Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression: Montage of the normalised CCA1-YFP expression of rhythmic cells from the root (bottom panel, first image taken after 46.1 hr in LL), lower hypocotyl (taken after 46.6 hr in LL), upper hypocotyl (taken after 46.7 hr) and cotyledon (top panel, taken after 46.9 hr in LL). (Gould et al., 2018, eLife)
Professor James Locke is a quantitative biologist who studies how noisy and dynamic gene networks regulate behaviour in plants and microbes.
He uses single-cell time-lapse microscopy, transcriptomics, stochastic modelling and synthetic biology to uncover how gene circuits generate pulsatile, oscillatory and heterogeneous expression patterns, and how these dynamics modulate development, stress responses and fitness in multicellular plants.
James studied Physics at the University of Warwick before completing Part III of the Mathematical Tripos in Cambridge. He then returned to Warwick for a joint PhD in Biology and Theoretical Physics with Andrew Millar and Matthew Turner, where he used iterative experiment–theory cycles to propose and validate a new feedback loop in the plant circadian clock. This work was recognised with a Promega Young Geneticist of the Year Award.
As an EMBO and Human Frontier Science Program Fellow in Michael Elowitz’s laboratory at Caltech, James developed quantitative single-cell imaging approaches and mathematical models that revealed how bacterial stress-response circuits use stochastic pulsing to generate phenotypic diversification. He also contributed to approaches for measuring gene expression dynamics in individual bacteria over many generations, which have been used in subsequent studies of microbial individuality and gene expression noise. For this work he was awarded the Merrimack–CSB2 Prize in Systems Biology in 2013.
Since 2012, James has led an interdisciplinary research group at the Sainsbury Laboratory, University of Cambridge, where he is now Professor of Quantitative Plant Development and Associate Director.
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms: Snapshots of the top of the live biofilms taken at 12 h intervals after inoculation shows development of a σB gradient of expression. (Nadezhdin et al., 2020, Nature Communications Research summary
Research areas
His group works across microbial and plant systems. In cyanobacteria, they showed how circadian clocks and environmental inputs jointly control cell size. In bacteria, they demonstrated that stochastic pulsing of gene expression allows cells to survive stress and form biofilm patterns.
In Arabidopsis, they explained how local coupling and spatial waves of gene expression coordinate single-cell clock rhythms across tissues, revealed significant transcriptional variability between isogenic seedlings, and uncovered how hormone-regulated bistable switches and transcriptional variability can account for natural differences in the timing and variability of seed germination.
Recent work has mapped how mixed positive and negative feedback loops generate diverse single-cell dynamics and how circadian clocks buffer environmental and molecular noise at the level of individual cells.
Environmental and molecular noise buffering by the cyanobacterial clock in individual cells: A time-lapse movie of a WT cyanobacteria strain in a Green Mother Machine. Credit: Sasha Eremina. (Eremina et al., 2025, Nat Commun) Research Summary
Funding
James’s research has been supported by long-term fellowships and competitive grants from the Gatsby Charitable Foundation, the European Commission, the European Research Council (ERC Starting Grant), the Leverhulme Trust, the Human Frontier Science Program, the Royal Society (including a University Research Fellowship and Enhancement Award), UK Research Councils (including BBSRC) and ARIA. He is a member of the BBSRC Pool of Experts, a former member of the Royal Society Diversity Committee, an Associate Editor of Royal Society Open Science, and co-author of the plant chapter for Principles of Development.
Former members of his group now work in academic and industry positions in the UK and abroad.
Publications
For a full and up-to-date list of publications, please see Google Scholar.
Selected Recent Publications
Z Nahas, AJ Bridgen, TE Loman, J Dillon, K Abley, DL Cano-Ramirez, F Ticchiarelli, M Seale, JCW Locke^, HMO Leyser^, A BRC1-modulated switch in auxin efflux accounts for the competition between Arabidopsis axillary buds, PLOS Biology, 2025; 23(9):e3003395. https://doi.org/10.1371/journal.pbio.3003395. Research summary
A Eremina, C Schwall, T Saez, L Witting, D Kohlheyer, BMC Martins^, P Thomas^, JCW Locke^, Environmental and molecular noise buffering by the cyanobacterial clock in individual cells, Nature Communications, 2025; 16:3566. Research summary
C Ye, CN Micklem, T Saez, AK Das, BMC Martins^, JCW Locke^, The cyanobacterial circadian clock couples to pulsatile processes using pulse amplitude modulation, Current Biology, 2024; 34(24):5796–5803.e6. Research summary
M Greenwood, IT Tokuda, JCW Locke^, A spatial model of the plant circadian clock reveals design principles for coordinated timing, Molecular Systems Biology, 2022; 18(3):e10140.
CP Schwall, TE Loman, BMC Martins, S Cortijo, C Villava, V Kusmartsev, T Livesey, T Saez, JCW Locke, Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit, Molecular Systems Biology, 2021; 17:e9832.
K Abley, P Formosa-Jordan, H Tavares, EYT Chan, M Afsharinafar, O Leyser^, JCW Locke^, An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time , eLife, 2021; 10:e59485. Research summary
E Nadezhdin, N Murphy, N Dalchau, A Phillips, JCW Locke, Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms, Nature communications, 2020; 11 (1), 1-12. Research summary
M Greenwood, M Domijan, PD Gould, AJW Hall, JCW Locke, Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana, PLoS biology, 2019; 17 (8), e3000407. Research summary and feature in The Coversation Plants can tell time even without a brain - here's how
S Cortijo, Z Aydin, S Ahnert, JCW Locke, Widespread inter-individual gene expression variability in Arabidopsis thaliana , Molecular systems biology, 2019; 15 (1), e8591. Research summary
O Patange, C Schwall, M Jones, C Villava, DA Griffith, A Phillips, JCW Locke, Escherichia coli can survive stress by noisy growth modulation, Nature communications, 2018; 9 (1), 1-11
BMC Martins, AK Tooke, P Thomas, JCW Locke, Cell size control driven by the circadian clock and environment in cyanobacteria, PNAS, 2018; (48), E11415-E11424
P Gould*, M Domijan*, M Greenwood, IT Tokuda, H Rees, L Kozma-Bognar, AJW Hall^, JCW Locke^, Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression, eLife, 2018; 7, e31700
Selected Recent Reviews
K Abley, R Goswami, JCW Locke, Bet-hedging and variability in plant development: seed germination and beyond, Philosophical Transactions of the Royal Society B, 2024; 379(1900):20230048
CN Micklem, JCW Locke, Cut the noise or couple up: Coordinating circadian and synthetic clocks, iScience, 2021; 24 (9), 103051
S Cortijo, JCW Locke, Does gene expression noise play a functional role in plants? Trends in Plant Science, 2020; 25 (10), 1041-1051
M Greenwood, JCW Locke, The circadian clock coordinates plant development through specificity at the tissue and cellular level, Current opinion in plant biology, 2020; 53, 65-72
*Joint first authors
^Joint corresponding authors
