could link together the computers in the Life Science Center computer class to perform our calculations.
We also settled on using Blast or HMMER algorithms for our software and that the best way would be to search among already translated sequences.
We discussed the possibilities of using different platforms for searching sequences with protein domain profiles.
Implementation:
- We settled on using Blast or HMMER algorithms for our software and that the best way would be to search among already translated sequences.
Photos from meeting with Kotryna Kvederavičiūtė
Prof. E. Sužiedėlienė and Dr. Justas Dapkūnas
Having the idea that we could extract light-modular transcription regulators from metagenomes, we searched for the way how to find sequences which our newly discovered protein bind to.
Our team met Dr. Justas Dapkūnas, who works in the field of bioinformatics as a researcher in the analysis of protein structure, surface properties, and interactions. We reasoned that by using bioinformatic tools, we could predict a DNA sequence that a protein of interest could bind to.
However, team members heard from Dr. Dapkūnas that this sort of protein structure modeling is a possible but extremely challenging task. The first difficulty stems from the fact that sometimes completely unrelated protein bind to the same DNA sequences, and other times homologous protein bind to entirely different DNA sequences. Secondly, it could be possible to predict the DNA sequence by docking a very closely related protein with a known structure to genomic DNA from the organism the protein of interest comes from. However, this method would not be possible, as our protein sequences would be gathered from metagenomic databases.
After this conversation with Dr. Dapkūnas, we understood that we would not be able to find the needed DNA sequence in silico and would have to find them by performing in vitro experimentation. Therefore, we asked Prof. Edita Sužiedėlienė to give us a piece of advice. She suggested performing double-stranded SELEX (Systematic evolution of ligands by exponential enrichment). This approach started by expressing our protein of interest fused with an affinity tag in E. coli. The next step would be immobilization of the protein on beads and bringing double-stranded chemically synthesized random nucleotide containing oligonucleotides. Professor Sužiedėlienė warned that the assay might be noisy; therefore, we should be prepared to optimize the conditions as much as possible.
Implementations:
- We understood that finding DNA binding sites in silico would be too challenging. Therefore, we decided to use in vitro method.
- We decided to use the double-stranded SELEX method to find the protein binding sites of the undescribed protein of our research.
Photos from meeting with Prof. E. Sužiedėlienė and Dr. Justas Dapkūnas
Irmantas Rokaitis
We decided that the best approach for searching for the protein binding sequence in DNA would be running five cycles of SELEX followed by EMSA (Electrophoretic Mobility Shift Assay) to separate the oligonucleotides that attach to the protein and those that do not. However, standard EMSA requires a radioactively labeled DNA sequence.
Irmantas Rokaitis is an MSc Student of biochemistry, currently working with the EMSA technique. As he has been a member of two previous iGEM teams, we decided to invite Irmantas to discuss lab safety. He told us that ordering radioactively labeled nucleotides is only possible under specific circumstances. He also said that if we were able to get everything needed, we should find a lab space that is suitable for this sort of work and meets all the requirements.
As an alternative to radioactively labeled nucleotides, he suggested us to use fluorescent-labeled DNA. Even though it has a lower sensitivity, it would be a much safer alternative.
Implementations:
- We settled on using fluorescent-labeled DNA for our following experiments instead of radioactively labeled nucleotides.
Photos from meeting with Irmantas Rokaitis
Biohackathon
During our annual Biohackathon: Lab issues event, four members of the Vilnius-Lithuania iGEM 2019 team were participating as an individual team; however, they could not compete for any of the prizes. This allowed us to get numerous consultations and discussions with top-level scientists and engineers in the field.
The team's initial software idea was to build a metagenomic analysis desktop app for finding a protein with desired characteristics that would use local system resources and would work on any operating system. Before even starting to write the code, our team had a set of concerns about the software being a desktop app, data cleaning, and hardware problems like storage and processing power.
Photos from BioHackathon
Michail Chrunov
After having our first consultation with Michail Chrunov, desktop software developer, a decision was made to create the software as a web service application. According to Mr. Chrunov, this would increase the reachability and would be more convenient for those who just want to try it without having to install or download additional files. Additionally, this way, the app would use our hardware so we could be sure the analysis to be completed without any hardware-related errors.
Implementation:
- We decided to build software as a web-service application instead of a desktop app.
Photos from BioHackathon
Dr. Justas Dapkūnas, Dr. Kliment Olechnovič, Kotryna Kvederavičiūtė
The next major challenge was solving one of the biggest problems in metagenomics, that is, removing the duplicates from the multi-million sequence FASTA format files and to standardize the sequences for further analysis. Although at first glance, it seemed like a simple enough problem, we later found out that it is a well-known ongoing issue within the bioinformatics field. We had lengthy consultations and discussions with Dr. Justas Dapkūnas, Dr. Kliment Olechnovič, and Kotryna Kvederavičiūtė, and it took us numerous hours until we came up with an algorithmic solution for the problem. After implementing it and improving the code, we ended up having a tool that not only removes duplicates but also standardizes and cleans up the data, which is a must-have for a flawless analysis.
Implementation:
- Solved the duplicate problem and implemented standardization & cleanup algorithms.
We then moved on to tackling the problem with space for data storage. Since metagenomic data collections take up terabytes of data, we figured that it wouldn’t be cost-effective to let every user store their data on our servers. Dr. Dapkūnas suggested that we could use the best-in-class clustering tool for this job, which takes out only a certain percentage of representative sequences and clusters them into a new, up to 70% smaller file. We were also told that if we are working with big data, the Apache Spark cluster-computing framework is a must.
The general discussions about our software included topics such as application, performance, legal rights, value, and its impact on the scientific community and the need for such software. We took in many opinions and suggestions from real professionals of their fields and came out of this event with a result we are proud of and hope it can make a breakthrough in the scientific community.
Photos from BioHackathon
Final Project
According to the feedback our team managed to implement our project from a transcriptional light-inducible system to a framework for a multilevel light-control in bacteria.
“Colight” - a multi-level collection of optogenetic tools for modular bacteria control. Our newly developed systems fulfill the gaps in optogenetic bacteria control in transcription regulation and open up a possibility of light control expression dynamics in plasmid copy number and post-translational levels.