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Items: 40

1.

Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times.

Liang X, Whitham JM, Holwerda EK, Shao X, Tian L, Wu YW, Lombard V, Henrissat B, Klingeman DM, Yang ZK, Podar M, Richard TL, Elkins JG, Brown SD, Lynd LR.

Biotechnol Biofuels. 2018 Sep 6;11:243. doi: 10.1186/s13068-018-1238-1. eCollection 2018.

2.

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

Cross KL, Chirania P, Xiong W, Beall CJ, Elkins JG, Giannone RJ, Griffen AL, Guss AM, Hettich RL, Joshi SS, Mokrzan EM, Martin RK, Zhulin IB, Leys EJ, Podar M.

MBio. 2018 Mar 13;9(2). pii: e02061-17. doi: 10.1128/mBio.02061-17.

3.

Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.

Lee LL, Blumer-Schuette SE, Izquierdo JA, Zurawski JV, Loder AJ, Conway JM, Elkins JG, Podar M, Clum A, Jones PC, Piatek MJ, Weighill DA, Jacobson DA, Adams MWW, Kelly RM.

Appl Environ Microbiol. 2018 Apr 16;84(9). pii: e02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1.

4.

The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum.

Verbeke TJ, Garcia GM, Elkins JG.

Biotechnol Biofuels. 2017 Nov 30;10:233. doi: 10.1186/s13068-017-0917-7. eCollection 2017.

5.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane.

Nickels JD, Chatterjee S, Mostofian B, Stanley CB, Ohl M, Zolnierczuk P, Schulz R, Myles DAA, Standaert RF, Elkins JG, Cheng X, Katsaras J.

J Phys Chem Lett. 2017 Sep 7;8(17):4214-4217. doi: 10.1021/acs.jpclett.7b01877. Epub 2017 Aug 23.

PMID:
28825491
6.

Corrigendum: Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Jul 27;7:46875. doi: 10.1038/srep46875.

7.

Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds.

Clarkson SM, Giannone RJ, Kridelbaugh DM, Elkins JG, Guss AM, Michener JK.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01313-17. doi: 10.1128/AEM.01313-17. Print 2017 Sep 15.

8.

The in vivo structure of biological membranes and evidence for lipid domains.

Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DAA, Standaert RF, Elkins JG, Katsaras J.

PLoS Biol. 2017 May 23;15(5):e2002214. doi: 10.1371/journal.pbio.2002214. eCollection 2017 May.

9.

Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Feb 23;7:43355. doi: 10.1038/srep43355. Erratum in: Sci Rep. 2017 Jul 27;7:46875.

10.

Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors.

Moon JW, Phelps TJ, Fitzgerald CL Jr, Lind RF, Elkins JG, Jang GG, Joshi PC, Kidder M, Armstrong BL, Watkins TR, Ivanov IN, Graham DE.

Appl Microbiol Biotechnol. 2016 Sep;100(18):7921-31. doi: 10.1007/s00253-016-7556-y. Epub 2016 Apr 27.

PMID:
27118014
11.

Cellulosic ethanol production via consolidated bioprocessing at 75 °C by engineered Caldicellulosiruptor bescii.

Chung D, Cha M, Snyder EN, Elkins JG, Guss AM, Westpheling J.

Biotechnol Biofuels. 2015 Oct 6;8:163. doi: 10.1186/s13068-015-0346-4. eCollection 2015.

12.

Determination of the cellulase activity distribution in Clostridium thermocellum and Caldicellulosiruptor obsidiansis cultures using a fluorescent substrate.

Morrell-Falvey JL, Elkins JG, Wang ZW.

J Environ Sci (China). 2015 Aug 1;34:212-8. doi: 10.1016/j.jes.2015.03.009. Epub 2015 May 30.

PMID:
26257364
13.

Expression of a heat-stable NADPH-dependent alcohol dehydrogenase in Caldicellulosiruptor bescii results in furan aldehyde detoxification.

Chung D, Verbeke TJ, Cross KL, Westpheling J, Elkins JG.

Biotechnol Biofuels. 2015 Jul 22;8:102. doi: 10.1186/s13068-015-0287-y. eCollection 2015.

14.

A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E.

Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG.

Biotechnol Biofuels. 2014 Dec 3;7(1):165. doi: 10.1186/s13068-014-0165-z. eCollection 2014.

15.

Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.

Vishnivetskaya TA, Hamilton-Brehm SD, Podar M, Mosher JJ, Palumbo AV, Phelps TJ, Keller M, Elkins JG.

Microb Ecol. 2015 Feb;69(2):333-45. doi: 10.1007/s00248-014-0500-8. Epub 2014 Oct 16.

PMID:
25319238
16.

Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy.

Wang ZW, Lee SH, Elkins JG, Li Y, Hamilton-Brehm S, Morrell-Falvey JL.

J Environ Sci (China). 2013 May 1;25(5):849-56.

PMID:
24218813
17.

Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass.

Cha M, Chung D, Elkins JG, Guss AM, Westpheling J.

Biotechnol Biofuels. 2013 Jun 3;6(1):85. doi: 10.1186/1754-6834-6-85.

18.

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.

Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K.

Nat Commun. 2013;4:1755. doi: 10.1038/ncomms2743.

PMID:
23612296
19.

Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

Elkins JG, Hamilton-Brehm SD, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Davenport KW, Detter JC, Han CS, Tapia R, Land ML, Hauser L, Kyrpides NC, Ivanova NN, Pagani I, Bruce D, Woyke T, Cottingham RW.

Genome Announc. 2013 Apr 11;1(2):e0016213. doi: 10.1128/genomeA.00162-13.

20.

Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

Hamilton-Brehm SD, Gibson RA, Green SJ, Hopmans EC, Schouten S, van der Meer MT, Shields JP, Damsté JS, Elkins JG.

Extremophiles. 2013 Mar;17(2):251-63. doi: 10.1007/s00792-013-0512-1. Epub 2013 Jan 24.

PMID:
23345010
21.

Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass-derived substrates.

Hamilton-Brehm SD, Vishnivetskaya TA, Allman SL, Mielenz JR, Elkins JG.

Methods Mol Biol. 2012;908:153-68. doi: 10.1007/978-1-61779-956-3_15.

PMID:
22843398
22.

Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.

Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, Yin Y, Xu Y, Kataeva I, Poole FL 2nd, Adams MW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser LJ, Cottingham RW, Hettich RL, Kelly RM.

J Bacteriol. 2012 Aug;194(15):4015-28. doi: 10.1128/JB.00266-12. Epub 2012 May 25.

23.

fSpatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum.

Wang ZW, Lee SH, Elkins JG, Morrell-Falvey JL.

AMB Express. 2011 Oct 7;1:30. doi: 10.1186/2191-0855-1-30.

24.

Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis.

Wang ZW, Hamilton-Brehm SD, Lochner A, Elkins JG, Morrell-Falvey JL.

Bioresour Technol. 2011 Feb;102(3):3155-62. doi: 10.1016/j.biortech.2010.10.104. Epub 2010 Oct 28.

PMID:
21075617
25.

Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T.

Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE.

J Bacteriol. 2010 Nov;192(22):6099-100. doi: 10.1128/JB.00950-10. Epub 2010 Sep 17.

26.

Engineered microbial systems for enhanced conversion of lignocellulosic biomass.

Elkins JG, Raman B, Keller M.

Curr Opin Biotechnol. 2010 Oct;21(5):657-62. doi: 10.1016/j.copbio.2010.05.008. Epub 2010 Jun 25. Review.

PMID:
20579868
27.

Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park.

Hamilton-Brehm SD, Mosher JJ, Vishnivetskaya T, Podar M, Carroll S, Allman S, Phelps TJ, Keller M, Elkins JG.

Appl Environ Microbiol. 2010 Feb;76(4):1014-20. doi: 10.1128/AEM.01903-09. Epub 2009 Dec 18.

28.

The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.

Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N.

BMC Genomics. 2009 Apr 2;10:145. doi: 10.1186/1471-2164-10-145.

29.

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.

Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH Jr, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO.

Genome Biol. 2008;9(11):R158. doi: 10.1186/gb-2008-9-11-r158. Epub 2008 Nov 10.

30.

A korarchaeal genome reveals insights into the evolution of the Archaea.

Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO.

Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8102-7. doi: 10.1073/pnas.0801980105. Epub 2008 Jun 5.

31.

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.

Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N.

J Bacteriol. 2008 Apr;190(8):2957-65. doi: 10.1128/JB.01949-07. Epub 2008 Feb 8.

33.

Regulation of the Phosphate Stress Response in Rhizobium meliloti by PhoB.

Al-Niemi TS, Summers ML, Elkins JG, Kahn ML, McDermott TR.

Appl Environ Microbiol. 1997 Dec;63(12):4978-81.

34.

Cloning and characterization of a second acid phosphatase from Sinorhizobium meliloti strain 104A14.

Deng S, Elkins JG, Da LH, Botero LM, McDermott TR.

Arch Microbiol. 2001 Oct;176(4):255-63.

PMID:
11685369
35.

Factors affecting catalase expression in Pseudomonas aeruginosa biofilms and planktonic cells.

Frederick JR, Elkins JG, Bollinger N, Hassett DJ, McDermott TR.

Appl Environ Microbiol. 2001 Mar;67(3):1375-9.

36.

Effect of catalase on hydrogen peroxide penetration into Pseudomonas aeruginosa biofilms.

Stewart PS, Roe F, Rayner J, Elkins JG, Lewandowski Z, Ochsner UA, Hassett DJ.

Appl Environ Microbiol. 2000 Feb;66(2):836-8.

37.

Quorum sensing in Pseudomonas aeruginosa controls expression of catalase and superoxide dismutase genes and mediates biofilm susceptibility to hydrogen peroxide.

Hassett DJ, Ma JF, Elkins JG, McDermott TR, Ochsner UA, West SE, Huang CT, Fredericks J, Burnett S, Stewart PS, McFeters G, Passador L, Iglewski BH.

Mol Microbiol. 1999 Dec;34(5):1082-93.

38.
39.

Protective role of catalase in Pseudomonas aeruginosa biofilm resistance to hydrogen peroxide.

Elkins JG, Hassett DJ, Stewart PS, Schweizer HP, McDermott TR.

Appl Environ Microbiol. 1999 Oct;65(10):4594-600.

40.

Expression and regulation of phosphate stress inducible genes in Sinorhizobium meliloti.

Summers ML, Elkins JG, Elliott BA, McDermott TR.

Mol Plant Microbe Interact. 1998 Nov;11(11):1094-101.

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