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Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

ABSTRACT: By using transcriptomics, we studied the spatiotemporal transcriptional changes in Escherichia coli biofilm colonies

ORGANISM(S): Escherichia coli

PROVIDER: GSE175768 | GEO | 2021/10/29

REPOSITORIES: GEO

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Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

Project description:Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

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Project description: Not available

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Escherichia coli colony biofilms: Interior vs. Exterior

Project description:Transcriptional profiling of Escherichia coli in the biofilm mode of growth. A comparison of the transcriptional profiles of the biofilm interior and perimeter.

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Surface topography guides morphology and spatial patterning of induced pluripotent stem cell colonies

Project description:The relevance of topographic cues for commitment of induced pluripotent stem cells (iPSCs) is largely unknown. In this study, we demonstrate that groove-ridge structures with a periodicity in the submicrometer range induce elongation of iPSC colonies, guide the orientation of apical actin fibers, and direct the polarity of cell division. Elongation of iPSC colonies impacts also on their intrinsic molecular patterning, which seems to be orchestrated from the rim of the colonies. BMP4-induced differentiation is enhanced in elongated colonies, and the submicron grooves impact on the spatial modulation of YAP activity upon induction with this morphogen. Interestingly, TAZ, a YAP paralog, shows distinct cytoskeletal localization in iPSCs. These findings demonstrate that topography can guide orientation and organization of iPSC colonies, which may affect the interaction between mechanosensors and mechanotransducers in iPSCs. For more information please check; https://cbit.maastrichtuniversity.nl/

2018-10-31 | E-MTAB-7327 | biostudies-arrayexpress

Nanotopography guides morphology and spatial patterning of induced pluripotent stem cell colonies

Project description:The role of topographic cues in controlling commitment of induced pluripotent stem cells (iPSCs) is largely unknown. Here we demonstrate that groove-ridge nanostructures induce the elongation of iPSC colonies, guide the orientation of apical actin fibers and direct the polarity of cell division. Elongation of iPSC colonies impacts also on the intrinsic molecular patterning which seems to be orchestrated starting from the rim of the colonies. We followed the hypothesis that nanotopography directly modulates the transcriptional program of iPSC, further to guiding the overall spatial organization of the colonies. Single iPSC were seeded on flat (PI flat) and nanostructured polyimide (PI 650) and gene expression profiles were analyzed after three days. No significant differences were observed when cells were kept under culture conditions that sustained pluripotency. Then, we analyzed gene expression changes upon two weeks of multi-lineage differentiation. Many genes revealed significant expression changes in the course of differentiation and this was more pronounced on PI flat as compared to PI 650. Comparison of iPSC that were either differentiated on flat or nanostructured biomaterials revealed differential expression of several genes. Noteworthy, among significantly regulated genes, the biggest fold change on PI 650 versus PI flat after differentiation was observed in ANKRD1, which is one of the best readouts of YAP/TAZ activity. Our study suggests that nanotopography impacts on orientation and organization of iPSC colonies and highlight a possible interaction between mechanosensors and mechanotransducers.

2017-09-18 | GSE84848 | GEO

The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

Project description:Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.

2022-08-26 | GSE184603 | GEO

Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry

Project description:This study investigates the metabolism and antibiotic inhibition in Escherichia coli and Bacillus subtilis colonies.

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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (bulk RNA-Seq)

2022-08-26 | GSE160665 | GEO

Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies

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