Nicholas Baltes
Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF. (2015). Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nature Plants. 15145: 1-4.
Cermak T, Baltes NJ, Cegan R, Zhang Y, Voytas DF (2015). High-frequency, precise modification of the tomato genome. Genome Biology. 16:232.
Lowder LG, Zhang D, Baltes NJ, Paul JW 3rd, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation.Plant Physiol. 169:971-85.
Baltes NJ, Voytas DF (2015). Enabling plant synthetic biology through genome engineering. Trends in Biotechnology. 33:120-31.
Ali Z, Abul-faraj A, Li L, Ghosh N, Piatek M, Mahjoub A, Aouida M, Piatek A, Baltes NJ, Voytas DF, Dinesh-Kumar S, Hahfouz MM (2015). Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Mol. Plant. 8:1288-91.
Qi Y, Starker CG, Zhang F, Baltes NJ, Voytas DF (2014). Tailor-made mutations in Arabidopsis using zinc finger nucleases. Methods Mol Biol. 1062:193-209.
Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF (2014). DNA replicons for plant genome engineering. Plant Cell. 26:151-63.
Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF (2013).Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3. 3:1707-15.
Curtin SJ, Anderson JE, Starker CG, Baltes NJ, Mani D, Voytas DF, Stupar RM (2013). Targeted mutagenesis for functional analysis of gene duplication in legumes. Methods Mol Biol. 1069:25-42.
Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM (2011). Targeted mutagenesis of duplicated genes in soybean with zinc finger nucleases. Plant Physiol. 156:466-73.
Sarah Bloch
Held, ME, Kolb, A, Perdue, S, Hsu, S, Bloch SE, Quin MB, Schmidt-Dannert, C, Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. SciReports 2016, 6:24359 DOI: 10.1038/srep24359
Bloch SE, Schmidt-Dannert C. Construction of a chimeric biosynthetic pathway for the de novo biosynthesis of rosmarinic acid in Eschericha coli. ChemBiochem 2014, 15:2393-2401.
Wawrzyn GT, Bloch SE, Schmidt-Dannert C. Discovery and characterization of terpenoid biosynthetic pathways of fungi. Methods Enzymol 2012; 515: 83-105. PMID: 22999171
Vick JE, Johnson ET, Choudhary S, Bloch SE, Lopez-Gellego F, Srivastava P, Tikh IB, Wawrzyn GT, Schmidt-Dannert C. Optimized compatible set of BioBrick™ vectors for metabolic pathway engineering. Appl Microbiol Biotechnol 2011; 92:1275–1286. PMID: 22033566
Stephan Cameron
Wackett, L.P., J. Frias, J.L. Seffernick, D. Sukovich, and S.M. Cameron (2007) Vibrio furnissii M1: Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype.Appl. Environ. Microbiol. 73: 7192-7198.
Cameron, S.M., K. Durchschein, J.E. Richman, M.J. Sadowsky and L.P. Wackett (2011) A new family of biuret hydrolases involved in s-triazine ring metabolism. ACS Catalysis 1(9):1075-1082.
Seffernick, J.L., J.S. Erickson, S.M. Cameron, S. Cho, A.G. Dodge, J. Richman, M.J. Sadowsky, and L.P. Wackett (2012) Defining the cyanuric acid hydrolase (AtzD)/barbiturase protein family. J. Bacteriol. 194:4579-4588.
Veronica Diaz-Rodriguez
Diaz-Rodriguez, V.; Ganusova, E.; Rappe, T. M.; Becker, J. M. & Distefano, M. D. (2015) Synthesis of Peptides Containing C-Terminal Esters Using Trityl Side-Chain Anchoring: Applications to the Synthesis of C-Terminal Ester Analogs of the Saccharomyces cerevisiae Mating Pheromone a-Factor.J. Org. Chem., 80, 11266. PMCID: in progress
Diaz-Rodriguez, V.; Mullen, D. G.; Ganusova, E.; Becker, J. M. & Distefano, M. D. (2012) Synthesis of Peptides Containing C-Terminal Methyl Esters Using Trityl Side-Chain Anchoring: Application to the Synthesis of a-Factor and a-Factor Analogs. Org. Lett., 14, 5648. PMCID: PMC3622458
Sarah Gruba
Finkenstaedt-Quinn, S.; Gruba, S.; & Haynes, C.L. (2016) Variations in Fusion Pore Formation in Cholesterol-Treated Platelets, Biophysical Journal, 110, 922 PMID: 26910428
Manning, B.M.; Meyer, A.F.; Gruba, S.M.; & Haynes, C.L. (2015) Single-Cell Analysis of Mast Cell Degranulation Induced by Airway Smooth Muscle-Secreted Chemokines, Biochimica et Biophysica Acta- General Subjects, 1850, 1862. PMID: 25986989
Gruba, S.M.; Koseoglu, S.; Meyer, A.F.; Meyer, B.M.; Maurer-Jones, M.A.; & Haynes, C.L. (2015) Platelet Membrane Variations and their Effects on δ-Granule Secretion Kinetics and Aggregation Spreading among Different Species, Biochimica et Biophysica Acta- Biomembranes, 1848, 1609. PMID: 25906946
Meyer, A.F.; Knutson, C.M.; Finkenstaedt-Quinn, S. A.; Gruba, S. M.; Meyer, B.M.; Thompson, J.W.; Maurer-Jones, M.A.; Halderman, S.; Tillman, A.S.; DeStefano, L.; & Haynes, C.L. (2014) Activities for Middle School Students To Sleuth a Chemistry Whodunit and Investigate the Scientific Method,Journal of Chemical Education, 91, 410.
Chan, J.D., Agbedanu, P.N., Zamanian, M., Gruba, S.M., Haynes, C.L., Day, T.A., Marchant, J.S., 2014, Death and Axes: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents,PLOS Pathogens, 10(2): e1003942.
Gruba, S.M., Meyer, A.F., Manning, B.M., Wang, Y., Thompson, J.W., Dalluge, J.J., and Haynes, C.L. (2014) Time- and Concentration-Dependent Effects of Exogenous Serotonin and Inflammatory Cytokines on Mast Cell Function, ACS Chemical Biology, 9, 503. PMID: 24586156
Ian Gunsolus
Hang, M.; Gunsolus, I.; Wayland, H.; Melby, E.; Mensch, A.; Hurley, K.; Pedersen, J.; Haynes, C.L.; Hamers, R. (2016) Impact of Nanoscale Lithium Nickel Manganese Cobalt Oxide (NMC) on the Bacterium Shewanella oneidensis MR-1, Chemistry of Materials, 28, 1092.
Gunsolus, I.L. & Haynes, C.L. (2016) Analytical Aspects of Nanotoxicology, Analytical Chemistry, 88 451. PMID: 26565109
Qiu, T. A.; Bozich, J. S.; Lohse, S. E.; Vartanian, A. M.; Jacob, L. M.; Meyer, B. M.; Gunsolus, I. L.; Niemuth, N. J.; Murphy, C. J.; Haynes, C. L.; & Klaper, R. D. (2015) Gene Expression Response of the Gram-negative Bacterium Shewanella oneidensis and the Water Flea Daphnia magna Exposed to Functionalized Gold Nanoparticles, Environmental Science: Nano, 2, 615.
Mousavi, M.P.S.; Gunsolus, I.; Perez de Jesus, C.E.; Lancaster, M.; Hussein, K.; Haynes, C.L.; Buhlmann, P. (2015) Dynamic Silver Speciation as Studied with Fluorous-phase Ion-selective Electrodes: Effect of Natural Organic Matter on the Toxicity and Speciation of Silver, Science of the Total Environment, 537, 453. PMID: 26284896
Jacobson, K.; Gunsolus, I.; Kuech, T.; Troiano, J.; Melby, E.; Lohse, S.; Hu, D.; Chrisler, W.; Murphy, C; Orr, G.; Geiger, F.; Haynes, C.L.; & Pedersen, J.A. (2015) Lipopolysaccharide Density and Structure Governs the Extent and Distance of Nanoparticle Interaction with Actual and Model Bacterial Outer Membranes, Environmental Science & Technology, 49, 10642. PMID: 26207769
Feng, Z.V., Gunsolus, I.L.; Qiu, T.A.; Hurley, K.R.; Nyberg, L.H.; Frew, H.; Johnson, K.P.; Vartanian, A.M.; Jacob, L.M.; Lohse, S.E.; Torelli, M.D.; Hamers, R.J.; Murphy, C.J.; & Haynes, C.L. (2015) Impacts of Gold Nanoparticle Charge and Ligand Type on Surface Binding and Toxicity to Gram-Negative and Gram-Positive Bacteria, Chemical Science, 6, 5186.
Gunsolus, I.L.; Mousavi, M.P.S.; Hussein, K.; Buhlmann, P.; & Haynes, C.L.; (2015) Effects of Humic and Fulvic Acids on Silver Nanoparticle Stability, Dissolution, and Toxicity, Environmental Science & Technology, 49, 8078. PMID: 26047330
Gunsolus, I.L.; Hu, D.; Mihai, C.; Lohse, S.E.; Lee, C.-S.; Torelli, M.D.; Hamers, R.J.; Murphy, C.J.; Orr, G.; and Haynes, C.L. (2014) Facile Method to Stain the Bacterial Cell Surface for Super-Resolution Fluorescence Microscopy, Analyst, 139(12) 3174-3178. PMID: 23701037
Maurer-Jones, M.A.; Gunsolus, I.; Meyer, B.; Christenson, C.; & Haynes, C.L. (2013) Impact of TiO2 Nanoparticles on Growth, Biofilm Formation, and Flavin Secretion in Shewanella oneidensis,Analytical Chemistry, 85, 5810. PMID: 23701037
Maurer-Jones, M.A.; Gunsolus, I.L.; Murphy, C.J.; & Haynes, C.L. (2013) Toxicity of Engineered Nanoparticles in the Environment, Analytical Chemistry, 85, 3036. PMID: 23427995
Timothy Johnson
Nicholls, D.P.; Oh S.H.; Johnson, T.W.; & Reitich, F. (2016) Launching surface plasmon waves via vanishingly small periodic gratings. J. Opt. Soc. Am. A Opt. Image. Sci. Vis. 33, 276. PMID: 26974896.
Kumar, S.; Johnson, T.W.; Wood, C.K.; Qu, T.; Wittenberg, N.J.; Otto, L.M.; Shaver, J.; Long, N.J.; Victora R.H.; Edel, J.B.; & Oh, S.H. (2016) Template-Stripped Multifunctional Wedge and Pyramid Arrays for Magnetic Nanofocusing and Optical Sensing. ACS Appl Mater Interfaces. [Epub ahead of print] PubMed PMID: 26837912.
Barik A, Cherukulappurath S, Wittenberg NJ, Johnson TW, Oh SH. Dielectrophoresis-Assisted Raman Spectroscopy of Intravesicular Analytes on Metallic Pyramids. Anal Chem. 2016 Feb 2;88(3):1704-10. doi:10.1021/acs.analchem.5b03719. Epub 2016 Jan 11. PubMed PMID: 26751756.
Yoo D, Johnson TW, Cherukulappurath S, Norris DJ, Oh SH. Template-Stripped Tunable Plasmonic Devices on Stretchable and Rollable Substrates. ACS Nano. 2015 Nov 24;9(11):10647-54. doi: 10.1021/acsnano.5b05279. Epub 2015 Oct 1. PubMed PMID: 26402066; PubMed Central PMCID: PMC4660390.
Otto LM, Mohr DA, Johnson TW, Oh SH, Lindquist NC.Polarization interferometry for real-time spectroscopic plasmonic sensing. Nanoscale. 2015 Mar 7;7(9):4226-33. doi: 10.1039/c4nr06586g. PubMed PMID: 25672889; PubMed Central PMCID: PMC4339257.
Kumar S, Cherukulappurath S, Johnson TW, Oh SH. Millimeter-Sized Suspended Plasmonic Nanohole Arrays for Surface-Tension-Driven Flow-Through SERS. Chem Mater. 2014 Nov 25;26(22):6523-6530. Epub 2014 Oct 20. PubMed PMID: 25678744; PubMed Central PMCID: PMC4311951.
Nicholls DP, Reitich F, Johnson TW, Oh SH. Fast high-order perturbation of surfaces methods for simulation of multilayer plasmonic devices and metamaterials. J Opt Soc Am A Opt Image Sci Vis. 2014 Aug 1;31(8):1820-31. doi: 10.1364/JOSAA.31.001820. PubMed PMID: 25121539.
Jose J, Kress S, Barik A, Otto LM, Shaver J, Johnson TW, Lapin ZJ, Bharadwaj P, Novotny L, Oh SH.Individual Template-Stripped Conductive Gold Pyramids for Tip-Enhanced Dielectrophoresis. ACS Photonics. 2014 May 21;1(5):464-470. Epub 2014 Apr 16. PubMed PMID: 25541619; PubMed Central PMCID: PMC4270414.
Wittenberg NJ, Johnson TW, Jordan LR, Xu X, Warrington AE, Rodriguez M, Oh SH. Formation of biomembrane microarrays with a squeegee-based assembly method. J Vis Exp. 2014 May 8;(87). doi: 10.3791/51501. PubMed PMID: 24837169; PubMed Central PMCID: PMC4032179.
Barik A, Otto LM, Yoo D, Jose J, Johnson TW, Oh SH. Dielectrophoresis-enhanced plasmonic sensing with gold nanohole arrays. Nano Lett. 2014;14(4):2006-12. doi: 10.1021/nl500149h. Epub 2014 Mar 27. PubMed PMID: 24646075; PubMed Central PMCID: PMC4083195.
Reitich F, Johnson TW, Oh SH, Meyer G. A fast and high-order accurate surface perturbation method for nanoplasmonic simulations: basic concepts, analytic continuation and applications. J Opt Soc Am A Opt Image Sci Vis. 2013 Nov 1;30(11):2175-87. doi: 10.1364/JOSAA.30.002175. PubMed PMID: 24322914.
Beams R, Smith D, Johnson TW, Oh SH, Novotny L, Vamivakas AN. Nanoscale fluorescence lifetime imaging of an optical antenna with a single diamond NV center. Nano Lett. 2013 Aug 14;13(8):3807-11. doi: 10.1021/nl401791v. Epub 2013 Jul 8. PubMed PMID: 23815462.
Im H, Bantz KC, Lee SH, Johnson TW, Haynes CL, Oh SH. Self-assembled plasmonic nanoring cavity arrays for SERS and LSPR biosensing. Adv Mater. 2013 May 21;25(19):2678-85. doi: 10.1002/adma.201204283. Epub 2013 Feb 22. PubMed PMID: 23436239.
Cherukulappurath S, Johnson TW, Lindquist NC, Oh SH. Template-stripped asymmetric metallic pyramids for tunable plasmonic nanofocusing. Nano Lett. 2013;13(11):5635-41. doi: 10.1021/nl403306n. Epub 2013 Oct 28. PubMed PMID: 24144067.
Lindquist NC, Johnson TW, Nagpal P, Norris DJ, Oh SH. Plasmonic nanofocusing with a metallic pyramid and an integrated C-shaped aperture. Sci Rep. 2013;3:1857. doi: 10.1038/srep01857. PubMed PMID: 23676841; PubMed Central PMCID: PMC3655335.
Lindquist NC, Johnson TW, Jose J, Otto LM, Oh SH. Ultrasmooth metallic films with buried nanostructures for backside reflection-mode plasmonic biosensing. Ann Phys. 2012 Nov;524(11):687-696. PubMed PMID: 24159227; PubMed Central PMCID: PMC3804426.
Johnson TW, Lapin ZJ, Beams R, Lindquist NC, Rodrigo SG, Novotny L, Oh SH. Highly reproducible near-field optical imaging with sub-20-nm resolution based on template-stripped gold pyramids. ACS Nano. 2012 Oct 23;6(10):9168-74. doi: 10.1021/nn303496g. Epub 2012 Sep 17. PubMed PMID: 22938087.
Wittenberg NJ, Johnson TW, Oh SH. High-density arrays of submicron spherical supported lipid bilayers. Anal Chem. 2012 Oct 2;84(19):8207-13. doi: 10.1021/ac3014274. Epub 2012 Sep 21. PubMed PMID: 22967217; PubMed Central PMCID: PMC3476481.
Wittenberg NJ, Im H, Johnson TW, Xu X, Warrington AE, Rodriguez M, Oh SH. Facile assembly of micro- and nanoarrays for sensing with natural cell membranes. ACS Nano. 2011 Sep 27;5(9):7555-64. doi: 10.1021/nn202554t. Epub 2011 Aug 17. PubMed PMID: 21842844; PubMed Central PMCID: PMC3183111.
Lindquist NC, Johnson TW, Norris DJ, Oh SH. Monolithic integration of continuously tunable plasmonic nanostructures. Nano Lett. 2011 Sep 14;11(9):3526-30. doi: 10.1021/nl2005737. Epub 2011 Aug 11. PubMed PMID: 21834564.
Im H, Lee SH, Wittenberg NJ, Johnson TW, Lindquist NC, Nagpal P, Norris DJ, Oh SH. Template-stripped smooth Ag nanohole arrays with silica shells for surface plasmon resonance biosensing. ACS Nano. 2011 Aug 23;5(8):6244-53. doi: 10.1021/nn202013v. Epub 2011 Jul 27. PubMed PMID: 21770414; PubMed Central PMCID: PMC3160512.
Nick Kotloski
Kane, A.L.; Brutinel, E.D.; Joo, H.; Maysonet Sanchez, R.; VanDrisse, C. M.; Kotloski, N.J.; & Gralnick, J. A. (2016) Formate metabolism in Shewanella oneidensis generates proton motive force and prevents growth without an electron acceptor. J Bacteriol. 198, 1337. PMID: 26883823
TerAvest, M.A.; Rosenbaum, M.A.; Kotloski, N.J.; Gralnick, J.A. & Angenent, L.T. 2014. Oxygen allows Shewanella oneidensis MR-1 to overcome mediator washout in a continuously-fed bioelectrochemical system. Biotechnol Bioeng. 111, 692. PMID: 24122485
Kotloski, N.J. & Gralnick, J.A. (2013) Flavin electron shuttles dominate extracellular electron transfer by Shewanella oneidensis. mBio. 4, e00553. PMCID: PMC3551548
Covington, E.D.; Gelbmann, C.B; Kotloski, N.J.; Gralnick, J.A. (2010) An essential role for UshA in processing of extracellular flavin electron shuttles by Shewanella oneidensis. Mol Microbiol. 78, 519. PMID: 20807196
Patrick Smadbeck
Smadbeck P. & Kaznessis, Y.N. (2015) On a theory of stability for nonlinear stochastic chemical reaction networks. J Chem Phys. 142, 184101. PMID: 25978877
Smadbeck, P. & Kaznessis Y.N. (2015) Chemical master equation closure for computer-aided synthetic biology. Methods Mol Biol.; 1244, 179. PMID: 25487098
Smadbeck, P. & Kaznessis, Y.N. (2014) Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks. Curr. Opin. Chem. Eng. 5, 90. PMID: 25215268
Smadbeck, P. & Kaznessis, Y.N. (2013) A closure scheme for chemical master equations. Proc. Natl. Acad. Sci. USA. A110, 14261. PMID: 23940327
Smadbeck, P. & Kaznessis, Y. (2012) Stochastic model reduction using a modified Hill-type kinetic rate law. J. Chem. Phys. 137, 234109. PMID: 23267473
Smadbeck, P. & Kaznessis, Y.N. (2012) Efficient Moment Matrix Generation for Arbitrary Chemical Networks. Chem. Eng. Sci. 84, 612.
Adam Woodruff
Xiong M, Deng J, Woodruff A, Zhu M, Park S, Li H, Fu Y, Zhang K. (2012) A Bio-Catalytic Approach to Aliphatic Ketones. Sci. Rep.
Zhang, K., Woodruff A., Xiong M., Zhou, J. and Dhande, Y.K. (2011) A Synthetic Metabolic Pathway for Production of Platform Chemical Isobutyric Acid. ChemSusChem. Jul 8. 4(8):1068-70.
Ping Yu, Yi-Shu Tai, Adam P Woodruff, Mingyong Xiong, Kechun Zhang, (2012) Engineering artificial metabolic pathways for biosynthesis, Current Opinion in Chemical Engineering, Volume 1, Issue 4, Pages 373-379