Selected Publications
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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:
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, 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.