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Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants.

Lee JH, Mazarei M, Pfotenhauer AC, Dorrough AB, Poindexter MR, Hewezi T, Lenaghan SC, Graham DE, Stewart CN Jr.

Front Plant Sci. 2020 Jan 31;10:1720. doi: 10.3389/fpls.2019.01720. eCollection 2019.


The RpoS Gatekeeper in Borrelia burgdorferi: An Invariant Regulatory Scheme That Promotes Spirochete Persistence in Reservoir Hosts and Niche Diversity.

Caimano MJ, Groshong AM, Belperron A, Mao J, Hawley KL, Luthra A, Graham DE, Earnhart CG, Marconi RT, Bockenstedt LK, Blevins JS, Radolf JD.

Front Microbiol. 2019 Aug 21;10:1923. doi: 10.3389/fmicb.2019.01923. eCollection 2019.


Temperature sensitivity of mineral-enzyme interactions on the hydrolysis of cellobiose and indican by β-glucosidase.

Yang Z, Liao Y, Fu X, Zaporski J, Peters S, Jamison M, Liu Y, Wullschleger SD, Graham DE, Gu B.

Sci Total Environ. 2019 Oct 10;686:1194-1201. doi: 10.1016/j.scitotenv.2019.05.479. Epub 2019 Jun 1.


Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales.

Wilpiszeski RL, Aufrecht JA, Retterer ST, Sullivan MB, Graham DE, Pierce EM, Zablocki OD, Palumbo AV, Elias DA.

Appl Environ Microbiol. 2019 Jul 1;85(14). pii: e00324-19. doi: 10.1128/AEM.00324-19. Print 2019 Jul 15. Review.


Expression of benzoyl-CoA metabolism genes in the lignocellulolytic host Caldicellulosiruptor bescii.

Sander K, Yeary M, Mahan K, Whitham J, Giannone RJ, Brown SD, Rodriguez M Jr, Graham DE, Hankoua B.

AMB Express. 2019 May 4;9(1):59. doi: 10.1186/s13568-019-0783-8.


Improved ZnS nanoparticle properties through sequential NanoFermentation.

Moon JW, Eskelsen JR, Ivanov IN, Jacobs CB, Jang GG, Kidder MK, Joshi PC, Armstrong BL, Pierce EM, Oremland RS, Phelps TJ, Graham DE.

Appl Microbiol Biotechnol. 2018 Oct;102(19):8329-8339. doi: 10.1007/s00253-018-9245-5. Epub 2018 Aug 4.


Characterization of iron oxide nanoparticle films at the air-water interface in Arctic tundra waters.

Jubb AM, Eskelsen JR, Yin X, Zheng J, Philben MJ, Pierce EM, Graham DE, Wullschleger SD, Gu B.

Sci Total Environ. 2018 Aug 15;633:1460-1468. doi: 10.1016/j.scitotenv.2018.03.332. Epub 2018 Apr 4.


Cryomilled zinc sulfide: A prophylactic for Staphylococcus aureus-infected wounds.

Tran PL, Li J, Lungaro L, Ramesh S, Ivanov IN, Moon JW, Graham DE, Hamood A, Wang J, Elfick AP, Rivero IV.

J Biomater Appl. 2018 Jul;33(1):82-93. doi: 10.1177/0885328218770530. Epub 2018 Apr 23.


Molecular Insights into Arctic Soil Organic Matter Degradation under Warming.

Chen H, Yang Z, Chu RK, Tolic N, Liang L, Graham DE, Wullschleger SD, Gu B.

Environ Sci Technol. 2018 Apr 17;52(8):4555-4564. doi: 10.1021/acs.est.7b05469. Epub 2018 Apr 5.


Impacts of Methane on Carbon Dioxide Storage in Brine Formations.

Soltanian MR, Amooie MA, Cole DR, Darrah TH, Graham DE, Pfiffner SM, Phelps TJ, Moortgat J.

Ground Water. 2018 Mar;56(2):176-186. doi: 10.1111/gwat.12633. Epub 2018 Jan 16.


Influence of Structural Defects on Biomineralized ZnS Nanoparticle Dissolution: An in-Situ Electron Microscopy Study.

Eskelsen JR, Xu J, Chiu M, Moon JW, Wilkins B, Graham DE, Gu B, Pierce EM.

Environ Sci Technol. 2018 Feb 6;52(3):1139-1149. doi: 10.1021/acs.est.7b04343. Epub 2018 Jan 12.


Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment.

Yang Z, Yang S, Van Nostrand JD, Zhou J, Fang W, Qi Q, Liu Y, Wullschleger SD, Liang L, Graham DE, Yang Y, Gu B.

Front Microbiol. 2017 Sep 19;8:1741. doi: 10.3389/fmicb.2017.01741. eCollection 2017.


UV-activated ZnO films on a flexible substrate for room temperature O2 and H2O sensing.

Jacobs CB, Maksov AB, Muckley ES, Collins L, Mahjouri-Samani M, Ievlev A, Rouleau CM, Moon JW, Graham DE, Sumpter BG, Ivanov IN.

Sci Rep. 2017 Jul 20;7(1):6053. doi: 10.1038/s41598-017-05265-5.


Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N-Nitroglycine by Variovorax sp. Strain JS1663.

Mahan KM, Zheng H, Fida TT, Parry RJ, Graham DE, Spain JC.

Appl Environ Microbiol. 2017 Jul 17;83(15). pii: e00457-17. doi: 10.1128/AEM.00457-17. Print 2017 Aug 1.


Warming increases methylmercury production in an Arctic soil.

Yang Z, Fang W, Lu X, Sheng GP, Graham DE, Liang L, Wullschleger SD, Gu B.

Environ Pollut. 2016 Jul;214:504-509. doi: 10.1016/j.envpol.2016.04.069. Epub 2016 Apr 29.


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.


Draft Genome Sequence of Streptomyces vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group.

Mahan KM, Klingeman DM, Hettich RL, Parry RJ, Graham DE.

Genome Announc. 2016 Jan 21;4(1). pii: e01582-15. doi: 10.1128/genomeA.01582-15.


Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.

Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12384-9. doi: 10.1073/pnas.1504986112. Epub 2015 Sep 21.


In situ capping for size control of monochalcogenide (ZnS, CdS and SnS) nanocrystals produced by anaerobic metal-reducing bacteria.

Jang GG, Jacobs CB, Ivanov IN, Joshi PC, Meyer HM, Kidder M, Armstrong BL, Datskos PG, Graham DE, Moon JW.

Nanotechnology. 2015 Aug 14;26(32):325602. doi: 10.1088/0957-4484/26/32/325602. Epub 2015 Jul 24.


Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry.

Mann BF, Chen H, Herndon EM, Chu RK, Tolic N, Portier EF, Roy Chowdhury T, Robinson EW, Callister SJ, Wullschleger SD, Graham DE, Liang L, Gu B.

PLoS One. 2015 Jun 12;10(6):e0130557. doi: 10.1371/journal.pone.0130557. eCollection 2015.


Stoichiometry and temperature sensitivity of methanogenesis and CO2 production from saturated polygonal tundra in Barrow, Alaska.

Roy Chowdhury T, Herndon EM, Phelps TJ, Elias DA, Gu B, Liang L, Wullschleger SD, Graham DE.

Glob Chang Biol. 2015 Feb;21(2):722-37. doi: 10.1111/gcb.12762. Epub 2014 Nov 26.


L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.

Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A.

Structure. 2014 Sep 2;22(9):1287-1300. doi: 10.1016/j.str.2014.07.002. Epub 2014 Aug 14.


Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation.

Li Y, Xu T, Tschaplinski TJ, Engle NL, Yang Y, Graham DE, He Z, Zhou J.

Biotechnol Biofuels. 2014 Feb 20;7(1):25. doi: 10.1186/1754-6834-7-25.


Engineering acidic Streptomyces rubiginosus D-xylose isomerase by rational enzyme design.

Waltman MJ, Yang ZK, Langan P, Graham DE, Kovalevsky A.

Protein Eng Des Sel. 2014 Feb;27(2):59-64. doi: 10.1093/protein/gzt062. Epub 2014 Jan 8.


Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL.

Biol Direct. 2013 Apr 22;8:9. doi: 10.1186/1745-6150-8-9.


Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media.

Kridelbaugh DM, Nelson J, Engle NL, Tschaplinski TJ, Graham DE.

Bioresour Technol. 2013 Feb;130:125-35. doi: 10.1016/j.biortech.2012.12.006. Epub 2012 Dec 27.


Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations.

Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M Jr, Liao JC, Schadt CW, Guss AM, Yang Y, Graham DE.

Biotechnol Biofuels. 2012 Jan 4;5(1):2. doi: 10.1186/1754-6834-5-2.


Microbes in thawing permafrost: the unknown variable in the climate change equation.

Graham DE, Wallenstein MD, Vishnivetskaya TA, Waldrop MP, Phelps TJ, Pfiffner SM, Onstott TC, Whyte LG, Rivkina EM, Gilichinsky DA, Elias DA, Mackelprang R, VerBerkmoes NC, Hettich RL, Wagner D, Wullschleger SD, Jansson JK.

ISME J. 2012 Apr;6(4):709-12. doi: 10.1038/ismej.2011.163. Epub 2011 Nov 17. No abstract available.


Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass.

Lochner A, Giannone RJ, Keller M, Antranikian G, Graham DE, Hettich RL.

J Proteome Res. 2011 Dec 2;10(12):5302-14. doi: 10.1021/pr200536j. Epub 2011 Nov 8.


Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis.

Lochner A, Giannone RJ, Rodriguez M Jr, Shah MB, Mielenz JR, Keller M, Antranikian G, Graham DE, Hettich RL.

Appl Environ Microbiol. 2011 Jun;77(12):4042-54. doi: 10.1128/AEM.02811-10. Epub 2011 Apr 15.


2-oxoacid metabolism in methanogenic CoM and CoB biosynthesis.

Graham DE.

Methods Enzymol. 2011;494:301-26. doi: 10.1016/B978-0-12-385112-3.00015-9.


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.


Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit.

Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE.

Biochemistry. 2010 Mar 30;49(12):2687-96. doi: 10.1021/bi901766z.


Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase.

Graham DE, Taylor SM, Wolf RZ, Namboori SC.

Biochem J. 2009 Dec 10;424(3):467-78. doi: 10.1042/BJ20090999.


Transcriptional regulation of the Escherichia coli gene rraB, encoding a protein inhibitor of RNase E.

Zhou L, Zhao M, Wolf RZ, Graham DE, Georgiou G.

J Bacteriol. 2009 Nov;191(21):6665-74. doi: 10.1128/JB.00344-09. Epub 2009 Aug 28.


Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins.

Boyd JM, Drevland RM, Downs DM, Graham DE.

J Bacteriol. 2009 Mar;191(5):1490-7. doi: 10.1128/JB.01469-08. Epub 2008 Dec 29.


Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae.

Smith CB, Graham DE.

J Bacteriol. 2008 Nov;190(22):7431-40. doi: 10.1128/JB.00652-08. Epub 2008 Sep 12.


Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis.

Drevland RM, Jia Y, Palmer DR, Graham DE.

J Biol Chem. 2008 Oct 24;283(43):28888-96. doi: 10.1074/jbc.M802159200. Epub 2008 Sep 2.


Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme.

Giles TN, Graham DE.

J Biol Chem. 2008 Sep 19;283(38):25829-38. doi: 10.1074/jbc.M802674200. Epub 2008 Jul 23.


Enzymatic analysis of uridine diphosphate N-acetyl-D-glucosamine.

Namboori SC, Graham DE.

Anal Biochem. 2008 Oct 1;381(1):94-100. doi: 10.1016/j.ab.2008.06.034. Epub 2008 Jun 27.


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.


Methanogens with pseudomurein use diaminopimelate aminotransferase in lysine biosynthesis.

Graham DE, Huse HK.

FEBS Lett. 2008 Apr 16;582(9):1369-74. doi: 10.1016/j.febslet.2008.03.021. Epub 2008 Mar 25.


Acetamido sugar biosynthesis in the Euryarchaea.

Namboori SC, Graham DE.

J Bacteriol. 2008 Apr;190(8):2987-96. doi: 10.1128/JB.01970-07. Epub 2008 Feb 8.


Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae.

Giles TN, Graham DE.

J Bacteriol. 2007 Oct;189(20):7376-83. Epub 2007 Aug 10.


Identification and characterization of archaeal and fungal tRNA methyltransferases.

Graham DE, Kramer G.

Methods Enzymol. 2007;425:185-209. Review.


Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase.

Lee C, Kramer G, Graham DE, Appling DR.

J Biol Chem. 2007 Sep 21;282(38):27744-53. Epub 2007 Jul 25.


Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii.

Drevland RM, Waheed A, Graham DE.

J Bacteriol. 2007 Jun;189(12):4391-400. Epub 2007 Apr 20.


Biosynthesis of phosphoserine in the Methanococcales.

Helgadóttir S, Rosas-Sandoval G, Söll D, Graham DE.

J Bacteriol. 2007 Jan;189(2):575-82. Epub 2006 Oct 27.

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