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Items: 43


Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents.

Stewart LC, Algar CK, Fortunato CS, Larson BI, Vallino JJ, Huber JA, Butterfield DA, Holden JF.

ISME J. 2019 Jul;13(7):1711-1721. doi: 10.1038/s41396-019-0382-3. Epub 2019 Mar 6.


Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer.

Topçuoğlu BD, Meydan C, Nguyen TB, Lang SQ, Holden JF.

Appl Environ Microbiol. 2019 Apr 18;85(9). pii: e00180-19. doi: 10.1128/AEM.00180-19. Print 2019 May 1.


Spectral and morphological characteristics of synthetic nanophase iron (oxyhydr)oxides.

Sklute EC, Kashyap S, Dyar MD, Holden JF, Tague T, Wang P, Jaret SJ.

Phys Chem Miner. 2018 Jan;45(1):1-26. doi: 10.1007/s00269-017-0897-y. Epub 2017 May 19.


Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea.

Kashyap S, Sklute EC, Dyar MD, Holden JF.

Front Microbiol. 2018 Jul 11;9:1550. doi: 10.3389/fmicb.2018.01550. eCollection 2018.


Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae.

Topçuoğlu BD, Meydan C, Orellana R, Holden JF.

Environ Microbiol. 2018 Mar;20(3):949-957. doi: 10.1111/1462-2920.14022. Epub 2017 Dec 29.


Biological iron-sulfur storage in a thioferrate-protein nanoparticle.

Vaccaro BJ, Clarkson SM, Holden JF, Lee DW, Wu CH, Poole Ii FL, Cotelesage JJH, Hackett MJ, Mohebbi S, Sun J, Li H, Johnson MK, George GN, Adams MWW.

Nat Commun. 2017 Jul 20;8:16110. doi: 10.1038/ncomms16110.


Broad substrate specificity of a hyperthermophilic α-glucosidase from Pyrobaculum arsenaticum.

Jung JH, Seo DH, Holden JF, Kim HS, Baik MY, Park CS.

Food Sci Biotechnol. 2016 Dec 31;25(6):1665-1669. doi: 10.1007/s10068-016-0256-7. eCollection 2016.


Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.

Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF.

Front Microbiol. 2016 Aug 5;7:1240. doi: 10.3389/fmicb.2016.01240. eCollection 2016.


Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate.

Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF.

Int J Syst Evol Microbiol. 2016 Sep;66(9):3372-3376. doi: 10.1099/ijsem.0.001201. Epub 2016 Jun 3.


Hydrogen Production and Enzyme Activities in the Hyperthermophile Thermococcus paralvinellae Grown on Maltose, Tryptone, and Agricultural Waste.

Hensley SA, Moreira E, Holden JF.

Front Microbiol. 2016 Feb 23;7:167. doi: 10.3389/fmicb.2016.00167. eCollection 2016.


Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge.

Lin TJ, Ver Eecke HC, Breves EA, Dyar MD, Jamieson JW, Hannington MD, Dahle H, Bishop JL, Lane MD, Butterfield DA, Kelley DS, Lilley MD, Baross JA, Holden JF.

Geochem Geophys Geosyst. 2016 Feb;17(2):300-323. doi: 10.1002/2015GC006091. Epub 2016 Jan 11.


Hydrogen and thiosulfate limits for growth of a thermophilic, autotrophic Desulfurobacterium species from a deep-sea hydrothermal vent.

Stewart LC, Llewellyn JG, Butterfield DA, Lilley MD, Holden JF.

Environ Microbiol Rep. 2016 Apr;8(2):196-200. doi: 10.1111/1758-2229.12368. Epub 2016 Jan 26.


Complete genome sequence of the hyperthermophilic methanogen Methanocaldococcus bathoardescens JH146(T) isolated from the basalt subseafloor.

Kim YT, Jung JH, Stewart LC, Kwon SW, Holden JF, Park CS.

Mar Genomics. 2015 Dec;24 Pt 3:229-30. doi: 10.1016/j.margen.2015.06.002. Epub 2015 Jun 18.


Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.

Wang DT, Gruen DS, Lollar BS, Hinrichs KU, Stewart LC, Holden JF, Hristov AN, Pohlman JW, Morrill PL, Könneke M, Delwiche KB, Reeves EP, Sutcliffe CN, Ritter DJ, Seewald JS, McIntosh JC, Hemond HF, Kubo MD, Cardace D, Hoehler TM, Ono S.

Science. 2015 Apr 24;348(6233):428-31. doi: 10.1126/science.aaa4326. Epub 2015 Mar 5.


Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent.

Stewart LC, Jung JH, Kim YT, Kwon SW, Park CS, Holden JF.

Int J Syst Evol Microbiol. 2015 Apr;65(Pt 4):1280-3. doi: 10.1099/ijs.0.000097. Epub 2015 Jan 29.


Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents.

Hensley SA, Jung JH, Park CS, Holden JF.

Int J Syst Evol Microbiol. 2014 Nov;64(Pt 11):3655-9. doi: 10.1099/ijs.0.066100-0. Epub 2014 Jul 31.


Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04.

Park KH, Jung JH, Park SG, Lee ME, Holden JF, Park CS, Woo EJ.

Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1659-68. doi: 10.1107/S1399004714006567. Epub 2014 May 30.


Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1.

Jeon EJ, Jung JH, Seo DH, Jung DH, Holden JF, Park CS.

Enzyme Microb Technol. 2014 Jun 10;60:9-15. doi: 10.1016/j.enzmictec.2014.03.009. Epub 2014 Mar 30.


Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys.

Lin TJ, Breves EA, Dyar MD, Ver Eecke HC, Jamieson JW, Holden JF.

Geobiology. 2014 May;12(3):200-11. doi: 10.1111/gbi.12083. Epub 2014 Mar 10.


Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1.

Jung JH, Kim YT, Jeon EJ, Seo DH, Hensley SA, Holden JF, Lee JH, Park CS.

J Biotechnol. 2014 Mar 20;174:14-5. doi: 10.1016/j.jbiotec.2014.01.022. Epub 2014 Jan 25.


Identification and characterization of an archaeal kojibiose catabolic pathway in the hyperthermophilic Pyrococcus sp. strain ST04.

Jung JH, Seo DH, Holden JF, Park CS.

J Bacteriol. 2014 Mar;196(5):1122-31. doi: 10.1128/JB.01222-13. Epub 2014 Jan 3.


Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.

Ver Eecke HC, Akerman NH, Huber JA, Butterfield DA, Holden JF.

Environ Microbiol Rep. 2013 Oct;5(5):665-71. doi: 10.1111/1758-2229.12065. Epub 2013 May 6.


Maltose-forming α-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04.

Jung JH, Seo DH, Holden JF, Park CS.

Appl Microbiol Biotechnol. 2014 Mar;98(5):2121-31. doi: 10.1007/s00253-013-5068-6. Epub 2013 Jul 25.


Molecular cloning and enzymatic characterization of cyclomaltodextrinase from hyperthermophilic archaeon Thermococcus sp. CL1.

Lee JE, Kim IH, Jung JH, Seo DH, Kang SG, Holden JF, Cha J, Park CS.

J Microbiol Biotechnol. 2013 Aug;23(8):1060-9.


Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1, isolated from a Paralvinella sp. polychaete worm collected from a hydrothermal vent.

Jung JH, Holden JF, Seo DH, Park KH, Shin H, Ryu S, Lee JH, Park CS.

J Bacteriol. 2012 Sep;194(17):4769-70. doi: 10.1128/JB.01016-12.


Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.

Ver Eecke HC, Butterfield DA, Huber JA, Lilley MD, Olson EJ, Roe KK, Evans LJ, Merkel AY, Cantin HV, Holden JF.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13674-9. doi: 10.1073/pnas.1206632109. Epub 2012 Aug 6.


Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04, isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge.

Jung JH, Lee JH, Holden JF, Seo DH, Shin H, Kim HY, Kim W, Ryu S, Park CS.

J Bacteriol. 2012 Aug;194(16):4434-5. doi: 10.1128/JB.00824-12.


Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea.

Oslowski DM, Jung JH, Seo DH, Park CS, Holden JF.

Appl Environ Microbiol. 2011 May;77(10):3169-73. doi: 10.1128/AEM.01366-10. Epub 2011 Mar 18.


Abundances of hyperthermophilic autotrophic Fe(III) oxide reducers and heterotrophs in hydrothermal sulfide chimneys of the northeastern Pacific Ocean.

Ver Eecke HC, Kelley DS, Holden JF.

Appl Environ Microbiol. 2009 Jan;75(1):242-5. doi: 10.1128/AEM.01462-08. Epub 2008 Oct 31.


Identification of membrane proteins in the hyperthermophilic archaeon pyrococcus furiosus using proteomics and prediction programs.

Holden JF, Poole Ii FL, Tollaksen SL, Giometti CS, Lim H, Yates Iii JR, Adams MW.

Comp Funct Genomics. 2001;2(5):275-88. doi: 10.1002/cfg.110.


Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum.

Feinberg LF, Srikanth R, Vachet RW, Holden JF.

Appl Environ Microbiol. 2008 Jan;74(2):396-402. Epub 2007 Nov 26.


Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.

Yennaco LJ, Hu Y, Holden JF.

Extremophiles. 2007 Sep;11(5):741-6. Epub 2007 May 9.


Characterization of dissimilatory Fe(III) versus NO3- reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum.

Feinberg LF, Holden JF.

J Bacteriol. 2006 Jan;188(2):525-31. Erratum in: J Bacteriol. 2006 Jun;188(11):4163.


Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.

Lim H, Eng J, Yates JR 3rd, Tollaksen SL, Giometti CS, Holden JF, Adams MW, Reich CI, Olsen GJ, Hays LG.

J Am Soc Mass Spectrom. 2003 Sep;14(9):957-70.


Microbe-metal interactions in marine hydrothermal environments.

Holden JF, Adams MW.

Curr Opin Chem Biol. 2003 Apr;7(2):160-5. Review.


Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean.

Holden JF, Takai K, Summit M, Bolton S, Zyskowski J, Baross JA.

FEMS Microbiol Ecol. 2001 Jun;36(1):51-60.


Determination of polydextrose in foods by ion chromatography: collaborative study.

Craig SA, Holden JF, Khaled MY.

J AOAC Int. 2001 Mar-Apr;84(2):472-8.


Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus.

Adams MW, Holden JF, Menon AL, Schut GJ, Grunden AM, Hou C, Hutchins AM, Jenney FE Jr, Kim C, Ma K, Pan G, Roy R, Sapra R, Story SV, Verhagen MF.

J Bacteriol. 2001 Jan;183(2):716-24.


Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus.

Hutchins AM, Holden JF, Adams MW.

J Bacteriol. 2001 Jan;183(2):709-15.


Determination of polydextrose as dietary fiber in foods.

Craig SA, Holden JF, Khaled MY, Craig SA, Holden JF, Khaled MY.

J AOAC Int. 2000 Jul-Aug;83(4):1006-12.


Overview of hyperthermophiles and their heat-shock proteins.

Baross JA, Holden JF.

Adv Protein Chem. 1996;48:1-34. Review. No abstract available.


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