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Jochen Kursawe

Publications and source records attributed to Jochen Kursawe.

2 recordsLinked to original sources

Robust cell tracking in epithelial tissues through identification of maximum common subgraphs

Tracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterising cell growth, proliferation, intercalation and apoptosis in epithelia helps us to understand how morphogenetic processes such as tissue invagination and extension are locally regulated and controlled. Accurate cell tracking requires correctly resolving cells entering or leaving the field of view between frames, cell neighbour exchanges, cell removals and cell divisions. However, current tracking methods for epithelial sheets are not robust to large morphogenetic deformations and require significant manual interventions. Here, we present a novel algorithm for epithelial cell tracking, exploiting the graph-theoretic concept of a maximum common subgraph to track cells between frames of a video. Our algorithm does not require the adjustment of tissue-specific parameters, and scales in sub-quadratic time with tissue size. It does not rely on precise positional information, permitting large cell movements between frames and enabling tracking in datasets acquired at low temporal resolution due to experimental constraints such as photoxicity. To demonstrate the method, we perform tracking on the Drosophila embryonic epidermis and compare cell-cell rearrangements to previous studies in other tissues. Our implementation is open source and generally applicable to epithelial tissues.

Bioengineering

Capabilities and Limitations of Tissue Size Control Through Passive Mechanical Forces

Embryogenesis is an extraordinarily robust process, exhibiting the ability to control tissue size and repair patterning defects in the face of environmental and genetic perturbations. The size and shape of a developing tissue is a function of the number and size of its constituent cells as well as their geometric packing. How these cellular properties are coordinated at the tissue level to ensure developmental robustness remains a mystery; understanding this process requires studying multiple concurrent processes that make up morphogenesis, including the spatial patterning of cell fates and apoptosis, as well as cell intercalations. In this work, we develop a computational model that aims to understand aspects of the robust pattern repair mechanisms of the Drosophila embryonic epidermal tissues. Size control in this system has previously been shown to rely on the regulation of apoptosis rather than proliferation; however, to date little work has been done to understand the role of cellular mechanics in this process. We employ a vertex model of an embryonic segment to test hypotheses about the emergence of this size control. Comparing the model to previously published data across wild type and genetic perturbations, we show that passive mechanical forces suffice to explain the observed size control in the posterior (P) compartment of a segment. However, observed asymmetries in cell death frequencies across the segment are demonstrated to require patterning of cellular properties in the model. Finally, we show that distinct forms of mechanical regulation in the model may be distinguished by differences in cell shapes in the P compartment, as quantified through experimentally accessible summary statistics, as well as by the tissue recoil after laser ablation experiments.\n\nAuthor SummaryDeveloping embryos are able to grow organs of the correct size even in the face of significant external perturbations. Such robust size control is achieved via tissue-level coordination of cell growth, proliferation, death and rearrangement, through mechanisms that are not well understood. Here, we employ computational modelling to test hypotheses of size control in the developing fruit fly. Segments in the surface tissues of the fruit fly embryo have been shown to achieve the same size even if the number of cells in each segment is perturbed genetically. We show that simple mechanical interactions between the cells of this tissue can recapitulate previously gathered data on tissue sizes and cell numbers. However, this simple model does not capture the experimentally observed spatial variation in cell death rates in this tissue, which may be explained through several adaptations to the model. These distinct adaptations may be distinguished through summary statistics of the tissue behaviour, such as statistics of cell shapes or tissue recoil after cutting. This work demonstrates how computational modelling can help investigate the complex mechanical interactions underlying tissue size and shape, which are important for understanding the underlying causes of birth defects and diseases driven by uncontrolled growth.

Developmental Biology