cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14854114
title: Rab3a, a small GTP-binding protein, is required for the stabilization of the murine leukaemia virus Gag protein

description: We recently identified a CD63-interacting protein to understand the role of CD63 in virion production of the human immunodeficiency virus type 1, and we have found that Rab3a forms a complex with CD63. In this study, we analysed the effect of Rab3a on virion production of the murine leukaemia virus (MLV), which is another member of the retrovirus family. We found that Rab3a silencing induced lysosomal degradation of the MLV Gag protein, and recovery of the Rab3a expression restored the level of the Gag protein through a complex formation of MLV Gag and Rab3a, indicating that Rab3a is required for MLV Gag protein expression. In contrast, CD63 silencing decreased the infectivity of released virions but had no effect on virion production, indicating that CD63 facilitates the infectivity of released MLV particles. Although Rab3a induced CD63 degradation in uninfected cells, the complex of MLV Gag and Rab3a suppressed the Rab3a-mediated CD63 degradation in MLV-infected cells. Finally, we found that the MLV Gag protein interacts with Rab3a to stabilize its own protein and CD63 that facilitates the infectivity of released MLV particles. Considering the involvement of Rab3a in lysosome trafficking to the plasma membrane, it may also induce cell surface transport of the MLV Gag protein.
DOI: 10.6084/m9.figshare.16864165.v1
title: Unexplored Cdc42 functions at the budding yeast nucleus suggested by subcellular localization

description: In budding yeast, the Rho-family GTPase Cdc42 has several functions that depend on its subcellular localization and the cell cycle stage. During bud formation, Cdc42 localizes to the plasma membrane at the bud tip and bud neck where it carries out functions in actin polymerization, spindle positioning, and exocytosis to ensure proper polarity development. Recent live-cell imaging analysis revealed a novel localization of Cdc42 to a discrete intracellular focus associated with the vacuole and nuclear envelope. The discovery of this novel Cdc42 localization led to the identification of a new function in ESCRT-mediated nuclear envelope sealing. However, other aspects of this intracellular localization and its functional implications were not explored. Here, we further characterize the Cdc42 focus and present several novel observations that suggest possible additional Cdc42 functions at the nucleus, including nucleus-vacuole junction formation, nuclear envelope tethering, nuclear migration, and nucleopodia formation.
DOI: 10.6084/m9.figshare.16699108
title: Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators

description: GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for <i>Dictyostelium</i> species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.
DOI: 10.6084/m9.figshare.16699108.v1
title: INTERACTOME AND EVOLUTIONARY CONSERVATION OF DICTYOSTELID SMALL GTPASES AND THEIR DIRECT REGULATORS

description: The GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under respectively positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signaling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoire, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unraveling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Almost completely assembled genomes and cell-type specific and developmental transcriptomes are available for <i>Dictyostelium</i> species that span the 0.5 billion years of evolution of the group from their unicellular ancestor. In this work, we identified all GTPases, GEFs and GAP from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and change in their functional domain architecture and in their developmental and cell-type specific expression. We performed hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlighted sets known to interact experimentally and many novel combinations. The work represents a valuable resource for research into all fields of cellular regulation.
DOI: 10.6084/m9.figshare.16699108.v2
title: Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators

description: GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for <i>Dictyostelium</i> species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.
DOI: 10.6084/m9.figshare.21512432
title: Small-molecule inhibitors of P-Rex guanine-nucleotide exchange factors

description: P-Rex1 and P-Rex2 are guanine-nucleotide exchange factors (GEFs) that activate Rac small GTPases in response to the stimulation of G protein-coupled receptors and phosphoinositide 3-kinase. P-Rex Rac-GEFs regulate the morphology, adhesion and migration of various cell types, as well as reactive oxygen species production and cell cycle progression. P-Rex Rac-GEFs also have pathogenic roles in the initiation, progression or metastasis of several types of cancer. With one exception, all P-Rex functions are known or assumed to be mediated through their catalytic Rac-GEF activity. Thus, inhibitors of P-Rex Rac-GEF activity would be valuable research tools. We have generated a panel of small-molecule P-Rex inhibitors that target the interface between the catalytic DH domain of P-Rex Rac-GEFs and Rac. Our best-characterized compound, P-Rex inhibitor 1 (PREX-in1), blocks the Rac-GEF activity of full-length P-Rex1 and P-Rex2, and of their isolated catalytic domains, <i>in vitro</i> at low-micromolar concentration, without affecting the activities of several other Rho-GEFs. PREX-in1 blocks the P-Rex1 dependent spreading of PDGF-stimulated endothelial cells and the production of reactive oxygen species in fMLP-stimulated mouse neutrophils. Structure-function analysis revealed critical structural elements of PREX-in1, allowing us to develop derivatives with increased efficacy, the best with an IC<sub>50</sub> of 2 µM. In summary, we have developed PREX-in1 and derivative small-molecule compounds that will be useful laboratory research tools for the study of P-Rex function. These compounds may also be a good starting point for the future development of more sophisticated drug-like inhibitors aimed at targeting P-Rex Rac-GEFs in cancer.
DOI: 10.6084/m9.figshare.21512432.v1
title: Small-molecule inhibitors of P-Rex guanine-nucleotide exchange factors

description: P-Rex1 and P-Rex2 are guanine-nucleotide exchange factors (GEFs) that activate Rac small GTPases in response to the stimulation of G protein-coupled receptors and phosphoinositide 3-kinase. P-Rex Rac-GEFs regulate the morphology, adhesion and migration of various cell types, as well as reactive oxygen species production and cell cycle progression. P-Rex Rac-GEFs also have pathogenic roles in the initiation, progression or metastasis of several types of cancer. With one exception, all P-Rex functions are known or assumed to be mediated through their catalytic Rac-GEF activity. Thus, inhibitors of P-Rex Rac-GEF activity would be valuable research tools. We have generated a panel of small-molecule P-Rex inhibitors that target the interface between the catalytic DH domain of P-Rex Rac-GEFs and Rac. Our best-characterized compound, P-Rex inhibitor 1 (PREX-in1), blocks the Rac-GEF activity of full-length P-Rex1 and P-Rex2, and of their isolated catalytic domains, <i>in vitro</i> at low-micromolar concentration, without affecting the activities of several other Rho-GEFs. PREX-in1 blocks the P-Rex1 dependent spreading of PDGF-stimulated endothelial cells and the production of reactive oxygen species in fMLP-stimulated mouse neutrophils. Structure-function analysis revealed critical structural elements of PREX-in1, allowing us to develop derivatives with increased efficacy, the best with an IC<sub>50</sub> of 2 µM. In summary, we have developed PREX-in1 and derivative small-molecule compounds that will be useful laboratory research tools for the study of P-Rex function. These compounds may also be a good starting point for the future development of more sophisticated drug-like inhibitors aimed at targeting P-Rex Rac-GEFs in cancer.
DOI: 10.6084/m9.figshare.14332990
title: Phylogenetic reconstruction and evolution of the Rab GTPase gene family in Amoebozoa

description: Rab GTPase is a paralog-rich gene family that controls the maintenance of the eukaryotic cell compartmentalization system. Diverse eukaryotes have varying numbers of Rab paralogs. Currently, little is known about the evolutionary pattern of Rab GTPase in most major eukaryotic ‘supergroups’. Here, we present a comprehensive phylogenetic reconstruction of the Rab GTPase gene family in the eukaryotic ‘supergroup’ Amoebozoa, a diverse lineage represented by unicellular and multicellular organisms. We demonstrate that Amoebozoa conserved 20 of the 23 ancestral Rab GTPases predicted to be present in the last eukaryotic common ancestor and massively expanded several ‘novel’ in-paralogs. Due to these ‘novel’ in-paralogs, the Rab family composition dramatically varies between the members of Amoebozoa; as a consequence, ‘supergroup’-based studies may significantly change our current understanding of the evolution and diversity of this gene family. The high diversity of the Rab GTPase gene family in Amoebozoa makes this ‘supergroup’ a key lineage to study and advance our knowledge of the evolution of Rab in Eukaryotes.
DOI: 10.6084/m9.figshare.14332990.v1
title: Phylogenetic reconstruction and evolution of the Rab GTPase gene family in Amoebozoa

description: Rab GTPase is a paralog-rich gene family that controls the maintenance of the eukaryotic cell compartmentalization system. Diverse eukaryotes have varying numbers of Rab paralogs. Currently, little is known about the evolutionary pattern of Rab GTPase in most major eukaryotic ‘supergroups’. Here, we present a comprehensive phylogenetic reconstruction of the Rab GTPase gene family in the eukaryotic ‘supergroup’ Amoebozoa, a diverse lineage represented by unicellular and multicellular organisms. We demonstrate that Amoebozoa conserved 20 of the 23 ancestral Rab GTPases predicted to be present in the last eukaryotic common ancestor and massively expanded several ‘novel’ in-paralogs. Due to these ‘novel’ in-paralogs, the Rab family composition dramatically varies between the members of Amoebozoa; as a consequence, ‘supergroup’-based studies may significantly change our current understanding of the evolution and diversity of this gene family. The high diversity of the Rab GTPase gene family in Amoebozoa makes this ‘supergroup’ a key lineage to study and advance our knowledge of the evolution of Rab in Eukaryotes.
DOI: 10.6084/m9.figshare.20473065.v1
title: Quantitation of RhoA activation: differential binding to downstream effectors

description: The small GTPase RhoA controls many important cellular processes through its ability to activate multiple downstream effector pathways. Most RhoA effectors contain a Rho-binding domain (RBD), and interaction between active RhoA and the RBD typically induces a conformational change in effectors that stimulates their recruitment or activity. Isolated GTPase binding domains fused to GST have been widely used in so-called pulldown assays to measure the activation state of other GTPases in cell lysates. Similarly, GST fusions containing the RBD of the RhoA effector Rhotekin have been widely adopted as a standardized tool for the measurement of RhoA activation. RBDs have also been used to generate fluorescent reporter constructs to localize sites of GTPase activation in intact cells. In this report, we demonstrate that not all forms of active RhoA are capable of interacting with the Rhotekin RBD. A constitutively active RhoA-G14V mutant, which interacted with the RBDs of ROCK2 and mDIA1, was unable to bind the Rhotekin RBD as evidenced by both conventional GST pulldown assay and our newly established BRET assay. Furthermore, active RhoA induced by different stimuli in cells also displayed binding preference for its diverse effectors. Our data demonstrate that RhoA may undergo effector-specific activation for differential regulation of its downstream pathways, and that RhoA activation should not be defined solely by its interaction with Rhotekin.
DOI: 10.6084/m9.figshare.14854114.v2
title: Rab3a, a small GTP-binding protein, is required for the stabilization of the murine leukaemia virus Gag protein

description: We recently identified a CD63-interacting protein to understand the role of CD63 in virion production of the human immunodeficiency virus type 1, and we have found that Rab3a forms a complex with CD63. In this study, we analysed the effect of Rab3a on virion production of the murine leukaemia virus (MLV), which is another member of the retrovirus family. We found that Rab3a silencing induced lysosomal degradation of the MLV Gag protein, and recovery of the Rab3a expression restored the level of the Gag protein through a complex formation of MLV Gag and Rab3a, indicating that Rab3a is required for MLV Gag protein expression. In contrast, CD63 silencing decreased the infectivity of released virions but had no effect on virion production, indicating that CD63 facilitates the infectivity of released MLV particles. Although Rab3a induced CD63 degradation in uninfected cells, the complex of MLV Gag and Rab3a suppressed the Rab3a-mediated CD63 degradation in MLV-infected cells. Finally, we found that the MLV Gag protein interacts with Rab3a to stabilize its own protein and CD63 that facilitates the infectivity of released MLV particles. Considering the involvement of Rab3a in lysosome trafficking to the plasma membrane, it may also induce cell surface transport of the MLV Gag protein.
DOI: 10.6084/m9.figshare.14854114.v1
title: Rab3a, a small GTP-binding protein, is required for the stabilization of the murine leukaemia virus gag protein

description: We recently identified a CD63-interacting protein to understand the role of CD63 in virion production of the human immunodeficiency virus type 1, and we have found that Rab3a forms a complex with CD63. In this study, we analysed the effect of Rab3a on virion production of the murine leukaemia virus (MLV), which is another member of the retrovirus family. We found that Rab3a silencing induced lysosomal degradation of the MLV Gag protein, and recovery of the Rab3a expression restored the level of the Gag protein through a complex formation of MLV Gag and Rab3a, indicating that Rab3a is required for MLV Gag protein expression. In contrast, CD63 silencing decreased the infectivity of released virions but had no effect on virion production, indicating that CD63 facilitates the infectivity of released MLV particles. Although Rab3a induced CD63 degradation in uninfected cells, the complex of MLV Gag and Rab3a suppressed the Rab3a-mediated CD63 degradation in MLV-infected cells. Finally, we found that the MLV Gag protein interacts with Rab3a to stabilize its own protein and CD63 that facilitates the infectivity of released MLV particles. Considering the involvement of Rab3a in lysosome trafficking to the plasma membrane, it may also induce cell surface transport of the MLV Gag protein.
DOI: 10.6084/m9.figshare.21638291
title: Unprocessed FASTQ Read Data From: Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

description: Unprocessed FASTQ read data from: Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli, 10.1021/acssynbio.5b00131 Tiles are labelled 1 through 11 for the proJK1-LGK selection or 1-2, 3-4 for the proNR2-LGK1 selection. Selection replicates are labelled -1 or -2 in the filename. The reference (or unselected) is labelled with U.
DOI: 10.6084/m9.figshare.21638291.v1
title: Unprocessed FASTQ Read Data From: Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

description: Unprocessed FASTQ read data from: Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli, 10.1021/acssynbio.5b00131 Tiles are labelled 1 through 11 for the proJK1-LGK selection or 1-2, 3-4 for the proNR2-LGK1 selection. Selection replicates are labelled -1 or -2 in the filename. The reference (or unselected) is labelled with U.
DOI: 10.6084/m9.figshare.21638198.v1
title: EBI Data_Final.xlsx

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.6084/m9.figshare.21638198.v2
title: Data for " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.6084/m9.figshare.21638198.v3
title: Data for " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.5281/zenodo.7375085
title: PERTEMUAN 12_29 NOVEMBER 2022_STUDY KASUS SIKLUS AKUNTANSI PERUSAHAAN JASA_PRAKTEK AKUNTANSI_UNIVERSITAS GRESIK_JAM 18.00-20.00

description: <strong>Capaian Pembelajaran Mata Kuliah (CPMK)</strong> Untuk mengetahui dan mengevaluasi pemahaman terkait dengan siklus akuntansi <strong>Indikator Pembelajaran</strong> 1. Tes Lisan 2. Tes Tulis
description: PERTEMUAN 12_29 NOVEMBER 2022_STUDY KASUS SIKLUS AKUNTANSI PERUSAHAAN JASA_PRAKTEK AKUNTANSI_UNIVERSITAS GRESIK_JAM 18.00-20.00
DOI: 10.5281/zenodo.7375084
title: PERTEMUAN 12_29 NOVEMBER 2022_STUDY KASUS SIKLUS AKUNTANSI PERUSAHAAN JASA_PRAKTEK AKUNTANSI_UNIVERSITAS GRESIK_JAM 18.00-20.00

description: <strong>Capaian Pembelajaran Mata Kuliah (CPMK)</strong> Untuk mengetahui dan mengevaluasi pemahaman terkait dengan siklus akuntansi <strong>Indikator Pembelajaran</strong> 1. Tes Lisan 2. Tes Tulis
description: PERTEMUAN 12_29 NOVEMBER 2022_STUDY KASUS SIKLUS AKUNTANSI PERUSAHAAN JASA_PRAKTEK AKUNTANSI_UNIVERSITAS GRESIK_JAM 18.00-20.00
DOI: 10.6084/m9.figshare.21638198
title: Data for " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.6084/m9.figshare.21638198.v5
title: Data for " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.6084/m9.figshare.21638198.v4
title: Data for " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder

description: The data for the paper " Dysfunction of External Switching and Backward Inhibition in Major Depressive Disorder "
DOI: 10.6084/m9.figshare.21639245
title: MOSCAP.xlsx

description: In the dataset, it ranges from 3 rooms with 20 cases to 20 rooms with 160 cases.
DOI: 10.6084/m9.figshare.21639245.v1
title: MOSCAP.xlsx

description: In the dataset, it ranges from 3 rooms with 20 cases to 20 rooms with 160 cases.
DOI: 10.26207/e4v3-b123
title: Genotyping of SECORE Outplanted Colonies in Curacao
DOI: 10.4225/08/5b31c59fca196
title: PaintCloud

description: A selection of 3D lidar SLAM point clouds colourised using an arbitrary mobile mapping device and an independent camera.