cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1436177
title: transcript GTF annotation of colon smooth muscle

description: transcript annotation of colon smooth muscle
DOI: 10.6084/m9.figshare.1436179.v1
title: smooth muscle cell in colon

description: smooth muscle cell in colon
DOI: 10.6084/m9.figshare.1436188.v4
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436179.v3
title: transcript GTF annotation of smooth muscle cells in colon

description: trascript annotation of smooth muscle cells in colon
DOI: 10.6084/m9.figshare.1436179.v2
title: transcript annotation of smooth muscle cells in colon

description: trascript annotation of smooth muscle cells in colon
DOI: 10.6084/m9.figshare.1436177.v1
title: transcript annotation of colon smooth muscle

description: transcript annotation of colon smooth muscle
DOI: 10.6084/m9.figshare.1436178.v1
title: transcript annotation of smooth muscle cells in jejunum

description: transcript annotation of smooth muscle cells in jejunum
DOI: 10.6084/m9.figshare.1436188.v5
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436175
title: transcript GTF annotation of PDGFRa+ cells in colon smooth muscle

description: transcript annotation of PDGFRa+ cells in colon smooth muscle
DOI: 10.6084/m9.figshare.1436176
title: transcript GTF annotation of jejunum smooth muscle

description: transcript annotation of jejunum smooth muscle
DOI: 10.6084/m9.figshare.1436172
title: transcript GTF annotation of PDGFRa+ cells in jejunum smooth muscle

description: transcript annotation of PDGFRa+ cells in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1436171
title: transcript GTF annotation of PDGFRa+ cells in colon mucosa

description: transcript annotation of PDGFRa+ cells in colon mucosa
DOI: 10.6084/m9.figshare.1436175.v2
title: transcript GTF annotation of PDGFRa+ cells in colon smooth muscle

description: transcript annotation of PDGFRa+ cells in colon smooth muscle
DOI: 10.6084/m9.figshare.1436188.v6
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436171.v2
title: transcript GTF annotation of PDGFRa+ cells in colon mucosa

description: transcript annotation of PDGFRa+ cells in colon mucosa
DOI: 10.6084/m9.figshare.1436172.v2
title: transcript GTF annotation of PDGFRa+ cells in jejunum smooth muscle

description: transcript annotation of PDGFRa+ cells in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1436175.v1
title: transcript annotation of PDGFRa+ cells in colon smooth muscle

description: transcript annotation of PDGFRa+ cells in colon smooth muscle
DOI: 10.6084/m9.figshare.1436176.v1
title: transcript annotation of jejunum smooth muscle

description: transcript annotation of jejunum smooth muscle
DOI: 10.6084/m9.figshare.1436168
title: Surf Paddling Data

description: These data are reported in a manuscript submitted to PLOS One
DOI: 10.6084/m9.figshare.1436170
title: transcript GTF annotation of all gastrointestinal samples

description: trascript annotation of all gastrointestinal samples
DOI: 10.6084/m9.figshare.1436188.v7
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436171.v1
title: transcript annotation of PDGFRa+ cells in colon mucosa

description: transcript annotation of PDGFRa+ cells in colon mucosa
DOI: 10.6084/m9.figshare.1436115
title: Data associated with "Sulfur Isotope Effects of Dissimilatory Sulfite Reductase"

description: Data files associated with Leavitt WD, Bradley AS, Santos AA, Pereira IAC and Johnston DT (2015) <strong>Sulfur Isotope Effects of Dissimilatory Sulfite Reductase</strong>. Front. Microbiol. 6:1392. doi: 10.3389/fmicb.2015.01392 There are four files in this fileset:1. <b>Dvulgaris_DsrAB.xlsx</b>Raw data and model output for <i>D vulgaris</i> experiment 2. <b>Afulgidis_DsrAB.xlsx</b>Raw data for <i>A. fulgidis</i> experiment 3. <b>Compilation_of_S_isotope_fractionation.xlsx</b>Compilation of S isotope fractionations from literature4. <b>Summary_stats_S_fractionation.xlsx</b>Statistics of literature S isotope compilation<br>
DOI: 10.6084/m9.figshare.1436170.v2
title: transcript GTF annotation of all gastrointestinal samples

description: trascript annotation of all gastrointestinal samples
DOI: 10.6084/m9.figshare.1436172.v1
title: transcript annotation of PDGFRa+ cells in jejunum smooth muscle

description: transcript annotation of PDGFRa+ cells in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1436095
title: Modeling the spatial dynamics of the Atlantic forest cover in Trajano de Moraes, Brazil

description: We mapped forest cover of Trajano de Moraes in five timeslots between years 1978 and 2014, and used the weights of evidence method for modeling spatial dynamics of this landscape, to understand where natural regeneration is occurring and which are the main factors related to this phenomenon. In forest cover maps, value 2 stands for class "Atlantic forest" and value 1 stands for class "matrix".
DOI: 10.6084/m9.figshare.1436170.v1
title: transcript annotation of all gastrointestinal samples

description: trascript annotation of all gastrointestinal samples
DOI: 10.6084/m9.figshare.1436188.v8
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436188.v10
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436188.v9
title: A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells

description: Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
DOI: 10.6084/m9.figshare.1436095.v2
title: Modeling the spatial dynamics of the Atlantic forest cover in Trajano de Moraes, Brazil

description: We mapped forest cover of Trajano de Moraes in five timeslots between years 1978 and 2014, and used the weights of evidence method for modeling spatial dynamics of this landscape, to understand where natural regeneration is occurring and which are the main factors related to this phenomenon. In forest cover maps, value 2 stands for class "Atlantic forest" and value 1 stands for class "matrix".
DOI: 10.6084/m9.figshare.1436095.v3
title: Modeling the spatial dynamics of the Atlantic forest cover in Trajano de Moraes, Brazil

description: We mapped forest cover of Trajano de Moraes in five timeslots between years 1978 and 2014, and used the weights of evidence method for modeling spatial dynamics of this landscape, to understand where natural regeneration is occurring and which are the main factors related to this phenomenon. In forest cover maps, value 2 stands for class "Atlantic forest" and value 1 stands for class "matrix".
DOI: 10.6084/m9.figshare.1436095.v4
title: Modeling the spatial dynamics of the Atlantic forest cover in Trajano de Moraes, Brazil

description: We mapped forest cover of Trajano de Moraes in five timeslots between years 1978 and 2014, and used the weights of evidence method for modeling spatial dynamics of this landscape, to understand where natural regeneration is occurring and which are the main factors related to this phenomenon. In forest cover maps, value 2 stands for class "Atlantic forest" and value 1 stands for class "matrix".
DOI: 10.6084/m9.figshare.1436095.v6
title: Modeling the spatial dynamics of the Atlantic forest cover in Trajano de Moraes, Brazil

description: We mapped forest cover of Trajano de Moraes in five timeslots between years 1978 and 2014, and used the weights of evidence method for modeling spatial dynamics of this landscape, to understand where natural regeneration is occurring and which are the main factors related to this phenomenon. In forest cover maps, value 2 stands for class "Atlantic forest" and value 1 stands for class "matrix".
DOI: 10.6084/m9.figshare.1436073
title: A new endothiodont dicynodont (Therapsida, Anomodontia) from the Permian Ruhuhu Formation (Songea Group) of Tanzania and its feeding system

description: ABSTRACTCranial material of the dicynodont <i>Endothiodon</i> from the middle fossiliferous horizon of the Permian Ruhuhu Formation (Ruhuhu Basin, Tanzania) is described as a new species, <i>E. tolani</i>. <i>Endothiodon tolani</i> is distinguished from other <i>Endothiodon</i> species by the absence of a pineal boss and the presence of tusks in most specimens. Although some parts of the Ruhuhu Formation probably correlate with the <i>Eodicynodon</i> or <i>Tapinocephalus</i> assemblage zones of the South African Karoo Basin, it is uncertain whether <i>E. tolani</i> is older than <i>E. bathystoma</i> or <i>E. mahalanobisi</i>. There is less evidence for extensive anteroposterior translation of the mandible in <i>E. tolani</i> than in other dicynodonts. The jaw joint is specialized for allowing some medial-lateral motion. Mastication involved unilateral chewing. Flexure of the postdentary bones relative to the fused dentaries permitted the posterolaterally directed rows of teeth on one side of the skull and mandible to move past one another. The long tooth rows and prominent horn-covered ridges and grooves on the palate and mandible of <i>Endothiodon</i> are unique among dicynodonts. Comparisons with other taxa suggest that its feeding system may have been specialized for cutting three-dimensional objects such as stems or rhizomes. The dicynodont feeding system is very stereotyped throughout the clade's history, but <i>Endothiodon</i> escaped the constraints that affected other dicynodonts, allowing it to evolve a unique skull morphology. This evolutionary flexibility did not translate into high taxonomic richness (we recognize only three species of <i>Endothiodon</i>), but <i>Endothiodon</i> was able to achieve high levels of relative abundance in some basins.http://zoobank.org/urn:lsid:zoobank.org:pub:9686F708-2E6E-40EB-956F-05659889684FSUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP