Similar Datasets
Project description:A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.
| S-EPMC11654995 | biostudies-literature
Project description:Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
2023-11-28 | GSE201858 | GEO
Project description:Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.
2023-11-28 | GSE201857 | GEO
Project description:Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.
2023-11-28 | GSE201855 | GEO
Project description:Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.
2023-12-21 | GSE251694 | GEO
Project description:Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.
2023-12-21 | GSE251695 | GEO
Project description:Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a cell slice. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics and spatial omics technologies.
| S-EPMC10555842 | biostudies-literature
Project description:Acetylcholine (ACh) is critical in controlling epithelial ion transport and hence water movements for gut hydration. Here we review the mechanism of cholinergic control of epithelial ion transport across the mammalian intestine. The cholinergic nervous system affects basal ion flux and can evoke increased active ion transport events. Most studies rely on measuring increases in short-circuit current (ISC = active ion transport) evoked by adding ACh or cholinomimetics to intestinal tissue mounted in Ussing chambers. Despite subtle species and gut regional differences, most data indicate that, under normal circumstances, the effect of ACh on intestinal ion transport is mainly an increase in Cl- secretion due to interaction with epithelial M3 muscarinic ACh receptors (mAChRs) and, to a lesser extent, neuronal M1 mAChRs; however, AChR pharmacology has been plagued by a lack of good receptor subtype-selective compounds. Mice lacking M3 mAChRs display intact cholinergically-mediated intestinal ion transport, suggesting a possible compensatory mechanism. Inflamed tissues often display perturbations in the enteric cholinergic system and reduced intestinal ion transport responses to cholinomimetics. The mechanism(s) underlying this hyporesponsiveness are not fully defined. Inflammation-evoked loss of mAChR-mediated control of epithelial ion transport in the mouse reveals a role for neuronal nicotinic AChRs, representing a hitherto unappreciated braking system to limit ACh-evoked Cl- secretion. We suggest that: i) pharmacological analyses should be supported by the use of more selective compounds and supplemented with molecular biology techniques targeting specific ACh receptors and signalling molecules, and ii) assessment of ion transport in normal tissue must be complemented with investigations of tissues from patients or animals with intestinal disease to reveal control mechanisms that may go undetected by focusing on healthy tissue only.
| S-EPMC2014671 | biostudies-other
Project description:Colorectal cancers (CRCs) are composed of an amalgam of cells with distinct genotypes and phenotypes. Here, we reveal a previously unappreciated heterogeneity in the biosynthetic capacities of CRC cells. We discover that the majority of ribosomal DNA transcription and protein synthesis in CRCs occurs in a limited subset of tumor cells that localize in defined niches. The rest of the tumor cells undergo an irreversible loss of their biosynthetic capacities as a consequence of differentiation. Cancer cells within the biosynthetic domains are characterized by elevated levels of the RNA polymerase I subunit A (POLR1A). Genetic ablation of POLR1A-high cell population imposes an irreversible growth arrest on CRCs. We show that elevated biosynthesis defines stemness in both LGR5+ and LGR5- tumor cells. Therefore, a common architecture in CRCs is a simple cell hierarchy based on the differential capacity to transcribe ribosomal DNA and synthesize proteins.
| S-EPMC9006079 | biostudies-literature
Project description:Saudi Arabia has no permanent lakes or rivers but has wet meadows, which are desert wetlands temporarily formed due to the seasonal rainfall. This work investigates the environmental variables' impact on the vegetation pattern in the desert-wetland ecosystem in Taif highlands. Forty-one stands were randomly selected representing three main habitats (wet meadows, slopes, and terraces) to study their floristic features and vegetation analysis. A total of 142 species were recorded belonging to 111 genera and 45 families in the desert wetlands of Taif Province. About 64.1% were natural plants, while 25.4% were segetal weeds, 7.7% were aquatic plants, and 2.8% were plants that escaped from cultivation. Therophytes dominated over the other life forms, and mono-regional taxa were the dominant chorotype. Multivariate analysis of the recorded plants produced eight vegetation groups; four of them (A: Potamogeton nodosus-Nasturtium officinale, B: Lemna gibba-Leptochloa fusca, C: Typha domingensis- Xanthium strumarium and D: Conyza stricta- Cyperus longus) represented the wet meadows, while two (E: Acacia gerrardii- Commicarpus plumbagineus and H: Osteospermum vaillantii- Eragrostis Pilosa) for slopes and other two (F: Argemone ochroleuca-Cyperus rotundus and G: Pulicaria undulata- Solanum incanum) for the desert terraces. The vegetation zonation was clear, which started from real aquatic species in the wet meadows passing through mixed vegetation in the slopes and ended with proper xerophytic vegetation in the terraces. Conyza stricta- Cyperus longus community had the highest species diversity, while that of Potamogeton nodosus-Nasturtium officinale had the lowest. The principal component analysis indicated that HCO3, NO3, Mg, Cl, Ca, and pH values were the most effective soil variable. The presence of several segetal weeds suggests the alteration of the natural status of the desert-wetland ecosystem, and thus the conservation of these natural habitats becomes urgent.
| S-EPMC8176040 | biostudies-literature