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Biology subjects

Abele, T.

Publications and source records attributed to Abele, T..

7 recordsLinked to original sources

Volume and surface methods for microparticle traction force microscopy: a computational and experimental comparison

It is an essential element of mechanobiology to measure the forces of biological cells. In microparticle traction force microscopy, they are inferred from the deformation of elastic microparticles. Two complementary variants have been introduced before: the volume method, which reconstructs surface stresses from the displacements of fiducial markers embedded inside the particles, and the surface method, which infers stresses directly from the deformation of the particle surface. However, a systematic comparison of the two methods has been lacking. Here, we quantitatively compare both approaches using simulated traction fields representing biologically relevant loading scenarios. We find that the surface method consistently reconstructs traction profiles with substantially lower errors than the volume method, which suffers from displacement tracking and stress calculation at the surface. At high noise levels, however, the performance gap becomes smaller. To compare the performance of the two methods in a realistic experimental setting, we developed DNA-based hydrogel microparticles equipped with both fluorescent surface labels and embedded fluorescent nanoparticles, enabling the direct comparison of the two methods within the same system. Compression experiments produced traction profiles consistent with Hertzian contact mechanics and confirmed the trends observed in the simulations. We also show that despite large experimental deformations and strains (both up to 20 percent), linear elasticity theory should still be valid. While our computational workflow establishes a framework to apply both methods, our experimental workflow establishes DNA microparticles as versatile and biocompatible probes for measuring cellular forces.

biophysics↗

Buoyancy-driven sorting of synthetic cells for nanopore activity

The development of sorting strategies that directly report on functional activity remains a bottleneck in synthetic cell research. Current methodologies typically rely on sequential label-dependent probing, which limits throughput. Here, we introduce a label-free, buoyancy-driven selection strategy in which the mode of separation and the mode of decision-making are intrinsically linked, coupling pore activity directly to the synthetic vesicles internal density in a one-pot assay. In this system, sorting emerges intrinsically: Giant unilamellar vesicles (GUVs) that contain a dense medium sediment by default, while only those with functional transmembrane pores undergo solute exchange, leading to density equilibration and flotation. We exploit this principle to separate pore-active from non-functional GUVs without external markers or imaging-based readouts. Using protein pores and DNA origami and DNA tile nanopores, we demonstrate that buoyancy-driven separation enables parallel functional assessment of heterogeneous populations and supports flow-based enrichment of highly active synthetic cells. By directly linking molecular transport performance to GUV buoyancy, this approach collapses decision-making into the physical separation process itself, providing a scalable platform for screening, sorting, and evolving membrane pores in synthetic cell systems.

biophysics↗

Automated Image-Based Cell Sorting by Targeted Photopolymerization

We present an automated image-based cell sorting method capable of a through-put of hundreds of cells per second. Our microscopy platform integrates automated image acquisition, machine-learning based classification and sub-sequent depletion of up to 99.98 % of negative cells by spatially controlled photo-encapsulation, preserving target cells for collection. Applied to peripheral blood mononuclear cells, the method achieves the label-free, morphology-based enrichment of activated T cells for downstream applications in biomedicine.

cell biology↗

Growth, dissolution and segregation of genetically encoded RNA droplets by ribozyme catalysis

Active droplets, membraneless compartments driven by internal chemical reactions, are compelling models for protocells and synthetic life. A central challenge is to program their dynamic behaviors using heritable genetic information, which would grant them the capacity to evolve. Here, we create transiently active RNA droplets by integrating sites for ribozyme catalysis directly into the sequence of self-assembling, four-arm RNA nanostars. To enable perfusion and observe the resulting dynamics over time, we develop a method for trapping individual droplets in hydrogel cages by targeted in situ photopolymerization. This enables us to quantify the sequence-programmable droplet dissolution and to control the degradation kinetics by choosing between fast (hammerhead) and slow (hairpin) ribozymes. Furthermore, we trigger the segregation of mixed droplet populations via the sequence-specific cleavage of a chimeric linker RNA. The droplet-encapsulated DNA templates code for the regrowth of new droplets, establishing the proof-of-principle for a minimal, genetically encoded cycle of dissolution and regrowth. By directly linking RNA sequence to droplet stability, composition, and life-cycle dynamics, our work provides a robust platform for engineering evolvable materials and advancing the bottom-up construction of synthetic cells.

synthetic biology↗

Minimal-invasive 3D laser printing of microimplants in organismo

Multi-photon 3D laser printing has gathered much attention in recent years as a means of manufacturing biocompatible scaffolds that can modify and guide cellular behavior in vitro. However, in vivo tissue engineering efforts have been limited so far to the implantation of beforehand 3D printed biocompatible scaffolds and in vivo bioprinting of tissue constructs from bioinks containing cells, biomolecules, and printable hydrogel formulations. Thus, a comprehensive 3D laser printing platform for in vivo and in situ manufacturing of microimplants raised from synthetic polymer-based inks is currently missing. Here we present a platform for minimal-invasive manufacturing of microimplants directly in the organism by one-photon photopolymerization and multi-photon 3D laser printing. Employing a commercially available elastomeric ink giving rise to biocompatible synthetic polymer-based microimplants, we demonstrate first applicational examples of biological responses to in situ printed microimplants in the teleost fish Oryzias latipes and in embryos of the fruit fly Drosophila melanogaster. This provides a framework for future studies addressing the suitability of inks for in vivo 3D manufacturing. Our platform bears great potential for the direct engineering of the intricate microarchitectures in a variety of tissues in model organisms and beyond.

bioengineering↗

Energetics and kinetics of membrane permeation of photoresists for bioprinting

Three-dimensional (3D) bioprinting is a promising technology which typically uses bioinks to pattern cells and their scaffolds. The selection of cytocompatible inks is critical for the printing success. In laserbased 3D bioprinting, photoresist molecules are used as bioinks. We propose that cytotoxicity can be a consequence of the interaction of photoresists with lipid membranes and their permeation into the cell. Here, molecular dynamics simulations and in vitro assays address this issue, retrieving partition coefficients, free energies, and permeabilities for eight commonly-used photoresists in model lipid bilayers. Crossing the hydrophobic center of the membrane constitutes the rate limiting step during permeation. In addition, three photoresists feature a preferential localization site at the acyl chain headgroup interface. Photoresist permeabilities range over eight orders of magnitude, with some molecules being membrane-permeable on bioprinting timescales. Moreover, permeation correlates well with the oil-water partition coefficients and is severely hampered by the lipid ordering imposed by the lipid saturation. Overall, the mechanism of interaction of photoresists with model lipid bilayers is provided here, helping to classify them according to their residence in the membrane and permeation through it. This is useful information to guide the selection of cytocompatible photoresists for 3D bioprinting.

biophysics↗

Effects of early life stress on bone homeostasis in mice and humans

Bone pathology is frequent in stressed individuals. A comprehensive examination of mechanisms linking life stress, depression and disturbed bone homeostasis is missing. In this translational study, mice exposed to early life stress (MSUS) were examined on bone microarchitecture (CT), metabolism (qPCR), and neuronal stress mediator expression (qPCR) and contrasted with a sample of depressive patients with or without early life stress by analyzing bone mineral density [BMD] (DXA) and metabolic changes in serum (osteocalcin, PINP, CTX-I). MSUS mice showed a significant decrease in NGF, NPYR1, VIPR1 and TACR1 expression, higher innervation density in bone and increased serum levels of CTX-I, suggesting a milieu in favor of catabolic bone turnover. MSUS mice had a significantly lower body weight compared to control mice, and this caused minor effects on bone micro-CT. Depressive patients with experiences of childhood neglect also showed a catabolic pattern. A significant reduction in BMD was observed in depressive patients with childhood abuse and stressful life events during childhood. Therefore, future studies on prevention and treatment strategies for both mental and bone disease should consider early life stress as a risk factor for bone pathologies.

physiology↗