'Neighbourhood watch' model: embryonic epiblast cells assess positional information in relation to their neighbours.
Ontology highlight
ABSTRACT:
SUBMITTER: Lee HC
PROVIDER: S-EPMC9188750 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Numerous organisms integrate information from multiple sources and express adaptive behaviours, but how they do so at different developmental stages remains to be identified. Seeds, which are the embryonic stage of plants, need to make decisions about the timing of emergence in response to environmental cues related to survival. We investigated the timing of emergence of Plantago asiatica (Plantaginaceae) seed while manipulating the presence of Trifolium repens seed and the relatedness of neighbouring P. asiatica seed. The relatedness of neighbouring P. asiatica seed and the presence of seeds of T. repens did not on their own influence the timing of P. asiatica emergence. However, when encountering a T. repens seed, a P. asiatica seed emerged faster in the presence of a sibling seed than in the presence of a non-sibling seed. Water extracts of seeds gave the same result. We show that P. asiatica seeds integrate information about the relatedness of neighbouring P. asiatica seeds and the presence of seeds of a different species via water-soluble chemicals and adjust their emergence behaviour in response. These findings suggest the presence of kin-dependent interspecific interactions.
| S-EPMC5489730 | biostudies-literature
Project description:The reproducibility and precision of biological patterning is limited by the accuracy with which concentration profiles of morphogen molecules can be established and read out by their targets. We consider four measures of precision for the Bicoid morphogen in the Drosophila embryo: the concentration differences that distinguish neighboring cells, the limits set by the random arrival of Bicoid molecules at their targets (which depends on absolute concentration), the noise in readout of Bicoid by the activation of Hunchback, and the reproducibility of Bicoid concentration at corresponding positions in multiple embryos. We show, through a combination of different experiments, that all of these quantities are approximately 10%. This agreement among different measures of accuracy indicates that the embryo is not faced with noisy input signals and readout mechanisms; rather, the system exerts precise control over absolute concentrations and responds reliably to small concentration differences, approaching the limits set by basic physical principles.
| S-EPMC2253670 | biostudies-literature
Project description:The brain has an extraordinary ability to create an internal spatial map of the external world [1]. This map-like representation of environmental surroundings is encoded through specific types of neurons, located within the hippocampus and entorhinal cortex, which exhibit spatially tuned firing patterns [2, 3]. In addition to encoding space, these neurons are believed to be related to contextual information and memory [4-7]. One class of such cells is the grid cells, which are located within the entorhinal cortex, presubiculum, and parasubiculum [3, 8]. Grid cell firing forms a hexagonal array of firing fields, a pattern that is largely thought to reflect the operation of intrinsic self-motion-related computations [9-12]. If this is the case, then fields should be relatively uniform in size, number of spikes, and peak firing rate. However, it has been suggested that this is not in fact the case [3, 13]. The possibility exists that local spatial information also influences grid cells, which-if true-would greatly change the way in which grid cells are thought to contribute to place coding. Accordingly, we asked how discriminable the individual fields of a given grid cell are by looking at the distribution of field firing rates and reproducibility of this distribution across trials. Grid fields were less uniform in intensity than expected, and the pattern of strong and weak fields was spatially stable and recurred across trials. The distribution remained unchanged even after arena rescaling, but not after remapping. This suggests that additional local information is being overlaid onto the global hexagonal pattern of grid cells.
| S-EPMC5558037 | biostudies-literature
Project description:A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.
| S-EPMC5038966 | biostudies-literature
Project description:We transcriptionally profiled the neuronal types of the zebrafish larvae optic tectum and matched them with their functional and morphological properties.
2024-11-13 | GSE269232 | GEO
Project description:The pluripotent state, which is first established in the primitive ectoderm cells of blastocysts, is lost progressively and irreversibly during subsequent development. For example, development of post-implantation epiblast cells from primitive ectoderm involves significant transcriptional and epigenetic changes, including DNA methylation and X chromosome inactivation, which create a robust epigenetic barrier and prevent their reversion to a primitive-ectoderm-like state. Epiblast cells are refractory to leukaemia inhibitory factor (LIF)-STAT3 signalling, but they respond to activin/basic fibroblast growth factor to form self-renewing epiblast stem cells (EpiSCs), which exhibit essential properties of epiblast cells and that differ from embryonic stem (ES) cells derived from primitive ectoderm. Here we show reprogramming of advanced epiblast cells from embryonic day 5.5-7.5 mouse embryos with uniform expression of N-cadherin and inactive X chromosome to ES-cell-like cells (rESCs) in response to LIF-STAT3 signalling. Cultured epiblast cells overcome the epigenetic barrier progressively as they proceed with the erasure of key properties of epiblast cells, resulting in DNA demethylation, X reactivation and expression of E-cadherin. The accompanying changes in the transcriptome result in a loss of phenotypic and epigenetic memory of epiblast cells. Using this approach, we report reversion of established EpiSCs to rESCs. Moreover, unlike epiblast and EpiSCs, rESCs contribute to somatic tissues and germ cells in chimaeras. Further studies may reveal how signalling-induced epigenetic reprogramming may promote reacquisition of pluripotency.
| S-EPMC3863718 | biostudies-literature
Project description:Habitat selection and dispersal behaviour are key processes in evolutionary ecology. Recent studies have suggested that individuals may use the reproductive performance of conspecifics as a source of public information on breeding patch quality for dispersal decisions, but experimental evidence is still limited for species breeding in aggregates, i.e. colonial species. We addressed this issue by manipulating the local breeding success of marked individuals and that of their neighbours on a series of breeding patches of a colonial seabird, the black-legged kittiwake (Rissa tridactyla). Based on previous observations in this species, we predicted that individuals that lost their eggs on successful patches would attend their nest and come back to it the year after at a higher rate than individuals that lost their eggs on patches where their neighbours were also in failure. As predicted, the attendance of breeders and prospectors was strongly affected by the local level of breeding success, resulting in differential site fidelity and recruitment. This suggests that individuals used information conveyed by conspecific breeding performance to make decisions relative to breeding site selection. This process can amplify the response of these populations to environmental change and may have contributed to the evolution of colonial breeding.
| S-EPMC2610090 | biostudies-literature
Project description:The temporal and stationary behavior of protein modification cascades has been extensively studied, yet little is known about the spatial aspects of signal propagation. We have previously shown that the spatial separation of opposing enzymes, such as a kinase and a phosphatase, creates signaling activity gradients. Here we show under what conditions signals stall in the space or robustly propagate through spatially distributed signaling cascades. Robust signal propagation results in activity gradients with long plateaus, which abruptly decay at successive spatial locations. We derive an approximate analytical solution that relates the maximal amplitude and propagation length of each activation profile with the cascade level, protein diffusivity, and the ratio of the opposing enzyme activities. The control of the spatial signal propagation appears to be very different from the control of transient temporal responses for spatially homogenous cascades. For spatially distributed cascades where activating and deactivating enzymes operate far from saturation, the ratio of the opposing enzyme activities is shown to be a key parameter controlling signal propagation. The signaling gradients characteristic for robust signal propagation exemplify a pattern formation mechanism that generates precise spatial guidance for multiple cellular processes and conveys information about the cell size to the nucleus.
| S-EPMC2654021 | biostudies-literature
Project description:Robust positioning of cells in a tissue against unavoidable noises is important for achieving normal and reproducible morphogenesis. The position in a tissue is represented by morphogen concentrations, and cells read them to recognize their spatial coordinates. From the engineering viewpoint, these positioning processes can be regarded as an information coding. Organisms are conjectured to adopt good coding designs with high reliability for a given number of available morphogen species and their chemical properties. To answer, quantitatively, the questions of how good coding is adopted, and subsequently when, where, and to what extent each morphogen contributes to positioning, we need a way to evaluate the goodness of coding. In this article, by introducing basic concepts of computer science, we mathematically formulate coding processes in morphogen-dependent positioning, and define some key concepts such as encoding, decoding, and positional information and its precision. We demonstrate the best designs for pairs of encoding and decoding rules, and show how those designs can be biologically implemented by using some examples. We also propose a possible procedure of data analysis to validate the coding optimality formulated here.
| S-EPMC3218323 | biostudies-literature
Project description:Injury is a common occurrence in the life of most if not all organisms. Because injury and the extent of damage inflicted are not predictable events, pre-existing tissues must somehow determine how much tissue needs to be restored. It has been known for over a century that amputation position along a proximal-distal (P/D) axis determines the regeneration speed of amputated limbs in regeneration-competent animals1. Yet, it is not clear how an injured limb conveys positional information during regeneration to faithfully restore pre-existing morphologies and functions. Here, we profiled millimetric caudal fins regenerating proximal and distal amputations in the African killifish (Nothobranchius furzeri). We report position-specific, differential modulation of the spatial distribution, duration, and magnitude of proliferation, and the possibility to predict blastema sizes. Regenerating fins profiled by single cell RNA sequencing identified a Transient Regeneration-Activated Cell State (TRACS) enriched in extracellular matrix (ECM) components and modifiers that is proportionally amplified to match a given amputation position. We located this transient cell state to the basal epidermis by gene expression and confocal microscopy, and propose a role for these cells in transducing positional information to the regeneration blastema. Understanding the temporal deployment of regenerative cell states may hold the key to set up a successful regeneration event in organisms with limited regenerative abilities such as humans.
2024-04-01 | GSE260629 | GEO