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Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways.

Garcia DC, Cheng X, Land ML, Standaert RF, Morrell-Falvey JL, Doktycz MJ.

ACS Chem Biol. 2019 Nov 18. doi: 10.1021/acschembio.9b00725. [Epub ahead of print]


Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange.

Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ.

Front Microbiol. 2019 Oct 1;10:2163. doi: 10.3389/fmicb.2019.02163. eCollection 2019.


Label-free time- and space-resolved exometabolite sampling of growing plant roots through nanoporous interfaces.

Patabadige DEW, Millet LJ, Aufrecht JA, Shankles PG, Standaert RF, Retterer ST, Doktycz MJ.

Sci Rep. 2019 Jul 16;9(1):10272. doi: 10.1038/s41598-019-46538-5.


Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network.

Aufrecht JA, Fowlkes JD, Bible AN, Morrell-Falvey J, Doktycz MJ, Retterer ST.

PLoS One. 2019 Jun 27;14(6):e0218316. doi: 10.1371/journal.pone.0218316. eCollection 2019.


Increasing access to microfluidics for studying fungi and other branched biological structures.

Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Miquel Guennoc C, Deveau A, Olsson S, Bonito G, Doktycz MJ, Retterer ST.

Fungal Biol Biotechnol. 2019 Jun 10;6:1. doi: 10.1186/s40694-019-0071-z. eCollection 2019. Erratum in: Fungal Biol Biotechnol. 2019 Jul 31;6:10.


Loss of carotenoids from membranes of Pantoea sp. YR343 results in altered lipid composition and changes in membrane biophysical properties.

Kumar SV, Taylor G, Hasim S, Collier CP, Farmer AT, Campagna SR, Bible AN, Doktycz MJ, Morrell-Falvey J.

Biochim Biophys Acta Biomembr. 2019 Jul 1;1861(7):1338-1345. doi: 10.1016/j.bbamem.2019.05.009. Epub 2019 May 14.


Exploration of the Biosynthetic Potential of the Populus Microbiome.

Blair PM, Land ML, Piatek MJ, Jacobson DA, Lu TS, Doktycz MJ, Pelletier DA.

mSystems. 2018 Oct 2;3(5). pii: e00045-18. doi: 10.1128/mSystems.00045-18. eCollection 2018 Sep-Oct.


Elucidating Duramycin's Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope.

Hasim S, Allison DP, Mendez B, Farmer AT, Pelletier DA, Retterer ST, Campagna SR, Reynolds TB, Doktycz MJ.

Front Microbiol. 2018 Feb 14;9:219. doi: 10.3389/fmicb.2018.00219. eCollection 2018.


Nano-Enabled Approaches to Chemical Imaging in Biosystems.

Retterer ST, Morrell-Falvey JL, Doktycz MJ.

Annu Rev Anal Chem (Palo Alto Calif). 2018 Jun 12;11(1):351-373. doi: 10.1146/annurev-anchem-061417-125635. Epub 2018 Feb 28. Review.


Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343.

Estenson K, Hurst GB, Standaert RF, Bible AN, Garcia D, Chourey K, Doktycz MJ, Morrell-Falvey JL.

J Proteome Res. 2018 Apr 6;17(4):1361-1374. doi: 10.1021/acs.jproteome.7b00708. Epub 2018 Feb 26.


Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome.

Timm CM, Carter KR, Carrell AA, Jun SR, Jawdy SS, Vélez JM, Gunter LE, Yang Z, Nookaew I, Engle NL, Lu TS, Schadt CW, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Pelletier DA, Weston DJ.

mSystems. 2018 Jan 23;3(1). pii: e00070-17. doi: 10.1128/mSystems.00070-17. eCollection 2018 Jan-Feb.


Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data.

Ievlev AV, Belianinov A, Jesse S, Allison DP, Doktycz MJ, Retterer ST, Kalinin SV, Ovchinnikova OS.

Sci Rep. 2017 Dec 6;7(1):17099. doi: 10.1038/s41598-017-17049-y.


Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis.

Hurst GB, Asano KG, Doktycz CJ, Consoli EJ, Doktycz WL, Foster CM, Morrell-Falvey JL, Standaert RF, Doktycz MJ.

Anal Chem. 2017 Nov 7;89(21):11443-11451. doi: 10.1021/acs.analchem.7b02555. Epub 2017 Oct 17.


Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform.

Aufrecht JA, Ryan JM, Hasim S, Allison DP, Nebenführ A, Doktycz MJ, Retterer ST.

J Vis Exp. 2017 Aug 15;(126). doi: 10.3791/55971.


In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale.

Anunciado DB, Nyugen VP, Hurst GB, Doktycz MJ, Urban V, Langan P, Mamontov E, O'Neill H.

J Phys Chem Lett. 2017 Apr 20;8(8):1899-1904. doi: 10.1021/acs.jpclett.7b00399. Epub 2017 Apr 13.


β-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity.

Hasim S, Allison DP, Retterer ST, Hopke A, Wheeler RT, Doktycz MJ, Reynolds TB.

Infect Immun. 2016 Dec 29;85(1). pii: e00601-16. doi: 10.1128/IAI.00601-16. Print 2017 Jan.


Correction: Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development.

Hansen RR, Timm AC, Timm CM, Bible AN, Morrell-Falvey JL, Pelletier DA, Simpson ML, Doktycz MJ, Retterer ST.

PLoS One. 2016 Jul 21;11(7):e0160135. doi: 10.1371/journal.pone.0160135. eCollection 2016.


Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.

Utturkar SM, Cude WN, Robeson MS Jr, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA.

Appl Environ Microbiol. 2016 Aug 30;82(18):5698-708. doi: 10.1128/AEM.01285-16. Print 2016 Sep 15.


While-you-wait proteins? Producing biomolecules at the point of need.

Mohr BP, Retterer ST, Doktycz MJ.

Expert Rev Proteomics. 2016 Aug;13(8):707-9. doi: 10.1080/14789450.2016.1209415. Epub 2016 Jul 18. No abstract available.


Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System.

Timm CM, Pelletier DA, Jawdy SS, Gunter LE, Henning JA, Engle N, Aufrecht J, Gee E, Nookaew I, Yang Z, Lu TY, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Weston DJ.

Front Plant Sci. 2016 Apr 26;7:497. doi: 10.3389/fpls.2016.00497. eCollection 2016.


Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development.

Hansen RH, Timm AC, Timm CM, Bible AN, Morrell-Falvey JL, Pelletier DA, Simpson ML, Doktycz MJ, Retterer ST.

PLoS One. 2016 May 6;11(5):e0155080. doi: 10.1371/journal.pone.0155080. eCollection 2016. Erratum in: PLoS One. 2016;11(7):e0160135.


A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization.

Bible AN, Fletcher SJ, Pelletier DA, Schadt CW, Jawdy SS, Weston DJ, Engle NL, Tschaplinski T, Masyuko R, Polisetti S, Bohn PW, Coutinho TA, Doktycz MJ, Morrell-Falvey JL.

Front Microbiol. 2016 Apr 18;7:491. doi: 10.3389/fmicb.2016.00491. eCollection 2016.


Toward Microfluidic Reactors for Cell-Free Protein Synthesis at the Point-of-Care.

Timm AC, Shankles PG, Foster CM, Doktycz MJ, Retterer ST.

Small. 2016 Feb 10;12(6):810-7. doi: 10.1002/smll.201502764. Epub 2015 Dec 22.


Microstencils to generate defined, multi-species patterns of bacteria.

Timm CM, Hansen RR, Doktycz MJ, Retterer ST, Pelletier DA.

Biomicrofluidics. 2015 Nov 12;9(6):064103. doi: 10.1063/1.4935938. eCollection 2015 Nov.


Fabrication of nanoporous membranes for tuning microbial interactions and biochemical reactions.

Shankles PG, Timm AC, Doktycz MJ, Retterer ST.

J Vac Sci Technol B Nanotechnol Microelectron. 2015 Nov;33(6):06FM03. Epub 2015 Oct 21.


Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA.

Front Microbiol. 2015 Oct 14;6:1118. doi: 10.3389/fmicb.2015.01118. eCollection 2015.


Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW.

Appl Environ Microbiol. 2015 Oct 30;82(1):375-83. doi: 10.1128/AEM.02612-15. Print 2016 Jan 1.


New surface radiolabeling schemes of super paramagnetic iron oxide nanoparticles (SPIONs) for biodistribution studies.

Nallathamby PD, Mortensen NP, Palko HA, Malfatti M, Smith C, Sonnett J, Doktycz MJ, Gu B, Roeder RK, Wang W, Retterer ST.

Nanoscale. 2015 Apr 21;7(15):6545-55. doi: 10.1039/c4nr06441k.


Modular microfluidics for point-of-care protein purifications.

Millet LJ, Lucheon JD, Standaert RF, Retterer ST, Doktycz MJ.

Lab Chip. 2015 Apr 21;15(8):1799-811. doi: 10.1039/c5lc00094g.


Microstructured block copolymer surfaces for control of microbe adhesion and aggregation.

Hansen RR, Shubert KR, Morrell-Falvey JL, Lokitz BS, Doktycz MJ, Retterer ST.

Biosensors (Basel). 2014 Mar 14;4(1):63-75. doi: 10.3390/bios4010063. eCollection 2014 Mar.


Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Oct;30(19):2709-16. doi: 10.1093/bioinformatics/btu391. Epub 2014 Jun 14.


Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor.

Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F.

Mol Plant Microbe Interact. 2014 Jun;27(6):546-56. doi: 10.1094/MPMI-09-13-0286-R.


Multi-input regulation and logic with T7 promoters in cells and cell-free systems.

Iyer S, Karig DK, Norred SE, Simpson ML, Doktycz MJ.

PLoS One. 2013 Oct 23;8(10):e78442. doi: 10.1371/journal.pone.0078442. eCollection 2013.


Thrombin-mediated transcriptional regulation using DNA aptamers in DNA-based cell-free protein synthesis.

Iyer S, Doktycz MJ.

ACS Synth Biol. 2014 Jun 20;3(6):340-6. doi: 10.1021/sb4000756. Epub 2013 Sep 26.


Volume labeling with Alexa Fluor dyes and surface functionalization of highly sensitive fluorescent silica (SiO2) nanoparticles.

Wang W, Nallathamby PD, Foster CM, Morrell-Falvey JL, Mortensen NP, Doktycz MJ, Gu B, Retterer ST.

Nanoscale. 2013 Nov 7;5(21):10369-75. doi: 10.1039/c3nr02639f. Epub 2013 Sep 12.


Enteroaggregative Escherichia coli: surface protein dispersin increases bacterial uptake of ciprofloxacin.

Mortensen NP, Boisen N, Carey S, Kennel SJ, Fowlkes JD, Doktycz MJ, Nataro JP, Allison DP.

Int J Antimicrob Agents. 2013 Nov;42(5):462-5. doi: 10.1016/j.ijantimicag.2013.07.007. Epub 2013 Aug 15.


Layer-by-layer templated assembly of silica at the nanoscale.

Hinestrosa JP, Sutton JE, Allison DP, Doktycz MJ, Messman JM, Retterer ST.

Langmuir. 2013 Feb 19;29(7):2193-9. doi: 10.1021/la3042204. Epub 2013 Feb 7.


Nanozymes for antiviral therapy.

Iyer S, Doktycz MJ.

Nanomedicine (Lond). 2012 Nov;7(11):1654-5. No abstract available.


Rationally designed vaccines.

Iyer S, Doktycz MJ.

Nanomedicine (Lond). 2012 Nov;7(11):1654. No abstract available.


Multilayered nanoparticles for siRNA delivery.

Iyer S, Doktycz MJ.

Nanomedicine (Lond). 2012 Nov;7(11):1653-4. No abstract available.


Shear-activated nanotherapeutics.

Iyer S, Doktycz MJ.

Nanomedicine (Lond). 2012 Nov;7(11):1653. doi: 10.2217/nnm.12.148. No abstract available.


Relating nanomaterial properties and microbial toxicity.

Suresh AK, Pelletier DA, Doktycz MJ.

Nanoscale. 2013 Jan 21;5(2):463-74. doi: 10.1039/c2nr32447d. Epub 2012 Dec 3. Review.


Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 Nov;194(21):5991-3. doi: 10.1128/JB.01243-12.


Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides.

Brown SD, Klingeman DM, Lu TY, Johnson CM, Utturkar SM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 May;194(9):2383-4. doi: 10.1128/JB.00198-12.


Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness.

Weston DJ, Pelletier DA, Morrell-Falvey JL, Tschaplinski TJ, Jawdy SS, Lu TY, Allen SM, Melton SJ, Martin MZ, Schadt CW, Karve AA, Chen JG, Yang X, Doktycz MJ, Tuskan GA.

Mol Plant Microbe Interact. 2012 Jun;25(6):765-78. doi: 10.1094/MPMI-09-11-0253.


Cytotoxicity induced by engineered silver nanocrystallites is dependent on surface coatings and cell types.

Suresh AK, Pelletier DA, Wang W, Morrell-Falvey JL, Gu B, Doktycz MJ.

Langmuir. 2012 Feb 7;28(5):2727-35. doi: 10.1021/la2042058. Epub 2012 Jan 23.


Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator.

Lian M, Collier CP, Doktycz MJ, Retterer ST.

Biomicrofluidics. 2012 Nov 7;6(4):44108. doi: 10.1063/1.4765337. eCollection 2012.


Expression optimization and synthetic gene networks in cell-free systems.

Karig DK, Iyer S, Simpson ML, Doktycz MJ.

Nucleic Acids Res. 2012 Apr;40(8):3763-74. doi: 10.1093/nar/gkr1191. Epub 2011 Dec 17.


Enzyme reactions in nanoporous, picoliter volume containers.

Siuti P, Retterer ST, Choi CK, Doktycz MJ.

Anal Chem. 2012 Jan 17;84(2):1092-7. doi: 10.1021/ac202726n. Epub 2011 Dec 27.


The chemotaxis-like Che1 pathway has an indirect role in adhesive cell properties of Azospirillum brasilense.

Siuti P, Green C, Edwards AN, Doktycz MJ, Alexandre G.

FEMS Microbiol Lett. 2011 Oct;323(2):105-12. doi: 10.1111/j.1574-6968.2011.02366.x. Epub 2011 Aug 16.

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