arXiv subjects

David Klenerman

Publications and source records attributed to David Klenerman.

7 recordsLinked to original sources

arXiv2026

A cell-level model to predict the spatiotemporal dynamics of neurodegenerative disease

A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation from cells that are already in a pathological, runaway aggregation state. To bridge this gap, we here develop a bottom-up physical model that explicitly incorporates these two fundamental cell-level drivers of protein aggregation dynamics. We show that our model naturally explains the characteristic long, slow development of pathology followed by a rapid acceleration, a hallmark of many neurodegenerative diseases. Furthermore, the model reveals the existence of a critical switch point at which the system's dynamics transition from being dominated by slow, spontaneous formation of diseased cells to being driven by fast propagation. This framework provides a robust physical foundation for interpreting pathological data and offers a method to predict which class of therapeutic strategies is best matched to the underlying drivers of a specific disease.

q-bio.QM↗

arXiv2025

A universal phase-plane model for in vivo protein aggregation

Neurodegenerative diseases are driven by the accumulation of protein aggregates in the brain of affected individuals. The aggregation behaviour in vitro is well understood and driven by the equilibration of a super-saturated protein solution to its aggregated equilibrium state. However, the situation is altered fundamentally in living systems where active processes consume energy to remove aggregates. It remains unclear how and why cells transition from a state with predominantly monomeric protein, which is stable over decades, to one dominated by aggregates. Here, we develop a simple but universal theoretical framework to describe cellular systems that include both aggregate formation and removal. Using a two-dimensional phase-plane representation, we show that the interplay of aggregate formation and removal generates cell-level bistability, with a bifurcation structure that explains both the emergence of disease and the effects of therapeutic interventions. We explore a wide range of aggregate formation and removal mechanisms and show that phenomena such as seeding arise robustly when a minimal set of requirements on the mechanism are satisfied. By connecting in vitro aggregation mechanisms to changes in cell state, our framework provides a general conceptual link between molecular-level therapeutic interventions and their impact on disease progression.

q-bio.BM↗

arXiv2021

Deformable and robust core-shell protein microcapsules templated by liquid-liquid phase separated microdroplets

Microcapsules are a key class of microscale materials with applications in areas ranging from personal care to biomedicine, and with increasing potential to act as extracellular matrix (ECM) models of hollow organs or tissues. Such capsules are conventionally generated from non-ECM materials including synthetic polymers. Here, we fabricated robust microcapsules with controllable shell thickness from physically- and enzymatically-crosslinked gelatin and achieved a core-shell architecture by exploiting a liquid-liquid phase separated aqueous dispersed phase system in a one-step microfluidic process. Microfluidic mechanical testing revealed that the mechanical robustness of thicker-shell capsules could be controlled through modulation of the shell thickness. Furthermore, the microcapsules demonstrated environmentally-responsive deformation, including buckling by osmosis and external mechanical forces. A sequential release of cargo species was obtained through the degradation of the capsules. Stability measurements showed the capsules were stable at 37 °C for more than two weeks. Finally, all-aqueous liquid-liquid phase separated and multiphase liquid-liquid phase separated systems were generated with the gel-sol transition of microgel precursors. These smart capsules are promising models of hollow biostructures, microscale drug carriers, and building blocks or compartments for active soft materials and robots.

cond-mat.soft↗

arXiv2021

Low Stress Ion Conductance Microscopy of Sub-Cellular Stiffness

Directly examining subcellular mechanics whilst avoiding excessive strain of a live cell requires the precise control of light stress on very small areas, which is fundamentally difficult. Here we use a glass nanopipet out of contact with the plasma membrane to both exert the stress on the cell and also accurately monitor cellular compression. This allows the mapping of cell stiffness at a lateral resolution finer than 100 nm. We calculate the stress a nanopipet exerts on a cell as the sum of the intrinsic pressure between the tip face and the plasma membrane plus its direct pressure on any glycocalyx, both evaluated from the gap size in terms of the ion current decrease. A survey of cell types confirms that an intracellular pressure of approximately 120 Pa begins to detach the plasma membrane from the cytoskeleton and reveals that the first 660 +/- 90 nm of compression of a neuron cell body is much softer than previous methods have been able to detect.

cond-mat.soft↗

arXiv2019

Spectrally-Resolved Photodynamics of Individual Emitters in Large-Area Monolayers of Hexagonal-Boron Nitride

Hexagonal boron nitride (h-BN) is a 2D, wide band-gap semiconductor that has recently been shown to display bright room-temperature emission in the visible region, sparking immense interest in the material for use in quantum applications. In this work, we study highly crystalline, single atomic layers of chemical vapour deposition (CVD)-grown hexagonal boron nitride and find predominantly one type of emissive state. Using a multidimensional super-resolution fluorescence microscopy technique we simultaneously measure spatial position, intensity and spectral properties of the emitters, as they are exposed to continuous wave illumination over minutes. As well as low emitter heterogeneity, we observe inhomogeneous broadening of emitter line-widths and power law dependency in fluorescence intermittency, this is in striking similarity to previous work on quantum dots. These results show that high control over h-BN growth and treatment can produce a narrow distribution of emitter type, and that surface interactions heavily influence the photodynamics. Furthermore, we highlight the utility of spectrally-resolved wide-field microscopy in the study of optically-active excitons in atomically thin two-dimensional materials.

physics.optics↗

arXiv2017

The 2015 super-resolution microscopy roadmap

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of 'super-resolution' far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of Journal of Physics D: Applied Physics addresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough discussion on the concepts underlying super-resolution optical microscopy, the potential of different approaches, the importance of label optimization (such as reversible photoswitchable proteins) and applications in which these methods will have a significant impact.

physics.bio-ph↗

arXiv2014

pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

Single molecule Förster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additional documentation including tutorials is hosted independently on ReadTheDocs. The code is available from the free hosting site Bitbucket. Through distribution of this software, we hope to lower the barrier for the adoption of smFRET experiments by other research groups and we encourage others to contribute modules for specific analysis needs.

cs.CE↗