Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A cellular basis for the mammalian nocturnal-diurnal switch

ABSTRACT: Mammalian colonization of daytime niches accelerated after the Cretaceous-Paleogene extinction. Diurnality subsequently evolved multiple times independently, but underlying mechanisms remain unclear. We identified a conserved cell-intrinsic signal inversion that may have facilitated transitions from nocturnality to diurnality. Diurnal and nocturnal mammalian cells respond oppositely to temperature and osmotic cycles, mirroring species’ activity patterns. Cells exhibited differential global responses to temperature changes, including the phosphoproteome and protein synthesis. Differences in mechanistic Target of Rapamycin (mTOR) signaling contribute to the inversion, with diurnal mammals evolutionarily converging on modifications to mTOR and With-no-lysine (WNK) kinase pathways. Treatments that reduced mTOR activity induced nocturnal-to-diurnal shifting at cellular, tissue, and organismal levels. Therefore, mTOR signaling integrates energetic state with environmental signals to help tune physiology to different temporal niches.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Skin, Fibroblast

SUBMITTER: Sew Peak-Chew

LAB HEAD: John S. O’Neill

PROVIDER: PXD067660 | Pride | 2026-03-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CRM5913_TMT16_MS2_phos_HS_F1.raw	Raw
	CRM5913_TMT16_MS2_phos_HS_F10.raw	Raw
	CRM5913_TMT16_MS2_phos_HS_F11.raw	Raw
	CRM5913_TMT16_MS2_phos_HS_F12.raw	Raw
	CRM5913_TMT16_MS2_phos_HS_F13.raw	Raw

Items per page:

1 - 5 of 70

Similar Datasets

Potential blood biomarkers for chronic traumatic encephalopathy: the multi-omics landscape of an observational cohort (serum exosomes miRNA microarray data)

Project description:Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts, which is susceptible in elderly people with declined mobility, athletes of full contact sports, military personnel and victims of domestic violence. It has been pathologically diagnosed in brain donors with a history of repetitive mild traumatic brain injury (rmTBI), but cannot be clinically diagnosed for a long time. By the continuous efforts by neuropathologists, neurologists and neuroscientists in recent 10 years, an expert consensus for the diagnostic framework of CTE was proposed in 2021 funded by the National Institute of Neurological Disorders and Stroke. The new consensus contributes to facilitating research in the field. However, it still needs to incorporate in-vivo biomarkers to further refine and validate the clinical diagnostic criteria. From this, a single-center, observational cohort study has been being conducted by Tianjin Medical University General Hospital since 2021. As a pilot study of this clinical trial, the present research recruited 4 pairs of gender- and age-matched rmTBI patients with healthy subjects. Their blood samples were collected for exosome isolation, and multi-omics screening to explore potential diagnostic biomarkers in blood and its exosomes.

2022-10-18 | E-MTAB-12329 | biostudies-arrayexpress

Potential blood biomarkers for chronic traumatic encephalopathy: the multi-omics landscape of an observational cohort (serum-free RNA microarray data)

2022-10-18 | E-MTAB-12330 | biostudies-arrayexpress

Potential blood biomarkers for chronic traumatic encephalopathy: the multi-omics landscape of an observational cohort (serum exosomes RNA microarray data)

2022-10-18 | E-MTAB-12331 | biostudies-arrayexpress

Macromolecular condensation buffers intracellular water potential

Project description:Optimum protein function and biochemical activity critically depends on water availability, because solvent thermodynamics drive protein folding and macromolecular interactions. Reciprocally, macromolecules restrict the movement of “structured” water molecules within their hydration layers, reducing the available “free” bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Within concentrated macromolecular solutions like the cytosol, we found modest changes in temperature greatly impact the water potential, and are counteracted by opposing changes in osmotic strength. Remarkably, this duality of temperature and osmotic strength allows simple manipulations of solvent thermodynamics to prevent cell death upon extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength that impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales, so we postulated the existence of a rapid compensatory response. We find this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically-disordered proteins. Formation or dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which in consequence is robustly buffered in the cytoplasm. Our results indicate biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function.

2023-09-22 | PXD044481 | Pride

Development of a SIN1 targeting inhibitor as a novel therapeutic approach for the treatment of malignancies

Project description:We have developed a novel mTOR pathway inhibitor via targeting SIN1. We used multiple proteomics analyses to determine mechanism of action of our novel Sin1 inhibitor and compare to other mTOR pathway inhibitors.

2026-01-26 | PXD040952 | Pride

Regulated biogenesis and targeting of monotopic squalene monooxygenase requires the GET pathway

Project description:This study investigated get3 mutant yeast cell. Proteins of the GET pathway are involved in targeting of C-terminally anchored transmembrane proteins and protection against lipotoxicity. Get3 cells revealed an altered ergosterol production and susceptibility towards a sterol synthesis inhibiting drug terbinafine. Furthermore, we identified a member of a non-canonical GET pathway client, a monotopic membrane protein squalene monooxygenase Erg1 that may be responsible for the susceptibility of Get3 mutant to lipotoxic agents.

2022-06-09 | PXD027705 | Pride

Circadian regulation of macromolecular complex turnover and proteome renewal

Project description:Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome- wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

2024-05-16 | PXD049176 | Pride

mTORC2-NDRG1-Cdc42 axis couples fasting to mitochondrial fission

Project description:Fasting triggers diverse physiological adaptations including increases in circulating fatty acids and mitochondrial respiration to facilitate organismal survival. The mechanisms driving mitochondrial adaptations and respiratory sufficiency during fasting remain incompletely understood. Here we show that fasting or lipid availability stimulates mTORC2 activity. Activation of mTORC2 and phosphorylation of its downstream target NDRG1 at Ser336 sustains mitochondrial fission and respiratory sufficiency. Timelapse imaging shows that NDRG1, but not phosphorylation-deficient NDRG1Ser336Ala mutant, engages with mitochondria to facilitate fission in both control and Drp1-deficient cells, reflecting independency from Drp1. Using proteomics, an siRNA screen, and epistasis experiments, we show that mTORC2-phosphorylated NDRG1 cooperates with small GTPase Cdc42 and effectors and regulators of Cdc42 to orchestrate fission. Accordingly, RictorKO, NDRG1Ser336Ala mutants, and Cdc42-deficient cells each display mitochondrial phenotypes reminiscent of fission failure. During nutrient surplus, mTOR complexes perform anabolic functions; however, paradoxical reactivation of mTORC2 during fasting unexpectedly drives mitochondrial fission and respiration.

2023-04-27 | PXD041696 | Pride

Development of gene expression profiles for pearl oyster Pinctada fucata exposed in near-future ocean warming and acidification.

Project description:To elucidate how does the gene expression profiles of whole transcriptome of P.fucata response to acute and gradual seawater acidification and warming, and which genes or functional gene clusters are involved in the stress response to enviromental stressors, we have employed microarray as a tool to identify genes in these stress. For acute temperature and acidity stress treatment, oysters were added into the tanks immediately with the maintaining conditions of temperature 25M-BM-11 M-BM-0C and 31M-BM-11 M-BM-0C, acidity pH7.8M-BM-10.05 and pH7.5M-BM-10.05, salinity 33M-BM-11M-bM-^@M-0 in recirculating seawater. The temperatures and pH values in the studies were near future levels and predicted for 2100 and 2300. The pallial zone of mantle were collected and preserved on the hours of 72 after treatment for subsequent studies. All the collected mantles above were snap-frozen in liquid nitrogen, and stored at -80M-BM-0C. The conditions of salinity 33M-BM-11M-bM-^@M-0, 19M-BM-11 M-BM-0C and pH8.1M-BM-10.05 (~380 ppm CO2) in pre-culture tanks was as a control. In total, 15 mantle tissue samples from 15 individuals were used for the microarray analysis and 3 samples were used as control .Three biological replicates were employed in each treatment.

2014-05-02 | E-GEOD-57171 | biostudies-arrayexpress

Comparative genomic hybridization by array of east haploid and heterozygous essential deletion pools treated with compounds synergistic with fluconazole to identify sensitive and resistant mutants

Project description:The haploid and the heterozygous essential S.cerevisiae deletion pools were grown in the presence of compounds that we found to be synergistic with fluconazole. We also treated the deletion pools with combinations of those drugs and fluconazole to interrogate the mechanism of action of the drug interactions. These experimental samples were hybridized against DMSO or water control samples. The resulting hybridization pattern informs about sensitive and resistant yeast deletion mutants.

2011-09-07 | E-MTAB-394 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data