Data underlying the publication: "Lateral induction limits the impact of cell connectivity on Notch signaling in arterial walls"

This study extends a previous 1D agent-based model for Notch signaling in arteries to a 2D formulation. This allows investigation of the effects of cell connectivity on the dynamics of arterial Notch signaling and VSMC phenotypes. Notch signaling for VSMCs with 2-6 neighbouring cells was analyzed. Computational results of the 1D and 2D formulations were also compared

Supplementary material from "Mesoscale substrate curvature overrules nanoscale contact guidance to direct bone marrow stromal cell migration"

The intrinsic architecture of biological tissues and of implanted biomaterials provides cells with large-scale geometrical cues. To understand how cells are able to sense and respond to complex structural environments, a deeper insight into the cellular response to multi-scale and conflicting geometrical cues is needed. In this study, we subjected human bone marrow stromal cells (hBMSCs) to mesoscale cylindrical surfaces (diameter 250–5000 µm) and nanoscale collagen fibrils (diameter 100–200 nm) that were aligned perpendicular to the cylinder axis. On flat surfaces and at low substrate curvatures (cylinder diameter d > 1000 µm), cell alignment and migration were governed by the nanoscale collagen fibrils, consistent with the contact guidance effect. With increasing surface curvature (decreasing cylinder diameter, d

Data underlying the publication: YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico

Data belonging to the article "YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico"It contains the MATLAB code used to run all simulations, the fitting algorithms and the code used to obtain all Figures.The study focused on the mechanoresponse of Notch and in turn, that of angiogenesis. We hypothesized that this response could be explained through Notch interactions with mechano-sensitive YAP/TAZ. The modeled implementation was used to also investigate and suggest avenues through which to steer angiogenesis; by cytoskeletal manipulations and heterogeneous stiffness patterns.DOI: https://doi.org/10.1038/s41540-024-00444-

Data underlying the publication: Computationally guided in-vitro vascular growth model reveals causal link between flow oscillations and disorganized neotissue

This repository contains the data and scripts required to reproduce the subfigures of figure 2 of: van Haaften et al 2021 "Computationally guided in-vitro vascular growth model reveals causal link between flow oscillations and disorganized neotissue" related to the computational simulations. More specifically, this repository contains:1) Datasets to visualize the time-averaged wall shear stress (TAWSS), oscillatory shear index (OSI) and the strain (ε) in graft at the venous anastomosis in Paraview. 2) Scripts and data to produce histograms of the time-averaged wall shear stress (TAWSS), oscillatory shear index (OSI) and the strain (ε) in the graft at the venous anastomosis in MATLA

Data underlying the publication: "Shear stress induces expression, intracellular reorganization and enhanced Notch activation potential of Jagged1”

Experimental data describing shear stress-induced effects on endothelial Jagged1. The data underlies the publication "Shear stress induces expression, intracellular reorganization and enhanced Notch activation potential of Jagged1

Microfluidic Models of Metastasis: In vitro approaches to study the tumor microenvironment - supplementary design and video files

Design files of microfluidic and peripheral devices designed in the PhD thesis "Microfluidic Models of Metastasis: In vitro approaches to study the tumor microenvironment" of Jelle J.F. Sleeboom, and 10 experimental videos. A catalogue record of the thesis is available from the Eindhoven University of Technology Library. ISBN: 978-90-386-5104-

Supplementary material from "Initial scaffold thickness affects the emergence of a geometrical and mechanical equilibrium in engineered cardiovascular tissues"

In situ cardiovascular tissue-engineering can potentially address the shortcomings of the current replacement therapies, in particular, their inability to grow and remodel. In native tissues, it is widely accepted that physiological growth and remodelling occurs to maintain a homeostatic mechanical state to conserve its function, regardless of changes in the mechanical environment. A similar homeostatic state should be reached for tissue-engineered (TE) prostheses to ensure proper functioning. For in situ tissue-engineering approaches obtaining such a state greatly relies on the initial scaffold design parameters. In this study, it is investigated if the simple scaffold design parameter initial thickness, influences the emergence of a mechanical and geometrical equilibrium state in in vitro TE constructs, which resemble thin cardiovascular tissues such as heart valves and arteries. Towards this end, two sample groups with different initial thicknesses of myofibroblast-seeded polycarpolactone-bisurea constructs were cultured for three weeks under dynamic loading conditions, while tracking geometrical and mechanical changes temporally using non-destructive ultrasound imaging. A mechanical equilibrium was reached in both groups, although at different magnitudes of the investigated mechanical quantities. Interestingly, a geometrically stable state was only established in the thicker constructs, while the thinner construct’s length continuously increased. This demonstrates that reaching geometrical and mechanical stability in TE constructs is highly dependent on functional scaffold design

Data underlying the publication "Computational characterization of the dish-in-a-dish, a high yield culture platform for endothelial shear stress studies on the orbital shaker"

Computational and experimental data on characterization and optimization of a dish-in-a-dish (DiaD) system for in vitro shear stress studies

Data underlying the publication: "A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarisation in renal epithelial cells"

The data and resulting publication show the role of integrins and Rho-GTPases in the establishment of apical-basal polarization in renal epithelial cells. The dataset contains the code for the 1D computational framework

Optogenetic control of NOTCH1 signaling

Abstract The Notch signaling pathway is a crucial regulator of cell differentiation as well as tissue organization, whose deregulation is linked to the pathogenesis of different diseases. NOTCH1 plays a key role in breast cancer progression by increasing proliferation, maintenance of cancer stem cells, and impairment of cell death. NOTCH1 is a mechanosensitive receptor, where mechanical force is required to activate the proteolytic cleavage and release of the Notch intracellular domain (NICD). We circumvent this limitation by regulating Notch activity by light. To achieve this, we have engineered an optogenetic NOTCH1 receptor (optoNotch) to control the activation of NOTCH1 intracellular domain (N1ICD) and its downstream transcriptional activities. Using optoNotch we confirm that NOTCH1 activation increases cell proliferation in MCF7 and MDA-MB-468 breast cancer cells in 2D and spheroid 3D cultures, although causing distinct cell-type specific migratory phenotypes. Additionally, optoNotch activation induced chemoresistance on the same cell lines. OptoNotch allows the fine-tuning, ligand-independent, regulation of N1ICD activity and thus a better understanding of the spatiotemporal complexity of Notch signaling. Video Abstrac