Future Leaders of Biophysics Thursday, March 27, 2025 2:00 PM (UK time)

We would like to welcome all attendees to this first Future Leaders in Biophysics webinar, housed via Cassyni on the Springer Nature Physics Seminars series supported by the International Union of Pure and Applied Biophysics (IUPAB). In this webinar, which is free to attend and will be recorded (subject to speakers' wishes), we wish to announce the winner of the annual prestigious Michèle Auger Award, connected with the Biophysical Reviews journal.

The meeting will honour the winner and top candidates for the Michèle Auger Award by giving them a chance to present their recent research and answer questions. Please do attend if you can and join us in celebrating the Future Leaders of Biophysics.

1. Introduction/housekeeping, Joshua Bayliss
2. IUPAB and its role in biophysics, Tony Watts
3. Biophysical Reviews Journal, Wilma Olson

Current research in biomechanics and mechanobiology faces critical limitations to control the mechanical environment (i.e., deformation, stiffness) of biological systems. A significant limitation exists in the real-time control and remote actuation of the mechanical environment. We present a novel experimental framework to modulate the mechanical properties of cell substrates using magnetorheological elastomers (MREs) and magneto-responsive hydrogels. We demonstrated reversible mechanical changes in substrates of more than one order of magnitude in stiffness and large local deformations (>30%). In parallel, we developed a multiscale computational model to guide the experimental testing. The whole experimental-computational framework is coupled to a customised imaging system for live cellular assays that allows for magneto-mechanical stimulation in real time. In addition, we coupled the system to nanoindentation instruments to enable the measurement of local changes in cellular mechanical properties during substrate deformation. Finally, the complete system is used to study the response of astrocytes to mechanical deformation by means of dynamic changes in morphology, stiffness and functional responses. Other applications of the system also allow for studying cell-extracellular matrix interactions under evolving mechanical scenarios or adapting the methods to tissue samples. These results offer direct benefits for health purposes by paving the path to models to simulate dynamic mechanistic-mediated biological processes as well as testing and design of new therapeutics.

Most traditional biological approaches analyse millions to billions of molecules, meaning that the behaviour of individual molecules is obscured by ensemble averaging. This limits their utility for looking at heterogeneous systems. This can limit their effectiveness for examining heterogeneous systems. In contrast, single-molecule approaches analyse molecules one at a time, allowing even the rarest species to be observed and characterised.

In my group, based in the School of Chemistry and the Institute for Repair and Regeneration at the University of Edinburgh, we build and use single-molecule instrumentation for studying complex biological systems. A major focus is on neurodegenerative disorders, such as Parkinson’s, Alzheimer’s and Amyotrophic Lateral Sclerosis. In these diseases, proteins can misfold and clump together to form aggregates, which are both low in abundance and highly heterogenous. Single-molecule techniques let us precisely determine the size, protein composition and structure of these, and we have utilised these in patient biofluids [1,2]. Our goal is to diagnose individuals before symptoms appear, enabling timely therapeutic interventions. We have applied these methods to analyse samples from recent phase-2 and phase-3 Parkinson’s drug trials.

Alongside single-molecule approaches, we have also developed super-resolution approaches to image proteins at the nanometre length scale, including a new approach that can be used in live cells [3–6]. We’ve also used these to visualise synaptic proteins in the brain, elucidating mechanisms of the memory storage [7,8].

Throughout my career, I have been fascinated by microscopy and driven to push the boundaries of what is possible to observe. The resolution of microscopy techniques is rapidly increasing, exemplified by the Cryo-EM resolution revolution. Atomic force microscopy (AFM) is capable of routinely imaging the double helix of DNA and variations within that structure (Pyne et al. 2014). However, AFM is still not routinely used to help solve problems inaccessible to the traditional tools of structural biology, in part due to a lack of accessible software pipelines designed to analyse this complex 3D data.

Extracting information from an image remains a major challenge for microscopy and imaging techniques that work at higher length scales, i.e., those of people, or planets. We have developed TopoStats, an open-source image analysis pipeline to extract quantitative information from raw AFM images of any biological molecule, from membrane proteins to living bacteria (Beton et al. 2021). We have recently shown that through a combination of high-resolution imaging and automated image analysis, we can explicitly determine the structure and topology of individual molecules of DNA (Holmes et al. 2025, Diggines et al. 2024).

Complexity in DNA structures, from defects and damage to the formation of alternative structures, plays a critical role in maintaining, regulating and disrupting the flow of cellular information within the genome. We have developed new tools in TopoStats to trace the structure of replication intermediates from Xenopus egg extracts and determine the extent of replication progression. We identify stalled complexes as theta structures, separating and quantifying the length of replicated and unreplicated DNA. In ~7% of complexes, we observe reversed forks of length ~20 nm, providing new insights into the likelihood of complex DNA structures forming in response to replication stress.

Beyond DNA alone, we use our pipeline to uncover the mechanism of action of new DNA-targeting anti-cancer therapeutics (Poole et al. 2025) and by incorporating deep learning models, can identify single proteins interacting within DNA-protein complexes. Looking forward, we are developing new tools to quantify the effect of complexity in DNA structure on protein recognition and activity.

Bacteria move through the rotation of large filaments know as flagella. Flagellar rotary motion is powered by a flagellar motor, driven by stator units (MotAB). The MotAB proteins convert the ion motive force across the bacterial inner membrane into rotation of the filament, but it was not understood how this occurred. Using cryo-EM we have determined structures of the MotAB complex, which we show has a 5:2 stoichiometry shared across different species. By visualizing MotAB in its plugged, inactive state, as well as mimics of its active state, we come up with models for how torque is generated in the flagellar motors, as well as how direction switching in the flagellar motor occurs. We also reveal our recent progress on how ion specificity is obtained and propose a mechanism for how stator units become active upon motor incorporation. I will also present results on a newly discovered bacteriophage defense system, Zorya, that uses a 5:2 motor complex to sense bacteriophage infection. Using a combination of structural biology, functional assays, light microscopy and mass spectrometry, we provide novel insight into the unique Zorya mechanism of action. We provide data indicating that Zorya detects phage infection by monitoring integrity of the peptidoglycan layer. Upon phage infection, the ZorAB motor proteins get activated and through a 700 Å long tail locally recruit and activate ZorD nuclease that can degrade the phage genome, halting the infection.