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Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris.

Oshlag JZ, Ma Y, Morse K, Burger BT, Lemke RA, Karlen SD, Myers KS, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2019 Nov 15. pii: AEM.01888-19. doi: 10.1128/AEM.01888-19. [Epub ahead of print]


Medium-chain fatty acid synthesis by Candidatus Weimeria bifida, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov.

Scarborough MJ, Myers KS, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2019 Nov 8. pii: AEM.02242-19. doi: 10.1128/AEM.02242-19. [Epub ahead of print]


Common principles and best practices for engineering microbiomes.

Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O'Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD.

Nat Rev Microbiol. 2019 Dec;17(12):725-741. doi: 10.1038/s41579-019-0255-9. Epub 2019 Sep 23. Review.


Integrated Omic Analyses Provide Evidence that a "Candidatus Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions.

Camejo PY, Oyserman BO, McMahon KD, Noguera DR.

mSystems. 2019 Jan 15;4(1). pii: e00193-18. doi: 10.1128/mSystems.00193-18. eCollection 2019 Jan-Feb.


Design and Assessment of Species-Level qPCR Primers Targeting Comammox.

Beach NK, Noguera DR.

Front Microbiol. 2019 Jan 31;10:36. doi: 10.3389/fmicb.2019.00036. eCollection 2019.


A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ.

J Biol Chem. 2019 Feb 8;294(6):1877-1890. doi: 10.1074/jbc.RA118.006548. Epub 2018 Dec 12.


Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome.

Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR.

mSystems. 2018 Nov 20;3(6). pii: e00221-18. doi: 10.1128/mSystems.00221-18. eCollection 2018 Nov-Dec.


Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production.

Scarborough MJ, Lynch G, Dickson M, McGee M, Donohue TJ, Noguera DR.

Biotechnol Biofuels. 2018 Jul 19;11:200. doi: 10.1186/s13068-018-1193-x. eCollection 2018.


Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ.

J Biol Chem. 2018 Apr 6;293(14):4955-4968. doi: 10.1074/jbc.RA117.001268. Epub 2018 Feb 15.


In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units.

Gall DL, Kontur WS, Lan W, Kim H, Li Y, Ralph J, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2018 Jan 17;84(3). pii: e02076-17. doi: 10.1128/AEM.02076-17. Print 2018 Feb 1.


Corrigendum to "Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors" [Water Res. 102 (2016) 125-137].

Camejo PY, Owen BR, Martirano J, Ma J, Kapoor V, Domingo JS, McMahon KD, Noguera DR.

Water Res. 2017 Dec 15;127:258. doi: 10.1016/j.watres.2017.10.056. No abstract available.


Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium "Candidatus Nitrospira nitrosa".

Camejo PY, Santo Domingo J, McMahon KD, Noguera DR.

mSystems. 2017 Sep 12;2(5). pii: e00059-17. doi: 10.1128/mSystems.00059-17. eCollection 2017 Sep-Oct.


Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides.

Burger BT, Imam S, Scarborough MJ, Noguera DR, Donohue TJ.

mSystems. 2017 Jun 6;2(3). pii: e00015-17. doi: 10.1128/mSystems.00015-17. eCollection 2017 May-Jun.


Metabolic network analysis reveals microbial community interactions in anammox granules.

Lawson CE, Wu S, Bhattacharjee AS, Hamilton JJ, McMahon KD, Goel R, Noguera DR.

Nat Commun. 2017 May 31;8:15416. doi: 10.1038/ncomms15416.


Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production.

Lemmer KC, Zhang W, Langer SJ, Dohnalkova AC, Hu D, Lemke RA, Piotrowski JS, Orr G, Noguera DR, Donohue TJ.

MBio. 2017 May 23;8(3). pii: e00513-17. doi: 10.1128/mBio.00513-17.


Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions.

Keene NA, Reusser SR, Scarborough MJ, Grooms AL, Seib M, Santo Domingo J, Noguera DR.

Water Res. 2017 Sep 15;121:72-85. doi: 10.1016/j.watres.2017.05.029. Epub 2017 May 13.


Biochemical transformation of lignin for deriving valued commodities from lignocellulose.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

Curr Opin Biotechnol. 2017 Jun;45:120-126. doi: 10.1016/j.copbio.2017.02.015. Epub 2017 Mar 24. Review.


Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure.

Bhattacharjee AS, Wu S, Lawson CE, Jetten MSM, Kapoor V, Domingo JWS, McMahon KD, Noguera DR, Goel R.

Environ Sci Technol. 2017 Apr 18;51(8):4317-4327. doi: 10.1021/acs.est.6b05855. Epub 2017 Mar 31.


Community Assembly and Ecology of Activated Sludge under Photosynthetic Feast-Famine Conditions.

Oyserman BO, Martirano JM, Wipperfurth S, Owen BR, Noguera DR, McMahon KD.

Environ Sci Technol. 2017 Mar 21;51(6):3165-3175. doi: 10.1021/acs.est.6b03976. Epub 2017 Mar 10.


Transformation of erythromycin during secondary effluent soil aquifer recharging: Removal contribution and degradation path.

Wei L, Qin K, Zhao N, Noguera DR, Qiu W, Zhao Q, Kong X, Zhang W, Kabutey FT.

J Environ Sci (China). 2017 Jan;51:173-180. doi: 10.1016/j.jes.2016.08.004. Epub 2016 Sep 5.


Adsorption of Cu2+ and Zn2+ by extracellular polymeric substances (EPS) in different sludges: Effect of EPS fractional polarity on binding mechanism.

Wei L, Li Y, Noguera DR, Zhao N, Song Y, Ding J, Zhao Q, Cui F.

J Hazard Mater. 2017 Jan 5;321:473-483. doi: 10.1016/j.jhazmat.2016.05.016. Epub 2016 Sep 14.


Transformation and speciation of typical heavy metals in soil aquifer treatment system during long time recharging with secondary effluent: Depth distribution and combination.

Wei L, Wang K, Noguera DR, Jiang J, Oyserman B, Zhao N, Zhao Q, Cui F.

Chemosphere. 2016 Dec;165:100-109. doi: 10.1016/j.chemosphere.2016.09.027. Epub 2016 Sep 15.


Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors.

Camejo PY, Owen BR, Martirano J, Ma J, Kapoor V, Santo Domingo J, McMahon KD, Noguera DR.

Water Res. 2016 Oct 1;102:125-137. doi: 10.1016/j.watres.2016.06.033. Epub 2016 Jun 16. Erratum in: Water Res. 2017 Dec 15;127:258.


Utilization of artificial recharged effluent as makeup water for industrial cooling system: corrosion and scaling.

Wei L, Qin K, Zhao Q, Noguera DR, Xin M, Liu C, Keene N, Wang K, Cui F.

Water Sci Technol. 2016;73(10):2559-69. doi: 10.2166/wst.2016.115.


Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria.

Oyserman BO, Moya F, Lawson CE, Garcia AL, Vogt M, Heffernen M, Noguera DR, McMahon KD.

ISME J. 2016 Dec;10(12):2931-2945. doi: 10.1038/ismej.2016.67. Epub 2016 Apr 29.


Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD.

J Biol Chem. 2016 May 6;291(19):10228-38. doi: 10.1074/jbc.M115.700427. Epub 2016 Mar 3.


Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin.

Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN Jr.

J Biol Chem. 2016 Mar 4;291(10):5234-46. doi: 10.1074/jbc.M115.694307. Epub 2015 Dec 4.


Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis.

Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD.

ISME J. 2016 Apr;10(4):810-22. doi: 10.1038/ismej.2015.155. Epub 2015 Nov 10.


Could in situ DNA-hybridization chain reaction enable simple and effective detection of identity and function in whole cell hybridizations?

Noguera DR.

Environ Microbiol. 2015 Aug;17(8):2559-61. doi: 10.1111/1462-2920.12969. Epub 2015 Aug 4. No abstract available.


Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris.

Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang W, Higbee A, Zhang Y, Coon JJ, Hodge DB, Donohue TJ, Noguera DR.

Environ Sci Technol. 2015 Jul 21;49(14):8914-22. doi: 10.1021/acs.est.5b02062. Epub 2015 Jul 9.


Dissolved organic matter removal during coal slag additive soil aquifer treatment for secondary effluent recharging: Contribution of aerobic biodegradation.

Wei L, Li S, Noguera DR, Qin K, Jiang J, Zhao Q, Kong X, Cui F.

J Environ Manage. 2015 Jun 1;156:158-66. doi: 10.1016/j.jenvman.2015.03.049. Epub 2015 Apr 2.


Oxygen-dependent regulation of bacterial lipid production.

Lemmer KC, Dohnalkova AC, Noguera DR, Donohue TJ.

J Bacteriol. 2015 May;197(9):1649-58. doi: 10.1128/JB.02510-14. Epub 2015 Mar 2.


An integrated approach to reconstructing genome-scale transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ.

PLoS Comput Biol. 2015 Feb 27;11(2):e1004103. doi: 10.1371/journal.pcbi.1004103. eCollection 2015 Feb.


CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria.

Imam S, Noguera DR, Donohue TJ.

MBio. 2015 Feb 3;6(1). pii: e02461-14. doi: 10.1128/mBio.02461-14.


Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen.

Fitzgerald CM, Camejo P, Oshlag JZ, Noguera DR.

Water Res. 2015 Mar 1;70:38-51. doi: 10.1016/j.watres.2014.11.041. Epub 2014 Dec 3.


Global analysis of photosynthesis transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ.

PLoS Genet. 2014 Dec 11;10(12):e1004837. doi: 10.1371/journal.pgen.1004837. eCollection 2014 Dec.


Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides.

Imam S, Fitzgerald CM, Cook EM, Donohue TJ, Noguera DR.

Photosynth Res. 2015 Feb;123(2):167-82. doi: 10.1007/s11120-014-0061-1. Epub 2014 Nov 27.


Mathematical tools to optimize the design of oligonucleotide probes and primers.

Noguera DR, Wright ES, Camejo P, Yilmaz LS.

Appl Microbiol Biotechnol. 2014 Dec;98(23):9595-608. doi: 10.1007/s00253-014-6165-x. Epub 2014 Oct 31. Review.


A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

Environ Sci Technol. 2014 Oct 21;48(20):12454-63. doi: 10.1021/es503886d. Epub 2014 Oct 1.


Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.

Wright ES, Yilmaz LS, Corcoran AM, Ökten HE, Noguera DR.

Appl Environ Microbiol. 2014 Aug;80(16):5124-33. doi: 10.1128/AEM.01685-14. Epub 2014 Jun 13.


Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates.

Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR.

Environ Microbiol. 2014 May;16(5):1354-65. doi: 10.1111/1462-2920.12259. Epub 2013 Sep 24.


Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Gall DL, Kim H, Lu F, Donohue TJ, Noguera DR, Ralph J.

J Biol Chem. 2014 Mar 21;289(12):8656-67. doi: 10.1074/jbc.M113.536250. Epub 2014 Feb 7.


Global insights into energetic and metabolic networks in Rhodobacter sphaeroides.

Imam S, Noguera DR, Donohue TJ.

BMC Syst Biol. 2013 Sep 13;7:89. doi: 10.1186/1752-0509-7-89.


Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate.

Jin M, Bothfeld W, Austin S, Sato TK, La Reau A, Li H, Foston M, Gunawan C, LeDuc RD, Quensen JF, McGee M, Uppugundla N, Higbee A, Ranatunga R, Donald CW, Bone G, Ragauskas AJ, Tiedje JM, Noguera DR, Dale BE, Zhang Y, Balan V.

Bioresour Technol. 2013 Nov;147:212-20. doi: 10.1016/j.biortech.2013.08.018. Epub 2013 Aug 14.


Benzoyl coenzyme a pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

J Bacteriol. 2013 Sep;195(18):4112-20. doi: 10.1128/JB.00634-13. Epub 2013 Jul 12.


Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.

Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ.

J Bacteriol. 2012 Dec;194(24):7016-7. doi: 10.1128/JB.01214-12.


Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.

Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR.

PLoS One. 2012;7(8):e43862. doi: 10.1371/journal.pone.0043862. Epub 2012 Aug 27.


Exploring the in situ accessibility of small subunit ribosomal RNA of members of the domains Bacteria and Eukarya to oligonucleotide probes.

Okten HE, Yilmaz LS, Noguera DR.

Syst Appl Microbiol. 2012 Dec;35(8):485-95. doi: 10.1016/j.syapm.2011.11.001. Epub 2012 Jan 20.


DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences.

Wright ES, Yilmaz LS, Noguera DR.

Appl Environ Microbiol. 2012 Feb;78(3):717-25. doi: 10.1128/AEM.06516-11. Epub 2011 Nov 18.


Maximizing reductant flow into microbial H2 production.

Kontur WS, Noguera DR, Donohue TJ.

Curr Opin Biotechnol. 2012 Jun;23(3):382-9. doi: 10.1016/j.copbio.2011.10.003. Epub 2011 Oct 28. Review.


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