Difference between revisions of "Template:Vilnius-Lithuania/JS/Integrated"

Latest revision as of 00:37, 28 October 2020

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let eventsDesc = {
    newteam: {
        title: 'Forming Vilnius-Lithuania iGEM 2020 team and receiving good practices',

desc: '

Our journey on Vilnius-Lithuania iGEM 2020 started when last year’s team formed a group of students from different disciplines: IT, medicine, biochemistry, genetics, biophysics, molecular biology and more.

', contr: '

One of the biggest help from previous Vilnius-Lithuania iGEM 2019 was coordinating the first months of our iGEM experience. We received a lot of good practices, starting from what is an iGEM project and what it consists of. They also gave us tips on planning our time, encouraged us to study the EdX course "Principles of Synthetic biology” and to read articles on synthetic biology.

The previous team gave us instructions to meet up a couple of times a week and to prepare presentations about previous iGEM projects that did well and that interest us. Last year’s team also encouraged us to start brainstorming ideas as soon as possible. Finally, they also highly suggested having a team-building session with the same instructor that they had last year since it helped to find each other’s strengths and weaknesses, it helped to bond and formed a strong team.

', adjust: '

While doing iGEM projects presentations, we learned a lot about the whole concept of it and edX course helped us to start thinking about ideas. We began brainstorming sessions soon after that. At first, we had a lot of ideas, but the majority of them were dismissed because it was unattainable or would take too much time. Once we found some possible ideas, we started researching it even more.

Due to the pandemic, we were not able to have team-buildingteam building with the help of professionals. However, we did an online team building virtually, which was both fun and beneficial. Later on, we had individual calls with our team leader where we talked about our goals for iGEM competition, what we want to learn and take away from this project.

', next: '

Our team had to continue researching literature and thinking of new ideas. Also, we got used to the working tempo and workload that being in an iGEM team requires. We continued to strengthen our team, learned to listen to everyone’s ideas and give all of them a chance in becoming a potential project, however, constructive criticism is always needed. After the team building session, we divided into smaller groups that did separate research into different ideas. This helped us to dive deeper into analysis and to determine which ideas are worth our time and could be a great project.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/9/90/T--Vilnius-Lithuania--integrated-forming.jpg',
    },
    coins: {
        title: 'Participated in international life sciences conference The COINS 2020',

desc: '

For the third time, Vilnius-Lithuania iGEM team has taken part in an international conference of life sciences The COINS 2020. During this event, our team not only presented oral and poster presentations about the 2019 Vilnius-Lithuania iGEM team project Colight, attended a company fair, did a workshop for high school students (hyperlink -> read more about these activities here) but also, had a lot of inspiring conversations with scientists from all around the world.

', contr: '

One of the biggest highlights of The COINS 2020 conference was an opportunity to meet and exchange thoughts with the Nobel prize laureate in Chemistry in 2004 Aaron Ciechanover.

During the conversation, he told us a lot about his research on the method that cells use to degrade and recycle proteins using ubiquitin. It was interesting not only to hear about his findings but also to discuss how scientists pick a field for their studies.

In addition to this, at this conference, we have met another inspiring scientist - prof. Peter Hagemann who won a Warren Alpert Foundation Prize for the discovery that led to the new technology - optogenetics.

Besides a brief discussion of last year’s Vilnius-Lithuania iGEM 2019 project Colight, our team was encouraged by him to discuss our ideas with specialists from different fields.

', adjust: '

Firstly, after these conversations, we decided to filter out our ideas by its global relevance and we asked ourselves if our project could solve some significant problems. Also, we were encouraged to discuss these preliminary ideas with specialists from different fields.

', next: '

To reject as many non-significant problems as possible and conduct broader research on arising issues with exogenous fish infections. Also, later on, we reached out with companies and other specialists to get a more comprehensive range of views on how we can implement our project in real life.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/1/19/T--Vilnius-Lithuania--integrated-coins.jpg'
    },
    pi1: {
        title: 'Presenting the idea to our PI prof. Rolandas Meškys',

desc: '

After gathering many diverse ideas we have decided to present them to distinguished prof. Rolandas Meškys who is the head of the Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center and has a vast knowledge regarding molecular biology, genetic engineering and biotechnology. He also was the PI of Vilnius-Lithuania iGEM 2019 team.

', contr: '

During the meeting, we presented and filtered out a lot of ideas for this year’s project, but the main focus was given to bacterial fish infections. More accurately, during this meeting, we were talking a lot about the detection and treatment strategies for fish who have been infected with F. columnare.

This discussion with the professor was an eye-opening experience because he pointed out many things which had not even been considered yet. For example, until the meeting, we had not thought about which genotype and serotype of the bacteria we should use for experiments. Also, we saw a huge need to dive deeper into the analysis of the mechanisms of the proteins which have depolymerase activity. Professor also suggested us to think more about alternative prevention strategies - from genetically engineered biological filters to vaccination.

', adjust: '

After this meeting, we gained more motivation and reasons to establish FlavoFlow as our 2020 iGEM project. Also, this led us to introduce the prevention part of our project. At the end of the meeting, we asked him if he could be our Principal Investigator and he kindly accepted this request.

', next: '

In order to progress onwards with our project, we had to do more research and complete detection and treatment parts. Also, we had to determine which protocols and parts will be used in the project. In addition, our team had to take a closer look into the possibilities of the prevention strategies and choose the most suitable one.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/4/49/T--Vilnius-Lithuania--integrated-meskys1.jpg'
    },
    fishfarms: {
        title: 'Talks with various fish farms to learn about the current situation of fish diseases',

desc: "

When our team was getting closer to choosing exogenous fish infections as our target for this year's project, we decided to gain more information about the situation of this kind of infections in our country. After a lot of research, we saw that it is quite hard to find statistics about diseases in aquaculture farms. Due to this reason, we started to talk about it with fish farms directly.

", contr: '

While making calls, we were yet undecided on what diseases exactly we will be focusing on during the project. Because of that, we called to farms which grow warm and cold-water fish. We asked if they encountered various outbreaks of infections in their farms and what are the next steps after they find out what causes the disease.

Also, we were interested to know if it is essential to identify the exact bacteria species which caused the infections as soon as possible. As we learned, nowadays, farmers need to send a live fish to the National Food and Veterinary Risk Assessment Institute of Lithuania, where it takes at least 2-3 days until the farmer gets preliminary results.

However, the biggest highlight of these phone calls was conversation with our future partners - rainbow trouts aquaculture farm FishNet. During the call, they said that only a few months ago they had a huge Flavobacterium outbreak in their farm and lost around 40 tonnes, which is equal to 125 000 euros, only in two weeks (keeping in mind that their farm gathers only 240 tonnes of fish per year - 50 tones of these losses are tremendous).

And the biggest problem is that they were not able to identify which of the flavobacterium caused these infections. Knowing that these bacteria are persistent and exist in aquaculture tanks all the time after fish immunity gets weaker, it will be almost impossible to choose an exact and most effective treatment as soon as possible.

', adjust: '

During these calls, we saw a huge need for point-of-care test development in Lithuania. It inspired us to pay more attention to this project part with the aim to find the most rapid and specific detection tool. Also, these conversations led us to choose our future partners for deeper analysis of the situation about exogenous fish infections in aquaculture farms.

', next: '

To make a deeper analysis on rapid detection tools for different pathogenic bacteria. Besides that, we saw that it would be great to obtain a view of this problem from a different perspective. Because of that, we decided to reach out to the National Food and Veterinary Risk Assessment Institute of Lithuania.

',

        mediaSrc: 'null'
    },
    nvrmi: {
        title: 'Consultation with the National Food and Veterinary Inspection (NFVRAI) specialist Darius Nienius',

desc: '

When we started to dive deeper into exogenous fish infections, a lot of questions about the situation in Lithuania rose up. With the purpose of getting practical insights into these diseases, we reached out to the specialist Darius Nienius from National Food and Veterinary Risk Assessment Institute.

', contr: '

During this meeting, Darius Nienius offered us a lot of practical insights from a governmental institution’s prism. At first, he gave us a few statistics about fish farms in Lithuania. Although, according to him, even if 90 % of aquaculture farms in our country grow carp, the most modern and responsible are the fisheries which grow salmon, trout or other cold-water fish. It is related to farming principles, which are based on ES requirements. Also, they are using RAS systems which are widely spread not only in Europe but also all around the world, so infections in these systems are relevant for a wide range of people.

However, the specialist confirmed that today NFVRAI does not have any certificated protocols for Flavobacterium spp. detection and that farmers can speculate about disease only from physical changes of fish. Furthermore, the conversation about detection methods of bacterial infections revealed a more significant problem – most of the farms do not take the risk of diseases seriously, and barely anyone sends fish specimens to NFVRAI for further investigation.

Besides of these problems related with pathogen detection, Darius Nienius also highlighted that today lots of farms treat fish symptomatically and choose an antibiotic according to whether the pathogenic bacteria is gram-negative or gram-positive, but they are not trying to identify an exact pathogenic bacteria with the purpose of adapting an accurate treatment method.

For the purpose of preventing infections, he stated the most effective prevention strategies in RAS aquaculture farms. According to him, it mainly includes usage of UV light, bacterial and mechanical filters, vaccination and strict control of the farming environment.

', adjust: '

Firstly, we concluded that Flavobacterium spp. definitely should be one of the main targets in our point-of-care diagnostic system development. Also, our treatment system should be directed to an exact bacteria species. This strategy could help to reduce antibiotics usage in aquaculture farms. Lastly, we pointed out that our aim to create a novel prevention method should be based on a filter or vaccine background.

', next: '

Reach out to the rainbow trout aquaculture farm FishNet with the purpose of obtaining a different perspective of the issue at hand. Also, discussion about the prevention of infections in RAS systems inspired us to pinpoint the pros and cons of bacterial filter and vaccine strategies.

',

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    },
    almira1: {
        title: 'Meeting about gold nanoparticles synthesis with prof. Almira Ramanavičienė',

desc: "

In April, we started to write protocols for experiments. At first, our team was confused and lost in the sea of different protocols to synthesize gold nanoparticles.

To clear things up we decided to have a virtual call with Vilnius University Professor Almira Ramanavičienė. Prof. A. Ramanavičienė is a group leader of the research group 'Nanotechnas' and has comprehensive experience in the synthesis of metallic and polymeric nanoparticles. Thus, we thought it would be great to discuss and take a deeper view of the gold nanoparticles synthesis protocol prepared by our team with her.

", contr: "

During the call, we talked about each step of the synthesis reaction and the professor gave us many great insights and advice which improved our protocol. She said that gold nanoparticles synthesized with tannic acid should not interfere with the further functionalization reaction and that newly synthesized solution must be kept at 4 degrees. Also it was very important to us to learn more about methods used to characterize gold nanoparticles.

Before the meeting we were pretty lost on how we should calculate gold nanoparticles concentration. Professor advised us that absorption spectra analysis is the easiest way to do this. She also encouraged us to try to measure its size by using a microscope. Finally, we discussed the possibility of synthesizing gold nanoparticles with the professor's help.

", adjust: '

After the call, we decided that it would be best if synthesis reactions would be performed in prof. A. Ramanavičienė’s laboratory where the necessary equipment and technical support would be available. Also, we decided to try out gold nanoparticles synthesized using tannic acid for the lateral flow assay test development - a method which we had not considered before.

', next: "

The professor’s laboratory was visited right after lockdown. During this meeting we finally synthesized gold nanoparticles and obtained a lot of practical information in synthesis protocols.

",

        mediaSrc: 'https://static.igem.org/mediawiki/2020/3/38/T--Vilnius-Lithuania--integrated-almira1.jpg'
    },
    fishnet1: {
        title: "Virtual meeting with rainbow trouts aquaculture farm 'FishNet'",

desc: '

In the middle of March we concluded that this year we will be focusing on the development of a comprehensive solution for exogenous bacterial fish diseases detection, treatment and prevention. However, even if we already knew a lot of crucial scientific information about these infections, it was important for us to gather as many different points of view as possible.

After a virtual meeting with the National Food and Veterinary Risk Assessment Institute of Lithuania, it became interesting and important to learn about the main bacterial infections directly from aquaculture farm owners. As we mentioned before, we decided to further collaborate with rainbow trout aquaculture farm FishNet. We have chosen this farm due to its responsible view of bacterial infections and openness to innovative exogenous fish infections solutions.

The farm also employs dr. Egidijus Leliūna, so it was very helpful to communicate with scientists who work in the industry and have a wider view of our target diseases. We conducted a deeper analysis of the principles of the RAS system and FishNet specialists told us even more about treatment and prevention strategies after seeing visual changes on fish.

', contr: '

Firstly, over the course of this meeting they suggested to concentrate on bacteria that could only affect cold-water fish. As the main pathogens, they excluded Yersinia ruckeri, Aeromonas salmonicida and Flavobacterium spp (F. columnare, F. psychrophilum and F. branchiophilum). Keeping in mind that each of Flavo can cause different diseases, it is crucial for them to be able to identify an exact Flavobacterium species as soon as possible in order to apply the most accurate treatment.

Besides bacterial diseases, representatives of FishNet aquaculture farm also talked about another problem – viral diseases. They said that it would be great to have some prevention tools for these diseases, since it is nearly impossible to prevent them by using filters or UV light.

After discussing what pathogens we should be focusing on, they also encouraged us to think about this detection tool not only from the scientific side. FishNet owner calculated that in two weeks Flavobacterium spp. can cause the death of 50 tonnes of fish, which equals to 125 000 euros of losses.

During the meeting, FishNet specialists also explained the main principles of the RAS system and paid a lot of attention to its filters, due to our preliminary idea of filters, which can catch Flavobacterium spp. directly.

', adjust: '

This meeting helped us choose three bacteria species as our target for rapid detection tool development – F. columnare, F. psychrophilum and F. branchiophilum. Furthermore, calculations of possible losses pointed out that we first needed to focus at point-of-care diagnostic tool robustness and specificity, and not on the test price.

Nonetheless, this discussion led us to change our prevention strategies. After we gained a lot of practical knowledge on bacterial filters in RAS systems, we realized that it would be more efficient to focus on subunit vaccines. That led us to reject our previous idea of creating a specific filter for Flavobacterium spp.

', next: '

Firstly we needed to make a deeper analysis of immunogenic proteins of bacterial and viral fish diseases that could be used as a vaccine. Also, we needed to start searching for different marker gene sequences that could help us to identify an exact Flavobacterium species.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/0/01/T--Vilnius-Lithuania--integrated-fishnet.jpg'
    },
    pi2: {
        title: 'Consultations with prof. Rolandas Meškys',

desc: '

After we decided to focus on the FlavoFlow project, quite a lot of questions arose during dry lab work. To tackle these questions we decided to have online consultation with our PI Rolandas Meškys.

', contr: '

From the numerous questions we had, the most important one for us was related with Flavobacterium bacteriophages, which proteins we wanted to use in our treatment strategy. Therefore, it was important for us to obtain as much knowledge related to this topic as possible.

During consultation, Rolandas Meškys suggested that we could possibly use Klebsiella species bacteria instead of Flavobacteria as Klebsiella was gram negative, uses the same autoinducer-2 quorum sensing system and has an ability to form biofilms.

Also, he mentioned that their department was working on Klebsiella phages. Due to this, our PI provided the plasmids with already cloned protein genes gp529, gp531 and gp533 thought to be exolysins for further treatment strategy development.

', adjust: '

Instead of using Flavobacterium phages we decided to use Klebsiella KV-3 phage RAK-2 exolysin in gene circuits of the treatment part .

', next: '

We had to induce the exolysin protein, purify it and test its activity on Klebsiella sp. bacteria.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/c/cc/T--Vilnius-Lithuania--integrated-meskys2.jpg'
    },
    fishnet2: {
        title: "Trip to 'FishNet' farm",

desc: '

Despite theoretical information about diseases caused by Flavobacterium spp. we wanted to see how it looks in a real farm and if there are any opportunities to collect specimens directly from fish gills. It was also important for us to understand how exactly RAS systems work in order to come up with the final treatment and prevention solutions.

', contr: '

When the lockdown was cancelled we finally had an opportunity to visit FishNet farm. Farm’s representatives Vaidas Juodis and Egidijus Leliūna showed us how persistent Flavobacterium spp. looks like and pointed out ways of taking fish samples. It was nice to hear that after so much time spent on this farm, they were already able to discrete sick fish by observing their eyes.

After we explained our project’s purpose it became clear that the point-of-care test would be used not only after seeing sick fish but also periodically with the purpose of observing its persistence over time.

This visit helped us to clearly understand how RAS and nutrition systems work. Also, it allowed us to make new insights into prevention and treatment strategies’ implementation.

', adjust: '

This visit helped us to understand the basics of the RAS system and how we can obtain samples directly from fish without committing any harm. Furthermore, during the conversation farmers suggested us to think not only about qualitative but also about quantitative detection tool development.

', next: '

We investigated whether we would be able to design a quantitative point-of-care detection tool. Also, discussions on how the final FlavoFlow detection kit should look like took place in the upcoming weeks.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/c/c6/T--Vilnius-Lithuania--integrated-fishnetTrip.mp4',
        video: true,
    },
    giedre: {
        title: 'Virtual consultation about helimerase with dr. Giedrė Tamulaitienė',

desc: '

When we decided to use the HDA amplification method to obtain ssDNA fragments for an LFA test, we started to think about how we could improve this method. After a lot of research we found out that one option to enhance the processivity of HDA reaction is to fuse helicase with polymerase.

However, with the discovery of this strategy a lot of questions followed up. To tackle those questions, we decided to reach out with dr. Giedrė Tamulaitienė who is a senior research associate at Vilnius University, Institute of Biotechnology and works directly with proteins who form interactions with DNA molecules.

', contr: '

One of the main questions for us was how can we improve this fusion strategy as well as to find out more ways of protein co-expression. She suggested us to focus on its co-expression at first. Giedrė gave advice to not to focus only on co-expressing TteUvrD and BstPol genes in different plasmids. Great option also could be the usage of plasmid with two MCS sites, where we express genes from only one plasmid.

', adjust: '

After this virtual meeting G. Tamulaitienė suggested for us to use pETDuet plasmid with the purpose of cloning both genes (TteUvrD and BstPol) into a single vector. This suggestion let us to reject the primary idea of two proteins co-expression from different plasmids. Also, she suggested to change BstPol purification tag from Histag to StrepII with the purpose of increasing the purification specificity.

', next: '

We changed in silico cloning strategy and ordered correct TteUvrD and BstPol genes.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/6/64/T--Vilnius-Lithuania--integrated-giedre.jpg'
    },
    vilnius: {
        title: "Meeting with Vilnius city administration for 'The 6th SynBio sense' project",

desc: '

One of our biggest Education and Public Engagement activities this year was <a target="_blank" href="https://2020.igem.org/Team:Vilnius-Lithuania/The_6th_SynBio_Sense">‘The 6th SynBio Sense’</a> project, the goal of which was to guide people of various ages through the basics of life sciences using Augmented Reality technology. We wanted to pursue this project in different cities of Lithuania and one of these was the capital - Vilnius. Our team met the representatives of the general education department to discuss the possibilities of implementing ‘The 6th SynBio Sense’ there.

', contr: '

It was the first official meeting for this project, therefore we gained valuable first-hand experience on how to work together with administration officials and what is the procedure for implementing projects like this. Also, we strengthened our entrepreneurial skills that eventually helped us throughout the whole year.

', adjust: '

After the meeting, based on received feedback, we wrote an official project specification and plan in order to request financial resources from the administration.

', next: '

Later in August we officially signed the agreement that ensured the financial backing for the implementation of ‘The 6th SynBio Sense’ project in Lithuania’s capital city Vilnius.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/3/3d/T--Vilnius-Lithuania--integrated-vilnius.jpg'
    },
    almira2: {
        title: 'Production of gold nanoparticles with prof. Almira Ramanavičienė',

desc: "

In the beginning of July two of our team members went to Vilnius University faculty of chemistry and geosciences to synthesize gold nanoparticles with professor's help. As mentioned before, professor Almira Ramanavičienė has a comprehensive experience in the synthesis of metallic nanoparticles.

", contr: "

Professor A. Ramanavičienė helped us with the process and we told her more about this year's iGEM project and further experiments to be done in the laboratory. Professor explained to us how synthesis reaction works in theory - that sodium citrate ions act as stabilizing agents and that tannic acid is used to control the size of gold nanoparticles. However, gold nanoparticles can be synthesized without tannic acid as well but boiling temperatures must be used. We took it into consideration and decided that if further experiments will be unsuccessful we will synthesize gold nanoparticles without tannic acid.

", adjust: "

After the meeting we successfully synthesized gold nanoparticles that were of perfect parameters which wouldn’t be the case if we would have done everything ourselves. The Professor's aid helped us to save valuable resource - time. Also we deepened our understanding in chemical synthesis of gold nanoparticles as well as their evaluation.

", next: '

Eventually we decided to keep in touch for further experiments with gold nanoparticles. Also we got previously synthesized nanoparticles without using tannic acid. It was decided to evaluate both types of gold nanoparticles in further experiments. The next step - functionalization with ssDNA probes was awaiting.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/7/7b/T--Vilnius-Lithuania--integrated-almira2.jpg'
    },
    kotryna: {
        title: 'Meeting about software development with dr. Kotryna Kvederavičiūtė',

desc: '

Our primary idea for software, which would significantly help our detection system, was to develop a universal primer and probe design algorithm for Helicase - Dependent Amplification (HDA) and Lateral Flow Assay (LFA). In order to do this, we consulted with one of the leading bioinformaticians in our university - dr. Kotryna Kvedaravičiūtė.

', contr: '

While the main steps of the algorithm were created earlier in June, in this meeting we received many tips on how we could improve it. For example, at first we were designing primers that were specific only to Flavobacterium but we learned that for a test like this, we should think broader and design specific primers for fish and other water organisms’ metagenomes as well.

', adjust: '

In the meeting we learned valuable things that helped us to design the second batch of primers and probes for the detection of Flavobacterium since the first one, designed entirely by us was not as specific as we wanted. As for software, the main problem we ran into a few weeks later was the lack of experimental data regarding the correct parameters for HDA primers and LFA probe design. After many discussions we decided to go the other way and develop <a target="_blank" href="https://2020.igem.org/Team:Vilnius-Lithuania/Software">onFlow</a>.

', next: '

We believe that this software would be very valuable for rapid bacterial species detection, yet at this moment there is insufficient data to create an accurate algorithm. Our team encourages future iGEM teams and researchers to further explore this idea.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/2/24/T--Vilnius-Lithuania--integrated-kotryna.jpg'
    },
    micromolds1: {
        title: "Designing 3D model of detection test case with 'Micromolds'",

desc: '

One of our point-of-care detection test traits should be its portability. To fulfil this criteria we concluded that it would be great to have a strip test case. After we started to search how we can create this test case, we saw that there are too many criterias for this type of test case development. Due to this we started to look further for the company who could help us with this product development.

And this is how we found plastic moulding company Micromolds. We chosen this company not only because of its excellence in this kind of projects, but also due to its social responsibility to work along with scientific communities and non-profit projects.

', contr: "

Micromolds mainly contributed in the design and manufacturing of a strip testing device. Before the meeting with micromolds representatives, we have imagined that the development of the test case will be easier. However, it was clear that for this strip test case it's important to know as many test dimensions as possible. Also, a big question on the strengths of fastening mechanisms has arisen.

Meeting also let us dive deeper into the main principles of 3D printing. We get acquitted that some complicated designs with small details intended for test stabilizing, are not possible due to limited 3D printing parameters.

", adjust: '

Even if a 3D printer is a cheap alternative for this type of cases printing, it has limited parameters, which does not allow it to print out. Before meeting with Micromolds we were not thinking that it is important to check the stability of membrane parts, but during brainstorm sessions we have decided to add some fasteners with the aim to stabilize membrane. So after this meeting we had to make a lot of different LFA test prototypes to check what parts of the test should be pressed against the protrusions in the test.

', next: '

Prepare a membrane prototype for more accurate test case dimensions calculations.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/7/7f/T--Vilnius-Lithuania--integrated-micromolds.jpg'
    },
    alytus: {
        title: "Meeting with Alytus city administration for 'The 6th SynBio sense' project",

desc: '

One of our biggest Education and Public Engagement activities this year was <a target="_blank" href="https://2020.igem.org/Team:Vilnius-Lithuania/The_6th_SynBio_Sense">‘The 6th SynBio Sense’</a> project the goal of which was to guide people of various ages through the basics of life sciences using Augmented Reality technology. We wanted to pursue this project in different cities of Lithuania and one of these was Alytus. Our team had the pleasure of meeting with the mayor Nerijus Cesiulis and his team to discuss the possibilities of implementing “The 6th SynBio Sense” there.

', contr: '

Unlike the first meeting in Vilnius, here we had the possibility to have a longer talk about this project and life sciences in general. At the meeting we gained valuable insight into how people with highly variable career paths (artists, administration officials, local museum staff) view and understand the main topics of life sciences.

', adjust: '

This helped us make some adjustments to the descriptions of the Augmented Reality scenes and make them even more understandable for a broader group of users. We also discussed the possibility of implementing this project by using large stickers rather than steel plates to make it more affordable which led to a faster realization of the project.

', next: '

Through continuous communication we designed the stickers that would be compliant with both parties’ requests and sent them out for the realization.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/1/10/T--Vilnius-Lithuania--integrated-alytus.jpg'
    },
    saulius: {
        title: "Meeting with lawyer Saulius Bareika to consult us about GDPR for 'The 6th SynBio sense' project",

desc: '

One of the newer concepts of developing ‘The 6th SynBio Sense’ project was to write our privacy policy. Since we do not have a member in our team, who is strongly familiar with GDPR and other privacy laws, we had a meeting with lawyer Saulius Bareika, who consulted us on how we should do it.

', contr: '

We received valuable information on the general structure of website’s privacy policy and what are the most important points that should be mentioned. Since our website does not require login, but uses phone camera access, cookies and Google Analytics, we received examples of some privacy policies that fall into a similar category as we do and it made a great impact for us in this area.

', adjust: '

Based on the given examples and tips, we wrote our privacy policy that complies with the GDPR. The policy was checked once again by lawyer Bareika to ensure that all required information is there.

', next: '

The privacy policy was uploaded to the website for “The 6th SynBio Sense” project and is now being used.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/8/84/T--Vilnius-Lithuania--integrated-saulius.jpg'
    },
    klaipeda: {
        title: "Meeting with Klaipėda city administration for 'The 6th SynBio sense' project",

desc: '

One of our biggest Education and Public Engagement activities this year was <a target="_blank" href="https://2020.igem.org/Team:Vilnius-Lithuania/The_6th_SynBio_Sense">“The 6th SynBio Sense”</a> project, the goal of which was to guide people of various ages through the basics of life sciences using Augmented Reality technology. We wanted to pursue this project in different cities of Lithuania and one of these was the third biggest - Klaipėda. Our team met with the representatives of the administration to discuss the possibilities of implementing “The 6th SynBio Sense” there.

', contr: '

After our presentation about the project, we had a successful brainstorming session with all the participants of the meeting. Not only did we discuss the location of the Augmented Reality stops, as we call them, but also different and exciting ways to promote the project.

', adjust: '

Since one of the participants of the meeting was a highly skilled artist, he helped us along the way of designing an eye-catching layout for the stickers and steel plates that would also fit the style of the city.

', next: '

Over a course of two months we managed to finally realize the project in Klaipėda. While the ongoing pandemic did stretch out the timeline of the release, it was the first city that successfully implemented the project. We were extremely pleased to implement not only hundreds of stickers placed all around the city, but also durable and long lasting steel plates that were placed on the benches located in the city center.

',

        mediaSrc: 'null'
    },
    paulius: {
        title: 'Meeting about helicase research with our advisor Paulius Toliušis',

desc: '

After we synthesized and purified helicase and polymerase we were interested in how we can determine its activity. Due to this we reached out with dr. Paulius Toliušis who is a junior researcher in Vilnius university Institute of Biotechnology Department of Protein-DNA Interactions.

', contr: '

Since Paulius Toliušis has worked a lot with helicases, it was very helpful to have a discussion about different helicases and what kind of experiments we should do in order to determine its processivity, melting temperature and other parameters. Furthermore, he pointed out that we will not be able to test helicase activity by using radiolabeled DNA. However, Paulius suggested us to base our experiments on SYBR intercalation into DNA.

Also, after we started to talk about methods on ssDNA, obtained after HDA assay, concentration measurements, he suggested us to measure it by using Qubit Fluorometric Quatitation.

', adjust: '

After we realized that we are not able to perform any experiments with radiolabeled parts, we have chosen to use SYBR GreenI dye for helicase and polymerase experiments. Also, he gave us insights on how we should plan our experiments. We were amazed by his passion for our project, so at the end of the meeting we suggested to him to become our advisor.

', next: '

Plan and perform future experiments with the TteUvrD helicase and Bst polymerase.

',

        mediaSrc: 'null'
    },
    juta: {
        title: "Meeting with Juta Rainytė and Dr. Rasa Petraitytė-Burneikienė",
        desc: "After numerous unsuccessful attempts to express an immunogenic protein in yeast, we decided to consult with PhD students Juta Rainytė and Dr. Rasa Petraitytė-Burneikienė, who work at the Vilnius University Life Sciences Center, the Department of Eukaryote Gene Engineering. ",
        contr: "Juta suggested different induction condition adjustments to optimize protein synthesis efficiency in S. cerevisiae and provided insight into our in silico constructs. Rasa advised us to try expressing the protein in different strains of S. cerevisiae and showed us alternative plasmid construction routes to improve the efficiency of protein purification.",
        adjust: "We decided to adapt the suggested strategies and to reject the idea of protein induction in Pichia Pastoris due to the experts' advice. In addition to this, Juta Rainytė and Dr. Rasa Petraitytė-Burneikienė kindly provided the necessary strains of S. cerevisiae for the suggested experiments.",
        next: "We needed to work on alternative plasmid construction routes and apply different induction conditions for yeast.",
        mediaSrc: 'null'
    },
    almira3: {
        title: 'Discussion with prof. A. Ramanavičienė about unsuccessful functionalization reaction',

desc: '

Professor A. Ramanavičienė has extensive experience not only in the synthesis processes of metallic polymers but also in surface modifications with different nanostructures and site-directed antibody and their fragments immobilization. For this reason this time we came to the professor with the gold nanoparticles functionalization with ssDNA probes problem.

', contr: '

During the meeting our team explained the problem and experiments to be performed with the gold nanoparticles to the professor. After, we discussed why the reaction would fail and lead to nanoparticle aggregation. Professor suggested trying multiple control experiments to determine which solution exactly causes the aggregation. Also, Professor told us more about different ways to functionalize gold nanoparticles with antibodies or DNA probes. We talked about how a low pH environment would be of immense importance for ssDNA probes with poly-A sequence conjugation to gold nanoparticles.

', adjust: '

After this meeting our team decided to omit the step of thiol group activation with DTT since it could be the cause of aggregation as well as to try a new method for gold nanoparticle functionalization based on low pH, because it is suitable for our probes created with poly-A sequence. All modifications worked and finally the reaction was successful.

', next: '

Having successfully conjugated gold nanoparticles to detection probes, the next step was to create and test a lateral flow assay test for the identification of two bacteria species: F. columnare and F. psychrophilum.

',

        mediaSrc: 'null'
    },
    micromolds3: {
        title: "Received final version of the detection test case from 'Micromolds'",

desc: '

People working at the Micromolds company, starting with their manager and ending with their engineering skills, were very accurate, clear and looked precisely into this task. Due to this, only after few improvements we were able to obtain the final detection test case.

', contr: '

During this meeting we talked about the principles of how this case was created. They explained to us why they made such decisions by creating the prototype and how the case could be improved in the future.

', adjust: '

Because we were satisfied with the final product, no further adjustments have been made.

', next: '

This receival allowed us to step closer towards the test’s implementation in the real world by creating a fully portable detection tool. Also, Micromolds gave us a template for 3D printing, so in the future other iGEM teams will be able to use it for their own diagnostic tool implementation.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/3/38/T--Vilnius-Lithuania--integrated-micromolds2.jpg'
    },
    taurage: {
        title: "Meeting with Tauragė city administration for 'The 6th SynBio sense' project",

desc: '

One of our biggest Education activities this year was <a target="_blank" href="https://2020.igem.org/Team:Vilnius-Lithuania/The_6th_SynBio_Sense">The 6th SynBio Sense” project</a>, the goal of which was to guide people of various ages through the basics of life sciences with Augmented Reality technology. We wanted to pursue this project in different cities of Lithuania and one of these was Tauragė. Our team had the pleasure of meeting the local museum director and his team to discuss the possibilities of implementing “The 6th SynBio Sense” there.

', contr: '

One of the goals of the project was to include not only the biggest cities of Lithuania but also some more sparsely populated areas that do not get as many life sciences directed activities like this one. At the meeting we had the chance not only to discuss the matters of the project but also to talk about the current situation of science education in Lithuania. We had an interesting discussion about the impact of genetically engineered organisms in our everyday lives and what their regulations are both worldwide and in the EU.

', adjust: '

This helped us to update our Augmented Reality scene about genetically engineered organisms, including both positive and negative aspects of it. It also inspired us to reach out to smaller cities, since the officials agreed that the lack of life sciences education in rural areas is a big problem.

', next: '

Right after the meeting we started the process of implementing the project in the city and it has been launched in a local park since the 21st of October.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/2/22/T--Vilnius-Lithuania--integrated-taurage.jpg'
    },
    contactfair: {
        title: 'Participating in the annual Vilnius University Contact Fair',

desc: '

Vilnius University students organize an annual contact fair, where the whole community is brought together. From a distinguished professor to a fresh first year student, from a start-up owner to a corporate company executive - everyone, that is or was a part of the university, is welcome to discuss, share ideas and network. We were invited to talk about the iGEM competition, our project as well as synthetic biology in general along with other student initiative representatives.

', contr: '

It was brought to our attention that a lot of the attendees thought about the science community as a closed up organization. Many were surprised to hear how students from different faculties, especially the humanities, can contribute to the iGEM competition or scientific research.

One of the attendees approached us with a question that led to a discussion on trust in science. He later thanked us for good arguments and emphasised that such conversations should be more public and heard by others.

', adjust: '

We became aware that there is a lack of science communication to the general public and that people are likely to believe conspiracy theories rather than facts if the problem is not properly addressed.

', next: '

Our team will emphasise the importance of science communication and public engagement to the Vilnius-Lithuania iGEM team 2021. In addition, we will try to be more public on our personal platforms and put more effort to communicate science after the competition.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/b/b7/T--Vilnius-Lithuania--integrated-contactfair.jpg'
    },
    sergej: {
        title: 'Meetings prof. Sergejus Borodinas and Arūnas Speičys',

desc: '

The subunit vaccines developed in our prevention system were encapsulated in alginate beads. To make the vaccine work in real life, all the environmental conditions have to be considered. As the vaccine travels through the fish digestive tract, it encounters both chemical and physical challenges. We decided to consult on the latter with Vilnius’ Gediminas Technical University professor Sergejus Borodinas and Arūnas Speičys, who are knowledgeable in physical properties of various materials as well as how to test them.

', contr: '

Professor consulted us on how the experiments should be implemented. He also suggested testing beads of a uniform size and see if they can withstand a standard pressure suggested in the articles rather than pressurizing them until breakage to get more accurate results. Arūnas Speičys instructed us on how to use the testing machine and helped with parameters’ calculations.

', adjust: '

We decided to test if the alginate beads could withstand a pressure that was suggested in the literature.

', next: '

With beads, capable of withstanding peristaltic movements of the fish gut, the vaccines are ready to be tested in vivo.

',

        mediaSrc: 'https://static.igem.org/mediawiki/2020/0/00/T--Vilnius-Lithuania--integrated-andrej.mp4',
        video: true,
    }
}