Biology subjects

Manca, M.

Publications and source records attributed to Manca, M..

4 recordsLinked to original sources

bioRxiv2025

Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative

The emergence of virtual human twins (VHT) in biomedical research has sparked interest in multiscale in silico modelling frameworks, particularly in their application bridging cellular to tissue levels. Among the diverse array of multiscale modelling tools, off-lattice center-based agent-based models (CBM) offer a promising approach due to their depiction of cells in 3D space, closely resembling biological reality. Despite the proliferation of CBM tools addressing various biomedical challenges, a comprehensive and systematic comparison among them has been elusive. This paper presents a community-driven benchmark initiative aimed at evaluating and comparing CBM for biomedical applications, akin to successful efforts in other scientific domains such as the Critical Assessment of Protein Structure Prediction (CASP). Enlisting developers from leading tools like BioDynaMo, Chaste, PhysiCell,TiSim, and CompuTiX, we devised a benchmark scope, defined metrics, and established reference datasets to ensure a meaningful and equitable evaluation. Unit tests targeting different solvers within these tools were designed, ranging from diffusion and mechanics to cell cycle simulations and growth scenarios. Results from these tests demonstrate varying tool implementations in handling diffusion, mechanics, and cell cycle equations, emphasising the need for standardised benchmarks and interoperability. Discussions among the community underscore the necessity for defining gold standards, fostering interoperability, and drawing lessons from analogous benchmarking experiences. The outcomes, disseminated through a public platform in collaboration with OpenEBench, aim to catalyse advancements in computational biology, offering a comprehensive resource for tool evaluation and guiding future developments in cell-level simulations. This initiative endeavours to strengthen and expand the computational biology simulation community through continued dissemination and performance-oriented benchmarking efforts to enable the use of VHT in biomedicine.

systems biology↗

bioRxiv2021

Structure of anchorless RML prion reveals motif variation between strains

Little is known about the structural basis of prion strains. Here we provide a high (3.0 [A]) resolution cryo-electron microscopy-based structure of brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register {beta}-sheet-based core. However, detailed comparisons reveal that variations in shared structural motifs provide a basis for prion strain determination. One-sentence summaryCryo-electron microscopy reveals a near-atomic structure of an infectious, brain-derived murine prion fibril and strain differences.

biochemistry↗

bioRxiv2020

BioDynaMo: an agent-based simulation platform for scalable computational biology research

MotivationAgent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. ResultsWe present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a general-purpose and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology, and epidemiology. For each use case we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baseline. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. AvailabilityBioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in supplementary information. Contactlukas.breitwieser@inf.ethz.ch, a.s.hesam@tudelft.nl, omutlu@ethz.ch, r.bauer@surrey.ac.uk Supplementary informationAvailable at https://doi.org/10.5281/zenodo.4501515.

systems biology↗

bioRxiv2020

Cholinergic modulation of membrane properties of calyx terminals in the vestibular periphery

Vestibular nerve afferents are divided into regular and irregular groups based on the variability of interspike intervals in their resting discharge. Most afferents receive inputs from bouton terminals that contact type II hair cells as well as from calyx terminals that cover the basolateral walls of type I hair cells. Calyces have an abundance of different subtypes of KCNQ (Kv7) potassium channels and muscarinic acetylcholine receptors (mAChRs) and receive cholinergic efferent inputs from neurons in the brainstem. We investigated whether mAChRs affected membrane properties and firing patterns of calyx terminals through modulation of KCNQ channel activity. Patch clamp recordings were performed from calyx terminals in central regions of the cristae of the horizontal and anterior canals in 13 - 18 day old Sprague-Dawley rats. KCNQ mediated currents were observed as voltage sensitive currents with slow kinetics (activation and deactivation), resulting in spike frequency adaptation so that calyces at best fired a single action potential at the beginning of a depolarizing step. Activation of mAChRs by application of oxotremorine methiodide or inhibition of KCNQ channels by linopirdine dihydrochloride decreased voltage activated currents by [~]30%, decreased first spike latencies by [~]40%, decreased spike thresholds by [~]50%, and resulted in continuous firing during depolarizing steps. Interestingly, some of the calyces showed spontaneous discharge in the presence of these drugs. Together, these findings suggest that cholinergic efferents can modulate the response properties and encoding of head movements by afferents.

neuroscience↗