A model of filamentous cyanobacteria leading to reticulate pattern formation.

The filamentous cyanobacterium, Pseudanabaena, has been shown to produce reticulate patterns that are thought to be the result of its gliding motility. Similar fossilized structures found in the geological record constitute some of the earliest signs of life on Earth. It is difficult to tie these fossils, which are billions of years old, directly to the specific microorganisms that built them. Identifying the physicochemical conditions and microorganism properties that lead microbial mats to form macroscopic structures can lead to a better understanding of the conditions on Earth at the dawn of life. In this article, a cell-based model is used to simulate the formation of reticulate patterns in cultures of Pseudanabaena. A minimal system of long and flexible trichomes capable of gliding motility is shown to be sufficient to produce stable patterns consisting of a network of streams. Varying model parameters indicate that systems with little to no cohesion, high trichome density and persistent movement are conducive to reticulate pattern formation, in conformance with experimental observations.

Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure.

Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display photomovement, by which a trichome modulates its gliding according to the incident light. The latter has been found to play an important role in guiding the trichomes to optimal lighting conditions, which can either inhibit the cells if the incident light is too weak, or damage the cells if too strong. We have developed a computational model for gliding filamentous photophobic cyanobacteria that allows us to perform simulations on the scale of a Petri dish using over 10(5) individual trichomes. Using the model, we quantify the effectiveness of one commonly observed photomovement strategy--photophobic responses--in distributing large populations of trichomes optimally over a light field. The model predicts that the typical observed length and gliding speeds of filamentous cyanobacteria are optimal for the photophobic strategy. Therefore, our results suggest that not just photomovement but also the trichome shape itself improves the ability of the cyanobacteria to optimize their light exposure.

A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering.

The gastrulation of Nematostella vectensis, the starlet sea anemone, is morphologically simple yet involves many conserved cell behaviors such as apical constriction, invagination, bottle cell formation, cell migration and zippering found during gastrulation in a wide range of more morphologically complex animals. In this article we study Nematostella gastrulation using a combination of morphometrics and computational modeling. Through this analysis we frame gastrulation as a non-trivial problem, in which two distinct cell domains must change shape to match each other geometrically, while maintaining the integrity of the embryo. Using a detailed cell-based model capable of representing arbitrary cell-shapes such as bottle cells, as well as filopodia, localized adhesion and constriction, we are able to simulate gastrulation and associate emergent macroscopic changes in embryo shape to individual cell behaviors. We have developed a number of testable hypotheses based on the model. First, we hypothesize that the blastomeres need to be stiffer at their apical ends, relative to the rest of the cell perimeter, in order to be able to hold their wedge shape and the dimensions of the blastula, regardless of whether the blastula is sealed or leaky. We also postulate that bottle cells are a consequence of cell strain and low cell-cell adhesion, and can be produced within an epithelium even without apical constriction. Finally, we postulate that apical constriction, filopodia and de-epithelialization are necessary and sufficient for gastrulation based on parameter variation studies.