Ljubljana

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== Project in brief ==
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Last year our team modified human cells by introducing a feedback device with a dominant-negative inhibitor under the control of the NFkapaB promotor, which decreased the damaging excessive response to the bacterial infection. In 2007, we are remaining in the domain of the potential applications of synthetic biology to improve human health.
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The goal of our project is to design cells that will be able to detect the invasion of a pathogen and defend the organism by either undergoing apoptosis (and destroying the invaded pathogen before it can replicate) or by mounting any other defense response. To our opinion, the main innovative aspect of the project will be to detect the invasion of the pathogen not based on any particular sequence (which can be avoided through point mutations of the pathogen) but rather by relying on the ''function'' of the pathogen, which is essential for its survival or pathogenicity. The ultimate goal of this approach would be to develop gene therapy against infectious diseases.
 
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In parallel with the research, we prepared a 12-pages [https://2007.igem.org/Image:BrochureSB07_LJU_TitlePage.jpg brochure] on Synthetic Biology and our project in Slovenian language, aimed at life science students and general audience.
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== Slovenian iGEM2007 team ==
 
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[[Image:Team2-small.jpg]]
 
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Ljubljana team in June 2007 (photo taken in the new meeting room at the [http://www.ki.si/index.php?id=117&no_cache=1&L=1 Natl. Institute of Chemistry]).<br>
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First row: Saša, Mojca, Katja, Anja, Nives; Second row: Roman, Mateja, Karolina, Gabi, Peter, Andrej, Rok, Marko D. (missing on the photo is Marko B.)
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<img src="https://static.igem.org/mediawiki/2007/7/73/VIROTRAP.jpg" width="633" height="200">
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'''undergraduate students''':<br>
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Marko Bitenc - Biotechnology 3rd year<br>
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Peter Cimermančič - Biochemistry 3rd year<br>
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Rok Gaber - Microbiology 3rd year<br>
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Saša Jereb - Biochemistry 2nd year<br>
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Katja Kolar - Biochemistry 2nd year<br>
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Anja Korenčič - Biochemistry 4th year<br>
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Andrej Ondračka - Biochemistry 3rd year<br>
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'''instructors''':<br>
 
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Roman Jerala - NIC - ''supervisor''<br>
 
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Marko Dolinar - FCCT - ''supervisor''<br>
 
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Mojca Benčina - NIC<br>
 
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Karolina Ivičak - NIC<br>
 
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Mateja Manček Keber - NIC <br>
 
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Gabriela Panter - NIC<br>
 
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Nives Škrlj - FCCT<br>
 
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== Ljubljana and hosting institutions ==
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      <p class="p1"><span><b>Synthetic biology provides the possibility to extend our defense against disease by employing our intelligence. In the spirit of synthetic biology we can combine different functional parts with known properties to assemble new cellular functions which do not yet exist in nature.</b></span></p>
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[http://www.ljubljana.si/en/ljubljana/ Ljubljana] (population 300.000) is the capital of [http://www.slovenia.si/ Slovenia] (population 2 million) and homes the largest of three universities in the country, [http://www.uni-lj.si University of Ljubljana] (UL). Most of the research work will be done at the [http://www.ki.si/index.php?id=117&no_cache=1&L=1 National Institute of Chemistry], [http://www.ki.si/index.php?id=192&no_cache=1&L=1 Laboratory of Biotechnology] and parts of it at the UL [http://www.fkkt.uni-lj.si/en/ Faculty of Chemistry and Chemical Technology], [http://openwetware.org/wiki/FCCT_Biochemistry_Lab Biochemistry Chair].
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== iGEM 2006 project ==
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Ljubljana team joined iGEM in 2006 and received the grand prize! The project focused on the signal transduction linked to development of sepsis. We engineered a negative feedback loop that inhibited excessive signalling via toll-like receptors. For more information, check the [https://2006.igem.org/wiki/index.php/Ljubljana%2C_Slovenia_2006 2006 wiki] or follow Alja's [http://partsregistry.org/movies/iGEM2006_ljubljana.mov presentation] at the Jamboree. We were also invited to [http://download.podcast.ethz.ch/media/MAVT-0001-00X/2007062409_dm.m4v present] our work at the 2007 SB 3.0 conference in Zurich.
 
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== ACKNOWLEDGEMENTS ==
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<h3><span>Abstract for nonspecialists</span></h3>
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<div align="justify">
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HIV-1 virus is one of the most difficult targets for therapy because it hijacks the cells of our immune system and particularly because the virus mutates rapidly making it drug resistant. Current therapy uses combinations of different drugs, since it is less probable for the virus to develop the resistance against all of them simultaneously.
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Our team would like to thank for the financial support to the organizations that made our research and attendance of the jamboree possible:
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We propose a different strategy, where we target a specific <b>FUNCTION</b> of virus, rather than any particular sequence. This viral function triggers a cellular response which can either employ antiviral defense or lead to a destruction of infected cells to prevent spread of the infection.
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AdFutura Public Fund,  
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Ministry of High Scool Education, Science and Technology of Slovenia,
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University of Ljubljana,
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Slovenian Biochemical Society,
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European Commission - Synbiocomm Project,
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National Institute of Chemistry,
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Lek - a Sandoz company.
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[[Image:logo_glava_AdFutura.gif]]
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The effect of mutations can thus be avoided since those mutations that cause the loss of the function also render the virus harmless. We successfully implemented two types of defense devices – one based on the viral attachment to the cell and another based on the viral maturation. In our system activation of any of them activates the antiviral cell defense or alternatively kills the infected cells, preventing further spread of infection. The same approach could be implemented for defense against other viral infections.
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[[Image:KIlogo.gif]]
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[[Image:menuleft_logo_unilj.gif]]
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[[Image:SBDLogoS.jpg]]
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[[Image:120px-EU-flag.gif]]
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[[Image:Lek-logo.jpg]]
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Special thanks are due to GeneArt for the support in synthesis of parts:
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[[Image:GeneArt.jpg]]
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          <object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" width="600" height="500" id="team2" > <param name="allowScriptAccess" value="sameDomain" /> <param name="movie" value="https://static.igem.org/mediawiki/2007/8/86/Split_ubiquitin.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffffff" /><embed src="https://static.igem.org/mediawiki/2007/8/86/Split_ubiquitin.swf" quality="high" bgcolor="#ffffff" width="600" height="500" name="team2" allowScriptAccess="sameDomain" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" />
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Animation of split-ubiquitin system.
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<h3><span>Scientific abstract</span></h3>
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We have devised a synthetic system of antiviral defense against the HIV-1 infection that is not sensitive to viral mutations, because it is based on viral functions. <b>Two essential viral functions</b> have been successfully implemented to activate the cellular defense – viral attachment to cells through a pair of surface receptors and processing of viral proteins by its own protease.
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Binding of virus to human T-cells causes formation of CD4-CCR5 heterodimers, which in our system reconstitutes the split ubiquitin. This protease cleaves-off the membrane-anchored T7 RNA polymerase from the membrane, directing it into the nucleus. T7 RNA polymerase provides the amplification of the signal and causes transcription of <b>versatile effector genes</b>, coding either for antiviral proteins or for caspase, which leads the infected cell into apoptosis thereby preventing further spread of viral infection. The same viral function was successfully utilized in the implementation of the split TEV protease system.
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The second implementation of this idea was to utilize the activity of HIV-protease, which is required for viral maturation and cleaves a specific amino acid sequence. This target sequence was engineered between the membrane anchor and T7 RNA polymerase. T7 RNA polymerase released from the membrane subsequently activates the defense similar to that described with the split protein system. <b>All three systems work in human cells.</b> We have prepared and tested many different constructs, contributing more than 70 new BioBricks and successfully demonstrated activation of response gene by infection of mammalian cell cultures with HIV-1 pseudovirus.
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  <p class="MsoNormal"><o:p><b>PLEDGE:</b> All experimental work on this project was performed from May to October 2007 by the undergraduate students participating in the team under the tutorial of instructors. All the students participated at iGEM for the first time.</o:p></p>
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  <td><a href="http://www.ki.si/">National Institute of Chemistry</a> <br>
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  <a href="http://www.ki.si/"><img border="0" src="https://static.igem.org/mediawiki/2007/2/29/KIlogo.gif" width="110" height="70"><br></a><br></td>
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<td>  </td><td>  </td><td>  </td><td>  </td>
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  <td><br><a href="http://www.uni-lj.si/en">University of Ljubljana</a> <br>
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  <a href="http://www.uni-lj.si/en/"><img border="0" src="https://static.igem.org/mediawiki/2007/3/33/UL-logo.jpg"> <br></a></td>
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    <div id="footer">______________________________________<br />
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      <a href="https://2007.igem.org/Ljubljana">Home</a>|
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<a href="https://2007.igem.org/Ljubljana/AIDSplague">Epidemics</a>
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<a href="https://2007.igem.org/Ljubljana">
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        <h3 class="menu"><span><a class="two" href="https://2007.igem.org/Ljubljana/AIDSplague">AIDS - Today's Plague</a></span></h3>
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        <ul>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/AIDSplague">Epidemics</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/HIVbacground">HIV-1 Infection Background</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/Currenttreatment">Current Disease Treatment</a>&nbsp; </li>
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        <h3 class="links"><span><a class="two" href="https://2007.igem.org/Ljubljana/Strategy">Project</a></span></h3>
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        <li><a class="one" href="https://2007.igem.org/Ljubljana/Strategy">Strategy</a>&nbsp; </li> 
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<li><a class="one" href="https://2007.igem.org/Ljubljana/implementation">Implementation</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/model">Model</a>&nbsp; </li>
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        <h3 class="resources"><span><a class="two" href="https://2007.igem.org/Ljubljana/results">Results</a></span></h3>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/subsystems">Subsystems Testing</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/finalsystem">Performance of the Final Functional Systems</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/biobricks">BioBricks</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/methods">Methods</a>&nbsp; </li>
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        <h3 class="results"><span><a class="two" href="https://2007.igem.org/Ljubljana/summary">Summary</a></span></h3>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/summary">Achievements</a>&nbsp; </li>
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          <li><a class="one" href="https://2007.igem.org/Ljubljana/summary">Prospects</a>&nbsp; </li>
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<div id="ldiscussion">
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        <h3 class="discussion"><span><a class="two" href="https://2007.igem.org/Ljubljana/team">Team</a></span></h3>
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<div id="ldiscussion">
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<ul><li><a class="one" href="https://2007.igem.org/Ljubljana/glossary">Glossary & References</a>&nbsp; </li>
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<li><a class="one" href="https://2007.igem.org/Ljubljana/acknowledgements">Acknowledgements</a>&nbsp; </li>
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Latest revision as of 18:36, 23 November 2007

Company Name



Synthetic biology provides the possibility to extend our defense against disease by employing our intelligence. In the spirit of synthetic biology we can combine different functional parts with known properties to assemble new cellular functions which do not yet exist in nature.

Abstract for nonspecialists

HIV-1 virus is one of the most difficult targets for therapy because it hijacks the cells of our immune system and particularly because the virus mutates rapidly making it drug resistant. Current therapy uses combinations of different drugs, since it is less probable for the virus to develop the resistance against all of them simultaneously. We propose a different strategy, where we target a specific FUNCTION of virus, rather than any particular sequence. This viral function triggers a cellular response which can either employ antiviral defense or lead to a destruction of infected cells to prevent spread of the infection. The effect of mutations can thus be avoided since those mutations that cause the loss of the function also render the virus harmless. We successfully implemented two types of defense devices – one based on the viral attachment to the cell and another based on the viral maturation. In our system activation of any of them activates the antiviral cell defense or alternatively kills the infected cells, preventing further spread of infection. The same approach could be implemented for defense against other viral infections.



Animation of split-ubiquitin system.

Scientific abstract

We have devised a synthetic system of antiviral defense against the HIV-1 infection that is not sensitive to viral mutations, because it is based on viral functions. Two essential viral functions have been successfully implemented to activate the cellular defense – viral attachment to cells through a pair of surface receptors and processing of viral proteins by its own protease. Binding of virus to human T-cells causes formation of CD4-CCR5 heterodimers, which in our system reconstitutes the split ubiquitin. This protease cleaves-off the membrane-anchored T7 RNA polymerase from the membrane, directing it into the nucleus. T7 RNA polymerase provides the amplification of the signal and causes transcription of versatile effector genes, coding either for antiviral proteins or for caspase, which leads the infected cell into apoptosis thereby preventing further spread of viral infection. The same viral function was successfully utilized in the implementation of the split TEV protease system. The second implementation of this idea was to utilize the activity of HIV-protease, which is required for viral maturation and cleaves a specific amino acid sequence. This target sequence was engineered between the membrane anchor and T7 RNA polymerase. T7 RNA polymerase released from the membrane subsequently activates the defense similar to that described with the split protein system. All three systems work in human cells. We have prepared and tested many different constructs, contributing more than 70 new BioBricks and successfully demonstrated activation of response gene by infection of mammalian cell cultures with HIV-1 pseudovirus.


PLEDGE: All experimental work on this project was performed from May to October 2007 by the undergraduate students participating in the team under the tutorial of instructors. All the students participated at iGEM for the first time.

National Institute of Chemistry



University of Ljubljana