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Items: 1 to 50 of 135

1.

Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting.

McDermott JE, Cort JR, Nakayasu ES, Pruneda JN, Overall C, Adkins JN.

PeerJ. 2019 Jun 7;7:e7055. doi: 10.7717/peerj.7055. eCollection 2019.

2.

Campylobacter jejuni Demonstrates Conserved Proteomic and Transcriptomic Responses When Co-cultured With Human INT 407 and Caco-2 Epithelial Cells.

Negretti NM, Clair G, Talukdar PK, Gourley CR, Huynh S, Adkins JN, Parker CT, Corneau CM, Konkel ME.

Front Microbiol. 2019 Apr 11;10:755. doi: 10.3389/fmicb.2019.00755. eCollection 2019.

3.

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White RA 3rd, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME, Blackwell M, Nicora CD, Kim YM, Reardon PN, Lipton MS, Adkins JN, Pett-Ridge J, Brodie EL.

Nat Microbiol. 2019 May;4(5):864-875. doi: 10.1038/s41564-019-0384-y. Epub 2019 Mar 11.

PMID:
30858574
4.

Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR.

Akberdin IR, Collins DA, Hamilton R, Oshchepkov DY, Shukla AK, Nicora CD, Nakayasu ES, Adkins JN, Kalyuzhnaya MG.

Front Microbiol. 2018 Nov 27;9:2735. doi: 10.3389/fmicb.2018.02735. eCollection 2018.

5.

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells.

Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO.

Analyst. 2019 Jan 28;144(3):794-807. doi: 10.1039/c8an01574k. Review.

PMID:
30507980
6.

Individual Variability of Protein Expression in Human Tissues.

Kushner IK, Clair G, Purvine SO, Lee JY, Adkins JN, Payne SH.

J Proteome Res. 2018 Nov 2;17(11):3914-3922. doi: 10.1021/acs.jproteome.8b00580. Epub 2018 Oct 18.

PMID:
30300549
7.

Multiple mechanisms drive phage infection efficiency in nearly identical hosts.

Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA 3rd, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB.

ISME J. 2018 Jun;12(6):1605-1618. doi: 10.1038/s41396-018-0099-8. Epub 2018 Mar 22.

8.

Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut.

Wu J, Sabag-Daigle A, Borton MA, Kop LFM, Szkoda BE, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim YM, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH, Ahmer BMM.

Infect Immun. 2018 Apr 23;86(5). pii: e00945-17. doi: 10.1128/IAI.00945-17. Print 2018 May.

9.

Comprehensive computational design of ordered peptide macrocycles.

Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D.

Science. 2017 Dec 15;358(6369):1461-1466. doi: 10.1126/science.aap7577.

10.

The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species.

Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME.

Sci Rep. 2017 Nov 13;7(1):15455. doi: 10.1038/s41598-017-15379-5.

11.

Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague.

Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW.

PLoS One. 2017 Aug 30;12(8):e0183478. doi: 10.1371/journal.pone.0183478. eCollection 2017.

12.

Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi.

Tan K, Deatherage Kaiser BL, Wu R, Cuff M, Fan Y, Bigelow L, Jedrzejczak RP, Adkins JN, Cort JR, Babnigg G, Joachimiak A.

Protein Sci. 2017 Sep;26(9):1738-1748. doi: 10.1002/pro.3209. Epub 2017 Jun 19.

13.

Redeploying β-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections.

Waters EM, Rudkin JK, Coughlan S, Clair GC, Adkins JN, Gore S, Xia G, Black NS, Downing T, O'Neill E, Kadioglu A, O'Gara JP.

J Infect Dis. 2017 Jan 1;215(1):80-87. doi: 10.1093/infdis/jiw461. Epub 2016 Nov 14.

14.

Identification of Novel Host Interactors of Effectors Secreted by Salmonella and Citrobacter.

Sontag RL, Nakayasu ES, Brown RN, Niemann GS, Sydor MA, Sanchez O, Ansong C, Lu SY, Choi H, Valleau D, Weitz KK, Savchenko A, Cambronne ED, Adkins JN.

mSystems. 2016 Jul 12;1(4). pii: e00032-15. eCollection 2016 Jul-Aug.

15.

Persister formation in Staphylococcus aureus is associated with ATP depletion.

Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung AL, Lewis K.

Nat Microbiol. 2016 Apr 18;1:16051. doi: 10.1038/nmicrobiol.2016.51.

PMID:
27572649
16.

Persister formation in Staphylococcus aureus is associated with ATP depletion.

Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung AL, Lewis K.

Nat Microbiol. 2016;1. pii: 16051. Epub 2016 Apr 18.

17.

Ecosystem Services Connect Environmental Change to Human Health Outcomes.

Bayles BR, Brauman KA, Adkins JN, Allan BF, Ellis AM, Goldberg TL, Golden CD, Grigsby-Toussaint DS, Myers SS, Osofsky SA, Ricketts TH, Ristaino JB.

Ecohealth. 2016 Sep;13(3):443-449. Epub 2016 Jun 29. No abstract available.

PMID:
27357081
18.

The landscape of viral proteomics and its potential to impact human health.

Oxford KL, Wendler JP, McDermott JE, White Iii RA, Powell JD, Jacobs JM, Adkins JN, Waters KM.

Expert Rev Proteomics. 2016 Jun;13(6):579-91. doi: 10.1080/14789450.2016.1184091. Epub 2016 May 26. Review.

PMID:
27133506
19.

ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response.

Li J, Overall CC, Johnson RC, Jones MB, McDermott JE, Heffron F, Adkins JN, Cambronne ED.

PLoS One. 2015 Sep 21;10(9):e0138466. doi: 10.1371/journal.pone.0138466. eCollection 2015.

20.

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens.

Elfenbein JR, Knodler LA, Nakayasu ES, Ansong C, Brewer HM, Bogomolnaya L, Adams LG, McClelland M, Adkins JN, Andrews-Polymenis HL.

PLoS Genet. 2015 Sep 14;11(9):e1005472. doi: 10.1371/journal.pgen.1005472. eCollection 2015 Sep.

21.

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.

Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD.

Sci Data. 2015 Aug 18;2:150041. doi: 10.1038/sdata.2015.41. eCollection 2015.

22.

Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis.

Nakayasu ES, Sydor MA, Brown RN, Sontag RL, Sobreira TJ, Slysz GW, Humphrys DR, Skarina T, Onoprienko O, Di Leo R, Deatherage Kaiser BL, Li J, Ansong C, Cambronne ED, Smith RD, Savchenko A, Adkins JN.

J Proteome Res. 2015 Sep 4;14(9):4029-38. doi: 10.1021/acs.jproteome.5b00574. Epub 2015 Aug 6.

23.

Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes.

Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R.

J Proteome Res. 2015 Aug 7;14(8):3123-35. doi: 10.1021/acs.jproteome.5b00052. Epub 2015 Jul 22.

PMID:
26143644
24.

Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression.

Li J, Overall CC, Nakayasu ES, Kidwai AS, Jones MB, Johnson RC, Nguyen NT, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN.

Front Microbiol. 2015 Feb 10;6:27. doi: 10.3389/fmicb.2015.00027. eCollection 2015.

25.

Global analysis of Salmonella alternative sigma factor E on protein translation.

Li J, Nakayasu ES, Overall CC, Johnson RC, Kidwai AS, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN.

J Proteome Res. 2015 Apr 3;14(4):1716-26. doi: 10.1021/pr5010423. Epub 2015 Feb 27.

26.

Electroporation of functional bacterial effectors into mammalian cells.

Sontag RL, Mihai C, Orr G, Savchenko A, Skarina T, Cui H, Cort JR, Adkins JN, Brown RN.

J Vis Exp. 2015 Jan 19;(95):52296. doi: 10.3791/52296.

27.

Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea.

Brown JN, Brewer HM, Nicora CD, Weitz KK, Morris MJ, Skabelund AJ, Adkins JN, Smith RD, Cho JH, Gelinas R.

BMC Med Genomics. 2014 Oct 5;7:58. doi: 10.1186/1755-8794-7-58.

28.

Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability.

Lu J, Wu R, Adkins JN, Joachimiak A, Glover JN.

Biochemistry. 2014 Sep 16;53(36):5810-9. doi: 10.1021/bi500244m. Epub 2014 Sep 2.

29.

A method to determine lysine acetylation stoichiometries.

Nakayasu ES, Wu S, Sydor MA, Shukla AK, Weitz KK, Moore RJ, Hixson KK, Kim JS, Petyuk VA, Monroe ME, Pasa-Tolic L, Qian WJ, Smith RD, Adkins JN, Ansong C.

Int J Proteomics. 2014;2014:730725. doi: 10.1155/2014/730725. Epub 2014 Jul 20.

30.

Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry.

Kronewitter SR, Marginean I, Cox JT, Zhao R, Hagler CD, Shukla AK, Carlson TS, Adkins JN, Camp DG 2nd, Moore RJ, Rodland KD, Smith RD.

Anal Chem. 2014 Sep 2;86(17):8700-10. doi: 10.1021/ac501839b. Epub 2014 Aug 21.

31.

Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO.

Eletsky A, Michalska K, Houliston S, Zhang Q, Daily MD, Xu X, Cui H, Yee A, Lemak A, Wu B, Garcia M, Burnet MC, Meyer KM, Aryal UK, Sanchez O, Ansong C, Xiao R, Acton TB, Adkins JN, Montelione GT, Joachimiak A, Arrowsmith CH, Savchenko A, Szyperski T, Cort JR.

PLoS One. 2014 Jul 10;9(7):e101787. doi: 10.1371/journal.pone.0101787. eCollection 2014.

32.

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN.

Protein Sci. 2014 Jun;23(6):747-59. doi: 10.1002/pro.2458. Epub 2014 Apr 3.

33.

Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens.

Zaborin A, Defazio JR, Kade M, Kaiser BL, Belogortseva N, Camp DG 2nd, Smith RD, Adkins JN, Kim SM, Alverdy A, Goldfeld D, Firestone MA, Collier JH, Jabri B, Tirrell M, Zaborina O, Alverdy JC.

Antimicrob Agents Chemother. 2014;58(2):966-77. doi: 10.1128/AAC.02183-13. Epub 2013 Nov 25.

34.

Activated ClpP kills persisters and eradicates a chronic biofilm infection.

Conlon BP, Nakayasu ES, Fleck LE, LaFleur MD, Isabella VM, Coleman K, Leonard SN, Smith RD, Adkins JN, Lewis K.

Nature. 2013 Nov 21;503(7476):365-70. doi: 10.1038/nature12790. Epub 2013 Nov 13.

35.

A semiautomated framework for integrating expert knowledge into disease marker identification.

Wang J, Webb-Robertson BJ, Matzke MM, Varnum SM, Brown JN, Riensche RM, Adkins JN, Jacobs JM, Hoidal JR, Scholand MB, Pounds JG, Blackburn MR, Rodland KD, McDermott JE.

Dis Markers. 2013;35(5):513-23. doi: 10.1155/2013/613529. Epub 2013 Oct 10.

36.

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.

Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR.

Bioinformatics. 2013 Nov 15;29(22):2900-8. doi: 10.1093/bioinformatics/btt493. Epub 2013 Aug 23.

37.

Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection.

Nakayasu ES, Tempel R, Cambronne XA, Petyuk VA, Jones MB, Gritsenko MA, Monroe ME, Yang F, Smith RD, Adkins JN, Heffron F.

Mol Cell Proteomics. 2013 Nov;12(11):3297-309. doi: 10.1074/mcp.M113.029850. Epub 2013 Aug 22.

38.

Diverse secreted effectors are required for Salmonella persistence in a mouse infection model.

Kidwai AS, Mushamiri I, Niemann GS, Brown RN, Adkins JN, Heffron F.

PLoS One. 2013 Aug 12;8(8):e70753. doi: 10.1371/journal.pone.0070753. eCollection 2013.

39.

Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze.

Merkley ED, Cort JR, Adkins JN.

J Struct Funct Genomics. 2013 Sep;14(3):77-90. doi: 10.1007/s10969-013-9160-z. Epub 2013 Aug 7. Review.

40.

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection.

Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN.

PLoS One. 2013 Jun 26;8(6):e67155. doi: 10.1371/journal.pone.0067155. Print 2013.

41.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.

Ansong C, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10153-8. doi: 10.1073/pnas.1221210110. Epub 2013 May 29.

42.

Evaluation of selected binding domains for the analysis of ubiquitinated proteomes.

Nakayasu ES, Ansong C, Brown JN, Yang F, Lopez-Ferrer D, Qian WJ, Smith RD, Adkins JN.

J Am Soc Mass Spectrom. 2013 Aug;24(8):1214-23. doi: 10.1007/s13361-013-0619-8. Epub 2013 May 7.

43.

Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.

Nakayasu ES, Brown RN, Ansong C, Sydor MA, Imtiaz S, Mihai C, Sontag R, Hixson KK, Monroe ME, Sobreira TJ, Orr G, Petyuk VA, Yang F, Smith RD, Adkins JN.

Mol Cell Proteomics. 2013 Aug;12(8):2136-47. doi: 10.1074/mcp.M112.026138. Epub 2013 May 2.

44.

The genome organization of Thermotoga maritima reflects its lifestyle.

Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K.

PLoS Genet. 2013 Apr;9(4):e1003485. doi: 10.1371/journal.pgen.1003485. Epub 2013 Apr 25.

45.

New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium.

Michalska K, Brown RN, Li H, Jedrzejczak R, Niemann GS, Heffron F, Cort JR, Adkins JN, Babnigg G, Joachimiak A.

J Struct Funct Genomics. 2013 Mar;14(1):1-10. doi: 10.1007/s10969-013-9151-0. Epub 2013 Apr 10.

46.

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.

Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN.

Mol Biosyst. 2013 Jun;9(6):1522-34. doi: 10.1039/c3mb25598k. Epub 2013 Apr 5.

47.

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

Merkley ED, Baker ES, Crowell KL, Orton DJ, Taverner T, Ansong C, Ibrahim YM, Burnet MC, Cort JR, Anderson GA, Smith RD, Adkins JN.

J Am Soc Mass Spectrom. 2013 Mar;24(3):444-9. doi: 10.1007/s13361-012-0565-x. Epub 2013 Feb 20.

48.

RNA type III secretion signals that require Hfq.

Niemann GS, Brown RN, Mushamiri IT, Nguyen NT, Taiwo R, Stufkens A, Smith RD, Adkins JN, McDermott JE, Heffron F.

J Bacteriol. 2013 May;195(10):2119-25. doi: 10.1128/JB.00024-13. Epub 2013 Feb 8.

49.

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.

Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT.

Chem Biol. 2013 Jan 24;20(1):123-33. doi: 10.1016/j.chembiol.2012.11.008.

50.

A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, Motin VL, Adkins JN.

Mol Biosyst. 2013 Jan 27;9(1):44-54. doi: 10.1039/c2mb25287b. Epub 2012 Nov 13.

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