http://2007.igem.org/wiki/index.php?title=Special:Contributions/AndrejO&feed=atom&limit=50&target=AndrejO&year=&month=2007.igem.org - User contributions [en]2024-03-29T00:37:45ZFrom 2007.igem.orgMediaWiki 1.16.5http://2007.igem.org/wiki/index.php/Ljubljana/AndrejOndrackaLjubljana/AndrejOndracka2008-01-12T16:43:47Z<p>AndrejO: </p>
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<h3><span>Andrej Ondračka</span></h3><br />
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At the beginning of my studies I became interested in structural biology and biomolecular spectroscopy. Later, I also discovered the magical world of synthetic and systems biology. Currently, I am equally interested in both.<br><br />
Besides science, I like music, philosophy, photography, and my great passion, travelling.<br><br />
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For any information about me don't hesitate to contact me on andrej (dot) ondracka (at) gmail (dot) com<br />
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</html></div>AndrejOhttp://2007.igem.org/wiki/index.php/Ljubljana/AndrejOndrackaLjubljana/AndrejOndracka2007-10-27T10:11:39Z<p>AndrejO: </p>
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At the beginning of my studies I became interested in structural biology and biomolecular spectroscopy. Later, I also discovered the magical world of synthetic and systems biology. Currently, I am equally interested in both.<br><br />
Besides science, I like music, philosophy, photography, and my great passion, travelling.<br><br />
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For any information about me don't hesitate to contact me on andrej_ondracka (at) yahoo.com<br />
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<h3><span>Performance of the Final Functional Systems</span></h3><br />
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<h3><span>Split systems based on heterodimerization</span></h3><br />
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Our results demonstrate that split-ubiquitin and split TEVP systems were activated by the HIV coat protein gp120 which causes dimerization of CD4 and CCR5 receptors. Activation was amplified by the T7 RNAP system connected to luciferase reporter. Figures 4 and 5 show normalized luciferase activities of gp120-stimulated cells, nonstimulated and control cells, respectively in the split ubiquitin (Fig. 4) and split TEVP (Fig.5) system.<br><br><br />
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<img src="https://static.igem.org/mediawiki/2007/2/2e/SASAslika1.jpg" width="633" height="380"><br><br />
<small> <b>Fig. 4. Viral envelope protein gp120 activates the split ubiquitin system.</b> Cells were transfected with CMV–CD4–CUb–T7RNA polymerase, CMV–CCR5–Nub, pT7-fLuc and CMV-rLuc reporter plasmids. 12 hours after transfection cells were activated with gp120 protein for additional 12 hours. Cells were lysed and luciferase activity was measured. The results were normalized for transfection efficiency and cell number using rLuc readings. Addition of gp120 clearly activated the split ubiquitin system as higher amounts of T7 promoter-regulated luciferase activity were measured. Luminescence was observed also in cells which were not stimulated, probably because of small level of spontaneusly dimerized CD4 and CCR5, as we used relatively strong promoter, which may cause high level receptors expression at the plasma membrane. T-test: p<0,01, ***; p<0,005, ****<br />
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<small><b>Fig. 5. Viral gp120 activates the split TEV protease system.</b> Cells were transfected with CMV–CD4–TEVC, CMV–CCR5–TEVN, myristoylation signal-TEVprotease site–T7 protease, pT7-fLuc and CMV-rLuc reporter plasmids. 12 hours after transfection cells were activated with gp120 protein for additional 12 hours. Cells were lysed and luciferase activity was measured. The results were normalized for transfection efficiency and cell number using rLuc readings. Addition of gp120 activated split TEV protease system as higher amounts of T7promoter luciferase were measured. Increased luminiscence was also observed in control cells, probably due to the same reason as in split ubiquitin experiment. T-test: p<0,1, *.T-test: p<0,005, ****.</small><br><br><br />
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<b>Interpretation of results:</b><br><br />
Firefly luciferase gene is regulated by the inducible T7 promoter, while renilla luciferase is under constitutive CMV promoter. The difference in luminescence of both luciferases is a consequence of different transfection efficiencies and cell number in different wells. Normalization means that we divide relative luminescence of firefly luciferase by relative luminescence of renilla luciferase. The ratio we get presents differences in promoter activity – the higher the ratio the more active promoter we have.<br><br><br />
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Measurements of luminescence revealed a higher firefly/renilla ratio in cells stimulated with viral protein gp120. A significant difference between stimulated and nonstimulated cells was observed. This is a strong evidence that the engineered device actually works as planned.<br><br><br />
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As seen in Figure 1, we could prove enhanced activation of T7 promoter in gp120 stimulated cells. To verify that the response is due only to T7 RNAP liberated from the ubiquitin fusion (and not e.g. by promoter leaking, spontaneous dimerization of CD4/CCR5, unspecific cleavage of membrane-attached T7 polymerase or unexpected activity of membrane-anchored T7 RNAP, we performed two additional control experiments.<br><br><br />
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Control 1: Cells were transfected with T7 promoter – firefly luciferase vector (and renilla luciferase for normalization standard). Only little background luminescence was detected. Control 2: Cells were transfected with both luciferase constructs and with CD4-CUb-T7 RNAP (control column in Figure 1). Luminescence was low, meaning that neither leaking of T7 promoter nor activity of T7 RNA polymerase on the plasma membrane (or its liberation from the bilayer) are the cause of T7 promoter activation.<br><br><br />
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Luminescence was observed also in non-stimulated cells. This could be due to spontaneous dimerization of CD4 and CCR5, probably because we used a relatively strong promoter which could lead to too many receptor molecules expressed and bound to the plasma membrane.<br><br><br />
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In the comparable experiment just with the split-TEVP attached to CD4 and CCR5 and T7 polymerase attached to the plasma membrane via a myristoyl group and connected to the receptor-split TEVP by a TEVP cleavage site. Results, presented in Figure 2 are highly comparable to those obtained with split ubiquitin, were controlled and interpreted as presented above for the split ubiquitin system.<br><br><br />
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In conclusion, with these experiments we proved that stimulation by HIV viral coat protein activated cellular response through both split-protein devices. We can expect that by replacing luciferase by an effector gene (caspase 3 or ß-interferon) cells would respond by activation of apoptosis or by synthesis of antiviral substances which would prevent the virus from spreading infection to healthy cells.<br><br><br />
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<b>Fluorescent confocal microscopy</b> was used to demonstrate the performance of the split TEV protease system and confirm luciferase data. Cells were transfected with CMV–CD4–TEVC, CMV–CCR5–TEVN and myristoylation signal–TEVprotease site–mCerulean. Fluorescence was detected at the plasma membrane, as expected (Fig. 6C). 22 hours after the transfection cells were stimulated with pseudovirus or gp120 protein and again observed 18 hours later. mCerulean was released from the membrane into cytosol in both cases (Fig. 6A and 6B). Additionally, membrane was stained after the stimulation to confirm the cytosolic localization, respectively (Fig. 6B).<br><br><br />
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<img src="https://static.igem.org/mediawiki/2007/b/b9/KATJA_slika6.jpg" width="633" height="217"><br><br />
<b><small>Fig. 6. HIV pseudovirus and gp120 protein activate split TEV protease system.</b> HEK293T cells were transfected with CMV–CD4–TEVC, CMV–CCR5–TEVN, myristoylation signal–TEVprotease site–mCerulean. 22 hours after transfection cells were stimulated with pseudovirus (A) or gp120 protein (B) for additional 18 hours. In both cases the split TEV protease system was activated and mCerulean reporter protein was released from membrane to cytosol. However, in unstimulated cells the system remained inactive and mCerulean was detected mainly at the plasma membrane (C).</small><br><br><br />
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We proposed that analogously T7 RNA polymerase fused to the receptor instead of mCerulean will be cleaved. Transfection with TEV protease cleavage site fused with T7 RNA polymerase with NLS and T7promoter–mCerulean was performed. Cells were stimulated with pseudovirus or gp120 protein 22 hours after transfection and again observed 18 hours later (Fig. 7). In stimulated cells intense expression of mCerulean was detected (Fig. 8A and 8B)whereas unstimulated cells remained clear (Fig. 7C). The system, using receptors CD4 and CCR5 with truncated cytoplasmic domains was also tested and resulted in similar results.<br><br><br />
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These experiments confirm that when activated, split TEV protease system releases T7 RNA polymerase from the membrane. Consequently T7 RNA polymerase translocates to the nucleus where it transcribes genes under the T7 promoter.<br><br><br />
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<b><small>Fig. 7. Activated split TEV protease system transcribes genes under the T7 promoter.</b> HEK293T cells were transfected with CMV–CD4–TEVC, CMV–CCR5–TEVN, myristoylation signal–TEVprotease site–T7 RNA polymerase-NLS and reporter plasmid T7-mCerulean. 22 hours after the transfection cells were stimulated with pseudovirus (A) or gp120 protein (B) for additional 18 hours. In both cases the split TEV protease system was activated, resulting in translocation of T7 RNA polymerase from the plasma membrane to the nucleus. Consequently mCerulean reporter protein was transcribed and detected in cytosol. In unstimulated cells the system remained inactive and no fluorescence at all was observed (C).</small><br><br />
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<h3><span>System based on the activation by HIV protease</span></h3><br />
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The process of system activation was observed using fluorescent confocal microscopy. Cells were transfected with CMV–CD4–HIV protease cleavage site–mCherry–NLS and optionally cotransfected with HIV protease on pNL4.3 plasmid. In cells without HIV protease fluorescence was detected at the plasma membrane (Fig. 8A), whereas in HIV protease cotransfected cells, fluorescent protein mCherry was released from the membrane and translocated to the nucleus (Fig. 8B). Similar results were obtained when mCherry was substituted with T7 RNA polymerase and additional construct pT7–mCerulean was transfected to detect the T7 RNA polymerase activity. In cells with HIV protease cotransfection, mCerulean was detected in cytosol (Fig. 9B), but no fluorescence at all was observed in the control experiment without of the HIV protease activity (Fig. 9A).<br><br><br />
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The system, using myristoylation signal instead of CD4 to anchor the T7 RNA polymerase to the membrane was also tested and we obtained similar results (data not shown).<br><br><br />
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We can conclude that in the presence of HIV protease, T7 RNA polymerase is released from the membrane and translocates to the nuceleus where it transcribes genes under the T7 promoter.<br><br><br />
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<b><small>Fig. 8. HIV protease cleaves the linker between the membrane anchor and mCherry.</b> HEK293T cells were transfected with CMV-CD4-HIVprotease cleavage site-mCherry-NLS (A) and additionally with HIV protease plasmid pNL4.3 (B). In cells without HIV protease, membrane localization of mCherry reporter protein was observed (A), but in the presence of HIV protease mCherry-NLS was released to cytosol and translocated to nucleus (B).</small><br><br><br />
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<b><small>Fig. 9. T7 RNA polymerase is activated by the cleavage of the linker on the membrane anchor by HIV protease.</b> HEK293T cells were transfected with CMV-CD4-HIVprotease cleavage site-T7 RNA polymerase-NLS, reporter plasmid T7-mCerulean (A) and additionally with HIV protease plasmid pNL4.3 (B). HIV protease cut off T7 RNA polymerase from the membrane, thus activating it. Consequently mCerulean under the T7 promoter was transcribed and detected in cytosol (B). In the absence of protease the system remained inactive and no fluorescence was observed (A).</small><br />
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<h3><span>Effector protein – caspase-3</span></h3><br />
<p class="p1"><span><br />
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Instead of reporter proteins effector proteins such as caspase-3 were used, which are close to the real application. Caspase-3, a cysteine peptidase, which is the main executioner of the apoptosis. We have selected caspase-3 since we wanted to induce apoptosis in HIV-infected cells so that HIV could not replicate and infect the surrounding cells. Apoptosis prevents any inflammation to the neighboring cells and provides for a "clean removal" of apoptotic cells.<br><br><br />
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Two constructs were prepared for testing the caspase-3 activity: CMV-Cas3 and pT7-Cas3. The first construct was used to test if the caspase-3 is active in transfected cells. The second construct with caspase-3 under the T7 promoter was used as our main effector. Caspase-3 will be transcribed only when active T7 RNA polymerase is present in cytosol or nucleus. This should happen when our devices are activated by HIV virus-induced receptor heterodimerization or by HIV protease, expressed in HIV infected cells.<br><br><br />
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ELISA was used to determine the amount of caspase-3 in cells – this indicates the apoptotic potential of our system. We wanted to show that amount of caspase-3 in cells infected with HIV protease is greater than in non-infected cells (Fig. 10). The amount of caspase-3 had to be carefully monitored since the expression of caspase-3 leads to apoptosis and killing the cells, which we then can not detect anymore. So, timing of ELISA tests was therefore very important.<br><br><br />
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<b><small>Fig. 10. Caspase-3 expression is enchanced in HIV-protease transfected cells.</b> HeLa cells were transfected with effector gene pT7-Cas3 alone or with effector gene and components of system based on activation by HIV protease activity: CD4 membrane receptor with bound T7 RNA polymerase via HIV protease cleavage site and HIV protease in pNL4.3 vector. ELISA test was made with antibodies against human caspase-3. Significant amount of caspase-3 was detected in nontransfected cells and in cells, transfected with pT7-Cas3 as well. Since ELISA can also detect inactive and endogenous caspase-3 and since certain amount of cells is always in apoptosis, we did not expect extremely low values in these two samples. Significantly elevated levels of caspase-3 were detected in cells, transfected with our system components, meaning that more caspase-3 is transcribed and activated cells after HIV protease cuts off T7 RNA polymerase from transmembrane receptor. In terms of our initial idea this means that HIV entry and HIV protease activity in infected cells could trigger apoptosis and thus prevent replication of virus. T-test: p<0,05, **; p<0,01, ***.</small><br><br><br />
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Flow cytometry using annexin V staining was used for detection of amount of apoptotic cells as a consequence of caspase 3 activity after system activation. We have transfected cells with components of our systems (that have been previously proved as functional) with caspase-3 under T7 promoter as an effector gene. As a positive control we used cells, transfected with CMV-Cas3 construct. Activation of apoptosis varies between different cell lines and also the efficiency between different inducers varies significantly. Although some apoptosis was detected still an additional optimization is needed to obtain reliable results.<br><br><br />
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Instead of caspase-3, which triggers apoptosis in HIV infected cells we could use effector proteins that would act as antiviral agents. Good example is interferon-β. Interferons are very important in antiviral defense. They are usually secreted as a consequence of elevated levels of dsRNA in cells. Its effects include prevention of viral replication and stimulation of the immune response. In extreme cases it can also trigger apoptosis, probably trough increased production of p53 gene product.<br><br><br />
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We have not directly tested the activity of human interferon-β in HIV-infected cells but have deposited BioBricks containing interferon-β, pT7-interferon-β and CMV-interferon-β to the Registry.<br><br><br />
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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><br />
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<h3><span>Abstract for nonspecialists</span></h3><br />
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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. <br />
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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.<br />
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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.<br />
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Animation of split-ubiquitin system.<br />
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<h3><span>Scientific abstract</span></h3><br />
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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.<br />
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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.<br />
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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.<br />
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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><br />
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<td><a href="http://www.uni-lj.si/en/">University of Ljubljana </a> <br><br />
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</html></div>AndrejOhttp://2007.igem.org/wiki/index.php/Ljubljana/SasaJerebLjubljana/SasaJereb2007-10-26T20:52:41Z<p>AndrejO: </p>
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<h3><span>Saša Jereb</span></h3><br />
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<br><br>Undergraduate student of Biochemistry.<br><br />
I decided to join iGEM team because I wanted to know what the term »synthetic biology« means in the lab. I enjoyed all the work a lot, except making agarose gels. In the future I'll work in a lab where they are buying them.<br><br />
When I grow up I'll be working on improving human health, in case I'll become a biochemist.<br />
In case not, I'll be an illustrator.<br />
If you want to know more about our project mail me: sasajereb at gmail. <br />
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</html></div>AndrejOhttp://2007.igem.org/wiki/index.php/Ljubljana/AndrejOndrackaLjubljana/AndrejOndracka2007-10-26T19:56:50Z<p>AndrejO: </p>
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<h3><span>Andrej Ondracka</span></h3><br />
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At start of my studies I became interested in structural biology and biomolecular spectroscopy. Later, I also discovered the magical world of synthetic and systems biology.<br> Currently, I am equally interested in both.<br />
Besides science, I like music, philosophy, photography, and my great passion, travelling.<br><br />
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For any information about me don't hesitate to contact me on andrej_ondracka (at) yahoo.com<br />
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<h3><span>Andrej Ondracka</span></h3><br />
<p class="p1"><span><br />
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<img src="https://static.igem.org/mediawiki/2007/b/b5/Andrej.JPG"<br />
width="600" height="450"><br />
</p><br />
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At start of my studies, I became interested in structural biology and biomolecular spectroscopy. Later, I also discovered the magical world of synthetic and systems biology.<br> Currently, I am equally interested in both.<br />
Besides science, I like music, philosophy, photography, and my great passion, travelling.<br><br />
<br />
For any information about me, don't hesitate to contact me on andrej_ondracka (at) yahoo.com<br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/acknowledgements">Acknowledgements</a>&nbsp; </li><br />
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<h3><span>Andrej Ondracka</span></h3><br />
<p class="p1"><span><br />
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<br><br />
<img src="https://static.igem.org/mediawiki/2007/b/b5/Andrej.JPG"<br />
width="600" height="450"><br />
</p><br />
<br><br />
At start of my studies, I became interested in structural biology and biomolecular spectroscopy. Later, I also discovered the magic world of synthetic and systems biology.<br> Currently, I am equally interested in both.<br />
Besides science, I like music, philosophy, photography, and my great passion, travelling.<br><br />
<br />
For any information about me, don't hesitate to contact me on andrej_ondracka (at) yahoo.com<br />
<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
</a></span></p><br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/finalsystem">Performance of the Final Functional Systems</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/biobricks">BioBricks</a>&nbsp; </li><br />
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</ul><br />
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<h3 class="results"><span><a class="two" href="https://2007.igem.org/Ljubljana/summary">Summary</a></span></h3><br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/achievements">Achievements</a>&nbsp; </li><br />
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<h3 class="discussion"><span><a class="two" href="https://2007.igem.org/Ljubljana/team">Team</a></span></h3><br />
<ul><br />
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<br><br><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/glossary">Terms & References</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/acknowledgements">Acknowledgements</a>&nbsp; </li><br />
</ul><br />
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<h3><span>Glossary</span></h3><br />
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<b>AIDS - </b> <small>Acquired immune deficiency syndrome is a collection of symptoms and infections resulting from the specific damage to the immune system caused by the human immunodeficiency virus (HIV) in humans. The late stage of the condition leaves individuals susceptible to opportunistic infections and tumors.</small> <br> <br><br />
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<b>Apoptosis - </b> <small> is a form of programmed cell death in multicellular organisms. It is one of the main types of programmed cell death and involves an orchestrated series of biochemical events leading to a characteristic cell morphology and death. </small><br><br><br />
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<b>Capsid - </b> <small>is the protective shell of protein that surrounds the genetic material of a virus.<br />
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<b>CCR5 - </b> <small>short for chemokine (C-C motif) receptor 5. CCR5 is predominantly expressed on T cells, macrophages, dendritic cells and microglia. HIV uses CCR5 or another protein, CXCR4, as a co-receptor to enter its target cells. CCR5 is likely the most physiologically important coreceptor during natural infection. </small><br><br><br />
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<b>CD4 - </b> <small>CD4 (cluster of differentiation 4) is a glycoprotein expressed on the surface of T helper cells, regulatory T cells, monocytes, macrophages, and dendritic cells. Like many cell surface receptors/markers, CD4 is a member of the immunoglobulin superfamily. CD4 is also a primary receptor used by HIV-1 to gain entry into host T cells.</small><br><br><br />
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<b>CXCR4 - </b> <small>also called fusin, this is one of two co receptors for HIV binding to the human cell, it is embedded in the T Cell membrane. The other co receptor is CCR5. </small><br><br><br />
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<b><i>Env - </i></b> <small>The envelope gene encodes the surface glycoprotein (SU) - transmembrane (TM) polyprotein. <i>Env</i> gene is located in the HIV genome.</small><br><br><br />
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<b><i>Gag - </i></b> <small>The <i>gag</i> (group specific antigen) gene encodes the viral matrix (MA) capsid (CA) and nucleoproteins (NC). <i>Gag</i> gene is located in the HIV genome.</small><br><br><br />
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<b>GFP - </b> <small>protein, comprised of 238 amino acids (26,9 kDa), originally isolated from the jellyfish. When GFP is exposed to blue light it fluoresces green and is therefore easy to detect on confocal microscope.</small><br><br><br />
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<b>gp41 - </b> <small>is a glycoprotein non-covalently bound to gp120, and provides the second step by which HIV enters the cell. It is originally buried within the viral envelope, but when gp120 binds to a CD4 receptor, gp120 changes its conformation causing gp41 to become exposed, where it can assist in fusion with the host cell.</small><br><br><br />
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<b>gp120 - </b> <small>is a glycoprotein exposed on the surface of the HIV envelope. The glycoprotein gp120 is anchored to the viral membrane through non-covalent bonds along with gp41, both coming from a cleaved protein, gp160. It infects any target cell with a CD4 receptor, particularly the helper T-cell, by binding to that receptor.</small><br><br><br />
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<b>HAART - </b> <small>Highly Active AntiRetroviral Therapy. Treatment for human immunodeficiency virus (HIV) infection that uses a combination of several antiretroviral drugs. The drugs inhibit the ability of the virus to multiply in the body, and they slow down the development of AIDS.</small><br><br><br />
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<b>HIV - </b> <small>Human immunodeficiency virus is a retrovirus that can lead to acquired immunodeficiency syndrome (AIDS). HIV infection leads to a progressive reduction in the number of T cells possessing CD4 receptors.</small><br><br><br />
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<b>HIV protease - </b> <small>aspartyl protease that is essential for the life-cycle of HIV. Inhibition of this protease prevents maturation of HIV particles. As such, many drugs have been developed (protease inhibitors) that target this enzyme. </small><br><br><br />
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<b>Integrase - </b> <small>an enzyme produced by a retrovirus (including HIV) that enables its genetic material to be integrated into the DNA of the infected cell. It is also produced by viruses containing double stranded DNAs for the same purpose. </small><br><br><br />
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<b>LTR - </b> <small>long terminal repeats (LTRs) are found in retroviral DNA flanking functional genes. The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (cDNA) and ultimately dsDNA (double-stranded DNA) with full LTRs. The LTRs then mediate integration of the retroviral DNA via an LTR specific transposase called integrase into another region of the chromosome. This is the basic mechanism used by HIV. LTRs also act as promoters/enhancers - when integrated into the host genome they influence the cell machinery which transcribes DNA to alter the amount of transcription which occurs</small><br><br><br />
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<b>NRTI - </b> <small>analogs of nucleosides/nucleotides (building blocks necessary for DNA synthesis). They inhibit the reverse transcriptase of HIV, thus inhibiting its replication and leading to decreased viral loads.</small><br><br><br />
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<b>NNRTI - </b> <small>non-nucleoside reverse transcriptase inhibitors, a family of reverse transcriptase inhibitors used as anti AIDS treatment.<br />
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<b>Polyprotein - </b> <small>protein that is cleaved after translation to produce several functionally distinct proteins. </small><br><br><br />
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<b><i>Pol - </i></b> <small>encodes the reverse transcriptase (RT) and an integrase (IN). <i>Pol</i> gene is located in the HIV genome.</small><br><br><br />
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<b>Retrovirus - </b> <small>is any virus belonging to the viral family Retroviridae. They are enveloped viruses possessing a RNA genome and replicate via DNA intermediate. Retroviruses rely on the enzyme reverse transcriptase to perform the reverse transcription of its genome from RNA into DNA, which can then be integrated into the host's genome with an integrase enzyme. The virus then replicates as part of the cell's DNA.</small><br><br><br />
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<b>Split protein system - </b> <small>Experimental procedure to detect protein-protein interactions that uses two fusion proteins (“hybrids”) which reconstitute an active transcription factor (or some other active protein) when the two fusion proteins interact. </small><br><br><br />
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<b>T-cells - </b> <small>belong to a group of white blood cells known as lymphocytes and play a central role in cell-mediated immunity. They attack virus-infected cells, foreign cells and cancer cells. T-cells also produce a number of substances that regulate the immune response.</small><br><br><br />
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<b>T7 RNA polymerase - </b> <small>catalyzes the formation of RNA in the 5'→ 3' direction. T7 RNA polymerase is extremely promoter-specific and only transcribes bacteriophage T7 DNA or DNA cloned downstream of a T7 promoter.</small><br><br><br />
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<b>TEV protease - </b> <small>highly site-specific protease that is found in the Tobacco Etch Virus (TEV). It is a cysteine protease. Advantages of this enzyme are its high specificity and its high activity rate.</small><br><br><br />
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<b>Ubiquitin - </b> <small> highly conserved small regulatory protein that is ubiquitous in eukaryotes. Ubiquitination refers to the post-translational modification of a protein by the covalent attachment (via an isopeptide bond) of one or more ubiquitin monomers. The most prominent function of ubiquitin is labeling proteins for proteasomal degradation.</small><br><br><br><br />
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<h3><span>References</span></h3><br />
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<h3><span>Marko Dolinar</span></h3><br />
<p class="p1"><span><br />
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Together with <a href="https://2007.igem.org/Ljubljana/RomanJerala">Roman Jerala</a>, I am co-supervisor of the Slovenian team. Five out of seven undergraduates in our team are or were my students. I teach molecular biology within the Biochemistry course and Recombinant DNA Technology theoretical and practical course here at the <a href="http://www.uni-lj.si/en/">University of Ljubljana</a> <a href="http://www.fkkt.uni-lj.si/en/">Faculty of Chemistry and Chemical Technology</a>. Our Biochemistry Chair presents itself <a href="http://openwetware.org/wiki/FCCT_Biochemistry_Lab">on OWW</a>.<br><br />
If you are fluent in Slovenian, visit my <a href="http://novebiologije.blogspot.com/">blog "New Biologies"</a> where I present and comment news from the field of molecular, synthetic, systems and related biologies.<br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/finalsystem">Performance of the Final Functional Systems</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/biobricks">BioBricks</a>&nbsp; </li><br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/achievements">Achievements</a>&nbsp; </li><br />
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<h3 class="discussion"><span><a class="two" href="https://2007.igem.org/Ljubljana/team">Team</a></span></h3><br />
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<br><br><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/glossary">Terms & References</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/acknowledgements">Acknowledgements</a>&nbsp; </li><br />
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<h3><span>Marko Dolinar</span></h3><br />
<p class="p1"><span><br />
<br />
<br><br><br><br />
<br><br><br><br><br />
Together with <a href="https://2007.igem.org/Ljubljana/RomanJerala">Roman Jerala</a>, I am co-supervisor of the Slovenian team. Five out of seven undergraduates in our team are or were my students. I teach molecular biology within the Biochemistry course and Recombinant DNA Technology theoretical and practical course here at the <a href="http://www.uni-lj.si/en/">University of Ljubljana</a> <a href="http://www.fkkt.uni-lj.si/en/">Faculty of Chemistry and Chemical Technology</a>. Our Biochemistry Chair presents itself <a href="http://openwetware.org/wiki/FCCT_Biochemistry_Lab">on OWW</a>.<br><br />
If you are fluent in Slovenian, visit my <a href="http://novebiologije.blogspot.com/">blog "New Biologies"</a> where I present and comment news from the field of molecular, synthetic, systems and related biologies.<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
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<ul><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/subsystems">Subsystems Testing</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/finalsystem">Performance of the Final Functional Systems</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/biobricks">BioBricks</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/methods">Methods</a>&nbsp; </li><br />
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<li><a class="one" href="https://2007.igem.org/Ljubljana/achievements">Achievements</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/prospects">Prospects</a>&nbsp; </li><br />
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<h3 class="discussion"><span><a class="two" href="https://2007.igem.org/Ljubljana/team">Team</a></span></h3><br />
<ul><br />
<br />
<br><br><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/glossary">Terms & References</a>&nbsp; </li><br />
<li><a class="one" href="https://2007.igem.org/Ljubljana/acknowledgements">Acknowledgements</a>&nbsp; </li><br />
</ul><br />
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