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Items: 48

1.

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.

Uritskiy GV, DiRuggiero J, Taylor J.

Microbiome. 2018 Sep 15;6(1):158. doi: 10.1186/s40168-018-0541-1.

2.

Fundamental drivers for endolithic microbial community assemblies in the hyperarid Atacama Desert.

Meslier V, Casero MC, Dailey M, Wierzchos J, Ascaso C, Artieda O, McCullough PR, DiRuggiero J.

Environ Microbiol. 2018 May;20(5):1765-1781. doi: 10.1111/1462-2920.14106. Epub 2018 Apr 10.

PMID:
29573365
3.

The Non-Coding Regulatory RNA Revolution in Archaea.

Gelsinger DR, DiRuggiero J.

Genes (Basel). 2018 Mar 5;9(3). pii: E141. doi: 10.3390/genes9030141. Review.

4.

Transitory microbial habitat in the hyperarid Atacama Desert.

Schulze-Makuch D, Wagner D, Kounaves SP, Mangelsdorf K, Devine KG, de Vera JP, Schmitt-Kopplin P, Grossart HP, Parro V, Kaupenjohann M, Galy A, Schneider B, Airo A, Frösler J, Davila AF, Arens FL, Cáceres L, Cornejo FS, Carrizo D, Dartnell L, DiRuggiero J, Flury M, Ganzert L, Gessner MO, Grathwohl P, Guan L, Heinz J, Hess M, Keppler F, Maus D, McKay CP, Meckenstock RU, Montgomery W, Oberlin EA, Probst AJ, Sáenz JS, Sattler T, Schirmack J, Sephton MA, Schloter M, Uhl J, Valenzuela B, Vestergaard G, Wörmer L, Zamorano P.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2670-2675. doi: 10.1073/pnas.1714341115. Epub 2018 Feb 26.

5.

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii.

Gelsinger DR, DiRuggiero J.

J Bacteriol. 2018 Apr 9;200(9). pii: e00779-17. doi: 10.1128/JB.00779-17. Print 2018 May 1.

6.

Across the tree of life, radiation resistance is governed by antioxidant Mn2+, gauged by paramagnetic resonance.

Sharma A, Gaidamakova EK, Grichenko O, Matrosova VY, Hoeke V, Klimenkova P, Conze IH, Volpe RP, Tkavc R, Gostinčar C, Gunde-Cimerman N, DiRuggiero J, Shuryak I, Ozarowski A, Hoffman BM, Daly MJ.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9253-E9260. doi: 10.1073/pnas.1713608114. Epub 2017 Oct 17.

7.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica.

Goordial J, Davila A, Lacelle D, Pollard W, Marinova MM, Greer CW, DiRuggiero J, McKay CP, Whyte LG.

ISME J. 2016 Jul;10(7):1613-24. doi: 10.1038/ismej.2015.239. Epub 2016 Jan 19.

8.

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert.

Goordial J, Davila A, Greer CW, Cannam R, DiRuggiero J, McKay CP, Whyte LG.

Environ Microbiol. 2017 Feb;19(2):443-458. doi: 10.1111/1462-2920.13353. Epub 2016 Jun 28.

PMID:
27129741
9.

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments.

Crits-Christoph A, Robinson CK, Ma B, Ravel J, Wierzchos J, Ascaso C, Artieda O, Souza-Egipsy V, Casero MC, DiRuggiero J.

Front Microbiol. 2016 Mar 9;7:301. doi: 10.3389/fmicb.2016.00301. eCollection 2016.

10.

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community.

Crits-Christoph A, Gelsinger DR, Ma B, Wierzchos J, Ravel J, Davila A, Casero MC, DiRuggiero J.

Environ Microbiol. 2016 Jun;18(6):2064-77. doi: 10.1111/1462-2920.13259. Epub 2016 Mar 21.

PMID:
26914534
11.

In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert.

Davila AF, Hawes I, Araya JG, Gelsinger DR, DiRuggiero J, Ascaso C, Osano A, Wierzchos J.

Front Microbiol. 2015 Oct 6;6:1035. doi: 10.3389/fmicb.2015.01035. eCollection 2015.

12.

Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert.

Wierzchos J, DiRuggiero J, Vítek P, Artieda O, Souza-Egipsy V, Škaloud P, Tisza M, Davila AF, Vílchez C, Garbayo I, Ascaso C.

Front Microbiol. 2015 Sep 10;6:934. doi: 10.3389/fmicb.2015.00934. eCollection 2015.

13.

Colonization patterns of soil microbial communities in the Atacama Desert.

Crits-Christoph A, Robinson CK, Barnum T, Fricke WF, Davila AF, Jedynak B, McKay CP, Diruggiero J.

Microbiome. 2013 Nov 20;1(1):28. doi: 10.1186/2049-2618-1-28.

14.

Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert.

Robinson CK, Wierzchos J, Black C, Crits-Christoph A, Ma B, Ravel J, Ascaso C, Artieda O, Valea S, Roldán M, Gómez-Silva B, DiRuggiero J.

Environ Microbiol. 2015 Feb;17(2):299-315. doi: 10.1111/1462-2920.12364. Epub 2014 Jan 28.

PMID:
24372972
15.

Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum.

Webb KM, Yu J, Robinson CK, Noboru T, Lee YC, DiRuggiero J.

Extremophiles. 2013 May;17(3):485-97. doi: 10.1007/s00792-013-0533-9. Epub 2013 Mar 27.

PMID:
23532412
16.

Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea.

Webb KM, DiRuggiero J.

Archaea. 2012;2012:845756. doi: 10.1155/2012/845756. Epub 2012 Nov 14. Erratum in: Archaea. 2013;2013:810286.

17.

A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum.

Robinson CK, Webb K, Kaur A, Jaruga P, Dizdaroglu M, Baliga NS, Place A, Diruggiero J.

J Bacteriol. 2011 Apr;193(7):1653-62. doi: 10.1128/JB.01310-10. Epub 2011 Jan 28.

18.

Coordination of frontline defense mechanisms under severe oxidative stress.

Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.

Mol Syst Biol. 2010 Jul;6:393. doi: 10.1038/msb.2010.50.

19.
20.

Salt shield: intracellular salts provide cellular protection against ionizing radiation in the halophilic archaeon, Halobacterium salinarum NRC-1.

Kish A, Kirkali G, Robinson C, Rosenblatt R, Jaruga P, Dizdaroglu M, DiRuggiero J.

Environ Microbiol. 2009 May;11(5):1066-78.

PMID:
19452594
21.

Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.

White JR, Escobar-Paramo P, Mongodin EF, Nelson KE, DiRuggiero J.

Appl Environ Microbiol. 2008 Oct;74(20):6447-51. doi: 10.1128/AEM.01024-08. Epub 2008 Aug 22.

22.

Rad50 is not essential for the Mre11-dependent repair of DNA double-strand breaks in Halobacterium sp. strain NRC-1.

Kish A, DiRuggiero J.

J Bacteriol. 2008 Aug;190(15):5210-6. doi: 10.1128/JB.00292-08. Epub 2008 May 23.

23.

A predictive model for transcriptional control of physiology in a free living cell.

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS.

Cell. 2007 Dec 28;131(7):1354-65.

24.

An integrated systems approach for understanding cellular responses to gamma radiation.

Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS.

Mol Syst Biol. 2006;2:47. Epub 2006 Sep 12.

25.

Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation.

Williams E, Lowe TM, Savas J, DiRuggiero J.

Extremophiles. 2007 Jan;11(1):19-29. Epub 2006 Aug 8. Erratum in: Extremophiles. 2007 Jan;11(1):31-2.

PMID:
16896524
26.

Evidence for genetic drift in the diversification of a geographically isolated population of the hyperthermophilic archaeon Pyrococcus.

Escobar-Páramo P, Ghosh S, DiRuggiero J.

Mol Biol Evol. 2005 Nov;22(11):2297-303. Epub 2005 Aug 3.

PMID:
16079249
27.

Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation.

Kottemann M, Kish A, Iloanusi C, Bjork S, DiRuggiero J.

Extremophiles. 2005 Jun;9(3):219-27. Epub 2005 Apr 21.

PMID:
15844015
28.

A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei.

Kanoksilapatham W, González JM, Maeder DL, DiRuggiero J, Robb FT.

Archaea. 2004 Oct;1(4):277-83.

29.

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J.

Genome Res. 2004 Jun;14(6):1025-35. Epub 2004 May 12.

30.

Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight.

Saffary R, Nandakumar R, Spencer D, Robb FT, Davila JM, Swartz M, Ofman L, Thomas RJ, DiRuggiero J.

FEMS Microbiol Lett. 2002 Sep 24;215(1):163-8.

31.

Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1.

Ward DE, Revet IM, Nandakumar R, Tuttle JH, de Vos WM, van der Oost J, DiRuggiero J.

J Bacteriol. 2002 May;184(9):2561-6.

32.

The RadB protein from Pyrococcus does not complement E. coli recA mutations in vivo.

Inwood W, Kane S, DiRuggiero J, Robb F, Clark AJ.

Mol Genet Genomics. 2001 Jun;265(4):683-6.

PMID:
11459188
33.

Glutamate dehydrogenases from hyperthermophiles.

Robb FT, Maeder DL, DiRuggiero J, Borges KM, Tolliday N.

Methods Enzymol. 2001;331:26-41. No abstract available.

PMID:
11265468
34.

Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology.

Robb FT, Maeder DL, Brown JR, DiRuggiero J, Stump MD, Yeh RK, Weiss RB, Dunn DM.

Methods Enzymol. 2001;330:134-57. No abstract available.

PMID:
11210495
35.

Evidence of recent lateral gene transfer among hyperthermophilic archaea.

Diruggiero J, Dunn D, Maeder DL, Holley-Shanks R, Chatard J, Horlacher R, Robb FT, Boos W, Weiss RB.

Mol Microbiol. 2000 Nov;38(4):684-93.

36.

Both RadA and RadB are involved in homologous recombination in Pyrococcus furiosus.

Komori K, Miyata T, DiRuggiero J, Holley-Shanks R, Hayashi I, Cann IK, Mayanagi K, Shinagawa H, Ishino Y.

J Biol Chem. 2000 Oct 27;275(43):33782-90.

38.

DNA repair systems in archaea: mementos from the last universal common ancestor?

DiRuggiero J, Brown JR, Bogert AP, Robb FT.

J Mol Evol. 1999 Oct;49(4):474-84.

PMID:
10486005
39.

Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.

Maeder DL, Weiss RB, Dunn DM, Cherry JL, González JM, DiRuggiero J, Robb FT.

Genetics. 1999 Aug;152(4):1299-305.

42.

Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus.

DiRuggiero J, Santangelo N, Nackerdien Z, Ravel J, Robb FT.

J Bacteriol. 1997 Jul;179(14):4643-5.

43.

Characterization of the reverse gyrase from the hyperthermophilic archaeon Pyrococcus furiosus.

Borges KM, Bergerat A, Bogert AM, DiRuggiero J, Forterre P, Robb FT.

J Bacteriol. 1997 Mar;179(5):1721-6.

44.

Enzymes of central nitrogen metabolism from hyperthermophiles: characterization, thermostability, and genetics.

Diruggiero J, Robb FT.

Adv Protein Chem. 1996;48:311-39. Review. No abstract available.

PMID:
8791628
45.
47.

Characterization, cloning, and in vitro expression of the extremely thermostable glutamate dehydrogenase from the hyperthermophilic Archaeon, ES4.

DiRuggiero J, Robb FT, Jagus R, Klump HH, Borges KM, Kessel M, Mai X, Adams MW.

J Biol Chem. 1993 Aug 25;268(24):17767-74.

48.

Regulation of ribosomal RNA transcription by growth rate of the hyperthermophilic Archaeon, Pyrococcus furiosus.

DiRuggiero J, Achenbach LA, Brown SH, Kelly RM, Robb FT.

FEMS Microbiol Lett. 1993 Aug 1;111(2-3):159-64.

PMID:
7691680

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