Selected Publications
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BioBits™ Explorer: A modular synthetic biology education kit
Huang A, Nguyen PQ, Stark JC, et al. BioBitsTM Explorer: A modular synthetic biology education kit. Science Advances. 2018;4(8):eaat5105. doi:10.1126/sciadv.aat5105. Hands-on demonstrations greatly enhance the teaching of science, technology, engineering, and mathematics (STEM) concepts and foster engagement and exploration in the sciences. While numerous chemistry and physics classroom demonstrations exist, few biology demonstrations are practical and accessible due to the challenges and concerns of growing living cells in classrooms. We introduce BioBits™ Explorer, a synthetic biology educational kit based on shelf-stable, freeze-dried, cell-free (FD-CF) reactions, which are activated by simply adding water. The FD-CF reactions engage the senses of sight, smell, and touch with outputs that produce fluorescence, fragrances, and hydrogels, respectively. We introduce components that can teach tunable protein expression, enzymatic reactions, biomaterial formation, and biosensors using RNA switches, some of which represent original FD-CF outputs that expand the toolbox of cell-free synthetic biology. The BioBits™ Explorer kit enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms. |
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BioBits™ Bright: A fluorescent synthetic biology education kit
Stark JC, Huang A, Nguyen PQ, et al. BioBitsTM Bright: A fluorescent synthetic biology education kit. Science Advances. 2018;4(8):eaat5107. doi:10.1126/sciadv.aat5107. Synthetic biology offers opportunities for experiential educational activities at the intersection of the life sciences, engineering, and design. However, implementation of hands-on biology activities in classrooms is challenging because of the need for specialized equipment and expertise to grow living cells. We present BioBits™ Bright, a shelfstable, just-add-water synthetic biology education kit with easy visual outputs enabled by expression of fluorescent proteins in freeze-dried, cell-free reactions. We introduce activities and supporting curricula for teaching the central dogma, tunable protein expression, and design-build-test cycles and report data generated by K-12 teachers and students. We also develop inexpensive incubators and imagers, resulting in a comprehensive kit costing <US$100 per 30-person classroom. The user-friendly resources of this kit promise to enhance biology education both inside and outside the classroom. |
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Portable, On-Demand Biomolecular Manufacturing.
Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ Cell. 2016 Sep 22;167(1):248-259.e12. doi: 0.1016/j.cell.2016.09.013. Synthetic biology uses living cells as molecular foundries for the biosynthesis of drugs, therapeutic proteins, and other commodities. However, the need for specialized equipment and refrigeration for production and distribution poses a challenge for the delivery of these technologies to the field and to low-resource areas. Here, we present a portable platform that provides the means for on-site, on-demand manufacturing of therapeutics and biomolecules. This flexible system is based on reaction pellets composed of freeze-dried, cell-free transcription and translation machinery, which can be easily hydrated and utilized for biosynthesis through the addition of DNA encoding the desired output. We demonstrate this approach with the manufacture and functional validation of antimicrobial peptides and vaccines and present combinatorial methods for the production of antibody conjugates and small molecules. This synthetic biology platform resolves important practical limitations in the production and distribution of therapeutics and molecular tools, both to the developed and developing world. |
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Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.
Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Cell. 2016 May 19;165(5):1255-66. doi: 10.1016/j.cell.2016.04.059. Epub 2016 May 6. The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. |
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Paper-based Synthetic Gene Networks.
Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Cell. 2014 Nov 6;159(4):940-54. doi: 10.1016/j.cell.2014.10.004. Epub 2014 Oct 23. Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. |
All Publications:
Perspective: Solidifying the impact of cell-free synthetic biology through lyophilization
Pardee, K. (2018). Perspective: Solidifying the Impact of Cell-Free Synthetic Biology Through Lyophilization. Biochemical Engineering Journal. https://doi.org/10.1016/J.BEJ.2018.07.008
BioBits™ Explorer: A modular synthetic biology education kit.
A. Huang, P. Q. Nguyen, J. C. Stark, M. K. Takahashi, N. Donghia, T. Ferrante, A. J. Dy, K. J. Hsu, R. S. Dubner, K. Pardee, M. C. Jewett, J. J. Collins, BioBits™ Explorer: A modular synthetic biology education kit. Sci. Adv. 4, eaat5105 (2018).
BioBits™ Bright: A fluorescent synthetic biology education kit.
Stark, J.C., Huang, A., Nguyen, P.Q., Dubner, R.S., Hsu, K.J., Ferrante, T.C., Anderson, M., Kanapskyte, A., Mucha, Q., Packett, J.S., Patel, P., Patel, R., Qaq, D., Zondor, T., Burke, J., Brand, L., Hill, L.R., Chellaswamy, J.F., Faheem, N., Fetherling, S., Gong, E., Gonzalzles, E.M., Granito, T., Koritsaris, J., Nguyen, B., Ottman, S., Palffy, C., Patel, A., Skweres, S., Slaton, A., Woods, T., Donghia, N., Pardee, K., Collins, J.J., Jewett, M.C., 2018. BioBits Bright: A fluorescent synthetic biology education kit. Science Advances accepted. doi:10.1126/sciadv.aat5107
Portable, On-Demand Biomolecular Manufacturing.
Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ Cell. 2016 Sep 22;167(1):248-259.e12. doi: 10.1016/j.cell.2016.09.013.
Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.
Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Cell. 2016 May 19;165(5):1255-66. doi: 10.1016/j.cell.2016.04.059. Epub 2016 May 6.
Synthetic biology devices for in vitro and in vivo diagnostics.
Slomovic S, Pardee K, Collins JJ. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14429-35. doi: 10.1073/pnas.1508521112. Review.
Deconstructing transcriptional heterogeneity in pluripotent stem cells.
Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ.Nature. 2014 Dec 4;516(7529):56-61. doi: 10.1038/nature13920.
Paper-based synthetic gene networks.
Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Cell. 2014 Nov 6;159(4):940-54. doi: 10.1016/j.cell.2014.10.004. Epub 2014 Oct 23.
Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions.
Faucon PC, Pardee K, Kumar RM, Li H, Loh YH, Wang X. PLoS One. 2014 Jul 24;9(7):e102873. doi: 10.1371/journal.pone.0102873. eCollection 2014.
Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction.
Pardee K, Necakov AS, Krause H. Subcell Biochem. 2011;52:123-53. doi: 10.1007/978-90-481-9069-0_6. Review.
The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis.
Horner MA, Pardee K, Liu S, King-Jones K, Lajoie G, Edwards A, Krause HM, Thummel CS. Genes Dev. 2009 Dec 1;23(23):2711-6. doi: 10.1101/gad.1833609.
Nuclear receptors homo sapiens Rev-erbbeta and Drosophila melanogaster E75 are thiolate-ligated heme proteins which undergo redox-mediated ligand switching and bind CO and NO.
Marvin KA, Reinking JL, Lee AJ, Pardee K, Krause HM, Burstyn JN. Biochemistry. 2009 Jul 28;48(29):7056-71. doi: 10.1021/bi900697c.
The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.
Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A.
PLoS Biol. 2009 Feb 24;7(2):e43. doi: 10.1371/journal.pbio.1000043.
The Drosophila nuclear receptor e75 contains heme and is gas responsive.
Reinking J, Lam MM, Pardee K, Sampson HM, Liu S, Yang P, Williams S, White W, Lajoie G, Edwards A, Krause HM. Cell. 2005 Jul 29;122(2):195-207.
Nuclear hormone receptors, metabolism, and aging: what goes around comes around. Transcription factors link lipid metabolism and aging-related processes.
Pardee K, Reinking J, Krause H. Sci Aging Knowledge Environ. 2004 Nov 24;2004(47):re8. Review.
Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction.
Pardee K, Necakov AS, Krause H. Subcell Biochem. 2011;52:123-53. doi: 10.1007/978-90-481-9069-0_6. Review.
The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis.
Horner MA, Pardee K, Liu S, King-Jones K, Lajoie G, Edwards A, Krause HM, Thummel CS. Genes Dev. 2009 Dec 1;23(23):2711-6. doi: 10.1101/gad.1833609.
P1 Trisaccharide (Galalpha1,4Galbeta1,4GlcNAc) synthesis by enzyme glycosylation reactions using recombinant Escherichia coli.
Liu Z, Lu Y, Zhang J, Pardee K, Wang PG. Appl Environ Microbiol. 2003 Apr;69(4):2110-5.
Structural proteomics: toward high-throughput structural biology as a tool in functional genomics.
Yee A, Pardee K, Christendat D, Savchenko A, Edwards AM, Arrowsmith CH. Acc Chem Res. 2003 Mar;36(3):183-9.
Pardee, K. (2018). Perspective: Solidifying the Impact of Cell-Free Synthetic Biology Through Lyophilization. Biochemical Engineering Journal. https://doi.org/10.1016/J.BEJ.2018.07.008
BioBits™ Explorer: A modular synthetic biology education kit.
A. Huang, P. Q. Nguyen, J. C. Stark, M. K. Takahashi, N. Donghia, T. Ferrante, A. J. Dy, K. J. Hsu, R. S. Dubner, K. Pardee, M. C. Jewett, J. J. Collins, BioBits™ Explorer: A modular synthetic biology education kit. Sci. Adv. 4, eaat5105 (2018).
BioBits™ Bright: A fluorescent synthetic biology education kit.
Stark, J.C., Huang, A., Nguyen, P.Q., Dubner, R.S., Hsu, K.J., Ferrante, T.C., Anderson, M., Kanapskyte, A., Mucha, Q., Packett, J.S., Patel, P., Patel, R., Qaq, D., Zondor, T., Burke, J., Brand, L., Hill, L.R., Chellaswamy, J.F., Faheem, N., Fetherling, S., Gong, E., Gonzalzles, E.M., Granito, T., Koritsaris, J., Nguyen, B., Ottman, S., Palffy, C., Patel, A., Skweres, S., Slaton, A., Woods, T., Donghia, N., Pardee, K., Collins, J.J., Jewett, M.C., 2018. BioBits Bright: A fluorescent synthetic biology education kit. Science Advances accepted. doi:10.1126/sciadv.aat5107
Portable, On-Demand Biomolecular Manufacturing.
Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ Cell. 2016 Sep 22;167(1):248-259.e12. doi: 10.1016/j.cell.2016.09.013.
Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.
Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Cell. 2016 May 19;165(5):1255-66. doi: 10.1016/j.cell.2016.04.059. Epub 2016 May 6.
Synthetic biology devices for in vitro and in vivo diagnostics.
Slomovic S, Pardee K, Collins JJ. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14429-35. doi: 10.1073/pnas.1508521112. Review.
Deconstructing transcriptional heterogeneity in pluripotent stem cells.
Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ.Nature. 2014 Dec 4;516(7529):56-61. doi: 10.1038/nature13920.
Paper-based synthetic gene networks.
Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Cell. 2014 Nov 6;159(4):940-54. doi: 10.1016/j.cell.2014.10.004. Epub 2014 Oct 23.
Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions.
Faucon PC, Pardee K, Kumar RM, Li H, Loh YH, Wang X. PLoS One. 2014 Jul 24;9(7):e102873. doi: 10.1371/journal.pone.0102873. eCollection 2014.
Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction.
Pardee K, Necakov AS, Krause H. Subcell Biochem. 2011;52:123-53. doi: 10.1007/978-90-481-9069-0_6. Review.
The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis.
Horner MA, Pardee K, Liu S, King-Jones K, Lajoie G, Edwards A, Krause HM, Thummel CS. Genes Dev. 2009 Dec 1;23(23):2711-6. doi: 10.1101/gad.1833609.
Nuclear receptors homo sapiens Rev-erbbeta and Drosophila melanogaster E75 are thiolate-ligated heme proteins which undergo redox-mediated ligand switching and bind CO and NO.
Marvin KA, Reinking JL, Lee AJ, Pardee K, Krause HM, Burstyn JN. Biochemistry. 2009 Jul 28;48(29):7056-71. doi: 10.1021/bi900697c.
The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.
Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A.
PLoS Biol. 2009 Feb 24;7(2):e43. doi: 10.1371/journal.pbio.1000043.
The Drosophila nuclear receptor e75 contains heme and is gas responsive.
Reinking J, Lam MM, Pardee K, Sampson HM, Liu S, Yang P, Williams S, White W, Lajoie G, Edwards A, Krause HM. Cell. 2005 Jul 29;122(2):195-207.
Nuclear hormone receptors, metabolism, and aging: what goes around comes around. Transcription factors link lipid metabolism and aging-related processes.
Pardee K, Reinking J, Krause H. Sci Aging Knowledge Environ. 2004 Nov 24;2004(47):re8. Review.
Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction.
Pardee K, Necakov AS, Krause H. Subcell Biochem. 2011;52:123-53. doi: 10.1007/978-90-481-9069-0_6. Review.
The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis.
Horner MA, Pardee K, Liu S, King-Jones K, Lajoie G, Edwards A, Krause HM, Thummel CS. Genes Dev. 2009 Dec 1;23(23):2711-6. doi: 10.1101/gad.1833609.
P1 Trisaccharide (Galalpha1,4Galbeta1,4GlcNAc) synthesis by enzyme glycosylation reactions using recombinant Escherichia coli.
Liu Z, Lu Y, Zhang J, Pardee K, Wang PG. Appl Environ Microbiol. 2003 Apr;69(4):2110-5.
Structural proteomics: toward high-throughput structural biology as a tool in functional genomics.
Yee A, Pardee K, Christendat D, Savchenko A, Edwards AM, Arrowsmith CH. Acc Chem Res. 2003 Mar;36(3):183-9.