RNA sequencing of chronically damage human colon organoids via Air-liquid interface submergence
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE178698 | GEO | 2021/06/23
REPOSITORIES: GEO
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Project description:RNA sequencing of chronically damage human colon organoids via Air-liquid interface submergence
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2019-12-29 | GSE127172 | GEO
Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence.
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Project description:Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.
2021-09-20 | GSE184340 | GEO
Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5–3 h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.
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Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5�� h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.
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Project description:The Air Liquid Interface Model of Gastric Mucosa allows to provide a fully polarized epithelium accessible to infection experiments with H.pylori. The influence of several factors on immune response has been studied.
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Project description:This SuperSeries is composed of the SubSeries listed below. The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
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