Team:Virginia/Papers
Sources
[1] A. H. Chen and P. A. Silver, “Designing biological compartmentalization,” Trends Cell Biol., vol. 22, no. 12, pp. 662–670, Dec. 2012, doi: 10.1016/j.tcb.2012.07.002.
[2] A. I. Romero-Pérez, R. M. Lamuela-Raventós, C. Andrés-Lacueva, and M. C. de La Torre-Boronat, “Method for the quantitative extraction of resveratrol and piceid isomers in grape berry skins. Effect of powdery mildew on the stilbene content,” J. Agric. Food Chem., vol. 49, no. 1, pp. 210–215, 2001.
[3] C. Chowdhury, S. Sinha, S. Chun, T. O. Yeates, and T. A. Bobik, “Diverse Bacterial Microcompartment Organelles,” Microbiol. Mol. Biol. Rev. MMBR, vol. 78, no. 3, pp. 438–468, Sep. 2014, doi: 10.1128/MMBR.00009-14.
[4] C. Lim, Z. Fowler, T. Hueller, S. Schaffer, and M. Koffas, “High-Yield Resveratrol Production in Engineered Escherichia coli,” Appl. Environ. Microbiol., vol. 77, pp. 3451–60, Mar. 2011, doi: 10.1128/AEM.02186-10.
[5] C. M. Insights, “Resveratrol Market to Surpass US$ 159.1 Million by 2026 – Coherent Market Insights,” GlobeNewswire News Room, 21-Nov-2018. [Online]. Available: https://www.globenewswire.com/news-release/2018/11/21/1655234/0/en/Resveratrol-Market-to-Surpass-US-159-1-Million-by-2026-Coherent-Market-Insights.html. [Accessed: 27-Oct-2020]
[6] Crowley et al., “Structural Insight into the Mechanisms of Transport across the Salmonella Enterica Pdu Microcompartment Shell.” 2010.
[7] D.-G. Wang, W.-Y. Liu, and G.-T. Chen, “A simple method for the isolation and purification of resveratrol from Polygonum cuspidatum,” Journal of Pharmaceutical Analysis, 10-Dec-2012. [Online]. Available: https://www.sciencedirect.com/science/article/pii/S2095177912001426. [Accessed: 27-Oct-2020]
[8] D.-K. Ro et al., “Production of the antimalarial drug precursor artemisinic acid in engineered yeast,” Nature, vol. 440, no. 7086, pp. 940–943, Apr. 2006, doi: 10.1038/nature04640.
[9] Fan and Bobik, “The N-Terminal Region of the Medium Subunit (PduD) Packages Adenosylcobalamin-Dependent Diol Dehydratase (PduCDE) into the Pdu Microcompartment.”2011.
[10] Garmann, Goldfain, and Manoharan, “Measurements of the Self-Assembly Kinetics of Individual Viral Capsids around Their RNA Genome.” 2009.
[11] Glazyrina J, Materne EM, Dreher T, Storm D, Junne S, Adams T, Greller G, Neubauer P. "High cell density cultivation and recombinant protein production with Escherichia coli in a rocking-motion-type bioreactor." Microb Cell Fact. 2010 May 30 9: 42. doi: 10.1186/1475-2859-9-42. p.4 left column 5th paragraph
[12] Innovations transforming economies and O. Lives, “The Bio Revolution,” Mckinsey.com. [Online]. Available: https://www.mckinsey.com/~/media/McKinsey/Industries/Pharmaceuticals%20and%20Medical%20Products/Our%20Insights/The%20Bio %20Revolution%20Innovations%20transforming%20economies%20societies%20and%20our%20lives/May_2020_MGI_Bio_Revolution _Report.pdf. [Accessed: 27-Oct-2020].
[13] J. B. Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement,” Mol. Cell, vol. 38, no. 2, pp. 305–315, Apr. 2010, doi: 10.1016/j.molcel.2010.04.008. [9] T. O. Yeates, J. Jorda, and T. A. Bobik, “The Shells of BMC-Type Microcompartment Organelles in Bacteria,” J. Mol. Microbiol. Biotechnol., vol. 23, no. 4–5, pp. 290–299, 2013, doi: 10.1159/000351347.
[14] J. Elbaz, P. Yin, and C. A. Voigt, “Genetic encoding of DNA nanostructures and their self-assembly in living bacteria,” Nat. Commun., vol. 7, no. 1, p. 11179, Apr. 2016, doi: 10.1038/ncomms11179.
[15] Jorda et al., “Exploring Bacterial Organelle Interactomes.” 2015.
[16] J. Rajawat and G. Jhingan, Chapter 1 - Mass spectroscopy, Data Processing Handbook for Complex Biological Data Sources, pp. 1-20, 2019.
[17] Juodeikis et al., “Effect of Metabolosome Encapsulation Peptides on Enzyme Activity, Coaggregation, Incorporation, and Bacterial Microcompartment Formation.” 2020.
[18] Kennedy et al., “Apparent Size and Morphology of Bacterial Microcompartments Varies with Technique.” 2020.
[19] M. Gearing, Plasmids 101: Golden Gate Cloning,addgene blog share science. [Online]. Available: https://blog.addgene.org/plasmids-101-golden-gate-cloning. [Accessed: 26-Oct-2020].
[20] M. Katz, H. P. Smits, J. Forster, and J. B. NIELSEN, “Metabolically engineered cells for the production of resveratrol or an oligomeric or glycosidically-bound derivative thereof,” US9404129B2, Aug. 02, 2016.
[21] M. Portincaso, A. Gourévitch, S. Gross-Selbeck, and T. Reichert, “How Deep Tech Can Help Shape the New Reality,” BCG Global, 21-Jul-2020. [Online]. Available: https://www.bcg.com/publications/2020/how-deep-tech-can-shape-post-covid-reality. [Accessed: 27-Oct-2020]
[22] M. Samejima and A. Attorney, “Efforts Towards Open Innovation,” Nedo.go.jp. [Online]. Available: https://www.nedo.go.jp/content/100889935.pdf. [Accessed: 27-Oct-2020].
[23] Nature News. [Online]. Available: https://www.nature.com/articles/d42473-020-00220-x. [Accessed: 27-Oct-2020].
[24] Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement.” 2010.
[25] Q. Wang et al., “Peanut by-products utilization technology,” in Peanuts: Processing Technology and Product Development, Elsevier, 2016, pp. 211–325.
[26] “Resveratrol Market size 2020 industry share, demand, top players, industry size, future growth by 2026,” MarketWatch, 19-Oct-2020. [Online]. Available: https://www.marketwatch.com/press-release/resveratrol-market-size-2020-industry-share-demand-top-players-industry-size-future-growth-by-2026-2020-10-18. [Accessed: 27-Oct-2020].
[27] R. J. Conrado et al., “DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency,” Nucleic Acids Res., vol. 40, no. 4, pp. 1879–1889, Feb. 2012, doi: 10.1093/nar/gkr888.
[28] Salis, Mirsky, and Voigt, “Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression.” 2009.
[29] S. D. Axen, O. Erbilgin, and C. A. Kerfeld, “A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method,” PLoS Comput. Biol., vol. 10, no. 10, Oct. 2014, doi: 10.1371/journal.pcbi.1003898.
[30] Synbiobeta.com. [Online]. Available: https://synbiobeta.com/wp-content/uploads/2018/11/Synbiobeta_Report_8.22.18_Chemicals_v3.pdf. [Accessed: 27-Oct-2020].
[31] “Synthetic biology is shaking up these 5 industries-Some of them might surprise you - SynBioBeta,” Synbiobeta.com, 11-Feb-2020. [Online]. Available: https://synbiobeta.com/synthetic-biology-is-shaking-up-these-5-industries-some-of-them-might-surprise-you/. [Accessed: 27-Oct-2020].
[32] “Team:British Columbia/project/vanillin - 2013.Igem.Org,” Igem.org. [Online]. Available: https://2013.igem.org/Team:British_Columbia/Project/Vanillin. [Accessed: 27-Oct-2020].
[33] T. O. Yeates, C. S. Crowley, and S. Tanaka, “Bacterial Microcompartment Organelles: Protein Shell Structure and Evolution,” Annu. Rev. Biophys., vol. 39, pp. 185–205, Jun. 2010, doi: 10.1146/annurev.biophys.093008.131418.
[34] Toyeates, English: Stylized view of the carboxysome and related bacterial structures such as the propanediol utilization (Pdu) and ethanolamine utilization (Eut) microcompartments. Distinct hexameric BMC shell proteins carrying out different functions in the shell are shown in different shades of blue. Pentameric vertex proteins are shown in magenta. Encapsulated enzymes are shown in green, organized in layers. [Image: T. Yeates]. 2013.
[35] Waters, Beginners Guide to Liquid Chromatography. [Online]. Available: https://www.waters.com/waters/en_US/HPLC---High-Performance-Liquid-Chromatography-Explained/nav.htm?cid=10048919. [Accessed: 26-Oct-2020].
[36] W. Zha, S. B. Rubin-Pitel, Z. Shao, and H. Zhao, “Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering,” Metab. Eng., vol. 11, no. 3, pp. 192–198, May 2009, doi: 10.1016/j.ymben.2009.01.005.
[37] Yang et al., “Decoding the Stoichiometric Composition and Organisation of Bacterial Metabolosomes.” 2020.
[38] Y. Tsai et al., “Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome,” PLoS Biol., vol. 5, no. 6, Jun. 2007, doi: 10.1371/journal.pbio.0050144.
[2] A. I. Romero-Pérez, R. M. Lamuela-Raventós, C. Andrés-Lacueva, and M. C. de La Torre-Boronat, “Method for the quantitative extraction of resveratrol and piceid isomers in grape berry skins. Effect of powdery mildew on the stilbene content,” J. Agric. Food Chem., vol. 49, no. 1, pp. 210–215, 2001.
[3] C. Chowdhury, S. Sinha, S. Chun, T. O. Yeates, and T. A. Bobik, “Diverse Bacterial Microcompartment Organelles,” Microbiol. Mol. Biol. Rev. MMBR, vol. 78, no. 3, pp. 438–468, Sep. 2014, doi: 10.1128/MMBR.00009-14.
[4] C. Lim, Z. Fowler, T. Hueller, S. Schaffer, and M. Koffas, “High-Yield Resveratrol Production in Engineered Escherichia coli,” Appl. Environ. Microbiol., vol. 77, pp. 3451–60, Mar. 2011, doi: 10.1128/AEM.02186-10.
[5] C. M. Insights, “Resveratrol Market to Surpass US$ 159.1 Million by 2026 – Coherent Market Insights,” GlobeNewswire News Room, 21-Nov-2018. [Online]. Available: https://www.globenewswire.com/news-release/2018/11/21/1655234/0/en/Resveratrol-Market-to-Surpass-US-159-1-Million-by-2026-Coherent-Market-Insights.html. [Accessed: 27-Oct-2020]
[6] Crowley et al., “Structural Insight into the Mechanisms of Transport across the Salmonella Enterica Pdu Microcompartment Shell.” 2010.
[7] D.-G. Wang, W.-Y. Liu, and G.-T. Chen, “A simple method for the isolation and purification of resveratrol from Polygonum cuspidatum,” Journal of Pharmaceutical Analysis, 10-Dec-2012. [Online]. Available: https://www.sciencedirect.com/science/article/pii/S2095177912001426. [Accessed: 27-Oct-2020]
[8] D.-K. Ro et al., “Production of the antimalarial drug precursor artemisinic acid in engineered yeast,” Nature, vol. 440, no. 7086, pp. 940–943, Apr. 2006, doi: 10.1038/nature04640.
[9] Fan and Bobik, “The N-Terminal Region of the Medium Subunit (PduD) Packages Adenosylcobalamin-Dependent Diol Dehydratase (PduCDE) into the Pdu Microcompartment.”2011.
[10] Garmann, Goldfain, and Manoharan, “Measurements of the Self-Assembly Kinetics of Individual Viral Capsids around Their RNA Genome.” 2009.
[11] Glazyrina J, Materne EM, Dreher T, Storm D, Junne S, Adams T, Greller G, Neubauer P. "High cell density cultivation and recombinant protein production with Escherichia coli in a rocking-motion-type bioreactor." Microb Cell Fact. 2010 May 30 9: 42. doi: 10.1186/1475-2859-9-42. p.4 left column 5th paragraph
[12] Innovations transforming economies and O. Lives, “The Bio Revolution,” Mckinsey.com. [Online]. Available: https://www.mckinsey.com/~/media/McKinsey/Industries/Pharmaceuticals%20and%20Medical%20Products/Our%20Insights/The%20Bio %20Revolution%20Innovations%20transforming%20economies%20societies%20and%20our%20lives/May_2020_MGI_Bio_Revolution _Report.pdf. [Accessed: 27-Oct-2020].
[13] J. B. Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement,” Mol. Cell, vol. 38, no. 2, pp. 305–315, Apr. 2010, doi: 10.1016/j.molcel.2010.04.008. [9] T. O. Yeates, J. Jorda, and T. A. Bobik, “The Shells of BMC-Type Microcompartment Organelles in Bacteria,” J. Mol. Microbiol. Biotechnol., vol. 23, no. 4–5, pp. 290–299, 2013, doi: 10.1159/000351347.
[14] J. Elbaz, P. Yin, and C. A. Voigt, “Genetic encoding of DNA nanostructures and their self-assembly in living bacteria,” Nat. Commun., vol. 7, no. 1, p. 11179, Apr. 2016, doi: 10.1038/ncomms11179.
[15] Jorda et al., “Exploring Bacterial Organelle Interactomes.” 2015.
[16] J. Rajawat and G. Jhingan, Chapter 1 - Mass spectroscopy, Data Processing Handbook for Complex Biological Data Sources, pp. 1-20, 2019.
[17] Juodeikis et al., “Effect of Metabolosome Encapsulation Peptides on Enzyme Activity, Coaggregation, Incorporation, and Bacterial Microcompartment Formation.” 2020.
[18] Kennedy et al., “Apparent Size and Morphology of Bacterial Microcompartments Varies with Technique.” 2020.
[19] M. Gearing, Plasmids 101: Golden Gate Cloning,addgene blog share science. [Online]. Available: https://blog.addgene.org/plasmids-101-golden-gate-cloning. [Accessed: 26-Oct-2020].
[20] M. Katz, H. P. Smits, J. Forster, and J. B. NIELSEN, “Metabolically engineered cells for the production of resveratrol or an oligomeric or glycosidically-bound derivative thereof,” US9404129B2, Aug. 02, 2016.
[21] M. Portincaso, A. Gourévitch, S. Gross-Selbeck, and T. Reichert, “How Deep Tech Can Help Shape the New Reality,” BCG Global, 21-Jul-2020. [Online]. Available: https://www.bcg.com/publications/2020/how-deep-tech-can-shape-post-covid-reality. [Accessed: 27-Oct-2020]
[22] M. Samejima and A. Attorney, “Efforts Towards Open Innovation,” Nedo.go.jp. [Online]. Available: https://www.nedo.go.jp/content/100889935.pdf. [Accessed: 27-Oct-2020].
[23] Nature News. [Online]. Available: https://www.nature.com/articles/d42473-020-00220-x. [Accessed: 27-Oct-2020].
[24] Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement.” 2010.
[25] Q. Wang et al., “Peanut by-products utilization technology,” in Peanuts: Processing Technology and Product Development, Elsevier, 2016, pp. 211–325.
[26] “Resveratrol Market size 2020 industry share, demand, top players, industry size, future growth by 2026,” MarketWatch, 19-Oct-2020. [Online]. Available: https://www.marketwatch.com/press-release/resveratrol-market-size-2020-industry-share-demand-top-players-industry-size-future-growth-by-2026-2020-10-18. [Accessed: 27-Oct-2020].
[27] R. J. Conrado et al., “DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency,” Nucleic Acids Res., vol. 40, no. 4, pp. 1879–1889, Feb. 2012, doi: 10.1093/nar/gkr888.
[28] Salis, Mirsky, and Voigt, “Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression.” 2009.
[29] S. D. Axen, O. Erbilgin, and C. A. Kerfeld, “A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method,” PLoS Comput. Biol., vol. 10, no. 10, Oct. 2014, doi: 10.1371/journal.pcbi.1003898.
[30] Synbiobeta.com. [Online]. Available: https://synbiobeta.com/wp-content/uploads/2018/11/Synbiobeta_Report_8.22.18_Chemicals_v3.pdf. [Accessed: 27-Oct-2020].
[31] “Synthetic biology is shaking up these 5 industries-Some of them might surprise you - SynBioBeta,” Synbiobeta.com, 11-Feb-2020. [Online]. Available: https://synbiobeta.com/synthetic-biology-is-shaking-up-these-5-industries-some-of-them-might-surprise-you/. [Accessed: 27-Oct-2020].
[32] “Team:British Columbia/project/vanillin - 2013.Igem.Org,” Igem.org. [Online]. Available: https://2013.igem.org/Team:British_Columbia/Project/Vanillin. [Accessed: 27-Oct-2020].
[33] T. O. Yeates, C. S. Crowley, and S. Tanaka, “Bacterial Microcompartment Organelles: Protein Shell Structure and Evolution,” Annu. Rev. Biophys., vol. 39, pp. 185–205, Jun. 2010, doi: 10.1146/annurev.biophys.093008.131418.
[34] Toyeates, English: Stylized view of the carboxysome and related bacterial structures such as the propanediol utilization (Pdu) and ethanolamine utilization (Eut) microcompartments. Distinct hexameric BMC shell proteins carrying out different functions in the shell are shown in different shades of blue. Pentameric vertex proteins are shown in magenta. Encapsulated enzymes are shown in green, organized in layers. [Image: T. Yeates]. 2013.
[35] Waters, Beginners Guide to Liquid Chromatography. [Online]. Available: https://www.waters.com/waters/en_US/HPLC---High-Performance-Liquid-Chromatography-Explained/nav.htm?cid=10048919. [Accessed: 26-Oct-2020].
[36] W. Zha, S. B. Rubin-Pitel, Z. Shao, and H. Zhao, “Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering,” Metab. Eng., vol. 11, no. 3, pp. 192–198, May 2009, doi: 10.1016/j.ymben.2009.01.005.
[37] Yang et al., “Decoding the Stoichiometric Composition and Organisation of Bacterial Metabolosomes.” 2020.
[38] Y. Tsai et al., “Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome,” PLoS Biol., vol. 5, no. 6, Jun. 2007, doi: 10.1371/journal.pbio.0050144.
