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Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat.

Steinke L, Slysz GW, Lipton MS, Klatt C, Moran JJ, Romine MF, Wood JM, Anderson G, Bryant DA, Ward DM.

Appl Environ Microbiol. 2020 Mar 18;86(7). pii: e01829-19. doi: 10.1128/AEM.01829-19. Print 2020 Mar 18.


Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation.

Daly P, Peng M, Mitchell HD, Kim YM, Ansong C, Brewer H, de Gijsel P, Lipton MS, Markillie LM, Nicora CD, Orr G, Wiebenga A, Hildén KS, Kabel MA, Baker SE, Mäkelä MR, de Vries RP.

Environ Microbiol. 2020 Mar;22(3):1154-1166. doi: 10.1111/1462-2920.14907. Epub 2020 Jan 6.


Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa.

Horta MAC, Thieme N, Gao Y, Burnum-Johnson KE, Nicora CD, Gritsenko MA, Lipton MS, Mohanraj K, de Assis LJ, Lin L, Tian C, Braus GH, Borkovich KA, Schmoll M, Larrondo LF, Samal A, Goldman GH, Benz JP.

Front Microbiol. 2019 Nov 1;10:2317. doi: 10.3389/fmicb.2019.02317. eCollection 2019.


In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing.

Evans MV, Getzinger G, Luek JL, Hanson AJ, McLaughlin MC, Blotevogel J, Welch SA, Nicora CD, Purvine SO, Xu C, Cole DR, Darrah TH, Hoyt DW, Metz TO, Lee Ferguson P, Lipton MS, Wilkins MJ, Mouser PJ.

ISME J. 2019 Nov;13(11):2690-2700. doi: 10.1038/s41396-019-0466-0. Epub 2019 Jun 26.


Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ.

Appl Environ Microbiol. 2019 May 30;85(12). pii: e00018-19. doi: 10.1128/AEM.00018-19. Print 2019 Jun 15.


Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White RA 3rd, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME, Blackwell M, Nicora CD, Kim YM, Reardon PN, Lipton MS, Adkins JN, Pett-Ridge J, Brodie EL.

Nat Microbiol. 2019 May;4(5):864-875. doi: 10.1038/s41564-019-0384-y. Epub 2019 Mar 11.


Multiomics resolution of molecular events during a day in the life of Chlamydomonas.

Strenkert D, Schmollinger S, Gallaher SD, Salomé PA, Purvine SO, Nicora CD, Mettler-Altmann T, Soubeyrand E, Weber APM, Lipton MS, Basset GJ, Merchant SS.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2374-2383. doi: 10.1073/pnas.1815238116. Epub 2019 Jan 18.


Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.


Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, Morgan DM, Wolfe RA, Sharma S, Carr TR, Cole DR, Mouser PJ, Lipton MS, Wilkins MJ, Wrighton KC.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6585-E6594. doi: 10.1073/pnas.1800155115. Epub 2018 Jun 25.


Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.

Booker AE, Borton MA, Daly RA, Welch SA, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Wolfe RA, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, Wilkins MJ.

mSphere. 2017 Jul 5;2(4). pii: e00257-17. doi: 10.1128/mSphereDirect.00257-17. eCollection 2017 Jul-Aug.


Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.


New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11.

Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC.

ISME J. 2017 Mar;11(3):691-703. doi: 10.1038/ismej.2016.150. Epub 2016 Dec 13.


Proteome Remodeling in Response to Sulfur Limitation in "Candidatus Pelagibacter ubique".

Smith DP, Nicora CD, Carini P, Lipton MS, Norbeck AD, Smith RD, Giovannoni SJ.

mSystems. 2016 Jul 12;1(4). pii: e00068-16. eCollection 2016 Jul-Aug.


Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 Oct 3;1(11):16210. doi: 10.1038/nmicrobiol.2016.210. No abstract available.


The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 May 16;1(8):16065. doi: 10.1038/nmicrobiol.2016.65. Erratum in: Nat Microbiol. 2016 Oct 03;1(11):16210.


Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions.

Anderson LN, Koech PK, Plymale AE, Landorf EV, Konopka A, Collart FR, Lipton MS, Romine MF, Wright AT.

ACS Chem Biol. 2016 Feb 19;11(2):345-54. doi: 10.1021/acschembio.5b00918. Epub 2015 Dec 22.


Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85.

Burnet MC, Dohnalkova AC, Neumann AP, Lipton MS, Smith RD, Suen G, Callister SJ.

PLoS One. 2015 Dec 2;10(12):e0143809. doi: 10.1371/journal.pone.0143809. eCollection 2015.


Correction: Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.

Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR.

PLoS One. 2015 Sep 23;10(9):e0139151. doi: 10.1371/journal.pone.0139151. eCollection 2015. No abstract available.


Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.

Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR.

PLoS One. 2015 Aug 28;10(8):e0134752. doi: 10.1371/journal.pone.0134752. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0139151.


The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.

Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD.

Sci Data. 2015 Aug 18;2:150041. doi: 10.1038/sdata.2015.41. eCollection 2015.


Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis.

Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS.

J Proteome Res. 2015 Mar 6;14(3):1361-75. doi: 10.1021/pr500983v. Epub 2015 Feb 3.


Proteome of Geobacter sulfurreducens in the presence of U(VI).

Orellana R, Hixson KK, Murphy S, Mester T, Sharma ML, Lipton MS, Lovley DR.

Microbiology. 2014 Dec;160(Pt 12):2607-2617. doi: 10.1099/mic.0.081398-0. Epub 2014 Oct 1.


Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification.

Keating DH, Zhang Y, Ong IM, McIlwain S, Morales EH, Grass JA, Tremaine M, Bothfeld W, Higbee A, Ulbrich A, Balloon AJ, Westphall MS, Aldrich J, Lipton MS, Kim J, Moskvin OV, Bukhman YV, Coon JJ, Kiley PJ, Bates DM, Landick R.

Front Microbiol. 2014 Aug 13;5:402. doi: 10.3389/fmicb.2014.00402. eCollection 2014.


Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection.

Qu Y, Feng J, Deng S, Cao L, Zhang Q, Zhao R, Zhang Z, Jiang Y, Zink EM, Baker SE, Lipton MS, Paša-Tolić L, Hu JZ, Wu S.

Fungal Genet Biol. 2014 Nov;72:207-215. doi: 10.1016/j.fgb.2014.08.001. Epub 2014 Aug 10.


The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation.

Huang EL, Aylward FO, Kim YM, Webb-Robertson BJ, Nicora CD, Hu Z, Metz TO, Lipton MS, Smith RD, Currie CR, Burnum-Johnson KE.

Environ Microbiol Rep. 2014 Aug;6(4):389-95. doi: 10.1111/1758-2229.12163. Epub 2014 Apr 27.


Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer.

Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF.

ISME J. 2014 Jul;8(7):1452-63. doi: 10.1038/ismej.2013.249. Epub 2014 Mar 13.


Automated data extraction from in situ protein-stable isotope probing studies.

Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TR, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS.

J Proteome Res. 2014 Mar 7;13(3):1200-10. doi: 10.1021/pr400633j. Epub 2014 Feb 21.


Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation.

Cao L, Tolić N, Qu Y, Meng D, Zhao R, Zhang Q, Moore RJ, Zink EM, Lipton MS, Paša-Tolić L, Wu S.

Anal Biochem. 2014 May 1;452:96-102. doi: 10.1016/j.ab.2014.01.003. Epub 2014 Jan 15.


Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium.

Smith DP, Thrash JC, Nicora CD, Lipton MS, Burnum-Johnson KE, Carini P, Smith RD, Giovannoni SJ.

mBio. 2013 Nov 26;4(6):e00133-12. doi: 10.1128/mBio.00133-12.


Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.

Taylor RC, Webb Robertson BJ, Markillie LM, Serres MH, Linggi BE, Aldrich JT, Hill EA, Romine MF, Lipton MS, Wiley HS.

Integr Biol (Camb). 2013 Nov;5(11):1393-406. doi: 10.1039/c3ib40120k. Epub 2013 Sep 30.


Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.

Nicora CD, Anderson BJ, Callister SJ, Norbeck AD, Purvine SO, Jansson JK, Mason OU, David MM, Jurelevicius D, Smith RD, Lipton MS.

Proteomics. 2013 Oct;13(18-19):2776-85. doi: 10.1002/pmic.201300003. Epub 2013 Aug 16.


Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.

Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, Weinstock GM, Gerardo NM, Suen G, Lipton MS, Currie CR.

Appl Environ Microbiol. 2013 Jun;79(12):3770-8. doi: 10.1128/AEM.03833-12. Epub 2013 Apr 12.


Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans.

Wu S, Brown RN, Payne SH, Meng D, Zhao R, Tolić N, Cao L, Shukla A, Monroe ME, Moore RJ, Lipton MS, Paša-Tolić L.

Int J Proteomics. 2013;2013:279590. doi: 10.1155/2013/279590. Epub 2013 Mar 10.


Automated immobilized metal affinity chromatography system for enrichment of Escherichia coli phosphoproteome.

Qu Y, Wu S, Zhao R, Zink E, Orton DJ, Moore RJ, Meng D, Clauss TR, Aldrich JT, Lipton MS, Paša-Tolić L.

Electrophoresis. 2013 Jun;34(11):1619-26. doi: 10.1002/elps.201200628. Epub 2013 May 8.


Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.

Wilkins MJ, Wrighton KC, Nicora CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE, Lipton MS.

PLoS One. 2013;8(3):e57819. doi: 10.1371/journal.pone.0057819. Epub 2013 Mar 5.


Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching.

Merkley ED, Anderson BJ, Park J, Belchik SM, Shi L, Monroe ME, Smith RD, Lipton MS.

J Proteome Res. 2012 Dec 7;11(12):6147-58. doi: 10.1021/pr3007914. Epub 2012 Nov 2.


Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.

Fang Y, Wilkins MJ, Yabusaki SB, Lipton MS, Long PE.

Appl Environ Microbiol. 2012 Dec;78(24):8735-42. doi: 10.1128/AEM.01795-12. Epub 2012 Oct 5.


Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.

Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF.

Science. 2012 Sep 28;337(6102):1661-5. Erratum in: Science. 2012 Nov 9;338(6108):742.


Impact of ArcA loss in Shewanella oneidensis revealed by comparative proteomics under aerobic and anaerobic conditions.

Yuan J, Wei B, Lipton MS, Gao H.

Proteomics. 2012 Jun;12(12):1957-69. doi: 10.1002/pmic.201100651.


Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142.

Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL.

PLoS Comput Biol. 2012;8(4):e1002460. doi: 10.1371/journal.pcbi.1002460. Epub 2012 Apr 5.


Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.

Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ, Goodwin LA, Smith RD, Lipton MS, Currie CR.

ISME J. 2012 Sep;6(9):1688-701. doi: 10.1038/ismej.2012.10. Epub 2012 Mar 1.


Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1.

Liu J, Wang Z, Belchik SM, Edwards MJ, Liu C, Kennedy DW, Merkley ED, Lipton MS, Butt JN, Richardson DJ, Zachara JM, Fredrickson JK, Rosso KM, Shi L.

Front Microbiol. 2012 Feb 8;3:37. doi: 10.3389/fmicb.2012.00037. eCollection 2012.


Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically.

Cao L, Bryant DA, Schepmoes AA, Vogl K, Smith RD, Lipton MS, Callister SJ.

Photosynth Res. 2012 Feb;110(3):153-68. doi: 10.1007/s11120-011-9711-8. Epub 2012 Jan 17.


Membrane stresses induced by overproduction of free fatty acids in Escherichia coli.

Lennen RM, Kruziki MA, Kumar K, Zinkel RA, Burnum KE, Lipton MS, Hoover SW, Ranatunga DR, Wittkopp TM, Marner WD 2nd, Pfleger BF.

Appl Environ Microbiol. 2011 Nov;77(22):8114-28. doi: 10.1128/AEM.05421-11. Epub 2011 Sep 23.


Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation.

Zhang H, Yang F, Qian WJ, Brown RN, Wang Y, Merkley ED, Park JH, Monroe ME, Purvine SO, Moore RJ, Shi L, Fredrickson JK, Paša-Tolić L, Smith RD, Lipton MS.

Anal Chem. 2011 Oct 1;83(19):7260-8. doi: 10.1021/ac2000829. Epub 2011 Sep 1. Erratum in: Anal Chem. 2012 Sep 4;84(17):7591. Merkley, Eric E [corrected to Merkley, Eric D].


Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures.

Chundawat SP, Lipton MS, Purvine SO, Uppugundla N, Gao D, Balan V, Dale BE.

J Proteome Res. 2011 Oct 7;10(10):4365-72. doi: 10.1021/pr101234z. Epub 2011 Jul 1.


Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: linking systems biology with vaccine development.

Adams LG, Khare S, Lawhon SD, Rossetti CA, Lewin HA, Lipton MS, Turse JE, Wylie DC, Bai Y, Drake KL.

Vaccine. 2011 Sep 22;29(41):7197-206. doi: 10.1016/j.vaccine.2011.05.080. Epub 2011 Jun 7.


Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pathway responses to B.melitensis, S.enterica Typhimurium and M.avium paratuberculosis.

Adams LG, Khare S, Lawhon SD, Rossetti CA, Lewin HA, Lipton MS, Turse JE, Wylie DC, Bai Y, Drake KL.

BMC Proc. 2011 Jun 3;5 Suppl 4:S6. doi: 10.1186/1753-6561-5-S4-S6.


Discovering mercury protein modifications in whole proteomes using natural isotope distributions observed in liquid chromatography-tandem mass spectrometry.

Polacco BJ, Purvine SO, Zink EM, Lavoie SP, Lipton MS, Summers AO, Miller SM.

Mol Cell Proteomics. 2011 Aug;10(8):M110.004853. doi: 10.1074/mcp.M110.004853. Epub 2011 Apr 30.


Large improvements in MS/MS-based peptide identification rates using a hybrid analysis.

Cannon WR, Rawlins MM, Baxter DJ, Callister SJ, Lipton MS, Bryant DA.

J Proteome Res. 2011 May 6;10(5):2306-17. doi: 10.1021/pr101130b. Epub 2011 Mar 30.


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