http://2014.igem.org/wiki/index.php?title=Special:Contributions/JamesLongAberdeen&feed=atom&limit=50&target=JamesLongAberdeen&year=&month=2014.igem.org - User contributions [en]2024-03-29T07:18:35ZFrom 2014.igem.orgMediaWiki 1.16.5http://2014.igem.org/Team:Aberdeen_Scotland/Project/DiseaseTeam:Aberdeen Scotland/Project/Disease2014-10-18T02:56:10Z<p>JamesLongAberdeen: </p>
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<h1>Trypanosomiasis</h1><br />
<h3>Human African Trypanosomiasis (Sleeping Sickness) Epidemiology</h3><br />
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<p>Over 98% of reported cases of Human African Trypanosomiasis (HAT) are caused by a chronic infection of parasite <i>Trypanosoma brucei gambiense</i>. Its vector is through the bite of an infected Tsetse fly in sub-saharan Africa.</p><br />
<p>WHO estimates as of 2014, 30,000 people are currently infected, with more than 80% of new cases occurring in Democratic Republic of the Congo.</p><br />
<center><img src="https://static.igem.org/mediawiki/2014/7/7b/Afr.png" width="60%" height="60%"></center><br />
<p><i>T.b. gambiense</i> sufferers may be infected for months or even years without major signs or symptoms of the disease. When more evident symptoms emerge, the patient is often already in an advanced disease stage where the central nervous system is affected.</p><br />
<p>During epidemic periods prevalence reached 50% in several villages in the Angola, Democratic Republic of Congo, and South Sudan. Sleeping sickness was the first or second greatest cause of mortality in those communities, ahead of even HIV/AIDS.<p><br />
<p>The World Health Organisation included HAT in its roadmap for elimination and control of neglected tropical diseases in 2012, setting a date of 2020 to eliminate the disease as a public health problem.</p><br />
<p>2% of reported cases are due to <i>T.b. rhodesiense</i>, which is an acute infection, however this figure may be skewed by the fact this develops rapidly, invading the central nervous system with symptoms appearing after only a few weeks or months. If it persists, infected have a similar prognosis of almost unanimous mortality.</p><br />
<p>Chagas disease of South America is of a different subgenus, <i>Trypanosoma cruzi</i>, and utilises a different vector, Triatominae (‘assassin bugs’).</p><br />
<h3>Disease Progression</h3><br />
<img src="https://static.igem.org/mediawiki/2014/c/cb/Trypanosoma-evansi-rat-blood-Giemsa-stain.jpg"><br />
Giemsa-stained trypanasoma parasites in blood<br />
<p><i>T. b. gambiense</i> stage 1 exists free in blood serum or lymph, usually pathogens like this will be quickly destroyed by an active immune response, however it exhibits antigenic variation of its LiTat1.3/1.5 coat that changes every 20 minutes with over 100 possible phenotypes encoded in its chromosome; this negates an active immunity from being effectively generated.</p><br />
<p>After a period of approximately 6 months it progresses to stage 2 where the parasite enters the central nervous system, here it is protected from an immune response and may proliferate at will. Clearer symptoms emerge at this point including muscle weakness, sleep disturbance, partial paralysis, parkinsonism, psychosis and other psychiatric symptoms, and coma. If untreated, <i>T. b. gambiense</i> almost always results in death.</p><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Project/DiseaseTeam:Aberdeen Scotland/Project/Disease2014-10-18T02:55:29Z<p>JamesLongAberdeen: </p>
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<p>Over 98% of reported cases of Human African Trypanosomiasis (HAT) are caused by a chronic infection of parasite <i>Trypanosoma brucei gambiense</i>. Its vector is through the bite of an infected Tsetse fly in sub-saharan Africa.</p><br />
<p>WHO estimates as of 2014, 30,000 people are currently infected, with more than 80% of new cases occurring in Democratic Republic of the Congo.</p><br />
<center><img src="https://static.igem.org/mediawiki/2014/7/7b/Afr.png" width="60%" height="60%"></center><br />
<p><i>T.b. gambiense</i> sufferers may be infected for months or even years without major signs or symptoms of the disease. When more evident symptoms emerge, the patient is often already in an advanced disease stage where the central nervous system is affected.</p><br />
<p>During epidemic periods prevalence reached 50% in several villages in the Angola, Democratic Republic of Congo, and South Sudan. Sleeping sickness was the first or second greatest cause of mortality in those communities, ahead of even HIV/AIDS.<p><br />
<p>The World Health Organisation included HAT in its roadmap for elimination and control of neglected tropical diseases in 2012, setting a date of 2020 to eliminate the disease as a public health problem.</p><br />
<p>2% of reported cases are due to <i>T.b. rhodesiense</i>, which is an acute infection, however this figure may be skewed by the fact this develops rapidly, invading the central nervous system with symptoms appearing after only a few weeks or months. If it persists, infected have a similar prognosis of almost unanimous mortality.</p><br />
<p>Chagas disease of South America is of a different subgenus, <i>Trypanosoma cruzi</i>, and utilises a different vector, Triatominae (‘assassin bugs’).</p><br />
<h3>Disease Progression</h3><br />
<img src="https://static.igem.org/mediawiki/2014/c/cb/Trypanosoma-evansi-rat-blood-Giemsa-stain.jpg"><br />
Giemsa-stained trypanasoma parasite in blood<br />
<p><i>T. b. gambiense</i> stage 1 exists free in blood serum or lymph, usually pathogens like this will be quickly destroyed by an active immune response, however it exhibits antigenic variation of its LiTat1.3/1.5 coat that changes every 20 minutes with over 100 possible phenotypes encoded in its chromosome; this negates an active immunity from being effectively generated.</p><br />
<p>After a period of approximately 6 months it progresses to stage 2 where the parasite enters the central nervous system, here it is protected from an immune response and may proliferate at will. Clearer symptoms emerge at this point including muscle weakness, sleep disturbance, partial paralysis, parkinsonism, psychosis and other psychiatric symptoms, and coma. If untreated, <i>T. b. gambiense</i> almost always results in death.</p><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Project/DiseaseTeam:Aberdeen Scotland/Project/Disease2014-10-18T02:55:00Z<p>JamesLongAberdeen: </p>
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</div> <br class="clear"> <!-- END OF HEAD --><br />
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<p>Over 98% of reported cases of Human African Trypanosomiasis (HAT) are caused by a chronic infection of parasite <i>Trypanosoma brucei gambiense</i>. Its vector is through the bite of an infected Tsetse fly in sub-saharan Africa.</p><br />
<p>WHO estimates as of 2014, 30,000 people are currently infected, with more than 80% of new cases occurring in Democratic Republic of the Congo.</p><br />
<center><img src="https://static.igem.org/mediawiki/2014/7/7b/Afr.png" width="60%" height="60%"></center><br />
<p><i>T.b. gambiense</i> sufferers may be infected for months or even years without major signs or symptoms of the disease. When more evident symptoms emerge, the patient is often already in an advanced disease stage where the central nervous system is affected.</p><br />
<p>During epidemic periods prevalence reached 50% in several villages in the Angola, Democratic Republic of Congo, and South Sudan. Sleeping sickness was the first or second greatest cause of mortality in those communities, ahead of even HIV/AIDS.<p><br />
<p>The World Health Organisation included HAT in its roadmap for elimination and control of neglected tropical diseases in 2012, setting a date of 2020 to eliminate the disease as a public health problem.</p><br />
<p>2% of reported cases are due to <i>T.b. rhodesiense</i>, which is an acute infection, however this figure may be skewed by the fact this develops rapidly, invading the central nervous system with symptoms appearing after only a few weeks or months. If it persists, infected have a similar prognosis of almost unanimous mortality.</p><br />
<p>Chagas disease of South America is of a different subgenus, <i>Trypanosoma cruzi</i>, and utilises a different vector, Triatominae (‘assassin bugs’).</p><br />
<h3>Disease Progression</h3><br />
<img src="https://static.igem.org/mediawiki/2014/c/cb/Trypanosoma-evansi-rat-blood-Giemsa-stain.jpg"><br />
giemsa stained trypanasoma in blood<br />
<p><i>T. b. gambiense</i> stage 1 exists free in blood serum or lymph, usually pathogens like this will be quickly destroyed by an active immune response, however it exhibits antigenic variation of its LiTat1.3/1.5 coat that changes every 20 minutes with over 100 possible phenotypes encoded in its chromosome; this negates an active immunity from being effectively generated.</p><br />
<p>After a period of approximately 6 months it progresses to stage 2 where the parasite enters the central nervous system, here it is protected from an immune response and may proliferate at will. Clearer symptoms emerge at this point including muscle weakness, sleep disturbance, partial paralysis, parkinsonism, psychosis and other psychiatric symptoms, and coma. If untreated, <i>T. b. gambiense</i> almost always results in death.</p><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/NotebookTeam:Aberdeen Scotland/Notebook2014-10-18T02:38:40Z<p>JamesLongAberdeen: </p>
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<h4>Initial brainstorming meetings (February-June)</h4><br />
<ul><br />
<li><br />
Our initial project ideas:<br><br />
<ol type="a"><br />
<li><b>Bacterial drones</b><br>Engineering bacteria to carry particular substances to specific locations via manipulation of chemotaxis</li><br />
<li><b>Defrosting streets in winter</b><br>To engineer bacteria expressing anti-freeze proteins from an arctic fish in order to provide an alternative for using salt in winter to defrost streets</li><br />
<li><b>Light sensor</b><br>Engineering bacteria that would sense the intensity of light in our surrounding and respond when it falls below a certain threshold by producing light (e.g. to keep optimal light levels when reading). Geobacter could be used since it can transmit an electric current</li><br />
<li><b>Tetrodotoxin detector</b><br>Designing a biosensor which would be able to detect lethal concentrations of tetrodotoxin in prepared Fugu fish, allowing a decision whether it is safe to consume</li><br />
<li><b>Recycling nappies</b><br>A bacterium which would be able to degrade a filling used in baby nappies</li><br />
<li><b>Polyester degradation</b><br>Engineering bacteria to degrade polyester and hence enable recycling of polyester based trash, e.g. margarine packages and yoga mats</li><br />
<li><b>Biological night light</b><br>Engineering plants to express luminescent luciferase in order to create a touch-activated night light for children which wouldn't require electricity</li><br />
<li><b>Bacterial pen</b><br>Filling a pen with bacteria manipulated to synthesize dye. Such a pen would never run out of ink as long as we would feed it with nitrogen and sugar. A water-soluble and insoluble dyes could be synthesized.</li><br />
<li><b>Supplementation of Vitamin C</b><br>Engineering probiotic bacteria to synthesize vitamin C in order to produce Vit. C fortified food products</li><br />
<li><b>Biofilm degradation</b><br>The idea is to engineer bacteria to synthesize an enzyme capable of degrading extracellular polymeric substances which create biofilms. This would ideally reduce biofilm-associated infections by disrupting quorum sensing, decreasing antibiotic resistance in bacteria and increasing their sensitivity to cleaning agents. Engineered bacteria could be incorporated into a toothpaste.</li><br />
<li><b>Water contamination detectors</b><br>Engineered bacteria would sense a presence of one of the following in water and respond via a colour change upon detection.<br />
<ol type="i"><br />
<li>Vibrio cholerae</li><br />
<li>Arsenic</li><br />
<li>Aluminium</li><br />
<li>Fluoride</li><br />
<li>Asbestos</li><br />
</ol><br />
</li><br />
<li><b>Greenhouse gas reduction bacteria</b><br>An anaerobic bacteria that uses NO2 to get Methane and then 'digests' Methane into CO2 and H20. The idea is to get the bacteria to stop at Methane and thus suck it from the atmosphere.</li><br />
<li><b>CO Detector bacteria</b><br>Use modified bacteria that is equipped with receptors for CO to signal a high concentration of CO in air. The bacteria could emit light, change colour or other type of signal.</li><br />
<li><b>Computer Bacteria</b><br>Use bacteria that conducts electricity and modify it in a way that it will conduct or not depending on a certain environmental condition. This way, we can make the bacteria mimic a computational process.</li><br />
<li><b>Fire detector bacteria</b><br>Fire detectors work by constantly checking for contamination in the air from smoke particles. They achieve this by flowing a current through a radioactive emitter, which decreases/stops emitting radiation when surrounded by smoke particles. This fall in current, triggers the detector. We could try imitating this behaviour with the electricity conducting bacteria, by making it not able to conduct electricity when smoke particles are with high concentration.</li><br />
<li><b>Bio-deodorant</b><br>A bacteria that would compete with the naturally-occurring skin bacteria by also metabolising secretions but crucially not producing smelly waste products. We really liked this one and it doesn't seem so far-fetched.</li><br />
<li><b>Contaminated water detector</b><br>Use E.coli to secrete colour in reaction to certain toxins in water. Problematic as in pure water witn only toxin diluted, there is no energy source for the bacteria.</li><br />
<li><b>Break down of oil spills</b><br>Make a bacteria break down oil into non-harmful matter in order to clean up oil spills.</li><br />
<li><b>Reduce saturated fat intake in humans</b><br>Use a similar idea to the previous one, but in this case, bacteria will extract saturated fat from food intake and make it indigestible or the bacteria itself could break it down to something less harmful.</li><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/NotebookTeam:Aberdeen Scotland/Notebook2014-10-18T02:37:01Z<p>JamesLongAberdeen: </p>
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<h4>Initial brainstorming meetings (February-June)</h4><br />
<ul><br />
<li><br />
Our initial project ideas:<br><br />
<ol type="a"><br />
<li><b>Bacterial drones</b><br>Engineering bacteria to carry particular substances to specific locations via manipulation of chemotaxis</li><br />
<li><b>Defrosting streets in winter</b><br>To engineer bacteria expressing anti-freeze proteins from an arctic fish in order to provide an alternative for using salt in winter to defrost streets</li><br />
<li><b>Light sensor</b><br>Engineering bacteria that would sense the intensity of light in our surrounding and respond when it falls below a certain threshold by producing light (e.g. to keep optimal light levels when reading). Geobacter could be used since it can transmit an electric current</li><br />
<li><b>Tetrodotoxin detector</b><br>Designing a biosensor which would be able to detect lethal concentrations of tetrodotoxin in prepared Fugu fish, allowing a decision whether it is safe to consume</li><br />
<li><b>Recycling nappies</b><br>A bacterium which would be able to degrade a filling used in baby nappies</li><br />
<li><b>Polyester degradation</b><br>Engineering bacteria to degrade polyester and hence enable recycling of polyester based trash, e.g. margarine packages and yoga mats</li><br />
<li><b>Biological night light</b><br>Engineering plants to express luminescent luciferase in order to create a touch-activated night light for children which wouldn't require electricity</li><br />
<li><b>Bacterial pen</b><br>Filling a pen with bacteria manipulated to synthesize dye. Such a pen would never run out of ink as long as we would feed it with nitrogen and sugar. A water-soluble and insoluble dyes could be synthesized.</li><br />
<li><b>Supplementation of Vitamin C</b><br>Engineering probiotic bacteria to synthesize vitamin C in order to produce Vit. C fortified food products</li><br />
<li><b>Biofilm degradation</b><br>The idea is to engineer bacteria to synthesize an enzyme capable of degrading extracellular polymeric substances which create biofilms. This would ideally reduce biofilm-associated infections by disrupting quorum sensing, decreasing antibiotic resistance in bacteria and increasing their sensitivity to cleaning agents. Engineered bacteria could be incorporated into a toothpaste.</li><br />
<li><b>Water contamination detectors</b><br>Engineered bacteria would sense a presence of one of the following in water and respond via a colour change upon detection.<br />
<ol type="i"><br />
<li>Vibrio cholerae</li><br />
<li>Arsenic</li><br />
<li>Aluminium</li><br />
<li>Fluoride</li><br />
<li>Asbestos</li><br />
</ol><br />
</li><br />
<li><b>Greenhouse gas reduction bacteria</b><br>An anaerobic bacteria that uses NO2 to get Methane and then 'digests' Methane into CO2 and H20. The idea is to get the bacteria to stop at Methane and thus suck it from the atmosphere.</li><br />
<li><b>CO Detector bacteria</b><br>Use modified bacteria that is equipped with receptors for CO to signal a high concentration of CO in air. The bacteria could emit light, change colour or other type of signal.</li><br />
<li><b>Computer Bacteria</b><br>Use bacteria that conducts electricity and modify it in a way that it will conduct or not depending on a certain environmental condition. This way, we can make the bacteria mimic a computational process.</li><br />
<li><b>Fire detector bacteria</b><br>Fire detectors work by constantly checking for contamination in the air from smoke particles. They achieve this by flowing a current through a radioactive emitter, which decreases/stops emitting radiation when surrounded by smoke particles. This fall in current, triggers the detector. We could try imitating this behaviour with the electricity conducting bacteria, by making it not able to conduct electricity when smoke particles are with high concentration.</li><br />
<li><b>Bio-deodorant</b><br>We really liked this one and it doesn't seem so far-fetched.</li><br />
<li><b>Contaminated water detector</b><br>Use E.coli to secrete colour in reaction to certain toxins in water. Problematic as in pure water witn only toxin diluted, there is no energy source for the bacteria.</li><br />
<li><b>Break down of oil spills</b><br>Make a bacteria break down oil into non-harmful matter in order to clean up oil spills.</li><br />
<li><b>Reduce saturated fat intake in humans</b><br>Use a similar idea to the previous one, but in this case, bacteria will extract saturated fat from food intake and make it indigestible or the bacteria itself could break it down to something less harmful.</li><br />
</ol><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/NotebookTeam:Aberdeen Scotland/Notebook2014-10-18T02:36:29Z<p>JamesLongAberdeen: </p>
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</div> <br class="clear"> <!-- END OF HEAD --><br />
<br />
<!-- PAGE CONTENT --><br />
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<h4>Initial brainstorming meetings (February-June)</h4><br />
<ul><br />
<li><br />
Our initial project ideas:<br><br />
<ol type="a"><br />
<li><b>Bacterial drones</b><br>Engineering bacteria to carry particular substances to specific locations via manipulation of chemotaxis</li><br />
<li><b>Defrosting streets in winter</b><br>To engineer bacteria expressing anti-freeze proteins from an arctic fish in order to provide an alternative for using salt in winter to defrost streets</li><br />
<li><b>Light sensor</b><br>Engineering bacteria that would sense the intensity of light in our surrounding and respond when it falls below a certain threshold by producing light (e.g. to keep optimal light levels when reading). Geobacter could be used since it can transmit an electric current</li><br />
<li><b>Tetrodotoxin detector</b><br>Designing a biosensor which would be able to detect lethal concentrations of tetrodotoxin in prepared Fugu fish, allowing a decision whether it is safe to consume</li><br />
<li><b>Recycling nappies</b><br>A bacterium which would be able to degrade a filling used in baby nappies</li><br />
<li><b>Polyester degradation</b><br>Engineering bacteria to degrade polyester and hence enable recycling of polyester based trash, e.g. margarine packages and yoga mats</li><br />
<li><b>Biological night light</b><br>Engineering plants to express luminescent luciferase in order to create a touch-activated night light for children which wouldn't require electricity</li><br />
<li><b>Bacterial pen</b><br>Filling a pen with bacteria manipulated to synthesize dye. Such a pen would never run out of ink as long as we would feed it with nitrogen and sugar. A water-soluble and insoluble dyes could be synthesized.</li><br />
<li><b>Supplementation of Vitamin C</b><br>Engineering probiotic bacteria to synthesize vitamin C in order to produce Vit. C fortified food products</li><br />
<li><b>Biofilm degradation</b><br>The idea is to engineer bacteria to synthesize an enzyme capable of degrading extracellular polymeric substances which create biofilms. This would ideally reduce biofilm-associated infections by disrupting quorum sensing, decreasing antibiotic resistance in bacteria and increasing their sensitivity to cleaning agents. Engineered bacteria could be incorporated into a toothpaste.</li><br />
<li><b>Water contamination detectors</b><br>Engineered bacteria would sense a presence of one of the following in water and respond via a colour change upon detection.<br />
<ol type="i"><br />
<li>Vibrio cholerae</li><br />
<li>Arsenic</li><br />
<li>Aluminium</li><br />
<li>Fluoride</li><br />
<li>Asbestos</li><br />
</ol><br />
</li><br />
<li><b>Greenhouse gas reduction bacteria</b><br>An anaerobic bacteria that uses NO2 to get Methane and then 'digests' Methane into CO2 and H20. The idea is to get the bacteria to stop at Methane and thus suck it from the atmosphere.</li><br />
<li><b>CO Detector bacteria</b><br>Use modified bacteria that is equipped with receptors for CO to signal a high concentration of CO in air. The bacteria could emit light, change colour or other type of signal.</li><br />
<li><b>Computer Bacteria</b><br>Use bacteria that conducts electricity and modify it in a way that it will conduct or not depending on a certain environmental condition. This way, we can make the bacteria mimic a computational process.</li><br />
<li><b>Fire detector bacteria</b><br>Fire detectors work by constantly checking for contamination in the air from smoke particles. They achieve this by flowing a current through a radioactive emitter, which decreases/stops emitting radiation when surrounded by smoke particles. This fall in current, triggers the detector. We could try imitating this behaviour with the electricity conducting bacteria, by making it not able to conduct electricity when smoke particles are with high concentration.</li><br />
<li><b>Bio-deodorant</b><br>James L's idea. We really liked this one and it doesn't seem so far-fetched.</li><br />
<li><b>Contaminated water detector</b><br>Use E.coli to secrete colour in reaction to certain toxins in water. Problematic as in pure water witn only toxin diluted, there is no energy source for the bacteria.</li><br />
<li><b>Break down of oil spills</b><br>Make a bacteria break down oil into non-harmful matter in order to clean up oil spills.</li><br />
<li><b>Reduce saturated fat intake in humans</b><br>Use a similar idea to the previous one, but in this case, bacteria will extract saturated fat from food intake and make it indigestible or the bacteria itself could break it down to something less harmful.</li><br />
</ol><br />
</li><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/ProjectTeam:Aberdeen Scotland/Project2014-10-18T02:33:19Z<p>JamesLongAberdeen: </p>
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<h1><i>E. coli</i>-based Trypanosomiasis Diagnostic System</h1><br />
<h3>Getting back at the Sleeping Sickness by detecting it early</h3><br />
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<p><i>E.coli </i> display of peptide mimotopes, integrated with quorum-sensing AND logic, for diagnosis of tropical diseases<br />
<i>Trypanosoma.b.gambiense</i>, the causative agent of Trypanosomiasis (African Sleeping Sickness) infects 30,000 people worldwide, with 60 million at disease risk.<br />
Unrecognised, this disease is fatal, but accurate diagnosis, relying on detection of patient serum antibodies against two different trypanosomal antigens, allows<br />
successful treatment. We engineered autotransporters Antigen 43 and ice-nucleation protein to successfully express surface epitopes in <i>E.coli</i> that mimic two different<br />
trypanosomal antigens. Two <i>E.coli</i> strains were generated, each expressing a distinct surface epitope and either a quorum sensing (QS) sender or receiver module<br />
respectively. Immune pull-down of each strain, and their subsequent co-culture, produced a quorum signal, indicating successful detection of two distinct antibody<br />
populations in a serum sample. We constructed a cheap, Raspberry Pi computer-controlled fluorimeter suitable for developing countries, showing it could detect QS<br />
fluorescence output. This novel application of antigen display, and quorum sensing to implement AND logic sensing, facilitates cheap, simple diagnosis of tropical<br />
diseases.</p><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:16:03Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/Device">Device Data</a></li><br />
<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<br />
This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here: http://parts.igem.org/Part:BBa_K1352003<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:15:30Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<br />
This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:14:45Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/Device">Device Data</a></li><br />
<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:14:05Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/Device">Device Data</a></li><br />
<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<br />
This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:13:46Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/Device">Device Data</a></li><br />
<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<br />
This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:12:59Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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INP+YFP+His<br />
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This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:12:35Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003Team:Aberdeen Scotland/Parts/ 20032014-10-18T02:12:07Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2003">Bba_K1352003</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006">Bba_K1352006</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_3013">Bba_k523013</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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This brick was successfully created but in an ampicillin backbone and as such was not physically submitted to iGEM, details about its characterisation can be found on the registry entry for it here:<br />
<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/AttributionsTeam:Aberdeen Scotland/Attributions2014-10-18T01:55:24Z<p>JamesLongAberdeen: </p>
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<h1>Attributions; what the Aberdeen iGEM team members did</h1><br />
<br />
<h3>Alpha Team – Ag43 Protein</h3><br />
<p><i>Team Members: Ana Maria Cujba and Martyna Sroka carried out the following work;</i></p><br />
<p>Alpha team took an Ag43 part produced by the 2012 Hokkaido University iGEM team, the goal at first appeared simple – insert a FLAG-tag-multiple-cloning-site (FLAG+MCS) into Ag43. However, two further problems had to be overcome first: 1. The part had six additional Pst1 sites (non-compliant with RFC-10) which did not appear in the registry sequence. These sites had to be removed. 2. Ag43 has beta hairpins, these are somewhat like Velcro and stick the cells together so that can form biofilms, for our assay these would lead to false-positives and two of them had to be removed. Only after solving those two problems, alpha team proceeded to insert FLAG+MCS; they also experimentally characterized all Ag43-related parts.</p><br />
<br />
<br><br />
<br />
<br />
<h3>Omega Team – INP</h3><br />
<p><i>Team Members: James Long and Joseph MacKinnon carried out the following work;</i></p><br />
<p>Omega team took an INP part produced by the 2011 Edinburgh University iGEM team, (this part is simply INP with engineered yellow fluorescent protein (eYFP) attached to the C-terminus). A FLAG(and HexaHis "His")-MCS had to be inserted onto the C-terminus of eYFP, although this is simple in theory it still took longer than expected, not only due to PCRs misbehaving, but more importantly the antibody test was negative and it was suspected that the eYFP (having its C and N termini on the same side) was shielding the FLAG/His tag. Because of this, the eYFP had to be removed and the FLAG tag attached to the C-terminus of INP.</p><br />
<br />
<br />
<br />
<br><br />
<br />
<br />
<h3>Modelling and GFP Detector</h3><br />
<p><i>Team Member: Konstantin Gizdov carried out the following work;</i></p><br />
<p>Mathematical modelling proved to be extremely useful to the team, it flagged up that an ELISA assay would probably not work, and as such when this gave poor results it was immediately abandoned in favour of a magnetic pull-down assay. It was also able to predict what the optimum ratio of “sender” to “receiver” cultures would be to give the best signal-to-noise ratio. As the ultimate goal of our project was to deploy a HAT detection kit in Africa, a cheap GFP detector would be needed, the only ones on the market are highly precise and expensive. A working DIY detector was created from off-the-shelf parts that cost less than £100 total and could be powered by a cheap solar-cell.</p><br />
<br />
<br />
<br><br />
<br />
<br />
<h3>Parts and Quorum Testing</h3><br />
<p><i>Team Member: James McAvoy carried out the following work;</i></p><br />
<p>This task can be split into three components. 1. Testing the individual expression of FLAG by Ag43 and INP use of anti-FLAG antibodies and fluorescence microscopy to see whether the plasmids worked. 2. Producing the composite cells (with Ag43 or INP plasmid, sender or receiver plasmid, and RFP identification plasmid all in the same cell). 3. Quorum-testing was a data-intensive task, these two cell cultures were tested with anti-GFP and anti-FLAG antibodies. At first ELISA-type assays were used to achieve this but these produced very poor results and were upgraded to a magnetic bead pull-down assay which were much better and gave us a proof-of-concept.</p><br />
<br />
<br />
<br><br />
<br />
<i>All submitted BioBrick parts were designed and created by our team:</i><br />
<br><br />
• Bba_K1352000 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K1352001 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K1352002 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K1352004 (Jamie Long, Joseph MacKinnon)<br />
<br><br />
• Bba_K1352006 (Jamie Long, Joseph MacKinnon)<br />
<br><br />
<br><br />
<i>All parts characterisation experiments were performed by the members of our team:</i><br />
<br><br />
• Bba_K759001 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K542009 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K346007 (Martyna Sroka, Ana-Maria Cujba)<br />
<br><br />
• Bba_K1090000 (James McAvoy)<br />
<br><br />
• Bba_T9002 (James McAvoy)<br />
<br><br />
The GFP detector was designed and built by Konstantin Gizdov.<br />
<br />
<br />
<br />
<h3>Special thanks to:</h3><br />
• Dr. Liesbeth Van Nieuwenhove, for putting us in touch with Professor Philippe Büscher<br />
<br><br />
• Professor Philippe Büscher, Head of the Unit of Parasite Diagnostics at Institute of Tropical Medicine Antwerp, for providing scientific expertise as well as supplying monoclonal antibodies and variable antigen type specific antisera<br />
<br><br />
• Dr. Kenneth Skeldon, Rhiannon Thompson and Heather Doran, for their help with preparation for our presentation at PechaKucha, Explorathon - European Researchers Night event<br />
<br><br />
• AU magazine, for publishing a series of blogpost about iGEM, synthetic biology and our project<br />
<br><br />
• Edinburgh University iGEM 2014 team, for organizing a meeting with Professor Muffy Calder, Chief Scientific Adviser for Scotland, at The Royal Society of Edinburgh<br />
<br><br />
• SULSA, for organizing Scottish iGEM teams meet-up and giving us a chance to present our project at the Synthetic Biology conference<br />
<br><br />
• Kim de Moura, for his advice and support during Scottish iGEM teams meet-up event<br />
<br><br />
• Kevin MacKenzie, for fluorescence microscopy training<br />
<br><br />
• University of Dundee, Sequencing Unit, for Sanger sequencing of our created BioBricks<br />
<br><br />
• Kelly Reid, Alison Davidson and other members of lab support team, for their patience, optimism and willingness to help<br />
<br><br />
• Dr Marco Thiel and the Institute for Complex Systems and Mathematical Biology, University of Aberdeen for proving us with specilised software support and initial building<br />
materials for the device (Arduino, RaspberryPi).<br />
<br><br />
• Last but not least - our supervisors: Dr Susan Black, Dr Rey Carabeo, Dr Alessandro Moura, Dr Berndt Müller, Dr Stefania Spanò and Prof Ian Stansfield, for their patience, scientific expertise and input during brainstorming sessions<br />
<br />
<br><br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<h3>We would like to extend our thanks to the organizations and companies that supported us and enabled our team to participate in this year's iGEM competition.</h3><br />
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<li><a href="http://arduino.cc/" title="Arduino"><img src="https://static.igem.org/mediawiki/2014/9/92/Arduino_logo.jpeg"></a></li><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Project/DeviceTeam:Aberdeen Scotland/Project/Device2014-10-17T23:59:41Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Project/Disease">The Disease</a></li><br />
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<h1>Portable Fluorescence Detector</h1><br />
<h3>The measurement device for automatically and efficiently analysing the test results on the go.</h3><br />
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<p>In order to be able to test a patient in the field, the assay needs to be analysed. As the assay results in the expression of GFP (Green Fluorescent Protein)<br />
production, it would have been next to impossible to make any meaningful measurements by hand. This is why our team has concentrated on designing a portable device that would<br />
aid the medical staff.</p><br />
<p>The operation of the device in question relies on several fundamental principles - the discrete nature of the activation and emission wavelengths for GFP, the<br />
filtering of UV light and the sensitivity range of LDRs (Light Dependent Resistors). Essentially, the device is going to measure the intensity of fluorescent light<br />
due to GFP illumination with UV light, in order to determine the amount (concentration) of GFP in the medium.</p><br />
<h3>The Measurement Chamber</h3><br />
<p>After the assay protocol has been finished, the cuvette is to be placed in the measurement chamber of the device. There a UV LED (Light Emitting Diode) with peak<br />
wavelength at 395 nm (the activation wavelength for GFP) shines through the cuvette and illuminates the GFP molecules in the medium. On the other side of the<br />
cuvette, after a UV filter and a Green (green pass-through) filter, the light intensity is measured by means of an LDR (Light Dependent Resistor).</p><br />
<img src="https://static.igem.org/mediawiki/2014/6/62/Chamber.png"><br />
<h3>Control Circuit</h3><br />
<p>The LDR is connected to an Arduino, that manages and supplies power to the measuring chamber and the measuring process. In order to improve<br />
on the noisy direct-measurement values, the Arduino communicates with a RaspberryPi, that uses Wolfram Mathematica 10 (incl) software for noise reduction and data<br />
analysis. In certain cases the RaspberryPi will be able to react to incoming data by adjusting the measurement procedure employed by the Arduino through the control<br />
API.</p><br />
<img src="https://static.igem.org/mediawiki/2014/1/18/Circuit.png"><br />
<h3>Portability</h3><br />
<p>The final milestone for the device is going to be portability. With the low-power nature of all the components in question, the device is able<br />
to operate from a small USB battery pack. The battery is charged in the mains or through a solar-panel charger. The market for such solar chargers is<br />
growing rapidly and they can be found at very affordable prices with good reliability.</p><br />
<h3>Price</h3><br />
<ul><br />
<li><br />
Price list by parts included:<br />
<ul><br />
<li>UV LED (395nm)<a href="http://uk.rs-online.com/web/p/uv-leds/7134894/"><sup>1</sup></a> <span style="float:right">£1.07</span></li><br />
<li>UV Filter<a href="http://www.epakelectronics.com/uv_filter_materials.htm"><sup>2</sup></a> <span style="float:right">£10.00</span></li><br />
<li><br />
Green Filter<a href="http://www.pnta.com/lighting/gels/lee/lee-filters-cl139-cool-led-primary-green/"><sup>3</sup></a><br />
<a href="http://www.leefilters.com/lighting/colour-details.html#CL139&filter=ld"><sup>4</sup></a> <span style="float:right">£4.26</span><br />
</li><br />
<li>LDR (Light Dependent Resistor)<br />
<a href="http://uk.rs-online.com/web/p/ldr-light-dependent-resistors/2341050/"><sup>5</sup></a> <span style="float:right">£0.91</span></li><br />
<li>Arduino UNO<a href="http://r.ebay.com/cDXfED"><sup>6</sup></a> <span style="float:right">£6.99</span></li><br />
<li>Raspberry Pi<a href="http://goo.gl/lRVsOO"><sup>7</sup></a> <span style="float:right">£25.80</span></li><br />
<li>Raspberry Pi Starter Kit<a href="http://goo.gl/InsQjb"><sup>8</sup></a> <span style="float:right">£15.00</span></li><br />
</ul><br />
</li><br />
<li><b>Total<span style="float:right">£64.03</span></b></li><br />
</ul><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Project/DeviceTeam:Aberdeen Scotland/Project/Device2014-10-17T23:57:41Z<p>JamesLongAberdeen: </p>
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<h3>The measurement device for automatically and efficiently analysing the test results on the go.</h3><br />
</div> <br class="clear"> <!-- END OF HEAD --><br />
<br />
<!-- PAGE CONTENT --><br />
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<p>In order to be able to test a patient in the field, the assay needs to be analysed. As the assay results in expressed in GFP (Green Fluorescent Protein)<br />
production, it is going to be very hard to make any meaningful measurements by hand. This is why our team has concentrated on designing a portable device that would<br />
aid the medical staff.</p><br />
<p>The operation of the device in question relies on several fundamental principles - the discrete nature of the activation and emission wavelengths for GFP, the<br />
filtering of UV light and the sensitivity range of LDRs (Light Dependent Resistors). Essentially, the device is going to measure the intensity of fluorescent light<br />
due to GFP illumination with UV light, in order to determine the amount (concentration) of GFP in the medium.</p><br />
<h3>The Measurement Chamber</h3><br />
<p>After the assay protocol has been finished, the cuvette is to be placed in the measurement chamber of the device. There a UV LED (Light Emitting Diode) with peak<br />
wavelength at 395 nm (the activation wavelength for GFP) shines through the cuvette and illuminates the GFP molecules in the medium. On the other side of the<br />
cuvette, after a UV filter and a Green (green pass-through) filter, the light intensity is measured by means of an LDR (Light Dependent Resistor).</p><br />
<img src="https://static.igem.org/mediawiki/2014/6/62/Chamber.png"><br />
<h3>Control Circuit</h3><br />
<p>The LDR is connected to an Arduino, that manages and supplies power to the measuring chamber and the measuring process. In order to improve<br />
on the noisy direct-measurement values, the Arduino communicates with a RaspberryPi, that uses Wolfram Mathematica 10 (incl) software for noise reduction and data<br />
analysis. In certain cases the RaspberryPi will be able to react to incoming data by adjusting the measurement procedure employed by the Arduino through the control<br />
API.</p><br />
<img src="https://static.igem.org/mediawiki/2014/1/18/Circuit.png"><br />
<h3>Portability</h3><br />
<p>The final milestone for the device is going to be portability. With the low-power nature of all the components in question, the device is able<br />
to operate from a small USB battery pack. The battery is charged in the mains or through a solar-panel charger. The market for such solar chargers is<br />
growing rapidly and they can be found at very affordable prices with good reliability.</p><br />
<h3>Price</h3><br />
<ul><br />
<li><br />
Price list by parts included:<br />
<ul><br />
<li>UV LED (395nm)<a href="http://uk.rs-online.com/web/p/uv-leds/7134894/"><sup>1</sup></a> <span style="float:right">£1.07</span></li><br />
<li>UV Filter<a href="http://www.epakelectronics.com/uv_filter_materials.htm"><sup>2</sup></a> <span style="float:right">£10.00</span></li><br />
<li><br />
Green Filter<a href="http://www.pnta.com/lighting/gels/lee/lee-filters-cl139-cool-led-primary-green/"><sup>3</sup></a><br />
<a href="http://www.leefilters.com/lighting/colour-details.html#CL139&filter=ld"><sup>4</sup></a> <span style="float:right">£4.26</span><br />
</li><br />
<li>LDR (Light Dependent Resistor)<br />
<a href="http://uk.rs-online.com/web/p/ldr-light-dependent-resistors/2341050/"><sup>5</sup></a> <span style="float:right">£0.91</span></li><br />
<li>Arduino UNO<a href="http://r.ebay.com/cDXfED"><sup>6</sup></a> <span style="float:right">£6.99</span></li><br />
<li>Raspberry Pi<a href="http://goo.gl/lRVsOO"><sup>7</sup></a> <span style="float:right">£25.80</span></li><br />
<li>Raspberry Pi Starter Kit<a href="http://goo.gl/InsQjb"><sup>8</sup></a> <span style="float:right">£15.00</span></li><br />
</ul><br />
</li><br />
<li><b>Total<span style="float:right">£64.03</span></b></li><br />
</ul><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/SafetyTeam:Aberdeen Scotland/Safety2014-10-17T23:18:31Z<p>JamesLongAberdeen: </p>
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<h3>We understand that safety is very important and so we made sure that we kept our lab work and genetic manipulations to high and agreed standards.</h3><br />
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<p>Safety, including genetic manipulation safety was of paramount importance for the whole team during the summer iGEM research period. All the procedures we carried out in the lab were guided by separate risk assessment documents that covered; biochemical reagent preparation; separation of nucleic acids on gels; visualisation of gels using UV light; use of the autoclave for sterilisation; use of the microwave to melt solid agar and gels. We spent the whole of week 1 of our 10 weeks in the lab working with our Instructors in the lab to ensure all our working practices were safe.</p><br />
<br />
<p>As important as general lab safety was genetic manipulation safety. iGEM Headquarters required us and all teams to liaise with their safety advisor throughout the project. However, before we could begin work on anything involving recombinant DNA at Aberdeen, we had first had to obtain permission from our local <a href="http://www.abdn.ac.uk/ims/documents/Foresterhill-Genetic-Modification-Safety-Information-Nov2013.pdf">Advisory Committee on Genetic Manipulation (ACGM) to carry out the project</a>. This involved (i) informal discussions with our ACGM chair to explain that the combination of genes we were intending to use could not exhibit any hazardous emergent properties, and that the genes we intending to manipulate were not inherently dangerous, and (ii) a formal application to the committee (linked, below) to set out the nature of the project and explain how its potential for causing harm through genetic manipulation was extremely low.</p><br />
<br />
<p> One problem we encountered was that the ACGM committee only meets quarterly, therefore any permissions we sought before the project began had to cover all directions the project might take! This was a serious iGEM disadvantage, since these projects can often take unexpected directions, and we may have wanted to manipulate new pieces of DNA not covered in the original ACGM application - this would have been impossible at Aberdeen under our ACGM regime. We therefore tried to make the ACGM application as broad as possible, covering all possible genes, promoters and plasmids we might conceivably use. We reflected that as synthetic biology develops in our and other Universities, ACGM oversight of projects will need to become more flexible, while still maintaining adequate safety oversight.</p> <br />
<br />
<p>You can find the specific details of what measures we took to ensure our work is safe for society, the environment and us in the document below.</p><br />
<br />
<br />
<a href="https://static.igem.org/mediawiki/2014/7/7c/IGEM_Aberdeen_2014_Safety_Form.pdf"><b>ACGM Genetic Permissions Application form [University of Aberdeen ACGM permission granted, June 2014]</b></a><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006Team:Aberdeen Scotland/Parts/ 20062014-10-17T21:12:54Z<p>JamesLongAberdeen: </p>
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<li class="curr"><a class="curr" href="#">Created</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<br />
K1352006 is a part which has a FLAG-tag octapeptide flanked by a multiple cloning site (MCS) inserted into Bba_K523013 (K523013 expresses ice nucleation protein (INP)); specifically, on the end of a linker, which is in turn on the C-terminus of INP and is in the same reading frame. The FLAG-tag is a BglII restriction site, followed by a FLAG octapeptide, followed by a HindIII restriction site; the sequence of which is as follows; the octapeptide is uppercase, the restriction sites are lowercase:<br />
(agatctGATTATAAAGATGATGATGATAAAaagctt)<br />
Attaching a FLAG-tag to the end of INP means that it will be expressed on the surface of the cell, the purpose of this is to allow the rapid insertion (via the MCS) of polypeptides (an antigen for example) to the C-terminus end of INP; this allows the surface expression of said polypeptide. For the 2014 Aberdeen iGEM project, this part was intended to be used as a trypanosome antigen displayer.<br />
<br />
Creation of INP-YFP-FLAG fragments followed by InFusion cloning Four infusion primers (primers with one homologous half (lower case) to the template, and one “overhang” half (upper case), the last 15 nucleotides of which is homologous to another DNA fragment) were designed.<br />
<br />
<br />
“INP-VEC-F” (CGCGGCCGCTTCTAGAttaatacgactcactataggg)<br><br />
<br />
“INP-Rem-R” (aagctttttatcatcatcatctttataatcagatctTCCCGCCACGCTGC)<br><br />
<br />
“INP-FLAG-F” (AGATCTGATTATAAAGATGATGATGATAAAAAGCTTtaataatactagcaacatatcataacggagtg) <br><br />
<br />
“INP-VEC-R” (AGCGGCCGCTACTAGTtataaacgcagaaaggccc) <br><br />
<br />
Two INP-YFP-FLAG fragments were created by PCR amplification, both use K523013 as the template, the first uses “INP-VEC-F” and “INP-FLAG-R” primers, the second uses “INP-VEC-R” and “INP-FLAG-F” primers. The Clontech InFusion kit was used to recombine the two INP-YFP-FLAG fragments with pSB1C3 backbone (cut with Xba1 and Spe1); this kit was followed according to the manufacturer’s instructions.<br />
<br />
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<br><br />
<font size="2">Figure 1; a Xba1 + HindIII restriction digest screen of recombinants. The recombinant which went on to become K1352006 is in lane 5. The “L” lane is DNA marker (ladder). The arrows are to highlight the distance travelled by the HindIII-negative recombinants.<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006Team:Aberdeen Scotland/Parts/ 20062014-10-17T21:04:16Z<p>JamesLongAberdeen: </p>
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<li class="curr"><a class="curr" href="#">Created</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004">Bba_K1352004</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
</ul><br />
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<br />
K1352006 is a part which has a FLAG-tag octapeptide flanked by a multiple cloning site (MCS) inserted into Bba_K523013 (K523013 expresses ice nucleation protein (INP)); specifically, on the end of a linker, which is in turn on the C-terminus of INP and is in the same reading frame. The FLAG-tag is a BglII restriction site, followed by a FLAG octapeptide, followed by a HindIII restriction site; the sequence of which is as follows; the octapeptide is uppercase, the restriction sites are lowercase:<br />
(agatctGATTATAAAGATGATGATGATAAAaagctt)<br />
Attaching a FLAG-tag to the end of INP means that it will be expressed on the surface of the cell, the purpose of this is to allow the rapid insertion (via the MCS) of polypeptides (an antigen for example) to the C-terminus end of INP; this allows the surface expression of said polypeptide. For the 2014 Aberdeen iGEM project, this part was intended to be used as a trypanosome antigen displayer.<br />
<br />
Creation of INP-YFP-FLAG fragments followed by InFusion cloning Four infusion primers (primers with one homologous half (lower case) to the template, and one “overhang” half (upper case), the last 15 nucleotides of which is homologous to another DNA fragment) were designed.<br />
<br />
<br />
“INP-VEC-F” (CGCGGCCGCTTCTAGAttaatacgactcactataggg)<br />
<br />
“INP-Rem-R” (aagctttttatcatcatcatctttataatcagatctTCCCGCCACGCTGC)<br />
<br />
“INP-FLAG-F” (AGATCTGATTATAAAGATGATGATGATAAAAAGCTTtaataatactagcaacatatcataacggagtg)<br />
<br />
“INP-VEC-R” (AGCGGCCGCTACTAGTtataaacgcagaaaggccc)<br />
<br />
Two INP-YFP-FLAG fragments were created by PCR amplification, both use K523013 as the template, the first uses “INP-VEC-F” and “INP-FLAG-R” primers, the second uses “INP-VEC-R” and “INP-FLAG-F” primers. The Clontech InFusion kit was used to recombine the two INP-YFP-FLAG fragments with pSB1C3 backbone (cut with Xba1 and Spe1); this kit was followed according to the manufacturer’s instructions.<br />
<br />
<br />
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<img src="https://static.igem.org/mediawiki/2014/5/55/2002fig2.png"><br />
<br><br />
<font size="2">Figure 1; a Xba1 + HindIII restriction digest screen of recombinants. The recombinant which went on to become K1352006 is in lane 5. The “L” lane is DNA marker (ladder). The arrows are to highlight the distance travelled by the HindIII-negative recombinants.<br />
<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004Team:Aberdeen Scotland/Parts/ 20042014-10-17T21:02:18Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2002">Bba_K1352002</a></li><br />
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
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<h1>INP+YFP+FLAG</h1><br />
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<br />
<br />
<br />
K1352004 is a part which has a FLAG-tag octapeptide flanked by a multiple cloning site (MCS) inserted into Bba_K523013 (K523013 expresses ice nucleation protein (INP) fused to yellow florescent protein (YFP) by a linker); specifically, on the end of the C-terminus of yellow florescence protein (YFP) and is in the same reading frame as INP+YFP. <br />
<br><br />
<br><br />
The FLAG-tag is a BglII restriction site, followed by a FLAG octapeptide, followed by a HindIII restriction site; the sequence of which is as follows; the octapeptide is uppercase, the restriction sites are lowercase:<br><br><br />
(agatctGATTATAAAGATGATGATGATAAAaagctt)<br><br><br />
Attaching a FLAG-tag to the end of YFP means that it will be expressed on the surface of the cell, the purpose of this is to allow the rapid insertion (via the MCS) of polypeptides (an antigen for example) to the C-terminus end of INP+YFP; this allows the surface expression of said polypeptide. For the 2014 Aberdeen iGEM project, this part was intended to be used as a trypanosome antigen displayer.<br><br><br />
<br />
Creation of INP-YFP-FLAG fragments followed by In-Fusion cloning Four infusion primers (primers with one homologous half (lower case) to the template, and one “overhang” half (upper case), the last 15 nucleotides of which is homologous to another DNA fragment) were designed.<br><br><br />
“INP-VEC-F” (CGCGGCCGCTTCTAGAttaatacgactcactataggg)<br><br />
“INP-FLAG-R” (AAGCTTTTTATCATCATCATCTTTATAATCAGATCTcttgtacagctcgtccatgc)<br><br />
“INP-FLAG-F” (AGATCTGATTATAAAGATGATGATGATAAAAAGCTTtaataatactagcaacatatcataacggagtg)<br><br />
“INP-VEC-R” (AGCGGCCGCTACTAGTtataaacgcagaaaggccc)<br><br><br />
Two INP-YFP-FLAG fragments were created by PCR amplification, both use K523013 as the template, the first uses “INP-VEC-F” and “INP-FLAG-R” primers, the second uses “INP-VEC-R” and “INP-FLAG-F” primers. The Clontech InFusion kit was used to recombine the two INP-YFP-FLAG fragments with pSB1C3 backbone (cut with Xba1 and Spe1); this kit was followed according to the manufacturer’s instructions.<br><br><br />
<br />
<h3>Confirmation of K1352004 DNA construct and the insertion of a MCS</h3><br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/5/5d/INPA_1.JPG"><br />
<br><br />
<font size="2">Fig.1&nbsp;&nbsp;&nbsp;&nbsp; Restriction digest verification of plasmids K1352004, K523013, and “INP-YFP-His” (a previously created plasmid which identical to K1352004 except that the FLAG tag is a 6xHis tag)<br><br />
<br><br />
Legends:<br><br />
L: 10,000bp – 500bp DNA marker “ladder”<br><br />
9: K1352004 plasmid undigested<br><br />
10: K1352004 plasmid digested with XbaI<br><br />
11: K1352004 plasmid digested with XbaI and HindIII<br><br />
12: K1352004 plasmid digested with XbaI and BglII<br><br />
<br><br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/2f/INP_2.JPG"><br />
<br><br />
<font size="2">Fig.2&nbsp;&nbsp;&nbsp;&nbsp;Restriction digest verification of plasmid K1352004<br />
<br><br><br />
Legends:<br><br />
L: 10,000bp – 500bp DNA marker “ladder”<br><br />
N: K1352004 plasmid digested with no enzymes<br><br />
E: K1352004 plasmid digested with EcoRI<br><br />
X: K1352004 plasmid digested with XbaI<br><br />
S: K1352004 plasmid digested with SpeI<br><br />
P: K1352004 plasmid digested with PstI<br><br />
EP: K1352004 plasmid digested with EcoRI and PstI<br><br />
SX: K1352004 plasmid digested with XbaI and Spe1<br><br />
<br><br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>DNA Sequencing</h3><br />
The recombinant plasmid was Sanger-sequenced with the following sequencing primers. “G101” is a reverse primer, the rest are forward primers. <br><br><br />
“G101” (attaccgcctttgagtgagc)<br><br />
“G100” (tgccacctgacgtctaagaa)<br><br />
“35 INP-SEQ 1” (ccgattcattaatgcagctgg)<br><br />
“36 INP-SEQ 2” (gaggttgctgttgccgac)<br><br />
“37 INP-SEQ 3” (ggtgtggaagccgacattc)<br><br><br />
The plasmid insert was found to be exactly as desired. Highlighted below is the MCS excerpt from the “G101” primer results (“G101” is a reverse primer which is why the sequence is in reverse complement).<br />
<br><br><br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/c/cd/MCS_in_INP-YFP-FLAG.JPG"><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>Florescence Microscopy</h3><br />
The following composite images were produced by superimposing a bright-field image with an YFP-filtered image.<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/d/d1/Fluorescence_negative_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel A; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a pSB1A3-transformed liquid cell culture (negative control) exhibiting no fluorescence as expected.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/22/K1352004_YFP_fluorescence.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel B; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K523013-transformed liquid cell culture exhibiting yellow fluorescence as expected.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/7/7f/K523013_positive_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel C; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K1352004-transformed liquid cell culture exhibiting yellow fluorescence.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>Western Blot</h3><br />
Westerm Blot was performed to confirm the presence and size of the translated INP-YFP-FLAG protein.<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/1/10/Western_blot_K1352004.png"><br />
<br><br />
<font size="2">Figure 4; &nbsp;&nbsp;&nbsp;&nbsp;Western Blot results.<br><br />
<br />
Legends (from left-to-right):<br><br />
1. Induced (with IPTG) K1352004 lysate probed with anti-FLAG antibody #1<br><br />
2. Induced (with IPTG) K1352004 lysate probed with anti-FLAG antibody #2<br><br />
3. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #1<br><br />
4. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #2<br><br />
5. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #3<br><br />
6. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #4<br><br />
7. Pre-stained protein marker “ladder” NuPAGE MES; From top to bottom in kDa: 188, 98 (orange), 62, 49, 38, 28, 17 (purple), 14, 6, 3<br><br />
The four Ag43 lanes act as a negative control, they also contain a single FLAG-tag but Ag43 is a heavier protein than INP and as such has a different banding pattern.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<h3>Discussion</h><br />
Conclusions The part is RFC 10 compatible. The construct sequence was produced exactly as designed; the full FLAG-tag – with BglII and HindIII sites – is present at the C-terminus of YFP. However, despite all this, possibly due to YFP’s C and N termini being on the same side of it, the FLAG-tag is not accessible to antibodies; it was for this reason that BBa_K1352006 was created.<br><br><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004Team:Aberdeen Scotland/Parts/ 20042014-10-17T21:01:27Z<p>JamesLongAberdeen: </p>
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<h1>INP+YFP+FLAG</h1><br />
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<br />
<br />
K1352004 is a part which has a FLAG-tag octapeptide flanked by a multiple cloning site (MCS) inserted into Bba_K523013 (K523013 expresses ice nucleation protein (INP) fused to yellow florescent protein (YFP) by a linker); specifically, on the end of the C-terminus of yellow florescence protein (YFP) and is in the same reading frame as INP+YFP. <br />
<br><br />
<br><br />
The FLAG-tag is a BglII restriction site, followed by a FLAG octapeptide, followed by a HindIII restriction site; the sequence of which is as follows; the octapeptide is uppercase, the restriction sites are lowercase:<br><br><br />
(agatctGATTATAAAGATGATGATGATAAAaagctt)<br><br><br />
Attaching a FLAG-tag to the end of YFP means that it will be expressed on the surface of the cell, the purpose of this is to allow the rapid insertion (via the MCS) of polypeptides (an antigen for example) to the C-terminus end of INP+YFP; this allows the surface expression of said polypeptide. For the 2014 Aberdeen iGEM project, this part was intended to be used as a trypanosome antigen displayer.<br><br><br />
<br />
Creation of INP-YFP-FLAG fragments followed by In-Fusion cloning Four infusion primers (primers with one homologous half (lower case) to the template, and one “overhang” half (upper case), the last 15 nucleotides of which is homologous to another DNA fragment) were designed.<br><br><br />
“INP-VEC-F” (CGCGGCCGCTTCTAGAttaatacgactcactataggg)<br><br />
“INP-FLAG-R” (AAGCTTTTTATCATCATCATCTTTATAATCAGATCTcttgtacagctcgtccatgc)<br><br />
“INP-FLAG-F” (AGATCTGATTATAAAGATGATGATGATAAAAAGCTTtaataatactagcaacatatcataacggagtg)<br><br />
“INP-VEC-R” (AGCGGCCGCTACTAGTtataaacgcagaaaggccc)<br><br><br />
Two INP-YFP-FLAG fragments were created by PCR amplification, both use K523013 as the template, the first uses “INP-VEC-F” and “INP-FLAG-R” primers, the second uses “INP-VEC-R” and “INP-FLAG-F” primers. The Clontech InFusion kit was used to recombine the two INP-YFP-FLAG fragments with pSB1C3 backbone (cut with Xba1 and Spe1); this kit was followed according to the manufacturer’s instructions.<br><br><br />
<br />
<h3>Confirmation of K1352004 DNA construct and the insertion of a MCS</h3><br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/5/5d/INPA_1.JPG"><br />
<br><br />
<font size="2">Fig.1&nbsp;&nbsp;&nbsp;&nbsp; Restriction digest verification of plasmids K1352004, K523013, and “INP-YFP-His” (a previously created plasmid which identical to K1352004 except that the FLAG tag is a 6xHis tag)<br><br />
<br><br />
Legends:<br><br />
L: 10,000bp – 500bp DNA marker “ladder”<br><br />
9: K1352004 plasmid undigested<br><br />
10: K1352004 plasmid digested with XbaI<br><br />
11: K1352004 plasmid digested with XbaI and HindIII<br><br />
12: K1352004 plasmid digested with XbaI and BglII<br><br />
<br><br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/2f/INP_2.JPG"><br />
<br><br />
<font size="2">Fig.2&nbsp;&nbsp;&nbsp;&nbsp;Restriction digest verification of plasmid K1352004<br />
<br><br><br />
Legends:<br><br />
L: 10,000bp – 500bp DNA marker “ladder”<br><br />
N: K1352004 plasmid digested with no enzymes<br><br />
E: K1352004 plasmid digested with EcoRI<br><br />
X: K1352004 plasmid digested with XbaI<br><br />
S: K1352004 plasmid digested with SpeI<br><br />
P: K1352004 plasmid digested with PstI<br><br />
EP: K1352004 plasmid digested with EcoRI and PstI<br><br />
SX: K1352004 plasmid digested with XbaI and Spe1<br><br />
<br><br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>DNA Sequencing</h3><br />
The recombinant plasmid was Sanger-sequenced with the following sequencing primers. “G101” is a reverse primer, the rest are forward primers. <br><br><br />
“G101” (attaccgcctttgagtgagc)<br><br />
“G100” (tgccacctgacgtctaagaa)<br><br />
“35 INP-SEQ 1” (ccgattcattaatgcagctgg)<br><br />
“36 INP-SEQ 2” (gaggttgctgttgccgac)<br><br />
“37 INP-SEQ 3” (ggtgtggaagccgacattc)<br><br><br />
The plasmid insert was found to be exactly as desired. Highlighted below is the MCS excerpt from the “G101” primer results (“G101” is a reverse primer which is why the sequence is in reverse complement).<br />
<br><br><br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/c/cd/MCS_in_INP-YFP-FLAG.JPG"><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>Florescence Microscopy</h3><br />
The following composite images were produced by superimposing a bright-field image with an YFP-filtered image.<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/d/d1/Fluorescence_negative_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel A; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a pSB1A3-transformed liquid cell culture (negative control) exhibiting no fluorescence as expected.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/22/K1352004_YFP_fluorescence.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel B; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K523013-transformed liquid cell culture exhibiting yellow fluorescence as expected.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/7/7f/K523013_positive_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel C; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K1352004-transformed liquid cell culture exhibiting yellow fluorescence.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<h3>Western Blot</h3><br />
Westerm Blot was performed to confirm the presence and size of the translated INP-YFP-FLAG protein.<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/1/10/Western_blot_K1352004.png"><br />
<br><br />
<font size="2">Figure 4; &nbsp;&nbsp;&nbsp;&nbsp;Western Blot results.<br><br />
<br />
Legends (from left-to-right):<br><br />
1. Induced (with IPTG) K1352004 lysate probed with anti-FLAG antibody #1<br><br />
2. Induced (with IPTG) K1352004 lysate probed with anti-FLAG antibody #2<br><br />
3. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #1<br><br />
4. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #2<br><br />
5. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #3<br><br />
6. Induced (with IPTG) Ag43-FLAG lysate probed with anti-FLAG antibody #4<br><br />
7. Pre-stained protein marker “ladder” NuPAGE MES; From top to bottom in kDa: 188, 98 (orange), 62, 49, 38, 28, 17 (purple), 14, 6, 3<br><br />
The four Ag43 lanes act as a negative control, they also contain a single FLAG-tag but Ag43 is a heavier protein than INP and as such has a different banding pattern.<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<h3>Discussion</h><br />
Conclusions The part is RFC 10 compatible. The construct sequence was produced exactly as designed; the full FLAG-tag – with BglII and HindIII sites – is present at the C-terminus of YFP. However, despite all this, possibly due to YFP’s C and N termini being on the same side of it, the FLAG-tag is not accessible to antibodies; it was for this reason that BBa_K1352006 was created.<br><br><br />
<br />
<br />
<br />
<br />
<br />
<p>of <i>E. coli</i>.</p><br />
<img src="https://static.igem.org/mediawiki/2014/2/2e/Ag43.jpg" alt="Ag43"><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2004Team:Aberdeen Scotland/Parts/ 20042014-10-17T20:55:34Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
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<h1>Background to Parts Design</h1><br />
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<br />
<br />
<br><br><br />
<br />
<br />
Ice Nucleation Protein (INP) Yellow Florescent Protein (YFP) FLAG-tag<br />
K1352004 is a part which has a FLAG-tag octapeptide flanked by a multiple cloning site (MCS) inserted into Bba_K523013 (K523013 expresses ice nucleation protein (INP) fused to yellow florescent protein (YFP) by a linker); specifically, on the end of the C-terminus of yellow florescence protein (YFP) and is in the same reading frame as INP+YFP. The FLAG-tag is a BglII restriction site, followed by a FLAG octapeptide, followed by a HindIII restriction site; the sequence of which is as follows; the octapeptide is uppercase, the restriction sites are lowercase:<br />
(agatctGATTATAAAGATGATGATGATAAAaagctt)<br />
Attaching a FLAG-tag to the end of YFP means that it will be expressed on the surface of the cell, the purpose of this is to allow the rapid insertion (via the MCS) of polypeptides (an antigen for example) to the C-terminus end of INP+YFP; this allows the surface expression of said polypeptide. For the 2014 Aberdeen iGEM project, this part was intended to be used as a trypanosome antigen displayer.<br />
<br />
Creation of INP-YFP-FLAG fragments followed by InFusion cloning Four infusion primers (primers with one homologous half (lower case) to the template, and one “overhang” half (upper case), the last 15 nucleotides of which is homologous to another DNA fragment) were designed.<br />
“INP-VEC-F” (CGCGGCCGCTTCTAGAttaatacgactcactataggg)<br />
“INP-FLAG-R” (AAGCTTTTTATCATCATCATCTTTATAATCAGATCTcttgtacagctcgtccatgc)<br />
“INP-FLAG-F” (AGATCTGATTATAAAGATGATGATGATAAAAAGCTTtaataatactagcaacatatcataacggagtg)<br />
“INP-VEC-R” (AGCGGCCGCTACTAGTtataaacgcagaaaggccc)<br />
Two INP-YFP-FLAG fragments were created by PCR amplification, both use K523013 as the template, the first uses “INP-VEC-F” and “INP-FLAG-R” primers, the second uses “INP-VEC-R” and “INP-FLAG-F” primers. The Clontech InFusion kit was used to recombine the two INP-YFP-FLAG fragments with pSB1C3 backbone (cut with Xba1 and Spe1); this kit was followed according to the manufacturer’s instructions.<br />
<br />
Confirmation of K1352004 DNA construct and the insertion of a MCS<br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/5/5d/INPA_1.JPG"><br />
<br><br />
<font size="2">Fig.1&nbsp;&nbsp;&nbsp;&nbsp; Restriction digest verification of plasmids K1352004, K523013, and “INP-YFP-His” (a previously created plasmid which identical to K1352004 except that the FLAG tag is a 6xHis tag)<br />
<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/2f/INP_2.JPG"><br />
<br><br />
<font size="2">Fig.2&nbsp;&nbsp;&nbsp;&nbsp;Restriction digest verification of plasmid K1352004<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/c/cd/MCS_in_INP-YFP-FLAG.JPG"><br />
<br><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/d/d1/Fluorescence_negative_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel A; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a pSB1A3-transformed liquid cell culture (negative control) exhibiting no fluorescence as expected.<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/2/22/K1352004_YFP_fluorescence.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel B; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K523013-transformed liquid cell culture exhibiting yellow fluorescence as expected.<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/7/7f/K523013_positive_control.PNG"><br />
<br><br />
<font size="2">Figure 3, Panel C; &nbsp;&nbsp;&nbsp;&nbsp;a composite fluorescence image – brightfield micrograph of a K1352004-transformed liquid cell culture exhibiting yellow fluorescence.<br />
<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<center><br />
<img src="https://static.igem.org/mediawiki/parts/1/10/Western_blot_K1352004.png"><br />
<br><br />
<font size="2">Figure 4; &nbsp;&nbsp;&nbsp;&nbsp;Western Blot to confirm the presence and size of the translated INP-YFP-FLAG protein<br />
<br />
<br><br />
<br />
</font><br />
</center><br />
<br><br><br />
<br />
<br />
<br />
<br />
<p>Antigen 43 (Ag43), the product of the </i>flu</i> gene, is a cell-surface autotransporter protein found in <i>Escherichia coli</i>. It is expressed at about 50,<br />
000 copies/cell and is initially synthesised as a precursor of 1039 amino acids. Upon removal of the signal peptide, the protein is transported to the cell surface<br />
and is composed of an α subunit (499 amino acids) at the N-terminus and a β subunit (488 amino acids) at the C-terminus. Ag43 is mainly known to induce cell-to-cell<br />
aggregation and be involved in biofilm formation. However, as the necessary information required for auto transportation resides in the protein itself, the main of<br />
our project was to use it as a platform for displaying specific peptides on the surface of <i>E. coli</i>.</p><br />
<img src="https://static.igem.org/mediawiki/2014/2/2e/Ag43.jpg" alt="Ag43"><br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006Team:Aberdeen Scotland/Parts/ 20062014-10-17T20:38:04Z<p>JamesLongAberdeen: </p>
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<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<font size="2">Figure 1; a Xba1 + HindIII restriction digest screen of recombinants. The recombinant which went on to become K1352006 is in lane 5. The “L” lane is DNA marker (ladder). The arrows are to highlight the distance travelled by the HindIII-negative recombinants.<br />
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</html></div>JamesLongAberdeenhttp://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2006Team:Aberdeen Scotland/Parts/ 20062014-10-17T20:37:34Z<p>JamesLongAberdeen: </p>
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<li class="curr"><a class="curr" href="#">Created</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2000">Bba_K1352000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2001">Bba_K1352001</a></li><br />
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<li class="curr"><a class="curr" href="#">Improved</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9001">Bba_K759001</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_2009">Bba_K542009</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_6007">Bba_K346007</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_0000">Bba_K1090000</a></li><br />
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts/_9002">Bba_T9002</a></li><br />
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<img src="https://static.igem.org/mediawiki/2014/5/55/2002fig2.png"><br />
<br><br />
<font size="2">Figure 1; a Xba1 + HindIII restriction digest screen of recombinants. The recombinant which went on to become K1352006 is in lane 5. The “L” lane is DNA marker (ladder). The arrows are to highlight the distance travelled by the HindIII-negative recombinants.<br />
<br />
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<font size="2">Fig.1&nbsp;&nbsp;&nbsp;&nbsp;Graphic representation of Ag43 autotransporter structure and process of autotransportation. <br />
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