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| - | [[Team:NTU-Singapore/Project | | + | [[Team:NTU-Singapore/Project | '''p'''Laq''U''<span class="sup">e</span> '''Out''!''''']] |
| - | + | [[Team:NTU-Singapore/Project/Approach | Research Approach]] | |
| - | [[Team:NTU-Singapore/Project/ | + | [[Team:NTU-Singapore/Project/Prototype/Sense | Sensing Device « ]] |
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| - | [[Team:NTU-Singapore/Project/Prototype/Sense | | + | |
[[Team:NTU-Singapore/Project/Prototype/Degrade | Degradation Device « ]] | [[Team:NTU-Singapore/Project/Prototype/Degrade | Degradation Device « ]] | ||
[[Team:NTU-Singapore/Project/Prototype/Image | Imaging Device « ]] | [[Team:NTU-Singapore/Project/Prototype/Image | Imaging Device « ]] | ||
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[[Team:NTU-Singapore/Project/References | References]] | [[Team:NTU-Singapore/Project/References | References]] | ||
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| - | + | # WHO Medical Centre (2009). "Cardiovascular diseases (CVDs)." from http://www.who.int/mediacentre/factsheets/fs317/en/index.html. | |
| - | + | # MayoClinic.com. (2008). "'''Definition of Arterioscleriosis.'''" from http://www.mayoclinic.com/health/arteriosclerosis-atherosclerosis/DS00525. | |
| - | + | # E. Galkina, K. Ley, “'''Immune and Inflammatory Mechanisms of Atherosclerosis'''” Annu. Rev. Immunol., vol 27, 165-97, 2009. | |
| - | + | # G. K. Hansson, Anna-Karin L. Robertson, C. Soderberg-Naucler, “'''Inflammation and Atherosclerosis'''” Annu. Rev. Pathol. Mech. Dis., vol 1, 297-329, 2006. | |
| - | + | # NIH. "'''How is Atherosclerosis Diagnosed?'''", from http://www.nhlbi.nih.gov/health/dci/Diseases/Atherosclerosis/Atherosclerosis_Diagnosis.html. | |
| - | + | # Anderson, T. J. M. (2003). "'''Nitric Oxide, Atherosclerosis and clinical relevance of endothelial dysfunction.'''" Heart Failure Reviews 8: 71 - 86. | |
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<div class="ref"> | <div class="ref"> | ||
| - | + | # S. Verma, M. R. Buchanan, T. J. Anderson, “'''Endothelial Function Testing as a Biomarker of Vascular Disease'''” Circulation, vol 108, 2054-2059, 2003. | |
| - | + | # W. Thomas, “'''Catch Bonds in Adhesion'''” Annu. Rev. Biomed. Eng., vol 10, 39-57, 2008. | |
| - | + | # L. M. Nilsson, W. E. Thomas, E. V. Sokurenko, V. Vogel, “'''Elevated Shear Stress Protects Escherichia Coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors'''” Applied and Environmental Microbiology, vol 72 no. 4, 3005-3010, 2006. | |
| - | + | # Eric Borges, W. T., Martin Steegmaier,* Thomas Moll,* Rupert Hallmann,§ Alf Hamann, and Dietmar Vestweber* (1997). "'''P-Selectin Glycoprotein Ligand-1 (PSGL-1) on T Helper 1 but Not on T Helper 2 Cells Binds to P-Selectin and Supports Migration into Inflamed Skin'''" Journal of Experimental Medicine 185. | |
| - | + | ||
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</div> | </div> | ||
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<div class="ref"> | <div class="ref"> | ||
| - | + | # Wilkinson, D. J. (2006). '''Stochastic modelling for systems biology'''. Boca Raton, FL, Taylor & Francis. | |
| - | + | # Dunn, I. J. (2003). '''Biological reaction engineering : dynamic modelling fundamentals with simulation examples.''' [Great Britain], Wiley-VCH. | |
| - | + | # Linkens, D. A. (1979). '''Biological systems, modelling, and control'''. Stevenage [Eng.] ; New York, P. Peregrinus on behalf of the Institution of Electrical Engineers. | |
| - | + | # Drubin, D. A., J. C. Way, et al. (2007). "'''Designing biological systems'''" Genes & Development 21(1): 242 - 254. | |
| - | + | # Murthy, D. N. P., N. W. Page, et al. (1990). '''Mathematical modelling : a tool for problem solving in engineering, physical, biological, and social sciences.''' Oxford ; New York, Pergamon Press. | |
| - | + | # Murphy, K., G. Balazsi, et al. (2007). "'''Combinatorial promoter design for engineering noisy gene expression.'''" Proc Natl Acad Sci USA 104: 12726 - 12731. | |
| - | + | # Naidoo, K. J. and Royal Society of Chemistry (Great Britain) (2006). '''Modelling molecular structure and reactivity in biological systems.''' Cambridge, Royal Society of Chemistry. | |
| - | + | # Garcia-Martinez, J., A. Aranda, et al. (2004). "'''Genomic run-on evaluates transcription rates for all yeast gens and identifies gene regulatory mechanisms.'''" Mol Cell 15: 303 - 313. | |
| - | + | # Ullner, E., A. Koseska, et al. (2008). "'''Multistability of synthetic genetic networks with repressive cell-to-cell communication.'''" Physical Review 78: 03904-1 - 03904-8. | |
| - | + | # Dennis, P. P., and H. Bremer. 1974. Differential rate of ribosomal protein synthesis in Escherichia coli B/r. J. Mol. Biol. 84:407–422. | |
| - | + | # Dennis, P. P., and M. Nomura. Stringent control of ribosomal protein gene expression in coli B/r. Proc Natl Acad Sci U S A. 1974 Oct71(10):3819-23 | |
| - | + | # Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004 Mar 2101(9):2758-63 | |
| - | + | # Dalbow and Young, Biochem J. 150:13-20 (1985) | |
| - | + | # Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan25(1):117-24. | |
| - | + | # El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22102(8):pp. 2736 | |
| - | + | ||
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</div> | </div> | ||
| - | == | + | == Sensing Device Resources == |
<div class="ref"> | <div class="ref"> | ||
| - | + | # D’Autre´aux, B., N. P. Tucker, et al. (2005). "'''A non-haem iron centre in the transcription factor NorR senses nitric oxide.'''" Nature 437(29): 769 -772. | |
| - | + | # Hutchings, M. I., N. Mandhana, et al. (2002). "'''The NorR protein of Escherichia coli activates expression of the Flavorbredoxin gene NorV in response to reactive nitrogen species.'''" Journal of bacteriology 184(16): 4640 - 4643. | |
| - | + | # Tucker, N. P., B. D. Autreaux, et al. (2006). "'''Mechanism of transcriptional regulation by Escherichia Coli nitric oxide sensor NorR.'''" Biochemical Society Transactions 34(1): 191 - 194. | |
| - | + | # Ferenc I. Tarr MD, P., Mária Sasvári MDb, Márton Tarr MD and Rozália Rácz MD (2005). "'''Evidence of Nitric Oxide Produced by the Internal Mammary Artery Graft in Venous Drainage of the Recipient Coronary Artery.'''" The Annals of Thoracic Surgery 80(5): 1728-1731. | |
| - | + | ||
</div> | </div> | ||
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<div class="ref"> | <div class="ref"> | ||
| - | + | # S. Ghosh, et al., "'''Molecular cloning and expression of rat hepatic neutral cholesteryl ester hydrolase,'''" Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism, vol. 1259, pp. 305-312, Dec 1995. | |
| - | + | # S. Ghosh, "'''Cholesteryl ester hydrolase in human monocyte/macrophage: cloning, sequencing, and expression of full-length cDNA'''" Physiological Genomics, vol. 2, pp. 1-8, Jan 2000. | |
| - | + | # B. Zhao, et al., "'''Macrophage-specific transgenic expression of cholesteryl ester hydrolase significantly reduces atherosclerosis and lesion necrosis in Ldlr(-)/(-) mice'''" Journal of Clinical Investigation, vol. 117, pp. 2983-2992, Oct 2007. | |
| - | + | # H. Okazaki, et al., "'''Elimination of cholesterol ester from macrophage foam cells by adenovirus-mediated gene transfer of hormone-sensitive lipase'''" Journal of Biological Chemistry, vol. 277, pp. 31893-31899, Aug 2002. | |
| - | + | # A. Sugihara, et al., "'''Purification and characterization of a novel cholesterol esterase from Pseudomonas aeruginosa, with its application to cleaning lipid-stained contact lenses'''" Bioscience Biotechnology and Biochemistry, vol. 66, pp. 2347-2355, Nov 2002. | |
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| - | + | ||
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</div> | </div> | ||
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<div class="ref"> | <div class="ref"> | ||
| - | + | # Kein, B. (2009). "'''Infrared Proteins Give Deep View Inside Living Animals.'''" from http://www.wired.com/wiredscience/2009/05/infraredcells/. | |
| - | + | # S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''” Science, vol 324, 804, 2009. | |
| - | + | # S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Supporting Online Material for Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''" Science, vol 324, 804, 2009. | |
| - | + | # N. C. Shaner, R. E. Campbell, P. A. Steinbach, B.N.G Giepmans, A.E. Palmer and R.Y. Tsien, “'''Improved Monomeric Red, Orange and Yellow Fluorescent Proteins derived from Discosoma sp. red fluorescent protein'''” Nature Biotechnology, vol 22, number 12, 2004. | |
| - | + | # C.T. Migita, X. Zhang, T. Yoshida, “'''Expression and Characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis'''” Eur J Biochem, vol 270, 687-698, 2003. | |
| - | + | ||
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</div> | </div> | ||
Latest revision as of 18:19, 21 October 2009
Literature & References
Atherosclerosis resources
- WHO Medical Centre (2009). "Cardiovascular diseases (CVDs)." from http://www.who.int/mediacentre/factsheets/fs317/en/index.html.
- MayoClinic.com. (2008). "Definition of Arterioscleriosis." from http://www.mayoclinic.com/health/arteriosclerosis-atherosclerosis/DS00525.
- E. Galkina, K. Ley, “Immune and Inflammatory Mechanisms of Atherosclerosis” Annu. Rev. Immunol., vol 27, 165-97, 2009.
- G. K. Hansson, Anna-Karin L. Robertson, C. Soderberg-Naucler, “Inflammation and Atherosclerosis” Annu. Rev. Pathol. Mech. Dis., vol 1, 297-329, 2006.
- NIH. "How is Atherosclerosis Diagnosed?", from http://www.nhlbi.nih.gov/health/dci/Diseases/Atherosclerosis/Atherosclerosis_Diagnosis.html.
- Anderson, T. J. M. (2003). "Nitric Oxide, Atherosclerosis and clinical relevance of endothelial dysfunction." Heart Failure Reviews 8: 71 - 86.
Catch-bonds resources
- S. Verma, M. R. Buchanan, T. J. Anderson, “Endothelial Function Testing as a Biomarker of Vascular Disease” Circulation, vol 108, 2054-2059, 2003.
- W. Thomas, “Catch Bonds in Adhesion” Annu. Rev. Biomed. Eng., vol 10, 39-57, 2008.
- L. M. Nilsson, W. E. Thomas, E. V. Sokurenko, V. Vogel, “Elevated Shear Stress Protects Escherichia Coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors” Applied and Environmental Microbiology, vol 72 no. 4, 3005-3010, 2006.
- Eric Borges, W. T., Martin Steegmaier,* Thomas Moll,* Rupert Hallmann,§ Alf Hamann, and Dietmar Vestweber* (1997). "P-Selectin Glycoprotein Ligand-1 (PSGL-1) on T Helper 1 but Not on T Helper 2 Cells Binds to P-Selectin and Supports Migration into Inflamed Skin" Journal of Experimental Medicine 185.
Biological modelling resources
- Wilkinson, D. J. (2006). Stochastic modelling for systems biology. Boca Raton, FL, Taylor & Francis.
- Dunn, I. J. (2003). Biological reaction engineering : dynamic modelling fundamentals with simulation examples. [Great Britain], Wiley-VCH.
- Linkens, D. A. (1979). Biological systems, modelling, and control. Stevenage [Eng.] ; New York, P. Peregrinus on behalf of the Institution of Electrical Engineers.
- Drubin, D. A., J. C. Way, et al. (2007). "Designing biological systems" Genes & Development 21(1): 242 - 254.
- Murthy, D. N. P., N. W. Page, et al. (1990). Mathematical modelling : a tool for problem solving in engineering, physical, biological, and social sciences. Oxford ; New York, Pergamon Press.
- Murphy, K., G. Balazsi, et al. (2007). "Combinatorial promoter design for engineering noisy gene expression." Proc Natl Acad Sci USA 104: 12726 - 12731.
- Naidoo, K. J. and Royal Society of Chemistry (Great Britain) (2006). Modelling molecular structure and reactivity in biological systems. Cambridge, Royal Society of Chemistry.
- Garcia-Martinez, J., A. Aranda, et al. (2004). "Genomic run-on evaluates transcription rates for all yeast gens and identifies gene regulatory mechanisms." Mol Cell 15: 303 - 313.
- Ullner, E., A. Koseska, et al. (2008). "Multistability of synthetic genetic networks with repressive cell-to-cell communication." Physical Review 78: 03904-1 - 03904-8.
- Dennis, P. P., and H. Bremer. 1974. Differential rate of ribosomal protein synthesis in Escherichia coli B/r. J. Mol. Biol. 84:407–422.
- Dennis, P. P., and M. Nomura. Stringent control of ribosomal protein gene expression in coli B/r. Proc Natl Acad Sci U S A. 1974 Oct71(10):3819-23
- Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004 Mar 2101(9):2758-63
- Dalbow and Young, Biochem J. 150:13-20 (1985)
- Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan25(1):117-24.
- El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22102(8):pp. 2736
Sensing Device Resources
- D’Autre´aux, B., N. P. Tucker, et al. (2005). "A non-haem iron centre in the transcription factor NorR senses nitric oxide." Nature 437(29): 769 -772.
- Hutchings, M. I., N. Mandhana, et al. (2002). "The NorR protein of Escherichia coli activates expression of the Flavorbredoxin gene NorV in response to reactive nitrogen species." Journal of bacteriology 184(16): 4640 - 4643.
- Tucker, N. P., B. D. Autreaux, et al. (2006). "Mechanism of transcriptional regulation by Escherichia Coli nitric oxide sensor NorR." Biochemical Society Transactions 34(1): 191 - 194.
- Ferenc I. Tarr MD, P., Mária Sasvári MDb, Márton Tarr MD and Rozália Rácz MD (2005). "Evidence of Nitric Oxide Produced by the Internal Mammary Artery Graft in Venous Drainage of the Recipient Coronary Artery." The Annals of Thoracic Surgery 80(5): 1728-1731.
Degradation Device Resources
- S. Ghosh, et al., "Molecular cloning and expression of rat hepatic neutral cholesteryl ester hydrolase," Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism, vol. 1259, pp. 305-312, Dec 1995.
- S. Ghosh, "Cholesteryl ester hydrolase in human monocyte/macrophage: cloning, sequencing, and expression of full-length cDNA" Physiological Genomics, vol. 2, pp. 1-8, Jan 2000.
- B. Zhao, et al., "Macrophage-specific transgenic expression of cholesteryl ester hydrolase significantly reduces atherosclerosis and lesion necrosis in Ldlr(-)/(-) mice" Journal of Clinical Investigation, vol. 117, pp. 2983-2992, Oct 2007.
- H. Okazaki, et al., "Elimination of cholesterol ester from macrophage foam cells by adenovirus-mediated gene transfer of hormone-sensitive lipase" Journal of Biological Chemistry, vol. 277, pp. 31893-31899, Aug 2002.
- A. Sugihara, et al., "Purification and characterization of a novel cholesterol esterase from Pseudomonas aeruginosa, with its application to cleaning lipid-stained contact lenses" Bioscience Biotechnology and Biochemistry, vol. 66, pp. 2347-2355, Nov 2002.
Imaging Device Resources
- Kein, B. (2009). "Infrared Proteins Give Deep View Inside Living Animals." from http://www.wired.com/wiredscience/2009/05/infraredcells/.
- S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome” Science, vol 324, 804, 2009.
- S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “Supporting Online Material for Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome" Science, vol 324, 804, 2009.
- N. C. Shaner, R. E. Campbell, P. A. Steinbach, B.N.G Giepmans, A.E. Palmer and R.Y. Tsien, “Improved Monomeric Red, Orange and Yellow Fluorescent Proteins derived from Discosoma sp. red fluorescent protein” Nature Biotechnology, vol 22, number 12, 2004.
- C.T. Migita, X. Zhang, T. Yoshida, “Expression and Characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis” Eur J Biochem, vol 270, 687-698, 2003.
