We are making all of the raw data generated as part of our publications available, please find it all here. The same link contains sequences of the most common strains we use in the lab. Collaborative publications might have raw data at other locations, listed in the publications themselves.

Schwarz-Linek J*, Negard LL*, Krasnopeeva E, Douarchec C, Arlt J, Martinez VA, Poon W**, Pilizota T** 'Motility turns sour: how a combination of environmental factors prevents swimming in dense suspensions of E. coli' (In preparation)

Tormena N, Pilizota T**, Voitchovsky K**. 'A minimalist model lipid system mimicking the biophysical properties Escherichia coli’s membrane' (bioarxiv)

Hegde S, Miroli D, Pilizota T. 'Cell envelope material properties and active repair determine the death time of Escherichia coli at high intracellular pressure' (In preparation)

Krasnopeeva E*, Le Nagard L*, Lo CJ, Pilizota T**. 'Nonlinear dependency of the bacterial flagellar motor speed on proton motive force and its consequences for swimming' (bioarxiv)

Tormena N, Pilizota T**, Voitchovsky K**. 'Substrate-induced molecular reorganization in supported lipid membranes' (In preparation)

2024
[35] Teraddot G, Krasnopeeva E, Swain S**, Pilizota T** 'Escherichia coli maintains pH via the membrane potential' PRX Life In Press;

[34] Lo WC, Krasnopeeva E, Pilizota T** 'Bacterial electrophysiology' Annual Review of biophysics 2024; Vol. 53:487-510.

2023
[33] Mancini L, Pilizota T** 'Environmental conditions define the energetics of bacterial dormancy and its antibiotic susceptibility' Biophys J 2023; Jul 4:S0006-3495(23)00411-3. doi: 10.1016/j.bpj.2023.06.023

[32] Schatz MF**, Cicuta P, Gordon VD, Pilizota T, Rodenborn B, Shattuck MD, Swinney HL 'Advancing Access to Cutting-Edge Tabletop Science' Annu Rev Fluid Mechanics 2023; 55:213-235

2022
[31] Honda T*, Cremer J*, Mancini L, Zhang Z, Pilizota T, Hwa T** 'Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions' PNAS 2022; 119 (37) e2110342119

[30] Voliotis M, Rosko J, Pilizota T, Liverpool T. 'Steady state running rate sets the speed and accuracy of accumulation of swimming bacteria' Biophys J 2022; 121(18):3435-3444

[29] Jaramillo-Riveri S, Broughton J, McVey A, Pilizota T, Scott M, El Karoui M. 'Growth-dependent heterogeneity in the DNA damage response in Escherichia coli' Mol Syst Biol 2022; 18(5):e10441

2021
[28] Wong F*, Wilson S*, Helbig R, Hegde S, Aftenieva O, Zheng H, Liu C, Pilizota T, Garner EC, Amir A**, Renner LD** 'Understanding Beta-Lactam-Induced Lysis at the Single-Cell Level' Front Microbiol 2021; 27;12:712007

[27] Le D, Krasnopeeva E*, Sinjab F*, Pilizota T**, Kim M** 'Active Efflux Leads to Heterogeneous Dissipation of Proton Motive Force by Protonophores in Bacteria' mBio 2021;12(4):e0067621

[26] Krasnopeeva E, Barboza-Perez U E, Rosko J, Pilizota T**, Lo C J** 'Bacterial Flagellar Motor as a Multimodal Biosensor' Methods 2021; 193:5-15

2020
[25] Schofiel Z*, Meloni G*, Tran P, Zerfass C, Sena G, Hayashi Y, Grant M, Contera SA, Minteer SD, Kim M, Prindle A, Rocha P, Djamgoz MBA, Pilizota T, Unwin PR, Asally M**, Soyer OS** 'Bioelectrical understanding and engineering of cell biology' J. R. Soc. Interface 2020;17: 20200013.

[24] Paraschiv A, Hegde S, Ganti R, Pilizota T, Saric A** 'Dynamic clustering regulates activity of mechanosensitive membrane channels' Phys Rev Lett 2020; 124:048102

[23] Mancini L, Tian T*, Terradot G*, Pu Y, Li Y, Lo CJ, Bai F, Pilizota T**. A general work-flow for characterization of Nernstian dyes and their effects on bacterial physiology. Biophys J 2020;118(1): 4-14

2019
[22] Wang YK*, Krasnopeeva E*, Lin SY, Bai F, Pilizota T**, Lo CJ**. Comparison of Escherichia coli surface attachment methods for single-cell microscopy. Scientific Reports 2019;9:19418

[21] Krasnopeeva E, Lo CJ, Pilizota T**. Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage. Biophys J 2019;116(12): 2390-2399

[20] Arlt J**, Martinez V A, Dawson A, Pilizota T and Poon W C K. Dynamics-dependent density distribution in active suspensions. Nature Communications 2019;10: 2321

2018
[19] Pilizota T, Ya Tang Yang**. 'Do it Yourself' microbial cultivation techniques for synthetic and systems biology: cheap, fun and flexible. Front. Microbiol. 2018;9: 1666

[18] Arlt J**, Martinez V A, Dawson A, Pilizota T and Poon W C K. Painting with light-powered bacteria. Nature Communications 2018;9: 768

2017
[17] Rosko J, Martinez V A, Poon W C K and Pilizota T**. Osmotaxis in Escherichia coli through changes in motor speed. PNAS September 2017; doi: 10.1073/pnas.1620945114

2016
[16] Stevenson K, McVey A F, Clark I B N, Swain P S and Pilizota T**. General calibration of microbial growth in microplate readers. Scientific Reports 2016;6:38828

[15] Swain P S**, Stevenson K, Leary A, Montano-Gutierrez L F, Clark I B N, Vogel J and Pilizota T. Inferring time-derivatives, including cell growth rates, using Gaussian processes. Nature Communications 2016;7:13766
Please use the GUI assosiated with this fitting method:
http://swainlab.bio.ed.ac.uk/software/fitderiv/

[14] Buda R*, Liu Y*, Yang J*, Hegde S*, Stevenson K, Bai F** and Pilizota T**. Dynamics of Escherichia coli's passive response to a sudden decreases in external osmolarity. PNAS September 2016, doi:10.1073/pnas.1522185113

[13] Fletcher KA, Pilizota T, Rhys-Davies P, French, CE. Characterization of the effects of n-butanol on the cell envelope of E. coli. Applied Microbiology and Biotechnology September 2016, 1-7. doi:10.1007/s00253-016-7771-6

[12] Schwarz-Linek J, Arlt J, Jepson A, Dawson A, Vissers T, Miroli D, Pilizota T, Martinez VA and Poon WCK. Escherichia coli as a model active colloid: a practical introduction, Colloids and Surfaces B: Bionterfaces January 2016, 137:2-16

Before 2016
[11] Pilizota T, Shaevitz JW. Origins of Escherichia coli growth rate and cell shape changes at high external osmolality. Biophys J October 2014, 107(8):1962-1969

[10] Lo CJ, Sowa Y, Pilizota T, Berry RM. The mechanism and kinetics of a sodium-driven bacterial flagellar motor. PNAS 2013 Jul;110(28):E2544-51 doi: 10.1073/pnas.1301664110

[9] Pilizota T, Shaevitz JW. Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli. Biophys J 18 June 2013, 104(12):2733-2742

[8] Bilyard T*, Nakanishi-Matsui* M, Steel BC, Pilizota T, Nord AL, Hosokawa H, Futai M, Berry RM. High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase. Philos Trans R Soc Lond B Biol Sci 24 December 2012. 368(1611):20120023

[7] Pilizota T, Shaevitz JW. Fast, Multiphase Volume Adaptation to Hyperosmotic Shock by Escherichia Coli. PlosOne 13 April 2012. 7(4):e35205

[6] Fan B*, Branch RW*, Nicolau DV*, Pilizota T, Maini PK, Berry RM. Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch. Science 2010 Feb; 327(5966): 685-9. (Mentioned in Perspectives: An Ensemble View of Allostery, Vincent J. Hilser, Science 5 February 2010: 653-654)

[5] Pilizota T*, Brown M*, Leake MC, Branch RW, Berry RM, Armitage JP. A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor. PNAS. 2009 Jul;106(28):11582-7. (Mentioned in 'In This Issue', PNAS 2009 106 (28) 11427-11428)

[4] Inoue Y, Lo CJ, Fukuoka H, Takahashi H, Sowa Y, Pilizota T, Wadhams G, Homma M, Berry RM, Ishijima A. Torque-speed relationships of Na+-driven chimeric flagellar motors in Escherichia coli. J Mol Biol. 2008 Mar; 376(5):1251-9.

[3] Lo CJ, Leake MC, Pilizota T, Berry RM. Non-equivalence of membrane voltage and ion-gradient as driving forces for the bacterial flagellar motor at low load. Biophys J. 2007 Jul; 93(1):294-302.

[2] Pilizota T, Bilyard T, Bai F, Hosokawa H, Futai M, Berry RM. A programmable optical angle clamp for rotary molecular motors, Biophys J. 2007 Jul; 93(1):264-275

[1] Pilizota T, Lucic B, Trinajstic N. Use of variable selection in modeling the secondary structural content of proteins from their composition of amino acid residues. J Chem Inf Comput Sci. 2004 Jan-Feb;44(1):113-21.


Protocols:
[1] Perez, UB, Krasnopeeva E, Rosko J, Pilizota T. Tunnel slide preparation for motor speed recordings. www.protocols.io 2021 March.

[2] Pilizota T, Rosko J, Krasnopeeva E. BFM speed recording with back-focal-plane interferometry. www.protocols.io 2021 March.

[3] Krasnopeeva E, Pilizota T. Cytoplasmic pH measurements with pHluorin. www.protocols.io 2021 March.


Book contributions:
[1] Pilizota T, Sowa Y, Berry RM. Chapter: Single-Molecule Studies of Rotary Proteins in Handbook of Single-Molecule Biophysics, Springer. 2009. Editors: Peter Hinterdorfer and Antoine van Oijen