Team:SDU-Denmark/Tour13

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

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)