Biology subjects

Smal, I.

Publications and source records attributed to Smal, I..

8 recordsLinked to original sources

bioRxiv2026

LiFT: Live foci tracking for quantitative analysis of DNA damage dynamics

Quantitative analysis of radiation induced DNA double strand breaks (DSBs) and their repair is essential for understanding and eventually contributing to improving radiation-based cancer therapies. Using live-cell microscopy, the formation and resolution of DSBs over time can be followed in individual cells through tracking of foci formed by accumulation of DSB repair proteins. However, manual analysis of such time-lapse datasets is a tedious time-consuming task that is prone to operator bias, affecting the reproducibility. Here, we present LiFT, an automated image analysis pipeline, specifically designed for robust quantification of DSB kinetics in live-cell imaging experiments. To quantify DSB kinetics, our pipeline first segments and tracks cell nuclei without requiring a nuclear stain. After correcting for inter-frame motion through image registration, automatic detection and tracking of foci within these nuclei enables direct quantification of the dynamics of individual repair events. Multiple algorithmic options were implemented for each step of the pipeline, ensuring more general applicability to potentially different imaging setups and applications. We evaluated the pipeline using PLC/PRF/5 cells and demonstrated its generalizability on U2OS-SSTR2 cells. Our results show that LiFT enables reproducible and scalable quantification of DSB dynamics, providing a broadly applicable framework to analyse live-cell imaging data in cancer research. To improve the adoption of LiFT, we made it available as an open-source Python package and provided a graphical user interface to select different methods and adjust method related parameters.

bioinformatics↗

bioRxiv2026

Multiscale three-dimensional ultrastructural mapping of intestinal tissues and organoids

Understanding cell biology in native environments requires imaging of subcellular organization in three dimensions. In the intestinal epithelium, multiple cell types organize along the crypt-villus axis, where cell-cell interfaces and subcellular architecture control cell differentiation, tissue organization and epithelial function. Resolving these features volumetrically remains challenging: light microscopy offers molecular specificity but has limited resolution, whereas electron microscopy provides ultrastructural detail but is poorly suited to volumetric acquisition combined with specific protein labeling. Here, we show that expansion microscopy enables the multiscale volumetric study of epithelial ultrastructure in tissue sections and organoid models. Using an optimized workflow, we resolve epithelial tissue architecture, cell types and subcellular features within volumes across scales. Application to a microvillus inclusion disease (MVID) organoid model revealed disease-associated ultrastructural phenotypes that were only observed using electron microscopy. Our results establish expansion microscopy as key technology for studying three-dimensional cell biology within intestinal tissue and tissue mimics.

cell biology↗

bioRxiv2026

System Identification and Control for Optogenetics in Mammalian Nucleocytoplasmic Transport

Optogenetics enables experiments in out-of-equilibrium conditions to clarify biological mechanisms and quantify biophysical parameters. However, modelling and control techniques to study mammalian cell biology under optogenetic perturbation remain underutilised. Here, we benchmark these methods within mammalian cells by steering nucleocytoplasmic transport via the optogenetic LEXY protein in outcome-driven microscopy. First, we employ system identification to obtain models that predict transport dynamics by minimising the prediction error. We quantify this prediction accuracy for one biophysical model and two black-box models. Second, we evaluate closed-loop control efficacy by steering transport along a predefined trajectory using model-free Proportional Integral (PI) control, model-based Linear Quadratic Regulation (LQR) and Model Predictive Control (MPC). Both the predictive models and the applied control techniques demonstrate robust performance against cell-to-cell variation. This biological variation is quantified by the parameter distributions obtained from model identification with single-cell trajectories. While we show that model-free techniques such as PI and gain-scheduled PI achieve steering without explict model knowledge, predictive architectures offer better performance under this cell-to-cell variation and time-varying setpoints. Moreover, black-box predictive accuracy suggests that this model-based control is possible, even when explicit mechanistic understanding is missing. Ultimately, we demonstrate that predictive modelling and optogenetics enable quantitative characterisation and precise manipulation of mammalian cells, while offering practical guidelines for the implementation of these techniques. SIGNIFICANCEOptogenetics provides the unique ability to steer cellular processes with light. Variable and localised light inputs allow us to extract more data and guide living cells to specific states. Despite this potential, application of predictive modelling and control techniques with optogenetics remain underutilised in mammalian cell biology. Here, we benchmark these techniques within mammalian cells to steer nucleocytoplasmic transport. Benchmarking these techniques demonstrates their direct applicability to mammalian systems, enabling the extraction of new biological insight in outcome-driven microscopy.

bioengineering↗

bioRxiv2024

Outcome-Driven Microscopy: Closed-Loop Optogenetic Control of Cell Biology

Smart microscopy is transforming biological imaging by integrating real-time analysis with adaptive acquisition to enhance imaging efficiency. Whereas many emerging implementations are event-driven and focus on on-demand data acquisition to reduce phototoxicity, we here present outcome-driven microscopy, which combines smart microscopy with optogenetics to achieve subcellular spatiotemporal control of biology to predefined outcomes. We validate this approach using light-based control of cell migration and nucleocytoplasmic transport, and demonstrate unprecedented spatiotemporal control over cellular behaviour.

cell biology↗

bioRxiv2024

KIF2A maintains cytokinesis in mouse embryonic stem cells by stabilising intercellular bridge microtubules

Cytokinesis, the final stage of cell division, serves to physically separate daughter cells while ensuring correct segregation of cellular components. In cultured naive mouse embryonic stem cells cytokinesis lasts unusually long but the underlying mechanisms are not well understood. Here, using cellular and in vitro approaches, we describe a novel function for the kinesin-13 member KIF2A in this process. In genome-engineered mouse embryonic stem cells we find that KIF2A mainly localises to spindle poles during metaphase and regulates spindle length in a manner consistent with its known role as microtubule minus-end depolymerase. By contrast, during cytokinesis we observe tight binding of KIF2A on the lattices of intercellular bridge microtubules. At this stage KIF2A maintains microtubule length and number, and controls microtubule acetylation. Based on in vitro experiments we propose that the conversion of KIF2A from a depolymerase to a stabiliser is driven both by the inhibition of its ATPase activity, which increases affinity for the lattice, and by a preference of KIF2A for compacted lattices. We propose that during cytokinesis KIF2A maintains the compacted microtubule state, thereby dampening acetylation. As KIF2A depletion causes pluripotency problems and affects mRNA homeostasis our results furthermore indicate that KIF2A-mediated microtubule stabilisation prolongs cytokinesis to maintain pluripotency.

cell biology↗

bioRxiv2023

Distinct mobility patterns of BRCA2 molecules at DNA damage sites

BRCA2 is an essential tumor suppressor protein involved in promoting faithful repair of DNA lesions. The activity of BRCA2 needs to be tuned precisely to be active when and where it is needed. Here, we quantified the spatio-temporal dynamics of BRCA2 in living cells using aberration-corrected multifocal microscopy (acMFM). Using multicolor imaging to identify DNA damage sites, we were able to quantify its dynamic motion patterns in the nucleus and at DNA damage sites. While a large fraction of BRCA2 molecules localized near DNA damage sites appear immobile, an additional fraction of molecules exhibits subdiffusive motion, providing a potential mechanism to retain an increased number of molecules at DNA lesions. Super-resolution microscopy revealed inhomogeneous localization of BRCA2 relative to other DNA repair factors at sites of DNA damage. This suggests the presence of multiple nanoscale compartments in the chromatin surrounding the DNA lesion, which could play an important role in the contribution of BRCA2 to the regulation of the repair process.

cell biology↗

bioRxiv2020

SMARCAD1 Mediated Active Replication Fork Stability Maintains Genome Integrity

Stalled fork protection pathway mediated by BRCA1/2 proteins is critical for replication fork stability that has implications in tumorigenesis. However, it is unclear if additional mechanisms are required to maintain replication fork stability. We describe a novel mechanism by which the chromatin remodeler SMARCAD1 stabilizes active replication forks that is essential for resistance towards replication poisons. We find that loss of SMARCAD1 results in toxic enrichment of 53BP1 at replication forks which mediates untimely dissociation of PCNA via the PCNA-unloader, ATAD5. Faster dissociation of PCNA causes frequent fork stalling, inefficient fork restart and accumulation of single-stranded DNA resulting in genome instability. Although, loss of 53BP1 in SMARCAD1 mutants restore PCNA levels, fork restart efficiency, genome stability and tolerance to replication poisons; this requires BRCA1 mediated fork protection. Interestingly, fork protection challenged BRCA1-deficient naive- or PARPi-resistant tumors require SMARCAD1 mediated active fork stabilization to maintain unperturbed fork progression and cellular proliferation.

cell biology↗

bioRxiv2020

Concerted action of kinesin-1 KIF5B and kinesin-3 KIF13B promotes efficient transport of exocytotic vesicles to microtubule plus ends

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.

cell biology↗