Find research datasets worth reusing

publicOct 2025View details →

Polycomb regulates sleep homeostasis in a specific group of cells in Drosophila brain

Open the record for dataset details and reuse information.

publicApr 2021View details →

Vacuolar sucrose homeostasis is critical for development, seed properties and survival of dark phases of Arabidopsis

Open the record for dataset details and reuse information.

publicJun 2025View details →

Brain-derived exosomal hemoglobin transfer contributes to neuronal mitochondrial homeostasis under hypoxia

Open the record for dataset details and reuse information.

publicMay 2023View details →

Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson’s disease

Open the record for dataset details and reuse information.

publicDec 2022View details →

Lipidomic datasets for: Transmembrane protein 135 regulates lipid homeostasis through its role in peroxisomal DHA metabolism

Open the record for dataset details and reuse information.

publicApr 2025View details →

Hoi1 targets the yeast BLTP2 protein to ER-PM contact sites to regulate lipid homeostasis

Open the record for dataset details and reuse information.

opencc-zeroJul 2020View details →

Data from: Body temperature, heart rate, and activity patterns of two boreal homeotherms in winter: homeostasis, allostasis, and ecological coexistence

<ol> <li>Organisms survive environmental variation by combining homeostatic regulation of critical states with allostatic variation of other traits, and species differences in these responses can contribute to coexistence in temporally-variable environments.</li> <li>In this paper, we simultaneously record variation in three functional traits – body temperature (Tb), heart rate, and activity - in relation to three forms of environmental variation – air temperature (Ta), photoperiod, and experimentally-manipulated resource levels – in free-ranging snowshoe hares and North American red squirrels to characterize distinctions in homeotherm responses to the extreme conditions of northern boreal winters.</li> <li>Hares and squirrels differed in the level and precision of Tb regulation, but also in the allostatic pathways necessary to maintain thermal homeostasis. Hares demonstrated a stronger metabolic pathway (through heart rate variation reflective of the thermogenesis), while squirrels demonstrated a stronger behavioral pathway (through activity variation that minimizes cold exposure).</li> <li>As intermediate-sized, winter-active homeotherms, hares and squirrels share many functional attributes, yet, through the integrated monitoring of multiple functional traits in response to shared environmental variation, our study reveals many pairwise species differences in homeostatic and allostatic traits, that both define and are defined by the natural history, functional niches, and coexistence of sympatric species.</li> </ol>

opencc-zeroSep 2020View details →

Data from: A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.

opencc-zeroOct 2020View details →

Networks of physiological adjustments and defenses, and their synergy with sodium (Na+) homeostasis explain the hidden variation for salinity tolerance across the cultivated Gossypium hirsutum germplasm

The abilities to mobilize and/or sequester excess ions within and outside the plant cell are important components of salt-tolerance mechanisms. Mobilization and sequestration of Na+ involves three transport systems facilitated by the plasma membrane H+/Na+ antiporter (SOS1), vacuolar H+/Na+ antiporter (NHX1), and Na+/K+ transporter in vascular tissues (HKT1). Many of these mechanisms are conserved across the plant kingdom. While Gossypium hirsutum (upland cotton) is significantly more salt-tolerant relative to other crops, the critical factors contributing to the phenotypic variation hidden across the germplasm have not been fully unraveled. In this study, the spatio-temporal patterns of Na+ accumulation along with other physiological and biochemical interactions were investigated at different severities of salinity across a meaningful genetic diversity panel across cultivated upland Gossypium. The aim was to define the importance of holistic or integrated effects relative to the direct effects of Na+ homeostasis mechanisms mediated by GhHKT1, GhSOS1, and GhNHX1. Multi-dimensional physio-morphometric attributes were investigated in a systems-level context using univariate and multivariate statistics, randomForest, and path analysis. Results showed that mobilized or sequestered Na+ contributes significantly to the baseline tolerance mechanisms. However, the observed variance in overall tolerance potential across a meaningful diversity panel were more significantly attributed to antioxidant capacity, maintenance of stomatal conductance, chlorophyll content, and divalent cation (Mg2+) contents other than Ca2+ through a complex interaction with Na+ homeostasis. The multi-tier macro-physiological, biochemical and molecular data generated in this study, and the networks of interactions uncovered strongly suggest that a complex physiological and biochemical synergy beyond the first-line-of defense (Na+ sequestration and mobilization) accounts for the total phenotypic variance across the primary germplasm of Gossypium hirsutum. These findings are consistent with the recently proposed Omnigenic Theory for quantitative traits and should contribute to a modern look at phenotypic selection for salt tolerance in cotton breeding.

opencc-by-4.0Oct 2020View details →

Ionic Homeostasis, Acid-Base Balance and the Risk of Citrate Accumulation in Patients After Cardiovascular Surgery Treated with Continuous Veno-venous Haemofiltration with Post-Dilution Regional Citrate Anticoagulation.

Data sets analyzed and described in the paper: "Ionic Homeostasis, Acid-Base Balance and the Risk of Citrate Accumulation in Patients After Cardiovascular Surgery Treated with Continuous Veno-venous Haemofiltration with Post-Dilution Regional Citrate Anticoagulation."

opencc-zeroDec 2017View details →

Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.

opencc-by-4.0Apr 2024View details →

Proteomics data for "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics"

Proteomics data used to generate results in "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics" as published in Cell Host and Microbe. <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00138-0">Manuscript Link</a>

opencc-zeroMar 2022View details →

Data from: Tree species with conservative foliar nutrient status and strong phosphorus homeostasis are regionally abundant in subtropical forests

Foliar nitrogen (N) or phosphorus (P) status and their stoichiometric homeostasis are integral parts of the plant nutrient economy that determines the success of plant species in environments where N or P limits plant growth. Despite growing evidence for higher predictability of stoichiometric homeostasis of N (HN) than that of P (HP) on plant species abundance in temperate grasslands, no previous studies explicitly examined how foliar N and P status modulate the relationships between stoichiometric homeostasis and species distribution (regional species abundance) of woody plants, especially in P-limited (sub)-tropical ecosystems. We hypothesized that species with a conservative foliar nutrient status but a higher HP (but not HN) would be regional abundant in P-limited forest. We measured foliar N (LNC) and P (LPC) contents of 54 woody species, community composition and soil N and P contents across 94 forest plots in Chinese subtropical forests. Then we evaluated the species' levels of N and P stoichiometric homeostasis and their regional abundance to test our hypotheses. HN and HP significantly increased with decreasing LNC and LPC. Foliar nutrient status positively correlated with the minimum values of both soil N and P contents, but only negatively associated with the maximum value of soil P content, indicating that conservative species can occupy a wider range of soil P- than N-based nutrient niche. Meanwhile, species abundance negatively correlated with LNC and LPC, and positively correlated with HN and HP. However, the structure equation model analysis showed that species abundance increased with decline of LNC but not yet with increased HN. In contrast, species abundance enhanced with increased HP and decreased LPC via HN, rather than directly with a decline of LPC. Synthesis. This study provides empirical evidence that species with conservative foliar nutrient status are more stable in terms of N and P stoichiometric homeostasis, and foliar N and P economy modulate species abundance distribution in different ways. Our results suggest that maintaining strong stoichiometric homeostasis of leaf P, while maintaining conservative economy of N, is a key physiochemical mechanism for shaping species abundance distribution in P-limited forests.

opencc-by-4.0May 2022View details →

Effect of Water Level and Submergence Time on Leaf Growth, Stoichiometry and Homeostasis of Carex brevicuspis

Water level and submergence time are important factors influencing plant growth and plant C:N:P characteristics in freshwater wetlands. However, the effect of their interaction on plant stoichiometry and homeostasis is far from clear. Here, we performed a controlled experiment using four water levels (0, 10, 20, and 40 cm, relative to the soil surface) and under three submergence times (30, 60, and 90 days) with the aim of investigating the changes in plant growth and stoichiometric characteristics, as well as the strength of N, P, and N:P homeostasis in C. brevicuspis in the Dongting Lake, China. Results showed that biomass, density, height, and total carbon (TC) decreased significantly with increasing water level; however, the latter total nitrogen (TN) and total phosphorus (TP) increased significantly. The highest TN and TP were at 40 cm water level, while the highest C:N, C:P, and N:P ratios were at 0 cm water level. Furthermore, significant stoichiometric homeostasis of C. brevicuspis was found for N (HN) and P (HP) except for N:P (HN:P). HN and HP decreased with increasing submergence time, and HN was consistently greater than HP, indicating that C. brevicuspis had a weak ability to maintain its internal P balance under long-term submergence. Therefore, the impact of water level and submergence time on plant growth and stoichiometric characteristics in this study, are applicable to the conservation and management of the wetlands dominated with C. brevicuspis.

opencc-by-4.0Oct 2024View details →

Supplementary Dataset for Membrane lipid homeostasis dually regulates conformational transition of phosphoethanolamine transferase EptA

Open the record for dataset details and reuse information.

opencc-zeroSep 2021View details →

Parasitic cnidarians (Myxozoa) do not retain key oxygen-sensing and homeostasis tool-kit genes: Transcriptome assemblies

For aerobic organisms, both the Hypoxia-Inducible Factor (HIF) pathway and the mitochondrial genomes are key players in regulating oxygen homeostasis. However, recent work has suggested that these mechanisms are not as highly conserved as previously thought, prompting more thorough surveys across animal higher taxonomic levels, which would in turn permit testing of hypotheses about the ecological conditions that may have facilitated evolutionary loss of such genes. The phylum Cnidaria is known to harbor wide variation in mitochondrial genome morphology, from typical single circular chromosomes to fragmented linear chromosomes. More recently, members of the cnidarian clade Myxozoa, comprising obligate endoparasites, were shown to have lost their mitochondrial genome, suggesting that variation in environmental oxygen availability may be a key determinant in the evolution of metabolic gene networks. Here, we surveyed genomes and transcriptomes across 42 cnidarian species for the presence of HIF pathway members (HIFa, EGLN, VHL), as well as for an assortment of hypoxia, mitochondrial, and stress-response toolkit genes. We find that presence of the HIF pathway, as well as number of genes associated with mitochondria, hypoxia, and stress response, do not vary based on mitochondrial genome morphology. More interestingly, we uncover evidence that myxozoans have lost the canonical HIF pathway repression machinery, potentially altering HIF pathway functionality to work under the specific conditions of their parasitic lifestyles. In addition, relative to other cnidarians, myxozoans show loss of large proportions of genes associated with the mitochondrion (~39%), and involved in response to hypoxia (~27.5%) and general stress (~32%). Our results provide additional evidence that the HIF regulatory machinery is evolutionarily labile and that variations in the canonical system have evolved in many animal groups.

opencc-by-4.0Sep 2022View details →

Fatty acids homeostasis during fasting predicts protection from chemotherapy toxicity

Fasting exerts beneficial effects in mice and humans, including protection from chemotherapy toxicity. To explore the involved mechanisms, we collect blood from humans and mice before and after 36 or 24 hours of fasting, respectively, and measure lipid composition of erythrocyte membranes, circulating micro RNAs (miRNAs), and RNA expression at peripheral blood mononuclear cells (PBMCs). Fasting coordinately affects the proportion of polyunsaturated versus saturated and monounsaturated fatty acids at the erythrocyte membrane; and reduces the expression of insulin signaling-related genes in PBMCs. When fasted for 24 hours before and 24 hours after administration of oxaliplatin or doxorubicin, mice show a strong protection from toxicity in several tissues. Erythrocyte membrane lipids and PBMC gene expression define two separate groups of individuals that accurately predict a differential protection from chemotherapy toxicity, with important clinical implications. Our results reveal a mechanism of fasting associated with lipid homeostasis, and provide biomarkers of fasting to predict fasting-mediated protection from chemotherapy toxicity.

opencc-by-4.0Dec 2022View details →

CD4 T cell receptor hierarchies are stable and independent of HIV-mediated dysregulation of immune homeostasis

LT-ART and A5248 folders contain preprocessed CyTOF files (FCS format) from a 31-marker mass cytometry panel to examine all major PBMC lineages and specifically CD4 and CD8 T cell memory dynamics in people with HIV (PWH) who are durably ART suppressed for an average of 6.7 years (LT-ART, n = 10) and PWH in the first 500 days following ART initiation (A5248, n = 10). The panel also includes markers of activation (HLA-DR, CD38, CCR5), activation/exhaustion (PD-1), proliferation (Ki67), survival (Bcl-2) and long-lived memory (CD127). Preprocessed annotated data objects (A5248_subsample.h5ad, LT-ART_subsample.h5ad) for unsupervised analysis can be accessed using the 'read_h5ad' function in Scanpy. CD4_MSI and CD8_MSI folders contain the MSI data for the Gamma fixed-effects regression models.  All source code for reproduction of the results can be found in the GitHub repository: <a href="https://github.com/glab-hiv/immune-recovery">https://github.com/glab-hiv/immune-recovery</a>

opencc-by-4.0Aug 2023View details →

ADAR1 Links R-Loop Homeostasis to ATR Activation in Replication Stress Response

Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.