Dataset Information

Cellular Dialogues: Cell-Cell Communication through Diffusible Molecules Yields Dynamic Spatial Patterns.

ABSTRACT: Cells form spatial patterns by coordinating their gene expressions. How a group of mesoscopic numbers (hundreds to thousands) of cells, without pre-existing morphogen gradients and spatial organization, self-organizes spatial patterns remains poorly understood. Of particular importance are dynamic spatial patterns such as spiral waves that perpetually move and transmit information. We developed an open-source software for simulating a field of cells that communicate by secreting any number of molecules. With this software and a theory, we identified all possible "cellular dialogues"-ways of communicating with two diffusing molecules-that yield diverse dynamic spatial patterns. These patterns emerge despite widely varying responses of cells to the molecules, gene-expression noise, spatial arrangements, and cell movements. A three-stage, "order-fluctuate-settle" process forms dynamic spatial patterns: cells form long-lived whirlpools of wavelets that, following erratic dynamics, settle into a dynamic spatial pattern. Our work helps in identifying gene-regulatory networks that underlie dynamic pattern formations.

SUBMITTER: Dang Y

PROVIDER: S-EPMC6975168 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundDynamical models are instrumental for exploring the way information required to generate robust developmental patterns arises from complex interactions among genetic and non-genetic factors. We address this fundamental issue of developmental biology studying the leaf and root epidermis of Arabidopsis. We propose an experimentally-grounded model of gene regulatory networks (GRNs) that are coupled by protein diffusion and comprise a meta-GRN implemented on cellularised domains.ResultsSteady states of the meta-GRN model correspond to gene expression profiles typical of hair and non-hair epidermal cells. The simulations also render spatial patterns that match the cellular arrangements observed in root and leaf epidermis. As in actual plants, such patterns are robust in the face of diverse perturbations. We validated the model by checking that it also reproduced the patterns of reported mutants. The meta-GRN model shows that interlinked sub-networks contribute redundantly to the formation of robust hair patterns and permits to advance novel and testable predictions regarding the effect of cell shape, signalling pathways and additional gene interactions affecting spatial cell-patterning.ConclusionThe spatial meta-GRN model integrates available experimental data and contributes to further understanding of the Arabidopsis epidermal system. It also provides a systems biology framework to explore the interplay among sub-networks of a GRN, cell-to-cell communication, cell shape and domain traits, which could help understanding of general aspects of patterning processes. For instance, our model suggests that the information needed for cell fate determination emerges from dynamic processes that depend upon molecular components inside and outside differentiating cells, suggesting that the classical distinction of lineage versus positional cell differentiation may be instrumental but rather artificial. It also suggests that interlinkage of nonlinear and redundant sub-networks in larger networks is important for pattern robustness. Pursuing dynamic analyses of larger (genomic) coupled networks is still not possible. A repertoire of well-characterised regulatory modules, like the one presented here, will, however, help to uncover general principles of the patterning-associated networks, as well as the peculiarities that originate diversity.

Project description:Attaining high crop yields and increasing carbon storage in agricultural soils, while avoiding negative environmental impacts on water quality, soil erosion, and biodiversity, requires accurate and precise management of crop inputs and management practices. The long-term analysis of spatial and temporal patterns of crop yields provides insights on how yields vary in a field, with parts of field constantly producing either high yields or low yields and other parts that fluctuate from one year to the next. The concept of yield stability has shown to be informative on how plants translate the effects of environmental conditions (e.g., soil, climate, topography) across the field and over the years in the final yield, and as a valuable layer in developing prescription maps of variable fertilizer rate inputs. Using known relationships between soil health and crop yields, we hypothesize that areas with measured constantly low yield will return low carbon to the soil affecting its heath. On this premises, yield stability zones (YSZ) provide an effective and practical integrative measure of the small-scale variability of soil health on a field relative basis. We tested this hypothesis by measuring various metrics of soil health from commercial farmers' fields in the north central Midwest of the USA in samples replicated across YSZ, using a soil test suite commonly used by producers and stakeholders active in agricultural carbon credits markets. We found that the use of YSZ allowed us to successfully partition field-relative soil organic carbon (SOC) and soil health metrics into statistically distinct regions. Low and stable (LS) yield zones were statistically lower in normalized SOC when compared to high and stable (HS) and unstable (US) yield zones. The drivers of the yield differences within a field are a series of factors ranging from climate, topography and soil. LS zones occur in areas of compacted soil layers or shallow soils (edge of the field) on steeper slopes. The US zones occurring with high water flow accumulation, were more dependent on topography and rainfall. The differences in the components of the overall soil health score (SHS) between these YSZ increased with sample depth suggesting a deeper topsoil in the US and HS zones, driven by the accumulation of water, nutrients, and carbon downslope. Comparison of the field management provided initial evidence that zero tillage reduces the magnitude of the variance in SOC and soil health metrics between the YSZ.

Dataset Information

Cellular Dialogues: Cell-Cell Communication through Diffusible Molecules Yields Dynamic Spatial Patterns.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets