Biology subjects

Sartori, P.

Publications and source records attributed to Sartori, P..

7 recordsLinked to original sources

bioRxiv2026

Tunable neuronal microenvironments drive distinct functional phenotypes in human iPSCs-derived dopaminergic neurons

Neuronal heterogeneity is a defining feature of complex neural circuits, where local differences in firing patterns, activity levels, and temporal dynamics shape information processing and emergent network activity. In adult neurons, this heterogeneity arises from a variety of known and unknown factors including the extracellular environment. Although neurons have been cultured on three-dimensional substrates, the effect of the microenvironments on their firing activity remains poorly understood. Here, we have synthesized two chitosan hydrogel systems seeded with human iPSCs-derived dopaminergic neurons as tunable platforms to control neuronal microenvironments. Both systems were formulated with the ability to incorporate carbon nanotubes (CNT), thus promoting neural interfacing. Calcium imaging combined with computational single-cell analysis demonstrated that supramolecular organization, hydration state, and general physicochemical properties differentially bias neuronal firing dynamics and synchrony leading to the emergence of distinct activity phenotypes despite identical cellular origin. These activity profiles were clustered through K-means and assigned to specific phenotypes including bursting irregular neurons, regular network contributors, or less active/quiescent neurons. Furthermore, CNTs incorporation enhanced local hydrogel compaction, resulting in unique active neuronal phenotypes, highlighting the potential of CNTs to modulate local cellular microenvironments. These findings establish tunable biomaterials as microenvironment contenders for controlling neuronal network state while giving insights on the interplay of different cues in promoting neuronal heterogeneity and functional phenotype relevant to neurodevelopment, neurodegeneration, and disease modelling.

neuroscience↗

bioRxiv2025

Model-based inference of cell cycle dynamics captures alterations of the DNA replication programme

The cell cycle of eukaryotic cells consists of several processes that must be carefully orchestrated and completed in a timely manner. Alterations in cell cycle dynamics have been linked to the onset of various diseases, underscoring the need for quantitative methods to analyze cell cycle progression. Here, using a combination of high-throughput experimental data and theoretical modeling, we develop RepliFlow, a model-based approach to infer cell cycle dynamics from flow cytometry data of DNA content in asynchronous cell populations. We model the DNA content distribution as the result of both noisy single-cell measurements and the populations age structure. We show that RepliFlow captures not only changes in the length of each cell cycle phase but also alterations in the underlying DNA replication dynamics. RepliFlow is species-agnostic and recapitulates results from more sophisticated analyses based on nucleotide incorporation. Finally, we propose a minimal DNA replication model that enables to derive microscopic insights about origin firing rates and replication fork speed from population-wide DNA content measurements. Our work presents a scalable framework for inferring cell cycle dynamics from flow cytometry data, enabling the characterization of replication program alterations.

systems biology↗

bioRxiv2024

Global comparative structural analysis of responses to protein phosphorylation

Post-translational modifications (PTMs), particularly protein phosphorylation, are key regulators of cellular processes, impacting numerous aspects of protein activity. Despite widespread phosphorylation of eukaryotic proteomes, the function of most phosphosites remains unknown. Elucidating the structural mechanisms underlying phosphorylation is crucial for understanding its regulatory roles. Here, we conducted a comparative structural analysis of phosphorylated and non-phosphorylated proteins taken from the Protein Data Bank (PDB). Our study systematically evaluates how phosphorylation affects backbone conformation, protein dynamics, and mechanical strain. We found that phosphorylation commonly induces small, stabilizing conformational changes through conformational selection and frequently modulates local residue fluctuations, influencing overall protein motion. Notably, a small but significant subset of phosphosites shows mechanical coupling with functional sites, aligning with the domino model of allosteric signal transduction. This work provides a foundation for studying phosphorylation and other PTMs in their structural context, which will guide the rational design of synthetic phosphosites and enable the engineering of PTM-driven regulatory circuits in synthetic biology.

bioinformatics↗

bioRxiv2024

Elastic analysis of structural ensemble reveals the energetic basis of hand-over-hand in a AAA+ motor

Proteins carry out cellular functions by changing their structure among a few conformations, each characterised by a different energy level. Therefore, structural changes, energy transformations, and protein function are intimately related. Despite its central importance, this relationship remains elusive. For example, while many hexameric ATPase motors are known to function using a hand-over-hand alternation of subunits, how energy transduction throughout the assembly structure drives the hand-over-hand mechanism is not known. In this work, we unravel the energetic basis of hand-over-hand in a model AAA+ motor, RuvB. To do so, we develop a general method to compute the residue-scale elastic pseudoenergy due to structure changes and apply it to RuvB structures, recently resolved through cryo-EM. This allows us to quantify how progression through RuvBs mechanochemical cycle translates into residue-scale energy transduction. In particular, we find that DNA binding is associated with overcoming a high energy barrier. This is possible through inter-subunit transmission of energy, and ultimately driven by nucleotide exchange. Furthermore, we show how this structure-inferred energetic quantification can be integrated into a non-equilibrium model of AAA+ assembly dynamics, consistent with single-molecule biophysics measurements. Overall, our work elucidates the energetic basis for the hand-over-hand mechanism in RuvBs cycle. Furthermore, it presents a generally applicable methodology for studying the energetics of conformational cycles in other proteins, allowing to quantitatively bridge data from structural biology and single-molecule biophysics. Author SummaryMolecular motors are proteins that transform chemical energy into motion. To do so, they change their shape through a highly organised cycle. How exactly these changes in shape translate into energy transformations that ultimately result in motion is still not fully understood. In our work, we combined tools from structural biology and biophysics to better quantify and model this process. We focused on RuvB, a motor made of six identical parts that work together to move DNA through its central pore. We first tracked how RuvBs shape changes and how much energy these changes involve, and then built a theoretical model that simulates its operational cycle. More broadly, our approach shows how studying protein energetics can connect the perspectives of structural biology and single-molecule biophysics, thus providing new ways to understand how molecular machines work.

biophysics↗

bioRxiv2024

Thermodynamic dissipation constrains metabolic versatility of unicellular growth

Metabolic versatility enables unicellular organisms to grow in vastly different environments. Since growth occurs far from thermodynamic equilibrium, the second law of thermodynamics has long been believed to pose key constraints to life. Yet, such constraints remain largely unknown. Here, we integrate published data spanning decades of experiments on unicellular chemotrophic growth and compute the corresponding thermodynamic dissipation. Due to its span in chemical substrates and microbial species, this dataset samples the versatility of metabolism. We find two empirical thermodynamic rules: first, the amount of energy dissipation per unit of biomass grown is largely conserved across metabolic types and domains of life; second, aerobic respiration exhibits a trade-off between dissipation and growth, reflecting in its high thermodynamic efficiency. By relating these rules to the fundamental thermodynamic forces that drive and oppose growth, our results show that dissipation imposes tight constraints on metabolic versatility.

biophysics↗

bioRxiv2023

Evolutionary conservation of mechanical strain distributions in functional transitions of protein structures

One of the tenets of molecular biology is that dynamic transitions between three-dimensional structures determine the function of proteins. Therefore, it seems only natural that evolutionary analysis of proteins, presently based mainly on their primary sequence, needs to shift its focus towards their function as assessed by corresponding structural transitions. This can be facilitated by recent progress in cryogenic electron microscopy that provides atomic structures of multiple conformational states for proteins and protein assemblies isolated from evolutionarily related species. In this work, we study evolutionary conservation of multi-protein assembly function by using mechanical strain as a quantitative footprint of structural transitions. We adopt the formalism of finite strain analysis, developed in condensed matter physics, and apply it, as a case study, to a classical multi-protein assembly, the ATP synthase. Our Protein Strain Analysis (PSA) provides a precise characterization of rotation domains that agrees with the present biophysical knowledge. In addition, we obtain a strain distribution on the protein structure associated with functional transitions. By analyzing in detail, the strain patterns of the chains responsible for ATP synthesis across distinct species, we show that they are evolutionarily conserved for the same functional transition. Such conservation is not revealed by displacement or rotation patterns. Furthermore, within each functional transition, we can identify conserved strain patterns for ATP synthases isolated from different organisms. The observed strain conservation across evolutionary distant species indicates that strain should be essential in future structure-based evolutionary studies of protein function.

biophysics↗

bioRxiv2019

Increasing demand for plasma membrane contributes to the energetic cost of early zebrafish embryogenesis.

How do early embryos apportion the resources stored in the sperm and egg? Recently, we established isothermal calorimetry (ITC) to measure heat dissipation by living zebrafish embryos and to estimate the energetics of specific developmental events. During the reductive cleavage divisions, the rate of heat dissipation increases from [~]60 nJ{middle dot}s-1 at the 2-cell stage to [~]90 nJ{middle dot}s-1 at the 1024-cell stage. Here we ask, which cellular process(es) drive these increasing energetic costs? We present evidence that the cost is due to the increase in the total surface area of all of the cells of the embryo. First, embryo volume stays constant during the cleavage stage, indicating that the increase is not due to growth. Second, the heat increase is blocked by nocodazole, which inhibits DNA replication, mitosis and cell division; this implicates some aspect of cell proliferation contributing to these costs. Third, the heat increase scales with total cell surface area rather than total cell number. Finally, the calculated costs of maintaining and assembling plasma membranes and associated proteins probably accounts for a significant proportion of the heat increase. Thus, the cells membrane is likely to contribute significantly to the total energy budget of the embryo.\n\nHighlight summary for TOCRodenfels et al. measure the energetic costs of early zebrafish development, using calorimetry. Embryonic heat dissipation increases, but, more slowly than the number of cells during early cleavage stage development. Instead, the heat dissipation scales with the energetic cost associated with maintaining and producing new plasma membrane.

developmental biology↗