Team:SDU-Denmark/Tour13

From 2013.igem.org

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<h2>A different wiki</h2>
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<h2>Attributions</h2>
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<h4></h4>
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<h4>Showing gratitude to those we could not have done without</h4>
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<a class="popupImg alignRight" style="width:300px" target="_blank"
 
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href="https://static.igem.org/mediawiki/2013/8/84/SDU2013_WikConstruction.jpg" title="Us, busy making the final touches for the Wiki before the wiki-freeze.">
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  <img src="https://static.igem.org/mediawiki/2013/8/84/SDU2013_WikConstruction.jpg" style="width:300px" />
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Us, busy making the final touches for the Wiki before the wiki-freeze.
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</a>
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<p class='intro'>
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<p>
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"I get by with a little help from my friends."
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<span class="intro">Most of our team members</span> have never tried creating a wiki, so when Heidi’s boyfriend Kenneth offered to help us out a bit, we were quick to accept. As a professional software developer, Kenneth had a unique perspective, which shone throughout our preliminary meetings. We set out to present the best, most intuitive wiki possible; to improve the standard wiki experience. This very wiki is the result, and below are the keys to the wiki.
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<b>- John Lennon </b>
</p>
</p>
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<p>
 
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<span class="intro">Better overview: A metro-map of all pages</span><br>
 
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A general issue observed on many wikis is that the user struggles to navigate. We designed a metro-style navigation bar at the top of each page, giving the user knowledge of his exact location.
 
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While allowing a custom experience and viewing order, the navigation bar ensures that the user is never lost.
 
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</p>
 
<p>
<p>
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<span class="intro">Smarter tour: Usable by both casual and thorough readers</span><br>
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<h4>Sponsors</h4>
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A lot of wiki-tours do a great job at introducing the reader to the project. However, users who want details are left to fend for themselves in a jungle of pages.
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Our fix: Allowing our readers the freedom to choose between a quick and a detailed tour by including all pages in our tour.</br>
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The result is an interactive wiki tour, which sets up a choice between digging deeper to detailed pages or fast-forward to the next major chapter. The two buttons (on the bottom of the screen) even have a small text explaining what you can expect to read on the coming pages. Also, take the time to click on our photos; this brings forward a detailed figure description.
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</p>
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<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/94/SDU2013_ERASynbio.png" style="width:280px" />
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<p>
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We would like to thank our sponsor <span class="intro"><a href="http://www.sdu.dk/en/" target="_blank">University of Southern Denmark</a></span> for giving us the funds for the project, making it possible for us to participate in iGEM. In particular, we would like to thank <b>Dean Henrik Pedersen</b> and <b>the Faculty of Science at University of Southern Denmark.</b> We would also like to thank <span class="intro"><a href="http://www.bionordika.dk/" target="_blank">Bionordika</a></span> for sponsoring the USER-enzymes. And a great thank to <span class="intro"><a href="http://www.erasynbio.eu/" target="_blank">ERASynBio</a></span> for sponsoring our trip to the World Championship in Boston.
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<span class="intro">Quicker navigation: Tour buttons and menu always visible</span><br>
 
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Additional ease of navigation was created by ensuring that tour-buttons and menu are always available - even when scrolling through the text! While searching for a topic of interest, a traditional menu as a means of a shortcut may be desirable. Such a menu allows users to access a specific page that they might wish to revisit. Perhaps a certain page sprung to mind after completing the tour, perhaps a user accesses our wiki looking for a particular subject. The menu makes such personalized experiences easier and more user-friendly.
 
</p>
</p>
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</br>
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<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/9b/SDU2013_BioNordika_Logo.jpg" style="width:300px" />
<p>
<p>
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<span class="intro">Tooltips: Simplifying the text</span><br>
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<h4>Laboratory support</h4>
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To reach broader audiences, we wanted our wiki articles to be easily understandable without compromising the scientific aspect.
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-
To solve this, we added <span class="tooltipLink">tooltips</span> <span class="tooltip"><span class="tooltipHeader">Tooltips</span>All tooltips are marked with bold, blue text to draw attention.</span> to many of our pages. The tooltips enable us to maintain short and precise texts with great scientific value, while explaining some of the more exotic words and abbreviations.</br>
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We also use tooltips when <span class="sourceReference">quoting a source without cluttering the text.</span>
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<span class="tooltip">
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  <span class="tooltipHeader">Source</span>
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  <i>A reference to our source will be placed here</i>
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</span>
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We would like to thank Associate Professor, Ph.D. <b>Jakob Møller Jensen & The Microbiology group</b>, and the rest of the <b>Department of Biochemistry and Molecular Biology</b> for letting us use their lab and equipment for the duration of the project.
</p>
</p>
 +
<p>
<p>
-
<span class="intro">Stay on track: Many external sites are shown as in-page dialogs</span><br>
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<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/97/SDU2013_SDU_Logo.jpg" style="width:300px" />
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Sometimes we link to external content, such as our submitted parts. These links will open inside the page using a dialog box, which can be easily closed by clicking the escape button in the top right corner. This helps users stay on track when browsing our wiki.
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<ul>
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<li>
 +
Our instructors Ph.D. Fellow <b>Kirstine Jacobsen,</b> Academic Assistant <b> Tina Kronborg,</b> and Ph.D <b>Ann Zahle Andersen</b> have been there for us all summer in our adversity and prosperity, an exceptional and gratefull thanks from us to them.<br>
 +
</li><li>
 +
Medical Laboratory Technician <b>Simon Rose</b> helped us tremendously with safety; introducing us to the laboratory as well as aiding with the safety form. <br>
 +
</li><li>
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Postdoc <b>Anders Boysen</b> helped troubleshoot when the PCR reactions were misbehaving.
 +
</li><li>
 +
Postdoc <b>Mikkel Jørgensen</b> gave us a lifesaving course in primer design.
 +
</li><li>
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Academic Assistant <b>Eva Lillebæk</b> answered our questions when needed in the everyday lab.
 +
</li><li>
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Associate Professor, dr. <b>Paul Stein</b> helped us with our characterization through NMR support.
 +
</li><li>
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Stud.cand.scient. <b>Lennart Bjerre Nielsen</b> and Ph.D. Fellow <b>Pernille Lassen</b> helped us with our characterization through MALDI support.
 +
</li><li>
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Academic Assistant, Ph.D. <b>Lise Junker Nielsen</b> helped us with our rubber purification process.
 +
</li><li>
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Ph.D. <b>Tine Daa Schrøder</b> helped us with our Dynamic Light Scattering measurements.
 +
</li><li>
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Head of Department (Institute of Chemical Engineering, Biotechnology and Environmental Technology), Professor, <b>Lars Porskjær Christensen</b>, Medical Laboratory Technician <b>Hanne V. Hemmingsen</b>, Medical Laboratory Technician <b>Dorthe Lillesø</b>, and Medical Laboratory Technichian <b>Brian Hermansen</b> all helped us with our GC characterization.
 +
</li>
 +
</ul>
</p>
</p>
 +
</br>
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<p>
-
<br>
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<h4>General support</h4>
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<p>
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<ul>
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<li>
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<h2>Compliance with the iGEM 2013 wiki requirements</h2>
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The iGEM team from <span class="intro">DTU</span> hosted an iGEM crash course in April. They introduced us to the USER-cloning technique, which we have used for the duration  of our project.
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The <a href="https://2013.igem.org/Requirements/Wiki" target="_blank">wiki requirements’</a> primary purpose is to ensure that the wiki will continue to function, even several years from now. Also, it is important that future teams can look to previous wikis and learn from them; hopefully resulting in even better wikis in the future in the spirit of iGEM’s community sharing.
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</li><li>
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<br><br>
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Innovation - & Entrepreneurship Expert <b>Sabina Kethelz</b> held a course in project management, giving us the tools to create a better group dynamic and to tackle any problem that arose.
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<span class="intro">All wiki requirements are met. </span>Below is an outline of focal points:<br>
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</li><li>
 +
Associate Professor, Ph.D. <b>Birthe Vester</b> gave a lecture on antibiotic resistance at the DK meet-up.
 +
</li><li>
 +
<b>DTU</b> and <span class="intro">UNIK-Copenhagen</span> iGEM teams visited us at the DK meet-up and gave us some great feedback at the workshop.
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</li><li>
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<a class="dialogLink" href="https://www.facebook.com/groups/162596843917752"><b>Bioscientific dissemination at SDU</b></a> gave us great feedback on our presentation in preparation of the jamboree.
 +
</li><li>
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Stud.cand.scient. <b>Claus Asger Lykkebo</b> did an amazing job, helping us designing and creating our own logo.
 +
</li>
 +
</ul>
</p>
</p>
 +
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</br>
<p>
<p>
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<span class="intro">All pages, images, and files are hosted on the 2013.igem.org server</span><br>
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<h4>Technical support</h4>
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This also includes all necessary javascript and JQuery code needed for the wiki to function properly.
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 +
<ul>
 +
<li>
 +
Associate Professor <b>Kristian Debrabant</b>, helped with the some of the technical programming for the modeling of our system.
 +
</li><li>
 +
Systems developer, datamatician <b>Kenneth Jensen</b> helped us a great deal with the creation of our wiki, teaching us how to create a userfriendly site. He also helped with the more complex programming, such as the tour menu, as well as helping with general layout and design issues<span class="tooltipLink">.</span><span class="tooltip"><span class="tooltipHeader">Zeus</span>Superman</span>
 +
</li>
 +
</ul>
</p>
</p>
 +
</br>
<p>
<p>
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<span class="intro">No flash was used in the making of this wiki</span><br>
 
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Since flash is not open-source, it would be impossible for other teams to see how it is made. Besides, flash is not visible from many <span class="tooltipLink">modern mobile devices</span><span class="tooltip"><span class="tooltipHeader">Modern mobile devices</span>iPhones, iPads, Windows Phone 8 and Windows tablets.
 
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</span>, which would make the wiki less accessible. Consequently, all animations were done using javascript.
 
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</p>
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<div class="imageGallery galleryMedium alignCenter">
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<p>
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<a class="galleryImg" target="_blank" href="https://static.igem.org/mediawiki/2013/3/31/SDU2013_Attri_1.JPG" title="We have shown USER-cloning to the public">
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<img src="https://static.igem.org/mediawiki/2013/a/af/SDU2013_Small_Attri_1.JPG">
 +
</a>
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<a class="galleryImg" target="_blank" href="https://static.igem.org/mediawiki/2013/c/c8/SDU2013_Attri_2.JPG" title="We had a great intro to USER cloning <Andreas is batman!> ">
 +
<img src="https://static.igem.org/mediawiki/2013/b/be/SDU2013_Small_Attri_2.JPG">
 +
</a>
 +
 
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<a class="galleryImg" target="_blank" href="https://static.igem.org/mediawiki/2013/8/8e/SDU2013_Attri_3.jpg" title="Great thanks to the other danish iGEM teams">
 +
<img src="https://static.igem.org/mediawiki/2013/e/e9/SDU2013_Small_Attri_3.jpg">
 +
</a>
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<span class="intro">Project description on front page</span><br>
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Us telling the public about USER-cloning and pictures from the DTU workshop.
-
To welcome new readers, the front page focuses on our project description.
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 +
</div>
</p>
</p>
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<p>
 
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<span class="intro">All pages are in the team namespace</span><br>
 
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We made sure that all our pages are created in the correct namespace, in our case under the <span class="spceialWord">Team:SDU-Denmark.</span>
 
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</p>
 
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<p>
 
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<span class="intro">There is a link to the completed safety form and an attributions section as part of the wiki</span><br>
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<br>
-
The completed safety form can be viewed on our <a href="https://2013.igem.org/Team:SDU-Denmark/Tour34">safety page.</a><br>
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The attributions page can be found <a href="https://2013.igem.org/Team:SDU-Denmark/Tour12">here.</a>
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-
</p>
 
<p>
<p>
-
<span class="intro">iGEM logo and user editing menu is found on the top of every page</span><br>
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<h4>Litterature support</h4>
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We kept the original iGEM logo in the header as a link to igem.org.
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The user editing menu is also visible on every page, just above our header. Note that the header collapses to save space, and you may have to scroll to the top of the page to view it, exactly as it does on the igem.org site. This way, menus are in their expected positions and easily accessible to future teams.
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<p>
 +
<span class="intro">The Team:</span><br>
 +
<ul><li>
 +
 +
Homepage of University of Southern Denmark. <a href="http://www.sdu.dk/en/Om_SDU" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
Odense Central Local History Library and City Archives. <a href="http://www.historienshus.dk/" target="_blank">(Link)</a>
 +
 +
</li></ul>
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</p><p>
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 +
 +
 +
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<span class="intro">The rubber issue: </span><br>
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<ul><li>
 +
Tanaka, Y., & J. T. Sakdapipanich. 2001. Chemical structure and occurrence of natural polyisoprenes, p. 1-25. In T. Koyama & A. Steinbüchel (ed.), Biopolymers, vol. 2. Polyisoprenoids. Wiley-VCH, Weinheim, Germany.
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<a href="http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527302212.html" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
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K.O. Omokhafe & J.E. Alika: Clonal stability of latex yield in eleven clones of <span class="specialWord">Hevea brasiliensis</span> Muell. Arg. Gen Mol Biol 2003, 26:313-317. <a href="http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000300016" target="_blank">(Link)</a>
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</li><li>
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The International Rubber Study Group IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>
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</li></ul>
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</p><p>
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<span class="intro">Current situation:</span><br>
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<ul>
 +
<li>
 +
The International Rubber Study Group IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>
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</li><li>
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International Smallholder Rubber Conference Phnom Penh, Cambodia  24 June 2009 Panel 4 : Prospects - IRSG
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</li><li>
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Rubber Statistical Bulletin, April - June 2013 edition by IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>
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</li><li>
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Threadingham, D., et al Synthetic rubber. In Ullmann's Encyclopedia of Industrial Chemistry, Bohnet, M., et al. (eds.), Wiley-VCH, Weinheim, 2006, Vol. A23 pp. 53-59, 93-97. <a href="http://onlinelibrary.wiley.com/doi/10.1002/14356007.a23_239.pub5/abstract" target="_blank">(Link)</a>
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</li><li>
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The Great Danish Encyclopedia <a href="http://www.denstoredanske.dk/Natur_og_milj%C3%B8/Botanik/Udenlandske_tr%C3%A6sorter/gummitr%C3%A6" target="_blank">(Link)</a>
 +
 +
</li><li>
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K.O. Omokhafe & J.E. Alika: Clonal stability of latex yield in eleven clones of <span class="specialWord">Hevea brasiliensis</span> Muell. Arg. Gen Mol Biol 2003, 26:313-317. <a href="http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000300016" target="_blank">(Link)</a>
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</li>
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</ul>
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</p><p>
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<span class="intro">The fatal future:</span><br>
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<ul><li>
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Li, H., et al: Demand for rubber is causing the loss of high diversity rain forest in SW China. Biodivers Conserv (2007) 16:1731–1745
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<a href="http://link.springer.com/chapter/10.1007%2F978-1-4020-6444-9_11" target="_blank">(Link)</a>
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</li><li>
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UN 2300 report <a href="http://www.un.org/esa/population/publications/longrange2/WorldPop2300final.pdf" target="_blank">(Link)</a>
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</ul></li>
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</p><p>
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<span class="intro">The production system:</span><br>
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<ul><li>
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Light DR, Dennis MS. Purification of a prenyltransferase that elongates cis-polyisoprene rubber from the latex of <span class="specialWord">Hevea brasiliensis</span>. J Biol Chem. 1989 Nov 5;264(31):18589-97. <a href="http://www.ncbi.nlm.nih.gov/pubmed/2808388" target="_blank">(Link)</a>
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 +
</li><li>
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem. 2013;82:497-530. doi: 10.1146/annurev-biochem-052010-100934.
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/23746261" target="_blank">(Link)</a>
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</li><li>
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Asawatreratanakul K, Zhang YW, Wititsuwannakul D, Wititsuwannakul R, Takahashi S, Rattanapittayaporn A, Koyama T. Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from <span class="specialWord">Hevea brasiliensis</span>. A key factor participating in natural rubber biosynthesis. Eur J Biochem. 2003 Dec;270(23):4671-80.
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/14622254" target="_blank">(Link)</a>
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</ul></li>
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 +
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</p><p>
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<span class="intro">Specifications:</span><br>
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<ul><li>
 +
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem. 2013;82:497-530. doi: 10.1146/annurev-biochem-052010-100934.
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23746261" target="_blank">(Link)</a>
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 +
</li><li>
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Alaxander Steinbüchel: Production of rubber-like polymers by microorganism, Current Opinion in Microbiology 2003. 6:261-270. (book) <a href="http://www.ncbi.nlm.nih.gov/pubmed/12831902" target="_blank">(Link)</a>
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 +
</ul></li>
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</p><p>
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<span class="intro">Modelling: </span><br>
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<ul><li>
 +
 +
<b>Dxs:</b>
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Sprenger GA, Schorken U, Wiegert T, Grolle S, De Graaf AA, Taylor
 +
SV, Begley TP, Bringer-Meyer S, Sahm H (1997) Identification
 +
of a thiamin-dependent synthase in <span class="specialWord">Escherichia coli</span> required for
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the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to
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isoprenoids, thiamin, and pyridoxol. Proc Natl Acad Sci USA
 +
94:12857–12862
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/9371765" target="_blank">(Link)</a>
 +
 +
 +
</li><li>
 +
 +
<b>Dxs:</b>
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 +
Miller B, Heuser T, Zimmer W (2000) Functional involvement of a
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deoxy-xylulose 5-phosphate reductoisomerase gene harboring
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locus of Synechococcus leopoliensis in isoprenoid biosynthesis.
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FEBS Lett 481:221–226
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/11007968" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
<b>Dxr:</b> 
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Koppisch AT, Fox DT, Blagg BS, Poulter CD. <span class="specialWord">E. coli</span> MEP synthase: steady-state kinetic analysis and substrate binding. Biochemistry. 2002 Jan 8;41(1):236-43.
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/11772021" target="_blank">(Link)</a>
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 +
</li><li>
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<b>IspD:</b>
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Richard SB, Lillo AM, Tetzlaff CN, Bowman ME, Noel JP, Cane DE. Kinetic analysis of <span class="specialWord">Escherichia coli</span> 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase, wild type and mutants, reveals roles of active site amino acids. Biochemistry. 2004 Sep 28;43(38):12189-97.
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/15379557" target="_blank">(Link)</a>
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 +
</li><li>
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<b>IspE:</b>
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Bernal C, Mendez E, Terencio J, Boronat A, Imperial S. A spectrophotometric assay for the determination of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase activity. Anal Biochem. 2005 May 15;340(2):245-51.
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/15840497" target="_blank">(Link)</a>
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 +
 +
</li><li>
 +
 +
<b>IspF:</b>
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Geist JG, Lauw S, Illarionova V, Illarionov B, Fischer M, Gräwert T, Rohdich F, Eisenreich W, Kaiser J, Groll M, Scheurer C, Wittlin S, Alonso-Gómez JL, Schweizer WB, Bacher A, Diederich F. Thiazolopyrimidine inhibitors of 2-methylerythritol 2,4-cyclodiphosphate synthase (IspF) from Mycobacterium tuberculosis and Plasmodium falciparum.
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 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/20480490" target="_blank">(Link)</a>
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 +
 +
 +
</li><li>
 +
 +
<b>IspG:</b>
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 +
Zepeck F, Gräwert T, Kaiser J, Schramek N, Eisenreich W, Bacher A, Rohdich F. Biosynthesis of isoprenoids. purification and properties of IspG protein from <span class="specialWord">Escherichia coli</span>. J Org Chem. 2005 Nov 11;70(23):9168-74.
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/16268586" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
<b>B<sub>1</sub> and B<sub>6</sub>:</b>
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 +
Yeh JI, Du S, Pohl E, Cane DE. Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate. Biochemistry. 2002 Oct 1;41(39):11649-57.
 +
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/12269807" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
<b>B<sub>1</sub> and B<sub>6</sub>:</b>
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 +
D. E. Cane, S. C. Du, J. K. Robinson, Y. J. Hsiung, I. D. Spenser. Biosynthesis of Vitamin B<sub>6</sub>: Enzymatic Conversion of 1-Deoxy-D-xylulose-5-phosphate to Pyridoxol Phosphate J. Am. Chem. Soc. 121,
 +
7722–7723 (1999).
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 +
<a href="http://pubs.acs.org/doi/pdf/10.1021/ja9914947" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
Bollenbach, T. et al. Non-optimal microbial response to antibiotics underlies suppressive drug interactions; Cell. 2009 November 13; 139(4): P. 707–718. <a href="http://download.cell.com/pdf/PIIS0092867409013154.pdf?intermediate=true" target="_blank" )="">(Link)</a>
 +
 +
 +
</li></ul>
 +
 +
 +
</p><p>
 +
 +
<span class="intro">Results: </span><br>
 +
 +
<ul><li>
 +
Fisher AJ, Rosenstiel TN, Shirk MC, Fall R. Nonradioactive assay for cellular dimethylallyl diphosphate. Anal Biochem. 2001 May 15;292(2):272-9.
 +
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/11355861" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
Donald L. Pavia and Gary M. Lampman. Introduction to Spectroscopy, International Edition 4e (Book) ISBN-13: 9780538734189 / ISBN-10: 0538734183
 +
 +
<a href="http://edu.cengage.co.uk/catalogue/product.aspx?isbn=0538734183" target="_blank">(Link)</a>
 +
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</li></ul>
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 +
</p><p>
 +
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<span class="intro">Rubber: </span><br>
 +
 +
<ul><li>
 +
Fisher AJ, Rosenstiel TN, Shirk MC, Fall R. Nonradioactive assay for cellular dimethylallyl diphosphate. Anal Biochem. 2001 May 15;292(2):272-9.
 +
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/11355861" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
Donald L. Pavia and Gary M. Lampman. Introduction to Spectroscopy, International Edition 4e (Book) ISBN-13: 9780538734189 / ISBN-10: 0538734183
 +
 +
<a href="http://edu.cengage.co.uk/catalogue/product.aspx?isbn=0538734183" target="_blank">(Link)</a>
 +
 +
</li><li>
 +
 +
Hyuneui L, Yeonhee L, Seunghee H, Youngsook Y, and Kang-Jin K. Investigation of Polystyrene, Polyisoprene, and Poly(2-vinylpyridine) using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Bull. Korean Chem. Soc. 1999, Vol. 20, No. 7 p. 853-856. <a href="http://pdf.lookchem.com/pdf/32/19391c15-f5be-4e7d-8b1d-7becdc30c921.pdf" target="_blank">(Link)</a>
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</li></ul>
</p>
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Latest revision as of 00:43, 29 October 2013

Bacteriorganic Rubber
iGEM logo
Introduction
Rubber issue
Production system
Process
Results
Future

Attributions

Showing gratitude to those we could not have done without

"I get by with a little help from my friends." - John Lennon

Sponsors

We would like to thank our sponsor University of Southern Denmark for giving us the funds for the project, making it possible for us to participate in iGEM. In particular, we would like to thank Dean Henrik Pedersen and the Faculty of Science at University of Southern Denmark. We would also like to thank Bionordika for sponsoring the USER-enzymes. And a great thank to ERASynBio for sponsoring our trip to the World Championship in Boston.


Laboratory support

We would like to thank Associate Professor, Ph.D. Jakob Møller Jensen & The Microbiology group, and the rest of the Department of Biochemistry and Molecular Biology for letting us use their lab and equipment for the duration of the project.

  • Our instructors Ph.D. Fellow Kirstine Jacobsen, Academic Assistant Tina Kronborg, and Ph.D Ann Zahle Andersen have been there for us all summer in our adversity and prosperity, an exceptional and gratefull thanks from us to them.
  • Medical Laboratory Technician Simon Rose helped us tremendously with safety; introducing us to the laboratory as well as aiding with the safety form.
  • Postdoc Anders Boysen helped troubleshoot when the PCR reactions were misbehaving.
  • Postdoc Mikkel Jørgensen gave us a lifesaving course in primer design.
  • Academic Assistant Eva Lillebæk answered our questions when needed in the everyday lab.
  • Associate Professor, dr. Paul Stein helped us with our characterization through NMR support.
  • Stud.cand.scient. Lennart Bjerre Nielsen and Ph.D. Fellow Pernille Lassen helped us with our characterization through MALDI support.
  • Academic Assistant, Ph.D. Lise Junker Nielsen helped us with our rubber purification process.
  • Ph.D. Tine Daa Schrøder helped us with our Dynamic Light Scattering measurements.
  • Head of Department (Institute of Chemical Engineering, Biotechnology and Environmental Technology), Professor, Lars Porskjær Christensen, Medical Laboratory Technician Hanne V. Hemmingsen, Medical Laboratory Technician Dorthe Lillesø, and Medical Laboratory Technichian Brian Hermansen all helped us with our GC characterization.


General support

  • The iGEM team from DTU hosted an iGEM crash course in April. They introduced us to the USER-cloning technique, which we have used for the duration of our project.
  • Innovation - & Entrepreneurship Expert Sabina Kethelz held a course in project management, giving us the tools to create a better group dynamic and to tackle any problem that arose.
  • Associate Professor, Ph.D. Birthe Vester gave a lecture on antibiotic resistance at the DK meet-up.
  • DTU and UNIK-Copenhagen iGEM teams visited us at the DK meet-up and gave us some great feedback at the workshop.
  • Bioscientific dissemination at SDU gave us great feedback on our presentation in preparation of the jamboree.
  • Stud.cand.scient. Claus Asger Lykkebo did an amazing job, helping us designing and creating our own logo.


Technical support

  • Associate Professor Kristian Debrabant, helped with the some of the technical programming for the modeling of our system.
  • Systems developer, datamatician Kenneth Jensen helped us a great deal with the creation of our wiki, teaching us how to create a userfriendly site. He also helped with the more complex programming, such as the tour menu, as well as helping with general layout and design issues.ZeusSuperman


Us telling the public about USER-cloning and pictures from the DTU workshop.


Litterature support

The Team:

  • Homepage of University of Southern Denmark. (Link)
  • Odense Central Local History Library and City Archives. (Link)

The rubber issue:

  • Tanaka, Y., & J. T. Sakdapipanich. 2001. Chemical structure and occurrence of natural polyisoprenes, p. 1-25. In T. Koyama & A. Steinbüchel (ed.), Biopolymers, vol. 2. Polyisoprenoids. Wiley-VCH, Weinheim, Germany. (Link)
  • K.O. Omokhafe & J.E. Alika: Clonal stability of latex yield in eleven clones of Hevea brasiliensis Muell. Arg. Gen Mol Biol 2003, 26:313-317. (Link)
  • The International Rubber Study Group IRSG (Link)

Current situation:

  • The International Rubber Study Group IRSG (Link)
  • International Smallholder Rubber Conference Phnom Penh, Cambodia 24 June 2009 Panel 4 : Prospects - IRSG
  • Rubber Statistical Bulletin, April - June 2013 edition by IRSG (Link)
  • Threadingham, D., et al Synthetic rubber. In Ullmann's Encyclopedia of Industrial Chemistry, Bohnet, M., et al. (eds.), Wiley-VCH, Weinheim, 2006, Vol. A23 pp. 53-59, 93-97. (Link)
  • The Great Danish Encyclopedia (Link)
  • K.O. Omokhafe & J.E. Alika: Clonal stability of latex yield in eleven clones of Hevea brasiliensis Muell. Arg. Gen Mol Biol 2003, 26:313-317. (Link)

The fatal future:

  • Li, H., et al: Demand for rubber is causing the loss of high diversity rain forest in SW China. Biodivers Conserv (2007) 16:1731–1745 (Link)
  • UN 2300 report (Link)

The production system:

  • Light DR, Dennis MS. Purification of a prenyltransferase that elongates cis-polyisoprene rubber from the latex of Hevea brasiliensis. J Biol Chem. 1989 Nov 5;264(31):18589-97. (Link)
  • Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem. 2013;82:497-530. doi: 10.1146/annurev-biochem-052010-100934. (Link)
  • Asawatreratanakul K, Zhang YW, Wititsuwannakul D, Wititsuwannakul R, Takahashi S, Rattanapittayaporn A, Koyama T. Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis. A key factor participating in natural rubber biosynthesis. Eur J Biochem. 2003 Dec;270(23):4671-80. (Link)

Specifications:

  • Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem. 2013;82:497-530. doi: 10.1146/annurev-biochem-052010-100934. (Link)
  • Alaxander Steinbüchel: Production of rubber-like polymers by microorganism, Current Opinion in Microbiology 2003. 6:261-270. (book) (Link)

Modelling:

  • Dxs: Sprenger GA, Schorken U, Wiegert T, Grolle S, De Graaf AA, Taylor SV, Begley TP, Bringer-Meyer S, Sahm H (1997) Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. Proc Natl Acad Sci USA 94:12857–12862 (Link)
  • Dxs: Miller B, Heuser T, Zimmer W (2000) Functional involvement of a deoxy-xylulose 5-phosphate reductoisomerase gene harboring locus of Synechococcus leopoliensis in isoprenoid biosynthesis. FEBS Lett 481:221–226 (Link)
  • Dxr: Koppisch AT, Fox DT, Blagg BS, Poulter CD. E. coli MEP synthase: steady-state kinetic analysis and substrate binding. Biochemistry. 2002 Jan 8;41(1):236-43. (Link)
  • IspD: Richard SB, Lillo AM, Tetzlaff CN, Bowman ME, Noel JP, Cane DE. Kinetic analysis of Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase, wild type and mutants, reveals roles of active site amino acids. Biochemistry. 2004 Sep 28;43(38):12189-97. (Link)
  • IspE: Bernal C, Mendez E, Terencio J, Boronat A, Imperial S. A spectrophotometric assay for the determination of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase activity. Anal Biochem. 2005 May 15;340(2):245-51. (Link)
  • IspF: Geist JG, Lauw S, Illarionova V, Illarionov B, Fischer M, Gräwert T, Rohdich F, Eisenreich W, Kaiser J, Groll M, Scheurer C, Wittlin S, Alonso-Gómez JL, Schweizer WB, Bacher A, Diederich F. Thiazolopyrimidine inhibitors of 2-methylerythritol 2,4-cyclodiphosphate synthase (IspF) from Mycobacterium tuberculosis and Plasmodium falciparum. (Link)
  • IspG: Zepeck F, Gräwert T, Kaiser J, Schramek N, Eisenreich W, Bacher A, Rohdich F. Biosynthesis of isoprenoids. purification and properties of IspG protein from Escherichia coli. J Org Chem. 2005 Nov 11;70(23):9168-74. (Link)
  • B1 and B6: Yeh JI, Du S, Pohl E, Cane DE. Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate. Biochemistry. 2002 Oct 1;41(39):11649-57. (Link)
  • B1 and B6: D. E. Cane, S. C. Du, J. K. Robinson, Y. J. Hsiung, I. D. Spenser. Biosynthesis of Vitamin B6: Enzymatic Conversion of 1-Deoxy-D-xylulose-5-phosphate to Pyridoxol Phosphate J. Am. Chem. Soc. 121, 7722–7723 (1999). (Link)
  • Bollenbach, T. et al. Non-optimal microbial response to antibiotics underlies suppressive drug interactions; Cell. 2009 November 13; 139(4): P. 707–718. (Link)

Results:

  • Fisher AJ, Rosenstiel TN, Shirk MC, Fall R. Nonradioactive assay for cellular dimethylallyl diphosphate. Anal Biochem. 2001 May 15;292(2):272-9. (Link)
  • Donald L. Pavia and Gary M. Lampman. Introduction to Spectroscopy, International Edition 4e (Book) ISBN-13: 9780538734189 / ISBN-10: 0538734183 (Link)

Rubber:

  • Fisher AJ, Rosenstiel TN, Shirk MC, Fall R. Nonradioactive assay for cellular dimethylallyl diphosphate. Anal Biochem. 2001 May 15;292(2):272-9. (Link)
  • Donald L. Pavia and Gary M. Lampman. Introduction to Spectroscopy, International Edition 4e (Book) ISBN-13: 9780538734189 / ISBN-10: 0538734183 (Link)
  • Hyuneui L, Yeonhee L, Seunghee H, Youngsook Y, and Kang-Jin K. Investigation of Polystyrene, Polyisoprene, and Poly(2-vinylpyridine) using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Bull. Korean Chem. Soc. 1999, Vol. 20, No. 7 p. 853-856. (Link)

Next chapter

Next chapter

Dig deeper

End of tour

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