Team:SDU-Denmark/Tour14

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Edible coli

Welcome

Interactive wiki-tour

Menu

Introduction

Edible coli

Process

Results

Policy and practices

Future

Attributions

"If you want to become a great chef, you have to work with great chefs" - Gordon Ramsay

Laboratory support

We would like to thank Associate Professor, Ph. D. Jakob Møller Jensen and the Microbiology group and also the rest of the Department of Biochemistry and Molecular Biology for letting us use their lab, providing laboratory equipment and guidance throughout our project.

Our instructors Academic Assistant Tina Kronborg, post doc Ann Zahle Andersen, stud.cand. Patrick Rosendahl Andreassen, stud.cand. Andreas Kjær and stud.cand. Thøger Jensen Krogh have adviced us the entire summer when crying for help. We are really grateful for all your advice in every situation.
Ph.D. fellow Maria Storm Mollerup helped us with general questions in the lab.
Academic assistant Eva Maria Sternkopf Lillebæk helped with tips and tricks to Western Blot and provided us with a Bacillus subtilis strain.
Ph.D. fellow Sabrina Brøner helped us getting doxycycline.
Post doc Anders Boysen assisted us with planning of Western Blots collaborated with materials to make them.
Medical Laboratory Technician Simon Rose introduced us to lab safety and behavior. Furthermore, he agreed to give an interview regarding our safety form.
From the University of Copenhagen professor, Ph.D., head of Section for Molecular Plant Biology, vice head of Copenhagen Plant science Centre Poul Erik Jensen who sent us a Synechocystis sp. PCC6803 strain.
Stud.Bsc.Sc. Kristian Davidsen from DTU provided us with USER polymerase.
Professor, Ph.D. Nils Joakim Færgeman pointed us to litterature to design a GC experiment and the toxicity assay on Caenorhabditis elegans.
Ph. D. fellow Eva Bang Harvald provided us with Caenorhabditis elegans and practical information about what to do with them.
Professor Dr. rer. nat. habil. Olaf-Georg Issinger provided us materials and facilities to do SDS-PAGE analysis.
Ph.D. fellow from University of Copenhagen Nana Cecilie Halmsted Kongsholm guided us while planning our ethics section.
Postdoctoral fellow at the Medical Research Council Julius Fredens provided us with a plasmid containing FAT-2 originating from Caenorhabditis elegans.
The SDU iGEM team 2013 has provided great inspiration for the making of our wiki.

Events support

We would like to thank everyone who has helped us promote our project and iGEM by helping us arrange our events.

Student house Odense arranged an event where we could talk about iGEM and synthetic biology and hold a quiz night.
Syddanske studerende let us promote our own project and iGEM by having us at the study trade fair.
IMCC (International Medical Cooperation Committee) let us promote our own project and iGEM by having us at the study trade fair and at sundhedsmekka.
The former SDU iGEM members who met with us and heard about our project and thoughts.

General support

We have received a lot of help during our project - also help that was not in the lab or specific for the execution of our project. We would like thank all the people that have helped us one way or another.

DTU (Technical University of Denmark) had arranged a crash course in the lab for Danish iGEM teams and introduced us to primers, USER cloning and the design of the team wiki.
KU (University of Copenhagen) arranged an ethics workshop for Danish iGEM teams.
YSB (young synthetic biologist) arranged and held the UK iGEM meet-up and allowed our team to join the meet up and told us more about synthetic biology and had arranged different workshops.
Everyone all over the world, who has answered our questionnaire about GMO and what they think about it being a food resource.
Jane Fornitz from the company Ibsing & Fornitz ApS introduced us to the different types of personalities and how to work together with different personalities - this has been a great help for the team work.
Doctor Yaa Difie-Osei from the National Biosafety Committee, Ghana and Professor George Armah from the Noguchi Memorial Institute for Medical Research gave us an interview to our Practices and Policy, regarding outreach and ethical considerations.
Bioscientific dissemination at SDU gave us great feedback on our presentation in preparation of the jamboree.
Stud. bac linguistics Klara Tandrup Pedersen helped us proofread our wiki.

Technical support

Post doc Ann Zahle Andersen helped us decode the programs used for modelling.
Stud.cand. Patrick Rosendahl Andreassen, stud.cand. Andreas Kjær and stud.cand. Thøger Jensen Krogh have assisted us with sequencing results.
Stud.cand. Thøger Jensen Krogh introduced us to designing our team wiki.

Modelling

Stud.cand. Nicky Cordua Mattsson adviced us with the modelling of our system.
Post doc Ann Zahle Andersen adviced us all the way with our model.

Litterature support

Edible coli:

WWF, Living Planet Report 2012: Biodiversity, biocapacity and better chioces. (Link)
Food and Agriculture Organization of the United Nations, 2014: Hunger Statistics. (Link)
Food and Agriculture Organization of the United Nations, 2014: Basic definitions. (Link)
Central intelligence Agency, 2014: The World Factbook. (link)
World Hunger, 2013: 2013 World Hunger and Poverty Facts and Statistics. (Link)
Save the Children, 2014: Where do we work.(Link)
Population media Center, 2009: Issue we Address. (Link)
FAO/WHO Expert Consultation: Carbohydrates in the human nutrition. FAO Food and Nutrition Paper, 1997. Vol. 66: Carbohydrates in the diet. (Link)
FAO Expert Consultation: Fats and fatty acids in human nutrition. FAO Food and Nutrition Paper, 2010. Vol. 91: p. 11-12. (Link)
WHO/FAO/UNU Expert Consultation: Protein and Amino Acid Requirement in Human Nutrition. WHO Technical Report Series, 2007. Vol. 935. (Link)
Center for Disease Control and Prevention, 2012: Nutrition for everyone. (Link)
NHC, 2011: Symptoms of malnutrition. (Link)
Contribution of Carbohydrates in Total Dietary Consumption: (Link)
FAO/WHO Expert Consultation: Carbohydrates in the human nutrition. FAO Food and Nutrition Paper, 1997. Vol. 66: Carbohydrates in the diet. (Link)
The World Bank, 2014: GNI per Capita, Atlas method (current US$). (Link)
Contribution of Proteins in Total Dietary Consumption: (Link)
WHO/FAO/UNU Expert Consultation: Protein and Amino Acid Requirement in Human Nutrition. WHO Technical Report Series, 2007. Vol. 935. (Link)
Consumption of Fats in Total Dietary Consumption: (Link)
FAO Expert Consultation: Fats and fatty acids in human nutrition. FAO Food and Nutrition Paper, 2010. Vol. 91: p. 11-12. (Link)
FAO: Chapter 7 - Food, nutrients and diets. (Link)
WHO/ FAO/ UNU Expert Consultation: Protein and Amino Acid Requirements in Human Nutrition, 2002. Vol. 935.
WHO/FAO/UNU Expert Consultation: Protein and Amino Acid Requirements in Human Nutrition. United Nations University, 2002. No. 935, p. 150-164. (Link)
Lynd, L.R., Weimer, P.J., van Zyl, P.H., and Isak, S.P.: Microbial Cellulose Utilization: Fundamentals and Biotechnology. Microbiology and Molecular Biology Reviews, 2002. Vol. 66:3, p. 506-577. (Link)
Lükcker, J., El Tamer, M.K., Schwab, W., Verstappen, F.V.A., van der Plas, L.H.V., Bouwmeester, H.J., and Verhoeven, H.A.: Monoterpene biosynthesis in lemon (Citrus Limon). European Journal of Biochemistry, 2002. Vol. 269:13, p. 3160-3171. (Link)
Kang, M.J., Lee, Y.M., Yoon, S.H., Kim, J.H., Ock, S.W., Jung, K.H., Shin, Y.C., Keasling, J.D., and Kim, S.W.: Identification of Genes Affecting Lycopene Accumulation in Escherichia coli Using a Shot-Gun Method. Biotechnology and Bioengineering, 2005. Vol. 91, p. 636-642. (Link)
Nelson, D.L. and Cox, M.M.:Lehninger – Principles of Biochemistry, fifth edition. W.H. Freeman and Company, 2008.
Ruiz-López, N., Sayanova, O., Napier, J.A., and Haslam, R.P.: Metabolic engineering of the omega-3 long chain polyunsaturated fatty acid biosynthetic pathway into transgenic plants. Journal of Experimental Botany, 2011. Vol. 63:7, p. 2397-2410. (Link)
Wada, H., Avelange-Macherel, M.H., and Murata, N.: The desA gene of the cyanobacterium Synechocystis sp. strain PCC6803 is the structural gene for delta 12 desaturase. Journal of Bacteriology, 1993. Vol. 175:18, p. 6056-6058. (Link)
Sakamoto, T., Wada, H., Ohmori, M., Murata, N.: Δ9 Acyl-Lipid Desaturases of Cyanobacteria. The Journal of Boilogical Chemistry, 1994. Vol. 269:14, p. 25576-25580. (Link)

Results:

Aagaard, L.., Amarzguioui, M., Sun, Guihua., Santos, L.C., Ehsani, A., Prydz, H. & Rossi, J.J.: A Facile Lentiviral Vector System for Ekspression of Doxycycline-Inducible dhRNAs: Knockdown of the Pre-miRNA Processing Enzyme Drosha. Molecular Therapy, 2007. 15:5, p. 938-945. (Link)
Kang, M.J., Lee, Y.M., Yoon, S.H., Kim, J.H., Ock, S.W., Jung, K.H., Shin, Y.C., Keasling, J.D., and Kim, S.W.: Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method. Biotechnology and Bioengineering, 2005, vol. 91:5, p. 636-642. (Link)
Mosbech, M., Kruse, R., Harvald, E. B., Olsen, A. S. B., Gallego, S. F., Hannibal-Bach, H. K., Ejsing, C. S. & Færgeman, N. J.: Functional Loss of Two Ceramide Synthases Elicits Autophagy-Dependent Lifespan Extension in C. elegans.: PLoS ONE, 2013. 8 vol:7. (Link)
Rodriguez, M., Snoek, L. B., Bono, M.D. & Kammenga, J. E.:Worms under stress: C. elegans sterss response and its relevance to complex human disease and aging. Trends in Genetics, 2013. Vol: 29, 6, p. 367-374. (Link)

Policy and Practices:

MicroBEnet: Microbial Myths: Common misconceptions about microbes (w/ some extra focus on those in the built environment), 2011. (Link)
Marris, C.: Public views on GMOs: deconstructing the myths. EMBO reports, 2001. Vol. 2 p. 545-548. (Link)
Gaskell, G., Stares, S., Allansdottir, A., Allum, N., Corchero, C., Fischler, C., Hampel, J., Jackson, J., Kronberger, N., Mejlgaard, N., Revuelta, G., Schreiner, C., Torgersen, H., and Wagner, W.: Europeans and Biotechnology in 2005: Patterns and Trends. Final report on Eurobarometer 64.3, 2006. P. 57. (Link)
Hancock, R.D.: Recent Patents on Vitamin C: Opportunities for Crop Improvement and Single-Step Biological Manufacture. Recent Patents on Food, Nutrition & Agriculture, 2009. Vol. 1, p. 39-49. (Link)
Sauer, M., Porro, D, Mattanovich, D., and Branduardi, P.: Microbial production of organic acids: expanding the market. Elsevier, 2008. Cell Press, vol. 26:2, p. 100-108. (Link)
GMO Compass, 2006: GM Microorganisms Taking the Place of Chemical Factories. (Link)
Berg, J., Tymoczko, J.L., and Stryer, L.: Biochemistry, Seventh Edition. W.H.Freeman & Co Ltd, 2011.
European Food Information Council, 1999: Lactic acid bacteria – their uses in food. (Link)
Microbiology online: Bacteria. (Link)
Gershon, E.: With you in the room, bacteria counts spike. Yale News, 2012. (Link)
Nielsen , J.: Betydningen af systembiologi for industriel bioteknologi. Biozoom, 2007. Vol. 2, p. 1-3.(Link)
Novo Nordisk: Use of gene technology at Novo Nordisk. (Link)
Homepage of iGEM: Synthetic Biology – based on standard parts. (Link)
Regulation (EC) No 1829/2003 of the European Parliament and of the Council of 22 September 2003 concerning the traceability and labelling of genetically modified organisms and the traceability of food and feed products produced from genetically modified organisms and amending Directive 2001/18/EC (Official Journal L 268, 18/10/2003 P. 0024 – 0028)
Save the Children, 2014: Where do we work. (Link)
NHC, 2011: Symptoms of malnutrition. (Link)
Central intelligence Agency, 2014: The World Factbook. (Link)
Food and Agriculture Organization of the United Nations, 2014: Hunger Statistics. (Link)
Marshall, S: Genetically Modified Organisms and Food. Nutrition & Food Science, 1994.94:1,4-7. (Link)
Mehta, M.: Public perceptions of genetically engineered foods: “Playing God” or trusting science Risk. Health, Safety and Environment, 2001. 12,205–220. (Link)
Davison, J.: GM plants: Science, politics and EC regulations. Plant Science, 2010. 178,94–98. (Link)
Paarlberg, R.: GMO foods and crops: Africa's choice. New Biotechnology, 2010.27:5,609–613. (Link)
Viljoen, C.D and Marx, G.M.: The implications for mandatory GM labelling under the Consumer Protection Act in South Africa. Food Control, 2013.31:2,387–391. (Link)
Mehta, M.: Public perceptions of genetically engineered foods: “Playing God” or trusting science Risk. Health, Safety and Environment, 2001. 12,205–220. (Link)
Einsiedel, E.F.: Mental Maps of Science: Knowledge and attitude Among Canadian Adults. Int J Public Opin Res, 1994.6:1,35-44. (Link)
Marris, C: Public views on GMOs: deconstructing the myths.EMBO reports, 2001.2:7,545-548. (Link)
FAO/WHO/UNU, expert consultation: Protein and amino acid requirements in human nutrition. World Health Organization,2007.935,1-265. (Link)
Peters, HP., Lang, JT., Sawicka, M., Hallman, WK: Culture and Technological Innovation: Impact of Institutional Trust and Appreciation of Nature on Attitudes towards Food Biotechnology in the USA and Germany. Int J Public Opin Res,2007.19:2,191-220. (Link)
Bartsch, D: GMO regulatory challenges and science: a European perspective. Journal of Consumer Protection and Food Safety,2014. 9:1,51–S58. (Link)
World Health Organization, 2014: WHO African region: Ghana. (Link)
World Health Organization, 2014: Country Cooperation Strategy at a glance: Ghana. (Link)
Food and Agriculture Organization of the United Nations, 2010: Nutrition Country Profile: Ghana. (Link)
Ademola A. Adenle, E. Jane Morris, Govindan Parayil: Status of development, regulation and adoption of GM agriculture in Africa: Views and positions of stakeholder groups. Food Policy, 2013:43,159-166. (Link)
Swallow, Dallas M: Genetics of Lactase Persistence and Lactoseintolerance. Annu.Rev.Genet, 2003.37:197-219. (Link)
Child Mortality Estimates, 2014: Under-five mortality rate. (Link)
World Health Organization, 2014: Country Cooperation Strategy at a glance. (Link)
The Mal-ED Network Investigators: The MAL-ED Study: A Multinational and Multidisciplinary Approach to Understand the Relationship Between Enteric Pathogens, Malnutrition, Gut Physiology, Physical Growth, Cognitive Development, and Immune Responses in Infants and Children Up to 2 Years of Age in Resource-Poor Environments. Clin Infect Dis,2014:59(4),193-206. (Link)