Team:ETH Zurich/References

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• Project
  • Project Description
  • Design
  • Applications
  • Achievements
  • Collaborations
  • Glossary
  • References
• Modeling
  • Overview
  • Lactate Module
  • AHL Module
  • Compartment Model
  • Reaction-Diffusion
  • Experiments Meet Modeling
  • Parameters
• Lab
  • Overview
  • Results
  • Chip Design
  • Experiments
  • Interlab Study
  • Safety
  • Notebook
  • Materials
• Human
  Practices
  • Overview
  • Medicine
  • Education
  • Awareness
  • Ethics
  • Business
  • Patents
• Parts
  • Overview
  • Basic
  • Composite
  • Part Collection
  • Characterization
• About Us
  • Team
  • Attributions
  • iGEM Team Roster

"What I cannot create I do not understand."
- Richard Feynmann

References

Description

• Aguilera, L., Campos, E., Giménez, R., Badía, J., Aguilar, J., & Baldoma, L. (2008). Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli. Journal of bacteriology, 190(8), 2997-3005.
• Autebert, J., Coudert, B., Champ, J., Saias, L., Guneri, E. T., Lebofsky, R., ... & Viovy, J. L. (2015). High purity microfluidic sorting and analysis of circulating tumor cells: towards routine mutation detection. Autebert, J., Coudert, B., Champ, J., Saias, L., Guneri, E. T., Lebofsky, R., ... & Viovy, J. L. (2015). High purity microfluidic sorting and analysis of circulating tumor cells: towards routine mutation detection. ,15(9), 2090-2101
• Chen, Z., Lu, W., Garcia-Prieto, C., & Huang, P. (2007). The Warburg effect and its cancer therapeutic implications. Journal of bioenergetics and biomembranes, 39(3), 267-274.
• Cooke, T., Reeves, J., Lanigan, A., & Stanton, P. (2001). HER2 as a prognostic and predictive marker for breast cancer. Annals of oncology, 12(suppl 1), S23-S28.
• Cooperberg, M. R., Broering, J. M., & Carroll, P. R. (2009). Risk assessment for prostate cancer metastasis and mortality at the time of diagnosis. Journal of the National Cancer Institute, 101(12), 878-887.
• van Engeland, M., Nieland, L. J., Ramaekers, F. C., Schutte, B., & Reutelingsperger, C. P. (1998). Annexin V-affinity assay: a review on an apoptosis detection system based on phosphatidylserine exposure. Cytometry,31(1), 1-9.
• Garcea, G., Neal, C. P., Pattenden, C. J., Steward, W. P., & Berry, D. P. (2005). Molecular prognostic markers in pancreatic cancer: a systematic review. European Journal of Cancer, 41(15), 2213-2236.
• Goentoro, L., Shoval, O., Kirschner, M. W., & Alon, U. (2009). The incoherent feedforward loop can provide fold-change detection in gene regulation. Molecular cell, 36(5), 894-899.
• Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. Cell,144(5), 646-674..
• Hawkins, T. E., Das, D., Young, B., & Moss, S. E. (2002). DT40 cells lacking the Ca²⁺-binding protein annexin 5 are resistant to Ca²⁺-dependent apoptosis. Proceedings of the National Academy of Sciences, 99(12), 8054-8059.
• International Agency for Research on Cancer. (2014). World cancer report 2014. Geneva: WHO.
• Ilie, M., Hofman, V., Long-Mira, E., Selva, E., Vignaud, J. M., Padovani, B., ... & Hofman, P. (2014). “Sentinel” Circulating Tumor Cells Allow Early Diagnosis of Lung Cancer in Patients with Chronic Obstructive Pulmonary Disease. PLoS One.,2014 Oct 31;9(10)
• Paik M. l., et al. Limitations of computerized tomography in staging invasive bladder cancer before radical cystectomy. (2000) The Journal of Urology Volume 163, Issue 6, Pages 1693–1696
• Msaouel, P., & Koutsilieris, M. (2011). Diagnostic value of circulating tumor cell detection in bladder and urothelial cancer: systematic review and meta-analysis. BMC cancer, ,11(1), 336
• Singhal, S., Vachani, A., Antin-Ozerkis, D., Kaiser, L. R., & Albelda, S. M. (2005). Prognostic implications of cell cycle, apoptosis, and angiogenesis biomarkers in non–small cell lung cancer: a review. Clinical Cancer Research,11(11), 3974-3986.
• Sleijfer, S., Gratama, J. W., Sieuwerts, A. M., Kraan, J., Martens, J. W., & Foekens, J. A. (2007). Circulating tumour cell detection on its way to routine diagnostic implementation?. European Journal of Cancer, 43(18), 2645-2650.
• Srivastava, R. K. (2001). TRAIL/Apo-2L: mechanisms and clinical applications in cancer. Neoplasia, 3(6), 535-546.
• Saxe, Charles. Unlocking the misteries of metastasis. American Cancer Society. 23 January 2013

Glossary

• Bratton, Donna L., et al. "Appearance of phosphatidylserine on apoptotic cells requires calcium-mediated nonspecific flip-flop and is enhanced by loss of the aminophospholipid translocase." Journal of Biological Chemistry 272.42 (1997): 26159-26165.
• Cáceres, G, Puskas, J. Circulating Tumor Cells: A Window Into Tumor Development and Therapeutic Effectiveness. Cancer control Vol. 22, No. 2 (2015)
• Kalluri, R., & Weinberg, R. A. (2009). The basics of epithelial-mesenchymal transition. The Journal of clinical investigation, 119(6), 1420.
• Miller, M. B., & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Reviews in Microbiology, 55(1), 165-199.
• Núñez, M. F., Kwon, O., Wilson, T. H., Aguilar, J., Baldoma, L., & Lin, E. C. (2002). Transport of L-lactate, D-lactate, and glycolate by the LldP and GlcA membrane carriers of Escherichia coli. Biochemical and biophysical research communications, 290(2), 824-829.
• Vander Heiden, M. G., Cantley, L. C., & Thompson, C. B. (2009). Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science, 324(5930), 1029-1033.
• Johnstone, R. W. et al. The TRAIL apoptotic pathway in cancer onset, progression and therapy. Nature Reviews Cancer 8, 782-798 (2008)

Experimental

• de Bruyne, M. et al. Cancer Letters Volume 332, Issue 2, (2013), Pages 175–183
• Chiu, T.-K. et al. Development of a Microfluidic-Based Optical Sensing Device for Label-Free Detection of Circulating Tumor Cells (CTCs) Through Their Lactic Acid Metabolism. Sensors (Basel) 15, 6789–6806 (2015).
• Gerke, V. Moss, S. E. Annexins: From Structure to Function. Physiological Reviews
• Leventis, P.A. and Grinstein, S.. The Distribution and Function of Phosphatidylserine in Cellular Membranes (2010)Annual Review in Biophysics 39:407–27
• Park, I. C., Park, M. J., Rhee, C. H., Lee, J. I., Choe, T. B., Jang, J. J., ... & Hong, S. I. (2001). Protein kinase C activation by PMA rapidly induces apoptosis through caspase-3/CPP32 and serine protease (s) in a gastric cancer cell line. International journal of oncology , 18(5), 1077-1083.
• Rieger, A. M., Nelson, K. L., Konowalchuk, J. D., & Barreda, D. R. (2011). Modified annexin V/propidium iodide apoptosis assay for accurate assessment of cell death. Journal of visualized experiments: JoVE, , (50).
• Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., & MacDonald, J. T. (2014). R2oDNA designer: computational design of biologically neutral synthetic DNA Sequences. ACS synthetic biology, ,3(8), 525-528
• http://www.researchgate.net/post/LDH_Assay_with_complete_media. 2015-08-10 Mol. Oncol. ,8, 232.
• Mandal (2014). pERK 1/2 inhibit Caspase-8 induced apoptosis in cancer cells by phosphorylating it in a cell cycle specific manner. Mol. Oncol. ,8, 232.
• Tian T., Salis, H. M. A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons. (2015) Nucleic Acids Research 43 (14): 7137-7151
• Thomas, W. D & Hersey, P. (1998) TNF-Related Apoptosis-Inducing Ligand (TRAIL) Induces Apoptosis in Fas Ligand-Resistant Melanoma Cells and Mediates CD4 T Cell Killing of Target Cells. The Journal of Immunology vol. 161 no. 5 2195-2200
• Vander Heiden, M.G. et al. Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. Science 22 Vol. 324 no. 5930 pp. 1029-1033 (2009)
• Zhang, L. & Fang. Mechanisms of resistance to TRAIL-induced apoptosis in cancer. Cancer Gene Therapy 12, 228–237 (2005)

Modeling

• Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold, and Ron Weiss. A synthetic multicellular system for programmed pattern formation. Nature, 434(7037):1130–1134, April 2005.
• Dong, J. M., Taylor, J. S., Latour, D. J., Iuchi, S., & Lin, E. C. (1993). Three overlapping lct genes involved in L-lactate utilization by Escherichia coli. Journal of bacteriology, 175(20), 6671-6678.
• Fatin-Rouge, N., Starchev, K., & Buffle, J. (2004). Size effects on diffusion processes within agarose gels. Biophysical Journal, 86(5), 2710-2719.
• Kaplan, H. B., & Greenberg, E. P. (1985). Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system. Journal of bacteriology, 163(3), 1210-1214.
• Stewart, P. S. (2003). Diffusion in biofilms. Journal of bacteriology, 185(5), 1485-1491.
• Trovato, A., Seno, F., Zanardo, M., Alberghini, S., Tondello, A., & Squartini, A. (2014). Quorum vs. diffusion sensing: a quantitative analysis of the relevance of absorbing or reflecting boundaries. FEMS microbiology letters, 352(2), 198-203.
• Lian-Hui Wang, Li-Xing Weng, Yi-Hu Dong, and Lian-Hui Zhang. Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase). Journal of Biological Chemistry, 279(14):13645–13651, April 2004.
• Marc Weber and Javier Buceta. Dynamics of the quorum sensing switch: stochastic and non-stationary effects.BMC Systems Biology, 7(1):6, January 2013.
• Kim, D., Kwon, Y.-K. and Cho, K.-H. (2008), The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks. Bioessays, 30: 1204–1211. doi: 10.1002/bies.20839

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