Dr Bruno Martins

Supervisor Details

Contact Details

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

Many organisms, from simple bacteria to complex mammals, have an internal ‘circadian’ clock that helps regulate essential life processes on a 24-hour cycle. The circadian clock is a network of interacting genes and proteins, which in turn interact with other processes in cells to switch genes on or off. Our goal is to understand both how and why the clock works together with these other processes, such as the cell cycle, metabolism or stress responses. To do so, we study the simplest known clock, which is found in photosynthetic cyanobacteria. By studying this simple system, we can establish general principles that we can then apply to more complicated organisms.

To test our hypothesis, we combine mathematical modelling – to quantitatively validate our understanding – with cutting-edge experimental techniques, including live imaging and synthetic biology. Our approach provides high-resolution data on the behaviour of individual cells (rather than whole populations averaged together). Differences between individual cells are often crucial to distinguish between hypotheses. It is also important that this data is dynamic, as otherwise causality is difficult to determine.

Understanding how the clock drives, and is in turn driven by, other cell processes is also the first step towards developing the capabilities to control it. Such control could be relevant for future research in other organisms as well as for applications in biomedicine and synthetic biology.

Scientific Inspiration

My scientific inspirations are François Jacob and Jacques Monod. For a few amazing years, they joined forces to create a new paradigm in both molecular and quantitative biology, by essentially discovering and creating a framework to explore the process of gene regulation. Their experiments and interpretation were highly creative and blended theoretical intuitions with solid empirical data. Throughout their lives, both also maintained and upheld strong humanist convictions.

Research Groups

Quantitative, Systems and Engineering Biology

Cells and Development

Environment and Ecology

Supervision Style

In three words or phrases: I am a laid-back and flexible supervisor. I think everyone is different and so each student may require a different supervision style from me. I will work with you to find the style that works the best, in order to maximise your chances of success and of enjoying your PhD.

My lab is an inclusive lab where we all strive to support one another without compromising our goals and standards of research.

Provision of Training

At the beginning of your PhD, I expect that I will be closely involved in your technical training and helping in setting up goals. As you progress, I expect you to become more independent and initiative taking. In a figurative sense, the PhD is a process of acquiring a licence to become an independent scientist. My role is to help you get it, but only you can get it.

Progression Monitoring and Management

We will meet once per week. In these meetings we will agree and review progress on both short and longer term goals. Biology can happen slowly, so I do not expect that there will be decisive progress every single week, but I believe it is important to maintain regular meetings.

Over time, I expect you to take ownership of the project and of your progress, but I will be available and expect you to come to me for troubleshooting. I have an open door policy and you can approach me at any time to discuss concerns, plans of action and experimental results.

Communication

Email is my preferred mode of written communication. WhatsApp chats and related apps are fine for short and quick communication, but communication by email stays on the record more easily.

Occasionally, I may email you outside working hours, but I do *not* expect you to reply until the next working day. I fully respect your right to a healthy work-life balance.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD study

At least once per week

In year 2 of PhD study

At least once per week

In year 3 of PhD study

At least once per week

The meetings will be face to face and I am usually contactable for an instant response (if required) on every working day.

Working Pattern

Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team.

Notice Period for Feedback

I need at least 2 week’s notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Coupling between the circadian clock, metabolism and the environment: a systems’ approach

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Coupling between the circadian clock, metabolism and the environment: a systems’ approach

Secondary Supervisor(s): Professor Orkun Soyer

University of Registration: University of Warwick

BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

The circadian clock is a gene circuit that generates 24-h cycles of gene expression in many organisms in anticipation of daily cycles of sunlight and temperature. In the cyanobacterium S. elongatus, which has the simplest clock we know of, most of the genome is under clock control. The cyanobacterial clock regulates many processes inside the cell, including metabolism, photosynthesis, cell growth and the cell division cycle. While the clock anticipates environmental change, it is also influenced by a variety of signalling cues. Light and temperature transitions reset the clock state and affect the cell size and division, but the effect of these signals on clock proteins is relayed through more fundamental quantities, such as redox metabolites and ATP/ADP ratios. These cues can be said to characterise the global energy state of the cell, but on the other hand the clock controls expression of most photosynthetic and metabolic proteins. This dynamic and bi-directional coupling between the circadian clock and metabolism likely holds the key to understanding the evolutionary significance of clocks at the most fundamental level (1, 2).

General Aim and Methodology

The aim of this project is to characterise the cross-talk between the circadian clock and metabolism and understand how this cross-talk coordinates cellular growth and division under different environmental scenarios. Using fluorescent reporters, the joint dynamics of the clock and metabolic enzymes will be measured using time-lapse microscopy (3) and microfluidics for thousands of individual cells. Cellular energetics (e.g. ATP/ADP ratios) will be monitored through ratiometric fluorescent reporters and complemented with high-throughput metabolomic profiling. These measurements will provide a comprehensive timeline of physiological changes throughout the 24-h cycle and of how cells allocate metabolic resources to time growth, cell division and DNA replication, which will allow us to create an integrated model of the coupling between the clock and metabolism. We will test this model using a combination of genetic and environmental perturbations in microfluidic devices. These results will allow us to understand why clocks offer a selective advantage, and thus reveal a mechanistic ‘logic’ that can be applied to other systems.

References

1. A. M. Puszynska, E. K. O’Shea, Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway. eLife 6, e23210 (2017).

2. G. Pattanayak, M. J. Rust, The Cyanobacterial Clock and Metabolism. Curr Opin Microbiol 18, 90–95 (2014).

3. B. M. Martins, A. K. Das, L. Antunes, J. C. Locke, Frequency doubling in the cyanobacterial circadian clock. Molecular Systems Biology 12, 896 (2016).

Previous Projects (2024-25)

Primary supervisor for:

The coupling between the circadian clock, metabolism and the environment: a systems’ approach

Previous Projects (2023-24)

Primary supervisor for:

The coupling between the circadian clock, metabolism and the environment: a systems’ approach