Understanding and control of electric communication in bacteria colonies, using machine learning

University of Reading

School of Biological Sciences

Project Description

Although initial discussions regarding bioelectricity and its role in the fundamental understanding of various cellular behaviours took place in the 1970s, the bioelectrical view of cells as a more general concept has remained limited to the fringes of biological research for five decades. Recent studies in diverse systems have shown that bioelectrical signals are at the core of cell–cell communication in micro-organisms, plants and animals. Bioelectricity can underpin efficient growth and antibiotic resistance in bacterial biofilms and organisation, morphogenesis and regeneration in mammalian and plant tissues. These findings, together with the bioengineering solution that externally-applied electric fields can modulate multicellular processes such as regeneration in plant and vertebrate tissue, have resulted in the recent proposition that microorganisms and multicellular organisation more broadly should be studied as a bioelectrical paradigm.

Electric communication in bacterial communities

Bacterial communities respond to environmental factors to survive in a changing environment. Demonstrating rich spatial patterns (body morphology), a bacterial community can control its shape as a whole colony to optimise the nutrition intake or minimise the effect of antibiotics. Recent studies have shown that responding to nutrition levels, bacteria cells at the periphery send electric signals to the centre of the colony aggregation, altering the the membrane potential to suppress their metabolic cycles. In other words, they electrically communicate with each other to pass sufficient nutrition to the centre, avoiding its depletion around the centre. In summary, individual bacteria cells can sense environmental factors, send electric signals to and from each other, and a whole colony goes through a decision-making process to choose a body morphology for adaptation.

Using a bacteria community, we aim to study

(1) the morphology of colony and electric patterns that facilitate control for adaptation to a changing environment,

(2) morphological computation based on reservoir computing, where the colony morphology is actually used for computation.

More prominently, we will actively enhance the computational ability by applying the external electric fields, and measure how the external field can shape the electric and morphological patterns in the bacteria community. To this end, machine learning will be used to optimise the feedback control using multiple input and output of electric stimulation.

Dr. Hayashi’s research spans the areas of complex physical systems, behavioural science and neuroscience, with specific expertise in: 1) non-equilibrium dynamics governing adaptive behaviour in physical and living systems; 2) neural/behavioural mechanisms of the closed brain-body loop for various living systems; and 3) mathematical models underpinning behaviour and activity of neural networks. Techniques include physio-chemical experiments, microbiological experiments, machine learning, electroencephalogram (EEG) measurement, and mathematical modelling. His lab’s website can be visited here.

Funding Information

This is a self-funded project.

Eligibility Requirements

Applicants should have a good degree (minimum of a UK Upper Second (2:1) undergraduate degree or equivalent) in Engineering and Biomedical Engineering or a strongly-related discipline. Applicants will also need to meet the University’s English Language requirements. We offer pre-sessional courses that can help with meeting these requirements.

Application Process

Submit an application for a PhD in Biomedical Engineering at http://www.reading.ac.uk/pgapply.

Further information

Enquiries: Dr. Yoshikatsu Hayashi, email: [email protected]

Supplementary Information

The University of Reading, located west of London, England, provides world-class research education programs. The University’s main Whiteknights Campus is set in 130 hectares of beautiful parkland, a 30-minute train ride to central London and 40 minutes from London Heathrow airport.

Our School of Biological Sciences conducts high-impact research, tackling current global challenges faced by society and the planet. Our research ranges from understanding and improving human health and combating disease, through to understanding evolutionary processes and uncovering new ways to protect the natural world. In 2020, we moved into a stunning new ~£60 million Health & Life Sciences building. This state-of-the-art facility is purpose-built for science research and teaching. It houses the Cole Museum of Zoology, a café and social spaces.

In the School of Biological Sciences, you will be joining a vibrant community of ~180 PhD students representing ~40 nationalities. Our students publish in high-impact journals, present at international conferences, and organise a range of exciting outreach and public engagement activities.

During your PhD at the University of Reading, you will expand your research knowledge and skills, receiving supervision in one-to-one and small group sessions. You will have access to cutting-edge technology and learn the latest research techniques. We also provide dedicated training in important transferable skills that will support your career aspirations. If English is not your first language, the University’s excellent International Study and Language Institute will help you develop your academic English skills.

The University of Reading is a welcoming community for people of all faiths and cultures. We are committed to a healthy work-life balance and will work to ensure that you are supported personally and academically.

References

1. Schofield, Z., Meloni, G. N., Tran, P., Zerfass, C., Sena, G., Hayashi, Y., Grant, M., Contera, S. A., Minteer, S. D., Kim, M., Prindle, A., Rocha, P., Djamgoz, M. B. A., Pilizota, T., Unwin, P. R., Asally, M. and Soyer, O. S. (2020) Bioelectrical understanding and engineering of cell biology. Journal of the Royal Society Interface, 17 (166). 20200013. ISSN 1742-5662 doi: https://doi.org/10.1098/rsif.2020.0013 http://centaur.reading.ac.uk/90915/1/rsif20200013.pdf
2. Stratford, J. P., Edwards, C. L. A., Ghanshyam, M. J., Malyshev, D., Delise, M. A., Hayashi, Y. and Asally, M. (2019) Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity. Proceedings of the National Academy of Sciences of the United States of America, 116 (19). pp. 9552-9557. ISSN 1091-6490 doi: https://doi.org/10.1073/pnas.1901788116 http://centaur.reading.ac.uk/83508/1/1901788116.full%20%281%29.pdf
Please also see Dr Hayashi’s profile: http://www.reading.ac.uk/biologicalsciences/SchoolofBiologicalSciences/Meetourteam/staff/y-hayashi.aspx

To apply for this PhD, please use the following application link: http://www.reading.ac.uk/pgapply

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