Quantification of social motility indicates different colony growth phases.

colonies of the flagellated parasite exhibit characteristic fingering instability patterns. To enable data-driven and data-validated mechanistic modelling of these complex growth processes, it is crucial to first establish appropriate quantitative metrics beyond qualitative image comparisons. We present a quantification approach based on two scale-free metrics designed to characterize the shape of two-dimensional colonies.

Aggregation of adult parasitic nematodes in sex-mixed groups analysed by transient anomalous diffusion formalism.

Intestinal parasitic worms are widespread throughout the world, causing chronic infections in humans and animals. However, very little is known about the locomotion of the worms in the host gut. We studied the movement of naturally infecting mice, and used as an animal model for roundworm infections.

Inference of alveolar capillary network connectivity from blood flow dynamics.

The intricate lung structure is crucial for gas exchange within the alveolar region. Despite extensive research, questions remain about the connection between capillaries and the vascular tree. We propose a computational approach combining three-dimensional (3-D) morphological modeling with computational fluid dynamics simulations to explore alveolar capillary network connectivity based on blood flow dynamics.

The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors.

Embryos develop in a concerted sequence of spatiotemporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analyzed so far.

Recognition and reconstruction of cell differentiation patterns with deep learning.

Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell communication to replicate common spatial arrangements like checkerboard and engulfing patterns.

Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing.

During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular signaling. We present an analytically tractable mathematical model based on signaling that reliably generates different cell type patterns with specified proportions.

Tissues as networks of cells: towards generative rules of complex organ development.

Network analysis is a well-known and powerful tool in molecular biology. More recently, it has been introduced in developmental biology. Tissues can be readily translated into spatial networks such that cells are represented by nodes and intercellular connections by edges.

Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus.

In interdisciplinary fields such as systems biology, good communication between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data.

Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach.

During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first decision, the trophectoderm and the inner cell mass are formed. Subsequently, the inner cell mass segregates into the epiblast and the primitive endoderm.

The transition from local to global patterns governs the differentiation of mouse blastocysts.

During mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterized by the expression of the transcription factors NANOG and GATA6, respectively. Here, we investigate the spatio-temporal distribution of NANOG and GATA6 expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single cell-based neighbourhood analyses.

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering.

During mammalian preimplantation, cells of the inner cell mass (ICM) adopt either an embryonic or an extraembryonic fate. This process is tightly regulated in space and time and has been studied previously in mouse embryos and embryonic stem cell models. Current research suggests that cell fates are arranged in a salt-and-pepper pattern of random cell positioning or a spatially alternating pattern.

The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.

A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS).

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields.

Contractile and mechanical properties of epithelia with perturbed actomyosin dynamics.

Mechanics has an important role during morphogenesis, both in the generation of forces driving cell shape changes and in determining the effective material properties of cells and tissues. Drosophila dorsal closure has emerged as a reference model system for investigating the interplay between tissue mechanics and cellular activity. During dorsal closure, the amnioserosa generates one of the major forces that drive closure through the apical contraction of its constituent cells.

Comparative Study of the Use of a Suturing System and Titanium Clips.

There is a need for secure and easy methods for suturing in laparoscopic surgery, no matter whether vessels are to be ligated, two structures sutured together, or the cystic duct is to be occluded in cholecystectomy. Laparoscopic suturing can be done with a suture, using automatic sewing devices or clips. Improper ligation of a vessel for example can result in bleeding, which is more difficult to treat in a laparoscopic procedure than in an open procedure.