cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7648775
title: VCP maintains lysosomal homeostasis and TFEB activity in differentiated skeletal muscle

description: Differentiated tissue is particularly vulnerable to alterations in protein and organelle homeostasis. The essential protein VCP, mutated in hereditary inclusion body myopathy, amyotrophic lateral sclerosis and frontotemporal dementia, is critical for efficient clearance of misfolded proteins and damaged organelles in dividing cells, but its role in terminally differentiated tissue affected by disease mutations is less clear. To understand the relevance of VCP in differentiated tissue, we inactivated it in skeletal muscle of adult mice. Surprisingly, knockout muscle demonstrated a necrotic myopathy with increased macroautophagic/autophagic proteins and damaged lysosomes. This was not solely due to a defect in autophagic degradation because age-matched mice with muscle inactivation of the autophagy essential protein, ATG5, did not demonstrate a myopathy. Notably, myofiber necrosis was preceded by upregulation of LGALS3/Galectin-3, a marker of damaged lysosomes, and TFEB activation, suggesting early defects in the lysosomal system. Consistent with that, myofiber necrosis was recapitulated by chemical induction of lysosomal membrane permeabilization (LMP) in skeletal muscle. Moreover, TFEB was activated after LMP in cells, but activation and nuclear localization of TFEB persisted upon VCP inactivation or disease mutant expression. Our data identifies VCP as central mediator of both lysosomal clearance and biogenesis in skeletal muscle. <b>Abbreviations:</b> AAA: ATPases Associated with diverse cellular Activities; TUBA1A/α-tubulin: tubulin alpha 1a; ATG5: autophagy related 5; ATG7: autophagy related 7; ACTA1: actin alpha 1, skeletal muscle; CLEAR: coordinated lysosomal expression and regulation; CTSB/D: cathepsin B/D; Ctrl: control; DAPI: diamidino-2-phenylindole; EBSS: Earle’s balanced salt solution; ELDR: endolysosomal damage response; ESCRT: endosomal sorting complexes required for transport; Gastroc/G: gastrocnemius; H&E: hematoxylin and eosin; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IBMPFD/ALS: inclusion body myopathy associated with Paget disease of the bone, frontotemporal dementia and amyotrophic lateral sclerosis; i.p.: intraperitoneal; LAMP1/2: lysosomal-associated membrane protein 1/2; LLOMe: Leu-Leu methyl ester hydrobromide; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; MTOR: mechanistic target of rapamycin kinase; MYL1: myosin light chain 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MSP: multisystem proteinopathy; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; Quad/Q: quadriceps; RHEB: Ras homolog, mTORC1 binding; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TA: tibialis anterior; siRNA: small interfering RNA; SQSTM1/p62, sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBS: Tris-buffered saline; TXFN, tamoxifen; UBXN6/UBXD1: UBX domain protein 6; VCP: valosin containing protein; WT: wild-type.
DOI: 10.7284/108625
title: TSG (Thermosalinograph) data collected during research cruise EN475 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648733
title: MTT-WS1-HaCaT-AMD3100.xlsx

description: To detect the effect of AMD3100 on cell viability of HaCaT and WS1 cells.
DOI: 10.6084/m9.figshare.7648733.v1
title: MTT-WS1-HaCaT-AMD3100.xlsx

description: To detect the effect of AMD3100 on cell viability of HaCaT and WS1 cells.
DOI: 10.6084/m9.figshare.7648775.v1
title: VCP maintains lysosomal homeostasis and TFEB activity in differentiated skeletal muscle

description: Differentiated tissue is particularly vulnerable to alterations in protein and organelle homeostasis. The essential protein VCP, mutated in hereditary inclusion body myopathy, amyotrophic lateral sclerosis and frontotemporal dementia, is critical for efficient clearance of misfolded proteins and damaged organelles in dividing cells, but its role in terminally differentiated tissue affected by disease mutations is less clear. To understand the relevance of VCP in differentiated tissue, we inactivated it in skeletal muscle of adult mice. Surprisingly, knockout muscle demonstrated a necrotic myopathy with increased macroautophagic/autophagic proteins and damaged lysosomes. This was not solely due to a defect in autophagic degradation because age-matched mice with muscle inactivation of the autophagy essential protein, ATG5, did not demonstrate a myopathy. Notably, myofiber necrosis was preceded by upregulation of LGALS3/Galectin-3, a marker of damaged lysosomes, and TFEB activation, suggesting early defects in the lysosomal system. Consistent with that, myofiber necrosis was recapitulated by chemical induction of lysosomal membrane permeabilization (LMP) in skeletal muscle. Moreover, TFEB was activated after LMP in cells, but activation and nuclear localization of TFEB persisted upon VCP inactivation or disease mutant expression. Our data identifies VCP as central mediator of both lysosomal clearance and biogenesis in skeletal muscle. <b>Abbreviations:</b> AAA: ATPases Associated with diverse cellular Activities; TUBA1A/α-tubulin: tubulin alpha 1a; ATG5: autophagy related 5; ATG7: autophagy related 7; ACTA1: actin alpha 1, skeletal muscle; CLEAR: coordinated lysosomal expression and regulation; CTSB/D: cathepsin B/D; Ctrl: control; DAPI: diamidino-2-phenylindole; EBSS: Earle’s balanced salt solution; ELDR: endolysosomal damage response; ESCRT: endosomal sorting complexes required for transport; Gastroc/G: gastrocnemius; H&E: hematoxylin and eosin; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IBMPFD/ALS: inclusion body myopathy associated with Paget disease of the bone, frontotemporal dementia and amyotrophic lateral sclerosis; i.p.: intraperitoneal; LAMP1/2: lysosomal-associated membrane protein 1/2; LLOMe: Leu-Leu methyl ester hydrobromide; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; MTOR: mechanistic target of rapamycin kinase; MYL1: myosin light chain 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MSP: multisystem proteinopathy; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; Quad/Q: quadriceps; RHEB: Ras homolog, mTORC1 binding; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TA: tibialis anterior; siRNA: small interfering RNA; SQSTM1/p62, sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBS: Tris-buffered saline; TXFN, tamoxifen; UBXN6/UBXD1: UBX domain protein 6; VCP: valosin containing protein; WT: wild-type.
DOI: 10.7284/108627
title: TSG (Thermosalinograph) data collected during research cruise EN475 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648775.v3
title: VCP maintains lysosomal homeostasis and TFEB activity in differentiated skeletal muscle

description: Differentiated tissue is particularly vulnerable to alterations in protein and organelle homeostasis. The essential protein VCP, mutated in hereditary inclusion body myopathy, amyotrophic lateral sclerosis and frontotemporal dementia, is critical for efficient clearance of misfolded proteins and damaged organelles in dividing cells, but its role in terminally differentiated tissue affected by disease mutations is less clear. To understand the relevance of VCP in differentiated tissue, we inactivated it in skeletal muscle of adult mice. Surprisingly, knockout muscle demonstrated a necrotic myopathy with increased macroautophagic/autophagic proteins and damaged lysosomes. This was not solely due to a defect in autophagic degradation because age-matched mice with muscle inactivation of the autophagy essential protein, ATG5, did not demonstrate a myopathy. Notably, myofiber necrosis was preceded by upregulation of LGALS3/Galectin-3, a marker of damaged lysosomes, and TFEB activation, suggesting early defects in the lysosomal system. Consistent with that, myofiber necrosis was recapitulated by chemical induction of lysosomal membrane permeabilization (LMP) in skeletal muscle. Moreover, TFEB was activated after LMP in cells, but activation and nuclear localization of TFEB persisted upon VCP inactivation or disease mutant expression. Our data identifies VCP as central mediator of both lysosomal clearance and biogenesis in skeletal muscle. <b>Abbreviations:</b> AAA: ATPases Associated with diverse cellular Activities; TUBA1A/α-tubulin: tubulin alpha 1a; ATG5: autophagy related 5; ATG7: autophagy related 7; ACTA1: actin alpha 1, skeletal muscle; CLEAR: coordinated lysosomal expression and regulation; CTSB/D: cathepsin B/D; Ctrl: control; DAPI: diamidino-2-phenylindole; EBSS: Earle’s balanced salt solution; ELDR: endolysosomal damage response; ESCRT: endosomal sorting complexes required for transport; Gastroc/G: gastrocnemius; H&E: hematoxylin and eosin; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IBMPFD/ALS: inclusion body myopathy associated with Paget disease of the bone, frontotemporal dementia and amyotrophic lateral sclerosis; i.p.: intraperitoneal; LAMP1/2: lysosomal-associated membrane protein 1/2; LLOMe: Leu-Leu methyl ester hydrobromide; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; MTOR: mechanistic target of rapamycin kinase; MYL1: myosin light chain 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MSP: multisystem proteinopathy; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; Quad/Q: quadriceps; RHEB: Ras homolog, mTORC1 binding; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TA: tibialis anterior; siRNA: small interfering RNA; SQSTM1/p62, sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBS: Tris-buffered saline; TXFN, tamoxifen; UBXN6/UBXD1: UBX domain protein 6; VCP: valosin containing protein; WT: wild-type.
DOI: 10.7284/107310
title: Winch data collected during research cruise EN475 using a Markey DUSH-5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648775.v2
title: VCP maintains lysosomal homeostasis and TFEB activity in differentiated skeletal muscle

description: Differentiated tissue is particularly vulnerable to alterations in protein and organelle homeostasis. The essential protein VCP, mutated in hereditary inclusion body myopathy, amyotrophic lateral sclerosis and frontotemporal dementia, is critical for efficient clearance of misfolded proteins and damaged organelles in dividing cells, but its role in terminally differentiated tissue affected by disease mutations is less clear. To understand the relevance of VCP in differentiated tissue, we inactivated it in skeletal muscle of adult mice. Surprisingly, knockout muscle demonstrated a necrotic myopathy with increased macroautophagic/autophagic proteins and damaged lysosomes. This was not solely due to a defect in autophagic degradation because age-matched mice with muscle inactivation of the autophagy essential protein, ATG5, did not demonstrate a myopathy. Notably, myofiber necrosis was preceded by upregulation of LGALS3/Galectin-3, a marker of damaged lysosomes, and TFEB activation, suggesting early defects in the lysosomal system. Consistent with that, myofiber necrosis was recapitulated by chemical induction of lysosomal membrane permeabilization (LMP) in skeletal muscle. Moreover, TFEB was activated after LMP in cells, but activation and nuclear localization of TFEB persisted upon VCP inactivation or disease mutant expression. Our data identifies VCP as central mediator of both lysosomal clearance and biogenesis in skeletal muscle. <b>Abbreviations:</b> AAA: ATPases Associated with diverse cellular Activities; TUBA1A/α-tubulin: tubulin alpha 1a; ATG5: autophagy related 5; ATG7: autophagy related 7; ACTA1: actin alpha 1, skeletal muscle; CLEAR: coordinated lysosomal expression and regulation; CTSB/D: cathepsin B/D; Ctrl: control; DAPI: diamidino-2-phenylindole; EBSS: Earle’s balanced salt solution; ELDR: endolysosomal damage response; ESCRT: endosomal sorting complexes required for transport; Gastroc/G: gastrocnemius; H&E: hematoxylin and eosin; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IBMPFD/ALS: inclusion body myopathy associated with Paget disease of the bone, frontotemporal dementia and amyotrophic lateral sclerosis; i.p.: intraperitoneal; LAMP1/2: lysosomal-associated membrane protein 1/2; LLOMe: Leu-Leu methyl ester hydrobromide; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; MTOR: mechanistic target of rapamycin kinase; MYL1: myosin light chain 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MSP: multisystem proteinopathy; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; Quad/Q: quadriceps; RHEB: Ras homolog, mTORC1 binding; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TA: tibialis anterior; siRNA: small interfering RNA; SQSTM1/p62, sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBS: Tris-buffered saline; TXFN, tamoxifen; UBXN6/UBXD1: UBX domain protein 6; VCP: valosin containing protein; WT: wild-type.
DOI: 10.7284/107253
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN476 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107316
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN476 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108634
title: Fluorometer data collected during research cruise EN476 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648607
title: Additional file 1: of Evolution of salivary glue genes in Drosophila species

description: Table S1. Number of gene copies for each family, and results of CAFE analysis for the glue gene families. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.7648607.v1
title: Additional file 1: of Evolution of salivary glue genes in Drosophila species

description: Table S1. Number of gene copies for each family, and results of CAFE analysis for the glue gene families. (XLSX 161 kb)
DOI: 10.7284/103241
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN476 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107313
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN476 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111982
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN476 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108629
title: Gyrocompass data collected during research cruise EN476 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108630
title: Gyrocompass data collected during research cruise EN476 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107315
title: Singlebeam Echosounder data collected during research cruise EN476 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108632
title: Speedlog data collected during research cruise EN476 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108631
title: TSG (Thermosalinograph) data collected during research cruise EN476 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648514
title: MOESM1 of Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein

description: Additional file 1: Table S1. Average protein abundances and fold changes for proteins from cytoplasmic (A), periplasmic (B) and insoluble/membrane (C) fractions.
DOI: 10.6084/m9.figshare.7648523
title: MOESM2 of Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein

description: Additional file 2: Table S2. Voronoi Treemap of log2 fold changes in protein abundance (E. coli CyDisCo vs. scFv and E. coli CyDisCo vs. mf_scFv).
DOI: 10.6084/m9.figshare.7648514.v1
title: MOESM1 of Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein

description: Additional file 1: Table S1. Average protein abundances and fold changes for proteins from cytoplasmic (A), periplasmic (B) and insoluble/membrane (C) fractions.
DOI: 10.6084/m9.figshare.7648523.v1
title: MOESM2 of Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein

description: Additional file 2: Table S2. Voronoi Treemap of log2 fold changes in protein abundance (E. coli CyDisCo vs. scFv and E. coli CyDisCo vs. mf_scFv).
DOI: 10.7284/108633
title: TSG (Thermosalinograph) data collected during research cruise EN476 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107314
title: Winch data collected during research cruise EN476 using a Markey DUSH-5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103242
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN477 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107317
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN477 using a Furuno GP-90D instrument system onboard the platform RV Endeavor
DOI: 10.7284/111981
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN477 using a Trimble NT-300D instrument system onboard the platform RV Endeavor
DOI: 10.7284/108638
title: Speedlog data collected during research cruise EN477 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107257
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN478 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107322
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN478 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648415
title: Additional file 2: of Prevalence and determinants of unmet need for family planning among married women in Ghana-a multinomial logistic regression analysis of the GDHS, 2014

description: Results log. (LOG 3 kb)
DOI: 10.6084/m9.figshare.7648421
title: MOESM2 of Ulcerative colitis: functional analysis of the in-depth proteome

description: Additional file 2. Complete list of identified proteins including UC/Healthy ratios and p-values, lists of gene ontology term enrichments, enriched functions discussed in the article and their proteins.
DOI: 10.6084/m9.figshare.7648415.v1
title: Additional file 2: of Prevalence and determinants of unmet need for family planning among married women in Ghana-a multinomial logistic regression analysis of the GDHS, 2014

description: Results log. (LOG 3 kb)
DOI: 10.6084/m9.figshare.7648421.v1
title: MOESM2 of Ulcerative colitis: functional analysis of the in-depth proteome

description: Additional file 2. Complete list of identified proteins including UC/Healthy ratios and p-values, lists of gene ontology term enrichments, enriched functions discussed in the article and their proteins.
DOI: 10.6084/m9.figshare.7648406
title: Additional file 1: of Prevalence and determinants of unmet need for family planning among married women in Ghana-a multinomial logistic regression analysis of the GDHS, 2014

description: Tabulation of unmet_need_tu. (XLS 1710 kb)
DOI: 10.7284/108646
title: Fluorometer data collected during research cruise EN478 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648406.v1
title: Additional file 1: of Prevalence and determinants of unmet need for family planning among married women in Ghana-a multinomial logistic regression analysis of the GDHS, 2014

description: Tabulation of unmet_need_tu. (XLS 1710 kb)
DOI: 10.7284/103243
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN478 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648382
title: MOESM5 of Prognostic role of PD-L1 for HCC patients after potentially curative resection: a meta-analysis

description: Additional file 5: Table S4. Meta-regression analysis for overall survival and recurrence-free survival.
DOI: 10.6084/m9.figshare.7648382.v1
title: MOESM5 of Prognostic role of PD-L1 for HCC patients after potentially curative resection: a meta-analysis

description: Additional file 5: Table S4. Meta-regression analysis for overall survival and recurrence-free survival.
DOI: 10.7284/107319
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN478 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111980
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN478 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648361
title: MOESM3 of Prognostic role of PD-L1 for HCC patients after potentially curative resection: a meta-analysis

description: Additional file 3: Table S3. Association of PD-L1 and clinicopathological features and tumour-infiltrating lymphocytes of the included studies.
DOI: 10.7284/108641
title: Gyrocompass data collected during research cruise EN478 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7648361.v1
title: MOESM3 of Prognostic role of PD-L1 for HCC patients after potentially curative resection: a meta-analysis

description: Additional file 3: Table S3. Association of PD-L1 and clinicopathological features and tumour-infiltrating lymphocytes of the included studies.