Synchronization of growth and self-organizing digit pattern by WNT signaling [ChIPseq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE275782 | GEO | 2024/08/30
REPOSITORIES: GEO
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Molecular analysis of the spatio-temporal dynamics of destabilization and self-reorganization underscore the crucial role of WNT and BMP signaling modulators as part of the Turing system.
2024-08-30 | GSE275783 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-08-28 | GSE275784 | GEO
Project description:Synchronization of growth and self-organizing digit pattern by WNT signaling [ChIPseq]
| PRJNA1152980 | ENA
Project description:Synchronization of growth and self-organizing digit pattern by WNT signaling
| PRJNA1152963 | ENA
Project description:Synchronization of growth and self-organizing digit pattern by WNT signaling [RNAseq]
| PRJNA1152978 | ENA
Project description:In this study we have utilized an optical clearing method to allow visualization of a heretofore undescribed subpleural acinar structural organization in the mammalian lung. The clearing method enables visualization of the lung structure deep below the visceral pleura in intact inflated lungs. In addition to confirming previous observations that the immediate subpleural alveoli are uniform in appearance, we document for the first time that the subpleural lung parenchyma is much more uniformly organized than the internal parenchyma. Specifically, we report that below the surface layer of alveoli, there is a striking parallel arrangement of alveolar ducts that all run perpendicular to the visceral pleural surface. A three dimensional visualization of alveolar ducts allowed for a calculation of the average inner to outer duct diameter ratio of 0.53 in these subpleural ducts. This unique, self-organizing parallel duct structure likely impacts both elastic recoil and the transmission of tethering forces in healthy and diseased lungs.
| S-EPMC7035422 | biostudies-literature
Project description:This study is devoted to the development of photonic patterns based on polystyrene spheres (PSS) incorporated in chitosan hydrogels by inkjet printing. Using this method, high-resolution encrypted images that became visible only in high humidity were obtained. Inks based on PSS with carboxylic groups on the surface were made, and their rheological parameters (viscosity, surface tension, and ζ-potential) were optimized according to the Ohnesorge theory. The obtained value of the ζ-potential indicated the stability of the synthesized colloidal inks. The dependences of the printing parameters on the concentration of ethylene glycol in PSS dispersion, the drop spacing, the shape of the printed pattern, waveform, the temperature of the printing process, and the degree of ordering of the PSS-based photonic crystal were investigated. The scanning electronic microscope (SEM) images confirmed that the optimal self-organization of PSS was achieved at the following values of 0.4% weight fraction (wt%) carboxylic groups, the drop spacing of 50 μm, and the temperature of the printing table of 25 °C. High-resolution microstructures were obtained by drop-on-demand printing with a deposited drophead diameter of 21 μm and an accuracy of ±2 μm on silicon and glass substrates. The deposition of chitosan-based hydrogels on the obtained polystyrene photonic crystals allowed reversibly changing the order of the diffraction lattice of the photonic crystal during the swelling of the hydrogel matrix, which led to a quick optical response in the daylight. The kinetics of the appearance of the optical response of the obtained coating were discussed. The simplicity of production, the speed of image appearance, and the ability to create high-resolution patterns determine the potential applications of the proposed systems as humidity sensors or anticounterfeiting coatings.
| S-EPMC7466399 | biostudies-literature
Project description:Species in nature are typically mobile over diverse distance scales, examples of which range from bacteria run to long-distance animal migrations. These behaviors can have a significant impact on biodiversity. Addressing the role of migration in biodiversity microscopically is fundamental but remains a challenging problem in interdisciplinary science. We incorporate both intra- and inter-patch migrations in stochastic games of cyclic competitions and find that the interplay between the migrations at the local and global scales can lead to robust species coexistence characterized dynamically by the occurrence of remarkable target-wave patterns in the absence of any external control. The waves can emerge from either mixed populations or isolated species in different patches, regardless of the size and the location of the migration target. We also find that, even in a single-species system, target waves can arise from rare mutations, leading to an outbreak of biodiversity. A surprising phenomenon is that target waves in different patches can exhibit synchronization and time-delayed synchronization, where the latter potentially enables the prediction of future evolutionary dynamics. We provide a physical theory based on the spatiotemporal organization of the target waves to explain the synchronization phenomena. We also investigate the basins of coexistence and extinction to establish the robustness of biodiversity through migrations. Our results are relevant to issues of general and broader interest such as pattern formation, control in excitable systems, and the origin of order arising from self-organization in social and natural systems.
| S-EPMC3654227 | biostudies-literature
Project description:MotivationChIPseq is rapidly becoming a common technique for investigating protein-DNA interactions. However, results from individual experiments provide a limited understanding of chromatin structure, as various chromatin factors cooperate in complex ways to orchestrate transcription. In order to quantify chromtain interactions, it is thus necessary to devise a robust similarity metric applicable to ChIPseq data. Unfortunately, moving past simple overlap calculations to give statistically rigorous comparisons of ChIPseq datasets often involves arbitrary choices of distance metrics, with significance being estimated by computationally intensive permutation tests whose statistical power may be sensitive to non-biological experimental and post-processing variation.ResultsWe show that it is in fact possible to compare ChIPseq datasets through the efficient computation of exact P-values for proximity. Our method is insensitive to non-biological variation in datasets such as peak width, and can rigorously model peak location biases by evaluating similarity conditioned on a restricted set of genomic regions (such as mappable genome or promoter regions). Applying our method to the well-studied dataset of Chen et al. (2008), we elucidate novel interactions which conform well with our biological understanding. By comparing ChIPseq data in an asymmetric way, we are able to observe clear interaction differences between cofactors such as p300 and factors that bind DNA directly.AvailabilitySource code is available for download at http://sonorus.princeton.edu/IntervalStats/IntervalStats.tar.gz.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC3339511 | biostudies-literature
Project description:Surface-attached microbial communities constitute a vast amount of life on our planet. They contribute to all major biogeochemical cycles, provide essential services to our society and environment, and have important effects on human health and disease. They typically consist of different interacting genotypes that arrange themselves non-randomly across space (referred to hereafter as spatial self-organization). While spatial self-organization is important for the functioning, ecology, and evolution of these communities, the underlying determinants of spatial self-organization remain unclear. Here, we performed a combination of experiments, statistical modeling, and mathematical simulations with a synthetic cross-feeding microbial community consisting of two isogenic strains. We found that two different patterns of spatial self-organization emerged at the same length and time scales, thus demonstrating pattern diversification. This pattern diversification was not caused by initial environmental heterogeneity or by genetic heterogeneity within populations. Instead, it was caused by nongenetic heterogeneity within populations, and we provide evidence that the source of this nongenetic heterogeneity is local differences in the initial spatial positionings of individuals. We further demonstrate that the different patterns exhibit different community-level properties; namely, they have different expansion speeds. Together, our results demonstrate that pattern diversification can emerge in the absence of initial environmental heterogeneity or genetic heterogeneity within populations and can affect community-level properties, thus providing novel insights into the causes and consequences of microbial spatial self-organization.
| S-EPMC8319339 | biostudies-literature