Difference between revisions of "Team:Vilnius-Lithuania/Collaborations"

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<h1 class="text-wall-heading">Collaborations</h1>
 
<h1 class="text-wall-heading">Collaborations</h1>
 
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     <h2 class="text-wall-area-box-heading">COLLABORATIONS</h2>
 
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         <p class="text-content">Our team has successfully and directly followed the meaning of the word “Collaboration”, which originated from Latin con- (“with”) and labōrō (“work”). We found several iGEM teams that we happily involved in our activities and dry lab development of SynDrop, as well as joined their initiatives and proposals. Entering into relations with like-minded people and broadening our scientific network came as mutual benefits which may evolve to common projects in the future as well.</p>
 
         <p class="text-content">Our team has successfully and directly followed the meaning of the word “Collaboration”, which originated from Latin con- (“with”) and labōrō (“work”). We found several iGEM teams that we happily involved in our activities and dry lab development of SynDrop, as well as joined their initiatives and proposals. Entering into relations with like-minded people and broadening our scientific network came as mutual benefits which may evolve to common projects in the future as well.</p>
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     <div class="modal-close"></div>
 
     <div class="modal-content">
 
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         <h1>Description</h1>
+
         <h1>Collaborations</h1>
 
         <p></p>
 
         <p></p>
 +
        <p>
 +
            <ul>
 +
                <li><strong>iGEM Teams Participating in Vilnius-Lithuania BioHackathon</strong></li>
 +
                <li><strong>iGEM Team Worldwide</strong></li>
 +
                <li><strong>iGEM Goes Green Survey</strong></li>
 +
                <li><strong>Exchanging Self-Designed Postcards</strong></li>
 +
            </ul>
 +
        </p>
 
         <p></p>
 
         <p></p>
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         <h2>What is SynORI?</h2>
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         <h1>iGEM Teams Self-Designed Postcards</h1>
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         <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
+
         <p></p>
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            and multi-plasmid systems precise, easy and on top of that - more functional.</p>
+
         <p>
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         <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
+
                As you may have already read in other sections of this wiki page, our team has organised BioHackathon - the international coding competition. Since symbiosis between Life Sciences and IT fields in Lithuania still is in its initial stage, we considered about gaining valuable experience from other countries, especially from other iGEM teams. Because of that we have invited iGEM teams to visit Vilnius and take part in 48 hours-lasting BioHackathon: Lab Issues event. As a result, team Aalto-Helsinki (Finland), team Lund (Sweden) and team Groningen (Netherlands) accepted the invitation. We considered it to be a very meaningful collaboration because everyone was working on the same goal – to create programmes or tools which were supposed to ease teams’ everyday laboratory life. Most of the BioHackathon ideas grew from from difficulties faced while working on their own iGEM projects. In that case, final applications and tools, created during BioHackathon, had improved their projects or at least relieved the realization of ideas. Some teams have been in touch with mentors after the event and received qualified advices. We have also used some created tools including team Lund search-engine that helped us in searching for particular BioBricks. Additionally, as team Aalto-Helsinki stated, it has been a great chance to learn about other iGEM projects, exchange knowledge and experience as well. As BioHackathon took place in the Life Sciences Center where the major part of our project development happened, teams had an opportunity to take a look at our laboratories and daily workspace. We strongly believe that such an event might become a pattern for the future collaborations.
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        <ol>
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−
            <li>Selecting the number of plasmid groups</li>
+
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            <li>Choosing the copy number of each group</li>
+
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            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
+
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        </ol>
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         </p>
 
         </p>
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+
        <p><mark>foto biohataka</mark></p>
 
         <p></p>
 
         <p></p>
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         <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
+
        <h1>iGEM Teams Worldwide</h1>
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            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
+
         <p></p>
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            copy number plasmid groups are not lost during the division.
+
        <p>
 +
                Many people and organisations are trying to reach the general public on social media by posting on Twitter, Linkedin, Facebook or Instagram. Our team is not an exception and we also have those accounts. But one of the most entertaining experience was to be a part of project @igem.teams.worldwide on Instagram, created by team Toulouse INSA-UPS. The main idea of the project is that various iGEM teams can manage this Instagram account for a week and introduce themselves by showing their casual life, laboratory issues and everything they imagine. We also had such an opportunity from 9th to 15th, July and it was a pleasure to share some brilliant daily routine moments, receive supportive comments about SynDrop project, gain more followers on our own Instagram account, and present Lithuania at once. It was not only an entertainment or a possibility to familiarize ourselves with other teams and their projects, but it has also induced our creativity in order to present ourselves differently.
 
         </p>
 
         </p>
 +
        <p><mark>Toulouse logo</mark></p>
 +
        <p></p>
 +
        <h1>iGEM goes green Survey</h1>
 
         <p></p>
 
         <p></p>
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        <div class="img-cont">
 
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            <img src="https://static.igem.org/mediawiki/parts/8/84/Collect.png" alt="img">
 
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            <div class="img-label">
 
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            </div>
 
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        </div>
 
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        <h2>Applications</h2>
 
 
         <p>
 
         <p>
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            <h5>Everyday lab work</h5>
+
                 Last year team TU Dresden 2017 initiated the project “iGEM goes green” intended to share the ecological improvements of their work. This year the team didn‘t take part in iGEM but team METU_HS_Ankara was so impressed by this idea that they decided to continue the project this year. After agreement and permissions from team TU Dresden were given, team METU_HS_Ankara has sent a Lab Poster and “iGEM Goes Green Guide” to us which were placed in our laboratory. Also they asked to enter our data on GHG Emissions Calculator, as well as share it in Lithuania widely. That helped us to turn our community’s attention to the environmental impact of a daily working routine and share eco-friendly thoughts in Lithuania too. For more information about the movement visit team METU_HS_Ankara page.  
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            <p>
+
                 https://2018.igem.org/Team:METU_HS_Ankara "Kristina"
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                 A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
+
        </p>
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                research to a particular plasmid copy number just because there are not enough right replicons to
+
        <p><mark>Ankara logo</mark></p>
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                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
+
        <p></p>
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                 suits your needs.</li>
+
        <h1>Dry Lab Collaborations</h1>
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            </p>
+
        <p></p>
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            <h5>Biological computing</h5>
+
        <p>
−
            <p>
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             <h2>eXplaY model in collaboration with team Groningen</h2>
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                The ability to choose a wide range of copy number options and their control types will make the
+
        </p>
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                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
+
        <p>
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                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
+
                 When team Groningen visited Vilnius and participated in the life sciences BioHackathon, we have exchanged ideas about modeling our project. We intended to design a liposome-surface display system and team Groningen was so interested in SynDrop idea, that they even offered some help. Finally, through this collaboration a molecular thermodynamics model, called eXplaY (hyperlink)"Kristina", was built.
−
                of multiple gene group expression.
+
        </p>
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            </p>
+
        <p></p>
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            <h5>Smart assembly of large protein complexes</h5>
+
        <p>
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            <p>
+
            <h2>Mathematical model for necessity of mRNA addition to IVTT system</h2>
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                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
+
−
                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
+
−
                the same type of control, and in addition can act in a group-specific manner.</p>
+
−
 
+
−
             <h5>Metabolic engineering</h5>
+
−
            <p>
+
−
                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
+
−
                 levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
+
−
                transcriptional control and synthetic ribosome binding sites in translational control are already
+
−
                widely used to maintain expression levels. In addition to current approaches, our framework allows a
+
−
                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
+
−
                search for perfect conditions a lot easier.
+
−
 
+
−
 
+
−
 
+
−
            </p>
+
−
 
+
−
 
+
 
         </p>
 
         </p>
 
         <p>
 
         <p>
 +
                While creating our cell-free system we had hypothesized the necessity of adding initial mRNA over single DNA into our liposomes. With the help of team Edinburgh, mathematical model"kristina" (hyperlink) proving our theoretical concept was designed. This model might be helpful for creating more efficient cell-free systems for membrane protein research.
 
         </p>
 
         </p>
−
         <table style="width:100%">
+
          
−
<thead>
+
−
<td align='center'>Species sign in ODE system</td>
+
−
<td align='center'>Species</td>
+
−
<td align='center'>Initial concentration (M)</td>
+
−
</thead>
+
−
<tbody>
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−
<tr>
+
−
<td align='center'>A</td>
+
−
<td align='center'>pDNA+RNA I+RNAII early</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>B</td>
+
−
<td align='center'>pDNA+RNA II short</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>RNAI</td>
+
−
<td align='center'>RNA I</td>
+
−
<td align='center'>1E-6</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>D</td>
+
−
<td align='center'>pDNA+RNA II long</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>E</td>
+
−
<td align='center'>pDNA+RNAII primer</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>F</td>
+
−
<td align='center'>RNA II long</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>G</td>
+
−
<td align='center'>pDNA</td>
+
−
<td align='center'>4E-8*</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>H</td>
+
−
<td align='center'>pDNA+RNA II+RNA I late</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>RNA II</td>
+
−
<td align='center'>RNA II</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
<tr>
+
−
<td align='center'>J</td>
+
−
<td align='center'>RNAI+RNAII</td>
+
−
<td align='center'>0</td>
+
−
</tr>
+
−
</tbody>
+
−
</table>
+
 
     </div>
 
     </div>
 
</div>
 
</div>

Revision as of 20:22, 17 October 2018

Collaborations

COLLABORATIONS

Our team has successfully and directly followed the meaning of the word “Collaboration”, which originated from Latin con- (“with”) and labōrō (“work”). We found several iGEM teams that we happily involved in our activities and dry lab development of SynDrop, as well as joined their initiatives and proposals. Entering into relations with like-minded people and broadening our scientific network came as mutual benefits which may evolve to common projects in the future as well.

Collaborations

  • iGEM Teams Participating in Vilnius-Lithuania BioHackathon
  • iGEM Team Worldwide
  • iGEM Goes Green Survey
  • Exchanging Self-Designed Postcards

iGEM Teams Self-Designed Postcards

As you may have already read in other sections of this wiki page, our team has organised BioHackathon - the international coding competition. Since symbiosis between Life Sciences and IT fields in Lithuania still is in its initial stage, we considered about gaining valuable experience from other countries, especially from other iGEM teams. Because of that we have invited iGEM teams to visit Vilnius and take part in 48 hours-lasting BioHackathon: Lab Issues event. As a result, team Aalto-Helsinki (Finland), team Lund (Sweden) and team Groningen (Netherlands) accepted the invitation. We considered it to be a very meaningful collaboration because everyone was working on the same goal – to create programmes or tools which were supposed to ease teams’ everyday laboratory life. Most of the BioHackathon ideas grew from from difficulties faced while working on their own iGEM projects. In that case, final applications and tools, created during BioHackathon, had improved their projects or at least relieved the realization of ideas. Some teams have been in touch with mentors after the event and received qualified advices. We have also used some created tools including team Lund search-engine that helped us in searching for particular BioBricks. Additionally, as team Aalto-Helsinki stated, it has been a great chance to learn about other iGEM projects, exchange knowledge and experience as well. As BioHackathon took place in the Life Sciences Center where the major part of our project development happened, teams had an opportunity to take a look at our laboratories and daily workspace. We strongly believe that such an event might become a pattern for the future collaborations.

foto biohataka

iGEM Teams Worldwide

Many people and organisations are trying to reach the general public on social media by posting on Twitter, Linkedin, Facebook or Instagram. Our team is not an exception and we also have those accounts. But one of the most entertaining experience was to be a part of project @igem.teams.worldwide on Instagram, created by team Toulouse INSA-UPS. The main idea of the project is that various iGEM teams can manage this Instagram account for a week and introduce themselves by showing their casual life, laboratory issues and everything they imagine. We also had such an opportunity from 9th to 15th, July and it was a pleasure to share some brilliant daily routine moments, receive supportive comments about SynDrop project, gain more followers on our own Instagram account, and present Lithuania at once. It was not only an entertainment or a possibility to familiarize ourselves with other teams and their projects, but it has also induced our creativity in order to present ourselves differently.

Toulouse logo

iGEM goes green Survey

Last year team TU Dresden 2017 initiated the project “iGEM goes green” intended to share the ecological improvements of their work. This year the team didn‘t take part in iGEM but team METU_HS_Ankara was so impressed by this idea that they decided to continue the project this year. After agreement and permissions from team TU Dresden were given, team METU_HS_Ankara has sent a Lab Poster and “iGEM Goes Green Guide” to us which were placed in our laboratory. Also they asked to enter our data on GHG Emissions Calculator, as well as share it in Lithuania widely. That helped us to turn our community’s attention to the environmental impact of a daily working routine and share eco-friendly thoughts in Lithuania too. For more information about the movement visit team METU_HS_Ankara page. https://2018.igem.org/Team:METU_HS_Ankara "Kristina"

Ankara logo

Dry Lab Collaborations

eXplaY model in collaboration with team Groningen

When team Groningen visited Vilnius and participated in the life sciences BioHackathon, we have exchanged ideas about modeling our project. We intended to design a liposome-surface display system and team Groningen was so interested in SynDrop idea, that they even offered some help. Finally, through this collaboration a molecular thermodynamics model, called eXplaY (hyperlink)"Kristina", was built.

Mathematical model for necessity of mRNA addition to IVTT system

While creating our cell-free system we had hypothesized the necessity of adding initial mRNA over single DNA into our liposomes. With the help of team Edinburgh, mathematical model"kristina" (hyperlink) proving our theoretical concept was designed. This model might be helpful for creating more efficient cell-free systems for membrane protein research.

invert