http://2013.igem.org/wiki/index.php?title=Special:Contributions/JunaidBabu&feed=atom&limit=50&target=JunaidBabu&year=&month=2013.igem.org - User contributions [en]2024-03-28T08:10:19ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:37:08Z<p>JunaidBabu: </p>
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:36:06Z<p>JunaidBabu: </p>
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Results<br />
</h2><br />
<hr class="featurette-divider"><br />
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<div class="row featurette"><br />
<p dir="ltr"><br />
<b><h3>EXPERIMENTAL RESULTS</h3></b><br />
</p><br />
<p dir="ltr"><br />
<b> 1] Preparation of the vector (pSB1C3 + BBa_F2620)</b><br />
<br/><br />
<br/><br />
<u> Result 1.1:</u> Our part of interest (BBa_F2620) was located in the 2013 Kit Plate 3, well 3P. It was reconstituted in 20 µL sterile water and 2 µL was<br />
transformed into E.coli DH5α cells. Mini-prep was performed to isolate the plasmid. The gel image is shown in Fig 1.1 below.</br><br />
<img<br />
src="https://lh4.googleusercontent.com/_ls5U61gqDNMPp-yD0xQi08tfxNmU1FV4AuVeJCc1vTafM0D6qWLTnqgS6OglsfxUV3udfg1VjOWYd6HPomK27q0T7oIY9cn1gaCXySmeGbXQE_Hz-QRKn6W"<br />
width="347px;"<br />
height="456px;"<br />
/><br />
<br/><br />
Fig 1.1: Plasmid Vector pSB1C3 isolation (3 kb each well)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.2:</u> The isolated plasmid was digested with <i>EcoR</i>1 and <i>Pst</i>1 to release BBa_F2620 from the pSB1C3 backbone. Fig 1.2 (gel image) shows release of the<br />
part BBa_F2620 (1061 bp) from the plasmid pSB1C3 (2070 bp).</br><br />
<img<br />
src="https://lh6.googleusercontent.com/kRJ7uW1GHamXbccbBu3L_WJe_xC1veiE-YEnRP2-MXaHd1o4VJAMLd4JzfLSd9rUfxDjpOyULNRA6z-ULxlOw3cEgKwU1AEkwrgkSRwrCYbHiDwyx5n7SYbx"<br />
width="308px;"<br />
height="263px;"<br />
/><br />
<br/><br />
<br/><br />
Fig 1.2: Restriction digestion image showing release of BBa_F2620 (2 kb+1 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.3:</u> Digestion of the plasmid vector with <i>Spe</i>1 and <i>Pst</i>1 gives the vector (3 kb) ready for ligation. Fig 1.3 shows the gel image after double<br />
digestion of the plasmid vector.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/nGxHsVn1zfjb9jKdvFES8ufDBfbe8nOrNfYBp0sG2MG13LCzKgoMltdxK7TRTKZoDvczAYBl2Qofck-gUBLchkOmFCJDDKCFiAnGpwnBwLZQMOJX-dlrpNhR"<br />
width="291px;"<br />
height="298px;"<br />
/><br />
<br/><br />
Fig 1.3: Double digested BBa_F2620 with <i>Spe</i>1 and <i>Pst</i>1 (3 kb)<br />
</p><br />
<p dir="ltr"><br />
<u>Result 1.4:</u> The vector was treated with calf intestinal alkaline phosphatase (CIP) to reduce the probability of getting self-ligated colonies. Fig 1.4<br />
shows the final gel image of the CIP-treated vector, ready for ligation.<br />
</br><img<br />
src="https://lh4.googleusercontent.com/hK2WT22UD8GoiWlgNsXpZNZ_OPq-z14s4V_ZkrNNHvNPRR2GAKsdQaIeLK-RUirY0b40jaNOl__GiTDIRd3UA3KiVnRFWiXp82EPTA6OHadhOKCkwp_RHYk1"<br />
width="237px;"<br />
height="266px;"<br />
/><br />
<br/><br />
Fig 1.4: CIP-treated vector (3 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b> 2] Isolation of insert (Gb3 mimic, 268 bp) </b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u> Result 2.1:</u> Gb3 mimic was delivered in pUC57 plasmid backbone. <i>E.coli</i> DH5α cells were transformed with pUC57. After primary culture, mini-prep was done to<br />
isolate the plasmid. Fig 2.1 shows the gel image of the isolated pUC57 plasmid containing Gb3 mimic insert.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/pPLOpHdOFbjGo5sR8x3WL656l8ijKFk_ex_q7khoJDJsmveUcbRtDPJ4LTRlDdSLaU9v7X-qgdDlcqiVRnEc_JuC5IolfXHcnzGdq6QYKwzoZuQyrmdx6nS_"<br />
width="275px;"<br />
height="240px;"<br />
/><br />
<br/><br />
Fig 2.1: Gel image of isolated pUC57 plasmid (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 2.2:</u> The pUC57 plasmid was then digested with <i>Spe</i>1 and <i>Pst</i>1 to show the release of Gb3 mimic insert. Fig 2.2 distinctly shows the two bands: a 2.7<br />
kb plasmid backbone (pUC57) and a 268 bp insert (Gb3 mimic).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3qEmbsGiZ6msjm3Hom00eFKyyDJ4S270UIrc9XPbcRBhISjwo4ms0Ij7SNsFsehoMSGdtzQCE20oontFXXa31AlCVdtjqJcDKnAxDhf22Qhb9qhMT8TIHLjb"<br />
width="412px;"<br />
height="265px;"<br />
/><br />
<br/><br />
Fig 2.2: Digestion of pUC57 to show release of interest (268 bp)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b>3] Cloning of insert (Gb3 mimic, 268 bp) in vector (BBa_F2620 in pSB1C3, 3 kb)</b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.1:</u> The digested insert was eluted and a ligation reaction between the vector (3 kb) and insert (268 bp) was set up. The clones were confirmed by digesting with <i>Spe</i>1 and <i>Pst</i>1. Fig 3.1 (gel image) shows two separate bands: one at 3 kb (corresponding to vector) and another at 268 bp (corresponding to insert).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/CSNwUCBKK153Y3ADOi4oyYb0h-aIRXYcyl1IRKs8tYd1jCqP8jwBYJ6EyhWG8sTcV4xnNw_MnXJqN6g38zOWXGPEYyyLHa7vxChJReKo36EVgGaJPvltv7b4"<br />
width="398px;"<br />
height="272px;"<br />
/><br />
<br/><br />
Fig 3.1: Restriction digest showing release of the cloned insert (268 bp) from vector (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.2:</u> The clones were further sequenced to confirm the successful cloning of the Gb3 mimic in pSB1C3. Fig 3.2 shows the sequencing results.<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
<img<br />
src="https://lh5.googleusercontent.com/OoqvSSdrtP16lQxYZWDa2NyMYnsCQ7whmrxoE4dGHrPsBtVFKH5zM5ZDKeZQ7SKGvLL0mjxGhNW4Xe1_66j_jCY8SSkLwnWAAlzl70ooJcmaa5diluEqL1nR03c8CfRZo_o"<br />
width="616px;"<br />
height="225px;"<br />
/><br />
<br/><br />
Fig 3.2: Sequencing of Gb3 mimic clones<br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<b>4] Cloning of I3A construct (3040 bp) in pSB1C3 downstream of BBa_F2620 </b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.1:</u> I3A construct (3040 bp) was delivered in pUC57. The plasmid backbone was restriction digested with <i>EcoR</i>1 and <i>Pst</i>1 to release the insert (I3A).<br />
Fig 4.1 shows the successfully isolated insert.<br />
</br><img<br />
src="https://lh3.googleusercontent.com/OA4FwlJaE1iK-0hQ8WJL69lmSCK-2ZMGvK22wuSv6sH8X8p-OmRflqG5DxNKA_vppIoheFD4fUSmbP9jKLsJSsT2v-zRpVEiJC2opqyh3S4dDtzpoVT9nd5c"<br />
width="250px;"<br />
height="228px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
Fig 4.1: Gel image showing isolated I3A insert (3040 bp)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.2:</u> The isolated insert was eluted and a ligation reaction was set up between the vector (pSB1C3+BBa_F2620, 3 kb) and the insert (I3A construct, 3040 bp). The clones were confirmed by digesting with <i>Spe</i>1 and <i>Pst</i>1. Fig 4.2 (gel image) shows two closely resolved yet separate bands. Upper band<br />
corresponds to the insert while lower band corresponds to the vector.</br><br />
<img<br />
src="https://lh5.googleusercontent.com/eMisU6QTF2HqDHYwfzfgTEzlbTxzaweNwGQLiiIlj2o2SeHO2L3GW9WJHg4I4vuXaa7V83pKHGQG7mxlPM8B_Uwyx2mLHMmbSt-AK8clgNmfvd-x-eb8Xw1I"<br />
width="344px;"<br />
height="274px;"<br />
/><br />
<br/><br />
Fig 4.2: Restriction digest showing separate bands of vector (bottom) and insert (top)<br />
</p><br />
<p dir="ltr"><br />
<b>5] Reverse-phase HPLC to detect presence of Gb3 mimic peptide.</b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u>Result 5.1:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next two peaks also share a common overlap region but they are just resolved.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3ZmPfcfkLi_aDaKldkv9wbPz9Wy0EMG9b8dSrAhjSp6jg1JxE4LLGdRPuAJCQQdvSvmnhQkHlNeeuuzUKMgpxBoKb4j8E9hH19Zx9kgBlSPMFJsFPim11c_e8MNlrhKNw0w"<br />
width="547px;"<br />
height="258px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of induced culture-spent medium run through a C18 column<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 5.2:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next peak is quite small compared to the corresponding peak for the induced culture. The fourth peak, in this case, is almost negligible. It is just a tiny crest.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/Akyi0tJS07oz5ac-dJQ4OgusaDKM5fA7XSt-_YYf5hOVpEkit1KNyl4o0JwY-v9Tei3xDeJGNw1rJhBOfpOZMievReCTSlMyJjAiAWbxkBLojh9OwtHi7remoBOzUlFQm-Y"<br />
width="624px;"<br />
height="293px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of non-induced culture-spent medium run through a C18 column.<br />
</p><br />
<br />
<br />
</div><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ResultsTeam:IIT Madras/Results2013-09-28T03:29:16Z<p>JunaidBabu: </p>
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Results<br />
</h2><br />
<hr class="featurette-divider"><br />
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<div class="row featurette"><br />
<p dir="ltr"><br />
<b><h3>EXPERIMENTAL RESULTS</h3></b><br />
</p><br />
<p dir="ltr"><br />
<b> 1] Preparation of the vector (pSB1C3 + BBa_F2620)</b><br />
<br/><br />
<br/><br />
<u> Result 1.1:</u> Our part of interest (BBa_F2620) was located in the 2013 Kit Plate 3, well 3P. It was reconstituted in 20 µL sterile water and 2 µL was<br />
transformed into E.coli DH5α cells. Mini-prep was performed to isolate the plasmid. The gel image is shown in Fig 1.1 below.</br><br />
<img<br />
src="https://lh4.googleusercontent.com/_ls5U61gqDNMPp-yD0xQi08tfxNmU1FV4AuVeJCc1vTafM0D6qWLTnqgS6OglsfxUV3udfg1VjOWYd6HPomK27q0T7oIY9cn1gaCXySmeGbXQE_Hz-QRKn6W"<br />
width="347px;"<br />
height="456px;"<br />
/><br />
<br/><br />
Fig 1.1: Plasmid Vector pSB1C3 isolation (3 kb each well)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.2:</u> The isolated plasmid was digested with <i>EcoR</i>1 and <i>Pst</i>1 to release BBa_F2620 from the pSB1C3 backbone. Fig 1.2 (gel image) shows release of the<br />
part BBa_F2620 (1061 bp) from the plasmid pSB1C3 (2070 bp).</br?<br />
<img<br />
src="https://lh6.googleusercontent.com/kRJ7uW1GHamXbccbBu3L_WJe_xC1veiE-YEnRP2-MXaHd1o4VJAMLd4JzfLSd9rUfxDjpOyULNRA6z-ULxlOw3cEgKwU1AEkwrgkSRwrCYbHiDwyx5n7SYbx"<br />
width="308px;"<br />
height="263px;"<br />
/><br />
<br/><br />
<br/><br />
Fig 1.2: Restriction digestion image showing release of BBa_F2620 (2 kb+1 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.3:</u> Digestion of the plasmid vector with <i>Spe</i>1 and <i>Pst</i>1 gives the vector (3 kb) ready for ligation. Fig 1.3 shows the gel image after double<br />
digestion of the plasmid vector.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/nGxHsVn1zfjb9jKdvFES8ufDBfbe8nOrNfYBp0sG2MG13LCzKgoMltdxK7TRTKZoDvczAYBl2Qofck-gUBLchkOmFCJDDKCFiAnGpwnBwLZQMOJX-dlrpNhR"<br />
width="291px;"<br />
height="298px;"<br />
/><br />
<br/><br />
Fig 1.3: Double digested BBa_F2620 with <i>Spe</i>1 and <i>Pst</i>1 (3 kb)<br />
</p><br />
<p dir="ltr"><br />
<u>Result 1.4:</u> The vector was treated with calf intestinal alkaline phosphatase (CIP) to reduce the probability of getting self-ligated colonies. Fig 1.4<br />
shows the final gel image of the CIP-treated vector, ready for ligation.<br />
</br><img<br />
src="https://lh4.googleusercontent.com/hK2WT22UD8GoiWlgNsXpZNZ_OPq-z14s4V_ZkrNNHvNPRR2GAKsdQaIeLK-RUirY0b40jaNOl__GiTDIRd3UA3KiVnRFWiXp82EPTA6OHadhOKCkwp_RHYk1"<br />
width="237px;"<br />
height="266px;"<br />
/><br />
<br/><br />
Fig 1.4: CIP-treated vector (3 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b> 2] Isolation of insert (Gb3 mimic, 268 bp) </b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u> Result 2.1:</u> Gb3 mimic was delivered in pUC57 plasmid backbone. <i>E.coli</i> DH5α cells were transformed with pUC57. After primary culture, mini-prep was done to<br />
isolate the plasmid. Fig 2.1 shows the gel image of the isolated pUC57 plasmid containing Gb3 mimic insert.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/pPLOpHdOFbjGo5sR8x3WL656l8ijKFk_ex_q7khoJDJsmveUcbRtDPJ4LTRlDdSLaU9v7X-qgdDlcqiVRnEc_JuC5IolfXHcnzGdq6QYKwzoZuQyrmdx6nS_"<br />
width="275px;"<br />
height="240px;"<br />
/><br />
<br/><br />
Fig 2.1: Gel image of isolated pUC57 plasmid (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 2.2:</u> The pUC57 plasmid was then digested with <i>Spe</i>1 and <i>Pst</i>1 to show the release of Gb3 mimic insert. Fig 2.2 distinctly shows the two bands: a 2.7<br />
kb plasmid backbone (pUC57) and a 268 bp insert (Gb3 mimic).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3qEmbsGiZ6msjm3Hom00eFKyyDJ4S270UIrc9XPbcRBhISjwo4ms0Ij7SNsFsehoMSGdtzQCE20oontFXXa31AlCVdtjqJcDKnAxDhf22Qhb9qhMT8TIHLjb"<br />
width="412px;"<br />
height="265px;"<br />
/><br />
<br/><br />
Fig 2.2: Digestion of pUC57 to show release of interest (268 bp)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b>3] Cloning of insert (Gb3 mimic, 268 bp) in vector (BBa_F2620 in pSB1C3, 3 kb)</b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.1:</u> The digested insert was eluted and a ligation reaction between the vector (3 kb) and insert (268 bp) was set up. The clones were confirmed by digesting with <i>Spe</i>1 and <i>Pst</i>1. Fig 3.1 (gel image) shows two separate bands: one at 3 kb (corresponding to vector) and another at 268 bp (corresponding to insert).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/CSNwUCBKK153Y3ADOi4oyYb0h-aIRXYcyl1IRKs8tYd1jCqP8jwBYJ6EyhWG8sTcV4xnNw_MnXJqN6g38zOWXGPEYyyLHa7vxChJReKo36EVgGaJPvltv7b4"<br />
width="398px;"<br />
height="272px;"<br />
/><br />
<br/><br />
Fig 3.1: Restriction digest showing release of the cloned insert (268 bp) from vector (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.2:</u> The clones were further sequenced to confirm the successful cloning of the Gb3 mimic in pSB1C3. Fig 3.2 shows the sequencing results.<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
<img<br />
src="https://lh5.googleusercontent.com/OoqvSSdrtP16lQxYZWDa2NyMYnsCQ7whmrxoE4dGHrPsBtVFKH5zM5ZDKeZQ7SKGvLL0mjxGhNW4Xe1_66j_jCY8SSkLwnWAAlzl70ooJcmaa5diluEqL1nR03c8CfRZo_o"<br />
width="616px;"<br />
height="225px;"<br />
/><br />
<br/><br />
Fig 3.2: Sequencing of Gb3 mimic clones<br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<b>4] Cloning of I3A construct (3040 bp) in pSB1C3 downstream of BBa_F2620 </b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.1:</u> I3A construct (3040 bp) was delivered in pUC57. The plasmid backbone was restriction digested with <i>EcoR</i>1 and <i>Pst</i>1 to release the insert (I3A).<br />
Fig 4.1 shows the successfully isolated insert.<br />
</br><img<br />
src="https://lh3.googleusercontent.com/OA4FwlJaE1iK-0hQ8WJL69lmSCK-2ZMGvK22wuSv6sH8X8p-OmRflqG5DxNKA_vppIoheFD4fUSmbP9jKLsJSsT2v-zRpVEiJC2opqyh3S4dDtzpoVT9nd5c"<br />
width="250px;"<br />
height="228px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
Fig 4.1: Gel image showing isolated I3A insert (3040 bp)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.2:</u> The isolated insert was eluted and a ligation reaction was set up between the vector (pSB1C3+BBa_F2620, 3 kb) and the insert (I3A construct, 3040 bp). The clones were confirmed by digesting with <i>Spe</i>1 and <i>Pst</i>1. Fig 4.2 (gel image) shows two closely resolved yet separate bands. Upper band<br />
corresponds to the insert while lower band corresponds to the vector.</br><br />
<img<br />
src="https://lh5.googleusercontent.com/eMisU6QTF2HqDHYwfzfgTEzlbTxzaweNwGQLiiIlj2o2SeHO2L3GW9WJHg4I4vuXaa7V83pKHGQG7mxlPM8B_Uwyx2mLHMmbSt-AK8clgNmfvd-x-eb8Xw1I"<br />
width="344px;"<br />
height="274px;"<br />
/><br />
<br/><br />
Fig 4.2: Restriction digest showing separate bands of vector (bottom) and insert (top)<br />
</p><br />
<p dir="ltr"><br />
<b>5] Reverse-phase HPLC to detect presence of Gb3 mimic peptide.</b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u>Result 5.1:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next two peaks also share a common overlap region but they are just resolved.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3ZmPfcfkLi_aDaKldkv9wbPz9Wy0EMG9b8dSrAhjSp6jg1JxE4LLGdRPuAJCQQdvSvmnhQkHlNeeuuzUKMgpxBoKb4j8E9hH19Zx9kgBlSPMFJsFPim11c_e8MNlrhKNw0w"<br />
width="547px;"<br />
height="258px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of induced culture-spent medium run through a C18 column<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 5.2:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next peak is quite small compared to the corresponding peak for the induced culture. The fourth peak, in this case, is almost negligible. It is just a tiny crest.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/Akyi0tJS07oz5ac-dJQ4OgusaDKM5fA7XSt-_YYf5hOVpEkit1KNyl4o0JwY-v9Tei3xDeJGNw1rJhBOfpOZMievReCTSlMyJjAiAWbxkBLojh9OwtHi7remoBOzUlFQm-Y"<br />
width="624px;"<br />
height="293px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of non-induced culture-spent medium run through a C18 column.<br />
</p><br />
<br />
<br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T03:25:28Z<p>JunaidBabu: </p>
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:13:01Z<p>JunaidBabu: </p>
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:11:29Z<p>JunaidBabu: </p>
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:09:07Z<p>JunaidBabu: </p>
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</a><br />
</li><br />
<li><br />
<a href="https://2013.igem.org/Team:IIT_Madras/Weekly"><br />
Weekly Summaries<br />
</a><br />
</li><br />
</ul><br />
</li><br />
<li><br />
<a href="https://2013.igem.org/Team:IIT_Madras/Attributions"><br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T03:07:24Z<p>JunaidBabu: </p>
<hr />
<div><html><br />
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display:none;<br />
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display: none;<br />
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visibility: visible;<br />
}<br />
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background: none;<br />
border: none;<br />
width: 100%}<br />
#bodyContent{<br />
<br />
width:100%;<br />
}<br />
#headingmain{<br />
font-size: 52px;<br />
position: absolute;<br />
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margin-right: auto;<br />
margin-top: 26px;<br />
}<br />
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text-align: center;<br />
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visibility: visible;<br />
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background: none;<br />
border: none;<br />
width: 100%}<br />
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width:100%;<br />
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}<br />
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font-family: 'Cantora One', sans-serif;<br />
}<br />
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position: absolute;<br />
margin-left: 140px;<br />
margin-right: auto;<br />
top: 45px;<br />
font-family: 'Rammetto One', cursive;<br />
">Indian Institute of Technology Madras</div><br />
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<img id="igem-logo" src="https://static.igem.org/mediawiki/2012/c/cc/Igem_logo_scaled.png" style="<br />
width: 129px;<br />
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Weekly Summaries<br />
</a><br />
</li><br />
</ul><br />
</li><br />
<li><br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T03:02:41Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<div class="container marketing"><br />
<div id="myCarousel" class="carousel slide"><br />
<br />
<ol class="carousel-indicators"><br />
<li data-target="#myCarousel" data-slide-to="0" class="active"></li><br />
<li data-target="#myCarousel" data-slide-to="1" class=""></li><br />
<li data-target="#myCarousel" data-slide-to="2" class=""></li><br />
<li data-target="#myCarousel" data-slide-to="3" class=""></li><br />
<li data-target="#myCarousel" data-slide-to="4" class=""></li><br />
</ol><br />
<div class="carousel-inner"><br />
<br />
<div class="item active"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG" alt="Second slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<!--<h1>The Team</h1><br />
<p>Cras justo odio, dapibus ac facilisis in, egestas eget quam. Donec id elit non mi porta gravida at eget metus. Nullam id dolor id nibh ultricies vehicula ut id elit.</p><br />
<p><a class="btn btn-large btn-primary" href="#">More info</a></p>--><br />
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</div><br />
</div><br />
</div><br />
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<img src="https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
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</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/4/40/SAM_0780.JPG/737px-SAM_0780.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
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</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
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</div><br />
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</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
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</div><br />
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<a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a><br />
<a class="right carousel-control" href="#myCarousel" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a><br />
</div><br />
<!--<br />
<br />
--></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T03:00:53Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<div class="container marketing"><br />
<div id="myCarousel" class="carousel slide"><br />
<br />
<ol class="carousel-indicators"><br />
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<br />
<div class="item active"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG" alt="Second slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<!--<h1>The Team</h1><br />
<p>Cras justo odio, dapibus ac facilisis in, egestas eget quam. Donec id elit non mi porta gravida at eget metus. Nullam id dolor id nibh ultricies vehicula ut id elit.</p><br />
<p><a class="btn btn-large btn-primary" href="#">More info</a></p>--><br />
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<br />
</div><br />
</div><br />
</div><br />
<br />
<br />
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<br />
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<img src="https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
<br />
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</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG" alt="Third slide" style="height: 100%; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
</div><br />
<a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a><br />
<a class="right carousel-control" href="#myCarousel" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a><br />
</div><br />
<!--<br />
<br />
--></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T02:59:45Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<div class="container marketing"><br />
<div id="myCarousel" class="carousel slide"><br />
<br />
<ol class="carousel-indicators"><br />
<li data-target="#myCarousel" data-slide-to="0" class="active"></li><br />
<li data-target="#myCarousel" data-slide-to="1" class=""></li><br />
<li data-target="#myCarousel" data-slide-to="2" class=""></li><br />
<li data-target="#myCarousel" data-slide-to="3" class=""></li><br />
</ol><br />
<div class="carousel-inner"><br />
<br />
<div class="item active"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG" alt="Second slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<!--<h1>The Team</h1><br />
<p>Cras justo odio, dapibus ac facilisis in, egestas eget quam. Donec id elit non mi porta gravida at eget metus. Nullam id dolor id nibh ultricies vehicula ut id elit.</p><br />
<p><a class="btn btn-large btn-primary" href="#">More info</a></p>--><br />
<br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
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<img src="https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
<br />
<br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
</div><br />
<a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a><br />
<a class="right carousel-control" href="#myCarousel" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a><br />
</div><br />
<!--<br />
<br />
--></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T02:59:26Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<div class="container marketing"><br />
<div id="myCarousel" class="carousel slide"><br />
<br />
<ol class="carousel-indicators"><br />
<li data-target="#myCarousel" data-slide-to="0" class="active"></li><br />
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<li data-target="#myCarousel" data-slide-to="2" class=""></li><br />
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</ol><br />
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<br />
<div class="item active"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG" alt="Second slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<!--<h1>The Team</h1><br />
<p>Cras justo odio, dapibus ac facilisis in, egestas eget quam. Donec id elit non mi porta gravida at eget metus. Nullam id dolor id nibh ultricies vehicula ut id elit.</p><br />
<p><a class="btn btn-large btn-primary" href="#">More info</a></p>--><br />
<br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPGg" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
<br />
<br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
</div><br />
<a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a><br />
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</div><br />
<!--<br />
<br />
--></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T02:58:56Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<div class="container marketing"><br />
<div id="myCarousel" class="carousel slide"><br />
<br />
<ol class="carousel-indicators"><br />
<li data-target="#myCarousel" data-slide-to="0" class="active"></li><br />
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<li data-target="#myCarousel" data-slide-to="3" class=""></li><br />
</ol><br />
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<br />
<div class="item active"><br />
<img src="https://static.igem.org/mediawiki/2013/d/db/Iitm13_Slide_1.jpg" alt="Second slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<!--<h1>The Team</h1><br />
<p>Cras justo odio, dapibus ac facilisis in, egestas eget quam. Donec id elit non mi porta gravida at eget metus. Nullam id dolor id nibh ultricies vehicula ut id elit.</p><br />
<p><a class="btn btn-large btn-primary" href="#">More info</a></p>--><br />
<br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPGg" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
<br />
<br />
</div><br />
</div><br />
<div class="item"><br />
<img src="https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG" alt="Third slide" style="height: 500px; width: 100%; display: block;"><br />
<div class="container"><br />
<div class="carousel-caption"><br />
<br />
</div><br />
</div><br />
</div><br />
</div><br />
<a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a><br />
<a class="right carousel-control" href="#myCarousel" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a><br />
</div><br />
<!--<br />
https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG<br />
--></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/GalleryTeam:IIT Madras/Gallery2013-09-28T02:53:49Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
https://static.igem.org/mediawiki/2013/thumb/7/77/DSCN3460.JPG/800px-DSCN3460.JPG<br />
https://static.igem.org/mediawiki/2013/thumb/c/c0/DSCN4173.JPG/800px-DSCN4173.JPG<br />
https://static.igem.org/mediawiki/2013/thumb/2/2c/SAM_0638.JPG/800px-SAM_0638.JPG<br />
https://static.igem.org/mediawiki/2013/thumb/f/f3/SAM_0640.JPG/800px-SAM_0640.JPG<br />
https://static.igem.org/mediawiki/2013/thumb/8/8f/SAM_0781.JPG/800px-SAM_0781.JPG</div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T02:52:33Z<p>JunaidBabu: </p>
<hr />
<div><html><br />
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<link href="//netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css" rel="stylesheet"><br />
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">Indian Institute of Technology Madras</div><br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/Templates/HeaderTeam:IIT Madras/Templates/Header2013-09-28T02:51:06Z<p>JunaidBabu: </p>
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_MadrasTeam:IIT Madras2013-09-28T02:47:52Z<p>JunaidBabu: </p>
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Shiga toxin, a worldwide menace, has killed over 1 million people to date and continues to afflict almost 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine amino acid Gb3 mimic peptide. We have engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of AHL(quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools.<br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:45:22Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="100%;"<br />
height="95px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak" width="250px" height="175px;" style="<br />
float: right;<br />
"><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
width="100%"<br />
height="95px;"<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:44:34Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="100%;"<br />
height="95px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="250px"<br />
height="175px;" float="right"<br />
<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
width="100%"<br />
height="95px;"<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:43:26Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
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<div class="container"><br />
<h2 align="center"><br />
Approach<br />
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<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="100%;"<br />
height="95px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="250px"<br />
height="195px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
width="100%"<br />
height="95px;"<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:42:38Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="100%;"<br />
height="95px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="150px;%"<br />
height="195px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
width="100%"<br />
height="95px;"<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:41:53Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="100%;"<br />
height="95px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="100%"<br />
height="95px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:40:23Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="624px;"<br />
height="53px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="203px;"<br />
height="113px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br></br></br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="50%;"<br />
/></br></br><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:39:28Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="624px;"<br />
height="53px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="203px;"<br />
height="113px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="90%;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:38:48Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<br />
<br />
<div class="container"><br />
<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="624px;"<br />
height="53px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="203px;"<br />
height="113px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br><br />
<img<br />
src="https://static.igem.org/mediawiki/2013/3/32/Iitm_pathway.jpg"<br />
width="247px;"<br />
height="176px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/File:Iitm_pathway.jpgFile:Iitm pathway.jpg2013-09-28T02:38:02Z<p>JunaidBabu: </p>
<hr />
<div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/AttributionsTeam:IIT Madras/Attributions2013-09-28T02:36:58Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Attributions<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
As is said popularly in society, “Team work is the secret that makes common people achieve uncommon results ” and let there be no doubt that there has been<br />
a long list of people and organizations that have helped us in many ways so that we can keep working towards this project independently and with our own<br />
creative ideas right since it’s conception.<br />
</p><br />
<p dir="ltr"><br />
First and foremost we are ever so grateful to the Department of Biotechnology, IIT Madras and more so to the Head of Department- Prof. Mukesh Doble and<br />
Senior Prof. K.B. Ramachandran for believing in the project and supporting it from the very beginning.<br />
<br />
<br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/2RPeihDYpMo5jUmNrIBHQ6iDFeUZbkWqBDpcF_S4PH8nd6Cf6EvlXTPbZBknuXQYWnYHpQ1n1gZbZcu80dH_xLQOWcHQr2Gxiq5R-5mRwVL_s2Oz4X5v86ieBeuHVzr4aT0"<br />
width="254px;"<br />
height="168px;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/YUodJQ4EIE-YcdJnghDpWg8nm3t4FX9vmP-O4u0gsjf6YBSOjZvl7pZ4zr5sprupfZtzGxuzPheVPKemY3RBiv7zj5surI-s8erhZ7p9xAQCSFt67JHVSsLorJq-o-iupQo"<br />
width="232px;"<br />
height="170px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. Mukesh Doble</br>Process control, </br>Chemical engineering, </br>I.I.T. Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. K B Ramachandran</br> Bioprocess Engineering Lab</td><br />
</tr><br />
</table><br />
<br />
</p><br />
<br />
<p ><br />
We would also like to thank the Cardiovascular Genetics Group mentored by our iGEM team Faculty Advisor Prof. N.R. Mahapatra for being generous with their<br />
lab resources and helping us out with advice on experimental design and running of experiments.</br><br />
<br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/JMtqkv3AE4XSwcOCAdB36X_wa5dYifqTK-7hC2NX9HlmRkTiCYxJM0LKrCdLL8XlgYwhueF2P6I_5vRFmxMkuFpUmT8Olf_xeSHXzNonGLTRYw9FvxEFVAF5yzNOZRQUL9g"<br />
width="433px;"<br />
height="324px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td><p style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Cardiovascular Genetics Lab, (From left to right) Prasanna ReddyAllu, Abrar Ali Khan, Binu Sasi, Vinayak Gupta, Bhargavi, Kalyani Ananthamohan<br />
<br />
</p></td><br />
</tr><br />
</table><br />
<br />
</br><br />
</p> <br />
<p dir="ltr"><br />
We are especially grateful to some graduate students who were kind enough to help us out with their abundant knowledge and with experiments that we had to<br />
do for the purpose of our project that they themselves were experts at. A big thank you to Parshuram J Sonawne for guiding us whenever we went to him<br />
whether it was with troubleshooting failed experiments or designing new ones. We also want to thank Prashant Kumar for giving us fast-track tutorials on<br />
peptide purification and helping us out on our experiments related to the same. And last but not the least, thanks to Vasanthan Ravichandran for helping us<br />
out with the HPLC experiments.<br />
</p><br />
<p dir="ltr"><br />
We feel truly blessed to have such a helpful and enthusiastic senior graduate students who were willing to help us in any way that they could.<br />
<table border="0" ><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/dqjRjrjL0_R-3KMmbrkNSx2pu_MQWlhTrcnvV__Rqeo9H_gnYCPznkfJY2WYs86Hg8r-bWGjioCK6xbWO28G-VPC07u4cH81tNnAGCtid7qrdeq9jN8OTqDFvnJ15cIGd7k"<br />
width="158px;"<br />
height="klasjglksa;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/zcbraxf7dSijW5L9qz0bxWs7s8eaU6PhTs2kj3At8v99c3Ptowy4Z6zj-9JuLkbjnSlX-OAxbjwIC7eVwmprHBK7z5-M2lrdKsn6N2gzPugzTeXZuzx87RYZFt7lHOSR6FM"<br />
width="216px;"<br />
height="180px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/RL2CQrwOiqaVSAWL_c6bvxwsUB0yBQ00KHWD-DimHUeOpMad615ASDazmtyczyPqaPqxo26oh8qZoHG-YoAqBUXTykMNBOSbj52eioiA72qaSwtl6gwXTvAxlbEFjDe51No"<br />
width="237px;"<br />
height="180px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Parshuram J Sonawane<br>Research Scholar,<br> Cardiovascular Genetics Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Prashant Kumar</br>Research Scholar, <br>Signal Transduction Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Vasanthan Ravichandras</br>Research Scholar, <br>Chemical Biology Lab, <br>IIT Madras</td><br />
</tr><br />
</table><br />
<br />
<br />
</p><br />
</br><br />
<p dir="ltr"><br />
We are extremely grateful to our ever supportive alumni- Dr. Shrikuman Sooryanarayanan, The Batch of 1979 (IIT Madras) Alumni fund and its Chairman, Dr.<br />
Dhinakar Kompala- for recognizing the value of our project, encouraging us to take it forward and for all the financial assistance they provided throughout<br />
the project. We would also like to acknowledge and thank Mr. Suresh at the International &amp; Alumni Relations Office and our Dean IAR, Dr. R. Nagarajan<br />
for their support and for helping us to get in touch with our alumni.<br />
</p><br />
<p dir="ltr"><br />
Finally we are very grateful to the center for Industrial Consultancy and Sponsored Research (IC &amp; SR) at IIT Madras for supporting our project and<br />
sponsoring it through their “Innovative Student Project” scheme for hi-tech undergraduate student projects.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<h3 style="text-align:center"><br />
OUR ORGANIZATIONAL SPONSORS<br />
</h3><br />
<p dir="ltr"><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/bZ8i_W3HSPHpDIq2Q7jLo9ynTS1mjrj_cE2ZcJ3oE6AQzpJWamRWxCYcSgdlaCKQV_D54Ztix-IjY6OTwgjgvBc8yCL8bIL0k0RI6vhS9-LflB2Bi4_sUVCR_3D4_2lBMms"<br />
width="240px;"<br />
height="359px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/JQ4eYtscY96GvK7x7GIDatc_YmNn6LtB4u9vuXK__9efWvfOPa1SuFJLjNhVYgLGRgB9SksNQGIqwMtZS6PCikMorzcPpXQe0XZ91IqPIkJJaYxiXExGgJX6oni-aEc-I1g"<br />
width="299px;"<br />
height="302px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/Ifa6GV5N3C7tvqfcjTKb38AgydenkH5Fq6LJLSgN4cQAWYleWVq1S2W9XbM7q6P5wF0Nzilr72oOMrxwqgaeMgwRXXpKb8by2ZbvaxBxd2s6GXUGtYmgQ7WRyRV-AuyxwWA"<br />
width="269px;"<br />
height="319px;"<br />
/></td><br />
</tr><br />
</table></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/AttributionsTeam:IIT Madras/Attributions2013-09-28T02:35:45Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Attributions<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
As is said popularly in society, “Team work is the secret that makes common people achieve uncommon results ” and let there be no doubt that there has been<br />
a long list of people and organizations that have helped us in many ways so that we can keep working towards this project independently and with our own<br />
creative ideas right since it’s conception.<br />
</p><br />
<p dir="ltr"><br />
First and foremost we are ever so grateful to the Department of Biotechnology, IIT Madras and more so to the Head of Department- Prof. Mukesh Doble and<br />
Senior Prof. K.B. Ramachandran for believing in the project and supporting it from the very beginning.<br />
<br />
<br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/2RPeihDYpMo5jUmNrIBHQ6iDFeUZbkWqBDpcF_S4PH8nd6Cf6EvlXTPbZBknuXQYWnYHpQ1n1gZbZcu80dH_xLQOWcHQr2Gxiq5R-5mRwVL_s2Oz4X5v86ieBeuHVzr4aT0"<br />
width="254px;"<br />
height="168px;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/YUodJQ4EIE-YcdJnghDpWg8nm3t4FX9vmP-O4u0gsjf6YBSOjZvl7pZ4zr5sprupfZtzGxuzPheVPKemY3RBiv7zj5surI-s8erhZ7p9xAQCSFt67JHVSsLorJq-o-iupQo"<br />
width="232px;"<br />
height="170px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. Mukesh Doble</br>Process control, </br>Chemical engineering, </br>I.I.T. Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. K B Ramachandran</br> Bioprocess Engineering Lab</td><br />
</tr><br />
</table><br />
<br />
</p><br />
<br />
<p ><br />
We would also like to thank the Cardiovascular Genetics Group mentored by our iGEM team Faculty Advisor Prof. N.R. Mahapatra for being generous with their<br />
lab resources and helping us out with advice on experimental design and running of experiments.</br><br />
<img<br />
src="https://lh5.googleusercontent.com/JMtqkv3AE4XSwcOCAdB36X_wa5dYifqTK-7hC2NX9HlmRkTiCYxJM0LKrCdLL8XlgYwhueF2P6I_5vRFmxMkuFpUmT8Olf_xeSHXzNonGLTRYw9FvxEFVAF5yzNOZRQUL9g"<br />
width="433px;"<br />
height="324px;"<br />
/></br><br />
</p> <p style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Cardiovascular Genetics Lab, (From left to right) Prasanna ReddyAllu, Abrar Ali Khan, Binu Sasi, Vinayak Gupta, Bhargavi, Kalyani Ananthamohan<br />
<br />
</p><br />
<p dir="ltr"><br />
We are especially grateful to some graduate students who were kind enough to help us out with their abundant knowledge and with experiments that we had to<br />
do for the purpose of our project that they themselves were experts at. A big thank you to Parshuram J Sonawne for guiding us whenever we went to him<br />
whether it was with troubleshooting failed experiments or designing new ones. We also want to thank Prashant Kumar for giving us fast-track tutorials on<br />
peptide purification and helping us out on our experiments related to the same. And last but not the least, thanks to Vasanthan Ravichandran for helping us<br />
out with the HPLC experiments.<br />
</p><br />
<p dir="ltr"><br />
We feel truly blessed to have such a helpful and enthusiastic senior graduate students who were willing to help us in any way that they could.<br />
<table border="0" ><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/dqjRjrjL0_R-3KMmbrkNSx2pu_MQWlhTrcnvV__Rqeo9H_gnYCPznkfJY2WYs86Hg8r-bWGjioCK6xbWO28G-VPC07u4cH81tNnAGCtid7qrdeq9jN8OTqDFvnJ15cIGd7k"<br />
width="158px;"<br />
height="klasjglksa;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/zcbraxf7dSijW5L9qz0bxWs7s8eaU6PhTs2kj3At8v99c3Ptowy4Z6zj-9JuLkbjnSlX-OAxbjwIC7eVwmprHBK7z5-M2lrdKsn6N2gzPugzTeXZuzx87RYZFt7lHOSR6FM"<br />
width="216px;"<br />
height="180px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/RL2CQrwOiqaVSAWL_c6bvxwsUB0yBQ00KHWD-DimHUeOpMad615ASDazmtyczyPqaPqxo26oh8qZoHG-YoAqBUXTykMNBOSbj52eioiA72qaSwtl6gwXTvAxlbEFjDe51No"<br />
width="237px;"<br />
height="180px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Parshuram J Sonawane<br>Research Scholar,<br> Cardiovascular Genetics Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Prashant Kumar</br>Research Scholar, <br>Signal Transduction Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Vasanthan Ravichandras</br>Research Scholar, <br>Chemical Biology Lab, <br>IIT Madras</td><br />
</tr><br />
</table><br />
<br />
<br />
</p><br />
</br><br />
<p dir="ltr"><br />
We are extremely grateful to our ever supportive alumni- Dr. Shrikuman Sooryanarayanan, The Batch of 1979 (IIT Madras) Alumni fund and its Chairman, Dr.<br />
Dhinakar Kompala- for recognizing the value of our project, encouraging us to take it forward and for all the financial assistance they provided throughout<br />
the project. We would also like to acknowledge and thank Mr. Suresh at the International &amp; Alumni Relations Office and our Dean IAR, Dr. R. Nagarajan<br />
for their support and for helping us to get in touch with our alumni.<br />
</p><br />
<p dir="ltr"><br />
Finally we are very grateful to the center for Industrial Consultancy and Sponsored Research (IC &amp; SR) at IIT Madras for supporting our project and<br />
sponsoring it through their “Innovative Student Project” scheme for hi-tech undergraduate student projects.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<h3 style="text-align:center"><br />
OUR ORGANIZATIONAL SPONSORS<br />
</h3><br />
<p dir="ltr"><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/bZ8i_W3HSPHpDIq2Q7jLo9ynTS1mjrj_cE2ZcJ3oE6AQzpJWamRWxCYcSgdlaCKQV_D54Ztix-IjY6OTwgjgvBc8yCL8bIL0k0RI6vhS9-LflB2Bi4_sUVCR_3D4_2lBMms"<br />
width="240px;"<br />
height="359px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/JQ4eYtscY96GvK7x7GIDatc_YmNn6LtB4u9vuXK__9efWvfOPa1SuFJLjNhVYgLGRgB9SksNQGIqwMtZS6PCikMorzcPpXQe0XZ91IqPIkJJaYxiXExGgJX6oni-aEc-I1g"<br />
width="299px;"<br />
height="302px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/Ifa6GV5N3C7tvqfcjTKb38AgydenkH5Fq6LJLSgN4cQAWYleWVq1S2W9XbM7q6P5wF0Nzilr72oOMrxwqgaeMgwRXXpKb8by2ZbvaxBxd2s6GXUGtYmgQ7WRyRV-AuyxwWA"<br />
width="269px;"<br />
height="319px;"<br />
/></td><br />
</tr><br />
</table></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/AttributionsTeam:IIT Madras/Attributions2013-09-28T02:35:18Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Attributions<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
As is said popularly in society, “Team work is the secret that makes common people achieve uncommon results ” and let there be no doubt that there has been<br />
a long list of people and organizations that have helped us in many ways so that we can keep working towards this project independently and with our own<br />
creative ideas right since it’s conception.<br />
</p><br />
<p dir="ltr"><br />
First and foremost we are ever so grateful to the Department of Biotechnology, IIT Madras and more so to the Head of Department- Prof. Mukesh Doble and<br />
Senior Prof. K.B. Ramachandran for believing in the project and supporting it from the very beginning.<br />
<br />
<br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/2RPeihDYpMo5jUmNrIBHQ6iDFeUZbkWqBDpcF_S4PH8nd6Cf6EvlXTPbZBknuXQYWnYHpQ1n1gZbZcu80dH_xLQOWcHQr2Gxiq5R-5mRwVL_s2Oz4X5v86ieBeuHVzr4aT0"<br />
width="254px;"<br />
height="168px;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/YUodJQ4EIE-YcdJnghDpWg8nm3t4FX9vmP-O4u0gsjf6YBSOjZvl7pZ4zr5sprupfZtzGxuzPheVPKemY3RBiv7zj5surI-s8erhZ7p9xAQCSFt67JHVSsLorJq-o-iupQo"<br />
width="232px;"<br />
height="170px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. Mukesh Doble</br>Process control, </br>Chemical engineering, </br>I.I.T. Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Dr. K B Ramachandran</br> Bioprocess Engineering Lab</td><br />
</tr><br />
</table><br />
<br />
</p><br />
<br />
<p ><br />
We would also like to thank the Cardiovascular Genetics Group mentored by our iGEM team Faculty Advisor Prof. N.R. Mahapatra for being generous with their<br />
lab resources and helping us out with advice on experimental design and running of experiments.<br />
<img<br />
src="https://lh5.googleusercontent.com/JMtqkv3AE4XSwcOCAdB36X_wa5dYifqTK-7hC2NX9HlmRkTiCYxJM0LKrCdLL8XlgYwhueF2P6I_5vRFmxMkuFpUmT8Olf_xeSHXzNonGLTRYw9FvxEFVAF5yzNOZRQUL9g"<br />
width="433px;"<br />
height="324px;"<br />
/></br><br />
</p> <p style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Cardiovascular Genetics Lab, (From left to right) Prasanna ReddyAllu, Abrar Ali Khan, Binu Sasi, Vinayak Gupta, Bhargavi, Kalyani Ananthamohan<br />
<br />
</p><br />
<p dir="ltr"><br />
We are especially grateful to some graduate students who were kind enough to help us out with their abundant knowledge and with experiments that we had to<br />
do for the purpose of our project that they themselves were experts at. A big thank you to Parshuram J Sonawne for guiding us whenever we went to him<br />
whether it was with troubleshooting failed experiments or designing new ones. We also want to thank Prashant Kumar for giving us fast-track tutorials on<br />
peptide purification and helping us out on our experiments related to the same. And last but not the least, thanks to Vasanthan Ravichandran for helping us<br />
out with the HPLC experiments.<br />
</p><br />
<p dir="ltr"><br />
We feel truly blessed to have such a helpful and enthusiastic senior graduate students who were willing to help us in any way that they could.<br />
<table border="0" ><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/dqjRjrjL0_R-3KMmbrkNSx2pu_MQWlhTrcnvV__Rqeo9H_gnYCPznkfJY2WYs86Hg8r-bWGjioCK6xbWO28G-VPC07u4cH81tNnAGCtid7qrdeq9jN8OTqDFvnJ15cIGd7k"<br />
width="158px;"<br />
height="klasjglksa;"<br />
/></td><br />
<td><img<br />
src="https://lh4.googleusercontent.com/zcbraxf7dSijW5L9qz0bxWs7s8eaU6PhTs2kj3At8v99c3Ptowy4Z6zj-9JuLkbjnSlX-OAxbjwIC7eVwmprHBK7z5-M2lrdKsn6N2gzPugzTeXZuzx87RYZFt7lHOSR6FM"<br />
width="216px;"<br />
height="180px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/RL2CQrwOiqaVSAWL_c6bvxwsUB0yBQ00KHWD-DimHUeOpMad615ASDazmtyczyPqaPqxo26oh8qZoHG-YoAqBUXTykMNBOSbj52eioiA72qaSwtl6gwXTvAxlbEFjDe51No"<br />
width="237px;"<br />
height="180px;"<br />
/></td><br />
</tr><br />
<tr><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Parshuram J Sonawane<br>Research Scholar,<br> Cardiovascular Genetics Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Prashant Kumar</br>Research Scholar, <br>Signal Transduction Lab, <br>IIT Madras</td><br />
<td style="<br />
font-size: 11px;<br />
line-height: 1;<br />
">Vasanthan Ravichandras</br>Research Scholar, <br>Chemical Biology Lab, <br>IIT Madras</td><br />
</tr><br />
</table><br />
<br />
<br />
</p><br />
</br><br />
<p dir="ltr"><br />
We are extremely grateful to our ever supportive alumni- Dr. Shrikuman Sooryanarayanan, The Batch of 1979 (IIT Madras) Alumni fund and its Chairman, Dr.<br />
Dhinakar Kompala- for recognizing the value of our project, encouraging us to take it forward and for all the financial assistance they provided throughout<br />
the project. We would also like to acknowledge and thank Mr. Suresh at the International &amp; Alumni Relations Office and our Dean IAR, Dr. R. Nagarajan<br />
for their support and for helping us to get in touch with our alumni.<br />
</p><br />
<p dir="ltr"><br />
Finally we are very grateful to the center for Industrial Consultancy and Sponsored Research (IC &amp; SR) at IIT Madras for supporting our project and<br />
sponsoring it through their “Innovative Student Project” scheme for hi-tech undergraduate student projects.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<h3 style="text-align:center"><br />
OUR ORGANIZATIONAL SPONSORS<br />
</h3><br />
<p dir="ltr"><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/bZ8i_W3HSPHpDIq2Q7jLo9ynTS1mjrj_cE2ZcJ3oE6AQzpJWamRWxCYcSgdlaCKQV_D54Ztix-IjY6OTwgjgvBc8yCL8bIL0k0RI6vhS9-LflB2Bi4_sUVCR_3D4_2lBMms"<br />
width="240px;"<br />
height="359px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/JQ4eYtscY96GvK7x7GIDatc_YmNn6LtB4u9vuXK__9efWvfOPa1SuFJLjNhVYgLGRgB9SksNQGIqwMtZS6PCikMorzcPpXQe0XZ91IqPIkJJaYxiXExGgJX6oni-aEc-I1g"<br />
width="299px;"<br />
height="302px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/Ifa6GV5N3C7tvqfcjTKb38AgydenkH5Fq6LJLSgN4cQAWYleWVq1S2W9XbM7q6P5wF0Nzilr72oOMrxwqgaeMgwRXXpKb8by2ZbvaxBxd2s6GXUGtYmgQ7WRyRV-AuyxwWA"<br />
width="269px;"<br />
height="319px;"<br />
/></td><br />
</tr><br />
</table></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/CodeRedTeam:IIT Madras/CodeRed2013-09-28T02:34:15Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Human Practices<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<div class="col-md-9"><br />
<iframe src="http://files.flipsnack.com/iframe/embed.html?hash=fdp0zfql&wmode=window&bgcolor=EEEEEE&t=1380286293" width="1140" height="500" seamless="seamless" scrolling="no" frameborder="0" allowtransparency="true"></iframe><br />
<br />
Links to Code Red in Regional Languages<br />
<a href="https://2013.igem.org/File:Code_Red_Guidebook.pdf" target="_blank"> English</a><br />
<br />
<a href="https://2013.igem.org/File:Code_Red_Hindi.pdf" target="_blank"> Hindi</a><br />
<br />
<a href="https://2013.igem.org/File:Code_Red_Marathi.pdf" target="_blank"> Marathi</a><br />
<br />
<a href="https://2013.igem.org/File:Code_Red_Tamil.pdf" target="_blank"> Tamil</a><br />
<br />
<a href="https://2013.igem.org/File:Code_Red_Telugu.pdf" target="_blank"> Telugu</a></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/OverviewTeam:IIT Madras/Overview2013-09-28T02:33:06Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Overview<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
Shiga toxin, a worldwide menace, has killed more than 1 million people to date and continues to afflict over 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to many complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine-amino acid Gb3 mimic peptide. We have already engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of an N-Acyl Homoserine Lactone (a quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). A polycistronic construct effecting I3A production is to be cloned downstream of the AHL-inducible promoter and detection of I3A is to be performed using mass spectrometry. We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools<br />
</div><br />
<br />
<br />
<hr class="featurette-divider"><br />
<br />
<br />
<br />
<br />
<br />
</html></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/SafetyTeam:IIT Madras/Safety2013-09-28T02:32:26Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<br />
<html><br />
<font style="calibri"><br />
<body ><br />
<div id="main_container" style="position:relative; top:-100px;><br />
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<html><br />
<head><br />
<body><br />
<head><style><br />
<br> <br><br />
body<br />
{<br />
background: #000;<br />
}<br />
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#aContent<br />
{<br />
background-color:#fff;<br />
margin: 50px auto;<br />
padding: 10px 10px 60px 10px;<br />
width: 800px;<br />
color: #000;<br />
}<br />
#bContent<br />
{<br />
background-color:#fff;<br />
margin: 50px auto;<br />
padding: 10px 10px 20px 10px;<br />
width: 800px;<br />
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</style><br />
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#menu a {position : relative; top:7px; text-decoration:none; color:white;} <br />
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<div id="aContent"><br />
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<h2 align="center"><br />
Safety Protocols<br />
</h2><br />
<hr class="featurette-divider"><br />
<p CLASS="justifyalign">Experiments were conducted in the Undergraduate lab of the <b>Dept. Of Biotechnology</b> at <b>IIT Madras</b>. The lab is confirmed to the standards for a bio-safety 1 lab according to the <b>Center for Disease Control and Prevention,Atlanta</b>. <b>Bio-safety Level 1</b> is suitable for work involving well-characterized agents not known to consistently cause disease in immunocompetent adult humans, and present minimal potential hazard to laboratory personnel and the environment. <b>BSL-1</b> laboratories are not necessarily separated from the general traffic patterns in the building. Work is typically conducted on open bench tops using standard microbiological practices. Special containment equipment or facility design is not required, but may be used as determined by appropriate risk assessment techniques. Laboratory personnel must have specific training in the procedures conducted in the laboratory and must be supervised by a scientist with training in microbiology or a related science.</p><br />
<br />
</body><br />
</html><br />
<br />
<u><b><br />
==Standard Microbiological Practices==<br />
</b></u><br />
<html><br />
<ol type="a"><br />
<li><b>Statement of Purpose (SOP)</b> have been developed and are kept for easy access which enlists all the safety measures each experiment should be abided for.</li><br />
<li>Access to the laboratory is limited or restricted at the discretion of the laboratory director when experiments or work with cultures and specimens are in progress.</li><br />
<li>People wash their hands after handling viable materials, after removing gloves, and before leaving the laboratory.</li><br />
<li>Eating, drinking, smoking, handling contact lenses, applying cosmetics, and storing food for human use are not permitted in the work areas. People who wear contact lenses in laboratories must wear goggles or a face shield. Food is stored outside the work area in cabinets or refrigerators designated and used for this purpose only.</li><br />
<li><b>Mouth pipetting </b> is prohibited .Instead <b>mechanical pipetting </b> devices are to be used.</li><br />
<li>Policies for the safe handling of sharp instruments are clearly instructed.</li><br />
<li>All procedures are performed carefully to minimize the creation of splashes or aerosols.</li><br />
<li>Work surfaces are <b>decontaminated</b> atleast once a day and after any spill of viable material.</li><br />
<li>All cultures, stocks, and other regulated wastes are decontaminated before disposal by an approved decontamination method for example <b>Autoclaving</b>. Materials to be decontaminated outside the immediate laboratory are to be placed in a durable, leakproof container and closed for transport from the laboratory. These materials are packaged in accordance with applicable local, state, and federal regulations before removing from the facility.</li><br />
</ol><br />
</html><br />
<b><u><br />
==Safety Equipment (Primary Barriers)==<br />
<br />
</u></b> <br />
<html><br />
<ol type="a"><br />
<li>Special containment devices or equipment such as a biological safety cabinet is generally not required for manipulations of agents assigned to <b>Bio-safety Level 1</b>.</li><br />
<li>It is recommended that laboratory coats, gowns, or uniforms be worn to prevent contamination or soiling of street clothes.</li><br />
<li>Gloves are must especially if there is a cut on the hand or if a rash is present. Alternatives to powdered latex gloves should be available.</li><br />
<li><b>Protective eyewear</b> should be worn while conducting experiments in which splashes of microorganisms or other hazardous materials are anticipated.</li><br />
</ol><br />
</html><br />
<b><u><br />
==Laboratory Facilities (Secondary Barriers)==<br />
<br />
</u></b> <br />
<html><br />
<ol type="a"><br />
<li>Laboratory has doors for access control.</li><br />
<li>A sink is provided in the Laboratory for washing hands.</li><br />
<li>The Laboratory is designed such that it can be easily cleaned.</li><br />
<li><b>Bench tops</b> are impervious to water and are resistant to moderate heat, organic solvents, acids, alkalis, and chemicals used to decontaminate the work surface and equipment.</li><br />
<li>Laboratory furniture is capable of supporting anticipated loadings and uses. Spaces between benches, cabinets, and equipments are accessible for cleaning.</li><br />
<li>It is made sure that the Laboratory is cut-off from the external environment.</li><br />
<li>We have an accesible compartment in the lab for <b>MSDS</b>(Materials Safety Data Sheet) where in we have a roster of all the chemicals and what needs to be done in case of accident. </li><br />
</ol><br />
</html><br />
<br />
<br />
<b><u><br />
==Simple Questions==<br />
</u> </b><br />
<html><br />
<b>1. Would any of your project ideas raise safety issues in terms of:<br />
<ul><li> researcher safety,<br />
<li> public safety, or<br />
<li> environmental safety?</ul></b><br />
<p><br />
<b><u>Researcher Safety</u></b><br/><br />
<ul><li><br />
<u><b>Chassis</b></u>: E.coli is the most commonly used gram-negative bacterial chassis in Molecular Biology. </br><br />
They are normal flora of the human gut, and can benefit their hosts by producing <b>Vitamin K2</b>,and by preventing the establishment of other pathogenic bacteria within the intestine. Some strains of E.coli are also pathogenic, associated with sever diarrhea.</br><br />
However the strains of E.coli used in lab are known to be non-pathogenic. However researchers are advised to use standard laboratory safety equipment and procedures while handling the cultures including wearing Lab coats, Safety Glasses etc.</li><br />
<li><u><b>EtBr</b></u>: Ethidium bromide is an intercalating agent and is/was commonly used as a fluorescent tag (nucleic acid stain) for agarose gel electrophoresis in our lab. Ethidium bromide is thought to act as a mutagen because it intercalates double stranded DNA (i.e. inserts itself between the strands), deforming the DNA. This could affect DNA biological processes, like <b>DNA replication</b> and <b>transcription</b>. <br />
Hence, we do not wash the gel in EtBr solution. Instead, EtBr is added in minimal concentration to the agar solution before it solidifies. It is strictly observed that gloves are used when handling EtBr or EtBr-containing gel. The gels are discarded considering them to be '<b>Hazardous Waste</b>'.</li><br />
<li><u><b>Sodium Azide</b></u>: Sodium Azide is a strong respiratory toxin which inhibits the activity of cytochrome oxidase and acts as a bacteriostat. It is however also highly toxic to mammals. Researchers are required to be extremely careful while handling sodium azide solutions and cultures with sodium azide. Lab Coats and Gloves are a must, they must also be informed about the hazards and the first aid procedures in case of azide spills. <br />
</ul><br />
</li><br />
<b><u>Public Safety</u></b><br />
<li>All work with live E.coli cells is carried out in the laminar hood that eliminates the possibility of any <b>GMO</b>(Genetically Modified Organisms) from being released out.</li><br />
<li>Laboratory has been provided with doors, as these GMO should not be readily accessible to unintended personnel.</li><br />
<li>It is made sure that appropriate measures for waste disposal are taken. Waste is not washed down the sink or thrown into public dust-bins.<li><br />
<b><u>Environment Safety</u></b><br />
<li>All contaminated waste is treated as '<b>Bio-Hazardous Waste</b>' and is decontaminated before being put into a red trash bag or a sealed medical waste box. The bio-hazard bag is placed in a pre-chosen area for pick up.</li><br />
<li>We believe extensively in the three <b>'R's - Reduce, Reuse and Recyle</b>. By considering these constraints, we have learnt to plan our experiments better.</li><br />
</ul><br />
</p><br />
<br />
<br />
<br><br />
<br><b><br />
2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,<br />
<ul><li> Did you document these issues in the Registry?<br />
<li> How did you manage to handle the safety issue?<br />
<li> How could other teams learn from your experience?<br />
</ul></b><br />
<p><br />
No. All bio-bricks made are according to the safety guidelines provided by the <b>Center for Disease Control and Prevention</b>. <br />
<br />
</p><br><br />
<br><b><br />
3. Is there a local biosafety group, committee, or review board at your institution?<br />
<ul><li> If yes, what does your local biosafety group think about your project?<br />
<li> If no, which specific biosafety rules or guidelines do you have to consider in your country?</ul></b><br />
<p><br />
Yes, our project is supported by the <b>Dept. of Biotechnology, IIT Madras</b>. They have provided us with <b>Biosafety level 1</b> facilities for all our experimental work.<br />
</p><br />
</p><br />
<hr/><br />
<p><b><u>References</u></b></p><br />
<ul><br />
<li>Cupillard, L. et al., 2005. Impact of plasmid supercoiling on the efficacy of a rabies DNA vaccines to protect cats. Vaccine 23: 1910-1916.</li><br />
<li>JM Tiedje et al., 1989. The planned introduction of genetically engineered organisms: Ecological considerations and recommendations Ecology, 70(2), 1989, pp. 298-315</li><br />
<li>Efstathia V. Scoulica. et al., Spread of blaVIM-1-producing e. coli in a university hospital in Greece. Genetic analysis of the integron carrying the blaVIM-1 metallo-β-lactamase gene,Diagnostic Microbiology and Infectious Disease Volume 48, Issue 3, March 2004, Pages 167-172</li><br />
</ul><br />
</font><br />
</html></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DryLabAndModellingTeam:IIT Madras/DryLabAndModelling2013-09-28T02:30:43Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Dry Lab and Modelling<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<h3><br />
BACKGROUND<br />
</h3><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-5c5da40e-617d-4c38-6216-33cc103221da"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity<br />
of a complex formed by two or more constituent molecules with known structures. Protein-ligand docking in particular, is very important because of its<br />
therapeutic applications in modern structure-based drug design.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Our team chose to do docking experiments in order to evaluate the binding characteristics of Shiga toxin and the peptide designed to neutralise it, as it<br />
is important to validate the results generated from experimental techniques.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since only the sequence of the peptide(WHWTWLSEY) was known, it was necessary to model the structure of the peptide. For this purpose, we used the online<br />
webserver, PEP-FOLD(Yimin SHEN et al.). PEP-FOLD is based on the concept of structural alphabet (SA) - i.e. a description of apolypeptidic conformation as<br />
a series of local canonical conformations, and uses a HMM (Hidden Markov Chain)-derived SA of 27 letters to describe proteins as series of overlapping<br />
fragments of four amino acids. PEP-FOLD is based on a two-step procedure:<br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
prediction of a limited set of SA letters at each position from peptide amino acid sequence<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
assembly of the prototype fragments associated with each SA letter using<br />
</p><br />
</li><br />
</ul><br />
<p dir="ltr"><br />
a greedy algorithm and a generic protein coarse-grained force field.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
As mentioned earlier, Shiga toxin binds to human Globotriaosylceramide (Gb3Cer) receptors which are present in the endothelium of mammalian cells. The<br />
crystal structure of Gb3 bound to Shiga toxin has already been determined by crystallization (PDB id - 1BOS) performed by Ling et.al. This structure was<br />
used in our experiments as a reference structure for carrying out docking studies.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Further work done by Miura et.al., on Gb3 mimicking peptides revealed the Molecular dynamics and binding characteristics of the truncated peptide<br />
considering only the first five amino residues of our peptide (WHWTWLSEY). In order to compare the docking characteristics of the entire peptide as opposed<br />
to the truncated peptide that was used in the publication, we carried out our bioinformatics experiments.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<h3><br />
TOOLS: HADDOCK<br />
</h3><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<a href="http://www.nmr.chem.uu.nl/haddock">HADDOCK</a><br />
(High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK can<br />
deal with a large class of modelling problems including protein-protein, protein-nucleic acids and protein-ligand complexes. For the purpose of our<br />
studies, we used the Easy Interface of the HADDOCK server which requires several parameters including active and passive residues.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since our peptide (WHWTWLSEY) is a Gb3 receptor mimic, it is reasonable to assume that the residues in Shiga toxin to which the peptide binds are the same<br />
ones to which Gb3 binds .<br />
</p><br />
<p dir="ltr"><br />
These active residues were obtained from PDB. These were found to be Lys(33), Asn(35),Asp(36), Asp(38), Thr(41), Glu(48), Thr(51), Asn(52), Arg(53),<br />
Trp(54), Asn(55), Thr(74), Asn(75), Gly(80), Gly(82), Phe(83).<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<h3><br />
RESULTS<br />
</h3><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
HADDOCK uses the HADDOCK score to rank the clusters generated during docking. This is a weighted sum of:<br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
Electrostatic energy (weight 0.2)<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
Van der Waals energy (weight 1.0)<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
Desolvation energy (weight 1.0)<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
Restraints violation energies (distance, SANI) (weight 0.1)<br />
</p><br />
</li><br />
</ul><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
According to this ranking score, we shortlisted the best models from the top 5 clusters.These were further analysed on the basis of low RMSD to the<br />
original structure of Gb3 bound to Shiga toxin.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<div dir="ltr"><br />
<table><br />
<colgroup><br />
<col width="82"/><br />
<col width="162"/><br />
<col width="240"/><br />
<col width="105"/><br />
</colgroup><br />
<tbody><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
Clusters<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
HADDOCK score<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
RMSD from structure of lowest energy<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
Z Score<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
1<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-110.4 +/- 6.1<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
0.4 +/- 0.2<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-1.5<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
2<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-100.8 +/- 6.2<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
1.6 +/- 0.3<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-0.9<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
3<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-93.6 +/- 10.2<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
1.0 +/- 0.3<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-0.5<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
4<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-91.2 +/- 3.9<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
2.4 +/- 0.0<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-0.3<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
5<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-70.9 +/- 7.4<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
2.2 +/- 0.2<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
0.9<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
6<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-69.0 +/- 4.9<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
2.0 +/- 0.1<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
1<br />
</p><br />
</td><br />
</tr><br />
<tr><br />
<td><br />
<p dir="ltr"><br />
7<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
-64.2 +/- 14.9<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
2.0 +/- 0.1<br />
</p><br />
</td><br />
<td><br />
<p dir="ltr"><br />
1.3<br />
</p><br />
</td><br />
</tr><br />
</tbody><br />
</table><br />
</div><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Cluster 1<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh3.googleusercontent.com/hxeLmE2qOTxmsAY209z0r91A_cEBTtR9mSCahhiXEmwgLJHrZaDunsNTEFXq8bLU2cSGkkn7ntXT8YSnsGxl_-gE-pVhQW5HGSRRgsUog4z4gOmV8M1-lVQ4SZ8QRPLNE5g"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
<td><img<br />
src="https://lh3.googleusercontent.com/SC2dirz7ALzkJh1QB713bRU1lS-0tHEyLy5zzUe6LPpHHwkN2vSQrJcmG_HayckeivnDRIuBQifrhNpxp3Ryj9IxnLOwEjLeQsIJTqCphNrPTVxW4V88iXApFpPJIUho_G0"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
</tr><br />
</table><br />
<br />
<br />
<br/><br />
<br/><br />
<br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Cluster 2<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh3.googleusercontent.com/k0pxy2LWHVS8vFpKLXMe-_zRxxbArJKt0KT46qzvNmxy7inGmLyOs5h2wNcZ6wBZBs-qLSLN19Oh82h-9gTtgvuTfJiAarTuMgCfW9i19FUaxxE0_DRYP-p97LQZhKkzNh8"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
<td><img<br />
src="https://lh6.googleusercontent.com/Cro5huqXLXr5NEAMnblMxHEVxOynnimzcZ0jUx99f_rzk2WyM4Yk3t0tMx5qsQ8NrZvHZtO0dViDnplRBOgVxOLqMvNO1F-8oatWX-NzwLegorMbFl0gEMWzxrOdkE1rRbU"<br />
width="579px;"<br />
height="393px;"<br />
/></td><br />
</tr><br />
</table><br />
<br />
<br />
<br/><br />
<br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Cluster 3<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh6.googleusercontent.com/GwUCFKWdhMo-bXdMuqJ0qel5PVhKZyp9rfSqfiExkknfrMfFJceTpG-7Fp-xdgmEGI5ig9YSzv_Cgmxs8P1i2Z6OFx116X0ZKb-xOV1J8ye2mbMETKSXuxADjzanoL2FCuc"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
<td><img<br />
src="https://lh3.googleusercontent.com/OCN3bQQ7ADAiKAYDitwqbJkZUYoIVMPmorbKeSeQwjCl5rNKQxHE2bfgbxA5XAO7tS3QZ4bcyXlh7KRbHHAOjHF24rjNVk1_CN25J8anYhx6WA8JViTasFOOxq3pHVz-orI"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
</tr><br />
</table><br />
<br />
<br/><br />
<br/><br />
<br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Cluster 4<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/AV9xRDfeJHMHZm-GHrXXqTpZujoOrmoblYCIIttdQYZeu_EB7ti2-V0pVg7IJCRiOqJ5l4UUyzoTxMl4fbi5k_yczlAEYIBOG5Wn55hQCcEtFbAFJOB61sb1mGHYAZTOJYM"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
<td><img<br />
src="https://lh6.googleusercontent.com/5TrVHjmhtnykLWa5JerFZcrOYoymbiZgpSr_f9GVPZOYPOjgYRhO0QP5G4ibS9Y5PX6WaKGfG4kJzsVYd-hlNGHctVnZzUa6tG_-rQnNVr54sGEw4_VtZxunhA9PuulJJMs"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
</tr><br />
</table><br />
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</strong><br />
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<p dir="ltr"><br />
Cluster 5<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<table border="0"><br />
<tr><br />
<td><img<br />
src="https://lh5.googleusercontent.com/z97FPlI3CPa_pkH1vCfh56oe5kn7Kmd0ISl2aNrV_GZAh2DsxtrUzgT7O5bEAOUjgXgNFOrxz6dnXg1iIXfc8-R30IVu8x6zoh8Jm5pRlOZDRJkYNO8gak0zOXOEm6FlqA8"<br />
width="624px;"<br />
height="423px;"<br />
/></td><br />
<td><img<br />
src="https://lh5.googleusercontent.com/dnjIhOzNTIeNCnNhYVZtsKsRIPx7_ZK37P4jGDJdNXvV5vrUsUVGRfKxjJUjFKdT1eaxcs_mZVPyxmFf634CU9bUbzJYPfioFR37efRiNLLgOEwOC1e-g7KDcEYGUu4jyoU"<br />
width="624px;"<br />
height="423px;"<br />
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<br/><br />
<br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Amongst the predicted results, Cluster 2 seems to be most suited as an interacting partner to Shiga toxin. This can be attributed to the optimum energy<br />
values assigned by HADDOCK as well as the high similarities of the binding modes of the peptide to the toxin as compared to the same of Gb3-Shiga toxin<br />
complex. This was analysed by the RMSD values as indicated by Pymol following structural alignment. The RMSD value obtained was 0.359.<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
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<h3><br />
SCOPE FOR FURTHER WORK<br />
</h3><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Our team intends to construct a peptide library using tools like SDM to create mutants of the peptide and analysing interactions of these with Shiga Toxin.<br />
We can also search for sequences homologous to the toxin which could be harmful in nature and test their interactions with peptide library.This is a<br />
high-throughput analysis and can be validated further by several wet lab techniques.<br />
</p><br />
</div><br />
</div><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ResultsTeam:IIT Madras/Results2013-09-28T02:25:02Z<p>JunaidBabu: </p>
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<h2 align="center"><br />
Results<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<p dir="ltr"><br />
<b><h3>EXPERIMENTAL RESULTS</h3></b><br />
</p><br />
<p dir="ltr"><br />
<b> 1] Preparation of the vector (pSB1C3 + BBa_F2620)</b><br />
<br/><br />
<br/><br />
<u> Result 1.1:</u> Our part of interest (BBa_F2620) was located in the 2013 Kit Plate 3, well 3P. It was reconstituted in 20 µL sterile water and 2 µL was<br />
transformed into E.coli DH5α cells. Mini-prep was performed to isolate the plasmid. The gel image is shown in Fig 1.1 below.</br><br />
<img<br />
src="https://lh4.googleusercontent.com/_ls5U61gqDNMPp-yD0xQi08tfxNmU1FV4AuVeJCc1vTafM0D6qWLTnqgS6OglsfxUV3udfg1VjOWYd6HPomK27q0T7oIY9cn1gaCXySmeGbXQE_Hz-QRKn6W"<br />
width="347px;"<br />
height="456px;"<br />
/><br />
<br/><br />
Fig 1.1: Plasmid Vector pSB1C3 isolation (3 kb each well)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.2:</u> The isolated plasmid was digested with <i>EcoR</i>1 and <i>Pst</i>1 to release BBa_F2620 from the pSB1C3 backbone. Fig 1.2 (gel image) shows release of the<br />
part BBa_F2620 (1061 bp) from the plasmid pSB1C3 (2070 bp).<br />
<img<br />
src="https://lh6.googleusercontent.com/kRJ7uW1GHamXbccbBu3L_WJe_xC1veiE-YEnRP2-MXaHd1o4VJAMLd4JzfLSd9rUfxDjpOyULNRA6z-ULxlOw3cEgKwU1AEkwrgkSRwrCYbHiDwyx5n7SYbx"<br />
width="308px;"<br />
height="263px;"<br />
/><br />
<br/><br />
<br/><br />
Fig 1.2: Restriction digestion image showing release of BBa_F2620 (2 kb+1 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 1.3:</u> Digestion of the plasmid vector with <i>Spe</i>1 and <i>Pst</i>1 gives the vector (3 kb) ready for ligation. Fig 1.3 shows the gel image after double<br />
digestion of the plasmid vector.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/nGxHsVn1zfjb9jKdvFES8ufDBfbe8nOrNfYBp0sG2MG13LCzKgoMltdxK7TRTKZoDvczAYBl2Qofck-gUBLchkOmFCJDDKCFiAnGpwnBwLZQMOJX-dlrpNhR"<br />
width="291px;"<br />
height="298px;"<br />
/><br />
<br/><br />
Fig 1.3: Double digested BBa_F2620 with <i>Spe</i>1 and <i>Pst</i>1 (3 kb)<br />
</p><br />
<p dir="ltr"><br />
<u>Result 1.4:</u> The vector was treated with calf intestinal alkaline phosphatase (CIP) to reduce the probability of getting self-ligated colonies. Fig 1.4<br />
shows the final gel image of the CIP-treated vector, ready for ligation.<br />
</br><img<br />
src="https://lh4.googleusercontent.com/hK2WT22UD8GoiWlgNsXpZNZ_OPq-z14s4V_ZkrNNHvNPRR2GAKsdQaIeLK-RUirY0b40jaNOl__GiTDIRd3UA3KiVnRFWiXp82EPTA6OHadhOKCkwp_RHYk1"<br />
width="237px;"<br />
height="266px;"<br />
/><br />
<br/><br />
Fig 1.4: CIP-treated vector (3 kb)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b> 2] Isolation of insert (Gb3 mimic, 268 bp) </b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u> Result 2.1:</u> Gb3 mimic was delivered in pUC57 plasmid backbone. <i>E.coli</i> DH5α cells were transformed with pUC57. After primary culture, mini-prep was done to<br />
isolate the plasmid. Fig 2.1 shows the gel image of the isolated pUC57 plasmid containing Gb3 mimic insert.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/pPLOpHdOFbjGo5sR8x3WL656l8ijKFk_ex_q7khoJDJsmveUcbRtDPJ4LTRlDdSLaU9v7X-qgdDlcqiVRnEc_JuC5IolfXHcnzGdq6QYKwzoZuQyrmdx6nS_"<br />
width="275px;"<br />
height="240px;"<br />
/><br />
<br/><br />
Fig 2.1: Gel image of isolated pUC57 plasmid (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 2.2:</u> The pUC57 plasmid was then digested with <i>Spe</i>1 and <i>Pst</i>1 to show the release of Gb3 mimic insert. Fig 2.2 distinctly shows the two bands: a 2.7<br />
kb plasmid backbone (pUC57) and a 268 bp insert (Gb3 mimic).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3qEmbsGiZ6msjm3Hom00eFKyyDJ4S270UIrc9XPbcRBhISjwo4ms0Ij7SNsFsehoMSGdtzQCE20oontFXXa31AlCVdtjqJcDKnAxDhf22Qhb9qhMT8TIHLjb"<br />
width="412px;"<br />
height="265px;"<br />
/><br />
<br/><br />
Fig 2.2: Digestion of pUC57 to show release of interest (268 bp)<br />
</p><br />
<br />
<p dir="ltr"><br />
<b>3] Cloning of insert (Gb3 mimic, 268 bp) in vector (BBa_F2620 in pSB1C3, 3 kb)</b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.1:</u> The digested insert was eluted and a ligation reaction between the vector (3 kb) and insert (268 bp) was set up. The clones were confirmed by digesting with <i>Spe</i>1 and <i>Pst</i>1. Fig 3.1 (gel image) shows two separate bands: one at 3 kb (corresponding to vector) and another at 268 bp (corresponding to insert).<br />
</br><img<br />
src="https://lh5.googleusercontent.com/CSNwUCBKK153Y3ADOi4oyYb0h-aIRXYcyl1IRKs8tYd1jCqP8jwBYJ6EyhWG8sTcV4xnNw_MnXJqN6g38zOWXGPEYyyLHa7vxChJReKo36EVgGaJPvltv7b4"<br />
width="398px;"<br />
height="272px;"<br />
/><br />
<br/><br />
Fig 3.1: Restriction digest showing release of the cloned insert (268 bp) from vector (3 kb)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 3.2:</u> The clones were further sequenced to confirm the successful cloning of the Gb3 mimic in pSB1C3. Fig 3.2 shows the sequencing results.<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
<img<br />
src="https://lh5.googleusercontent.com/OoqvSSdrtP16lQxYZWDa2NyMYnsCQ7whmrxoE4dGHrPsBtVFKH5zM5ZDKeZQ7SKGvLL0mjxGhNW4Xe1_66j_jCY8SSkLwnWAAlzl70ooJcmaa5diluEqL1nR03c8CfRZo_o"<br />
width="616px;"<br />
height="225px;"<br />
/><br />
<br/><br />
Fig 3.2: Sequencing of Gb3 mimic clones<br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<b>4] Cloning of I3A construct (3040 bp) in pSB1C3 downstream of BBa_F2620 </b><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.1:</u> I3A construct (3040 bp) was delivered in pUC57. The plasmid backbone was restriction digested with <i>EcoR</i>1 and <i>Pst</i>1 to release the insert (I3A).<br />
Fig 4.1 shows the successfully isolated insert.<br />
</br><img<br />
src="https://lh3.googleusercontent.com/OA4FwlJaE1iK-0hQ8WJL69lmSCK-2ZMGvK22wuSv6sH8X8p-OmRflqG5DxNKA_vppIoheFD4fUSmbP9jKLsJSsT2v-zRpVEiJC2opqyh3S4dDtzpoVT9nd5c"<br />
width="250px;"<br />
height="228px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
Fig 4.1: Gel image showing isolated I3A insert (3040 bp)<br />
</p><br />
<p align="CENTER"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
<u>Result 4.2:</u> The isolated insert was eluted and a ligation reaction was set up between the vector (pSB1C3+BBa_F2620, 3 kb) and the insert (I3A construct, 3040 bp). The clones were confirmed by digesting with Spe1 and Pst1. Fig 4.2 (gel image) shows two closely resolved yet separate bands. Upper band<br />
corresponds to the insert while lower band corresponds to the vector.<br />
<img<br />
src="https://lh5.googleusercontent.com/eMisU6QTF2HqDHYwfzfgTEzlbTxzaweNwGQLiiIlj2o2SeHO2L3GW9WJHg4I4vuXaa7V83pKHGQG7mxlPM8B_Uwyx2mLHMmbSt-AK8clgNmfvd-x-eb8Xw1I"<br />
width="344px;"<br />
height="274px;"<br />
/><br />
<br/><br />
Fig 4.2: Restriction digest showing separate bands of vector (bottom) and insert (top)<br />
</p><br />
<p dir="ltr"><br />
<b>5] Reverse-phase HPLC to detect presence of Gb3 mimic peptide.</b><br />
<br/><br />
</p><br />
<p dir="ltr"><br />
<u>Result 5.1:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next two peaks also share a common overlap region but they are just resolved.<br />
</br><img<br />
src="https://lh5.googleusercontent.com/3ZmPfcfkLi_aDaKldkv9wbPz9Wy0EMG9b8dSrAhjSp6jg1JxE4LLGdRPuAJCQQdvSvmnhQkHlNeeuuzUKMgpxBoKb4j8E9hH19Zx9kgBlSPMFJsFPim11c_e8MNlrhKNw0w"<br />
width="547px;"<br />
height="258px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of induced culture-spent medium run through a C18 column<br />
</p><br />
<br />
<p dir="ltr"><br />
<u>Result 5.2:</u> The spent medium corresponding to the induced culture was run through a C18 column. Fig 5.1 shows the chromatogram corresponding to the same.<br />
The first two peaks almost coincide with each other. The next peak is quite small compared to the corresponding peak for the induced culture. The fourth peak, in this case, is almost negligible. It is just a tiny crest.<br />
</br><img<br />
src="https://lh6.googleusercontent.com/Akyi0tJS07oz5ac-dJQ4OgusaDKM5fA7XSt-_YYf5hOVpEkit1KNyl4o0JwY-v9Tei3xDeJGNw1rJhBOfpOZMievReCTSlMyJjAiAWbxkBLojh9OwtHi7remoBOzUlFQm-Y"<br />
width="624px;"<br />
height="293px;"<br />
/><br />
<br/><br />
Fig 5.1: Chromatogram of non-induced culture-spent medium run through a C18 column.<br />
</p><br />
<br />
<br />
</div><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/ApproachTeam:IIT Madras/Approach2013-09-28T02:24:20Z<p>JunaidBabu: </p>
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<h2 align="center"><br />
Approach<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<p dir="ltr"><br />
The IIT Madras iGEM 2013 project involves a novel and holistic two fold approach to combating the issue of Shiga toxin. In the first part of our project,<br />
we plan to express and export a small Gb3 mimic peptide in <i>E. coli</i>, which is an effective anti-toxin against the deadly Shiga toxin. It was originally<br />
identified by enriching a phage display library, and was subsequently found to inhibit Shiga-toxicity by binding to the one of the B subunits of the<br />
toxin1. This novel peptide is not naturally occurring and has to be produced synthetically for any kind of biological studies.<br />
</p><br />
<p dir="ltr"><br />
The design of our team’s system not only allows the expression of this 9 AA peptide in a biological system, but also allows its secretion to the<br />
extracellular region of the cell after it has been synthesized in the cell. This aspect was specifically designed into the system to make the downstream<br />
processing more convenient. The design also allows for endogenous control over expression of the anti-toxin peptide.<br />
</p><br />
<p dir="ltr"><br />
More specifically, in order to incorporate ease of downstream processing, we synthesized the coding sequence of this peptide with the OmpF signal sequence<br />
upstream since OmpF has been reported to effectively export small peptides upto approximately 3.5 kDa outside the cell. For endogenous control of protein<br />
production, we clone this entire construct downstream a previously characterized iGEM part- BBa_F2620, an AHL induced LuxR promoter. Theoretically, this<br />
allows us to control the amount of peptide produced depending on the concentration of AHL in the rumen of cattle.<br />
<img<br />
src="https://lh6.googleusercontent.com/hqQmO4TSof1LdRZAxyYEadzqXYGyaNq5M2G5r9oSOqoIopbxsaW_gy8pztzGD56sHGYF2xe-P_wGxEPIJOhRZCJmkBeriyXqM-rwaXN_bScTEotKujv6u1kxFvJEjY0XSh4"<br />
width="624px;"<br />
height="53px;"<br />
/></p><br />
</br></br><p style="<br />
font-size: 12px;<br />
"> Fig.1: Conceptual Schematic of the Gb3 mimic peptide gene construct.</p><br />
</p><br />
<p dir="ltr"><br />
We propose to validate the peptide produced by HPLC since the small size of the peptide does not justify running SDS PAGE.<br />
</p><br />
<p dir="ltr"><br />
The second part of our approach involves attacking the very core mechanism that leads to the production of the toxin in the first place- the formation of a<br />
biofilm, specifically, the biofilm formed by <i>E. coli</i> O157:H7 in the gastrointestinal tract of the cattle.<br />
</p><br />
<p dir="ltr"><br />
<strong id="docs-internal-guid-3b519947-6163-3e92-c372-7bf748abcd26"><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
To accomplish this, we have chosen a small biomolecule which is known to be a potent inhibitor of O157:H7 biofilm- indole-3-acetaldehyde (I3A). I3A acts by<br />
repressing two very important curli forming operons, csgBAC and csgDEFG thereby inhibiting the bacteria from attaching to the gastro-intestinal (GI) tract.<br />
The reasons for choosing this specific inhibitor are elucidated below-<br />
</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
</strong><br />
</p><br />
<ul><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A is a natural compound and present as an intermediate in Indole-3-Acetic Acid (IAA) synthesis pathway in plants.<br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/rgbFdPKRXUyHZKd-6c48WDeZ-cW7385ZdO29U-Q0trwhBq0wI6Q2kAYFa9uydxMp3YGpVSgcmCHhgwCGA20keTrexOUvIcvvWjPPf8NveuqlTxWFx5vgFBWLAjFGNuaf-ak"<br />
width="203px;"<br />
height="113px;"<br />
/><br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The precursor molecule required for I3A production is tryptophan which is abundantly present in the cell.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A does not kill the bacteria but simply inhibits them from colonizing the GI tract, and hence it is highly unlikely that the O157:H7 would<br />
develop any sort of resistance against it.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
The enzymes (Tryptophan Transaminase (TAA1) and Indole Pyruvate Decarboxylase (IPDC) required for conversion of tryptophan to I3A do not have<br />
post-translational modifications and hence can be expressed in functionally active forms in <i>E. coli</i>.<br />
</p><br />
</li><br />
<li dir="ltr"><br />
<p dir="ltr"><br />
I3A has not previously been reported to be bio-synthetically produced.<br />
</p><br />
</li><br />
</ul><br />
<br />
<img<br />
src="https://lh3.googleusercontent.com/e8QM3M9AXtkRUL-3SZJ8Oa_ngju5gALahIlNRJpxUECmcUEL7WA4MNfY_tPfqRi17L3fvFU4wkiwGdP5PLJ0F0f8RRdHevMPz2D3gdPod-KR21xW06FiOihm8esfjGSNtiY"<br />
<br />
/><br />
<br />
</br></br><br />
<p style="<br />
font-size: 12px;">Fig 2: Conceptual Schematic of the gene construct for I3A producing system.</p><br />
<p dir="ltr"><br />
<strong><br />
<br/><br />
<br/><br />
</strong><br />
</p><br />
<p dir="ltr"><br />
Since we need I3A to be produced in accordance with AHL abundance in rumen of cattle, we have designed and synthesized a polycistronic construct of TAA1<br />
and IPDC and cloned it under the control of the same AHL-inducible pLuxR promoter system as used in the first construct.</br><br />
<img<br />
src="https://lh4.googleusercontent.com/0F9PJdZHFz3uM-tF09ssOfih9Diyg2N-bokE4GTZSlHy6bnWqYKfx_JWejhoSJihbgZ__on_KPywNxNQCirinaRCKUcJY03izOv1gvMJmD_u7nwtLKqVpQnJ_RJNcRteQsc"<br />
width="247px;"<br />
height="176px;"<br />
/><br />
</p><br />
<p dir="ltr"><br />
We plan to validate this second half of our project by testing for the small molecule indole with an indole test after expression of the given enzymes in<br />
bacteria which inhabit the GI tract of cattle e.g. <i>Lactococcus lactis</i>. We expect that indole will be secreted out of the cells and show a positive result<br />
with the indole test hence, successful production of indole in indole negative bacterial strain- <i>Lactococcus lactis</i>.<br />
</p><br />
<br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_MadrasTeam:IIT Madras2013-09-28T02:23:28Z<p>JunaidBabu: </p>
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Shiga toxin, a worldwide menace, has killed over 1 million people to date and continues to afflict almost 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine amino acid Gb3 mimic peptide. We have engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of AHL(quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools.<br />
</div><br />
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<img src="https://static.igem.org/mediawiki/2013/6/61/Iitm13_team_pic.JPG" width="100%" style="<br />
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</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_MadrasTeam:IIT Madras2013-09-28T02:21:37Z<p>JunaidBabu: </p>
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Shiga toxin, a worldwide menace, has killed over 1 million people to date and continues to afflict almost 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine amino acid Gb3 mimic peptide. We have engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of AHL(quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools.<br />
</div><br />
<div class="col-md-3"><br />
<img src="https://static.igem.org/mediawiki/2013/6/61/Iitm13_team_pic.JPG" width="100%" style="<br />
padding-top: 60px;<br />
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<br />
</div><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_MadrasTeam:IIT Madras2013-09-28T02:20:19Z<p>JunaidBabu: </p>
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<marquee behavior="scroll" direction="left" style="<br />
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Shiga toxin, a worldwide menace, has killed over 1 million people to date and continues to afflict almost 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine amino acid Gb3 mimic peptide. We have engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of AHL(quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools.<br />
</div><br />
<div class="col-md-3"><br />
https://static.igem.org/mediawiki/2013/6/61/Iitm13_team_pic.JPG<br />
</div><br />
<hr class="featurette-divider"><br />
</div></div>JunaidBabuhttp://2013.igem.org/File:Iitm13_team_pic.JPGFile:Iitm13 team pic.JPG2013-09-28T02:19:30Z<p>JunaidBabu: </p>
<hr />
<div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:14:55Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
align="middle" src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:14:40Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<style><br />
img {<br />
position: relative;<br />
margin-left: 50%;<br />
margin-top: 50%;<br />
}<br />
</style><br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
align="middle" src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:14:09Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<style><br />
img {<br />
position: relative;<br />
top: 50%;<br />
left: 50%;<br />
margin-left: -(Y/2)px;<br />
margin-top: -(Y/2)px;<br />
}<br />
</style><br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
align="middle" src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:13:50Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<style><br />
img {<br />
position: absolute;<br />
top: 50%;<br />
left: 50%;<br />
margin-left: -(Y/2)px;<br />
margin-top: -(Y/2)px;<br />
}<br />
</style><br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
align="middle" src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:12:58Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
align="middle" src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabuhttp://2013.igem.org/Team:IIT_Madras/DesignTeam:IIT Madras/Design2013-09-28T02:07:54Z<p>JunaidBabu: </p>
<hr />
<div>{{:Team:IIT Madras/Templates/Header}}<html><br />
<br />
<br />
<div class="container"><br />
<br />
<br />
<br />
<br />
<hr class="featurette-divider"><br />
<h2 align="center"><br />
Novel Design Considerations<br />
</h2><br />
<hr class="featurette-divider"><br />
<br />
<div class="row featurette"><br />
<br />
<p dir="ltr"><br />
Creating synthetic biological products and playing around with life is no child’s play hence, as aptly put by Voltaire and famously resonated on multiple<br />
occasions like in the blockbuster movie Spiderman, “With great power, comes great responsibility” . We realize that synthetic biology and the ability to<br />
manipulate biological systems is an exceptional power and on this platform of open source distribution of knowledge as provided by iGEM, it is important to<br />
use this tremendous power wisely.<br />
</p><br />
<p dir="ltr"><br />
Keeping this in mind, our team has designed novel genetic constructs that when used are agreeable to the environment, are safe, controllable, provide<br />
flexibility and yet, can be easily shared with and used by other enthusiasts of synthetic biology via this revolution in synthetic biology that is iGEM.<br />
</p><br />
<p dir="ltr"><br />
Our team project involves tackling the very complex problem of Shiga toxin by production of two very simple biomolecules – a 9 AA peptide sequence and a<br />
small biomolecule, indole-3-acetaldehyde. Both the deliverables of the project are environment friendly with no unforeseen ability to have any kind of<br />
negative impact.<br />
</p><br />
<p dir="ltr"><br />
The promoter system chosen for both the constructs is the pLuxR system so that the anti-toxin and the small molecule biofilm inhibitor are produced only in<br />
cattle rumen at the appropriate AHL concentration only. Theoretically, this allows endogenous control over the synthesis of final products in the cattle<br />
and practically, it allows us to precisely control how we produce our two potent biomolecules in the lab.<br />
</p><br />
<p dir="ltr"><br />
And finally, probably the most important aspects of our design is the flexibility that it offers in terms of sharing it with other synthetic biology<br />
enthusiasts and the ease with which they can modify our genetic constructs to meet their design requirements.<br />
</p><br />
<p dir="ltr"><br />
We have created a “Modular Plug-and-Play system” which simply means that we have designed our system in such a way that before every modular element used<br />
(RBS, Protein Coding Region and terminator) we have a restriction site before it so that individual parts can be isolated and different models of the same<br />
construct can be created based on the purposes of your experimentation. The introduction of restriction sites in the stuffer region between the RBS and<br />
Protein coding region for example allows you to choose and isolate these parts separately and design new constructs accordingly. A pictorial representation<br />
of the Plug-and-Play system has been given below for both the Gb3 construct and the I3A constructs and the use of restriction enzymes to create modular<br />
elements can be seen.<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/zhObwAdGNVoCYmbCukl-CkKvsaQSMa8PpgYK8mto1WFJzGB2D9Dvmj5GJcI1qgK85fd5ZqBgm3nekscAonHjQ8Q5bDoVjFflJqXXENFwdbZbGljFIFkLmN8p1KwcNzi-m5I"<br />
width="533px;"<br />
height="129px;"<br />
/><br />
<br/><br />
<img<br />
src="https://lh4.googleusercontent.com/GAhfsl96Uf6sm4U9cL9u1EV9RSGvnNZ6SiHw5a8w_RIlM1NPiUzRiUUz_nx7dUUSl5ykSF5BEonU4kC1dX5WubMlps2pCVtpX1tyNg21op4UwnBePOMC44QqEDvTZISd9qg"<br />
width="346px;"<br />
height="112px;"<br />
/><br />
<img<br />
src="https://lh5.googleusercontent.com/TrxaYR_HJK1F-Zmr0rkVifDwnoWHLeqGZ5kdYtAk_Xp3eC_4e8bv7h1ew_mNVzNpguOfm7r_8NRkqG_X3kVlUxAjw9VibvYbLgUdZtRLxXhNdYUOKdxwjcDGzE_5ZiR9FKI"<br />
width="213px;"<br />
height="104px;"<br />
/><br />
<p dir="ltr"><br />
Using different restriction enzymes, the modular elements can be plugged and played accordingly.<br />
</p><br />
<div><br />
<br/><br />
</div></div>JunaidBabu