Template:Team:Bonn:NetworkData

From 2013.igem.org

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content.childs=[18,32,33,34];
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content.titleShort = 'Methods of Induction';
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content.titleLong = 'Methods of Induction';
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content.summary= 'Introduction into several methods of Induction and their usage.';
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content.text= 'Regulating protein levels and conformation is a basic feature of any living organism, helping to maintain homeostasis and maximize efficiency while also increasing its versatility and adaptability. Thus, it is of great interest for basic research where tools are needed to provide protein regulation artificially. High spatiotemporal control is vital for essays which study protein function<sup><a href=#1>[1]</a></sup>, since often exact concentration or conformation is needed. In synthetic biology this is of particular importance since biochemical circuits rely on accurate mechanisms of control and oftentimes employ multiple means of induction.<sup><a href=#2>[2]</a></sup> However there is a multitude of methods available to induce changes in protein structure or expression.<sup><a href=#1>[1]</a><a href=#3>[3]</a><a href=#4>[4]</a><a href=#5>[5]</a><a href=#6>[6]</a></sup>Yet each technique has its own assets and drawbacks which are examined more closely in the following paragraphs.</br>
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<h2>References:</h2>
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<p><a name=1>1.</a> <a href=http://www.ncbi.nlm.nih.gov/pubmed/18272963> Amy B Tyszkiewicz & Tom W Muir: <i>Activation of protein splicing with light in yeast.</i> “Nature Methods” | Vol.5 No.4 | 303 (April 2008)</a></p>
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<p><a name=2>2.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955201>X. Gu, M. Trybilo, S. Ramsay,M. Jensen, R. Fulton, S. Rosser, and D. Gilbert <i>Engineering a novel self-powering electrochemical biosensor.</i> “Systems and Synthetic Biology”4(3) (Sep 2010)</a></p>
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<p><a name=3>3.</a> <a href=http://www.ncbi.nlm.nih.gov/pubmed/?term=Heat-induced%20conformational%20change%20and%20increased%20chaperone%20activity%20of%20lens%20alpha-crystallin> Das BK, Liang JJ, Chakrabarti B. <i>Heat-induced conformational change and increased chaperone activity of lens alpha-crystallin.</i> “Current Eye Research”  Apr;16(4):303-9  (1997)</a></p>
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<p><a name=4>4.</a> <a href=http://www.ncbi.nlm.nih.gov/pubmed/23359284> Yang J, Yang H, Sun X, Delaloye K, Yang X, Moller A, Shi J, Cui J. <i>Interaction between residues in the Mg2+-binding site regulates BK channel activation.</i> “The journal of general physiology” (Feb 2013)</a></p>
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<p><a name=5>5.</a> <a href=http://www.ncbi.nlm.nih.gov/pubmed/10537212> Richard DJ, Sawers G, Sargent F, McWalter L, Boxer DH. <i>Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli.</i> “Microbiology”145 ( Pt 10)  (Oct 1999)</a></p>
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<p><a name=6>6.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC97448/> Maen Qa'Dan, Lea M. Spyres, and Jimmy D. Ballard <i>pH-Induced Conformational Changes in Clostridium difficile Toxin B.</i> “Infection and Immunity” 68(5) (May 2000)</a></p>';
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content.type='Background';
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case 18:
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content.i = 32;
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content.parents=[17];
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content.titleShort ='Chemical';
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content.titleLong ='Chemical induction';
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content.summary= "this is a summary6";
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content.text= 'Chemical induction can be used to provide both expressional and structural changes in proteins.<sup><a href=#1>[1]</a></sup><sup><a href=#2>[2]</a></sup> As an advantage it is highly reliable and tunable which renders it very useful for ensuring constant expression levels.<sup><a href=#1>[1]</a></sup> Several promoters such as pBad which is inducible with arabinose or pLac which is inducible with IPTG are frequently used for such purpose.<sup><a href=#6>[6]</a></sup> Yet changes in protein expression require large timescales i.e. tens of minutes to hours, whereas structural changes such as dimerization (for example rapamycin induced dimerization of FRB and FKBP12<sup><a href=#4>[4]</a></sup>) occur much faster i.e. seconds to minutes.<sup><a href=#2>[2]</a></sup> <div align="center"><a href=https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg><img src=https://static.igem.org/mediawiki/2013/8/8c/BonnRapamycin3D.jpg height=260 width=260></a></br><i>A 3D Structure of Rapamycin </i></div> However compared to other methods of induction such temporal resolution is inferior. Additionally there are several problems arising from the use of chemical agents. Firstly to come into effect any molecule has to penetrate the cell membrane thus either being actively ingested by the cell or diffusing passively through it, which becomes a severe hindrance when none of these requirements are met.<sup><a href=#4>[4]</a></sup>  Secondly any chemical can be bioactive and hence interfere with the cells metabolism or other substances.<sup><a href=#1>[1]</a></sup>  Also specificity can be a problem especially in vivo, where often several cell types in multicellular organisms are effected. <sup><a href=#5>[5]</a></sup> Sub cellular spatial resolution can be difficult to achieve since molecules are subject to diffusion. It can be concluded that spatiotemporal resolution is low in chemically induced systems. <div align="center"><a href=https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg><img src=https://static.igem.org/mediawiki/2013/0/0f/BonnLacOperon.jpg height=260 width=260></a></br><i>The Lac Operon: Origin of the Lac1 Promoter</i></div>
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<h2>References:</h2>
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<p><a name=1>1.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16554/>J. Keith Joung, Elizabeth I. Ramm, and Carl O. Pabo: <i>A bacterial two-hybrid selection system for studying protein–DNA and protein–protein interactions.</i> “PNAS” (June 2000)</a></p>
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<p><a name=2>2.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368803/>Takafumi Miyamoto, Robert DeRose, Allison Suarez, Tasuku Ueno, Melinda Chen, Tai-ping Sun, Michael J. Wolfgang, Chandrani Mukherjee, David J. Meyers, and Takanari Inoue: <i>Rapid and Orthogonal Logic Gating with a Gibberellin-induced Dimerization System. </i>“Nature chemical biology” 8, 465–470 (2012) </a></p>
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<p><a name=3>3.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724991/>Adilson José da Silva, Antônio Carlos Luperni Horta, Ana Maria Velez, Mônica Rosas C Iemma, Cíntia Regina Sargo, Raquel LC Giordano, Maria Teresa M Novo, Roberto C Giordano, and Teresa Cristina Zangirolami: <i>Non-conventional induction strategies for production of subunit swine erysipelas vaccine antigen in rE. coli fed-batch cultures</i> “Springerplus”2, 322 (2013)</a></p>
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<p><a name=4>4.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133816/>Andrei V. Karginov, Yan Zou, David Shirvanyants, Pradeep Kota, Nikolay V. Dokholyan, Douglas D. Young, Klaus M. Hahn, and Alexander Deiters: <i>Light-regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP </i>“Journal of the American Chemical Society” 133(3) 420-423 (2011)</a></p>
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<p><a name=5>5.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529099/>Yuan Mei and Feng Zhang:<i>Molecular Tools and Approaches for Optogenetics</i> “Biological Psychatry”(2012)</a></p>
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<p><a name=6>6.</a> <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711423/>Jarno Mäkelä, Meenakshisundaram Kandhavelu, Samuel M. D. Oliveira, Jerome G. Chandraseelan, Jason Lloyd-Price, Juha Peltonen, Olli Yli-Harja and Andre S. Ribeiro:<i> In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter</i> “Nucleic Acids Research” (2013)"; </a></p>
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content.type='Background';
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case 33:

Revision as of 17:47, 1 October 2013

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