References

Biology

Iron metabolism and iron associated diseases in humans

• Casarrubea, D., Viatte, L., Hallas, T., Vasanthakumar, A., Eisenstein, R.S., Schümann, K., Hentze, M.W., and Galy, B. (2013). Abnormal body iron distribution and erythropoiesis in a novel mouse model with inducible gain of iron regulatory protein (IRP)-1 function. Journal of Molecular Medicine 91, 871–881.
• Ganz, T., and Nemeth, E. (2011). Hepcidin and Disorders of Iron Metabolism. Annual Review of Medicine 62, 347–360.
• Hentze, M.W., Muckenthaler, M.U., Galy, B., and Camaschella, C. (2010). Two to Tango: Regulation of Mammalian Iron Metabolism. Cell 142, 24–38. (link to the pdf)
• Nicolas, G. (2004). Hepcidin, a candidate modifier of the hemochromatosis phenotype in mice. Blood 103, 2841–2843. (link to the pdf)
• Nicolas, G., Bennoun, M., Devaux, I., Beaumont, C., Grandchamp, B., Kahn, A., and Vaulont, S. (2001). From the Cover: Lack of hepcidin gene expression and severe tissue iron overload in upstream stimulatory factor 2 (USF2) knockout mice. Proceedings of the National Academy of Sciences 98, 8780–8785. (link to the pdf)
  
• Pantopoulos, K., Porwal, S.K., Tartakoff, A., and Devireddy, L. (2012). Mechanisms of Mammalian Iron Homeostasis. Biochemistry 51, 5705–5724.
• Viatte, L. (2006). Chronic hepcidin induction causes hyposideremia and alters the pattern of cellular iron accumulation in hemochromatotic mice. Blood 107, 2952–2958. (link to the pdf)
  

FUR and iron metabolism in bacteria

• Ahmad, R., Brandsdal, B.O., Michaud-Soret, I., and Willassen, N.-P. (2009). Ferric uptake regulator protein: Binding free energy calculations and per-residue free energy decomposition. Proteins: Structure, Function, and Bioinformatics 75, 373–386. (link to the pdf)
• Andrews, S.C., Robinson, A.K., and Rodríguez-Quiñones, F. (2003). Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215–237. (link to the pdf)
• Escolar, L. , Pérez-Martín, J., and De Lorenzo, V. (1991). Opening the Iron Box: Transcriptional Metalloregulation by the Fur Protein. Journal of Bacteriology 181,20. (link to the pdf)
• Guerinot, M.L. (1994). Microbial iron transport. Annu. Rev. Microbiol. 48, 743–772.
• Oglesby-Sherrouse, A.G., and Murphy, E.R. (2013). Iron-responsive bacterial small RNAs: variations on a theme. Metallomics 5, 276.
• Pecqueur, L. (2006). Structural Changes of Escherichia coli Ferric Uptake Regulator during Metal-dependent Dimerization and Activation Explored by NMR and X-ray Crystallography. Journal of Biological Chemistry 281, 21286–21295. (link to the pdf)
• Schilling, C.H., Held, L., Torre, M., and Saier, M.H., Jr (2000). GRASP-DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs. J. Mol. Microbiol. Biotechnol. 2, 495–500. (link to the pdf)
• Tiss, A., Barre, O., Michaud-Soret, I., and Forest, E. (2005). Characterization of the DNA-binding site in the ferric uptake regulator protein from Escherichia coli by UV crosslink to the pdfing and mass spectrometry. FEBS Letters 579, 5454–5460. (link to the pdf)
• Tsolis, R., Baumler, A.J., Stojiljkovic, I., and Heffron, F. (1995). Fur regulon of Salmonella typhimurium: identification of new iron-regulated genes. Journal of Bacteriology 177, 4628–4637. (link to the pdf)
• Valdebenito, M., Crumbliss, A.L., Winkelmann, G., and Hantke, K. (2006). Environmental factors influence the production of enterobactin, salmochelin, aerobactin, and yersiniabactin in Escherichia coli strain Nissle 1917. International Journal of Medical Microbiology 296, 513–520.
• Visca, P., Leoni, L., Wilson, M.J., and Lamont, I.L. (2002). Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas. Mol. Microbiol. 45, 1177–1190. (link to the pdf)
• Zhang, Z., Gosset, G., Barabote, R., Gonzalez, C.S., Cuevas, W.A., and Saier, M.H. (2005). Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli. Journal of Bacteriology 187, 980–990. (link to the pdf)

Siderophores

• Hider, R.C. Siderophore mediated absorption of iron. In Siderophores from Microorganisms and Plants. (Berlin, Heidelberg: Springer Berlin Heidelberg), pp. 25–87.
• Matzanke, B.F. Siderophores and Iron Metabolism - Structures, Functions, Role in Infection and Potential as a Novel Class of Antibiotics. (link to the pdf)
• Raymond, K.N. (2003). Bioinorganic Chemistry Special Feature: Enterobactin: An archetype for microbial iron transport. Proceedings of the National Academy of Sciences 100, 3584–3588. (link to the pdf)
• Zheng, T., Bullock, J.L., and Nolan, E.M. (2012). Siderophore-Mediated Cargo Delivery to the Cytoplasm of Escherichia coli and Pseudomonas aeruginosa : Syntheses of Monofunctionalized Enterobactin Scaffolds and Evaluation of Enterobactin–Cargo Conjugate Uptake. Journal of the American Chemical Society 134, 18388–18400.

Microbiot, probiotic, safety

• Arribas, B., Rodríguez-Cabezas, M., Camuesco, D., Comalada, M., Bailón, E., Utrilla, P., Nieto, A., Concha, A., Zarzuelo, A., and Gálvez, J. (2009). A probiotic strain of Escherichia coli , Nissle 1917, given orally exerts local and systemic anti-inflammatory effects in lipopolysaccharide-induced sepsis in mice. British Journal of Pharmacology 157, 1024–1033. (link to the pdf)
• Bermúdez-Humarán, L.G., Aubry, C., Motta, J.-P., Deraison, C., Steidler, L., Vergnolle, N., Chatel, J.-M., and Langella, P. (2013). Engineering lactococci and lactobacilli for human health. Current Opinion in Microbiology 16, 278–283.
• Deriu, E., Liu, J.Z., Pezeshki, M., Edwards, R.A., Ochoa, R.J., Contreras, H., Libby, S.J., Fang, F.C., and Raffatellu, M. (2013). Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron. Cell Host & Microbe 14, 26–37.
• Hancock, V., Dahl, M., and Klemm, P. (2010). Probiotic Escherichia coli strain Nissle 1917 outcompetes intestinal pathogens during biofilm formation. Journal of Medical Microbiology 59, 392–399. (link to the pdf)
• Saarela, M., Mogensen, G., Fondén, R., Mättö, J., and Mattila-Sandholm, T. (2000). Probiotic bacteria: safety, functional and technological properties. Journal of Biotechnology 84, 197–215.
• Skaar, E.P. (2010). The Battle for Iron between Bacterial Pathogens and Their Vertebrate Hosts. PLoS Pathogens 6, e1000949. (link to the pdf)
• Snydman, D.R. (2008). The Safety of Probiotics. Clinical Infectious Diseases 46, S104–S111. (link to the pdf)

Protocols

• Louden, B.C., Haarmann, D., and Lynne, A. (2011). Use of Blue Agar CAS Assay for Siderophore Detection. Journal of Microbiology & Biology Education 12,.(link to the pdf)

Modeling

• Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., "BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions", BMC Bioinformatics, 11:213, (2010).
• Orth, Jeffrey D., Ines Thiele, and Bernhard Ø. Palsson. "What is flux balance analysis?." Nature biotechnology 28.3 (2010): 245-248.
• Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. 2013 COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Bio 7:74.
• B. Hari, S. Bakalis, P. Fryer (2012). Computational Modeling and Simulation of the Human Duodenum (link to the pdf)

Philosophy

• Anders G.(1980). Die Antiquiertheit des Menschen 2. Über die Zerstörung des Lebens im Zeitalter der dritten industriellen Revolution (The Outdatedness of Human Beings 2. On the Destruction of Life in the Era of the Third Industrial Revolution). C. H. Beck, Munich
• Simondon G. (1958). Du mode d'existence des objets techniques(On the Mode of Existence of Technical Objects). Aubier
• Brown N. (2003). Hope Against Hype – Accountability in Biopasts, Presents and Futures. Science Studies