cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28399830.v2
title: ESRRA (estrogen related receptor, alpha) induces ribosomal protein RPLP1-mediated adaptive hepatic translation during prolonged starvation

description: Protein translation is an energy-intensive ribosome-driven process that is reduced during nutrient scarcity to conserve cellular resources. During prolonged starvation, cells selectively translate specific proteins to enhance their survival (adaptive translation); however, this process is poorly understood. Accordingly, we analyzed protein translation and mRNA transcription by multiple methods <i>in vitro</i> and <i>in vivo</i> to investigate adaptive hepatic translation during starvation. While acute starvation suppressed protein translation in general, proteomic analysis showed that prolonged starvation selectively induced translation of lysosome and autolysosome proteins. Significantly, the expression of the orphan nuclear receptor, ESRRA (estrogen related receptor, alpha) increased during prolonged starvation and served as a master regulator of this adaptive translation by transcriptionally stimulating <i>Rplp1</i> (ribosomal protein lateral stalk subunit P1) gene expression. Overexpression or siRNA knockdown of <i>Esrra in vitro</i> or <i>in vivo</i> led to parallel changes in <i>Rplp1</i> gene expression, lysosome and macroautophagy/autophagy protein translation, and autophagy activity. Remarkably, we have found that ESRRA had dual functions by not only regulating transcription but also controlling adaptive translation via the ESRRA-RPLP1-lysosome-autophagy pathway during prolonged starvation.
DOI: 10.6084/m9.figshare.28399830.v1
title: ESRRA (estrogen related receptor, alpha) induces ribosomal protein RPLP1-mediated adaptive hepatic translation during prolonged starvation

description: Protein translation is an energy-intensive ribosome-driven process that is reduced during nutrient scarcity to conserve cellular resources. During prolonged starvation, cells selectively translate specific proteins to enhance their survival (adaptive translation); however, this process is poorly understood. Accordingly, we analyzed protein translation and mRNA transcription by multiple methods <i>in vitro</i> and <i>in vivo</i> to investigate adaptive hepatic translation during starvation. While acute starvation suppressed protein translation in general, proteomic analysis showed that prolonged starvation selectively induced translation of lysosome and autolysosome proteins. Significantly, the expression of the orphan nuclear receptor, ESRRA (estrogen related receptor, alpha) increased during prolonged starvation and served as a master regulator of this adaptive translation by transcriptionally stimulating <i>Rplp1</i> (ribosomal protein lateral stalk subunit P1) gene expression. Overexpression or siRNA knockdown of <i>Esrra in vitro</i> or <i>in vivo</i> led to parallel changes in <i>Rplp1</i> gene expression, lysosome and macroautophagy/autophagy protein translation, and autophagy activity. Remarkably, we have found that ESRRA had dual functions by not only regulating transcription but also controlling adaptive translation via the ESRRA-RPLP1-lysosome-autophagy pathway during prolonged starvation.
DOI: 10.6084/m9.figshare.28505442
title: A bacterial RING ubiquitin ligase triggering stepwise degradation of BRISC via TOLLIP-mediated selective autophagy manipulates host inflammatory response

description: Numerous bacterial pathogens have evolved tactics to interfere with the host ubiquitination network to evade clearance by the innate immune system. Nevertheless, the subtle antagonism between a bacterial ubiquitinase and a host deubiquitinase, through which they modify their respective targets within a multifaceted network, has yet to be characterized. BRCC3 isopeptidase complex (BRISC) is a newly identified K63-specific deubiquitinase complex that plays a crucial role in cellular signaling pathways such as inflammation. NleG, a type III secretion system (T3SS) effector, contains a conserved RING E3 ubiquitin ligase domain that interacts with host ubiquitination machinery, along with a distinct substrate-recognition domain that targets host proteins. Here, one particular variant, NleG6, was identified as mediating K27- and K29-linked polyubiquitination at residues K89 and K114 of ABRAXAS2/FAM175B, a scaffolding protein within the BRISC complex, leading to its degradation through TOLLIP (toll interacting protein)-mediated selective autophagy. Further investigations elucidated that ABRAXAS2 degradation triggered the subsequent degradation of adjacent BRCC3, which in turn, hindered TNIP1/ABIN1 degradation, ultimately inhibiting NFKB/NF-κB (nuclear factor kappa B)-mediated inflammatory responses. This chain of events offers valuable insights into the NFKB activation by the K63-specific deubiquitinating role of BRISC, unveiling how bacteria manipulate ubiquitin regulation and selective autophagy within the BRISC network to inhibit the host’s inflammatory response and thus dominate a pathogen-host tug-of-war. <b>Abbreviations:</b> 3-MA: 3-methyladenine; A/E: attaching and effacing; ATG7: autophagy related 7; BafA1: bafilomycin A<sub>1</sub>; BNIP3L/Nix: BCL2 interacting protein 3 like; BRISC: BRCC3 isopeptidase complex; Cas9: CRISPR-associated system 9; co-IP: co-immunoprecipitation; CQ: chloroquine; CRISPR: clustered regulatory interspaced short palindromic repeat; DAPI: 4’,6-diamidino2-phenylindole; DMSO: dimethyl sulfoxide; DUB: deubiquitinating enzyme; <i>E. coli</i>: <i>Escherichia coli</i>; EHEC: enterohemorrhagic <i>Escherichia coli</i>; EPEC: enteropathogenic <i>Escherichia coli</i>; GFP: green fluorescent protein; LEE: locus of enterocyte effacement; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MG132: cbz-leu-leu-leucinal; MOI: multiplicity of infection; NBR1: NBR1 autophagy cargo receptor; NC: negative control; NFKB/NF-κB: nuclear factor kappa B; NH<sub>4</sub>Cl: ammonium chloride; OPTN: optineurin; SQSTM1/p62: sequestosome 1; sgRNAs: small guide RNAs; T3SS: type III secretion system; TNF: tumor necrosis factor; TOLLIP: toll interacting protein; TRAF: TNF receptor associated factor; TUBB: tubulin beta class I; WCL: whole cell lysate; WT: wide type.
DOI: 10.6084/m9.figshare.28505442.v1
title: A bacterial RING ubiquitin ligase triggering stepwise degradation of BRISC via TOLLIP-mediated selective autophagy manipulates host inflammatory response

description: Numerous bacterial pathogens have evolved tactics to interfere with the host ubiquitination network to evade clearance by the innate immune system. Nevertheless, the subtle antagonism between a bacterial ubiquitinase and a host deubiquitinase, through which they modify their respective targets within a multifaceted network, has yet to be characterized. BRCC3 isopeptidase complex (BRISC) is a newly identified K63-specific deubiquitinase complex that plays a crucial role in cellular signaling pathways such as inflammation. NleG, a type III secretion system (T3SS) effector, contains a conserved RING E3 ubiquitin ligase domain that interacts with host ubiquitination machinery, along with a distinct substrate-recognition domain that targets host proteins. Here, one particular variant, NleG6, was identified as mediating K27- and K29-linked polyubiquitination at residues K89 and K114 of ABRAXAS2/FAM175B, a scaffolding protein within the BRISC complex, leading to its degradation through TOLLIP (toll interacting protein)-mediated selective autophagy. Further investigations elucidated that ABRAXAS2 degradation triggered the subsequent degradation of adjacent BRCC3, which in turn, hindered TNIP1/ABIN1 degradation, ultimately inhibiting NFKB/NF-κB (nuclear factor kappa B)-mediated inflammatory responses. This chain of events offers valuable insights into the NFKB activation by the K63-specific deubiquitinating role of BRISC, unveiling how bacteria manipulate ubiquitin regulation and selective autophagy within the BRISC network to inhibit the host’s inflammatory response and thus dominate a pathogen-host tug-of-war. <b>Abbreviations:</b> 3-MA: 3-methyladenine; A/E: attaching and effacing; ATG7: autophagy related 7; BafA1: bafilomycin A<sub>1</sub>; BNIP3L/Nix: BCL2 interacting protein 3 like; BRISC: BRCC3 isopeptidase complex; Cas9: CRISPR-associated system 9; co-IP: co-immunoprecipitation; CQ: chloroquine; CRISPR: clustered regulatory interspaced short palindromic repeat; DAPI: 4’,6-diamidino2-phenylindole; DMSO: dimethyl sulfoxide; DUB: deubiquitinating enzyme; <i>E. coli</i>: <i>Escherichia coli</i>; EHEC: enterohemorrhagic <i>Escherichia coli</i>; EPEC: enteropathogenic <i>Escherichia coli</i>; GFP: green fluorescent protein; LEE: locus of enterocyte effacement; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MG132: cbz-leu-leu-leucinal; MOI: multiplicity of infection; NBR1: NBR1 autophagy cargo receptor; NC: negative control; NFKB/NF-κB: nuclear factor kappa B; NH<sub>4</sub>Cl: ammonium chloride; OPTN: optineurin; SQSTM1/p62: sequestosome 1; sgRNAs: small guide RNAs; T3SS: type III secretion system; TNF: tumor necrosis factor; TOLLIP: toll interacting protein; TRAF: TNF receptor associated factor; TUBB: tubulin beta class I; WCL: whole cell lysate; WT: wide type.
DOI: 10.6084/m9.figshare.28399945
title: Heat-shock chaperone HSPB1 mitigates poly-glycine-induced neurodegeneration via restoration of autophagic flux

description: The CGG repeat expansions in the 5’-UTR regions of certain genes have been implicated in various neurodegenerative and muscular disorders. However, the underlying pathogenic mechanisms are not well understood. In this study, we explore the role of the small molecular chaperone HSPB1 in counteracting neurodegeneration induced by poly-glycine (poly-G) aggregates. Employing a reporter system, we demonstrate that CGG repeat expansions within the 5’-UTR of the <i>GIPC1</i> gene produce poly-G proteins, by repeat-associated non-AUG (RAN) translation. Through proximity labeling and subsequent mass spectrometry analysis, we characterize the composition of poly-G insoluble aggregates and reveal that these aggregates sequester key macroautophagy/autophagy receptors, SQSTM1/p62 and TOLLIP. This sequestration disrupts MAP1LC3/LC3 recruitment and impairs autophagosome formation, thereby compromising the autophagic pathway. Importantly, we show that HSPB1 facilitates the dissociation of these receptors from poly-G aggregates and consequently restores autophagic function. Overexpressing HSPB1 alleviates poly-G-induced neurodegeneration in mouse models. Taken together, these findings highlight a mechanistic basis for the neuroprotective effects of HSPB1 and suggest its potential as a therapeutic target in treating poly-G-associated neurodegenerative diseases. <b>Abbreviations</b>: AD: Alzheimer disease; AIF1/Iba1: allograft inflammatory factor 1; Baf A<sub>1</sub>: bafilomycin A<sub>1</sub>; BFP: blue fluorescent protein; CQ: chloroquine; EIF2A/eIF-2α: eukaryotic translation initiation factor 2A; FRAP: fluorescence recovery after photobleaching; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFAP: glial fibrillary acidic protein; GFP: green fluorescent protein; HSPB1: heat shock protein family B (small) member 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; NOTCH2NLC: notch 2 N-terminal like C; PD: Parkinson disease; PFA: paraformaldehyde; poly-A: poly-alanine; poly-G: poly-glycine; poly-R: poly-arginine; RAN translation: repeat-associated non-AUG translation; RBFOX3/NeuN: RNA binding fox-1 homolog 3; STED: stimulated emission depletion; TARDBP/TDP-43: TAR DNA binding protein; TG: thapsigargin; TOLLIP: toll interacting protein
DOI: 10.6084/m9.figshare.28399945.v1
title: Heat-shock chaperone HSPB1 mitigates poly-glycine-induced neurodegeneration via restoration of autophagic flux

description: The CGG repeat expansions in the 5’-UTR regions of certain genes have been implicated in various neurodegenerative and muscular disorders. However, the underlying pathogenic mechanisms are not well understood. In this study, we explore the role of the small molecular chaperone HSPB1 in counteracting neurodegeneration induced by poly-glycine (poly-G) aggregates. Employing a reporter system, we demonstrate that CGG repeat expansions within the 5’-UTR of the <i>GIPC1</i> gene produce poly-G proteins, by repeat-associated non-AUG (RAN) translation. Through proximity labeling and subsequent mass spectrometry analysis, we characterize the composition of poly-G insoluble aggregates and reveal that these aggregates sequester key macroautophagy/autophagy receptors, SQSTM1/p62 and TOLLIP. This sequestration disrupts MAP1LC3/LC3 recruitment and impairs autophagosome formation, thereby compromising the autophagic pathway. Importantly, we show that HSPB1 facilitates the dissociation of these receptors from poly-G aggregates and consequently restores autophagic function. Overexpressing HSPB1 alleviates poly-G-induced neurodegeneration in mouse models. Taken together, these findings highlight a mechanistic basis for the neuroprotective effects of HSPB1 and suggest its potential as a therapeutic target in treating poly-G-associated neurodegenerative diseases. <b>Abbreviations</b>: AD: Alzheimer disease; AIF1/Iba1: allograft inflammatory factor 1; Baf A<sub>1</sub>: bafilomycin A<sub>1</sub>; BFP: blue fluorescent protein; CQ: chloroquine; EIF2A/eIF-2α: eukaryotic translation initiation factor 2A; FRAP: fluorescence recovery after photobleaching; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFAP: glial fibrillary acidic protein; GFP: green fluorescent protein; HSPB1: heat shock protein family B (small) member 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; NOTCH2NLC: notch 2 N-terminal like C; PD: Parkinson disease; PFA: paraformaldehyde; poly-A: poly-alanine; poly-G: poly-glycine; poly-R: poly-arginine; RAN translation: repeat-associated non-AUG translation; RBFOX3/NeuN: RNA binding fox-1 homolog 3; STED: stimulated emission depletion; TARDBP/TDP-43: TAR DNA binding protein; TG: thapsigargin; TOLLIP: toll interacting protein
DOI: 10.6084/m9.figshare.28467238
title: Autophagy induced by mechanical stress sensitizes cells to ferroptosis by NCOA4-FTH1 axis

description: Ferroptosis is an iron-dependent regulated form of cell death implicated in various diseases, including cancers, with its progression influenced by iron-dependent peroxidation of phospholipids and dysregulation of the redox system. Whereas the extracellular matrix of tumors provides mechanical cues influencing tumor initiation and progression, its impact on ferroptosis and its mechanisms remains largely unexplored. In this study, we reveal that heightened mechanical tension sensitizes cells to ferroptosis, whereas decreased mechanics confers resistance. Mechanistically, reduced mechanical tension reduces intracellular free iron levels by enhancing FTH1 protein expression. Additionally, low mechanics significantly diminishes NCOA4, pivotal in mediating FTH1 phase separation-induced ferritinophagy. Targeting NCOA4 effectively rescues ferroptosis susceptibility under low mechanical tension through modulation of FTH1 phase separation-driven autophagy. In conclusion, our findings demonstrate that mechanics regulates iron metabolism via NCOA4-FTH1 phase separation-mediated autophagy, thereby influencing ferroptosis sensitivity and offering promising therapeutic avenues for future exploration. <b>Abbreviations:</b> ACO1: aconitase 1; ATG5: autophagy related 5; DMSO: dimethyl sulfoxide; EGFP: enhanced green fluorescent protein; FACS: fluorescence-activated cell sorting; FER-1: ferrostatin-1; FTH1: ferritin heavy chain 1; FTL: ferritin light chain; GPX4: glutathione peroxidase 4; IR: ionizing radiation; IREB2: iron responsive element binding protein 2; NCOA4: nuclear receptor coactivator 4; NFE2L2: NFE2 like bZIP transcription factor 2; NOPP: norepinephrine; PBS: phosphate-buffered saline; PI: propidium iodide; RSL3: (1S,3 R)-RSL3; TCGA: The Cancer Genome Atlas; WWTR1: WW domain containing transcription regulator 1; YAP1: Yes1 associated transcriptional regulator.
DOI: 10.6084/m9.figshare.28467238.v1
title: Autophagy induced by mechanical stress sensitizes cells to ferroptosis by the NCOA4-FTH1 axis

description: Ferroptosis is an iron-dependent regulated form of cell death implicated in various diseases, including cancers, with its progression influenced by iron-dependent peroxidation of phospholipids and dysregulation of the redox system. Whereas the extracellular matrix of tumors provides mechanical cues influencing tumor initiation and progression, its impact on ferroptosis and its mechanisms remains largely unexplored. In this study, we reveal that heightened mechanical tension sensitizes cells to ferroptosis, whereas decreased mechanics confers resistance. Mechanistically, reduced mechanical tension reduces intracellular free iron levels by enhancing FTH1 protein expression. Additionally, low mechanics significantly diminishes NCOA4, pivotal in mediating FTH1 phase separation-induced ferritinophagy. Targeting NCOA4 effectively rescues ferroptosis susceptibility under low mechanical tension through modulation of FTH1 phase separation-driven autophagy. In conclusion, our findings demonstrate that mechanics regulates iron metabolism via NCOA4-FTH1 phase separation-mediated autophagy, thereby influencing ferroptosis sensitivity and offering promising therapeutic avenues for future exploration.
DOI: 10.6084/m9.figshare.28467238.v2
title: Autophagy induced by mechanical stress sensitizes cells to ferroptosis by NCOA4-FTH1 axis

description: Ferroptosis is an iron-dependent regulated form of cell death implicated in various diseases, including cancers, with its progression influenced by iron-dependent peroxidation of phospholipids and dysregulation of the redox system. Whereas the extracellular matrix of tumors provides mechanical cues influencing tumor initiation and progression, its impact on ferroptosis and its mechanisms remains largely unexplored. In this study, we reveal that heightened mechanical tension sensitizes cells to ferroptosis, whereas decreased mechanics confers resistance. Mechanistically, reduced mechanical tension reduces intracellular free iron levels by enhancing FTH1 protein expression. Additionally, low mechanics significantly diminishes NCOA4, pivotal in mediating FTH1 phase separation-induced ferritinophagy. Targeting NCOA4 effectively rescues ferroptosis susceptibility under low mechanical tension through modulation of FTH1 phase separation-driven autophagy. In conclusion, our findings demonstrate that mechanics regulates iron metabolism via NCOA4-FTH1 phase separation-mediated autophagy, thereby influencing ferroptosis sensitivity and offering promising therapeutic avenues for future exploration. <b>Abbreviations:</b> ACO1: aconitase 1; ATG5: autophagy related 5; DMSO: dimethyl sulfoxide; EGFP: enhanced green fluorescent protein; FACS: fluorescence-activated cell sorting; FER-1: ferrostatin-1; FTH1: ferritin heavy chain 1; FTL: ferritin light chain; GPX4: glutathione peroxidase 4; IR: ionizing radiation; IREB2: iron responsive element binding protein 2; NCOA4: nuclear receptor coactivator 4; NFE2L2: NFE2 like bZIP transcription factor 2; NOPP: norepinephrine; PBS: phosphate-buffered saline; PI: propidium iodide; RSL3: (1S,3 R)-RSL3; TCGA: The Cancer Genome Atlas; WWTR1: WW domain containing transcription regulator 1; YAP1: Yes1 associated transcriptional regulator.
DOI: 10.6084/m9.figshare.28467081
title: Latino Intergenerational Communication and Attitudes Regarding Climate Change

description: Heightened environmental concerns of Latinx communities have been identified by various surveys, contradicting a common misconception that marginalized communities are disinterested in environmental issues. Using the state of Texas as a case study, Mexican-American climate perceptions are analyzed through semi-structured interviews with twenty individuals in Spanish and English. The themes of generation, acculturation, familism, and household finances are found to be prevalent in this segment of Latinx respondents, as ways of articulating perspectives related to climate change. We show how these topics emerge in response to standard questions about climate change, indicating a distinct climate change discourse. This leads to suggestions of specific interventions in how scholars and policy-makers can engage with Latinx climate discourse.
DOI: 10.6084/m9.figshare.28467081.v1
title: Latino Intergenerational Communication and Attitudes Regarding Climate Change

description: Heightened environmental concerns of Latinx communities have been identified by various surveys, contradicting a common misconception that marginalized communities are disinterested in environmental issues. Using the state of Texas as a case study, Mexican-American climate perceptions are analyzed through semi-structured interviews with twenty individuals in Spanish and English. The themes of generation, acculturation, familism, and household finances are found to be prevalent in this segment of Latinx respondents, as ways of articulating perspectives related to climate change. We show how these topics emerge in response to standard questions about climate change, indicating a distinct climate change discourse. This leads to suggestions of specific interventions in how scholars and policy-makers can engage with Latinx climate discourse.
DOI: 10.15468/dl.8uqayv
title: Occurrence Download

description: A dataset containing 1965 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Global caridean shrimp fauna"
 ]
}

 The dataset includes 1965 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002595-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/qjpvyc
title: Archeologisch Bureauonderzoek netversterking Ameland Achtendijk – Slattendijk – Grote Miedenweg – Zuidergrieweg – Oude Grazingweg, gemeente Ameland

description: In opdracht van Qterra B.V. heeft T&A Survey te Amsterdam in april 2025 een archeologisch bureauonderzoek uitgevoerd. Het betreft geplande werkzaamheden op het eiland Ameland.
DOI: 10.25921/xg33-1n83
title: High-resolution coastal acidification monitoring data collected in seven estuaries along the US East Coast, US West Coast and Gulf of Mexico from 2015-04-23 to 2020-07-29 (NCEI Accession 0225225)

description: This dataset includes high-frequency (hourly to sub-hourly) coastal acidification time-series data collected during nine deployments in the aforementioned seven estuaries along the US East Coast, US West Coast and Gulf of Mexico from 2015-04-23 to 2020-07-29. These data include water temperature, salinity, partial pressure of carbon dioxide (pCO2) in water, dissolved oxygen (DO) in water, and pH on the total scale. The instruments used to collected these data include Sunburst SAMI-CO2, Pro-Oceanus CO2-Pro CV and a LiCOr LI-820 CO2 gas analyzers for autonomous pCO2 measurements, Sea-Bird SeapHOx and SeaFET instruments for pH measurements, Sea-Bird SeapHOx and Aanderaa Oxygen Optode instruments for DO measurements, and YSI water sensing instrument packages for measurements of conductivity (salinity), temperature and depth. Beginning in 2015, the U.S. Environmental Protection Agency’s (EPA) National Estuary Program (NEP) started a collaboration with partners in seven estuaries along the East Coast (Barnegat Bay; Casco Bay), West Coast (Santa Monica Bay; San Francisco Bay; Tillamook Bay), and the Gulf of Mexico (GOM) Coast (Tampa Bay; Mission-Aransas Estuary) of the United States to expand the use of autonomous monitoring partial pressure of carbon dioxide (pCO2) and pH sensors to evaluate carbonate chemistry in the estuarine environment.