Team:SDU-Denmark/Tour13

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<h2>Attributions</h2>
<h4>Showing gratitude to those we could not have done without</h4>





<p class='intro'>
"I get by with a little help from my friends."
<b>- John Lennon </b>
</p>



<p>

<h4>Sponsors</h4>

<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/94/SDU2013_ERASynbio.png" style="width:280px" />


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. 

</p>
</br>

<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/9b/SDU2013_BioNordika_Logo.jpg" style="width:300px" />
<p>

<h4>Laboratory support</h4>




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>

<img class="alignRight" src="https://static.igem.org/mediawiki/2013/9/97/SDU2013_SDU_Logo.jpg" style="width:300px" />

<ul>
<li>
Our instructors Ph.D. Fellow <b>Kirstine Jacobsen,</b> Academic Assistant <br> Tina Kronborg,</br> and Ph.D <br>Ann Zahle Andersen</br> 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>
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>
Academic Assistant <b>Eva Lillebæk</b> answered our questions when needed in the everyday lab.
</li><li>
Associate Professor, dr. <b>Paul Stein</b> helped us with our characterization through NMR support.
</li><li>
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>
Academic Assistant, Ph.D. <b>Lise Junker Nielsen</b> helped us with our rubber purification process.
</li><li>
Ph.D. <b>Tine Daa Schrøder</b> helped us with our Dynamic Light Scattering measurements.
</li><li>
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>


</br>
<p>

<h4>General support</h4>

<ul>
<li>

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.
</li><li>
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.
</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.
</li><li>
<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>
Stud.cand.scient. <b>Claus Asger Lykkebo</b> did an amazing job, helping us designing and creating our own logo. 

</li>
</ul>
</p>


</br>

<p>

<h4>Technical support</h4>

<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>
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<p>


<div class="imageGallery galleryMedium alignCenter">

<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">
 <img src="https://static.igem.org/mediawiki/2013/a/af/SDU2013_Small_Attri_1.JPG">
</a>

<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>

<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>

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

</div>

</p>






<br>





<p>

<h4>Litterature support</h4>

<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>

</p><p>




<span class="intro">The rubber issue: </span><br>
<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.

<a href="http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527302212.html" target="_blank">(Link)</a>

</li><li>

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. <a href="http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000300016" target="_blank">(Link)</a>

</li><li>

The International Rubber Study Group IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>

</li></ul>

</p><p>


<span class="intro">Current situation:</span><br>
<ul>
<li>
The International Rubber Study Group IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>

</li><li>
International Smallholder Rubber Conference Phnom Penh, Cambodia  24 June 2009 Panel 4 : Prospects - IRSG
</li><li>
Rubber Statistical Bulletin, April - June 2013 edition by IRSG <a href="http://www.rubberstudy.com/pub-stats-bulletin.aspx" target="_blank">(Link)</a>

</li><li>

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>

</li><li>

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>

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. <a href="http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000300016" target="_blank">(Link)</a>

</li>
</ul>

</p><p>

<span class="intro">The fatal future:</span><br>
<ul><li>
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
<a href="http://link.springer.com/chapter/10.1007%2F978-1-4020-6444-9_11" target="_blank">(Link)</a>



</li><li>

UN 2300 report <a href="http://www.un.org/esa/population/publications/longrange2/WorldPop2300final.pdf" target="_blank">(Link)</a>

</ul></li>

</p><p>

<span class="intro">The production system:</span><br>

<ul><li>
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. <a href="http://www.ncbi.nlm.nih.gov/pubmed/2808388" target="_blank">(Link)</a>

</li><li>

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>


</li><li>

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.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/14622254" target="_blank">(Link)</a>


</ul></li>



</p><p>

<span class="intro">Specifications:</span><br>

<ul><li>

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>

</li><li>

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>

</ul></li>



</p><p>


<span class="intro">Modelling: </span><br>

<ul><li>

<b>Dxs:</b>

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
<a href="http://www.ncbi.nlm.nih.gov/pubmed/9371765" target="_blank">(Link)</a>


</li><li>

<b>Dxs:</b>

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

<a href="http://www.ncbi.nlm.nih.gov/pubmed/11007968" target="_blank">(Link)</a>

</li><li>

<b>Dxr:</b>  
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.

<a href="http://www.ncbi.nlm.nih.gov/pubmed/11772021" target="_blank">(Link)</a>

</li><li>

<b>IspD:</b> 
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.

<a href="http://www.ncbi.nlm.nih.gov/pubmed/15379557" target="_blank">(Link)</a>

</li><li>

<b>IspE:</b>

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.

<a href="http://www.ncbi.nlm.nih.gov/pubmed/15840497" target="_blank">(Link)</a>


</li><li>

<b>IspF:</b>
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.

<a href="http://www.ncbi.nlm.nih.gov/pubmed/20480490" target="_blank">(Link)</a>



</li><li>

<b>IspG:</b>

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.
<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>

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>

 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).

<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">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></ul>
</p>


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