Cellular automata modeling suggests symmetric stem-cell division, cell death, and cell drift as key mechanisms driving adult spinal cord growth in teleost fish

Probabilistic cellular automata modelling of intercellular interactions in airways: complex pattern formation in patients with chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a highly prevalent lung disease characterized by chronic inflammation and tissue remodeling possibly induced by unusual interactions between fibrocytes and CD8+ T lymphocytes in the peribronchial area. To investigate this phenomenon, we developed a probabilistic cellular automata type model where the two types of cells follow simple local interaction rules taking into account cell death, proliferation, migration and infiltration. We conducted a rigorous mathematical analysis using multiscale experimental data obtained in control and disease conditions to estimate the model's parameters accurately. The simulation of the model is straightforward to implement, and two distinct patterns emerged that we can analyse quantitatively. In particular, we show that the change in fibrocyte density in the COPD condition is mainly the consequence of their infiltration into the lung during exacerbations, suggesting possible explanations for experimental observations in normal and COPD tissue. Our integrated approach that combines a probabilistic cellular automata model and experimental findings will provide further insights into COPD in future studies.

Adult neurogenesis in the central nervous system of teleost fish: from stem cells to function and evolution

Adult neurogenesis, the generation of functional neurons from adult neural stem cells in the central nervous system (CNS), is widespread, and perhaps universal, among vertebrates. This phenomenon is more pronounced in teleost fish than in any other vertebrate taxon. There are up to 100 neurogenic sites in the adult teleost brain. New cells, including neurons and glia, arise from neural stem cells harbored both in neurogenic niches and outside these niches (such as the ependymal layer and parenchyma in the spinal cord, respectively). At least some, but not all, of the stem cells are of astrocytic identity. Aging appears to lead to stem cell attrition in fish that exhibit determinate body growth but not in those with indeterminate growth. At least in some areas of the CNS, the activity of the neural stem cells results in additive neurogenesis or gliogenesis - tissue growth by net addition of cells. Mathematical and computational modeling has identified three factors to be crucial for sustained tissue growth and correct formation of CNS structures: symmetric stem cell division, cell death and cell drift due to population pressure. It is hypothesized that neurogenesis in the CNS is driven by continued growth of corresponding muscle fibers and sensory receptor cells in the periphery to ensure a constant ratio of peripheral versus central elements. This 'numerical matching hypothesis' can explain why neurogenesis has ceased in most parts of the adult CNS during the evolution of mammals, which show determinate growth.

The Neurosphere Simulator: An educational online tool for modeling neural stem cell behavior and tissue growth

Until very recently, distance education, including digital science labs, served a rather small portion of postsecondary students in the United States and many other countries. This situation has, however, dramatically changed in 2020 in the wake of the COVID-19 pandemic, which forced colleges to rapidly transit from face-to-face instructions to online classes. Here, we report the development of an interactive simulator that is freely available on the web (http://neurosphere.cos.northeastern.edu/) for teaching lab classes in developmental biology. This simulator is based on cellular automata models of neural-stem-cell-driven tissue growth in the neurosphere assay. By modifying model parameters, users can explore the role in tissue growth of several developmental mechanisms, such as regulation of mitosis or apoptotic cell death by contact inhibition. Besides providing an instantaneous animation of the simulated development of neurospheres, the Neurosphere Simulator tool offers also the possibility to download data for detailed analysis. The simulator function is complemented by a tutorial that introduces students to computational modeling of developmental processes.

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We developed an interactive neurosphere simulator.

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Simulations are based on cellular automata models of neurosphere growth.

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This educational tool is freely available on the web.

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The simulator can be used for online lab classes in developmental biology.

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Students explore through exercises mechanisms of stem-cell-driven tissue growth.