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HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways_CAL27_RNAseq_Control

RNA-seq data from CAL27 cells 3 days after transfection with one of three control non-targeting siRNAs. The transfection was performed in triplicate and analyzed with paired-end reads. See DOI: 10.5281/zenodo.7839102 for the CAL27 siHAPSTR1 dataset. See DOI: 10.5281/zenodo.7839096 for the CAL27 siHUWE1 dataset.

HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways_CAL27_RNAseq_siHAPSTR1

RNA-seq data from CAL27 cells transfected with one of three siRNAs targeting human HAPSTR1. Each transfection was performed in triplicate and analyzed with paired-end reads. See DOI:10.5281/zenodo.7839090 for the CAL27 siControl dataset. See DOI: 10.5281/zenodo.7839096 for the CAL27 siHUWE1 dataset.

Dataset for Optimal reactive nitrogen control pathways identified for cost-effective PM2.5 mitigation in Europe

This folder includes six folders: The "Nr anthropogenic emissions" folder includes the anthropogenic Nr emissions used in the baseline simulations for January, April, July, and October 2015. The "Concentration" folder includes daily surface ammonia (NH3), nitric acid (HNO3), nitrate (NO3-), ammonium (NH4+), sulfate (SO42-), and fine particulate matter (PM2.5) concentrations for January, April, July, and October 2015 from WRF-Chem simulations (one BASE simulation and twelve sensitivity simulations as stated in Method). The "N-share" folder includes the N-share caused by anthropogenic Nr (NH3 and NOx)/ NH3/NOx emissions in 2015. The "Health" folder includes the PM2.5-related premature deaths from WRF-Chem combined with GEMM simulations in 2015.  The "Instant efficiency" folder includes the instant efficiency of Nr/ NH3/NOx emission controls from WRF-Chem simulations in 2015.  The "G ratio" folder includes the G ratio from WRF-Chem simulations for the year 2015 and the indicator months (January, April, July, and October).  For any questions, please contact Zehui Liu Email: liuzh18@pku.edu.cn

Simulation Data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"

Molecular dynamics simulation data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"

opencc-zeroMay 2023View details →

Data from: Rotavirus NSP1 subverts the antiviral oligoadenylate synthetase-RNase L pathway by inducing RNase L degradation

<div>The interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway plays a critical role in antiviral immunity. Group A rotaviruses, including the simian SA11 strain, inhibit this pathway through two activities: an E3-ligase related activity of NSP1 that degrades proteins necessary for IFN signaling, and a phosphodiesterase (PDE) activity of VP3 that hydrolyzes the RNase L-activator 2′,5′-oligoadenylate. Unexpectedly, we found that a recombinant (r) SA11 double mutant virus deficient in both activities (rSA11-VP3H797R-NSP1ΔC17) retained the ability to prevent RNase L activation. Mass spectrometry led to the discovery that NSP1 interacts with RNase L in rSA11-infected HT29 cells. This interaction was confirmed through copulldown assay of cells transiently expressing NSP1 and RNase L. Immunoblot analysis showed that infection with wild-type rSA11 virus, rSA11-VP3H797R-NSP1ΔC17 double mutant virus, or single mutant forms of the latter virus all resulted in the depletion of endogenous RNase L. The loss of RNase L was reversed by addition of the neddylation inhibitor MLN4924, but not the proteasome inhibitor MG132. Analysis of additional mutant forms of rSA11 showed that RNase L degradation no longer occurred when either the N-terminal RING domain of NSP1 was mutated or the C-terminal 98 amino acids of NSP1 were deleted. The C-terminal RNase L degradation domain is positioned upstream and is functionally independent of the NSP1 domain necessary for inhibiting IFN expression. Our studies reveal a new role for NSP1 and its E3-ligase related activity as an antagonist of RNase L and uncover a novel virus-mediated strategy of inhibiting the OAS-RNase L pathway.</div>

opencc-by-4.0Jun 2023View details →

Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1

Raw experimental data for the manuscript entitled 'Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1'. This includes the data underlying all figures, DESeq2 files, modeling and MD simulations, and chemical compound characterization (NMR, LC-MS, HRMS). Also, the custom Matlab script to analyse cilium intensity from microscopy images is included (cilia-track_v4.0).

opencc-by-4.0Dec 2022View details →

Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways

Mass spectrometry-based proteomics source data.

opencc-by-4.0Jun 2023View details →

Deep decarbonisation pathways of the energy system in times of unprecedented uncertainty in the energy sector. Energy Policy (2023). Supplementary Information on Assumptions and Results

This dataset supplements the article with the title "Deep decarbonisation pathways of the energy system in times of unprecedented uncertainty in the energy sector", published in Energy Policy.  The dataset contains the following: <ul> <li>The Latin Hypercube Sample of the multipliers that are applied to the key input parameters of ETSAP-TIAM in order to generate 1000 different states of the world regarding economic and demographic growth, energy resources potentials, energy technology costs, climate sensitivity and radiative forcing, LULUCF CO2 sink potential, CO2 sequestration potential, and decoupling between energy consumption and economic development. The multipliers are sampled from the underlying probability distributions described in the article. </li> <li>The results (at the global scale) from four scenario families for each one of the 1000 wofld states. These scenario families are: <ul> <li>BASE_SSP2: Describes the development of the global energy system consistent with recent trends and policies.</li> <li>2C_SSP2: Introduces to the BASE_SSP2 scenario a global constraint of 2 °C as the maximum post-industrial temperature change from 2020 to 2100.</li> <li>2C_SSP2_DA30: Delayed climate action. The climate change mitigation policies of 2C_SSP2 start in 2030. </li> <li>1p5c_OS_SSP2: Introduces to the BASE_SSP2 scenario a global constraint of 1.5 °C as the maximum post-industrial temperature change from 2020 onwards to 2100</li> </ul> </li> </ul> Key results included in the dataset are: Temperature change,  Radiative Forcing, GHG concentrations, CO2 emissions, Marginal abatement cost, Electricity Supply Primary Energy Consumption, and Annual Total Global Energy System Cost. The dataset also includes sectoral results regarding energy consumption and use, such as shares of different electric uses, shares of hydrogen consumption in end-use sectors, hydrogen supply, Demand electrification by sector, Renewable energy consumption by sector, Alternative fuels consumption in transport, and Total final energy consumption by sector.

opencc-by-4.0Jul 2023View details →

Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models

GraphPad Prism files containing source data for figures included in the manuscript "Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models", by Dwidar et al., published in mBio.

opencc-zeroAug 2023View details →

Early onset of urea synthesis and ammonia detoxification pathways in three terrestrially developing frogs

Frogs evolved terrestrial development multiple times, necessitating mechanisms to avoid ammonia toxicity at early stages. Urea synthesis from ammonia is a key adaptation that reduces water dependence after metamorphosis. We tested for early expression and plasticity of enzymatic mechanisms of ammonia detoxification in three terrestrial-breeding frogs: foam-nest-dwelling larvae of Leptodactylus fragilis (Lf) and arboreal embryos of Hyalinobatrachium fleischmanni (Hf) and Agalychnis callidryas (Ac). Activity of two ornithine-urea cycle (OUC) enzymes, arginase and CPSase 1, and levels of their products urea and CP in tissues were high in Lf regardless of nest hydration but reduced in experimental low- vs. high-ammonia environments. High OUC activity in wet and dry nests, comparable to that under experimental high ammonia, suggests terrestrial Lf larvae maintain high capacity for urea excretion regardless of their immediate risk of ammonia toxicity. This may aid survival through unpredictably long waiting periods before rain enables their transition to water. Moderate levels of urea and CP were present in Hf and Ac tissues and enzymatic activities were lower than in Lf. In both species, embryos in drying clutches can hatch and enter the water early, behaviorally avoiding ammonia toxicity. Moreover, glutamine synthetase is active in early stages of all three species, condensing ammonia and glutamate to glutamine as another mechanism of detoxification. Enzyme activity appeared highest in Lf, although substrate and product levels were higher in Ac and Lf. Our results reveal that multiple biochemical mechanisms of ammonia detoxification occur in early life stages of anuran lineages that evolved terrestrial development.

opencc-by-4.0Aug 2023View details →

Simplified Preservation of Equal Pathways Solid Element

The files contain the raw data of the experiments shown in the article: "Simple Preservation of Equal Pathways Solid Element".

opencc-by-4.0Aug 2023View details →

C. intestinalis larval behavior dataset with perturbations of neurotransmitter and neuromodulator pathways

C. intestinalis larval behavior dataset with perturbations of neurotransmitter and neuromodulator pathways

opencc-zeroAug 2023View details →

Net-zero 1.5 °C sectorial pathways for G20 countries: energy and emissions data to inform science-based decarbonization targets

This data for global, regional (EU-27), and country-specific (G20 member countries) energy and emission pathways required to achieve a defined carbon budget of under 450 Gt/CO2, developed to limit the mean global temperature rise to 1.5°C, over 50% likelihood. The data were calculated with the 1.5°C sectorial pathways of the One Earth Climate Model—an integrated energy assessment model devised at the University of Technology Sydney (UTS). The data consist of the following six zip-folder datasets (refer to Section 2 for an explanation of the data): 1. Appendix folder: Each file contains one worksheet, which summarizes the overall 1.5°C scenario. 2. Sector folder (XLSX): Each file contains one worksheet, which summarizes the industry sectors analysed. 3. Sector folder (CSV): The data contained are the same as those described in point 2. 4. Sector emissions folder: Each file contains one worksheet, which summarizes the total annual emissions for each industry sector. 5. Scope emissions folder (XLSX): Each file contains one worksheet, which summarizes the total annual emissions for each industry sector—with the additional specificity of emission scope. 6. Scope emissions folder (CSV): The data contained are the same as those described in point 5.

Numerical Output for Analysis of Atlantic Water Pathways in Fram Strait

This dataset contains data for the publication: Shifts of the Recirculation Pathways in central Fram Strait drive Atlantic Intermediate Water Variability on Northeast Greenland shelf (McPherson et al., JGR Oceans).

opencc-zeroSep 2023View details →

Data from: Hydroxymethylbutenyl diphosphate accumulation reveals MEP pathway regulation for high CO2-induced suppression of isoprene emission

Isoprene is emitted by some plants and is the most abundant biogenic hydrocarbon entering the atmosphere. Multiple studies have elucidated protective roles of isoprene against several environmental stresses, including high temperature, excessive ozone, and herbivory attack. However, isoprene emission adversely affects atmospheric chemistry by contributing to ozone production and aerosol formation. Thus, understanding the regulation of isoprene emission in response to varying environmental conditions, for example elevated CO2, is critical to comprehend how plants will respond to climate change. Isoprene emission decreases with increasing CO2 concentration; however, the underlying mechanism of this response is currently unknown. We demonstrated that high-CO2-mediated suppression of isoprene emission is independent of photosynthesis and light intensity, but it is reduced with increasing temperature. Furthermore, we measured methylerythritol 4-phosphate pathway metabolites in poplar leaves harvested at ambient and high CO2 to identify why isoprene emission is reduced under high CO2. We found that hydroxymethylbutenyl diphosphate (HMBDP) was increased and dimethylallyl diphosphate (DMADP) decreased at high CO2. This implies that high CO2 impeded the conversion of HMBDP to DMADP, possibly through the inhibition of HMBDP reductase activity, resulting in reduced isoprene emission. We further demonstrated that although this phenomenon appears similar to ABA-dependent stomatal regulation, it is unrelated as abscisic acid treatment did not alter the effect of elevated CO2 on the suppression of isoprene emission. Thus, this study provides a comprehensive understanding of the regulation of the MEP pathway and isoprene emission in the face of increasing CO2.

Lunar ejecta origin of near-Earth asteroid Kamo`oalewa is compatible with rare orbital pathways

Outcomes of numerical simulations for orbital elements and collisional states of test particles launched from the surface of the Moon as described by: Castro-Cisneros, Malhotra, Rosengren (2023). Lunar ejecta origin of near-Earth asteroid Kamo`oalewa is compatible with rare orbital pathways. Accepted for publication in Communications Earth & Environment.

opencc-zeroSep 2023View details →

Dietary shifts increase the feasibility of 1.5°C pathways

A transition to healthy diets like the EAT-Lancet Planetary Health Diet could considerably reduce GHG emissions. However, the specific contributions of dietary shifts for the feasibility of 1.5°C pathways remain unclear. Here, we use the open-source Integrated Assessment Modeling (IAM) framework REMIND-MAgPIE to compare 1.5°C pathways with and without dietary shifts. We find that a flexitarian diet increases the feasibility of the Paris Agreement climate goals in different ways: The reduction of GHG emissions related to dietary shifts, especially methane from ruminant enteric fermentation, increases the 1.5°C-compatible carbon budget. Therefore, dietary shifts allow us to achieve the same climate outcome with less carbon dioxide removal (CDR) and less stringent CO2 emission reductions in the energy system, which reduces pressure on GHG prices, energy prices and food expenditures. This dataset provides raw data for all figures shown in the paper. It includes data for three scenarios: SSP2-NDC, SSP2-1.5°C and SSP2-1.5°C-DietShift. All data is at global level and for the period 2020-2100. Raw data for each figure panel is provided on individual data sheets in a single .xlsx file. The structure of the data is identical on each sheet, organized in columns for model, scenario, region, variable, unit, year and value.

Data for: Sources, pathways and behaviour of cave air CO2 using carbon isotopes

Raw data for all figures in the manuscript by Krajnc et al. to be published by Geochimica et Cosmochimica Acta as "Sources, pathways and behaviour of cave air CO2 using carbon isotopes".

Pathway enrichment of 5 chronic pain types

Pathway enrichment analysis was performed on the phenotypes investigated in our study: chronic neck, back, hip and knee pain and chronic headaches. The VEGAS2Pathway tool was used.