Biology subjects

Fischer, S. C.

Publications and source records attributed to Fischer, S. C..

10 recordsLinked to original sources

bioRxiv2026

Dynamic coupling of cell fate specification and cell sorting during mouse preimplantation development

During preimplantation development in mice, cells of the inner cell mass undergo a cell fate decision to become either Epiblast (Epi) or Primitive Endoderm (PrE) cells. Cell fate patterns during this stage range from an alternating pattern at the beginning to the separation of Epi and PrE at the end. Several mechanisms guiding this decision and pattern formation have been proposed, including intra- and intercellular signalling, cell division and cell sorting. The current understanding is that signalling generates the cell fates and subsequent sorting introduces the spatial cell fate separation. We used agent-based modelling to investigate whether cell differentiation and cell sorting can act concurrently and how their relative contributions to pattern formation may change over time. Comparing our model to experimental data for mouse blastocysts and ICM organoids, we find two mechanistic regimes that can produce the experimentally observed spatial separation: (i) simultaneous long-range intercellular signalling and cell sorting, and (ii) a gradual transition from short-range signalling to cell sorting, in which the timing is mediated via reducing cell fate plasticity. While the second agrees better with existing experimental evidence for late blastocysts, the first might still be relevant for early and mid blastocysts. Together, our results refine the sequential view of Epi/PrE patterning by showing that fate specification and cell sorting can be dynamically coupled, with their relative contributions changing over the course of blastocyst development.

developmental biology↗

bioRxiv2025

An agent-based model of Trypanosoma brucei social motility to explore determinants of colony pattern formation

In vitro colonies of the unicellular parasite Trypanosoma brucei expand radially and establish fingering instabilities, a collective behavior known as social motility. The underlying mechanisms are thought to involve single-cell motility, chemical communication among cells, and mechanical interactions with the liquid boundary, but their relative contributions remain unclear. We aimed to determine which of the mechanisms are necessary to quantitatively reproduce the morphological characteristics of social motility. We developed a two-dimensional agent-based model that simulates colonies of 105 - 106 cells at single-cell resolution--two to four orders of magnitude larger than previous models. Cells are represented as point particles executing directional random walks with auto-chemotactic alignment, combined with reflective and mutable boundaries and exponential colony growth. The model was quantitatively evaluated by applying our previously established morphology metrics. We show quantitative agreement of the simulation results and experimental data in terms of colony morphology. Parameter exploration revealed that finger formation arises within a narrow range of trypanosome motility parameters that balance stochasticity and alignment, while boundary conditions modulate the speed of colony expansion. The diffusion coefficient of the chemotactic signal is the key determinant of pattern formation. Realistic behavior occurs at 2x 10-11 - 10-10 m2/s which corresponds to molecules of 12.1-1690 kDa. These results demonstrate that complex colony morphologies can emerge from minimal cell-level rules, suggesting testable hypotheses for the molecular drivers of trypanosome social motility. Furthermore, our approach provides a framework for dissecting the interplay between motility, signaling, and mechanical confinement in other microbial systems exhibiting collective behavior. Author summaryIn vitro colonies of the unicellular parasite Trypanosoma brucei expand radially and form finger-like patterns, a behavior known as social motility. The ability of trypanosomes to exhibit social motility has been linked to their successful journey through their insect vector, the tsetse fly, which facilitates their survival and spreading between hosts. However, the mechanisms driving this behavior are not yet clear. Experimental data suggest that the movement and growth of individual cells, their interactions with each other, and their effects on colony boundaries may all play a role. These different factors are difficult to separate in experiments. We employed mathematical modeling to investigate the relative importance of these factors and developed a model that represents individual cells. The simulations reproduced finger formation patterns similar to those observed in experiments. The results show that complex colony shapes can emerge from simple cell behaviors. We also found that the speed at which a signaling chemical spreads between cells is crucial, and that the predicted values do not match the properties of the chemicals that have been proposed so far. Identifying and testing candidate signaling molecules in experiments could be the next step. Additionally, our approach may also aid in understanding collective behaviors in other microorganisms.

biophysics↗

bioRxiv2025

Wnt/β-catenin signalling assists cell fate decision making in the early mouse embryo

Cell fate choice is a key event happening during preimplantation mouse development. From embryonic day 3.5 (E3.5) to E4.5, the inner cell mass (ICM) differentiates into epiblast (Epi, NANOG expressing cells) and primitive endoderm (PrE, GATA6, SOX17 and/or GATA4 expressing cells). The mechanism by which ICM cells differentiate into Epi cells and PrE cells remains partially unknown. FGF/ERK has been proposed as the main signalling pathway for this event, but it does not explain co-expression of NANOG and GAT6 or how the cell fate choice is initiated. In this study, we investigate whether Wnt/{beta}-catenin signalling also plays a role. To this end, we use two in vitro models based on inducible GATA6 expression: one in 2D, and another in 3D, namely ICM organoids. By combining these in vitro models with in vivo mouse embryos, chemical and classical genetics, and quantitative 3D immunofluorescence analyses, we propose a dual role for Wnt/{beta}-catenin signalling. We find that {beta}-catenin, acting alongside FGF/ERK signalling, helps to guide the cell fate choice towards PrE. Additionally, by regulating GATA6 and GATA4 stability, {beta}-catenin further facilitates this choice. To summarise, we observe that pathway activation promotes PrE differentiation, while its inhibition stalls it. SUMMARY STATEMENTWnt/{beta}-catenin signalling promotes PrE fate in mouse preimplantation embryos.

developmental biology↗

bioRxiv2025

Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in-situ sequencing (mudRapp-seq)

Influenza A viruses (IAV) contain eight negative-sense single-stranded viral RNA (vRNA) molecules, which are transcribed into mRNA and replicated via complementary RNA (cRNA). These processes are tightly regulated, but the precise molecular mechanisms governing the switch from transcription to replication remain elusive. Here, we introduce multiple direct-RNA assisted padlock probing in combination with in situ sequencing (mudRapp-seq) to visualize the transcription and replication of all eight IAV vRNA and mRNA molecules at the single-cell level. We demonstrate that direct RNA padlock probing is three times more efficient than conventional probes that target cDNA. Individual probes showed variations in efficiency, partly due to the RNA structure of the target, which was mitigated by employing multiple padlock probes per target. Applying mudRapp-seq to an infection time course, we observed early mRNA expression, followed by vRNA accumulation approximately 3 hours later. Individual viral segments exhibited differential expression, particularly in the mRNA population. Both bulk and single-cell analyses revealed a correlation between the expression of M mRNA and the onset of the transcription-to-replication switch. Our findings demonstrate that mudRapp-seq offers significant potential for elucidating viral replication mechanisms and may be applicable to studying other RNA viruses and cellular RNA processes.

microbiology↗

bioRxiv2024

Quantification of Trypanosoma Brucei social motilityindicates different colony growth phases

In vitro colonies of the flagellated parasite Trypanosoma brucei grow in characteristic fingering instability patterns. The underlying cause of this this type of collective migration and the associated behavior called social motility remains a topic of intense debate in the scientific community. In order to study these mechanisms in detail, it is crucial to develop quantitative methods to assess and measure social motility patterns at the level of the whole colony beyond qualitative image comparisons. Here, we show a quantification of the growth process based on two scale free metrics designed to quantify the shape of two-dimensional colonies. While initially developed for yeast colonies, we adapted, modified and extended the analysis pipeline for the Trypanosoma system. Combining the quantitative measurements with colony growth simulations based on the Eden model, we discovered two distinct growth phases in social motility showing colonies: In the first phase, the colonies shown mainly circular expansion and later switch to an almost exclusive finger growing phase. These phases are robust when increasing the number of cells as well as upon partial inhibition of the finger formation. A newly developed anisotropy index shows that upon partial inhibition the anisotropy in the colony increases over time. Our results provide objective measurements that help advance the understanding of social motility of trypanosomes. Furthermore, our approach is suitable as a blueprint for investigations of other colony forming cells such as yeast or bacteria.

biophysics↗

bioRxiv2024

Anomalous diffusion analysis reveals cooperative locomotion of adult parasitic nematodes in sex-mixed groups.

Parasitic worms are widespread throughout the world and causing agents of chronic infections in humans and animals. The majority of these pathogens parasitize the gut of the infected hosts, however very little is known about the locomotion of the worms dwelling the gut. We studied the movement of Heligmosomoides bakeri (previously Heligmosomoides polygyrus), a natural infection of mice and usually used as animal model to study the roundworm infections. We investigated the locomotion of H. bakeri in simplified environments mimicking key physical features of the intestinal lumen, i.e. various medium viscosities, and a periodical intestinal villi topography. The non-periodical nematode motion in these settings could be described by anomalous diffusion theory. Fascinatingly, an oriented, super-diffusive locomotion of nematodes in sex-mixed groups were detected, in the sense of a cooperative, but not collective (swarm-like) migration stimulated by mating and reproduction, while individual nematodes moved randomly, following a diffusive motion regime. High mucus-like medium viscosity and villi topography, representing physical constraints of nematode locomotion, slowed down but did not prevent this cooperative migration. Additionally, the mean displacement rate of nematodes in sex-mixed groups of 6{middle dot}10-4 mm/s in viscous mucus-like medium are in good agreement with estimates of nematode migration velocities between 10-4 to 10-3 mm/s in the gut. Thus, our data indicate the intestinal nematodes motion to be non-periodic and random but triggered to be oriented by kin of the different sex.

biophysics↗

bioRxiv2024

Inference of alveolar capillary network connectivity from blood flow dynamics

The intricate structure of the lungs is essential for the gas exchange within the alveolar region. Despite extensive research on the pulmonary vasculature, there are still unresolved questions regarding the connection between capillaries and the vascular tree. A major challenge is obtaining comprehensive experimental data that integrates morphological and physiological aspects. We propose a computational approach that combines data-driven 3D morphological modeling with computational fluid dynamics simulations. This method enables investigating the connectivity of the alveolar capillary network with the vascular tree based on the dynamics of blood flow. We developed 3D sheet-flow models to accurately represent the morphology of the alveolar capillary network and conducted computational fluid dynamics simulations to predict flow velocities and pressure distributions. Our approach focuses on leveraging functional features to identify the most plausible architecture of the system. For given capillary flow velocities and arteriole-to-venule pressure drops, we deduce details about arteriole connectivity. Preliminary connectivity analyses for non-human species indicate that their alveolar capillary network of a single alveolus is linked to at least two arterioles with diameters of 20 {micro}m or a single arteriole with a minimum diameter of 30 {micro}m. Our study provides insights into the structure of the pulmonary microvasculature by evaluating blood flow dynamics. This inverse approach represents a new strategy to exploit the intricate relationship between morphology and physiology, applicable to other tissues and organs. In the future, the availability of experimental data will play a pivotal role in validating and refining the hypotheses analyzed with our computational models. New and noteworthyThe alveolus is pivotal for gas exchange. Due to its complex morphology and dynamic nature, structural experimental studies are challenging. Computational modeling offers an alternative. We developed a databased 3D model of the alveolar capillary network and performed blood flow simulations within it. Choosing a novel perspective, we inferred structure from function. We systematically varied properties of vessels connected to our capillary network and compared simulation results with experimental data to obtain plausible vessel configurations.

physiology↗

bioRxiv2021

Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus

In interdisciplinary fields such as systems biology, close collaboration 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. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest. We defined a new spatio-temporal model for gas exchange in the human alveolus and implemented it in an interactive simulation software named Alvin. In Alvin, the course of the simulation can be traced in a three-dimensional rendering of an alveolus and dynamic plots. The user can interact by configuring essential model parameters. Alvin allows to run and compare multiple simulation instances simultaneously. The mathematical model was developed with the aim of visualization and the simulation software was engineered based on a requirements analysis. Our work resulted in an integrative gas exchange model and an interactive application that exceed the current standards. We exemplified the use of Alvin for research by identifying unknown dependencies in published experimental data. Employing a detailed questionnaire, we showed the benefits of Alvin for education. We postulate that interactive, visual simulation of theoretical models, as we have implemented with Alvin on respiratory processes in the alveolus, can be of great help for communication between specialists and thereby advancing research.

bioinformatics↗

bioRxiv2019

Cell Fate Clusters in ICM Organoids Arise from Cell Fate Heredity & Division - a Modeling Approach

During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first cell fate decision, cells become either part of an outer trophectoderm or part of the inner cell mass. Subsequently, the inner cell mass (ICM) segregates into an embryonic and an extraembryonic lineage, giving rise to the epiblast and the primitive endoderm, respectively. Inner cell mass organoids represent an experimental model system for preimplantation development, mimicking the second cell fate decision taking place in in vivo mouse embryos. In a previous study, the spatial pattern of the different cell lineage types was investigated. The study revealed that cells of the same fate tend to cluster stronger than expected for purely random cell fate decisions. Three major processes are hypothesised to contribute to the final cell fate arrangements at the mid and late blastocysts or 24 h old and 48 h old ICM organoids, respectively: 1) intra- and intercellular chemical signalling; 2) a cell sorting process; 3) cell proliferation. In order to quantify the influence of cell proliferation on the emergence of the observed cell lineage type clustering behaviour, we developed an agent-based model. Hereby, cells are mechanically interacting with direct neighbours, and exert adhesion and repulsion forces. The model was applied to compare several current assumptions of how inner cell mass neighbourhood structures are generated. We tested how different assumptions regarding cell fate switches affect the observed neighbourhood relationships. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. The model further shows that the observed neighbourhood structures can emerge due to cell fate heredity during cell division and allows the inference of a time point for the cell fate decision. STATEMENT OF SIGNIFICANCECell fate decisions in early embryogenesis have been considered random events, causing a random cell fate distribution. Using an agent-based mathematical model, fitted to ICM organoid data, we show that the assumed random distribution of cell fates occurs only for a short time interval, as cell fate heredity and cell division quickly lead to spatial cell fate clustering. Our results show that neighbourhood clustering can emerge without specific neighbourhood interactions affecting the cell fate decision. The approach indicates four consecutive phases of early development: 1) co-expression of cell fate markers, 2) cell fate decision, 3) division and local cell fate clustering, and 4) phase separation, whereby only the phases 1-3 occur in ICM organoids during the first 24h of growth.

systems biology↗

bioRxiv2017

Three-dimensional cell neighbourhood impacts differentiation in the inner mass cells of the mouse blastocyst

During mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterised by the transcription factors NANOG and GATA6, respectively. Here, we present quantitative three-dimensional single cell-based neighbourhood analyses to investigate the spatial distribution of NANOG and GATA6 expression in the ICM of the mouse blastocyst. The cell neighbourhood is characterised by the expression levels of the fate markers in the surrounding cells, together with the number of surrounding cells and cell position. We find that cell neighbourhoods are established in early blastocysts and different for cells expressing different levels of NANOG and GATA6. Highest NANOG expressing cells occupy specific positions within the ICM and are surrounded by 9 neighbours, while GATA6 expressing cells cluster according to their GATA6 levels. The analysis of mutants reveals that NANOG local neighbourhood is regulated by GATA6.\n\nSummary statementThree-dimensional cell neighbourhood, which includes fate marker levels, number of neighbouring cells and cell position, determines cell fate decision in early mouse embryos.

developmental biology↗