Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 84

1.

Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1.

Fu Y, He L, Reeve J, Beck DAC, Lidstrom ME.

MBio. 2019 Apr 9;10(2). pii: e00406-19. doi: 10.1128/mBio.00406-19.

2.

Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa.

Pesesky MW, Tilley R, Beck DAC.

Plasmid. 2019 Mar;102:10-18. doi: 10.1016/j.plasmid.2019.02.003. Epub 2019 Feb 22.

PMID:
30797764
4.

Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C.

Gilman A, Fu Y, Hendershott M, Chu F, Puri AW, Smith AL, Pesesky M, Lieberman R, Beck DAC, Lidstrom ME.

PeerJ. 2017 Oct 20;5:e3945. doi: 10.7717/peerj.3945. eCollection 2017.

5.

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations.

Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, Berube PM, Lowe TM, Moffett JW, Devol AH, Baliga NS, Arp DJ, Sayavedra-Soto LA, Hackett M, Armbrust EV, Ingalls AE, Stahl DA.

ISME J. 2018 Feb;12(2):508-519. doi: 10.1038/ismej.2017.186. Epub 2017 Oct 20.

6.

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection.

Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ.

Nat Microbiol. 2017 Nov;2(11):1493-1499. doi: 10.1038/s41564-017-0021-6. Epub 2017 Sep 18.

7.

DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies.

Ziels RM, Sousa DZ, Stensel HD, Beck DAC.

ISME J. 2018 Jan;12(1):112-123. doi: 10.1038/ismej.2017.143. Epub 2017 Sep 12.

8.

Long-chain fatty acid feeding frequency in anaerobic codigestion impacts syntrophic community structure and biokinetics.

Ziels RM, Beck DAC, Stensel HD.

Water Res. 2017 Jun 15;117:218-229. doi: 10.1016/j.watres.2017.03.060. Epub 2017 Mar 31.

PMID:
28402870
9.

Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq.

Hendrickson EL, Beck DA, Miller DP, Wang Q, Whiteley M, Lamont RJ, Hackett M.

Front Microbiol. 2017 Feb 28;8:261. doi: 10.3389/fmicb.2017.00261. eCollection 2017.

10.

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions.

Krause SM, Johnson T, Samadhi Karunaratne Y, Fu Y, Beck DA, Chistoserdova L, Lidstrom ME.

Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):358-363. doi: 10.1073/pnas.1619871114. Epub 2016 Dec 27.

11.

Quorum Sensing in a Methane-Oxidizing Bacterium.

Puri AW, Schaefer AL, Fu Y, Beck DAC, Greenberg EP, Lidstrom ME.

J Bacteriol. 2017 Feb 14;199(5). pii: e00773-16. doi: 10.1128/JB.00773-16. Print 2017 Mar 1.

12.

MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense.

Chu F, Beck DA, Lidstrom ME.

PeerJ. 2016 Sep 7;4:e2435. doi: 10.7717/peerj.2435. eCollection 2016.

13.

Microbial community adaptation influences long-chain fatty acid conversion during anaerobic codigestion of fats, oils, and grease with municipal sludge.

Ziels RM, Karlsson A, Beck DAC, Ejlertsson J, Yekta SS, Bjorn A, Stensel HD, Svensson BH.

Water Res. 2016 Oct 15;103:372-382. doi: 10.1016/j.watres.2016.07.043. Epub 2016 Jul 20.

PMID:
27486949
14.

Difference in C3-C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1.

Fu Y, Beck DA, Lidstrom ME.

BMC Microbiol. 2016 Jul 19;16(1):156. doi: 10.1186/s12866-016-0778-4.

15.

A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

Yu Z, Krause SM, Beck DA, Chistoserdova L.

Front Microbiol. 2016 Jun 15;7:946. doi: 10.3389/fmicb.2016.00946. eCollection 2016.

16.

Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance.

Hu B, Yang YM, Beck DA, Wang QW, Chen WJ, Yang J, Lidstrom ME, Yang S.

Biotechnol Biofuels. 2016 Apr 11;9:84. doi: 10.1186/s13068-016-0497-y. eCollection 2016.

17.

Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1).

de la Torre A, Metivier A, Chu F, Laurens LM, Beck DA, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG.

Microb Cell Fact. 2015 Nov 25;14:188. doi: 10.1186/s12934-015-0377-3.

18.

Potential for using a hermetically-sealed, positive-pressured isocage system for studies involving germ-free mice outside a flexible-film isolator.

Paik J, Pershutkina O, Meeker S, Yi JJ, Dowling S, Hsu C, Hajjar AM, Maggio-Price L, Beck DA.

Gut Microbes. 2015 Jul 4;6(4):255-65. doi: 10.1080/19490976.2015.1064576. Epub 2015 Jul 15.

19.

Monitoring the dynamics of syntrophic β-oxidizing bacteria during anaerobic degradation of oleic acid by quantitative PCR.

Ziels RM, Beck DA, Martí M, Gough HL, Stensel HD, Svensson BH.

FEMS Microbiol Ecol. 2015 Apr;91(4). pii: fiv028. doi: 10.1093/femsec/fiv028. Epub 2015 Mar 19.

PMID:
25873606
20.

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation.

Hernandez ME, Beck DA, Lidstrom ME, Chistoserdova L.

PeerJ. 2015 Feb 24;3:e801. doi: 10.7717/peerj.801. eCollection 2015.

21.

Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates.

Beck DA, McTaggart TL, Setboonsarng U, Vorobev A, Goodwin L, Shapiro N, Woyke T, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L.

Environ Microbiol. 2015 Mar;17(3):547-54. doi: 10.1111/1462-2920.12736. Epub 2015 Feb 11.

PMID:
25683159
22.

C₁-Pathways in Methyloversatilis universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies.

Good NM, Lamb A, Beck DA, Martinez-Gomez NC, Kalyuzhnaya MG.

Microorganisms. 2015 Apr 9;3(2):175-97. doi: 10.3390/microorganisms3020175.

23.

Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria.

McTaggart TL, Beck DA, Setboonsarng U, Shapiro N, Woyke T, Lidstrom ME, Kalyuzhnaya MG, Chistoserdova L.

Microorganisms. 2015 Mar 20;3(1):94-112. doi: 10.3390/microorganisms3010094.

24.

Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense.

Puri AW, Owen S, Chu F, Chavkin T, Beck DA, Kalyuzhnaya MG, Lidstrom ME.

Appl Environ Microbiol. 2015 Mar;81(5):1775-81. doi: 10.1128/AEM.03795-14. Epub 2014 Dec 29.

25.

Ethylmalonyl coenzyme A mutase operates as a metabolic control point in Methylobacterium extorquens AM1.

Good NM, Martinez-Gomez NC, Beck DA, Lidstrom ME.

J Bacteriol. 2015 Feb 15;197(4):727-35. doi: 10.1128/JB.02478-14. Epub 2014 Dec 1.

26.

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response.

Oshkin IY, Beck DA, Lamb AE, Tchesnokova V, Benuska G, McTaggart TL, Kalyuzhnaya MG, Dedysh SN, Lidstrom ME, Chistoserdova L.

ISME J. 2015 May;9(5):1119-29. doi: 10.1038/ismej.2014.203. Epub 2014 Oct 21.

27.

Proteomics of Fusobacterium nucleatum within a model developing oral microbial community.

Hendrickson EL, Wang T, Beck DA, Dickinson BC, Wright CJ, J Lamont R, Hackett M.

Microbiologyopen. 2014 Oct;3(5):729-51. doi: 10.1002/mbo3.204. Epub 2014 Aug 25.

28.

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

Rysavy SJ, Beck DA, Daggett V.

Protein Sci. 2014 Nov;23(11):1584-95. doi: 10.1002/pro.2537. Epub 2014 Sep 3.

29.

The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes.

Beck DA, McTaggart TL, Setboonsarng U, Vorobev A, Kalyuzhnaya MG, Ivanova N, Goodwin L, Woyke T, Lidstrom ME, Chistoserdova L.

PLoS One. 2014 Jul 24;9(7):e102458. doi: 10.1371/journal.pone.0102458. eCollection 2014.

30.

Highly efficient methane biocatalysis revealed in a methanotrophic bacterium.

Kalyuzhnaya MG, Yang S, Rozova ON, Smalley NE, Clubb J, Lamb A, Gowda GA, Raftery D, Fu Y, Bringel F, Vuilleumier S, Beck DA, Trotsenko YA, Khmelenina VN, Lidstrom ME.

Nat Commun. 2013;4:2785. doi: 10.1038/ncomms3785.

PMID:
24302011
31.

Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation.

Vorobev A, Beck DA, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L.

PeerJ. 2013 Jul 25;1:e115. doi: 10.7717/peerj.115. Print 2013.

32.

Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis.

Krumholz LR, Wang L, Beck DA, Wang T, Hackett M, Mooney B, Juba TR, McInerney MJ, Meyer B, Wall JD, Stahl DA.

Microbiology. 2013 Oct;159(Pt 10):2162-8. doi: 10.1099/mic.0.063818-0. Epub 2013 Jul 10.

PMID:
23842468
33.

Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium.

Khmelenina VN, Beck DA, Munk C, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Scholz M, Teshima H, Xu Y, Chain P, Bringel F, Vuilleumier S, Dispirito A, Dunfield P, Jetten MS, Klotz MG, Knief C, Murrell JC, Op den Camp HJ, Sakai Y, Semrau J, Svenning M, Stein LY, Trotsenko YA, Kalyuzhnaya MG.

Genome Announc. 2013 Jun 27;1(4). pii: e00053-13. doi: 10.1128/genomeA.00053-13.

34.

A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae.

Beck DA, Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L.

PeerJ. 2013 Feb 19;1:e23. doi: 10.7717/peerj.23. Print 2013.

35.

Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis.

Hirano T, Beck DA, Wright CJ, Demuth DR, Hackett M, Lamont RJ.

Mol Oral Microbiol. 2013 Feb;28(1):70-81. doi: 10.1111/omi.12007. Epub 2012 Nov 1.

36.

Multimolecule test-tube simulations of protein unfolding and aggregation.

McCully ME, Beck DA, Daggett V.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17851-6. doi: 10.1073/pnas.1201809109. Epub 2012 Oct 22.

37.

Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.

McCully ME, Beck DA, Daggett V.

Protein Eng Des Sel. 2013 Jan;26(1):35-45. doi: 10.1093/protein/gzs063. Epub 2012 Sep 25.

38.

Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant.

Hirano T, Beck DA, Demuth DR, Hackett M, Lamont RJ.

Front Cell Infect Microbiol. 2012 Jun 12;2:79. doi: 10.3389/fcimb.2012.00079. eCollection 2012.

39.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

Toofanny RD, Simms AM, Beck DA, Daggett V.

BMC Bioinformatics. 2011 Aug 10;12:334. doi: 10.1186/1471-2105-12-334.

40.

An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis.

Beck DA, Hendrickson EL, Vorobev A, Wang T, Lim S, Kalyuzhnaya MG, Lidstrom ME, Hackett M, Chistoserdova L.

J Bacteriol. 2011 Sep;193(18):4758-65. doi: 10.1128/JB.05375-11. Epub 2011 Jul 15.

41.

Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae.

Lapidus A, Clum A, Labutti K, Kaluzhnaya MG, Lim S, Beck DA, Glavina Del Rio T, Nolan M, Mavromatis K, Huntemann M, Lucas S, Lidstrom ME, Ivanova N, Chistoserdova L.

J Bacteriol. 2011 Aug;193(15):3757-64. doi: 10.1128/JB.00404-11. Epub 2011 May 27.

42.

Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium.

Ojala DS, Beck DA, Kalyuzhnaya MG.

Methods Enzymol. 2011;495:99-118. doi: 10.1016/B978-0-12-386905-0.00007-3.

PMID:
21419917
43.

Functional metagenomics of methylotrophs.

Kalyuzhnaya MG, Beck DA, Chistoserdova L.

Methods Enzymol. 2011;495:81-98. doi: 10.1016/B978-0-12-386905-0.00006-1.

PMID:
21419916
44.

Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera.

Kalyuzhnaya MG, Beck DA, Vorobev A, Smalley N, Kunkel DD, Lidstrom ME, Chistoserdova L.

Int J Syst Evol Microbiol. 2012 Jan;62(Pt 1):106-11. doi: 10.1099/ijs.0.029165-0. Epub 2011 Feb 18.

PMID:
21335496
45.

Amending greenroof soil with biochar to affect runoff water quantity and quality.

Beck DA, Johnson GR, Spolek GA.

Environ Pollut. 2011 Aug-Sep;159(8-9):2111-8. doi: 10.1016/j.envpol.2011.01.022. Epub 2011 Feb 12.

PMID:
21320738
46.

Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.

McCully ME, Beck DA, Fersht AR, Daggett V.

Biophys J. 2010 Sep 8;99(5):1628-36. doi: 10.1016/j.bpj.2010.06.040.

47.

Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy.

Hendrickson EL, Beck DA, Wang T, Lidstrom ME, Hackett M, Chistoserdova L.

J Bacteriol. 2010 Oct;192(19):4859-67. doi: 10.1128/JB.00512-10. Epub 2010 Jul 16.

48.

Dynameomics: a comprehensive database of protein dynamics.

van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD, Benson NC, Anderson PC, Merkley ED, Rysavy S, Bromley D, Beck DA, Daggett V.

Structure. 2010 Mar 14;18(4):423-35. doi: 10.1016/j.str.2010.01.012.

49.

Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics.

Kalyuzhnaya MG, Beck DA, Suciu D, Pozhitkov A, Lidstrom ME, Chistoserdova L.

ISME J. 2010 Mar;4(3):388-98. doi: 10.1038/ismej.2009.117. Epub 2009 Nov 19.

PMID:
19924155
50.

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.

Beck DA, Alonso DO, Inoyama D, Daggett V.

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12259-64. doi: 10.1073/pnas.0706527105. Epub 2008 Aug 19.

Supplemental Content

Support Center