cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13365290.v1
title: The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer

description: Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in <i>MAP1LC3B</i> expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function. <b>Abbreviations</b>: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.
DOI: 10.6084/m9.figshare.13050508.v1
title: Essential role of autophagy in restricting poliovirus infection revealed by identification of an ATG7 defect in a poliomyelitis patient

description: Paralytic poliomyelitis is a rare disease manifestation following poliovirus (PV) infection. The disease determinants remain largely unknown. We used whole exome sequencing to uncover possible contributions of host genetics to the development of disease outcome in humans with poliomyelitis. We identified a patient with a variant in <i>ATG7</i>, an important regulatory gene in the macroautophagy/autophagy pathway. PV infection did not induce a prominent type I interferon response, but rather activated autophagy in neuronal-like cells, and this was essential for viral control. Importantly, virus-induced autophagy was impaired in patient fibroblasts and associated with increased viral burden and enhanced cell death following infection. Lack of ATG7 prevented control of infection in neuronal-like cells, and reconstitution of patient cells with wild-type ATG7 reestablished autophagy-mediated control of infection. Collectively, these data suggest that ATG7 defect contributes to host susceptibility to PV infection and propose autophagy as an unappreciated antiviral effector in viral infection in humans.
DOI: 10.6084/m9.figshare.13058168.v1
title: Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, <i>Saccharomyces cerevisiae</i>

description: Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
DOI: 10.6084/m9.figshare.12998620.v1
title: Selective autophagy regulates heat stress memory in <i>Arabidopsis</i> by NBR1-mediated targeting of HSP90 and ROF1

description: In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS in <i>Arabidopsis thaliana</i>. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of an <i>nbr1</i>-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression of <i>HSP</i> genes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation of <i>NBR1</i> resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. <b>Abbreviations:</b> AIM: Atg8-interacting motif; ATG: autophagy-related; BiFC: bimolecular fluorescence complementation; ConA: concanamycinA; CoIP: co-immunoprecipitation; DMSO: dimethyl sulfoxide; FKBP: FK506-binding protein; FBPASE: fructose 1,6-bisphosphatase; GFP: green fluorescent protein; HS: heat stress; HSF: heat shock factor; HSFA2: heat shock factor A2; HSP: heat shock protein; HSP90: heat shock protein 90; LC-MS/MS: Liquid chromatography-tandem mass spectrometry; 3-MA: 3-methyladenine; NBR1: next-to-BRCA1; PQC: protein quality control; RFP: red fluorescent protein; ROF1: rotamase FKBP1; TF: transcription factor; TUB: tubulin; UBA: ubiquitin-associated; YFP: yellow fluorescent protein
DOI: 10.6084/m9.figshare.13073197.v1
title: Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs

description: Mitochondria-associated membranes (MAMs) are essential communication subdomains of the endoplasmic reticulum (ER) that interact with mitochondria. We previously demonstrated that, upon macroautophagy/autophagy induction, AMBRA1 is recruited to the BECN1 complex and relocalizes to MAMs, where it regulates autophagy by interacting with raft-like components. ERLIN1 is an endoplasmic reticulum lipid raft protein of the prohibitin family. However, little is known about its association with the MAM interface and its involvement in autophagic initiation. In this study, we investigated ERLIN1 association with MAM raft-like microdomains and its interaction with AMBRA1 in the regulation of the autophagic process. We show that ERLIN1 interacts with AMBRA1 at MAM raft-like microdomains, which represents an essential condition for autophagosome formation upon nutrient starvation, as demonstrated by knocking down <i>ERLIN1</i> gene expression. Moreover, this interaction depends on the “integrity” of key molecules, such as ganglioside GD3 and MFN2. Indeed, knocking down ST8SIA1/GD3-synthase or MFN2 expression impairs AMBRA1-ERLIN1 interaction at the MAM level and hinders autophagy. In conclusion, AMBRA1-ERLIN1 interaction within MAM raft-like microdomains appears to be pivotal in promoting the formation of autophagosomes. <b>Abbreviations:</b> ACSL4/ACS4: acyl-CoA synthetase long chain family member 4; ACTB/β-actin: actin beta; AMBRA1: autophagy and beclin 1 regulator 1; ATG14: autophagy related 14; BECN1: beclin 1; CANX: calnexin; Cy5: cyanine 5; ECL: enhanced chemiluminescence; ER: endoplasmic reticulum; ERLIN1/KE04: ER lipid raft associated 1; FB1: fumonisin B1; FE: FRET efficiency; FRET: Förster/fluorescence resonance energy transfer; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD3: aNeu5Ac(2-8)aNeu5Ac(2-3)bDGalp(1-4)bDGlcp(1-1)ceramide; HBSS: Hanks’ balanced salt solution; HRP: horseradish peroxidase; LMNB1: lamin B1; mAb: monoclonal antibody; MAMs: mitochondria-associated membranes; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; MYC/cMyc: proto-oncogene, bHLH transcription factor; P4HB: prolyl 4-hydroxylase subunit beta; pAb: polyclonal antibody; PE: phycoerythrin; SCAP/SREBP: SREBF chaperone; SD: standard deviation; ST8SIA1: ST8 alpha-N-acetyl-neuraminide alpha-2,8 sialyltransferase 1; SQSTM1/p62: sequestosome 1; TOMM20: translocase of outer mitochondrial membrane 20; TUBB/beta-tubulin: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VDAC1/porin: voltage dependent anion channel 1.
DOI: 10.6084/m9.figshare.13157977.v1
title: PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation

description: Macroautophagy/autophagy is an evolutionarily conserved intracellular pathway for the degradation of cytoplasmic materials. Under stress conditions, autophagy is upregulated and double-membrane autophagosomes are formed by the expansion of phagophores. The ATG16L1 precursor fusion contributes to development of phagophore structures and is critical for the biogenesis of autophagosomes. Here, we discovered a novel role of the protein tyrosine phosphatase PTPN9 in the regulation of homotypic ATG16L1 vesicle fusion and early autophagosome formation. Depletion of PTPN9 and its <i>Drosophila</i> homolog Ptpmeg2 impaired autophagosome formation and autophagic flux. PTPN9 colocalized with ATG16L1 and was essential for homotypic fusion of ATG16L1<sup>+</sup> vesicles during starvation-induced autophagy. We further identified the Q-SNARE VTI1B as a substrate target of PTPN9 phosphatase. Like PTPN9, the VTI1B nonphosphorylatable mutant but not the phosphomimetic mutant enhanced SNARE complex assembly and autophagic flux. Our findings highlight the important role of PTPN9 in the regulation of ATG16L1<sup>+</sup> autophagosome precursor fusion and autophagosome biogenesis through modulation of VTI1B phosphorylation status. <b>Abbreviations:</b> csw: corkscrew; EBSS: Earle’s balanced salt solution; ERGIC: ER-Golgi intermediate compartment; ESCRT: endosomal sorting complexes required for transport; mop: myopic; NSF: N-ethylmaleimide-sensitive factor; PAS: phagophore assembly site; PolyQ: polyglutamine; PtdIns3P: phosphatidylinositol-3-phosphate; PTK: protein tyrosine kinase; PTM: posttranslational modification; PTP: protein tyrosine phosphatase; PTPN23/HD-PTP: protein tyrosine phosphatase non-receptor type 23; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; STX7: syntaxin 7; STX8: syntaxin 8; STX17: syntaxin 17; VAMP3: vesicle associated membrane protein 3; VAMP7: vesicle associated membrane protein 7; VTI1B: vesicle transport through interaction with t-SNAREs 1B; YKT6: YKT6 v-SNARE homolog; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.
DOI: 10.6084/m9.figshare.13269950.v2
title: A tecpr2 knockout mouse exhibits age-dependent neuroaxonal dystrophy associated with autophagosome accumulation

description: Mutations in the coding sequence of human <i>TECPR2</i> were recently linked to spastic paraplegia type 49 (SPG49), a hereditary neurodegenerative disorder involving intellectual disability, autonomic-sensory neuropathy, chronic respiratory disease and decreased pain sensitivity. Here, we report the generation of a novel CRISPR-Cas9 <i>tecpr2</i> knockout (<i>tecpr2</i><sup>−/−</sup>) mouse that exhibits behavioral pathologies observed in SPG49 patients. <i>tecpr2</i><sup>−/−</sup> mice develop neurodegenerative patterns in an age-dependent manner, manifested predominantly as neuroaxonal dystrophy in the gracile (GrN) and cuneate nuclei (CuN) of the medulla oblongata in the brainstem and dorsal white matter column of the spinal cord. Age-dependent correlation with accumulation of autophagosomes suggests compromised targeting to lysosome. Taken together, our findings establish the <i>tecpr2</i> knockout mouse as a potential model for SPG49 and ascribe a new role to TECPR2 in macroautophagy/autophagy-related neurodegenerative disorders.
DOI: 10.6084/m9.figshare.13526158.v1
title: Autophagy inhibition rescues structural and functional defects caused by the loss of mitochondrial chaperone <i>Hsc70-5</i> in <i>Drosophila</i>

description: We investigated in larval and adult <i>Drosophila</i> models whether loss of the mitochondrial chaperone <i>Hsc70-5</i> is sufficient to cause pathological alterations commonly observed in Parkinson disease. At affected larval neuromuscular junctions, no effects on terminal size, bouton size or number, synapse size, or number were observed, suggesting that we studied an early stage of pathogenesis. At this stage, we noted a loss of synaptic vesicle proteins and active zone components, delayed synapse maturation, reduced evoked and spontaneous excitatory junctional potentials, increased synaptic fatigue, and cytoskeleton rearrangements. The adult model displayed ATP depletion, altered body posture, and susceptibility to heat-induced paralysis. Adult phenotypes could be suppressed by knockdown of <i>dj-1β, Lrrk, DCTN2-p50, DCTN1-p150, Atg1, Atg101, Atg5, Atg7</i>, and <i>Atg12</i>. The knockdown of components of the macroautophagy/autophagy machinery or overexpression of human <i>HSPA9</i> broadly rescued larval and adult phenotypes, while disease-associated <i>HSPA9</i> variants did not. Overexpression of <i>Pink1</i> or promotion of autophagy exacerbated defects. <b>Abbreviations:</b> AEL: after egg laying; AZ: active zone; brp: bruchpilot; Csp: cysteine string protein; dlg: discs large; eEJPs: evoked excitatory junctional potentials; GluR: glutamate receptor; H<sub>2</sub>O<sub>2</sub>: hydrogen peroxide; mEJP: miniature excitatory junctional potentials; MT: microtubule; NMJ: neuromuscular junction; PD: Parkinson disease; <i>Pink1</i>: PTEN-induced putative kinase 1; PSD: postsynaptic density; SSR: subsynaptic reticulum; SV: synaptic vesicle; VGlut: vesicular glutamate transporter.
DOI: 10.5281/zenodo.5567616
title: Impact of 3D Cloud Structures on the Atmospheric Trace Gas Products from UV-VIS Sounders: Synthetic dataset for validation of trace gas retrieval algorithms

description: This data set is described in detail in a paper submitted to AMTD: <strong>Impact of 3D Cloud Structures on the Atmospheric Trace Gas Products from UV-VIS Sounders - Part I: Synthetic dataset for validation of trace gas retrieval algorithms</strong> by Claudia Emde, Huan Yu, Arve Kylling, Michel van Roozendael, Kerstin Stebel, Ben Veihelmann, and<br> Bernhard Mayer The subdirectory <em>boxcloud</em> includes synthetic reflectances for clearsky, 1D cloud and box cloud. The subdirectory <em>les_cloud</em> includes synthetic reflectances for the LES cloud scenario for low earth orbit (<em>leo</em>) and geostationary orbit (<em>geo</em>). All data are provided in <em>netcdf</em> format.
DOI: 10.5281/zenodo.5567615
title: Impact of 3D Cloud Structures on the Atmospheric Trace Gas Products from UV-VIS Sounders: Synthetic dataset for validation of trace gas retrieval algorithms

description: This data set is described in detail in a paper submitted to AMTD: <strong>Impact of 3D Cloud Structures on the Atmospheric Trace Gas Products from UV-VIS Sounders - Part I: Synthetic dataset for validation of trace gas retrieval algorithms</strong> by Claudia Emde, Huan Yu, Arve Kylling, Michel van Roozendael, Kerstin Stebel, Ben Veihelmann, and<br> Bernhard Mayer The subdirectory <em>boxcloud</em> includes synthetic reflectances for clearsky, 1D cloud and box cloud. The subdirectory <em>les_cloud</em> includes synthetic reflectances for the LES cloud scenario for low earth orbit (<em>leo</em>) and geostationary orbit (<em>geo</em>). All data are provided in <em>netcdf</em> format.
DOI: 10.6084/m9.figshare.14055143.v1
title: Pushing barcodes to their limits: phylogenetic placement of Fontigens Pilsbry, 1933 (Caenogastropoda: Littorinimorpha: Truncatelloidea) and elevation of Fontigentidae Taylor, 1966

description: Tree files from Gladstone and Whelan.
DOI: 10.5281/zenodo.5567741
title: Dataset comparing different skewness methods tested in "Quantifying and comparing radiation damage in the Protein Data Bank"

description: Dataset comparing five different skewness metrics (including the Bnet metric) across 23 radiation damage datasets in the publication "Quantifying and comparing radiation damage in the Protein Data Bank"
DOI: 10.5281/zenodo.5567740
title: Dataset comparing different skewness methods tested in "Quantifying and comparing radiation damage in the Protein Data Bank"

description: Dataset comparing five different skewness metrics (including the Bnet metric) across 23 radiation damage datasets in the publication "Quantifying and comparing radiation damage in the Protein Data Bank"
DOI: 10.25810/c862-0e81.42
title: US Television Coverage of Climate Change or Global Warming, 2000-2021 - September 2021

description:         The Media and Climate Change Observatory Data monitors 127 sources (across newspapers, radio and TV) in 59 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.6084/m9.figshare.16785829
title: Data for 'Stomatal density in Pinus sylvestris as an indicator of temperature rather than CO2: evidence from a pan-European transect'

description: This dataset consists of combined field transect data and data from a provenance trial. Geographic coordinates and selected Worldclim climatic parameters (mean annual temperature, mean temperature of the warmest quarter and mean annual precipitation) for each sampling site or the original provenance site.are given. For each sampling site we give mean needle length, width, and stomatal traits for each needle surface (number of stomatal rows and stomatal density) as well as the projected stomatal density..
DOI: 10.6084/m9.figshare.16785829.v2
title: Data for 'Stomatal density in Pinus sylvestris as an indicator of temperature rather than CO2: evidence from a pan-European transect'

description: This dataset consists of combined field transect data and data from a provenance trial. Geographic coordinates and selected Worldclim climatic parameters (mean annual temperature, mean temperature of the warmest quarter and mean annual precipitation) for each sampling site or the original provenance site.are given. For each sampling site we give mean needle length, width, and stomatal traits for each needle surface (number of stomatal rows and stomatal density) as well as the projected stomatal density..
DOI: 10.6084/m9.figshare.16785829.v1
title: Data for Marek et al. 'Stomatal density in Pinus sylvestris as an indicator of temperature rather than CO2: evidence from a pan-European transect'

description: This dataset consists of combined field transect data and data from a provenance trial. Geographic coordinates and selected Worldclim climatic parameters (mean annual temperature, mean temperature of the warmest quarter and mean annual precipitation) for each sampling site or the original provenance site.are given. For each sampling site we give mean needle length, width, and stomatal traits for each needle surface (number of stomatal rows and stomatal density) as well as the projected stomatal density..
DOI: 10.6084/m9.figshare.13040474
title: Code Review Histories of Gerrit (QT, Eclipse, Wireshark, LibreOffice) and GitHub (GitHub Desktop, VSCode, TensorFlow, Django) Projects

description: <i><b>Code Review Histories of Gerrit (QT, Eclipse, Wireshark, LibreOffice) and GitHub (GitHub Desktop, VSCode, TensorFlow, Django) Projects.</b></i><i><b><br></b></i><i><b>The data is fetched by using the tool: Perceval (https://github.com/chaoss/grimoirelab-perceval).<br></b></i><b><br></b>
DOI: 10.6084/m9.figshare.15157240
title: Anillin/Mid1p interacts with the ESCRT-associated protein Vps4p and mitotic kinases to regulate cytokinesis in fission yeast

description: Cytokinesis is the final stage of the cell cycle which separates cellular constituents to produce two daughter cells. Using the fission yeast <i>Schizosaccharomyces pombe</i> we have investigated the role of various classes of proteins involved in this process. Central to these is anillin/Mid1p which forms a ring-like structure at the cell equator that predicts the site of cell separation through septation in fission yeast. Here we demonstrate a direct physical interaction between Mid1p and the endosomal sorting complex required for transport (ESCRT)-associated protein Vps4p, a genetic interaction of the <i>mid1</i> and <i>vps4</i> genes essential for cell viability, and a requirement of Vps4p for the correct cellular localization of Mid1p. Furthermore, we show that Mid1p is phosphorylated by aurora kinase, a genetic interaction of the <i>mid1</i> and the aurora kinase <i>ark1</i> genes is essential for cell viability, and that Ark1p is also required for the correct cellular localization of Mid1p. We mapped the sites of phosphorylation of Mid1p by human aurora A and the polo kinase Plk1 and assessed their importance in fission yeast by mutational analysis. Such analysis revealed serine residues S332, S523 and S531 to be required for Mid1p function and its interaction with Vps4p, Ark1p and Plo1p. Combined these data suggest a physical interaction between Mid1p and Vps4p important for cytokinesis, and identify phosphorylation of Mid1p by aurora and polo kinases as being significant for this process.