Resources Barrick Lab Website – We use a lot of these protocols, including media recipes, cloning techniques, transformation and conjugation procedures, and other project-specific activities. Relevant literature: Caffeinated Coli Project: Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5. Erik M. Quandt, Michael J. Hammerling, Ryan M. Summers, Peter B. Otoupal, Ben Slater, Razan N. Alnahhas, Aurko Dasgupta, James L. Bachman, Mani V. Subramanian, Jeffrey E. Barrick. (2013). ACS synthetic biology, 2(6), 301–307. https://doi.org/10.1021/sb4000146 Bioassay for Determining the Concentrations of Caffeine and Individual Methylxanthines in Complex Samples. Alejandro E. Gutierrez, Prachi Shah, Abigail E. Rex, Tien C. Nguyen, Saamiha P. Kenkar, Jeffrey E. Barrick, Dennis M. Mishler. (2019). Appl Environ Microbiol. https://doi.org/10.1128/AEM.01965-19 Evolutionary Stability Project: Predicting the genetic stability of engineered DNA sequences with the EFM calculator. Benjamin R. Jack, Sean P. Leonard, Dennis M. Mishler, Brian A. Renda, Dacia Leon, Gabriel A. Suárez, Jeffrey E. Barrick. (2015). ACS Synthetic Biology. 4(8):939-943. https://doi.org/10.1021/acssynbio.5b00068 Designing and engineering evolutionary robust genetic circuits. Sean C. Sleight, Bryan A. Bartley, Jane A. Lieviant, Herbert M. Sauro. (2010). J Biol Eng 4, 12 . https://doi.org/10.1186/1754-1611-4-12 Bee Project: The Neonicotinoid Insecticide Imidacloprid Disrupts Bumblebee Foraging Rhythms and Sleep. Kiah Tasman, Sean A. Rands, James J. L. Hodge (2020) iScience; 23(12): 101827. https://doi.org/10.1016/j.isci.2020.101827 Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids. Leonard SP, Perutka J, Powell JE, Geng P, Richhart DD, Byrom M, Kar S, Davies BW, Ellington AD, Moran NA, Barrick JE. (2018) ACS Synthetic Biology; 7(5):1279-1290. https://doi.org/10.1021/acssynbio.7b00399 Circadian foraging rhythms of bumblebees monitored by radio-frequency identification. Jürgen Stelzer R, Stanewsky R, Chittka L. J Biol Rhythms. (2010); 25(4):257-67. https://doi.org/10.1177/0748730410371750. Daily changes in ultraviolet light levels can synchronize the circadian clock of bumblebees (Bombus terrestris). Chittka L, Stelzer RJ, Stanewsky R. (2013) Chronobiology International. 30(4):434-42. https://doi.org/10.3109/07420528.2012.741168. Cyanobacteria Project: Characterizing and Genetically Modifying Oscillatoria to Degrade BPA. Grace Long (2017) [Unpublished Undergraduate Thesis]. http://hdl.handle.net/2152/65180 Using fungible biosensors to evolve improved alkaloid biosyntheses. Simon d’Oelsnitz, Wantae Kim, Nathaniel T. Burkholder, Kamyab Javanmardi, Ross Thyer, Yan Zhang, Hal S. Alper, Andrew D. Ellington (2022). Nat Chem Biology. (9):981-989. https://10.1038/s41589-022-01072-w Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Adam J. Meyer, Thomas H. Segall-Shapiro, Emerson Glassey, Jing Zhang, Christopher A. Voigt (2019). Nat Chem Biol 15, 196–204 https://doi.org/10.1038/s41589-018-0168-3 A family of synthetic riboswitches adopts a kinetic trapping mechanism. Dennis M. Mishler & Justin P. Gallivan (2014). Nucleic Acids Research 42, 10, 6753–6761, https://doi.org/10.1093/nar/gku262
