Team:Stanford/Attributions

Attributions

Contributions By The Team

It is important to note that every member of the 2021 Stanford iGEM Team played a significant role in the completion and success of CitrusSafe. Each member was a part of multiple sub-teams where they were able to focus their efforts on more specific tasks. In addition, some members worked on independent aspects of the project. In this section, we will discuss each member’s specific contribution to this project’s success.

Aaron: Aaron worked in the Experimental design subgroup and worked on literature review for the first part of the summer, as well as working on methods for the Quantification part of our project, researching various methods.

Allison: Allison worked on the Integrated Human Practices team, the Collaboration team, worked on literature review for our project as part of the Experimental Design team, and worked on the Education team. She worked on the policy brief for the Integrated Human Practices, and was instrumental in putting together our Speaker Series that helped bring awareness to the grapefruit-drug interaction problem and brought together students and faculty to learn about synthetic biology.

Andre: Andre worked on the Experimental Design subgroup and worked on literature review and ideation.

Jay: Jay worked on the Experimental Design subgroup and worked on literature review, as well as created graphics for our promotional video.

Josh: Joshua worked on literature review in the first part of the summer, and then worked primarily within the Integrated Human Practices and Education subteams. While interested in the experimental elements of the project, Josh spent much of his time organizing the speaker series and speaking with experienced bioengineers, building information that he used to build the policy brief alongside Allison. He was glad for the opportunity to learn about all the different parts of a bioengineering project, as well as contributing his interests and experience to the different aspects of the project.

Maya: Maya was part of the Experimental Design, Collaboration, and Modeling team. She worked on literature review and needfinding for the first part of the summer, and then transitioned to helping design plasmids and researching experimental design and helping with determining viable techniques for our project. She enjoyed combining and working on her research and design skills, and is grateful to be connected to a wider group of students who are interested in Synthetic Biology from across the world.

Nathan: Nathan was a part of the Integrated Human Practices sub-team and the Experimental sub-team. As well as being part of these sub-teams, Nathan also worked on the promotional video with the help of Jay (animations) and Sophia Aujero (editing). Whether it be in the lab or behind a computer, Nathan has worked on various aspects of this year’s iGEM project.

William: William worked on the Modeling and Experimental Design subgroup, and his work was instrumental in helping us come up with a quantitative model for enzyme kinetics. He also worked on our Contribution aspect of the project.

Contributions From Outside the Team

We would like to give a special thanks to Professor Drew Endy, Professor Stanley Qi, Dr. Prashanth Srinivasan, Lauren Ramlan (as well as the entire iGEM 2020 team), and the Uytengsu Teaching Laboratory. In addition, we would like to thank the following people for their contribution to our project:

Matt Carter - helped with ideation and learning about experimental techniques
Dr. Bailey - helped with ideation and background information about grapefruit-drug interaction
Dr. Sonnenburg - helped with ideation and experimental design
Sophia Aujero - helped with promotional video
Dr. Jennifer Brophy - helped with ideation and experimental design
Dr. Relman - helped with ideation and experimental design
Dr. Megan Palmer - helped with Integrated Human Practices
Miroslav Gasparek - helped with Integrated Human Practices
Dr. Zelda Love - helped with Integrated Human Practices
Sarah Yribarren - advised on website

Citations

Not all of these citations are referenced in the wiki, but we used them all for ideating and coming up with the idea, so have included all useful references throughout our project.

Bagga, D., Reichert, J. L., Koschutnig, K., Aigner, C. S., Holzer, P., Koskinen, K., Moissl-Eichinger, C., & Schöpf, V. (2018). Probiotics drive gut microbiome triggering emotional brain signatures. Gut microbes, 9(6), 486–496. https://doi.org/10.1080/19490976.2018.1460015

Bailey, D.G. (2017), Predicting clinical relevance of grapefruit–drug interactions: a complicated process. J Clin Pharm Ther, 42: 125-127. https://doi.org/10.1111/jcpt.12463

Bailey, D. G., Malcolm, J., Arnold, O., & Spence, J. D. (1998). Grapefruit juice-drug interactions. British journal of clinical pharmacology, 46(2), 101–110. https://doi.org/10.1046/j.1365-2125.1998.00764.x

Bailey, D. G., Dresser, G., & Arnold, J. M. O. (2013). Grapefruit–medication interactions: Forbidden fruit or avoidable consequences? Canadian Medical Association Journal, 185(4), 309 LP – 316. https://doi.org/10.1503/cmaj.120951

Bibi, Z. Role of cytochrome P450 in drug interactions. Nutr Metab (Lond) 5, 27 (2008). https://doi.org/10.1186/1743-7075-5-27

Brophy, J., Voigt, C. Principles of genetic circuit design. Nat Methods 11, 508–520 (2014). https://doi.org/10.1038/nmeth.2926

Bushra, R., Aslam, N., & Khan, A. Y. (2011). Food-drug interactions. Oman medical journal, 26(2), 77–83. https://doi.org/10.5001/omj.2011.21

Cohen, M. B., Schuler, M. A., & Berenbaum, M. R. (1992). A host-inducible cytochrome P-450 from a host-specific caterpillar: molecular cloning and evolution. Proceedings of the National Academy of Sciences of the United States of America, 89(22), 10920–10924. https://doi.org/10.1073/pnas.89.22.10920

Dahan, A., Altman, H. Food–drug interaction: grapefruit juice augments drug bioavailability—mechanism, extent and relevance. Eur J Clin Nutr 58, 1–9 (2004). https://doi.org/10.1038/sj.ejcn.1601736

De Castro, W. V., Mertens-Talcott, S., Rubner, A., Butterweck, V., & Derendorf, H. (2006). Variation of flavonoids and furanocoumarins in grapefruit juices: a potential source of variability in grapefruit juice-drug interaction studies. Journal of agricultural and food chemistry, 54(1), 249–255. https://doi.org/10.1021/jf0516944

Delaforge, M., Pruvost, A., Perrin, L., & André, F. (2005). CYTOCHROME P450-MEDIATED OXIDATION OF GLUCURONIDE DERIVATIVES: EXAMPLE OF ESTRADIOL-17β-GLUCURONIDE OXIDATION TO 2-HYDROXY-ESTRADIOL-17β-GLUCURONIDE BY CYP 2C8. Drug Metabolism and Disposition, 33(3), 466 LP – 473. https://doi.org/10.1124/dmd.104.002097

Dixon, T. A., Williams, T. C., & Pretorius, I. S. (2021). Sensing the future of bio-informational engineering. Nature communications, 12(1), 388. https://doi.org/10.1038/s41467-020-20764-2

Dongfack, M. D., Lallemand, M. C., Kuete, V., Mbazoa, C. D., Wansi, J. D., Trinh-van-Dufat, H., Michel, S., & Wandji, J. (2012). A new sphingolipid and furanocoumarins with antimicrobial activity from Ficus exasperata. Chemical & pharmaceutical bulletin, 60(8), 1072–1075. https://doi.org/10.1248/cpb.c12-00279

Dou, J. and Bennett, M.R. (2018), Synthetic Biology and the Gut Microbiome. Biotechnol. J., 13: 1700159. https://doi.org/10.1002/biot.201700159

Dugrand-Judek, A., Olry, A., Hehn, A., Costantino, G., Ollitrault, P., Froelicher, Y., & Bourgaud, F. (2015). The Distribution of Coumarins and Furanocoumarins in Citrus Species Closely Matches Citrus Phylogeny and Reflects the Organization of Biosynthetic Pathways. PloS one, 10(11), e0142757. https://doi.org/10.1371/journal.pone.0142757

“Furanocoumarins.” Furanocoumarins - an Overview | ScienceDirect Topics, https://www.sciencedirect.com/topics/neuroscience/furanocoumarins.

Gao, Y. D., Zhao, Y., & Huang, J. (2014). Metabolic modeling of common Escherichia coli strains in human gut microbiome. BioMed research international, 2014, 694967. https://doi.org/10.1155/2014/694967

Ge, X., Yang, H., Bednarek, M. A., Galon-Tilleman, H., Chen, P., Chen, M., Lichtman, J. S., Wang, Y., Dalmas, O., Yin, Y., Tian, H., Jermutus, L., Grimsby, J., Rondinone, C. M., Konkar, A., & Kaplan, D. D. (2018). LEAP2 Is an Endogenous Antagonist of the Ghrelin Receptor. Cell metabolism, 27(2), 461–469.e6. https://doi.org/10.1016/j.cmet.2017.10.016

Girennavar, B., Poulose, S. M., Jayaprakasha, G. K., Bhat, N. G., & Patil, B. S. (2006). Furocoumarins from grapefruit juice and their effect on human CYP 3A4 and CYP 1B1 isoenzymes. Bioorganic & medicinal chemistry, 14(8), 2606–2612. https://doi.org/10.1016/j.bmc.2005.11.039

Gong, Y., Li, T., Feng, Y. et al. The function of two P450s, CYP9M10 and CYP6AA7, in the permethrin resistance of Culex quinquefasciatus . Sci Rep 7, 587 (2017). https://doi.org/10.1038/s41598-017-00486-0

González Canga, A., Fernández Martínez, N., Sahagún Prieto, A. M., García Vieitez, J. J., Díez Liébana, M. J., Díez Láiz, R., & Sierra Vega, M. (2010). Dietary fiber and its interaction with drugs. Nutricion hospitalaria, 25(4), 535–539.

Grötzinger, C., Kneifel, J., Patschan, D., Schnoy, N., Anagnostopoulos, I., Faiss, S., Tauber, R., Wiedenmann, B., & Gessner, R. (2001). LI-cadherin: a marker of gastric metaplasia and neoplasia. Gut, 49(1), 73–81. https://doi.org/10.1136/gut.49.1.73

Guo, L. Q., & Yamazoe, Y. (2004). Inhibition of cytochrome P450 by furanocoumarins in grapefruit juice and herbal medicines. Acta pharmacologica Sinica, 25(2), 129–136.

Guttman, Y., Yedidia, I., Nudel, A., Zhmykhova, Y., Kerem, Z., & Carmi, N. (2020). New grapefruit cultivars exhibit low cytochrome P4503A4-Inhibition activity. Food and Chemical Toxicology, 137, 111135. https://doi.org/10.1016/J.FCT.2020.111135 Hills, R. D., Jr, Pontefract, B. A., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2019). Gut Microbiome: Profound Implications for Diet and Disease. Nutrients, 11(7), 1613. https://doi.org/10.3390/nu11071613

J. Agric. Food Chem. 2008, 56, 24, 12064–12068, Publication Date:November 14, 2008 https://doi.org/10.1021/jf802713g

Jones, D.R., Smith, M.B., McLean, R. et al. Engineering dual-glycan responsive expression systems for tunable production of heterologous proteins in Bacteroides thetaiotaomicron. Sci Rep 9, 17400 (2019). https://doi.org/10.1038/s41598-019-53726-w

Kastl, A. J., Terry, N. A., Wu, G. D., & Albenberg, L. G. (2020). The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions. Cellular and Molecular Gastroenterology and Hepatology, 9(1), 33–45. https://doi.org/10.1016/J.JCMGH.2019.07.006

Kelly, S. L., & Kelly, D. E. (2013). Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 368(1612), 20120476. https://doi.org/10.1098/rstb.2012.0476

Kumar, S., Earla, R., Jin, M., Mitra, A. K., & Kumar, A. (2010). Effect of ethanol on spectral binding, inhibition, and activity of CYP3A4 with an antiretroviral drug nelfinavir. Biochemical and biophysical research communications, 402(1), 163–167. https://doi.org/10.1016/j.bbrc.2010.10.014

Kurnik, D., Wood, A. J., & Wilkinson, G. R. (2006). The erythromycin breath test reflects P-glycoprotein function independently of cytochrome P450 3A activity. Clinical pharmacology and therapeutics, 80(3), 228–234. https://doi.org/10.1016/j.clpt.2006.06.002

Li, W., Berenbaum, M. R., & Schuler, M. A. (2001). Molecular analysis of multiple CYP6B genes from polyphagous Papilio species. Insect Biochemistry and Molecular Biology, 31(10), 999–1011. https://doi.org/10.1016/S0965-1748(01)00048-0

Li, W., Schuler, M. A., & Berenbaum, M. R. (2003). Diversification of furanocoumarin-metabolizing cytochrome P450 monooxygenases in two papilionids: Specificity and substrate encounter rate. Proceedings of the National Academy of Sciences, 100(suppl 2), 14593 LP – 14598. https://doi.org/10.1073/pnas.1934643100

Li, W., Schuler, M. A., & Berenbaum, M. R. (2003). Diversification of furanocoumarin-metabolizing cytochrome P450 monooxygenases in two papilionids: Specificity and substrate encounter rate. Proceedings of the National Academy of Sciences, 100(suppl 2), 14593 LP – 14598. https://doi.org/10.1073/pnas.1934643100

Liang, W.-J., Wilson, K. J., Xie, H., Knol, J., Suzuki, S., Rutherford, N. G., Henderson, P. J. F., & Jefferson, R. A. (2005). The gusBC Genes of Escherichia coli Encode a Glucuronide Transport System. Journal of Bacteriology, 187(7), 2377–2385. https://doi.org/10.1128/JB.187.7.2377-2385.2005

Liu, W., Zhi, D., Wang, L., Yang, A., Zhang, L., Ahiasi-Mensah, J., & He, X. (2020). Differences in xanthotoxin metabolites in seven mammalian liver microsomes. Experimental and therapeutic medicine, 20(4), 3846–3852. https://doi.org/10.3892/etm.2020.9098

Lown, K. S., Bailey, D. G., Fontana, R. J., Janardan, S. K., Adair, C. H., Fortlage, L. A., Brown, M. B., Guo, W., & Watkins, P. B. (1997). Grapefruit juice increases felodipine oral availability in humans by decreasing intestinal CYP3A protein expression. The Journal of clinical investigation, 99(10), 2545–2553. https://doi.org/10.1172/JCI119439

Lynch, T., & Price, A. (2007). The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects. American family physician, 76(3), 391–396.

Mertens-Talcott, S.U., Zadezensky, I., De Castro, W.V., Derendorf, H. and Butterweck, V. (2006), Grapefruit-Drug Interactions: Can Interactions With Drugs Be Avoided?. The Journal of Clinical Pharmacology, 46: 1390-1416. https://doi.org/10.1177/0091270006294277

Meyer, A.J., Segall-Shapiro, T.H., Glassey, E. et al. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat Chem Biol 15, 196–204 (2019). https://doi.org/10.1038/s41589-018-0168-3

Mrad, M. F., Mouawad, C. A., Al-Hariri, M., Eid, A. A., Alam, J., & Habib, A. (2012). Statins modulate transcriptional activity of heme-oxygenase-1 promoter in NIH 3T3 Cells. Journal of cellular biochemistry, 113(11), 3466–3475. https://doi.org/10.1002/jcb.24223

Myung, K., Manthey, J.A. & Narciso, J.A. Binding of furanocoumarins in grapefruit juice to Aspergillus niger hyphae. Appl Microbiol Biotechnol 78, 401–407 (2008). https://doi.org/10.1007/s00253-007-1326-9

Myung, K., Manthey, J. A., & Narciso, J. A. (2013). Protein Sequestration of Lipophilic Furanocoumarins in Grapefruit Juice. Journal of Agricultural and Food Chemistry, 61(3), 667–673. https://doi.org/10.1021/jf304271s

Myung, K., Narciso, J. A., & Manthey, J. A. (2008). Removal of furanocoumarins in grapefruit juice by edible fungi. Journal of Agricultural and Food Chemistry, 56(24), 12064–12068. https://doi.org/10.1021/jf802713g

Ogu, C. C., & Maxa, J. L. (2000). Drug interactions due to cytochrome P450. Proceedings (Baylor University. Medical Center), 13(4), 421–423. https://doi.org/10.1080/08998280.2000.11927719

Paine, M. F., Widmer, W. W., Hart, H. L., Pusek, S. N., Beavers, K. L., Criss, A. B., Brown, S. S., Thomas, B. F., & Watkins, P. B. (2006). A furanocoumarin-free grapefruit juice establishes furanocoumarins as the mediators of the grapefruit juice-felodipine interaction. The American journal of clinical nutrition, 83(5), 1097–1105. https://doi.org/10.1093/ajcn/83.5.1097

Paine, M. F., Hart, H. L., Ludington, S. S., Haining, R. L., Rettie, A. E., & Zeldin, D. C. (2006). The human intestinal cytochrome P450 "pie". Drug metabolism and disposition: the biological fate of chemicals, 34(5), 880–886. https://doi.org/10.1124/dmd.105.008672

Pawełczyk, T., & Kłoszewska, I. (2008). Interakcje leków psychotropowych z sokiem grejpfrutowym: korzyści i potencjalne ryzyko [Grapefruit juice interactions with psychotropic drugs: advantages and potential risk]. Przeglad lekarski, 65(2), 92–95.

Pidkovka, N., Rachkevych, O., & Belkhiri, A. (2021). Extrahepatic cytochrome P450 epoxygenases: pathophysiology and clinical significance in human gastrointestinal cancers. Oncotarget, 12(4), 379–391. https://doi.org/10.18632/oncotarget.27893

Regueiro, J., Vallverdú-Queralt, A., Negreira, N., Simal-Gándara, J., & Lamuela-Raventós, R. M. (2014). Identification and Quantification of Grapefruit Juice Furanocoumarin Metabolites in Urine: An Approach Based on Ultraperformance Liquid Chromatography Coupled to Linear Ion Trap-Orbitrap Mass Spectrometry and Solid-Phase Extraction Coupled to Ultraperformance Liquid Chromatography Coupled to Triple Quadrupole-Tandem Mass Spectrometry. Journal of Agricultural and Food Chemistry, 62(9), 2134–2140. https://doi.org/10.1021/jf405701a

Rivory, L.P., Slaviero, K.A., Hoskins, J.M. et al. The Erythromycin Breath Test For the Prediction of Drug Clearance. Clin Pharmacokinet 40, 151–158 (2001). https://doi.org/10.2165/00003088-200140030-00001

Seden, K., Dickinson, L., Khoo, S. et al. Grapefruit-Drug Interactions. Drugs 70, 2373–2407 (2010). https://doi.org/10.2165/11585250-000000000-00000

Sevrioukova I. F. (2019). Structural Insights into the Interaction of Cytochrome P450 3A4 with Suicide Substrates: Mibefradil, Azamulin and 6',7'-Dihydroxybergamottin. International journal of molecular sciences, 20(17), 4245. https://doi.org/10.3390/ijms20174245

Sharma, A., Chaudhuri, T.K. Revisiting Escherichia coli as microbial factory for enhanced production of human serum albumin. Microb Cell Fact 16, 173 (2017). https://doi.org/10.1186/s12934-017-0784-8

Shuaichen, L., & Guangyi, W. (2018). Bioinformatic analysis reveals CYP2C9 as a potential prognostic marker for HCC and liver cancer cell lines suitable for its mechanism study. Cellular and molecular biology (Noisy-le-Grand, France), 64(7), 70–74.

Srinivas N. R. (2016). Clinical drug-drug interactions of bosentan, a potent endothelial receptor antagonist, with various drugs: Physiological role of enzymes and transporters. General physiology and biophysics, 35(3), 243–258. https://doi.org/10.4149/gpb_2015050\

Takahashi, M., Onozawa, S., Ogawa, R., Uesawa, Y. and Echizen, H. (2015), Predictive performance of three practical approaches for grapefruit juice-induced 2-fold or greater increases in AUC of concomitantly administered drugs. J Clin Pharm Ther, 40: 91-97. https://doi.org/10.1111/jcpt.12231

Thelen, K., & Dressman, J. B. (2009). Cytochrome P450-mediated metabolism in the human gut wall. The Journal of pharmacy and pharmacology, 61(5), 541–558. https://doi.org/10.1211/jpp/61.05.0002

Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical journal, 474(11), 1823–1836. https://doi.org/10.1042/BCJ20160510

Trumble, J T, Moar, W J, Brewer, M J, & Carson, W G. Impact of UV radiation on activity of linear furanocoumarins and Bacillus thuringiensis var. kurstaki against Spodoptera exigua: Implications for tritrophic interactions. United States. https://doi.org/10.1007/BF01395603

Uesawa, Y., & Mohri, K. (2006). The use of heat treatment to eliminate drug interactions due to grapefruit juice. Biological & pharmaceutical bulletin, 29(11), 2274–2278. https://doi.org/10.1248/bpb.29.2274

Uesawa, Y., & Mohri, K. (2006). UV-irradiated grapefruit juice loses pharmacokinetic interaction with nifedipine in rats. Biological & pharmaceutical bulletin, 29(6), 1286–1289. https://doi.org/10.1248/bpb.29.1286

Wang, Y. H., Wei, K. Y., & Smolke, C. D. (2013). Synthetic biology: advancing the design of diverse genetic systems. Annual review of chemical and biomolecular engineering, 4, 69–102. https://doi.org/10.1146/annurev-chembioeng-061312-103351

Widmer, W. and Haun, C. (2005), Variation in Furanocoumarin Content and New Furanocoumarin Dimers in Commercial Grapefruit (Citrus paradisi Macf.) Juices. Journal of Food Science, 70: C307-C312. https://doi.org/10.1111/j.1365-2621.2005.tb07178.x

Won, C. S., Lan, T., Vandermolen, K. M., Dawson, P. A., Oberlies, N. H., Widmer, W. W., Scarlett, Y. V., & Paine, M. F. (2013). A modified grapefruit juice eliminates two compound classes as major mediators of the grapefruit juice-fexofenadine interaction: an in vitro-in vivo "connect". Journal of clinical pharmacology, 53(9), 982–990. https://doi.org/10.1002/jcph.136

Yu, T., Wang, X., Zhu, G., Han, C., Su, H., Liao, X., Yang, C., Qin, W., Huang, K., & Peng, T. (2018). The prognostic value of differentially expressed CYP3A subfamily members for hepatocellular carcinoma. Cancer management and research, 10, 1713–1726. https://doi.org/10.2147/CMAR.S159425

Zhimou Wen, Sanjeewa Rupasinghe, Guodong Niu, May R. Berenbaum, Mary A. Schuler, CYP6B1 and CYP6B3 of the Black Swallowtail (Papilio polyxenes): Adaptive Evolution through Subfunctionalization, Molecular Biology and Evolution, Volume 23, Issue 12, December 2006, Pages 2434–2443, https://doi.org/10.1093/molbev/msl118

Zhou, J., Wen, Q., Li, S. F., Zhang, Y. F., Gao, N., Tian, X., Fang, Y., Gao, J., Cui, M. Z., He, X. P., Jia, L. J., Jin, H., & Qiao, H. L. (2016). Significant change of cytochrome P450s activities in patients with hepatocellular carcinoma. Oncotarget, 7(31), 50612–50623. https://doi.org/10.18632/oncotarget.9437