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Application of Transposon Insertion Sequencing to Agricultural Science.

Fabian BK, Tetu SG, Paulsen IT.

Front Plant Sci. 2020 Mar 18;11:291. doi: 10.3389/fpls.2020.00291. eCollection 2020. Review.


Subsurface Stappia: Success Through Defence, Specialisation and Putative Pressure-Dependent Carbon Fixation.

Vick SHW, Greenfield P, Willows RD, Tetu SG, Midgley DJ, Paulsen IT.

Microb Ecol. 2019 Dec 11. doi: 10.1007/s00248-019-01471-y. [Epub ahead of print]


Rapid microevolution of biofilm cells in response to antibiotics.

Penesyan A, Nagy SS, Kjelleberg S, Gillings MR, Paulsen IT.

NPJ Biofilms Microbiomes. 2019 Nov 6;5:34. doi: 10.1038/s41522-019-0108-3. eCollection 2019.


Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams.

Vick SHW, Greenfield P, Tetu SG, Midgley DJ, Paulsen IT.

Sci Rep. 2019 Nov 7;9(1):16186. doi: 10.1038/s41598-019-52846-7.


Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol.

Espinosa MI, Williams TC, Pretorius IS, Paulsen IT.

Synth Syst Biotechnol. 2019 Oct 16;4(4):180-188. doi: 10.1016/j.synbio.2019.10.001. eCollection 2019 Dec.


The Role of Zinc Efflux during Acinetobacter baumannii Infection.

Alquethamy SF, Adams FG, Naidu V, Khorvash M, Pederick VG, Zang M, Paton JC, Paulsen IT, Hassan KA, Cain AK, McDevitt CA, Eijkelkamp BA.

ACS Infect Dis. 2020 Jan 10;6(1):150-158. doi: 10.1021/acsinfecdis.9b00351. Epub 2019 Nov 8.


Short-chain diamines are the physiological substrates of PACE family efflux pumps.

Hassan KA, Naidu V, Edgerton JR, Mettrick KA, Liu Q, Fahmy L, Li L, Jackson SM, Ahmad I, Sharples D, Henderson PJF, Paulsen IT.

Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):18015-18020. doi: 10.1073/pnas.1901591116. Epub 2019 Aug 15.


QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance.

de Witt RN, Kroukamp H, Van Zyl WH, Paulsen IT, Volschenk H.

FEMS Yeast Res. 2019 Aug 1;19(5). pii: foz047. doi: 10.1093/femsyr/foz047.


Who eats what? Unravelling microbial conversion of coal to methane.

Vick SHW, Gong S, Sestak S, Vergara TJ, Pinetown KL, Li Z, Greenfield P, Tetu SG, Midgley DJ, Paulsen IT.

FEMS Microbiol Ecol. 2019 Jul 1;95(7). pii: fiz093. doi: 10.1093/femsec/fiz093.


Catabolism of Nucleic Acids by a Cystic Fibrosis Pseudomonas aeruginosa Isolate: An Adaptive Pathway to Cystic Fibrosis Sputum Environment.

Kumar SS, Penesyan A, Elbourne LDH, Gillings MR, Paulsen IT.

Front Microbiol. 2019 May 31;10:1199. doi: 10.3389/fmicb.2019.01199. eCollection 2019.


Plastic leachates impair growth and oxygen production in Prochlorococcus, the ocean's most abundant photosynthetic bacteria.

Tetu SG, Sarker I, Schrameyer V, Pickford R, Elbourne LDH, Moore LR, Paulsen IT.

Commun Biol. 2019 May 14;2:184. doi: 10.1038/s42003-019-0410-x. eCollection 2019.


Evolutionary engineering in Saccharomyces cerevisiae reveals a TRK1-dependent potassium influx mechanism for propionic acid tolerance.

Xu X, Williams TC, Divne C, Pretorius IS, Paulsen IT.

Biotechnol Biofuels. 2019 Apr 23;12:97. doi: 10.1186/s13068-019-1427-6. eCollection 2019.


Interactions of an Emerging Fungal Pathogen Scedosporium aurantiacum with Human Lung Epithelial Cells.

Kaur J, Kautto L, Penesyan A, Meyer W, Elbourne LDH, Paulsen IT, Nevalainen H.

Sci Rep. 2019 Mar 22;9(1):5035. doi: 10.1038/s41598-019-41435-3.


Microbial communities are sensitive indicators for freshwater sediment copper contamination.

Sutcliffe B, Hose GC, Harford AJ, Midgley DJ, Greenfield P, Paulsen IT, Chariton AA.

Environ Pollut. 2019 Apr;247:1028-1038. doi: 10.1016/j.envpol.2019.01.104. Epub 2019 Jan 30.


Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia's Northern Oceanic Ecoregions.

Moore LR, Huang T, Ostrowski M, Mazard S, Kumar SS, Gamage HKAH, Brown MV, Messer LF, Seymour JR, Paulsen IT.

Front Microbiol. 2019 Jan 23;9:3356. doi: 10.3389/fmicb.2018.03356. eCollection 2018.


Identification of Novel Acinetobacter baumannii Host Fatty Acid Stress Adaptation Strategies.

Jiang JH, Hassan KA, Begg SL, Rupasinghe TWT, Naidu V, Pederick VG, Khorvash M, Whittall JJ, Paton JC, Paulsen IT, McDevitt CA, Peleg AY, Eijkelkamp BA.

mBio. 2019 Feb 5;10(1). pii: e02056-18. doi: 10.1128/mBio.02056-18.


The Role of the CopA Copper Efflux System in Acinetobacter baumannii Virulence.

Alquethamy SF, Khorvash M, Pederick VG, Whittall JJ, Paton JC, Paulsen IT, Hassan KA, McDevitt CA, Eijkelkamp BA.

Int J Mol Sci. 2019 Jan 29;20(3). pii: E575. doi: 10.3390/ijms20030575.


Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams.

Vick SHW, Greenfield P, Pinetown KL, Sherwood N, Gong S, Tetu SG, Midgley DJ, Paulsen IT.

iScience. 2019 Feb 22;12:152-167. doi: 10.1016/j.isci.2019.01.011. Epub 2019 Jan 11.


Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary.

Varkey D, Mazard S, Jeffries TC, Hughes DJ, Seymour J, Paulsen IT, Ostrowski M.

PLoS One. 2018 Dec 26;13(12):e0209857. doi: 10.1371/journal.pone.0209857. eCollection 2018.


Dual Transcriptomics of Host-Pathogen Interaction of Cystic Fibrosis Isolate Pseudomonas aeruginosa PASS1 With Zebrafish.

Kumar SS, Tandberg JI, Penesyan A, Elbourne LDH, Suarez-Bosche N, Don E, Skadberg E, Fenaroli F, Cole N, Winther-Larsen HC, Paulsen IT.

Front Cell Infect Microbiol. 2018 Nov 22;8:406. doi: 10.3389/fcimb.2018.00406. eCollection 2018.


Screening of candidate substrates and coupling ions of transporters by thermostability shift assays.

Majd H, King MS, Palmer SM, Smith AC, Elbourne LD, Paulsen IT, Sharples D, Henderson PJ, Kunji ER.

Elife. 2018 Oct 15;7. pii: e38821. doi: 10.7554/eLife.38821.


Fiber Supplements Derived From Sugarcane Stem, Wheat Dextrin and Psyllium Husk Have Different In Vitro Effects on the Human Gut Microbiota.

Gamage HKAH, Tetu SG, Chong RWW, Bucio-Noble D, Rosewarne CP, Kautto L, Ball MS, Molloy MP, Packer NH, Paulsen IT.

Front Microbiol. 2018 Jul 20;9:1618. doi: 10.3389/fmicb.2018.01618. eCollection 2018.


Blueprints for Biosensors: Design, Limitations, and Applications.

Carpenter AC, Paulsen IT, Williams TC.

Genes (Basel). 2018 Jul 26;9(8). pii: E375. doi: 10.3390/genes9080375. Review.


Genome-based evolutionary history of Pseudomonas spp.

Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q, Shapiro N, Hassan KA, Varghese N, Elbourne LDH, Paulsen IT, Kyrpides N, Woyke T, Loper JE.

Environ Microbiol. 2018 Jun;20(6):2142-2159. doi: 10.1111/1462-2920.14130. Epub 2018 Jul 22.


Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome.

Mavrodi DV, Mavrodi OV, Elbourne LDH, Tetu S, Bonsall RF, Parejko J, Yang M, Paulsen IT, Weller DM, Thomashow LS.

Front Plant Sci. 2018 Mar 21;9:345. doi: 10.3389/fpls.2018.00345. eCollection 2018.


Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii.

Liu Q, Hassan KA, Ashwood HE, Gamage HKAH, Li L, Mabbutt BC, Paulsen IT.

J Antimicrob Chemother. 2018 Jun 1;73(6):1492-1500. doi: 10.1093/jac/dky034.


Pacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens.

Hassan KA, Liu Q, Elbourne LDH, Ahmad I, Sharples D, Naidu V, Chan CL, Li L, Harborne SPD, Pokhrel A, Postis VLG, Goldman A, Henderson PJF, Paulsen IT.

Res Microbiol. 2018 Sep - Oct;169(7-8):450-454. doi: 10.1016/j.resmic.2018.01.001. Epub 2018 Feb 2. Review.


Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.

Shah BS, Ashwood HE, Harrop SJ, Farrugia DN, Paulsen IT, Mabbutt BC.

PLoS One. 2018 Jan 19;13(1):e0191610. doi: 10.1371/journal.pone.0191610. eCollection 2018.


A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria.

Li L, Tetu SG, Paulsen IT, Hassan KA.

Methods Mol Biol. 2018;1700:221-235. doi: 10.1007/978-1-4939-7454-2_12.


Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments.

Sutcliffe B, Chariton AA, Harford AJ, Hose GC, Stephenson S, Greenfield P, Midgley DJ, Paulsen IT.

Microb Ecol. 2018 May;75(4):970-984. doi: 10.1007/s00248-017-1102-z. Epub 2017 Nov 11.


Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro.

Gamage HKAH, Tetu SG, Chong RWW, Ashton J, Packer NH, Paulsen IT.

Sci Rep. 2017 Oct 30;7(1):14312. doi: 10.1038/s41598-017-14707-z.


Effects of uranium concentration on microbial community structure and functional potential.

Sutcliffe B, Chariton AA, Harford AJ, Hose GC, Greenfield P, Elbourne LDH, Oytam Y, Stephenson S, Midgley DJ, Paulsen IT.

Environ Microbiol. 2017 Aug;19(8):3323-3341. doi: 10.1111/1462-2920.13839. Erratum in: Environ Microbiol. 2017 Nov;19(11):4799.


Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach.

Paulsen IT, Cain AK, Hassan KA.

Mob Genet Elements. 2017 Mar 31;7(3):1-7. doi: 10.1080/2159256X.2017.1313805. eCollection 2017.


The putative drug efflux systems of the Bacillus cereus group.

Hassan KA, Fagerlund A, Elbourne LDH, Vörös A, Kroeger JK, Simm R, Tourasse NJ, Finke S, Henderson PJF, Økstad OA, Paulsen IT, Kolstø AB.

PLoS One. 2017 May 4;12(5):e0176188. doi: 10.1371/journal.pone.0176188. eCollection 2017.


Global Gene Expression Profile of Acinetobacter baumannii During Bacteremia.

Murray GL, Tsyganov K, Kostoulias XP, Bulach DM, Powell D, Creek DJ, Boyce JD, Paulsen IT, Peleg AY.

J Infect Dis. 2017 Feb 15;215(suppl_1):S52-S57. doi: 10.1093/infdis/jiw529.


Characterization and Vaccine Potential of Membrane Vesicles Produced by Francisella noatunensis subsp. orientalis in an Adult Zebrafish Model.

Lagos L, Tandberg JI, Repnik U, Boysen P, Ropstad E, Varkey D, Paulsen IT, Winther-Larsen HC.

Clin Vaccine Immunol. 2017 May 5;24(5). pii: e00557-16. doi: 10.1128/CVI.00557-16. Print 2017 May.


Zinc stress induces copper depletion in Acinetobacter baumannii.

Hassan KA, Pederick VG, Elbourne LD, Paulsen IT, Paton JC, McDevitt CA, Eijkelkamp BA.

BMC Microbiol. 2017 Mar 11;17(1):59. doi: 10.1186/s12866-017-0965-y.


Yeast's balancing act between ethanol and glycerol production in low-alcohol wines.

Goold HD, Kroukamp H, Williams TC, Paulsen IT, Varela C, Pretorius IS.

Microb Biotechnol. 2017 Mar;10(2):264-278. doi: 10.1111/1751-7915.12488. Epub 2017 Jan 13. Review.


TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life.

Elbourne LD, Tetu SG, Hassan KA, Paulsen IT.

Nucleic Acids Res. 2017 Jan 4;45(D1):D320-D324. doi: 10.1093/nar/gkw1068. Epub 2016 Nov 28.


A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus.

Pitt FD, Millard A, Ostrowski M, Dervish S, Mazard S, Paulsen IT, Zubkov MV, Scanlan DJ.

Front Microbiol. 2016 Oct 14;7:1592. eCollection 2016.


Genomics and the evolution of antibiotic resistance.

Gillings MR, Paulsen IT, Tetu SG.

Ann N Y Acad Sci. 2017 Jan;1388(1):92-107. doi: 10.1111/nyas.13268. Epub 2016 Oct 21. Review.


Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics.

Tandberg JI, Lagos LX, Langlete P, Berger E, Rishovd AL, Roos N, Varkey D, Paulsen IT, Winther-Larsen HC.

PLoS One. 2016 Oct 20;11(10):e0165099. doi: 10.1371/journal.pone.0165099. eCollection 2016.


Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii.

Hassan KA, Cain AK, Huang T, Liu Q, Elbourne LD, Boinett CJ, Brzoska AJ, Li L, Ostrowski M, Nhu NT, Nhu Tdo H, Baker S, Parkhill J, Paulsen IT.

mBio. 2016 Sep 6;7(5). pii: e01200-16. doi: 10.1128/mBio.01200-16.


Disruption of Transporters Affiliated with Enantio-Pyochelin Biosynthesis Gene Cluster of Pseudomonas protegens Pf-5 Has Pleiotropic Effects.

Lim CK, Penesyan A, Hassan KA, Loper JE, Paulsen IT.

PLoS One. 2016 Jul 21;11(7):e0159884. doi: 10.1371/journal.pone.0159884. eCollection 2016.


Pseudomonas aeruginosa Cell Membrane Protein Expression from Phenotypically Diverse Cystic Fibrosis Isolates Demonstrates Host-Specific Adaptations.

Kamath KS, Pascovici D, Penesyan A, Goel A, Venkatakrishnan V, Paulsen IT, Packer NH, Molloy MP.

J Proteome Res. 2016 Jul 1;15(7):2152-63. doi: 10.1021/acs.jproteome.6b00058. Epub 2016 Jun 9.


Tiny Microbes with a Big Impact: The Role of Cyanobacteria and Their Metabolites in Shaping Our Future.

Mazard S, Penesyan A, Ostrowski M, Paulsen IT, Egan S.

Mar Drugs. 2016 May 17;14(5). pii: E97. doi: 10.3390/md14050097. Review.


Synthetic Evolution of Metabolic Productivity Using Biosensors.

Williams TC, Pretorius IS, Paulsen IT.

Trends Biotechnol. 2016 May;34(5):371-381. doi: 10.1016/j.tibtech.2016.02.002. Epub 2016 Mar 3. Review.


Rapid multiplexed phenotypic screening identifies drug resistance functions for three novel efflux pumps in Acinetobacter baumannii.

Li L, Hassan KA, Brown MH, Paulsen IT.

J Antimicrob Chemother. 2016 May;71(5):1223-32. doi: 10.1093/jac/dkv460. Epub 2016 Jan 31.


Bacillus cereus efflux protein BC3310 - a multidrug transporter of the unknown major facilitator family, UMF-2.

Kroeger JK, Hassan K, Vörös A, Simm R, Saidijam M, Bettaney KE, Bechthold A, Paulsen IT, Henderson PJ, Kolstø AB.

Front Microbiol. 2015 Oct 12;6:1063. doi: 10.3389/fmicb.2015.01063. eCollection 2015.


Effects of low temperature on tropical and temperate isolates of marine Synechococcus.

Varkey D, Mazard S, Ostrowski M, Tetu SG, Haynes P, Paulsen IT.

ISME J. 2016 May;10(5):1252-63. doi: 10.1038/ismej.2015.179. Epub 2015 Oct 23.

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