Dynamical states of self-organised waves in a giant unicellular green alga

Associated manuscript:Afik, Liu and Meyerowitz (2023) : “Macroscopic waves, biological clocks and morphogenesis driven by light in a giant unicellular green alga.” bioRxiv. https://doi.org/10.1101/2023.02.22.529174.AbstractA hallmark of self-organisation in living systems is their capacity to stabilise their own dynamics, often appearing to anticipate and act upon potential outcomes. <i>Caulerpa brachypus </i>is a marine green alga consisting of differentiated organs resembling leaves, stems and roots. While an individual can exceed a metre in size, it is a single multinucleated giant cell. Thus <i>Caulerpa</i> presents the mystery of morphogenesis on macroscopic scales in the absence of cellularization.The experiments reported here reveal self-organised waves of greenness --- chloroplasts --- that propagate throughout the alga in anticipation of the day-night light cycle. Using dynamical systems analysis we show that these waves are coupled to a self-sustained oscillator, and demonstrate their entrainment to light. Under constant conditions light intensity affects the natural period and drives transition to temporal disorder. Moreover, we find distinct morphologies depending on light temporal patterns, suggesting waves of chlorophyll could link biological oscillators to metabolism and morphogenesis in this giant single-celled organism.Suggested setupDownload all files to one folder, and extract the compressed files.Environment setupDownload and install miniforge#mambaforge ; other conda based installations should work as well.Run in command line:<pre><pre>_{mamba update}_-n_base_-c_{conda-forge conda}<br>_{mamba create}_-n_eaDataLab_python₌₃_.10<br>_{mamba activate eaDataLab}<br>_{mamba install}_-n_{eaDataLab jupyterlab}_{# optional : jupyterlab-git}<br>_{mamba install}_-n_{eaDataLab hvplot pandas pyarrow ipympl}_{# optional : zarr dask-image scikit-image scikit-learn napari pytables tabulate python-graphviz} <br>_{mamba install}_-n_{eaDataLab watermark}</pre></pre>init jupyter lab<pre><pre>^{jupyter lab EA_TJBL_EMM_2023_SI_Fig2.ipynb}<br></pre></pre>