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http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T04:03:22Z
<p>Jhonatan: </p>
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<h1><a href="#"></a></h1> <br />
<h2><span></span></h2><br />
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<br />
<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<p>Lissania Guerra-Calderas<br><br />
<br><br />
Contribution: Butanol Production Pathway, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="257" class="right"></p><br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés<br><br />
<p>Contribution: Project Management, design and development of regulatory systems, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos<br><br />
<p>Contribution: Characterization and measurement protocols, BioBrick Designer and outreach activities. <br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) <br><br />
Contact: maritere1011@hotmail.com.<br><br />
</p><br />
<p><br><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
</p><br />
<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute (IPN).<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer and outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute (IPN). ao.patricia@hotmail.com </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="155" height="215" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Contribution: Mathematical Modeling. Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD<br><br />
<p>Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD<br><br />
<p>Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<p>&nbsp;</p><img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute (IPN).</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD<br><br />
<p>Resarcher 3A, SNI II. Leader instructor; he has a PhD in biochemical sciences from Institute for Biotechnology of National Autonomous University of Mexico (UNAM). He is the current leader of Systems and Synthetic Biology Lab in CINVESTAV Irapuato. His research interest is focused in the perception of environmental signals, information processing and transcriptional regulation in bacteria model, topological analysis, dynamic and modeling of biological networks, the design and construction of circuits, modules and genetic and metabolic systems, and the design and construction of self-replicating molecular and autoreproducible systems. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD<br><br />
<p>Researcher at Institute of Cell Physiology IFC-UNAM.<br />
He is an expert in Purple Non-Sulfur Photosynthetic Bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig PhD<br><br />
<p>Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura<br><br />
<p>Researcher, Dra. Zárate Segura belong to Interdisciplinary Unit for Biotechnology, IPN </p><br />
<p>&nbsp;</p><br />
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<li><a href="Gallery.htm">Gallery</a></li><br />
<li><a href="Acknowledgments.htm">Acknowledgments</a></li><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T04:02:04Z
<p>Jhonatan: </p>
<hr />
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<div id="context"> <br />
<br />
<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<p>Lissania Guerra-Calderas<br><br />
<br><br />
Contribution: Butanol Production Pathway, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="257" class="right"></p><br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés<br><br />
<p>Contribution: Project Management, design and development of regulatory systems, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos<br><br />
<p>Contribution: Characterization and measurement protocols, BioBrick Designer and outreach activities. <br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) <br><br />
Contact: maritere1011@hotmail.com.<br><br />
</p><br />
<p><br><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
</p><br />
<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute (IPN).<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer and outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute (IPN). ao.patricia@hotmail.com </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="155" height="215" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Contribution: Mathematical Modeling. Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD<br><br />
<p>Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD<br><br />
<p>Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<p>&nbsp;</p><img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute (IPN).</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD<br><br />
<p>Resarcher 3A, SNI II. Leader instructor; he has a PhD in biochemical sciences from Institute for Biotechnology of National Autonomous University of Mexico (UNAM). He is the current leader of Systems and Synthetic Biology Lab in CINVESTAV Irapuato. His research interest is focused in the perception of environmental signals, information processing and transcriptional regulation in bacteria model, topological analysis, dynamic and modeling of biological networks, the design and construction of circuits, modules and genetic and metabolic systems, and the design and construction of self-replicating molecular and autoreproducible systems. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD Researcher at Institute of Cell Physiology IFC-UNAM.<br />
He is an expert in Purple Non-Sulfur Photosynthetic Bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura PhD Researcher, at IPN. Dra. Zárate Segura has a PhD in Bioprocess from Interdisciplinary Unit for Biotechnology, National Polytechnic Institute. </p><br />
<p>&nbsp;</p><br />
</div><br />
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<li><a href="Acknowledgments.htm">Acknowledgments</a></li><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T04:00:06Z
<p>Jhonatan: </p>
<hr />
<div><html xmlns="http://www.w3.org/1999/xhtml"><br />
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<!-- end #header --><br />
<div id="page"><br />
<div id="context"> <br />
<br />
<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<p>Lissania Guerra-Calderas<br><br />
<br><br />
Contribution: Butanol Production Pathway, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="257" class="right"></p><br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés<br><br />
<p>Contribution: Project Management, design and development of regulatory systems, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos<br><br />
<p>Contribution: Characterization and measurement protocols, BioBrick Designer and outreach activities. <br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) <br><br />
Contact: maritere1011@hotmail.com.<br><br />
</p><br />
<p><br><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
</p><br />
<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute (IPN).<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer and outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute (IPN). ao.patricia@hotmail.com </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="155" height="215" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Contribution: Mathematical Modeling. Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<p>&nbsp;</p><img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute (IPN).</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD Resarcher 3A, SNI II. Leader instructor; he has a PhD in biochemical sciences from Institute for Biotechnology of National Autonomous University of Mexico (UNAM). He is the current leader of Systems and Synthetic Biology Lab in CINVESTAV Irapuato. His research interest is focused in the perception of environmental signals, information processing and transcriptional regulation in bacteria model, topological analysis, dynamic and modeling of biological networks, the design and construction of circuits, modules and genetic and metabolic systems, and the design and construction of self-replicating molecular and autoreproducible systems. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD Researcher at Institute of Cell Physiology IFC-UNAM.<br />
He is an expert in Purple Non-Sulfur Photosynthetic Bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura PhD Researcher, at IPN. Dra. Zárate Segura has a PhD in Bioprocess from Interdisciplinary Unit for Biotechnology, National Polytechnic Institute. </p><br />
<p>&nbsp;</p><br />
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<li><a href="Gallery.htm">Gallery</a></li><br />
<li><a href="Acknowledgments.htm">Acknowledgments</a></li><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T03:58:11Z
<p>Jhonatan: </p>
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<br />
<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<p>Lissania Guerra-Calderas<br><br />
<br><br />
Contribution: Butanol Production Pathway, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="235" class="right"></p><br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés<br><br />
<p>Contribution: Project Management, design and development of regulatory systems, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos<br><br />
<p>Contribution: Characterization and measurement protocols, BioBrick Designer and outreach activities. <br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) <br><br />
Contact: maritere1011@hotmail.com.<br><br />
</p><br />
<p><br><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
</p><br />
<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute (IPN).<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer and outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute (IPN). ao.patricia@hotmail.com </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="174" height="243" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Contribution: Mathematical Modeling. Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<p>&nbsp;</p><img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute (IPN).</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD Resarcher 3A, SNI II. Leader instructor; he has a PhD in biochemical sciences from Institute for Biotechnology of National Autonomous University of Mexico (UNAM). He is the current leader of Systems and Synthetic Biology Lab in CINVESTAV Irapuato. His research interest is focused in the perception of environmental signals, information processing and transcriptional regulation in bacteria model, topological analysis, dynamic and modeling of biological networks, the design and construction of circuits, modules and genetic and metabolic systems, and the design and construction of self-replicating molecular and autoreproducible systems. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD Researcher at Institute of Cell Physiology IFC-UNAM.<br />
He is an expert in Purple Non-Sulfur Photosynthetic Bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura PhD Researcher, at IPN. Dra. Zárate Segura has a PhD in Bioprocess from Interdisciplinary Unit for Biotechnology, National Polytechnic Institute. </p><br />
<p>&nbsp;</p><br />
</div><br />
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<div id="updates" class="orangebox"><br />
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<ul><br />
<li><a href="Members.htm" target="_parent">Members</a></li><br />
<li><a href="Institute.htm">Institute</a></li><br />
<li><a href="Gallery.htm">Gallery</a></li><br />
<li><a href="Acknowledgments.htm">Acknowledgments</a></li><br />
</ul><br />
<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T03:56:16Z
<p>Jhonatan: </p>
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<br />
<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<p>Lissania Guerra-Calderas<br><br />
<br><br />
Contribution: Butanol Production Pathway, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="235" class="right"></p><br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés<br><br />
<p>Contribution: Project Management, design and development of regulatory systems, BioBrick Designer and outreach activities.<br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM)<br><br />
Contact: jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos<br><br />
<p>Contribution: Characterization and measurement protocols, BioBrick Designer and outreach activities. <br><br />
4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) <br><br />
Contact: maritere1011@hotmail.com.<br><br />
</p><br />
<p><br><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
</p><br />
<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute (IPN).<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer and outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute (IPN). ao.patricia@hotmail.com </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="174" height="243" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
<p>Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Contribution: Mathematical Modeling. Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<p>&nbsp;</p><img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute (IPN).</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD Resarcher 3A, SNI II. Leader instructor; he has a PhD in biochemical sciences from Institute for Biotechnology of National Autonomous University of Mexico (UNAM). He is the current leader of Systems and Synthetic Biology Lab in CINVESTAV Irapuato. His research interest is focused in the perception of environmental signals, information processing and transcriptional regulation in bacteria model, topological analysis, dynamic and modeling of biological networks, the design and construction of circuits, modules and genetic and metabolic systems, and the design and construction of self-replicating molecular and autoreproducible systems. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD Researcher at Institute of Cell Physiology IFC-UNAM.<br />
He is an expert in Purple Non-Sulfur Photosynthetic Bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura PhD Researcher, at IPN. Dra. Zárate Segura has a PhD in Bioprocess from Interdisciplinary Unit for Biotechnology, National Polytechnic Institute. </p><br />
<p>&nbsp;</p><br />
</div><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/oxigenresponse.htm
Team/CINVESTAV-IPN-UNAM MX/oxigenresponse.htm
2012-10-27T03:36:58Z
<p>Jhonatan: </p>
<hr />
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<br />
<h1><em>Oxygen Control System!</em></h1><br />
<p id="text2"> PrrA/PrrB two component system</p><br />
<p>This system remains inactive under high oxygen tension, when oxygen<br />
concentration decreases, it is possible the GFP transcription. (See Rhodofactory section for<br />
a complete explanation).<br><br><br />
<br />
We made two BioBricks (BBa_K776019 y BBa_K776021) to test the Oxygen<br />
Control System, each one has GFP as a reporter gene and the functionality was related to<br />
the fluorescence detection.</p><br />
<div align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/c/c5/Osy01.jpg"><br />
<p>Figure 1. This BioBrick will show if our dependent promoter is functional, using the<br />
constitutive (or natural) system from <em>R. sphaeroides</em> or the orthologue system from <em>R.<br />
palustris.</em></p><br />
</div><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/0/06/Osy02.jpg" width="562" height="192"><br />
<p>Figure 2. This BioBrick will show if our complete system is functional because probably<br />
we need a synthetic system to promote GFP expression by binding its target sequence<br />
(dependent promoter) in <em>R. palustris.</em></p><br />
</div><br />
<p>Both systems were cloned in pRK415 because this is a vector for Purple Non-Sulfur<br />
Photosynthetic Bacteria, the plasmids were introduced in <em>R. sphaeroides</em> and <em>R. palustris</em>,<br />
by biparental and triparental conjugation.</p><br />
<p>The measurement approach we used was:<br />
<li>Fluorescence Microscopy: To have a qualitative detection of GFP in these bacteria.</li><br />
<li>Flow Cytometry: To have a quantitative detection of GFP expression, we calculated the<br />
percentage of bacterial population expressing GFP (GFP+) in 1000 bacteria.</li><br><br />
</p><br />
<p>We used 3 environmental growing conditions:<br />
<li>Aerobic/Darkness</li><br />
<li>Anaerobic/Light</li><br />
<li>Anaeroibic/darkness</li></p><br />
<p>For all data results, we considered a negative control: <em>Rhodobacter sphaeroides</em> or <em>Rhodopseudomonas palustris</em>, conjugated bacteria with pRK415 vector without BioBrick.</p> <br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/7/73/Osy03.jpg" width="563" height="452"><br />
<img src="https://static.igem.org/mediawiki/2012/e/ec/Osy04.jpg" width="563" height="452"><br />
<p>Figure 3. Percentage of bacterial population expressing GFP.<br><br />
</p><br />
</div><br />
<div align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/Osy05.jpg" width="556" height="384"><br />
<p>Figure 4. Representative images obtained by fluorescence microscopy, where our systems<br />
were functional in the expected conditions.</p><br />
</div><br />
<p id="text2">Discussion</p><br />
<p>In <em>R. sphaeroides</em>, as we can see in figure 3 and 4, there was low GFP expression, probably<br />
because growing conditions were microaerophilic instead of extrictly anaerobic. In<br />
anaerobic conditions PrrB autophosphorylates and passes a phosphate group to PrrA, this<br />
activated PrrA binds its promoter sequence to start GFP expression. Furthermore, when<br />
we introduced the complete system (BBa_K776021), actually we are overexpressing the<br />
regulatory proteins and the signaling could not be fully controlled.<br><br />
<br><br />
<br />
In <em>R. palustris</em>, we had GFP expression in PrrA dependent promoter (BBa_K776019), maybe<br />
because orthologous proteins activated it. The complete system (BBa_K776021) also<br />
was functional but in a lower level, assumably due to the interference of other proteins that regulate photosynthetic genes.<br><br />
<br> <br />
The GFP expression that we did not expected was in aerobic condition in the complete system, probably<br />
is due to the complexity of the regulatory network where this system is involved.<br />
</p><br />
<p id="text2">Conclusion</p><br />
<p> Our two BioBricks (K776019 and BBa_K776021) are functional in two photosynthetic<br />
bacteria <em>R. palustris</em> and <em>R. sphaeroides</em>, both in anaerobic/light expected condition. This is a functional system for controlling genetic<br />
expression with Oxygen tension.</p><br />
<br />
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<br />
<h2>Results</h2><br />
<ul><br />
<li><a href="Biobricks.htm" target="_parent">Biobricks</a></li><br />
<li><a href="Lightandoxre.htm">Light and oxygen response</a></li><br />
<li><a href="Notebook.htm">Notebook</a></li><br />
<li><a href="oxigenresponse.htm">Oxygen response</a></li><br />
<li><a href="Protocol.htm">Protocols</a></li><br />
</ul><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Biobricks.htm
Team/CINVESTAV-IPN-UNAM MX/Biobricks.htm
2012-10-27T03:35:33Z
<p>Jhonatan: </p>
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<h1><em>Biobricks!</em></h1><br />
<p id="text2">Favorite</p><br />
<table border="1" align="center" cellpadding="0" cellspacing="0" bordercolor="#999999"><br />
<tr><br />
<td width="140" bgcolor="#1054BB"><p align="center" class="Estilo2">&nbsp;<u>Name</u></p> </td><br />
<td width="115" bgcolor="#1054BB"><p align="center" class="Estilo2">Type</p></td><br />
<td width="106" bgcolor="#1054BB"><p align="center" class="Estilo2">Description</p></td><br />
<td width="139" bgcolor="#1054BB"><p align="center" class="Estilo2">Desing by</p></td><br />
<td width="58" bgcolor="#1054BB"><p align="center" class="Estilo2">Lenght (bp)</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776018">BBa_K776018</a><u> </u></p><br />
</td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">PpsR Promoter + GFP</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
<td><p align="center">1140</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776019">BBa_K776019</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">PrrA promoter + GFP</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
<td><p align="center">1070</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776020">BBa_K776020</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Complete system (concentration dependent promoter Light)</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
<td><p align="center">4060</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776021">BBa_K776021</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Complete system (dependent promoter oxygen concentration)</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
<td><p align="center">3865</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776027">BBa_K776027</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23101</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776028">BBa_K776028</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23102</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776029">BBa_K776029</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23104</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776030">BBa_K776030</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23107</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776031">BBa_K776031</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23108</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776032">BBa_K776032</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23111</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong>W </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776033">BBa_K776033</a><u> </u></p> </td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Measurement Kit J23115</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
<td><p align="center">970</p></td><br />
</tr><br />
</table><br />
<br><br />
<br><br />
<br />
<hr><br />
<p id="text2">Other parts</p><br />
<table border="1" cellpadding="0" cellspacing="0" bordercolor="#999999"><br />
<tr><br />
<td width="116" bgcolor="#1054BB"><p align="center" class="Estilo3"><u>Name </u></p></td><br />
<td width="134" bgcolor="#1054BB"><p align="center" class="Estilo3">Type</p></td><br />
<td width="152" bgcolor="#1054BB"><p align="center" class="Estilo3">Description</p></td><br />
<td width="158" bgcolor="#1054BB"><p align="center" class="Estilo3">Desing by</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776000">BBa_K776000</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PpsR Promoter</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776001">BBa_K776001</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PrrA Promoter</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776002">BBa_K776002</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PrrA</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776003">BBa_K776003</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PrrB</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776004">BBa_K776004</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PrrC</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776005">BBa_K776005</a></strong><strong> </strong></p></td><br />
<td><p align="center">Coding</p></td><br />
<td><p align="center">PpsR</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776006">BBa_K776006</a></strong><strong> </strong></p></td><br />
<td><p align="center">Translational_Unit</p></td><br />
<td><p align="center">RBS + PrrA</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776007">BBa_K776007</a></strong><strong> </strong></p></td><br />
<td><p align="center">Translational_Unit</p></td><br />
<td><p align="center">RBS + PrrB</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776008">BBa_K776008</a></strong><strong> </strong></p></td><br />
<td><p align="center">Translational_Unit</p></td><br />
<td><p align="center">RBS + PrrC</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776009">BBa_K776009</a></strong><strong> </strong></p></td><br />
<td><p align="center">Translational_Unit</p></td><br />
<td><p align="center">RBS + AppA</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776010">BBa_K776010</a></strong><strong> </strong></p></td><br />
<td><p align="center">Translational_Unit</p></td><br />
<td><p align="center">RBS + PpsR</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776011">BBa_K776011</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">PrrA/PrrB</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776012">BBa_K776012</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">PrrC DT</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776013">BBa_K776013</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">Prom J23104 + AppA</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776014">BBa_K776014</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">PpsR DT</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776015">BBa_K776015</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">PrrA/PrrB/PrrC</p></td><br />
<td><p align="center">Lissania Ximena Guerra-Calderas</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776016">BBa_K776016</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">Prom J23104 + AppA + PpsR + DT</p></td><br />
<td><p align="center">Jhonatan Alejandro Hernandez-Valdes</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776017">BBa_K776017</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">Prom J23104 + PrrA + PrrB + PrrC + DT</p></td><br />
<td><p align="center">Patricia Elizabeth Arias Orozco</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776022">BBa_K776022</a></strong><strong> </strong></p></td><br />
<td><p align="center">Intermediate</p></td><br />
<td><p align="center">AppA-PpsR-ETFA/ETFB</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776023">BBa_K776023</a></strong><strong> </strong></p></td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">EAB ABC</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776024">BBa_K776024</a></strong><strong> </strong></p></td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">PrrA Promotor BB DT</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776025">BBa_K776025</a></strong><strong> </strong></p></td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">Complete system (Promoter PpSR)</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
<tr><br />
<td><p align="center"><strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K776026">BBa_K776026</a></strong><strong> </strong></p></td><br />
<td><p align="center">Composite</p></td><br />
<td><p align="center">System ABC BB EA</p></td><br />
<td><p align="center">Maritere Uriostegui-Arcos</p></td><br />
</tr><br />
</table><br />
<p>&nbsp;</p><br />
</div><br />
<div id="sidebar"><br />
<div id="updates" class="orangebox"><br />
<br />
<h2>Results</h2><br />
<ul><br />
<li><a href="Biobricks.htm" target="_parent">Biobricks</a></li><br />
<li><a href="Lightandoxre.htm">Light and oxygen response</a></li><br />
<li><a href="Notebook.htm">Notebook</a></li><br />
<li><a href="oxigenresponse.htm">Oxygen response</a></li><br />
<li><a href="Protocol.htm">Protocols</a></li><br />
</ul><br />
</div><br />
</div> <br />
<div style="clear: both;">&nbsp;</div><br />
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<p align="center"> <strong>Rhodofactory 2012</strong> </p><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Construction.htm
Team/CINVESTAV-IPN-UNAM MX/Construction.htm
2012-10-27T03:34:10Z
<p>Jhonatan: </p>
<hr />
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<h1><em>Construction!</em></h1><br />
<p id="text2"> iGEM PROMOTER CHARACTERIZATION</p><br />
<br />
<p>We need to use a medium strength promoter for our constructions, so we characterize different promoters constitutive belonging to the isolated family from Anderson collection (J23101, J23102, J23104, J23107, J23108, J2311, and J23115) these promoters were assemble with GFP to determine promoter strength, using Victor X3 Multilabel Plate Reader.<br><br />
<br><br />
<img src="https://static.igem.org/mediawiki/2012/e/e8/Pfigura1.jpg" alt="figura1" width="570" height="180"></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/0/03/Pfigura2.jpg" alt="figura2" width="394" height="179"><br><br />
<br><br />
<img src="https://static.igem.org/mediawiki/2012/3/39/PFigura3.jpg" alt="Figura3" width="566" height="328"> </div><br />
<br><br />
<div align="center"></div><br />
<br><br />
<p id="text2"> Result</p><br />
<p>The characterization of the BioBricks shown in the following table:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/0/02/PFigura4.jpg" alt="Figura4" width="349" height="157"></div><br />
<br><br />
<img src="https://static.igem.org/mediawiki/2012/5/5b/PFigura5.jpg" alt="Figura5" width="282" height="477" class="left"><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>The constructions that were made, were confirmed by double digestions. The following image shows a gel double digestion with XbaI and SpeI for confirmatory promoter constructs:</p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<p>The constructions were cultivated in LB petri dishes with chloramphenicol and they were observated at UV light after it’s incubation.</p><br />
<div align="center"><br />
<p><img src="https://static.igem.org/mediawiki/2012/7/7a/PFigura6.jpg" alt="Figura6" width="263" height="247" class="left"><img src="https://static.igem.org/mediawiki/2012/e/e4/PFigura7.jpg" alt="Figura7" width="249" height="248" > <img src="https://static.igem.org/mediawiki/2012/0/0b/PFigura8.jpg" width="397" height="384"></p><br><br />
</div><br />
<p>In the following graphs there is shown the GFP expression in function of th time and the realtive promoter force. </p><img src="https://static.igem.org/mediawiki/2012/7/72/PFigura9.jpg" alt="Figura9" width="563" height="345"><br />
<br />
<p><br><br />
With the previous results of the characterization of the promoters there is concluded that the promoter J23107, is the strongest because it produces more RPUs.<br><br><br />
After characterization, J23104 promoter was chosen for construction of the system of regulation of light and oxygen dependent.</p><br />
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http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Light_Response.htm
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<p>Jhonatan: </p>
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<h1><em>Light & Oxygen Response: AppA/PpsR <br /><br />Regulation System! </em></h1><br />
<p>This is a repressor/antirepressor system, which under high oxygen tension; PpsR represses GFP expression by avoiding RNA polymerase binding <br />
the promoter sequence.<br />
When oxygen concentration decreases and in presence of light AppA has a conformational change and can bind with PpsR, this complex prevents the union of<br />
PpsR to its target sequence, thus GFP expression can begin.<br><br />
<br />
(See the next video for a visual explanation).</p><br />
<div align="center"><iframe width="480" height="360" src="http://www.youtube.com/embed/XBNRLq9pL8c" frameborder="0" allowfullscreen></iframe></div><br><br />
<p id="text2">Our biobricks </p><br />
<p>The first biobrick consists in the complete light-oxygen dependent system, AppA and PpsR, each one with Ribosome Binding Site, under a<br />
Medium strength promoter (J23104), this first biobrick also it has the PpsR dependent promoter and GFP as a reporter gene.</p><br />
<img src="https://static.igem.org/mediawiki/2012/b/b6/Rodo02.jpg" alt="rodo02" width="568" height="107"><br><br />
<p><br><br />
The second circuit is just the PpsR dependent promoter and GFP as a reporter gene.</p><br />
<img src="https://static.igem.org/mediawiki/2012/a/a1/Rodo03.jpg" alt="rodo03" width="562" height="252"><br />
<p id="text2">We were inspired in:</p><br />
<p><br />
This system is inspired in AppA/PpsR repressor/antirepressor system from Rhodobacter sphaeroides. The PpsR protein is a master repressor of<br />
Photosynthesis (PS) genes (Moskvin and Gomelsky 2005). Inactivation of the ppsR gene is enough to turn on PS gene expression and formation<br />
of the photosynthetic apparatus even at a high oxygen concentration, whereas ppsR overexpression is sufficient to block PS development even<br />
in the absence of oxygen. PpsR directly represses transcription of most carotenoid and pigment synthesis genes, photosystems operons, and<br />
genes involved in tetrapyrrole biosynthesis (Gomelsky and Kaplan 1995). The upstream regions of these genes contain two PpsR binding sites,<br />
TGTcN10gACA.<br><br><br />
<br />
A second protein called AppA, which has no known homologues, plays a role in controlling gene expression in <em>R. sphaeroides</em> in response to both<br />
light and O2 by acting as an antirepressor of PpsR. Our parts (appa, ppsr and ppsr-promoter) were synthesized by Genescript, and are codon<br />
optimized for <em>R. sphaeroides.</em></p><br />
<hr><br />
<p id="refe">References<br><br />
<br />
1. Gomelsky L., Moskvin L., Stenzel A., Jones D., Donohue T. and Gomelsky M.(2008) <strong>Hierarchical Regulation of Photosynthesis<br />
Gene Expression by the Oxygen-Responsive PrrBA and AppA-PpsR Systems of <em>Rhodobacter sphaeroides.</em></strong> J. Bacteriol.<br />
Dec. 2008, p. 8106–8114 Vol. 190, No. 24<br><br />
<br />
2. Moskvin, O. V., L. Gomelsky, and M. Gomelsky. (2005). <strong>Transcriptome analysis of the <em>Rhodobacter sphaeroides</em> PpsR<br />
regulon: PpsR as a master regulator of photosystem development.</strong> J. Bacteriol. 187:2148–2156.<br><br />
<br />
3. Gomelsky, M., and S. Kaplan. (1995). <strong>Genetic evidence that PpsR from <em>Rhodobacter sphaeroides.</em> 2.4.1 functions as a<br />
repressor of puc and bchF expression.</strong> J. Bacteriol. 177:1634–1637. <br><br />
4. Gomelsky, M., and S. Kaplan. (1995). <strong>AppA, a novel gene encoding a transacting factor involved in the regulation of<br />
photosynthesis gene expression in <em>Rhodobacter sphaeroides.</em> 2.4.1.</strong> J. Bacteriol. 177:4609–4618.<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Overview.htm
Team/CINVESTAV-IPN-UNAM MX/Overview.htm
2012-10-27T03:30:11Z
<p>Jhonatan: </p>
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<h1><em>Overview! </em></h1><br />
<p>The purple non-sulfur photosynthetic bacteria (PNSB) belong to the alpha-proteobacteria group, because of their genetic regulatory systems<br />
which coordinate different metabolic states, these microorganisms are able to grow under a wide variety of environmental conditions (1).<br><br><br />
<br />
Specifically, our project aims to isolate two genetic control systems based on <em>Rhodobacter sphaeroides</em> photosynthesis cluster regulation. The first one is the<br />
oxygen dependant system PrrA/PrrB, when oxygen tension is high it remains inactive, and when the oxygen is low it activates gene expression<br />
(2). The second system is the light and oxygen mediated system AppA/PpsR that represses gene expression under aerobic conditions and allows<br />
transcription in the absence of oxygen and presence light (3).<br><br><br />
<br />
To achieve this goal we designed two genetic biobrick in which GFP expression is oxygen and light-dependent by the antirepression of PpsR and<br />
oxygen dependent by the activation of PrrA/B system. The lab work is accompanied by a computational model, which will provide a way of<br />
testing our knowledge of these systems.<br><br><br />
<br />
Once, we have characterized the functionality of these regulatory systems we aim to take advantage of <em>Rhodopseudomonas palustris’</em> metabolic versatility, and use<br />
this bacteria as a microbial factory, that could work for the production of metabolites with economic value products using CO2 as carbon source.<br><br><br />
<br />
We are planning to use the S04147 clostridial butanol production operon (University of Alberta iGEM Team 2007) to evaluate the synthesis of<br />
this biofuel, linking it to our control systems. This would provide an interesting way to produce butanol using CO2 as carbon source under<br />
anaerobic photosynthetic conditions.</p><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Rule-Based.htm
Team/CINVESTAV-IPN-UNAM MX/Rule-Based.htm
2012-10-27T01:36:18Z
<p>Jhonatan: </p>
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<h1><em>Simulation of Promoters behavior using a <br /><br />Rule-Based model.!</em></h1><br />
<p>Like we said before the proteins in our regulatory system PpsR, AppA and PrrA belong to<br />
acomplex regulatory network and they all work together to control genetic expression and<br />
induce all the metabolic changes in Rhodobacter sphaeroides.<br><br><br />
<br />
<br />
We already developed one model based on ODEs, but since this is the first time there has<br />
been an attempted to build BioBricks using photosynthetic bacteria, we wanted to try<br />
another model to simulate promoters behavior under the same conditions that were tested<br />
in the lab and see if they correlated.<br><br><br />
<br />
<br />
Using a rule-based model we were able to evaluate site specific details about protein-<br />
protein interaction and for this part we focused mainly on interactions of the domains<br />
between PpsR, AppA and PrrA.<br><br><br />
<br />
<br />
The following scheme, Figure 1, shows a complex network, in where our main proteins are<br />
involved and the intermediate molecules that help establish the interactions. And the<br />
Figure 2, shows the reduced and oxidized form of AppA and PpsR.</p><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/Rule01.jpg" width="284" height="296"><img src="https://static.igem.org/mediawiki/2012/4/4e/Rule02.jpg" width="284" height="296"><br />
<p>Simulation of Promoters behavior using a Rule- Based model.<br />
Like we said before the proteins in our regulatory system PpsR, AppA and PrrA belong to<br />
acomplex regulatory network and they all work together to control genetic expression and<br />
induce all the metabolic changes in Rhodobacter sphaeroides.<br />
We already developed one model based on ODEs, but since this is the first time there has<br />
been an attempted to build BioBricks using photosynthetic bacteria, we wanted to try<br />
another model to simulate promoters behavior under the same conditions that were tested<br />
in the lab and see if they correlated.<br />
Using a rule-based model we were able to evaluate site specific details about protein-<br />
protein interaction and for this part we focused mainly on interactions of the domains<br />
between PpsR, AppA and PrrA.<br />
The following scheme, Figure 1, shows a complex network, in where our main proteins are<br />
involved and the intermediate molecules that help establish the interactions. And the<br />
Figure 2, shows the reduced and oxidized form of AppA and PpsR.<br />
<strong><br><br />
<br><br />
The tetramers with intramolecular disulfide bonds (S-S)</strong> and thiol groups (SH) denote the<br />
oxidized and the reduced form of the PpsR repressor, respectively. The AppA protein has<br />
an FAD and a heme cofactor attached where h+ and h–denote the oxidized and reduced<br />
form of the heme cofactor (TspO).</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/08/Rule03.jpg" width="566" height="379"><br />
<p>Aerobically, the volume of electron flow through the cbb3 oxidase is sufficient to generate an<br />
inhibitory signal keeping the PrrBA system inactive and no GFP expression, because the Quinone<br />
Pool is maximally oxidized, which is mirrored in the redox state of AppA, keeping PpsR active.<br><br />
<br><br />
<br />
As O2 tensions diminish, the volume of electron flow through the cbb3 oxidase decreases as well<br />
and the PrrBA system becomes active through an autophosphorylation of PrrB and transfer of this<br />
phosphate group to PrrA.</p><br />
<p id="text2">Parameters:</p><br />
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<p>Reference: <a href="http://bionumbers.hms.harvard.edu/" target="_blank">http://bionumbers.hms.harvard.edu/</a> and literature, the rest of the constants were<br />
assumed second-order rate constants.</p><br />
<p id="text2">Model Construction</p><br />
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<p id="text2">Overall conclusion about the models.</p><br />
<p>Well, but we have two almost completely different models, the question is why use two<br />
models for the same phenomenon? Well, that's because the perspective of each model,<br />
the pros and cons of them. Using two models gives us the opportunity to see two<br />
perspectives that help us understand the phenomenon.<br><br />
<br><br />
<br />
On one hand, the differential equations describing protein concentrations and its<br />
relationship to oxygen and light, while the rule-based model allows us to observe<br />
interactions between molecules, considering agents in agents in a confined space. In other<br />
words, the first model allows us to see the system as a whole while the latter sees it as the<br />
aggregation of various agents.</p><br />
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<li><a href="Differential.htm">Differential equations modeling</a></li><br />
<li><a href="Rule-Based.htm">Rule-Based model</a></li><br />
<li><a href="Cellular.htm">Cellular Automata</a></li><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Rule-Based.htm
Team/CINVESTAV-IPN-UNAM MX/Rule-Based.htm
2012-10-27T01:35:51Z
<p>Jhonatan: </p>
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<h1><em>Simulation of Promoters behavior using a Rule-Based model.!</em></h1><br />
<p>Like we said before the proteins in our regulatory system PpsR, AppA and PrrA belong to<br />
acomplex regulatory network and they all work together to control genetic expression and<br />
induce all the metabolic changes in Rhodobacter sphaeroides.<br><br><br />
<br />
<br />
We already developed one model based on ODEs, but since this is the first time there has<br />
been an attempted to build BioBricks using photosynthetic bacteria, we wanted to try<br />
another model to simulate promoters behavior under the same conditions that were tested<br />
in the lab and see if they correlated.<br><br><br />
<br />
<br />
Using a rule-based model we were able to evaluate site specific details about protein-<br />
protein interaction and for this part we focused mainly on interactions of the domains<br />
between PpsR, AppA and PrrA.<br><br><br />
<br />
<br />
The following scheme, Figure 1, shows a complex network, in where our main proteins are<br />
involved and the intermediate molecules that help establish the interactions. And the<br />
Figure 2, shows the reduced and oxidized form of AppA and PpsR.</p><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/Rule01.jpg" width="284" height="296"><img src="https://static.igem.org/mediawiki/2012/4/4e/Rule02.jpg" width="284" height="296"><br />
<p>Simulation of Promoters behavior using a Rule- Based model.<br />
Like we said before the proteins in our regulatory system PpsR, AppA and PrrA belong to<br />
acomplex regulatory network and they all work together to control genetic expression and<br />
induce all the metabolic changes in Rhodobacter sphaeroides.<br />
We already developed one model based on ODEs, but since this is the first time there has<br />
been an attempted to build BioBricks using photosynthetic bacteria, we wanted to try<br />
another model to simulate promoters behavior under the same conditions that were tested<br />
in the lab and see if they correlated.<br />
Using a rule-based model we were able to evaluate site specific details about protein-<br />
protein interaction and for this part we focused mainly on interactions of the domains<br />
between PpsR, AppA and PrrA.<br />
The following scheme, Figure 1, shows a complex network, in where our main proteins are<br />
involved and the intermediate molecules that help establish the interactions. And the<br />
Figure 2, shows the reduced and oxidized form of AppA and PpsR.<br />
<strong><br><br />
<br><br />
The tetramers with intramolecular disulfide bonds (S-S)</strong> and thiol groups (SH) denote the<br />
oxidized and the reduced form of the PpsR repressor, respectively. The AppA protein has<br />
an FAD and a heme cofactor attached where h+ and h–denote the oxidized and reduced<br />
form of the heme cofactor (TspO).</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/08/Rule03.jpg" width="566" height="379"><br />
<p>Aerobically, the volume of electron flow through the cbb3 oxidase is sufficient to generate an<br />
inhibitory signal keeping the PrrBA system inactive and no GFP expression, because the Quinone<br />
Pool is maximally oxidized, which is mirrored in the redox state of AppA, keeping PpsR active.<br><br />
<br><br />
<br />
As O2 tensions diminish, the volume of electron flow through the cbb3 oxidase decreases as well<br />
and the PrrBA system becomes active through an autophosphorylation of PrrB and transfer of this<br />
phosphate group to PrrA.</p><br />
<p id="text2">Parameters:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4e/Rule04.jpg" width="566"><br />
</div><br />
<p>Reference: <a href="http://bionumbers.hms.harvard.edu/" target="_blank">http://bionumbers.hms.harvard.edu/</a> and literature, the rest of the constants were<br />
assumed second-order rate constants.</p><br />
<p id="text2">Model Construction</p><br />
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<p id="text2">Overall conclusion about the models.</p><br />
<p>Well, but we have two almost completely different models, the question is why use two<br />
models for the same phenomenon? Well, that's because the perspective of each model,<br />
the pros and cons of them. Using two models gives us the opportunity to see two<br />
perspectives that help us understand the phenomenon.<br><br />
<br><br />
<br />
On one hand, the differential equations describing protein concentrations and its<br />
relationship to oxygen and light, while the rule-based model allows us to observe<br />
interactions between molecules, considering agents in agents in a confined space. In other<br />
words, the first model allows us to see the system as a whole while the latter sees it as the<br />
aggregation of various agents.</p><br />
</div><br />
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<h2>Modeling</h2><br />
<ul><br />
<li><a href="Tools.htm" target="_parent">Tools we used</a></li><br />
<li><a href="Differential.htm">Differential equations modeling</a></li><br />
<li><a href="Rule-Based.htm">Rule-Based model</a></li><br />
<li><a href="Cellular.htm">Cellular Automata</a></li><br />
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Jhonatan
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2012-10-27T01:32:54Z
<p>Jhonatan: </p>
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Jhonatan
http://2012.igem.org/File:Graficas.swf
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2012-10-27T01:32:20Z
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Jhonatan
http://2012.igem.org/File:Modeloconstruccion.swf
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2012-10-27T01:31:42Z
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Jhonatan
http://2012.igem.org/File:Rule04.jpg
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2012-10-27T01:30:57Z
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Jhonatan
http://2012.igem.org/File:Rule03.jpg
File:Rule03.jpg
2012-10-27T01:30:23Z
<p>Jhonatan: </p>
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Jhonatan
http://2012.igem.org/File:Rule02.jpg
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2012-10-27T01:29:51Z
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Jhonatan
http://2012.igem.org/File:Rule01.jpg
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2012-10-27T01:29:26Z
<p>Jhonatan: </p>
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Cellular.htm
Team/CINVESTAV-IPN-UNAM MX/Cellular.htm
2012-10-27T01:26:24Z
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<h1><em>Strange variant of cellular automata for <br /><br />the simulation of a bio-reactor!</em></h1><br />
<br />
<p id="text2">Introduction</p><br />
<p><br />
First of all: why use cellular automata if any linear models are easier to analyze? Well, first it looks great.<br />
</p><center><br />
<img src="https://static.igem.org/mediawiki/2012/5/50/CA1.gif" alt="This look great, no?"></center><br />
<p>Second, depending on the configuration of the Cellular Automaton(CA) "how do you look", the CA is more realistic and we it can provide enough data for other models. In fact, is just what took place in this model.<br />
</p><p>Imagine that we are scientists with more resources in the world and that we can generate hundreds of experiments in the conditions we want to feed our prediction models. The CA allows us to do this with the only drawback that we hate our CPU.<br />
</p><h2>Brief History</h2><br />
<p>Cellular automata are a mathematical model developed by Konrad Zuse and Stanislaw Ulam, but was better known and developed by a guy named John Vonn Neumann who loved parallel computing, but, as usual, history remembers him as the father of sequential computing.<br />
</p><p>Later, during the disruptive and flowery decade of 60's, a crazy mathematical said "oh, it would be great to do a math game where no players" (you know, the time before tetris and farmville), and created the world famous "Game of Life". The name of this cool mathematician was John Horton Conway. The really curious thing about this game was that, unlike tetris and Farmville, is a universal machine,is that you can solve almost any problem with it.<br />
</p><p>For this reason lot of scientists began to study seriously about the CA. Primarily a physicist a bit eccentric named Steven Wolfram, he study until the 90's, He used cellular automata to deal a coup against traditional scientific methodology, emphasizing the importance of simulations and modeling computer as unquestionable substitutes of the traditional experimentation.<br />
</p><h2>How To?</h2><br />
<center><img src="https://static.igem.org/mediawiki/2012/b/b8/Resistentbacter.gif" alt="A very Resistent bacterium"></center><br />
<p>How does a cellular automaton work? Well, imagine a group of guys in a dance floor. One of these says, "Well, If I'm the only one who is dancing or there is only one person dancing, I think that i'm don't i will not be a laughing stock" and "If more than 4 people are dancing, the better is stop of dance, it's uncomfortable dancing among many people ". And of course "else, i dancing all the night". Now, imagine that all people think the same track, that's basically a CA: a set of individuals (cells) that act similarly and simultaneously within a (lattice).<br />
</p><p>But, think more applied: if instead of teenage dancers, bacteria were willing to eat? Instead of a dance floor, outside a bioreactor? There are a more couple of questions to answer: If you want to feed the bacteria, the amount of food that is around you is also important, and we should consider adding it, and if they are fed well, they can not go to the bathroom to leave their waste , so we must take into account their waste.<br />
</p><p>Well, this is a brief description of our model, we have a bioreactor cells, bacteria, food and debris. That is, a lattice and three types of cells that fill it.<br />
</p><p>What else do we need to know? In the past example we said, "I need two or three people so that I can dance", but as we speak now of bacteria and food, we say "I need amount n of food and amout m of other bacteria that can feed with me", because , you know, no one likes to eat alone.<br />
</p><p>But we can go further in this model. Suppose the bioreactor gives us ideal conditions every so often and eliminates food waste produced and they distributed throughout the lattice.<br />
</p><p>In our model, we decided to have two lattices: one for our friend Rhodobacter, where there may be a bacterium or may be not that. And another lattice with the same number of squares, but with x percent of food, "y" percent of wastes and z percent for other resources. In this way we can generate simple rules:<br />
</p><ul><br />
<li>If, for example, among all the cells I have around, sum at least 2 complete squares, the bacter will survive.</li><br />
<li>However, If there more than 5 boxes of waste, the bacterium die.</li><br />
<li>If at least two bacteria and exist enough food, namely more than 2 squares of food, grow a new bacteria.</li><br />
</ul><br />
<p>Thus, the CA showed a more realistic simulation, but mostly we will get data from simulation models can feed others.<br />
</p><p>The two main disadvantages of the CA is the CPU time needed to calculate the simulation and randomness that can have its outcome, in other words, depending on how initialize living cells and the percentage that we decide to add for each compound in the second lattice.<br />
</p><p>The first problem is easy to solve: the current CPU is fast enough to avoid problems in these calculations.<br />
</p><p>The second problem is harder to solve. There are several methods, our personal favorite, another mathematical model: perform multiple simulations with different distributions of bacteria and its results are added to a probability function that characterizes certain experiment.<br />
<br />
<br />
<br />
</p><br />
<a href="https://2012.igem.org/File:GUI_prototype_for_cellular_automata.png"><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Cellular.htm
Team/CINVESTAV-IPN-UNAM MX/Cellular.htm
2012-10-27T01:24:51Z
<p>Jhonatan: </p>
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<h1><em>Strange variant of cellular automata for <br /><br />the simulation of a bio-reactor!</em></h1><br />
<br />
<p id="text2">Introduction</p><br />
<p><br />
First of all: why use cellular automata if any linear models are easier to analyze? Well, first it looks great.<br />
</p><center><br />
<img src="https://static.igem.org/mediawiki/2012/5/50/CA1.gif" alt="This look great, no?"></center><br />
<p>Second, depending on the configuration of the Cellular Automaton(CA) "how do you look", the CA is more realistic and we it can provide enough data for other models. In fact, is just what took place in this model.<br />
</p><p>Imagine that we are scientists with more resources in the world and that we can generate hundreds of experiments in the conditions we want to feed our prediction models. The CA allows us to do this with the only drawback that we hate our CPU.<br />
</p><h2>Brief History</h2><br />
<p>Cellular automata are a mathematical model developed by Konrad Zuse and Stanislaw Ulam, but was better known and developed by a guy named John Vonn Neumann who loved parallel computing, but, as usual, history remembers him as the father of sequential computing.<br />
</p><p>Later, during the disruptive and flowery decade of 60's, a crazy mathematical said "oh, it would be great to do a math game where no players" (you know, the time before tetris and farmville), and created the world famous "Game of Life". The name of this cool mathematician was John Horton Conway. The really curious thing about this game was that, unlike tetris and Farmville, is a universal machine,is that you can solve almost any problem with it.<br />
</p><p>For this reason lot of scientists began to study seriously about the CA. Primarily a physicist a bit eccentric named Steven Wolfram, he study until the 90's, He used cellular automata to deal a coup against traditional scientific methodology, emphasizing the importance of simulations and modeling computer as unquestionable substitutes of the traditional experimentation.<br />
</p><h2>How To?</h2><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/Resistentbacter.gif" alt="A very Resistent bacterium"><br />
<p>How does a cellular automaton work? Well, imagine a group of guys in a dance floor. One of these says, "Well, If I'm the only one who is dancing or there is only one person dancing, I think that i'm don't i will not be a laughing stock" and "If more than 4 people are dancing, the better is stop of dance, it's uncomfortable dancing among many people ". And of course "else, i dancing all the night". Now, imagine that all people think the same track, that's basically a CA: a set of individuals (cells) that act similarly and simultaneously within a (lattice).<br />
</p><p>But, think more applied: if instead of teenage dancers, bacteria were willing to eat? Instead of a dance floor, outside a bioreactor? There are a more couple of questions to answer: If you want to feed the bacteria, the amount of food that is around you is also important, and we should consider adding it, and if they are fed well, they can not go to the bathroom to leave their waste , so we must take into account their waste.<br />
</p><p>Well, this is a brief description of our model, we have a bioreactor cells, bacteria, food and debris. That is, a lattice and three types of cells that fill it.<br />
</p><p>What else do we need to know? In the past example we said, "I need two or three people so that I can dance", but as we speak now of bacteria and food, we say "I need amount n of food and amout m of other bacteria that can feed with me", because , you know, no one likes to eat alone.<br />
</p><p>But we can go further in this model. Suppose the bioreactor gives us ideal conditions every so often and eliminates food waste produced and they distributed throughout the lattice.<br />
</p><p>In our model, we decided to have two lattices: one for our friend Rhodobacter, where there may be a bacterium or may be not that. And another lattice with the same number of squares, but with x percent of food, "y" percent of wastes and z percent for other resources. In this way we can generate simple rules:<br />
</p><ul><br />
<li>If, for example, among all the cells I have around, sum at least 2 complete squares, the bacter will survive.</li><br />
<li>However, If there more than 5 boxes of waste, the bacterium die.</li><br />
<li>If at least two bacteria and exist enough food, namely more than 2 squares of food, grow a new bacteria.</li><br />
</ul><br />
<p>Thus, the CA showed a more realistic simulation, but mostly we will get data from simulation models can feed others.<br />
</p><p>The two main disadvantages of the CA is the CPU time needed to calculate the simulation and randomness that can have its outcome, in other words, depending on how initialize living cells and the percentage that we decide to add for each compound in the second lattice.<br />
</p><p>The first problem is easy to solve: the current CPU is fast enough to avoid problems in these calculations.<br />
</p><p>The second problem is harder to solve. There are several methods, our personal favorite, another mathematical model: perform multiple simulations with different distributions of bacteria and its results are added to a probability function that characterizes certain experiment.<br />
<br />
<br />
<br />
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Team/CINVESTAV-IPN-UNAM MX/results.htm
2012-10-27T01:01:59Z
<p>Jhonatan: </p>
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Jhonatan
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2012-10-27T01:00:50Z
<p>Jhonatan: </p>
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Cellular.htm
Team/CINVESTAV-IPN-UNAM MX/Cellular.htm
2012-10-27T00:37:32Z
<p>Jhonatan: </p>
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<h1><em>Strange variant of cellular automata for <br /><br />the simulation of a bio-reactor!</em></h1><br />
<br />
<p id="text2">Introduction</p><br />
<p><br />
First of all: why use cellular automata if any linear models are easier to analyze? Well, for starters look great.<br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/5/50/CA1.gif" alt="This look great, no?"><br />
<p>Second, depending on the configuration of the cellular automaton "how you look", the CA is more realistic and we can provide sufficient data to feed other models. In fact, is just what took place in this model.<br />
</p><p>Imagine that we are scientists with more material resources in the world and that we can generate hundreds of experiments in the conditions we want to feed our prediction models. Well, the CA allows us to do this with the only drawback that we hate our CPU.<br />
</p><h2>Brief History</h2><br />
<p>Cellular automata are a mathematical model developed by Konrad Zuse and Stanislaw Ulam, but was better known and developed by a guy named John Vonn Neumann who loved parallel computing, but, as usual, history remembers him as the father of sequential computing.<br />
</p><p>Later, during the disruptive and flowery decade of 60's, a crazy mathematical said "oh, it would be great to do a math game where no players" (you know, the time before tetris and farmville), and created the world famous "Game of Life". The name of this cool mathematician was John Horton Conway. The really curious thing about this game was that, unlike tetris and Farmville, is a universal machine,is that you can solve almost any problem with it.<br />
</p><p>For this reason lot of scientists began to study seriously about the CA. Primarily a physicist a bit eccentric named Steven Wolfram, he study until the 90's, He used cellular automata to deal a coup against traditional scientific methodology, emphasizing the importance of simulations and modeling computer as unquestionable substitutes of the traditional experimentation.<br />
</p><h2>How To?</h2><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/Resistentbacter.gif" alt="A very Resistent bacterium"><br />
<p>How does a cellular automaton? Well, imagine a group of guys in a dance floor. One of these says, "Well, If I'm the only one who is dancing or there is only one person dancing, I think that i'm don't i will not be a laughing stock" and "If more than 4 people are dancing, the better is stop of dance, it's uncomfortable dancing among many people ". And of course "else, i dancing all the night". Now, imagine that all people think the same track, that's basically a CA: a set of individuals (cells) that act similarly and simultaneously within a (lattice).<br />
</p><p>But, think more applied: if instead of teenage dancers, bacteria were willing to eat? Instead of a dance floor, outside a bioreactor? There are a more couple of questions to answer: If you want to feed the bacteria, the amount of food that is around you is also important, and we should consider adding it, and if they are fed well, they can not go to the bathroom to leave their waste , so we must take into account their waste.<br />
</p><p>Well, this is a brief description of our model, we have a bioreactor cells, bacteria, food and debris. That is, a lattice and three types of cells that fill it.<br />
</p><p>What else do we need to know? In the past example we said, "I need two or three people so that I can dance", but as we speak now of bacteria and food, we say "I need amount n of food and amout m of other bacteria that can feed with me", because , you know, no one likes to eat alone.<br />
</p><p>But we can go further in this model. Suppose the bioreactor gives us ideal conditions every so often and eliminates food waste produced and they distributed throughout the lattice.<br />
</p><p>In our model, we decided to have two lattices: one for our friend Rhodobacter, where there may be a bacterium or may be not that. And another lattice with the same number of squares, but with x percent of food, "y" percent of wastes and z percent for other resources. In this way we can generate simple rules:<br />
</p><ul><br />
<li>If, for example, among all the cells I have around, sum at least 2 complete squares, the bacter will survive.</li><br />
<li>However, If there more than 5 boxes of waste, the bacterium die.</li><br />
<li>If at least two bacteria and exist enough food, namely more than 2 squares of food, grow a new bacteria.</li><br />
</ul><br />
<p>Thus, the CA showed a more realistic simulation, but mostly we will get data from simulation models can feed others.<br />
</p><p>The two main disadvantages of the CA is the CPU time needed to calculate the simulation and randomness that can have its outcome, in other words, depending on how initialize living cells and the percentage that we decide to add for each compound in the second lattice.<br />
</p><p>The first problem is easy to solve: the current CPU is fast enough to avoid problems in these calculations.<br />
</p><p>The second problem is harder to solve. There are several methods, our personal favorite, another mathematical model: perform multiple simulations with different distributions of bacteria and its results are added to a probability function that characterizes certain experiment.<br />
<br />
<br />
<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Ownership.htm
Team/CINVESTAV-IPN-UNAM MX/Ownership.htm
2012-10-27T00:32:27Z
<p>Jhonatan: </p>
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<h1><em>Intellectual Property Strategy for Synbio <br /><br />Research in Mexico!</em></h1><br />
<p id="text2">Stage 1: Intellectual Property vs. Open Source report</p><br />
<p>With the objective to provide a wide vision of this topic, we are trying to open a national discussion for the creation and adoption of a strategy for intellectual property and open source for the development of synthetic biology in Mexico. The first stage consists in define the status of this issue. We´re going to introduce some concepts related to open source and intellectual property.</p><br />
<p id="text2"><img src="https://static.igem.org/mediawiki/2012/1/1b/Owner01.jpg" alt="owner01" width="560" height="345"></p><br />
<p id="text2">Stage 1 Summary</p><br />
<p>Patents were created as a way to provide financial incentives for inventors to undertake research, by allowing them to exclude competitors from exploiting their invention for a specified period of time. There is the risk that it could hinder those conducting important research or providing needed services downstream, and can inhibit cumulative innovation (2).<br><br><br />
Considerable historical evidence, including evidence from many important industries of the twentieth century, suggests that the transaction costs associated with developing broad patents on foundational research can slow growth in the industry (1). There is a real risk that patent thickets will hinder the ability to do research and commercialize applications in synbio.<br><br><br />
<br />
<br />
The Biobrick foundation and many synbio leaders support the open source (OS) to ensure the advance of synbio. Nevertheless, there are many questions to solve in order to reach the ideal strategy, especially in iGEM and the Registry of Standard Biological Parts (RSPB). There are many problems in the implementation of open source, to be success, the OS strategy should incorporate a strong intellectual property structure that allow the open access and use to the protected parts, but also avoid any misuse of these parts. <br><br />
<br><br />
Imagine that a foundational advance biobrick from the registry is not protected by any intellectual property modality; Many researchers have freely used this biobrick for the construction of useful devices; someone even used it for a commercial development and decided to patent the resultant device. One year earlier of this patent application, a giant corporation takes this idea and develops a tool based on it; they decide to patent this tool, what happen if the company decides to assert the researcher? Every aspect of this issue must to be perfectly clear to avoid that kind of problems<br />
Already we are beginning to see problematic foundational patents that could impede the potential of the technology (8). Some synbio leaders propose to use intellectual property rights to create a “commons” in the same way as software developers, by using the copyright and copyleft modalities of IP. <br><br />
<br><br />
<br />
<br />
The Biobrick foundation has partially solved the Intellectual Property issue by implementing its Biobrick Public Agreement, which is a new legal instrument for sharing synthetic biological parts. The simplicity of the BPA should help the synbio community grow without the cost or complexity of navigating the patent system. Those who wish to continue to use the patent system and other intellectual property frameworks (outside of the sharing system established via the BPA) are free to do so (9)<br />
Synthetic biology is trying to make biology easier to engineer, by introducing some ideas of many areas of engineering to life sciences, the core proposal is the standardization of biological parts. Our proposal is to incorporate standardization to synbio IP issues.<br><br />
<br><br />
<br />
<br />
Sometimes is better to patent a synbio invention, sometimes is better to give invention to the world for its free use, in other cases special strategies should be adopted. Application of BPA must be complemented by other standard procedures for each case. It is necessary to define what should be patented according to this. An interdisciplinary committee must be integrated to discuss this categorization and those standard procedures.<br><br />
<br><br />
<br />
<br />
Check out the complete report here:</p><br />
<p><a href="https://static.igem.org/mediawiki/2012/3/36/Intellectual_Property_report.pdf" target="_parent">Intellectual Property<br />
vs. Open Source</a></p><br />
<hr><br />
<p id="refe">References<br><br />
<br />
1 Merges RP, Nelson RR (1990) <strong>On the complex economics of patent scope.</strong> Columbia Law Rev<br><br />
<br />
2 World Health Organization (2005) <strong>Genetics, genomics and the patenting of DNA : review of potential implications for health in developing countries.</strong><br><br />
<br />
3 European group on ethics in science and new technologies to the European commission (2009) <strong>Ethics of synthetic biology European Union,</strong> 2010. ISBN 978-92-79-13829-4 doi: 10.2796/10789<br><br />
<br />
4 Organization for Economic Co-operation and Development (2010) <strong>Symposium on Opportunities and Challenges in the Emerging Field of Synthetic Biology OECD,</strong> Royal Society 2010<br><br />
<br />
5 Mexican Association for Synthetic Biology (2009) <strong>Strategic guidelines for synthetic biology industries in developing countries</strong><br><br />
<br />
6. Rai A, Boyle J (2007) <strong>Synthetic biology: Caught between property rights, the public domain, and the commons.</strong> PLoS Biol 5(3): e58. doi:10.1371/journal.pbio.0050058<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Members.htm
Team/CINVESTAV-IPN-UNAM MX/Members.htm
2012-10-27T00:31:26Z
<p>Jhonatan: </p>
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<h1><em>Members!</em></h1><br />
<p id="text2"> Students</p></br><br />
<img src="https://static.igem.org/mediawiki/2012/9/95/Diez.jpg" alt="diez" width="172" height="235" class="left"><br />
<br><br />
<br><br />
<br><br />
<p>Lissania Guerra-Calderas Contribution: Butanol Production System and BioBrick Designer, outreach activities. 4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) lissxgc.89@gmail.com.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Ocho.jpg" width="172" height="235" class="right"></p><br />
<br><br />
<br />
<br />
<p>Jhonatan Alejandro Hernández-Valdés Contribution: Project Management, design and development of regulatory systems, BioBrick Designer, outreach activities. 4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) jhonatanhv@hotmail.com.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/8/84/Once.jpg" alt="once" width="164" height="211" class="left"><br><br />
Maritere Uriostegui-Arcos Contribution: Characterization and measurement protocols. BioBrick Designer, outreach activities. 4th year undergraduate of Pharmaceutical and Biological Chemistry, at Faculty of Chemistry. National Autonomous University of Mexico (UNAM) maritere1011@hotmail.com.<br><br />
</p><br />
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<br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Nueve.jpg" alt="nueve" width="163" height="237" class="right"><br><br />
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<p>&nbsp;</p><br />
<p>Anna Karen Hernández-Gallardo Contribution: Mathematical modeling, 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology<br />
National Polytechnic Institute<br />
.</p><br />
<p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/1/16/Tre.jpg" alt="tre" width="171" height="246" class="left"></p><br />
<p>Patricia Arias-Orozco Contribution: Design and development of regulatory systems, BioBrick Designer, outreach activities. 4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology National Polytechnic Institute. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/4/45/Uno.jpg" alt="uno" width="174" height="243" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Daniel Domínguez-Gómez <br><br />
<p>Contribution: Outreach activities.<br> <br />
4th year undergraduate Biotechnological Engineering, Interdisciplinary Unit for Biotechnology, National Polytechnic Institute.<br><br />
<p></p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/4/43/Siete.jpg" alt="siete" width="167" height="234" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Ivan Lopez-Flores Mathematical Team: Mathematical modeling Computational Systems Engineering, Superior School for Computation National Polytechnic Institute National Polytechnic Institute <br><br />
<br><br />
<br><br />
<br><br />
<br />
</p><br />
<br />
<h1>Advisors</h1><br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Catorce.jpg" alt="catorce" width="168" height="244" class="left"><p>&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>Karen Nava Castro PhD Contribution: Flow Cytometry Expert. Researcher at Institute of Biomedical Research, Field of study: Immunology. National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/c/c8/Quince.jpg" alt="quince" width="161" height="221" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Jorge Morales Montor PhD Contribution: Dry lab support Researcher at Institute of Biomedical Research (IIB, UNAM) Field of study: Neuoimmunoendocrinology National Autonomous University of Mexico, UNAM. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Dos.jpg" alt="dos" width="194" height="270" class="left"><br />
<p>Daniel Federico Hernandez Gardiol Contribution: Mathematical model Systems Biologist: Universidad de la Republica (Montevideo, Uruguay) Bioengineering Masters Student: Ecole Polytechnique Federal de Lausanne (Lausanne, Switzerland) National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/0d/Cinco1.jpg" alt="cinco" width="173" height="205" class="right"><p>&nbsp;</p><br />
<p>Fernando G. Bastida-González Contribution: Wet lab support, Master in Health science at Superior Medicine School at National Polytechnic Institute.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<h1>Instructors</h1><br><br />
<br />
<p><img src="https://static.igem.org/mediawiki/2012/e/e9/Tres.jpg" alt="tres" width="166" height="227" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Agustino Martínez-Antonio PhD Resarcher 3A, SNI I Genetic Engineering Department, CINVESTAV Irapuato.</p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><br><br />
<img src="https://static.igem.org/mediawiki/2012/6/67/Seis.jpg" alt="seis" width="161" height="209" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Fernando Suaste-Olmos PhD Researcher at Institute of Cell Physiology IFC-UNAM.<br />
Expert in Photosynthetic bacteria. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/9/98/Doce.jpg" alt="dice" width="173" height="205" class="left"></p><br />
<p>&nbsp;</p><br />
<p>Nuria Sánchez-Puig Researcher at Institute of Chemistry UNAM Dr. Sanchez-Puig has a PhD from the Center for Protein Engineering, Cambridge, UK. </p><br />
<p>&nbsp;</p><p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2012/a/ad/Dieciseis.jpg" alt="dieciseis" width="150" height="204" class="right"></p><br />
<p>&nbsp;</p><br />
<p>Paola Zárate-Segura PhD Researcher, at IPN. Dra. Zárate Segura has a PhD in Bioprocess from Interdisciplinary Unit for Biotechnology, National Polytechnic Institute. </p><br />
<p>&nbsp;</p><br />
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http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Cellular.htm
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<p>Jhonatan: </p>
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<h1><em>Strange variant of cellular automata for <br /><br />the simulation of a bio-reactor!<em></h1><br />
<br />
<p id="text2">Introduction</p><br />
<p><br />
First of all: why use cellular automata if any linear models are easier to analyze? Well, for starters look great.<br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/5/50/CA1.gif" alt="This look great, no?"><br />
<p>Second, depending on the configuration of the cellular automaton "how you look", the CA is more realistic and we can provide sufficient data to feed other models. In fact, is just what took place in this model.<br />
</p><p>Imagine that we are scientists with more material resources in the world and that we can generate hundreds of experiments in the conditions we want to feed our prediction models. Well, the CA allows us to do this with the only drawback that we hate our CPU.<br />
</p><h2>Brief History</h2><br />
<p>Cellular automata are a mathematical model developed by Konrad Zuse and Stanislaw Ulam, but was better known and developed by a guy named John Vonn Neumann who loved parallel computing, but, as usual, history remembers him as the father of sequential computing.<br />
</p><p>Later, during the disruptive and flowery decade of 60's, a crazy mathematical said "oh, it would be great to do a math game where no players" (you know, the time before tetris and farmville), and created the world famous "Game of Life". The name of this cool mathematician was John Horton Conway. The really curious thing about this game was that, unlike tetris and Farmville, is a universal machine,is that you can solve almost any problem with it.<br />
</p><p>For this reason lot of scientists began to study seriously about the CA. Primarily a physicist a bit eccentric named Steven Wolfram, he study until the 90's, He used cellular automata to deal a coup against traditional scientific methodology, emphasizing the importance of simulations and modeling computer as unquestionable substitutes of the traditional experimentation.<br />
</p><h2>How To?</h2><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/Resistentbacter.gif" alt="A very Resistent bacterium"><br />
<p>How does a cellular automaton? Well, imagine a group of guys in a dance floor. One of these says, "Well, If I'm the only one who is dancing or there is only one person dancing, I think that i'm don't i will not be a laughing stock" and "If more than 4 people are dancing, the better is stop of dance, it's uncomfortable dancing among many people ". And of course "else, i dancing all the night". Now, imagine that all people think the same track, that's basically a CA: a set of individuals (cells) that act similarly and simultaneously within a (lattice).<br />
</p><p>But, think more applied: if instead of teenage dancers, bacteria were willing to eat? Instead of a dance floor, outside a bioreactor? There are a more couple of questions to answer: If you want to feed the bacteria, the amount of food that is around you is also important, and we should consider adding it, and if they are fed well, they can not go to the bathroom to leave their waste , so we must take into account their waste.<br />
</p><p>Well, this is a brief description of our model, we have a bioreactor cells, bacteria, food and debris. That is, a lattice and three types of cells that fill it.<br />
</p><p>What else do we need to know? In the past example we said, "I need two or three people so that I can dance", but as we speak now of bacteria and food, we say "I need amount n of food and amout m of other bacteria that can feed with me", because , you know, no one likes to eat alone.<br />
</p><p>But we can go further in this model. Suppose the bioreactor gives us ideal conditions every so often and eliminates food waste produced and they distributed throughout the lattice.<br />
</p><p>In our model, we decided to have two lattices: one for our friend Rhodobacter, where there may be a bacterium or may be not that. And another lattice with the same number of squares, but with x percent of food, "y" percent of wastes and z percent for other resources. In this way we can generate simple rules:<br />
</p><ul><br />
<li>If, for example, among all the cells I have around, sum at least 2 complete squares, the bacter will survive.</li><br />
<li>However, If there more than 5 boxes of waste, the bacterium die.</li><br />
<li>If at least two bacteria and exist enough food, namely more than 2 squares of food, grow a new bacteria.</li><br />
</ul><br />
<p>Thus, the CA showed a more realistic simulation, but mostly we will get data from simulation models can feed others.<br />
</p><p>The two main disadvantages of the CA is the CPU time needed to calculate the simulation and randomness that can have its outcome, in other words, depending on how initialize living cells and the percentage that we decide to add for each compound in the second lattice.<br />
</p><p>The first problem is easy to solve: the current CPU is fast enough to avoid problems in these calculations.<br />
</p><p>The second problem is harder to solve. There are several methods, our personal favorite, another mathematical model: perform multiple simulations with different distributions of bacteria and its results are added to a probability function that characterizes certain experiment.<br />
<br />
<br />
<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Cellular.htm
Team/CINVESTAV-IPN-UNAM MX/Cellular.htm
2012-10-27T00:26:07Z
<p>Jhonatan: </p>
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<h1><em>Strange variant of cellular automata for the simulation of <br /><br />a bio-reactor!<em></h1><br />
<br />
<p id="text2">Introduction</p><br />
<p><br />
First of all: why use cellular automata if any linear models are easier to analyze? Well, for starters look great.<br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/5/50/CA1.gif" alt="This look great, no?"><br />
<p>Second, depending on the configuration of the cellular automaton "how you look", the CA is more realistic and we can provide sufficient data to feed other models. In fact, is just what took place in this model.<br />
</p><p>Imagine that we are scientists with more material resources in the world and that we can generate hundreds of experiments in the conditions we want to feed our prediction models. Well, the CA allows us to do this with the only drawback that we hate our CPU.<br />
</p><h2>Brief History</h2><br />
<p>Cellular automata are a mathematical model developed by Konrad Zuse and Stanislaw Ulam, but was better known and developed by a guy named John Vonn Neumann who loved parallel computing, but, as usual, history remembers him as the father of sequential computing.<br />
</p><p>Later, during the disruptive and flowery decade of 60's, a crazy mathematical said "oh, it would be great to do a math game where no players" (you know, the time before tetris and farmville), and created the world famous "Game of Life". The name of this cool mathematician was John Horton Conway. The really curious thing about this game was that, unlike tetris and Farmville, is a universal machine,is that you can solve almost any problem with it.<br />
</p><p>For this reason lot of scientists began to study seriously about the CA. Primarily a physicist a bit eccentric named Steven Wolfram, he study until the 90's, He used cellular automata to deal a coup against traditional scientific methodology, emphasizing the importance of simulations and modeling computer as unquestionable substitutes of the traditional experimentation.<br />
</p><h2>How To?</h2><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/Resistentbacter.gif" alt="A very Resistent bacterium"><br />
<p>How does a cellular automaton? Well, imagine a group of guys in a dance floor. One of these says, "Well, If I'm the only one who is dancing or there is only one person dancing, I think that i'm don't i will not be a laughing stock" and "If more than 4 people are dancing, the better is stop of dance, it's uncomfortable dancing among many people ". And of course "else, i dancing all the night". Now, imagine that all people think the same track, that's basically a CA: a set of individuals (cells) that act similarly and simultaneously within a (lattice).<br />
</p><p>But, think more applied: if instead of teenage dancers, bacteria were willing to eat? Instead of a dance floor, outside a bioreactor? There are a more couple of questions to answer: If you want to feed the bacteria, the amount of food that is around you is also important, and we should consider adding it, and if they are fed well, they can not go to the bathroom to leave their waste , so we must take into account their waste.<br />
</p><p>Well, this is a brief description of our model, we have a bioreactor cells, bacteria, food and debris. That is, a lattice and three types of cells that fill it.<br />
</p><p>What else do we need to know? In the past example we said, "I need two or three people so that I can dance", but as we speak now of bacteria and food, we say "I need amount n of food and amout m of other bacteria that can feed with me", because , you know, no one likes to eat alone.<br />
</p><p>But we can go further in this model. Suppose the bioreactor gives us ideal conditions every so often and eliminates food waste produced and they distributed throughout the lattice.<br />
</p><p>In our model, we decided to have two lattices: one for our friend Rhodobacter, where there may be a bacterium or may be not that. And another lattice with the same number of squares, but with x percent of food, "y" percent of wastes and z percent for other resources. In this way we can generate simple rules:<br />
</p><ul><br />
<li>If, for example, among all the cells I have around, sum at least 2 complete squares, the bacter will survive.</li><br />
<li>However, If there more than 5 boxes of waste, the bacterium die.</li><br />
<li>If at least two bacteria and exist enough food, namely more than 2 squares of food, grow a new bacteria.</li><br />
</ul><br />
<p>Thus, the CA showed a more realistic simulation, but mostly we will get data from simulation models can feed others.<br />
</p><p>The two main disadvantages of the CA is the CPU time needed to calculate the simulation and randomness that can have its outcome, in other words, depending on how initialize living cells and the percentage that we decide to add for each compound in the second lattice.<br />
</p><p>The first problem is easy to solve: the current CPU is fast enough to avoid problems in these calculations.<br />
</p><p>The second problem is harder to solve. There are several methods, our personal favorite, another mathematical model: perform multiple simulations with different distributions of bacteria and its results are added to a probability function that characterizes certain experiment.<br />
<br />
<br />
<br />
</p><br />
<a href="https://2012.igem.org/File:GUI_prototype_for_cellular_automata.png"><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Tools.htm
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2012-10-27T00:23:44Z
<p>Jhonatan: </p>
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<h1><em>Some of the tools that we used during the <br /><br />modeling process.!</em></h1><br />
<p id="text2">Wolfram Research Mathematica</p><br />
<p>Mathematica is a general computer software system and language intended for mathematical and<br />
other applications. You can use Mathematica as: A numerical and symbolic calculator where you<br />
type in questions, and Mathematica prints out answers, a visualization system for functions and<br />
data, a high-level programming language in which you can create programs, large and small ones.<br />
and a modeling and data analysis environment.</p><br />
<p id="text2">Rule-Based Modeling of Biochemical Systems with BioNetGen</p><br />
<br />
<p>Rule-based modeling involves the representation of molecules as structured objects and molecular<br />
interactions as rules for transforming the attributes of these objects.The approach is notable in that<br />
it allows one to systematically incorporate site-specific details about protein-protein interactions into<br />
a model. BioNetGen allows a user to create a computational model that characterizes the dynamics<br />
of a signal transduction system, and that accounts comprehensively and precisely for specified<br />
enzymatic activities, potential post-translational modifications and interactions of the domains of<br />
signaling molecules. The output defines and parameterizes the network of molecular species that<br />
can arise during signaling and provides functions that relate model variables to experimental<br />
readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis<br />
of proteomic data and mechanistic studies of signal transduction.<br />
</p><br />
<p>For further details go to:</p><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Oxigen_Response.htm
Team/CINVESTAV-IPN-UNAM MX/Oxigen Response.htm
2012-10-27T00:22:05Z
<p>Jhonatan: </p>
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<h1><em>Oxygen Control System: PrrA/PrrB two <br /><br />component regulation system! </em></h1><br />
<p>This regulatory system is able to sense oxygen concentration and send a response, under high oxygen tension, the system remains inactive, when oxygen concentration decreases PrrB (Histidine sensor kinase) turns active through an autophosphorylation with help of PrrC, which receive the signal from electron transport chain. Then PrrB transfer a phosphate group to PrrA that directly binds promoter and recruits RNA polymerase to start GFP transcription.<br />
<br />
<br />
(See the next video for a visual explanation).</p><br />
<div align="center"><iframe width="480" height="360" src="http://www.youtube.com/embed/pgp6DzpNyA0" frameborder="0" allowfullscreen></iframe></div><br><br />
<p id="text2">Our biobricks </p><br />
<p>The first biobrick consists in the complete oxygen dependent system, PrrA, PrrB and PrrC, each one with a Ribosome Binding Site, under a<br />
Medium strength promoter (J23104), this first biobrick also it has the PrrA dependent promoter and GFP as a reporter gene</p><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/Rodo04.jpg" alt="rodo04" width="560" height="116"><br><br />
<p><br><br />
The second biobrick is just the PrrA dependent promoter and GFP as a reporter gene.</p><br />
<p align="center"><img src="https://static.igem.org/mediawiki/2012/1/16/Rodo05.jpg" alt="rodo05" width="450" height="249"></p><br />
<p id="text2">We were inspired in:</p><br />
<p>This system is inspired in PrrBCA two component system from <em>R. sphaeroides</em>, which is a master regulator involved in expression of<br />
approximately 850 genes, >20% of the genome (Kaplan & Eraso 2005) This system coordinately controls genes involved in the complex switch<br />
between aerobic and anaerobic conditions and the optimum use of reducing power. It also regulates gene expression involved in<br />
photosynthesis, carbon dioxide fixation, nitrogen fixation, hydrogen uptake, aerotaxis, denitrification, electron transport, aerobic and anaerobic<br />
respiration, and heme biosynthesis, and others. Thus emphasizing its global role (Elsen et.al 2004, Kaplan & Eraso 2005, Zeilstra-Ryalls &<br />
Kaplan 2004).</p><br />
<hr><br />
<p id="refe">References<br><br />
1.<br />
Kaplan S, Eraso J, Roh JH. (2005). <strong>Interacting regulatory networks in the facultative<br />
photosynthetic bacterium, <em>Rhodobacter sphaeroides</em> 2.4.1.</strong> Biochem. Soc. Trans. 33:51–55<br><br />
<br />
2.<br />
Zeilstra-Ryalls JH, Kaplan S. (2004). <strong>Oxygen intervention in the regulation of gene xpression: the photosynthetic<br />
bacterial paradigm.</strong> Cell. Mol. Life Sci. 61:417–36<br><br />
<br />
3.<br />
Eraso JM, Kaplan S (2009) <strong>Regulation of gene expression by PrrA in <em>Rhodobacter sphaeroides</em> 2.4.1: role of<br />
polyamines and DNA topology.</strong> J Bacteriol 2009, 191(13):4341-4352.<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Light_Response.htm
Team/CINVESTAV-IPN-UNAM MX/Light Response.htm
2012-10-27T00:21:39Z
<p>Jhonatan: </p>
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<h1><em>Light & Oxygen Response: AppA/PpsR <br /><br />Regulation System! </em></h1><br />
<p>This is a repressor/antirepressor system, which under high oxygen tension; PpsR represses GFP expression by avoiding RNA polymerase binding <br />
the promoter sequence.<br><br />
<br />
When oxygen concentration decreases AppA has a conformational change and can bind with PpsR, this complex prevents the union of<br />
PpsR to its target sequence, thus GFP expression can begin.<br><br />
<br />
(See the next video for a visual explanation).</p><br />
<div align="center"><iframe width="480" height="360" src="http://www.youtube.com/embed/XBNRLq9pL8c" frameborder="0" allowfullscreen></iframe></div><br><br />
<p id="text2">Our biobricks </p><br />
<p>The first biobrick consists in the complete light-oxygen dependent system, AppA and PpsR, each one with Ribosome Binding Site, under a<br />
Medium strength promoter (J23104), this first biobrick also it has the PpsR dependent promoter and GFP as a reporter gene.</p><br />
<img src="https://static.igem.org/mediawiki/2012/b/b6/Rodo02.jpg" alt="rodo02" width="568" height="107"><br><br />
<p><br><br />
The second circuit is just the PpsR dependent promoter and GFP as a reporter gene.</p><br />
<img src="https://static.igem.org/mediawiki/2012/a/a1/Rodo03.jpg" alt="rodo03" width="562" height="252"><br />
<p id="text2">We were inspired in:</p><br />
<p><br />
This system is inspired in AppA/PpsR repressor/antirepressor system from Rhodobacter sphaeroides. The PpsR protein is a master repressor of<br />
Photosynthesis (PS) genes (Moskvin and Gomelsky 2005). Inactivation of the ppsR gene is enough to turn on PS gene expression and formation<br />
of the photosynthetic apparatus even at a high oxygen concentration, whereas ppsR overexpression is sufficient to block PS development even<br />
in the absence of oxygen. PpsR directly represses transcription of most carotenoid and pigment synthesis genes, photosystems operons, and<br />
genes involved in tetrapyrrole biosynthesis (Gomelsky and Kaplan 1995). The upstream regions of these genes contain two PpsR binding sites,<br />
TGTcN10gACA.<br><br />
<br />
A second protein called AppA, which has no known homologues, plays a role in controlling gene expression in <em>R. sphaeroides</em> in response to both<br />
light and O2 by acting as an antirepressor of PpsR. Our parts (appa, ppsr and ppsr-promoter) were synthesized by Genescript, and are codon<br />
optimized for <em>R. sphaeroides.</em></p><br />
<hr><br />
<p id="refe">References<br><br />
<br />
1. Gomelsky L., Moskvin L., Stenzel A., Jones D., Donohue T. and Gomelsky M.(2008) <strong>Hierarchical Regulation of Photosynthesis<br />
Gene Expression by the Oxygen-Responsive PrrBA and AppA-PpsR Systems of <em>Rhodobacter sphaeroides.</em></strong> J. Bacteriol.<br />
Dec. 2008, p. 8106–8114 Vol. 190, No. 24<br><br />
<br />
2. Moskvin, O. V., L. Gomelsky, and M. Gomelsky. (2005). <strong>Transcriptome analysis of the <em>Rhodobacter sphaeroides</em> PpsR<br />
regulon: PpsR as a master regulator of photosystem development.</strong> J. Bacteriol. 187:2148–2156.<br><br />
<br />
3. Gomelsky, M., and S. Kaplan. (1995). <strong>Genetic evidence that PpsR from <em>Rhodobacter sphaeroides.</em> 2.4.1 functions as a<br />
repressor of puc and bchF expression.</strong> J. Bacteriol. 177:1634–1637. <br><br />
4. Gomelsky, M., and S. Kaplan. (1995). <strong>AppA, a novel gene encoding a transacting factor involved in the regulation of<br />
photosynthesis gene expression in <em>Rhodobacter sphaeroides.</em> 2.4.1.</strong> J. Bacteriol. 177:4609–4618.<br />
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Jhonatan
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Team/CINVESTAV-IPN-UNAM MX/home.htm
2012-10-27T00:20:26Z
<p>Jhonatan: </p>
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<h1><em>Rhodofactory, controlling genetic expression: an oxygen <br /><br />and light response!</em></h1><br />
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<p>The metabolic versatility of purple non-sulfur photosynthetic bacteria allows them to grow in light,<br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Differential.htm
Team/CINVESTAV-IPN-UNAM MX/Differential.htm
2012-10-27T00:19:18Z
<p>Jhonatan: </p>
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<h1><em>Differential equations modeling the <br /><br />interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d9/Grafidif04.jpg" width="400" height="291"><br />
<img src="https://static.igem.org/mediawiki/2012/d/dc/Grafidif02.jpg" width="414" height="321"><br />
<img src="https://static.igem.org/mediawiki/2012/6/63/Grafidif03.jpg" width="414" height="321"><br />
<img src="https://static.igem.org/mediawiki/2012/d/db/Grafidif01.jpg" width="420" height="307"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="https://static.igem.org/mediawiki/2012/8/8b/Interactive_Graphical_AP.zip" target="_parent">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Differential.htm
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<br />
<h1><em>Differential equations modeling the interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d9/Grafidif04.jpg" width="400" height="291"><br />
<img src="https://static.igem.org/mediawiki/2012/d/dc/Grafidif02.jpg" width="414" height="321"><br />
<img src="https://static.igem.org/mediawiki/2012/6/63/Grafidif03.jpg" width="414" height="321"><br />
<img src="https://static.igem.org/mediawiki/2012/d/db/Grafidif01.jpg" width="420" height="307"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="https://static.igem.org/mediawiki/2012/8/8b/Interactive_Graphical_AP.zip" target="_parent">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Differential.htm
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<h1><em>Differential equations modeling the interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d9/Grafidif04.jpg" width="568" height="425"><br />
<img src="https://static.igem.org/mediawiki/2012/d/dc/Grafidif02.jpg" width="568" height="425"><br />
<img src="https://static.igem.org/mediawiki/2012/6/63/Grafidif03.jpg" width="568" height="425"><br />
<img src="https://static.igem.org/mediawiki/2012/d/db/Grafidif01.jpg" width="568" height="425"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="https://static.igem.org/mediawiki/2012/8/8b/Interactive_Graphical_AP.zip" target="_parent">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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<li><a href="Cellular.htm">Cellular Automata</a></li><br />
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<h1><em>Differential equations modeling the interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fa/Dife08.png" width="568" height="425"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="https://static.igem.org/mediawiki/2012/8/8b/Interactive_Graphical_AP.zip" target="_parent">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Differential.htm
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<p>Jhonatan: </p>
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<h1><em>Differential equations modeling the interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fa/Dife08.png" width="568" height="425"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="https://static.igem.org/mediawiki/2012/8/8b/Interactive_Graphical_AP.zip" target="_blank">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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2012-10-26T23:20:36Z
<p>Jhonatan: </p>
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Jhonatan
http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Differential.htm
Team/CINVESTAV-IPN-UNAM MX/Differential.htm
2012-10-26T23:18:23Z
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<h1><em>Differential equations modeling the interactions between AppA and PpsR.!</em></h1><br />
<p>The proteins in our regulatory system constitute a network of intermingling elements<br />
whose behavior can be narrow into seven reactions. Primarily in this part of the modeling<br />
we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it<br />
using a system of ordinary differential equations.The system’s repressive activity varies<br />
with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly<br />
these two variables affect the overall repressive level of PpsR over the expression of PS<br />
genes.<br />
</p><br />
<p id="text2">Model Construction.</p><br />
<br />
<p>To do this we based ourselves on a previous work that had attempted to study this same<br />
regulatory system. [Pandey et al, 2011]. Therefore the mathematical model we developed is<br />
based on the ODEs and kinetic parameters outlined there.<br><br><br />
<br />
<br />
The following are its assumptions and basis:<br />
AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms:<br><br />
<br><br />
<br />
1. By reducing a disulfide bond in PpsR.<br><br />
<br />
2. By a blue-light-dependent sequestration of PpsR proteins into transcriptionally inactive<br />
complexes.<br><br />
<br />
At first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR<br />
(P4+), which occurs independently of the light conditions.The molecular mechanism of<br />
this two-electron transfer is not yet clear.<br><br><br />
<br />
<br />
Some experiments have shown that both PpsR and AppA have two redox-active Thiol<br />
groups that can form intramolecular disulfide bonds with a similar midpoint potential,<br />
according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br><br />
<br />
</div><br />
<p><br><br />
Then at the second level of regulation, the reduced form of AppA can form a complex with<br />
reduced PpsR. During the complex formation, one AppA molecule is associated with two<br />
PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable<br />
tetramer in solution.<br><br />
<br><br />
<br />
However there is a point were complex formation is inhibited by high intensities of blue-<br />
light irradiation (LI ¼ 900mmol/m2s). A subsequent study found that AppA responds to<br />
blue light over several orders of magnitude down to 0.2 mmol/m2s.</p><br />
<p>Other experiments indicate that light absorption induces a structural change in the BLUF<br />
domain of AppA, which results in interactions with its C-terminal part, thereby causing the<br />
dissociation of PpsR.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/3/33/Dife02.png"><br><br />
<br />
</div><br />
<p><br><br />
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han<br />
et al, 2007 according to which AppA utilizes heme as a cofactor, bound to its C-terminal<br />
domain, to sense the cytosolic redox conditions, according to this equation:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/6f/Dife03.png"><br />
</div><br />
<p><br><br />
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible:<br />
(kpr <sup>-</sup> &lt;&lt; kpr <sup>+</sup>), as suggested by the experiments of Masuda and Bauer, 2002.PpsR<br />
would have to be reoxidized through an AppA-independent mechanism. To account for<br />
this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen<br />
concentration as:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/5/5c/Dife04.png"><br />
</div><br />
<p><br><br />
Finally we assumed mass-action kinetics for the reactions above and the following are the<br />
set of ordinary differential equations established:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fc/Dife05.png" width="565" height="313"></div><br />
<p><br><br />
Were the total amounts of PpsR and AppA molecules are conserved according to:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/d/d7/Dife06.png"></div><br />
<P><br><br />
Later on we reduced this set of ODEs into seven basic reactions, to simplify the code<br />
written in Mathematica.</P><br />
<p>This is the code written in Mathematica.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/Dife07.png"> <br />
</div><br />
<p><br><br />
In addition to contacting the responsible authors and discussing this model, we chose to<br />
improve it based on recent publications and preliminary experimental results i.e. we<br />
introduced a more subtle way light and oxygen affects the protein concentration dynamic,<br />
which is exactly what we were interested in understanding better.</p><br />
<p id="text2">Differential equations Results:</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fa/Dife08.png" width="568" height="425"><br />
<p>Figure1. Steady state behavior of reduced PpsR (P4+), oxidized PpsR (P4-) and the<br />
AppA-PpsR complex as a function of oxygen concentration and light irradiance.</p> <br />
</div><br />
<p>If we assumed that the reduction of PpsR by AppA in Equation 1.</p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/4/4b/Dife01.png" width="301" height="76"><br></div><br />
<p><br><br />
Is effectively irreversible when <em><strong>Keq>>1</strong></em></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/f/f1/Dife09.png" width="100" height="66"></div><br />
<p><br><br />
We obtain a fifth order polynomial equation that admits at most five real roots,<br />
corresponding to five possible stationary states. (Graphics above).</p><br />
<p>For them to be biologically meaningful we require that they fall within the interval [0,1].<br />
Using our differential equations system we calculated protein concentrations at stable<br />
steady states and assumed this to be a natural “resting”, or homeostatic, state given a set<br />
of parameters, oxygen and light intensities. As such, this gave us a steady state total<br />
repressive force, in essence, as a function of oxygen tension and light intensity. This is<br />
because PpsR/AppA’s total repressive strength is a function of the concentrations of both<br />
its oxidative and reduced state.<br><br />
<br><br />
<br />
Since this was all done in Mathematica, we were also able to generate an interactive<br />
graphical representation of the repressive strength over a range of conditions.</p><br />
<p>Download the code:<a href="diferentialequiation/Interactive Graphical AP.nb" target="_blank">Interactive Graphical AP</a></p><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2012/6/64/Dife10.png" width="561" height="282"><br />
<p>This is how it will look like when you run the program.</p></div><br />
<p><br><br />
With this model, we can make predictions in sillico as to how the organism will react to a<br />
given environmental surrounding and then go back to the lab and validate that prediction.<br />
Also, since we have are able to manipulate the values of the parameters in an easy and<br />
intuitive way, we can explore the parameter space and visually observe the change in the<br />
concentration curves, which can be of interest to, not only us, but other people that might<br />
not be interested in all the math behind interphase.<br><br />
<br><br />
<br />
<br />
This parameter tweaking allows us to compare experimental data against sillico<br />
predictions; the only difference is that if we focus on the parameters, this can actually give<br />
us hints respect to the still-blurred nature of Protein-Protein and Protein-Environment<br />
mechanisms that exist in this extremely versatile cell. </p><br />
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Jhonatan
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