cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13073197.v3
title: Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs

description: Mitochondria-associated membranes (MAMs) are essential communication subdomains of the endoplasmic reticulum (ER) that interact with mitochondria. We previously demonstrated that, upon macroautophagy/autophagy induction, AMBRA1 is recruited to the BECN1 complex and relocalizes to MAMs, where it regulates autophagy by interacting with raft-like components. ERLIN1 is an endoplasmic reticulum lipid raft protein of the prohibitin family. However, little is known about its association with the MAM interface and its involvement in autophagic initiation. In this study, we investigated ERLIN1 association with MAM raft-like microdomains and its interaction with AMBRA1 in the regulation of the autophagic process. We show that ERLIN1 interacts with AMBRA1 at MAM raft-like microdomains, which represents an essential condition for autophagosome formation upon nutrient starvation, as demonstrated by knocking down <i>ERLIN1</i> gene expression. Moreover, this interaction depends on the “integrity” of key molecules, such as ganglioside GD3 and MFN2. Indeed, knocking down ST8SIA1/GD3-synthase or MFN2 expression impairs AMBRA1-ERLIN1 interaction at the MAM level and hinders autophagy. In conclusion, AMBRA1-ERLIN1 interaction within MAM raft-like microdomains appears to be pivotal in promoting the formation of autophagosomes. <b>Abbreviations:</b> ACSL4/ACS4: acyl-CoA synthetase long chain family member 4; ACTB/β-actin: actin beta; AMBRA1: autophagy and beclin 1 regulator 1; ATG14: autophagy related 14; BECN1: beclin 1; CANX: calnexin; Cy5: cyanine 5; ECL: enhanced chemiluminescence; ER: endoplasmic reticulum; ERLIN1/KE04: ER lipid raft associated 1; FB1: fumonisin B1; FE: FRET efficiency; FRET: Förster/fluorescence resonance energy transfer; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD3: aNeu5Ac(2-8)aNeu5Ac(2-3)bDGalp(1-4)bDGlcp(1-1)ceramide; HBSS: Hanks’ balanced salt solution; HRP: horseradish peroxidase; LMNB1: lamin B1; mAb: monoclonal antibody; MAMs: mitochondria-associated membranes; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; MYC/cMyc: proto-oncogene, bHLH transcription factor; P4HB: prolyl 4-hydroxylase subunit beta; pAb: polyclonal antibody; PE: phycoerythrin; SCAP/SREBP: SREBF chaperone; SD: standard deviation; ST8SIA1: ST8 alpha-N-acetyl-neuraminide alpha-2,8 sialyltransferase 1; SQSTM1/p62: sequestosome 1; TOMM20: translocase of outer mitochondrial membrane 20; TUBB/beta-tubulin: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VDAC1/porin: voltage dependent anion channel 1.
DOI: 10.6084/m9.figshare.12998620.v2
title: Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1

description: In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS in <i>Arabidopsis thaliana</i>. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of an <i>nbr1</i>-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression of <i>HSP</i> genes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation of <i>NBR1</i> resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. <b>Abbreviations:</b> AIM: Atg8-interacting motif; ATG: autophagy-related; BiFC: bimolecular fluorescence complementation; ConA: concanamycinA; CoIP: co-immunoprecipitation; DMSO: dimethyl sulfoxide; FKBP: FK506-binding protein; FBPASE: fructose 1,6-bisphosphatase; GFP: green fluorescent protein; HS: heat stress; HSF: heat shock factor; HSFA2: heat shock factor A2; HSP: heat shock protein; HSP90: heat shock protein 90; LC-MS/MS: Liquid chromatography-tandem mass spectrometry; 3-MA: 3-methyladenine; NBR1: next-to-BRCA1; PQC: protein quality control; RFP: red fluorescent protein; ROF1: rotamase FKBP1; TF: transcription factor; TUB: tubulin; UBA: ubiquitin-associated; YFP: yellow fluorescent protein
DOI: 10.6084/m9.figshare.13073197.v2
title: Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs

description: Mitochondria-associated membranes (MAMs) are essential communication subdomains of the endoplasmic reticulum (ER) that interact with mitochondria. We previously demonstrated that, upon macroautophagy/autophagy induction, AMBRA1 is recruited to the BECN1 complex and relocalizes to MAMs, where it regulates autophagy by interacting with raft-like components. ERLIN1 is an endoplasmic reticulum lipid raft protein of the prohibitin family. However, little is known about its association with the MAM interface and its involvement in autophagic initiation. In this study, we investigated ERLIN1 association with MAM raft-like microdomains and its interaction with AMBRA1 in the regulation of the autophagic process. We show that ERLIN1 interacts with AMBRA1 at MAM raft-like microdomains, which represents an essential condition for autophagosome formation upon nutrient starvation, as demonstrated by knocking down <i>ERLIN1</i> gene expression. Moreover, this interaction depends on the “integrity” of key molecules, such as ganglioside GD3 and MFN2. Indeed, knocking down ST8SIA1/GD3-synthase or MFN2 expression impairs AMBRA1-ERLIN1 interaction at the MAM level and hinders autophagy. In conclusion, AMBRA1-ERLIN1 interaction within MAM raft-like microdomains appears to be pivotal in promoting the formation of autophagosomes. <b>Abbreviations:</b> ACSL4/ACS4: acyl-CoA synthetase long chain family member 4; ACTB/β-actin: actin beta; AMBRA1: autophagy and beclin 1 regulator 1; ATG14: autophagy related 14; BECN1: beclin 1; CANX: calnexin; Cy5: cyanine 5; ECL: enhanced chemiluminescence; ER: endoplasmic reticulum; ERLIN1/KE04: ER lipid raft associated 1; FB1: fumonisin B1; FE: FRET efficiency; FRET: Förster/fluorescence resonance energy transfer; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD3: aNeu5Ac(2-8)aNeu5Ac(2-3)bDGalp(1-4)bDGlcp(1-1)ceramide; HBSS: Hanks’ balanced salt solution; HRP: horseradish peroxidase; LMNB1: lamin B1; mAb: monoclonal antibody; MAMs: mitochondria-associated membranes; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; MYC/cMyc: proto-oncogene, bHLH transcription factor; P4HB: prolyl 4-hydroxylase subunit beta; pAb: polyclonal antibody; PE: phycoerythrin; SCAP/SREBP: SREBF chaperone; SD: standard deviation; ST8SIA1: ST8 alpha-N-acetyl-neuraminide alpha-2,8 sialyltransferase 1; SQSTM1/p62: sequestosome 1; TOMM20: translocase of outer mitochondrial membrane 20; TUBB/beta-tubulin: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VDAC1/porin: voltage dependent anion channel 1.
DOI: 10.5517/ccdc.csd.cc292xz9
title: CCDC 2117981: Experimental Crystal Structure Determination

description: Related Article: Madalin Damoc, Alexandru-Constantin Stoica, Diana Blaj, Ana-Maria Macsim, Mihaela Dascalu, Corneliu Cojocaru, Sergiu Shova, Maria Cazacu|2022|J.Mol.Struct.|1269|133760|doi:10.1016/j.molstruc.2022.133760
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc292y0c
title: CCDC 2117982: Experimental Crystal Structure Determination

description: Related Article: Madalin Damoc, Alexandru-Constantin Stoica, Diana Blaj, Ana-Maria Macsim, Mihaela Dascalu, Corneliu Cojocaru, Sergiu Shova, Maria Cazacu|2022|J.Mol.Struct.|1269|133760|doi:10.1016/j.molstruc.2022.133760
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc292y1d
title: CCDC 2117983: Experimental Crystal Structure Determination

description: Related Article: Madalin Damoc, Alexandru-Constantin Stoica, Diana Blaj, Ana-Maria Macsim, Mihaela Dascalu, Corneliu Cojocaru, Sergiu Shova, Maria Cazacu|2022|J.Mol.Struct.|1269|133760|doi:10.1016/j.molstruc.2022.133760
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29bs4l
title: CCDC 2125519: Experimental Crystal Structure Determination

description: Related Article: Tuncay Yeşilkaynak, Fatma Nur Özkömeç, Mustafa Çeşme, Ruken Esra Demirdöğen, Emine Kutlu, Hatice Mehtap Kutlu, Fatih Mehmet Emen|2022|J.Mol.Struct.|1269|133758|doi:10.1016/j.molstruc.2022.133758
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29bvzh
title: CCDC 2125607: Experimental Crystal Structure Determination

description: Related Article: Tuncay Yeşilkaynak, Fatma Nur Özkömeç, Mustafa Çeşme, Ruken Esra Demirdöğen, Emine Kutlu, Hatice Mehtap Kutlu, Fatih Mehmet Emen|2022|J.Mol.Struct.|1269|133758|doi:10.1016/j.molstruc.2022.133758
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24pyb4
title: CCDC 1987296: Experimental Crystal Structure Determination

description: Related Article: Yahya Bahrouni, Brahim Ayed|2022|J.Mol.Struct.|1269|133757|doi:10.1016/j.molstruc.2022.133757
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25625/rhf7bu/o2xekb
title: Soil GHG fluxes in trop. vegetable farms.tab

description: Field-based quantification of soil N2O, CH4, and CO2 fluxes and soil controlling factors on an Andosol soil in Leyte, Philippines
DOI: 10.25625/rhf7bu
title: Replication Data for: Soil greenhouse gas fluxes in tropical vegetable farms, using forest as a reference

description: Data on the field-based measurements of soil N2O, CO2, and CH4 fluxes and soil-controlling factors in small-scale vegetable farms and secondary forest on an Andosol soil in Leyte, Philippines
DOI: 10.5281/zenodo.6903613
title: pLV[Exp]-U6&gt;NT-Seq1-hPGK&gt;mApple

description: Plasmid vector encoding a non-targeting sgRNA sequence under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6903612
title: pLV[Exp]-U6&gt;NT-Seq1-hPGK&gt;mApple

description: Plasmid vector encoding a non-targeting sgRNA sequence under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6903553
title: V5-KANSL1 pLVX-EF1α-IRES-Puro

description: Human KANSL1 cDNA with N-terminal V5 tag cloned into the pLVX-EF1α-IRES-Puro plasmid (EcoRI and SpeI restriction sites) from Clontech, Takara Bio.
DOI: 10.5281/zenodo.6903552
title: V5-KANSL1 pLVX-EF1α-IRES-Puro

description: Human KANSL1 cDNA with N-terminal V5 tag cloned into the pLVX-EF1α-IRES-Puro plasmid (EcoRI and SpeI restriction sites) from Clontech, Takara Bio.
DOI: 10.6084/m9.figshare.19076750
title: Jorge-Smeding et al 2022 - Suppl. Tables S1, S2, S3, S4

description: Supplementary Metarial
DOI: 10.5281/zenodo.6957034
title: T25 Analogs: Virtual Library

description: The virtual library containing approx. 50k peptide dendrimers
DOI: 10.5281/zenodo.6957033
title: T25 Analogs: Virtual Library

description: The virtual library containing approx. 50k peptide dendrimers
DOI: 10.34740/kaggle/dsv/4023702
title: Performance Data
DOI: 10.25430/researchdata.cab.unipd.it.00000681
title: New couples during lockdown

description: Data were collected online from November 2020 to April 2021 through Qualtrics, while the recruitment took place by sharing a link accompanied by a short message introducing the research on social medias. Overall, the study lasted approximately 20 minutes. Participants took part in the research on a voluntary basis and were asked to fill a consent form, which also explained the objectives and methodology of the research, as well as that the answers were collected confidentially.
DOI: 10.5281/zenodo.6957188
title: Forschungsdatenmanagement in Aus- und Weiterbildung: Überblick über Studiengänge und Kurse in Deutschland (02/22)

description: Projektarbeit im Seminar <em>BdK7.3.1 Infrastrukturen für Forschungsdaten</em> [WS 2021/2022] bei Prof. Dr. Mirjam Blümm<br> Studiengang: Bibliothek und digitale Kommunikation, Technische Hochschule Köln
DOI: 10.5281/zenodo.6957187
title: Forschungsdatenmanagement in Aus- und Weiterbildung: Überblick über Studiengänge und Kurse in Deutschland (02/22)

description: Projektarbeit im Seminar <em>BdK7.3.1 Infrastrukturen für Forschungsdaten</em> [WS 2021/2022] bei Prof. Dr. Mirjam Blümm<br> Studiengang: Bibliothek und digitale Kommunikation, Technische Hochschule Köln
DOI: 10.6084/m9.figshare.20424600
title: 211223 Tables.pdf

description: The Role of Lung Ultrasound in the Assessment of Acute Respiratory Failure
DOI: 10.6084/m9.figshare.20424600.v1
title: 211223 Tables.pdf

description: The Role of Lung Ultrasound in the Assessment of Acute Respiratory Failure
DOI: 10.6084/m9.figshare.19741999
title: analysis_dataset

description: Dataset of bird detection data and all elevation and habitat covariates
DOI: 10.5281/zenodo.6957214
title: Machine Learning Ready Induced Seismicity Data

description: This dataset contains previously published data on induced seismicity that has been processed to be machine learning ready.<br> <br> The data contains time series of the cumulative number of seismic events in certain areas and the corresponding pressures induced from injecting fluids into the ground. The natural task is to forecast future seismicity given past seismicity and pressures. These datasets aim to require as little seismology experience as necessary to prepare the data for forecasting algorithms. <br> <br> Data is provided for different locations. For Decatur Illinois, the seismic data was taken from Williams-Stroud et al., 2018 and the pressure data originated from Luu et al., 2022. Data aggregated over the whole region lies in the temporal_datasets/decatur_illinois/ folder. The region was further subdivided into subregions and the corresponding data stored separately (e.g. in loc1). The Kansas data originated from Cochran et al., 2018 and is further divided into subregions. The Cushing, Oklahoma is adapted from Skoumal et al., 2020. Each seismic file contains the following columns: epoch latitude longitude depth easting northing magnitude. The epoch corresponds to the number of seconds since a certain date (e.g. November 17, 2011 for Decatur). Each seismic event corresponds to one row in the file. <br> <br> Each pressure file contains the following columns: epoch pressure dpdt. dpdt is the derivative of pressure.
DOI: 10.5281/zenodo.6907572
title: Machine Learning Ready Induced Seismicity Data

description: This dataset contains previously published data on induced seismicity that has been processed to be machine learning ready.<br> <br> The data contains time series of the cumulative number of seismic events in certain areas and the corresponding pressures induced from injecting fluids into the ground. The natural task is to forecast future seismicity given past seismicity and pressures. These datasets aim to require as little seismology experience as necessary to prepare the data for forecasting algorithms. <br> <br> Data is provided for different locations. For Decatur Illinois, the seismic data was taken from Williams-Stroud et al., 2018 and the pressure data originated from Luu et al., 2022. Data aggregated over the whole region lies in the temporal_datasets/decatur_illinois/ folder. The region was further subdivided into subregions and the corresponding data stored separately (e.g. in loc1). The Kansas data originated from Cochran et al., 2018 and is further divided into subregions. The Cushing, Oklahoma is adapted from Skoumal et al., 2020. Each seismic file contains the following columns: epoch latitude longitude depth easting northing magnitude. The epoch corresponds to the number of seconds since a certain date (e.g. November 17, 2011 for Decatur). Each seismic event corresponds to one row in the file. <br> <br> Each pressure file contains the following columns: epoch pressure dpdt. dpdt is the derivative of pressure.
DOI: 10.5517/ccdc.csd.cc271lrn
title: CCDC 2057121: Experimental Crystal Structure Determination

description: Related Article: Liping Tang, Tianju Jiang, Xiling Dai, Xin Zhang, Cai Jiang, Nina Wang, Guozheng Huang, Jianguo Cao|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b4tt4
title: CCDC 2149596: Experimental Crystal Structure Determination

description: Related Article: Clément Brouillac, Wan-Shan Shen, Joëlle Rault-Berthelot, Cassandre Quinton, Zuo-Quan Jiang and Cyril Poriel|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b4tv5
title: CCDC 2149597: Experimental Crystal Structure Determination

description: Related Article: Clément Brouillac, Wan-Shan Shen, Joëlle Rault-Berthelot, Cassandre Quinton, Zuo-Quan Jiang and Cyril Poriel|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27p458
title: CCDC 2075889: Experimental Crystal Structure Determination

description: Related Article: Liang Guo|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bm3qt
title: CCDC 2163326: Experimental Crystal Structure Determination

description: Related Article: Liang Guo|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bm3rv
title: CCDC 2163327: Experimental Crystal Structure Determination

description: Related Article: Liang Guo|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bm3sw
title: CCDC 2163328: Experimental Crystal Structure Determination

description: Related Article: Liang Guo|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bm459
title: CCDC 2163340: Experimental Crystal Structure Determination

description: Related Article: Yan Huang, Lianpeng Tong|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bm5z4
title: CCDC 2163396: Experimental Crystal Structure Determination

description: Related Article: Selmi Ahmed|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.