cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23629236
title: High-resolution visualization and assessment of basal and OXPHOS-induced mitophagy in H9c2 cardiomyoblasts

description: Mitochondria are susceptible to damage resulting from their activity as energy providers. Damaged mitochondria can cause harm to the cell and thus mitochondria are subjected to elaborate quality-control mechanisms including elimination via lysosomal degradation in a process termed mitophagy. Basal mitophagy is a house-keeping mechanism fine-tuning the number of mitochondria according to the metabolic state of the cell. However, the molecular mechanisms underlying basal mitophagy remain largely elusive. In this study, we visualized and assessed the level of mitophagy in H9c2 cardiomyoblasts at basal conditions and after OXPHOS induction by galactose adaptation. We used cells with a stable expression of a pH-sensitive fluorescent mitochondrial reporter and applied state-of-the-art imaging techniques and image analysis. Our data showed a significant increase in acidic mitochondria after galactose adaptation. Using a machine-learning approach we also demonstrated increased mitochondrial fragmentation by OXPHOS induction. Furthermore, super-resolution microscopy of live cells enabled capturing of mitochondrial fragments within lysosomes as well as dynamic transfer of mitochondrial contents to lysosomes. Applying correlative light and electron microscopy we revealed the ultrastructure of the acidic mitochondria confirming their proximity to the mitochondrial network, ER and lysosomes. Finally, exploiting siRNA knockdown strategy combined with flux perturbation with lysosomal inhibitors, we demonstrated the importance of both canonical as well as non-canonical autophagy mediators in lysosomal degradation of mitochondria after OXPHOS induction. Taken together, our high-resolution imaging approaches applied on H9c2 cells provide novel insights on mitophagy during physiologically relevant conditions. The implication of redundant underlying mechanisms highlights the fundamental importance of mitophagy. <b>Abbreviations:</b> ATG: autophagy related; ATG7: autophagy related 7; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; CLEM: correlative light and electron microscopy; EGFP: enhanced green fluorescent protein; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; OXPHOS: oxidative phosphorylation; PepA: pepstatin A; PLA: proximity ligation assay; PRKN: parkin RBR E3 ubiquitin protein ligase; RAB5A: RAB5A, member RAS oncogene family; RAB7A: RAB7A, member RAS oncogene family; RAB9A: RAB9A, member RAS oncogene family; ROS: reactive oxygen species; SIM: structured illumination microscopy; siRNA: short interfering RNA; SYNJ2BP: synaptojanin 2 binding protein; TEM: transmission electron microscopy; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1.
DOI: 10.6084/m9.figshare.23629236.v1
title: High-resolution visualization and assessment of basal and OXPHOS-induced mitophagy in H9c2 cardiomyoblasts

description: Mitochondria are susceptible to damage resulting from their activity as energy providers. Damaged mitochondria can cause harm to the cell and thus mitochondria are subjected to elaborate quality-control mechanisms including elimination via lysosomal degradation in a process termed mitophagy. Basal mitophagy is a house-keeping mechanism fine-tuning the number of mitochondria according to the metabolic state of the cell. However, the molecular mechanisms underlying basal mitophagy remain largely elusive. In this study, we visualized and assessed the level of mitophagy in H9c2 cardiomyoblasts at basal conditions and after OXPHOS induction by galactose adaptation. We used cells with a stable expression of a pH-sensitive fluorescent mitochondrial reporter and applied state-of-the-art imaging techniques and image analysis. Our data showed a significant increase in acidic mitochondria after galactose adaptation. Using a machine-learning approach we also demonstrated increased mitochondrial fragmentation by OXPHOS induction. Furthermore, super-resolution microscopy of live cells enabled capturing of mitochondrial fragments within lysosomes as well as dynamic transfer of mitochondrial contents to lysosomes. Applying correlative light and electron microscopy we revealed the ultrastructure of the acidic mitochondria confirming their proximity to the mitochondrial network, ER and lysosomes. Finally, exploiting siRNA knockdown strategy combined with flux perturbation with lysosomal inhibitors, we demonstrated the importance of both canonical as well as non-canonical autophagy mediators in lysosomal degradation of mitochondria after OXPHOS induction. Taken together, our high-resolution imaging approaches applied on H9c2 cells provide novel insights on mitophagy during physiologically relevant conditions. The implication of redundant underlying mechanisms highlights the fundamental importance of mitophagy. <b>Abbreviations:</b> ATG: autophagy related; ATG7: autophagy related 7; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; CLEM: correlative light and electron microscopy; EGFP: enhanced green fluorescent protein; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; OXPHOS: oxidative phosphorylation; PepA: pepstatin A; PLA: proximity ligation assay; PRKN: parkin RBR E3 ubiquitin protein ligase; RAB5A: RAB5A, member RAS oncogene family; RAB7A: RAB7A, member RAS oncogene family; RAB9A: RAB9A, member RAS oncogene family; ROS: reactive oxygen species; SIM: structured illumination microscopy; siRNA: short interfering RNA; SYNJ2BP: synaptojanin 2 binding protein; TEM: transmission electron microscopy; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1.
DOI: 10.6084/m9.figshare.23646393
title: The autophagic protein FYCO1 controls TNFRSF10/TRAIL receptor induced apoptosis and is inactivated by CASP8 (caspase 8)

description: Apoptosis is a tightly controlled cell death program executed by proteases, the so-called caspases. It plays an important role in tissue homeostasis and is often dysregulated in cancer. Here, we identified FYCO1, a protein that promotes microtubule plus end-directed transport of autophagic and endosomal vesicles as a molecular interaction partner of activated CASP8 (caspase 8). The absence of FYCO1 sensitized cells to basal and TNFSF10/TRAIL-induced apoptosis by receptor accumulation and stabilization of the Death Inducing Signaling Complex (DISC). Loss of FYCO1 resulted in impaired transport of TNFRSF10B/TRAIL-R2/DR5 (TNF receptor superfamily member 10b) to the lysosomes in TNFSF10/TRAIL-stimulated cells. More in detail, we show that FYCO1 interacted via its C-terminal GOLD domain with the CCZ1-MON1A complex, which is necessary for RAB7A activation and for the fusion of autophagosomal/endosomal vesicles with lysosomes. We demonstrated that FYCO1 is a novel and specific CASP8 substrate. The cleavage at aspartate 1306 resulted in the release of the C-terminal GOLD domain, inactivating FYCO1 function, and allowing for the progression of apoptosis. Furthermore, the lack of FYCO1 resulted in a stronger and prolonged formation of the TNFRSF1A/TNF-R1 signaling complex. Thus, FYCO1 limits the ligand-induced and steady-state signaling of TNFR-superfamily members, providing a control mechanism that fine-tunes both apoptotic and inflammatory answers. <b>Abbreviations</b>: AP: affinity purification; CHX: cycloheximide; co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeats; DISC: death-inducing signaling complex; DR: death receptors; doxy: doxycycline; GEF: guanine nucleotide exchange factor; ind: inducible; KD: knockdown; KO: knockout; MS: mass spectrometry; shRNA: short hairpin RNA; siRNA: small interfering RNA; TIP: two-step co-immunoprecipitation; WB: western blot.
DOI: 10.6084/m9.figshare.23646393.v1
title: The autophagic protein FYCO1 controls TNFRSF10/TRAIL receptor induced apoptosis and is inactivated by CASP8 (caspase 8)

description: Apoptosis is a tightly controlled cell death program executed by proteases, the so-called caspases. It plays an important role in tissue homeostasis and is often dysregulated in cancer. Here, we identified FYCO1, a protein that promotes microtubule plus end-directed transport of autophagic and endosomal vesicles as a molecular interaction partner of activated CASP8 (caspase 8). The absence of FYCO1 sensitized cells to basal and TNFSF10/TRAIL-induced apoptosis by receptor accumulation and stabilization of the Death Inducing Signaling Complex (DISC). Loss of FYCO1 resulted in impaired transport of TNFRSF10B/TRAIL-R2/DR5 (TNF receptor superfamily member 10b) to the lysosomes in TNFSF10/TRAIL-stimulated cells. More in detail, we show that FYCO1 interacted via its C-terminal GOLD domain with the CCZ1-MON1A complex, which is necessary for RAB7A activation and for the fusion of autophagosomal/endosomal vesicles with lysosomes. We demonstrated that FYCO1 is a novel and specific CASP8 substrate. The cleavage at aspartate 1306 resulted in the release of the C-terminal GOLD domain, inactivating FYCO1 function, and allowing for the progression of apoptosis. Furthermore, the lack of FYCO1 resulted in a stronger and prolonged formation of the TNFRSF1A/TNF-R1 signaling complex. Thus, FYCO1 limits the ligand-induced and steady-state signaling of TNFR-superfamily members, providing a control mechanism that fine-tunes both apoptotic and inflammatory answers. <b>Abbreviations</b>: AP: affinity purification; CHX: cycloheximide; co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeats; DISC: death-inducing signaling complex; DR: death receptors; doxy: doxycycline; GEF: guanine nucleotide exchange factor; ind: inducible; KD: knockdown; KO: knockout; MS: mass spectrometry; shRNA: short hairpin RNA; siRNA: small interfering RNA; TIP: two-step co-immunoprecipitation; WB: western blot.
DOI: 10.15468/dl.txg4ch
title: Occurrence Download

description: A dataset containing 3600 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heteranthera limosa (Sw.) Willd."
 ]
}

 The dataset includes 3600 records from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qn4jzy
title: Occurrence Download

description: A dataset containing 7276 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Najas flexilis (Willd.) Rostk. & W.L.E.Schmidt"
 ]
}

 The dataset includes 7276 records from 253 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011789-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpeuh9
title: Occurrence Download

description: A dataset containing 60661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "Geometry POLYGON((112.34294 24.01862,113.64929 23.99706,113.65146 24.45881,113.65303 25.09172,113.04008 25.09461,112.34227 25.10753,112.35128 24.52596,112.34962 24.44752,112.34294 24.01862))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 60661 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011788-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4d6vxe
title: Occurrence Download

description: A dataset containing 3734 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex oligosperma Michx."
 ]
}

 The dataset includes 3734 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011792-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzxspe
title: Occurrence Download

description: A dataset containing 2010 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Najas gracillima (A.Braun ex Engelm.) Magnus"
 ]
}

 The dataset includes 2010 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011793-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k46sv9
title: Occurrence Download

description: A dataset containing 672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "TaxonKey is Macaca fascicularis (Raffles, 1821)"
 ]
}

 The dataset includes 672 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011796-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n7c58t
title: Occurrence Download

description: A dataset containing 1361 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyperus prolifer Lam."
 ]
}

 The dataset includes 1361 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011795-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2s7mbw
title: Occurrence Download

description: A dataset containing 15315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.11_1",
 "OccurrenceStatus is Present",
 "Year 2004-2023"
 ]
}

 The dataset includes 15315 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011794-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qn7286
title: Occurrence Download

description: A dataset containing 2390 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyperus reflexus Vahl"
 ]
}

 The dataset includes 2390 records from 188 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011797-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27184395
title: SPMIL_main_code

description: SPMIL main code
DOI: 10.6084/m9.figshare.27184395.v2
title: SPMIL_main_code

description: SPMIL main code
DOI: 10.6084/m9.figshare.27184395.v1
title: SPMIL_main_code

description: SPMIL main code
DOI: 10.15468/dl.5cfbbx
title: Occurrence Download

description: A dataset containing 127919 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potamogeton perfoliatus L."
 ]
}

 The dataset includes 127919 records from 746 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011790-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qehofd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "LastInterpreted 2014-01-01-2014-01-01",
 "Year is greater than or equal to 1980",
 {
 "or" : [
 "TaxonKey is Aves",
 "TaxonKey is Amphibia",
 "TaxonKey is Mammalia",
 "TaxonKey is Reptilia",
 "TaxonKey is Plantae"
 ]
 },
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002487-190320150433242/datasets/export for details.
DOI: 10.15468/dl.92qmtd
title: Occurrence Download

description: A dataset containing 1281537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas platyrhynchos Linnaeus, 1758",
 "HasCoordinate is true",
 "Month is August",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1281537 records from 705 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049413-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jyzq84
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Mimochroa albifrons (Moore, 1888)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007126-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9hqvj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "LastInterpreted 2014-01-01-2014-01-01",
 "Year is greater than or equal to 1980",
 {
 "or" : [
 "TaxonKey is Aves",
 "TaxonKey is Amphibia",
 "TaxonKey is Mammalia",
 "TaxonKey is Reptilia",
 "TaxonKey is Plantae"
 ]
 },
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002494-190320150433242/datasets/export for details.
DOI: 10.15468/dl.gaqea9
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is DECAF - AUTEC Sperm Whales - Multiple Sensors - Samples"
 ]
}

 The dataset includes 49 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005642-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fbdprb
title: Occurrence Download

description: A dataset containing 324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Burmannia flava Mart.",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 324 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007124-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bzq4xf
title: Occurrence Download

description: A dataset containing 29564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pterocles alchata (Linnaeus, 1766)"
 ]
}

 The dataset includes 29564 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020252-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzkub3
title: Occurrence Download

description: A dataset containing 316714 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Circus pygargus (Linnaeus, 1758)"
 ]
}

 The dataset includes 316714 records from 1172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020234-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtm7fg
title: Occurrence Download

description: A dataset containing 9620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present",
 "TaxonKey is Vultur gryphus Linnaeus, 1758"
 ]
}

 The dataset includes 9620 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001238-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e96w3j
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Decapterus tabl Berry, 1968",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001239-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.578sjy
title: Occurrence Download

description: A dataset containing 14614 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-123.20511 40.62693,-123.09504 40.62693,-123.09504 42.01909,-123.20511 42.01909,-123.20511 40.62693))",
 "Geometry POLYGON((-123.02915 42.00073,-123.16961 40.45343,-122.84522 39.23182,-122.06369 38.55271,-121.19877 38.0808,-119.87752 38.883,-119.88634 42.01557,-123.02915 42.00073))"
 ]
 },
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 14614 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001240-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vwnfu
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Decapterus russelli (Rüppell, 1830)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 52 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001241-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3n6t2e
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pristipomoides filamentosus (Valenciennes, 1830)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 40 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001242-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yg3jfc
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is South America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Cereus horrispinus Backeb."
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001245-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s23jnn
title: Occurrence Download

description: A dataset containing 19636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calonectris leucomelas (Temminck, 1836)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19636 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001244-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.