cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11798499
title: Long-lived mice with reduced growth hormone signaling have a constitutive upregulation of hepatic chaperone-mediated autophagy

description: Chaperone-mediated autophagy (CMA) is the most selective form of lysosomal proteolysis. CMA modulates proteomic organization through selective protein degradation, with targets including metabolic enzymes, cell growth regulators, and neurodegeneration-related proteins. CMA activity is low in <i>ad libitum</i>-fed rodents but is increased by prolonged fasting. AKT negatively regulates CMA at the lysosomal membrane by phosphorylating and inhibiting the CMA regulator GFAP. We have previously reported that long-lived <i>Pou1f1/Pit1</i> mutant (Snell) mice and <i>ghr</i> (growth hormone receptor) knockout mice (<i>ghr</i> KO) have lower AKT activity when fed compared to littermate controls, suggesting the hypothesis that these mice have increased baseline CMA activity. Here, we report that liver lysosomes from fed Snell dwarf mice and <i>ghr</i> KO mice have decreased GFAP phosphorylation and increased CMA substrate uptake activity. Liver lysosomes isolated from fed Snell dwarf mice and <i>ghr</i> KO mice injected with the protease inhibitor leupeptin had increased accumulation of endogenous CMA substrates, compared to littermate controls, suggesting an increase in CMA <i>in vivo</i>. Mice with liver-specific ablation of GH (growth hormone) signaling did not have increased liver CMA, suggesting that a signaling effect resulting from a loss of growth hormone in another tissue causes enhanced CMA in Snell dwarf and <i>ghr</i> KO mice. Finally, we find Snell dwarf mice have decreased protein levels (in liver and kidney) of CIP2A, a well-characterized CMA target protein, without an associated change in <i>Cip2a</i> mRNA. Collectively, these data suggest that CMA is enhanced downstream of an endocrine change resulting from whole-body ablation of GH signaling. <b>Abbreviations:</b> CMA: chaperone-mediated autophagy; GH: growth hormone; <i>ghr</i> KO: growth hormone receptor knockout; LAMP2A: splice variant 1 of <i>Lamp2</i> transcript; LC3-I: non-lipidated MAP1LC3; LC3-II: lipidated MAP1LC3; Li<i>-ghr</i> KO: liver-specific <i>ghr</i> knockout; MA: macroautophagy; MTORC1: mechanistic target of rapamycin kinase complex 1; MTORC2: mechanistic target of rapamycin kinase complex 2; PBS: phosphate-buffered saline.
DOI: 10.6084/m9.figshare.11880837.v1
title: Autophagy interferes with human cytomegalovirus genome replication, morphogenesis, and progeny release

description: Viral infections are often accompanied by the induction of autophagy as an intrinsic cellular defense mechanism. Herpesviruses have developed strategies to evade autophagic degradation and to manipulate autophagy of the host cells to their benefit. Here we addressed the role of macroautophagy/autophagy in human cytomegalovirus replication and for particle morphogenesis. We found that proteins of the autophagy machinery localize to cytoplasmic viral assembly compartments and enveloped virions in the cytoplasm. Surprisingly, the autophagy receptor SQSTM1/p62 was also found to colocalize with HCMV capsids in the nucleus of infected cells. This finding indicates that the autophagy machinery interacts with HCMV already at the early nuclear stages of particle morphogenesis. The membrane-bound form of LC3 and several autophagy receptors were packaged into extracellular HCMV virions. This suggested that autophagic membranes were included during secondary envelopment of HCMV virions. To further address the importance of autophagy in HCMV infection, we generated an HCMV mutant that expressed a dominant-negative version of the protease ATG4B (BAD-ATG4B<sup>C74A</sup>). The proteolytic activity of ATG4B is required for LC3 cleavage, priming it for membrane conjugation. Surprisingly, both genome replication and virus release were enhanced in cells infected with BAD-ATG4B<sup>C74A</sup>, compared to control strains. These results show that autophagy operates as an antiviral process during HCMV infection but is dispensable for secondary HCMV particle envelopment. <b>Abbreviations:</b> ATG: autophagy-related; BAC: bacterial artificial chromosome; BECN1: beclin 1; CPE: cytopathic effect; cVACs: cytoplasmic viral assembly compartments; d.p.i.: days post-infection; DB: dense body; EBV: Epstein-Barr virus; galK: galactokinase; HCMV: human cytomegalovirus; HFF: human foreskin fibroblasts; IE: immediate-early; IRS: internal repeat short; LC3: MAP1LC3A/B; m.o.i.; multiplicity of infection; MCP: major capsid protein; Pp: phosphoprotein; sCP/UL48a: smallest capsid protein; TRS: terminal repeat short; UL: unique long; US: unique short
DOI: 10.6084/m9.figshare.11896938
title: Mutant HTT (huntingtin) impairs mitophagy in a cellular model of Huntington disease

description: The precise degradation of dysfunctional mitochondria by mitophagy is essential for maintaining neuronal homeostasis. HTT (huntingtin) can interact with numerous other proteins and thereby perform multiple biological functions within the cell. In this study, we investigated the role of HTT during mitophagy and analyzed the impact of the expansion of its polyglutamine (polyQ) tract. HTT is involved in different mitophagy steps, promoting the physical proximity of different protein complexes during the initiation of mitophagy and recruiting mitophagy receptors essential for promoting the interaction between damaged mitochondria and the nascent autophagosome. The presence of the polyQ tract in mutant HTT affects the formation of these protein complexes and determines the negative consequences of mutant HTT on mitophagy, leading to the accumulation of damaged mitochondria and an increase in oxidative stress. These outcomes contribute to general mitochondrial dysfunction and neurodegeneration in Huntington disease. <b>Abbreviations</b>: AMPK: AMP-activated protein kinase; ATG13: autophagy related 13; BECN1: beclin 1, autophagy related; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; CCCP: carbonyl cyanide 3-chlorophenyl hydrazone; DMEM: Dulbecco’s modified eagle medium; EDTA: ethylene-diamine-tetra-acetic acid; EGFP: enhanced green fluorescent protein; EGTA: ethylene glycol bis(2-aminoethyl ether)tetraacetic acid; FUNDC1: FUN14 domain containing 1; HD: Huntington disease; HRP: horseradish peroxidase; HTT: huntingtin; LC3-II: lipidated form of MAP1LC3/LC3; mtDNA: mitochondrial deoxyribonucleic acid; MTDR: MitoTracker Deep Red; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1, autophagy cargo receptor; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; OCR: oxygen consumption rate; OPTN: optineurin; OXPHOS: oxidative phosphorylation; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PINK1: PTEN induced putative kinase 1; PLA: proximity ligation assay; PMSF: phenylmethylsulfonyl fluoride; polyQ: polyglutamine; PtdIns3K: phosphatidylinositol 3-kinase; ROS: reactive oxygen species; Rot: rotenone; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SEM: standard error of the mean; SQSTM1/p62: sequestosome 1; TMRM: tetramethylrhodamine methyl ester; UB: ubiquitin; ULK1: unc-51 like kinase 1.
DOI: 10.6084/m9.figshare.11871186.v1
title: The neurosteroid allopregnanolone protects retinal neurons by effects on autophagy and GABRs/GABA<sub>A</sub> receptors in rat glaucoma models

description: In an <i>ex vivo</i> rat glaucoma model using dissected retinas, the neurosteroid allopregnanolone (AlloP) protects retinal ganglion cells (RGCs) via GABR/GABA<sub>A</sub> receptors. To determine the involvement of macroautophagy/autophagy in neuroprotection by AlloP, we examined the effects of autophagy activators, rapamycin and torin 2, and autophagy inhibitors, bafilomycin A<sub>1</sub> and SAR405, on retinal retinal morphology and expression of MAP1 LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) and SQSTM1 (sequestosome 1). Administration of rapamycin or torin 2 exerted partial histological neuroprotection, while combined administration of AlloP with bafilomycin A<sub>1</sub> or SAR405 induced severe degeneration in a hyperbaric condition. Electron microscopic analyses showed that the addition of AlloP significantly increased autophagosomes and degenerative autophagic vacuoles in the retinal nerve fiber layer. Immunoblotting showed that the addition of AlloP or autophagic activators increased the lipidated form of LC3B (LC3B-II) and suppressed SQSTM1. Moreover, bafilomycin A<sub>1</sub> increased LC3B-II and SQSTM1 protein levels in the presence of AlloP without changes in corresponding mRNAs compared to AlloP-treated retinas in a hyperbaric condition. These data indicate that AlloP likely induces a protective form of autophagy in this model. In an <i>in vivo</i> rat model of glaucoma, we also observed neuroprotective effects of AlloP. Injection of polystyrene microbeads into the anterior chamber increased intraocular pressure about 3-fold and induced RGC apoptosis. A single intravitreal injection of AlloP or autophagy activators prevented apoptosis and protected RGCs with autophagy activation. We conclude that AlloP may serve as a potential therapeutic agent for the treatment of glaucoma via diverse mechanisms. <b>Abbreviations:</b> 2HBCD: 2-Hydroxypropyl)-β-cyclodextrin; 3-MA: 3-methyladenine; AlloP: allopregnanolone; AP: autophagosome; AVd: degradative autophagic vacuoles; GCL: ganglion cell layer; INL: inner nuclear layer; IOP: intraocular pressure; IPL: inner plexiform layer; LC3B-I: cytosolic form of LC3B; LCB-II: lipidated form of LC3B; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; mPTP: mitochondrial permeability transition pore; NDS: neuronal damage score; NFL: nerve fiber layer; OH: ocular hypertension; ON: optic nerve; ONL: outer nuclear layer; OPL: outer plexiform layer; p-STR: scotopic threshold response; RGC: retinal ganglion cells; RT-PCR: real-time reverse transcription polymerase chain reaction; SQSTM1: sequestosome 1; TUNEL: TdT-mediated dUTP Nick End Labeling
DOI: 10.6084/m9.figshare.11798499.v1
title: Long-Lived Mice with Reduced Growth Hormone Signaling Have a Constitutive Upregulation of Hepatic Chaperone-Mediated Autophagy

description: Chaperone-mediated autophagy (CMA) is a selective, vesicle-independent, lysosomal degradation pathway for intracellular proteins. CMA modulates proteomic organization through selective protein degradation, with targets including metabolic enzymes, regulators of cell growth, and neurodegeneration-related proteins. CMA activity is low in <i>ad libitum</i>-fed rodents but is increased by prolonged fasting (&gt;16 h). AKT negatively regulates CMA activity at the lysosomal membrane by phosphorylating and inhibiting the CMA regulator GFAP. We have previously reported that long-lived <i>Pou1f1/Pit1</i> mutant (Snell) mice and <i>ghr</i> (growth hormone receptor) knockout mice (<i>ghr</i> KO) have lower AKT activity when fed compared to littermate controls, suggesting the hypothesis that these mice have increased baseline CMA activity. Here, we report that liver lysosomes from fed Snell dwarf mice and <i>ghr</i> KO mice have decreased GFAP phosphorylation and increased CMA substrate uptake activity. Liver lysosomes isolated from fed Snell dwarf mice and <i>ghr</i> KO mice injected with the protease inhibitor leupeptin had increased accumulation of endogenous CMA substrates, compared to littermate controls, suggesting an increase in CMA <i>in vivo</i>. Mice with liver-specific ablation of GH (growth hormone) signaling did not have increased liver CMA, suggesting that a signaling effect resulting from a loss of growth hormone in another tissue causes enhanced CMA in Snell dwarf and <i>ghr</i> KO mice. Finally, we find Snell dwarf mice have decreased protein levels (in liver and kidney) of CIP2A, a well-characterized CMA target protein, without an associated change in <i>Cip2a</i> mRNA. Collectively, these data suggest that CMA is enhanced downstream of an endocrine change resulting from whole-body ablation of GH signaling.
DOI: 10.6084/m9.figshare.11896938.v1
title: Mutant HTT (huntingtin) impairs mitophagy in a cellular model of Huntington disease

description: The precise degradation of dysfunctional mitochondria by mitophagy is essential for maintaining neuronal homeostasis. HTT (huntingtin) can interact with numerous other proteins and thereby perform multiple biological functions within the cell. In this study, we investigated the role of HTT during mitophagy and analyzed the impact of the expansion of its polyglutamine (polyQ) tract. HTT is involved in different mitophagy steps, promoting the physical proximity of different protein complexes during the initiation of mitophagy and recruiting mitophagy receptors essential for promoting the interaction between damaged mitochondria and the nascent autophagosome. The presence of the polyQ tract in mutant HTT affects the formation of these protein complexes and determines the negative consequences of mutant HTT on mitophagy, leading to the accumulation of damaged mitochondria and an increase in oxidative stress. These outcomes contribute to general mitochondrial dysfunction and neurodegeneration in Huntington disease. <b>Abbreviations</b>: AMPK: AMP-activated protein kinase; ATG13: autophagy related 13; BECN1: beclin 1, autophagy related; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; CCCP: carbonyl cyanide 3-chlorophenyl hydrazone; DMEM: Dulbecco’s modified eagle medium; EDTA: ethylene-diamine-tetra-acetic acid; EGFP: enhanced green fluorescent protein; EGTA: ethylene glycol bis(2-aminoethyl ether)tetraacetic acid; FUNDC1: FUN14 domain containing 1; HD: Huntington disease; HRP: horseradish peroxidase; HTT: huntingtin; LC3-II: lipidated form of MAP1LC3/LC3; mtDNA: mitochondrial deoxyribonucleic acid; MTDR: MitoTracker Deep Red; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1, autophagy cargo receptor; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; OCR: oxygen consumption rate; OPTN: optineurin; OXPHOS: oxidative phosphorylation; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PINK1: PTEN induced putative kinase 1; PLA: proximity ligation assay; PMSF: phenylmethylsulfonyl fluoride; polyQ: polyglutamine; PtdIns3K: phosphatidylinositol 3-kinase; ROS: reactive oxygen species; Rot: rotenone; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SEM: standard error of the mean; SQSTM1/p62: sequestosome 1; TMRM: tetramethylrhodamine methyl ester; UB: ubiquitin; ULK1: unc-51 like kinase 1.
DOI: 10.25919/tmxh-nr13
title: Parkes observations for project P574 semester 2020OCTS_10

description: We request time to observe 260 pulsars on a regular basis to provide the accurate ephemerides necessary for the detection and characterisation of gamma-ray pulsars with the Fermi satellite. The main science goals are to increase the number of known gamma-ray pulsars (both radio-loud and radio-quiet), to determine accurate pulse profiles, and to characterise their high energy (phase-resolved) spectra. In the radio, the observations will also allow us to find glitches, characterise timing noise, investigate dispersion and rotation measure variability, and enhance our knowledge of single pulse phenomenology. To date, we are (co-)authors on over 80 papers arising from the collaboration and P574 data. The data have contributed to the PhD theses of students from Bordeaux, Oxford, Manchester, Stanford, and Swinburne.
DOI: 10.6084/m9.figshare.14378630
title: Dataset D3106 and Dataset D4802

description: Datasets used in manuscript "Predicting subcellular location of protein with evolution information and sequence-based deep learning"
DOI: 10.6084/m9.figshare.14378582.v1
title: LoMarloweZhang2021_ProbabilityMatching_Data.zip

description: This is the dataset for the paper ``To maximize or randomize? An experimental study of probability matching in financial decision making'' authored by Andrew W. Lo, Katherine P. Marlowe, and Ruixun Zhang.
DOI: 10.6084/m9.figshare.14378582
title: LoMarloweZhang2021_ProbabilityMatching_Data.zip

description: This is the dataset for the paper ``To maximize or randomize? An experimental study of probability matching in financial decision making'' authored by Andrew W. Lo, Katherine P. Marlowe, and Ruixun Zhang.
DOI: 10.5281/zenodo.4666824
title: Analytical Results - California wind and solar resource droughts

description: Analytical results for Rinaldi et al., Wind and Solar Resource Droughts in California Highlight the Benefits of Long-Term Storage and Integration with the Western Interconnect, ES&T (2021), https://doi.org/10.1021/acs.est.0c07848. For model code and input data, see https://github.com/carnegie/SEM_public/tree/Rinaldi_et_al_2021.
DOI: 10.5281/zenodo.4666823
title: Analytical Results - California wind and solar resource droughts

description: Analytical results for Rinaldi et al., Wind and Solar Resource Droughts in California Highlight the Benefits of Long-Term Storage and Integration with the Western Interconnect, ES&T (2021), https://doi.org/10.1021/acs.est.0c07848. For model code and input data, see https://github.com/carnegie/SEM_public/tree/Rinaldi_et_al_2021.
DOI: 10.5281/zenodo.4667171
title: mosartwmpy tutorial data 1981-05

description: Input data for following along with the mosartwmpy model tutorial: https://github.com/IMMM-SFA/mosartwmpy
DOI: 10.5281/zenodo.4171148
title: Sweet spheres - Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles

description: This archive accompanies our manuscript "Sweet spheres - Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles". Here, we studied the composition, functional diversity and gene expression of marine bacterial communities in a mixed pool of alginate and pectin particles. This Github repo describes the entire workflow. The raw sequencing data is available at Bioproject PRJEB38771. This archive contains the following data: 1) Assembled and Prokka-annotated metagenome contigs (MetaG_contigs.gb) 2) Summary and translations of predicted genes (MetaG_genes.faa; MetaG_genes.txt; MetaG_translations.txt) 3) Prokka-annotated metagenome-assembled genomes (MAG21, Col-24, Ten-26, Gla-32, Psyb-57, Psym-73) 4) Transcript abundances (MetaT_raw.csv, MetaT_TPM.csv) 5) Protocol for combined DNA/RNA extraction
DOI: 10.5281/zenodo.4171147
title: Sweet spheres - Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles

description: This archive accompanies our manuscript "Sweet spheres - Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles". Here, we studied the composition, functional diversity and gene expression of marine bacterial communities in a mixed pool of alginate and pectin particles. This Github repo describes the entire workflow. The raw sequencing data is available at Bioproject PRJEB38771. This archive contains the following data: 1) Assembled and Prokka-annotated metagenome contigs (MetaG_contigs.gb) 2) Summary and translations of predicted genes (MetaG_genes.faa; MetaG_genes.txt; MetaG_translations.txt) 3) Prokka-annotated metagenome-assembled genomes (MAG21, Col-24, Ten-26, Gla-32, Psyb-57, Psym-73) 4) Transcript abundances (MetaT_raw.csv, MetaT_TPM.csv) 5) Protocol for combined DNA/RNA extraction
DOI: 10.5066/p9rtbf7l
title: Lake Erie Fish Community Data, 2013-2020

description: Assessing the distribution and abundance of both predator and prey (forage) fish species is a cornerstone of ecosystem-based fishery management, and supports decision making that considers food-web interactions. In support of binational Great Lakes fishery management the objectives of this survey were to: provide estimates of densities of key forage and predator species in the western basin of Lake Erie, to assess seasonal and spatial distributions of fishes in tandem with water quality information, and to assess year class strength. A systematic grid sampling approach with 41 stations was sampled via bottom trawl during June (Spring) and September (Autumn), starting in 2013. This data release adds 2020 data to the set for a total of eight years observation using the same gear and sampling design.
DOI: 10.6084/m9.figshare.12615713.v1
title: Data from: Marine zooplankton, mini-barcodes, and DNA metabarcoding: The case for taxon-specific primers

description: <b>Abstract</b><b><br></b>DNA metabarcoding is an emerging tool for rapid species identification, with output data that can be applied to describe communities and provide biodiversity estimates. The approach utilizes high-throughput sequencing and target-specific markers to simultaneously identify multiple species present in taxonomically complex samples. Successful identification at species-level relies on genetic markers that cover a broad taxonomic range yet retain sufficient sequence divergence to resolve species; and on DNA reference libraries that link individual sequences to taxonomic descriptions. Here, we provide a versatile metabarcoding protocol for biomonitoring of bulk marine zooplankton samples targeting taxa with life-history stages important to commercial fisheries, such as prawns, shrimps, crabs, lobsters, and fish. Taxon-specific DNA mini-barcode primers were designed to amplify variable portions of the mitochondrial cytochrome c oxidase subunit I (COI) gene region and used together with primers already available in the literature. A series of tests were conducted on artificially assembled mock (with known species ratios) and coastal zooplankton communities to determine the efficiency of the selected protocol and primers. The use of a single primer pair versus primer cocktails (multiple primer sets) was assessed by evaluating species detection rates. Primer cocktails significantly increased the overall species detection in all samples. Taxon-specific primers increased the detection rate of target taxa when compared to using the universal primer set, highlighting the importance of accurate taxon-specific primer design for metabarcoding applications. The protocol developed, provides a rapid and cost-effective tool for biomonitoring of zooplankton communities in marine pelagic environments.<br>The data added to figshare includes the raw sequence data generated for each mock community using next-generation sequencing and Sanger sequences downloaded from GenBank to create the local reference library.
DOI: 10.5281/zenodo.4667276
title: Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

description: SNP data used in: Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp) Genotypic_data_368_colorado.csv: SNP data for 368 accessions in the UCR Minicore.<br> Genotypic_data_292_florida.csv: SNP data for 292 accessions evaluated in Florida. Adapted from Munoz-Amatriain, Maria, et al. "The UCR Minicore: a valuable resource for cowpea research and breeding." bioRxiv (2021) https://doi.org/10.1101/2021.02.09.430326
DOI: 10.5281/zenodo.4667275
title: Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

description: SNP data used in: Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp) Genotypic_data_368_colorado.csv: SNP data for 368 accessions in the UCR Minicore.<br> Genotypic_data_292_florida.csv: SNP data for 292 accessions evaluated in Florida. Adapted from Munoz-Amatriain, Maria, et al. "The UCR Minicore: a valuable resource for cowpea research and breeding." bioRxiv (2021) https://doi.org/10.1101/2021.02.09.430326