cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12907482
title: PDPK1 regulates autophagosome biogenesis by binding to PIK3C3

description: PDPK1 (3-phosphoinositide dependent protein kinase 1) is a phosphorylation-regulated kinase that plays a central role in activating multiple signaling pathways and cellular processes. Here, this study shows that PDPK1 turns on macroautophagy/autophagy as a SUMOylation-regulated kinase. <i>In vivo</i> data demonstrate that the SUMO modification of PDPK1 is a physiological feature in the brain and that it can be induced by viral infections. The SUMOylated PDPK1 regulates its own phosphorylation and subsequent activation of the AKT1 (AKT serine/threonine kinase 1)-MTOR (mechanistic target of rapamycin kinase) pathway. However, SUMOylation of PDPK1 is inhibited by binding to PIK3C3 (phosphatidylinositol 3-kinase catalytic subunit type 3). The nonSUMOylated PDPK1 then tethers LC3 to the endoplasmic reticulum to initiate autophagy, and it acts as a key component in forming the autophagic vacuole. Collectively, this study reveals the intricate molecular regulation of PDPK1 by post-translational modification in controlling autophagosome biogenesis, and it highlights the role of PDPK1 as a sensor of cellular stress and regulator of autophagosome biogenesis. <b>Abbreviations:</b> AKT1: AKT serine/threonine kinase 1; ATG14: autophagy related 14; Co-IP: co-immunoprecipitation; ER: endoplasmic reticulum; hpi: hours post-infection; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; pAb: polyclonal antibody; PDPK1: 3-phosphoinositide dependent protein kinase 1; PI3K: phosphoinositide 3-kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic, subunit type 3; RPS6KB1: ribosomal protein S6 kinase B1; SGK: serum/glucocorticoid regulated kinase; SQSTM1: sequestosome 1; SUMO: small ubiquitin like modifier; UBE2I/UBC9: ubiquitin conjugating enzyme E2 I; UVRAG: UV radiation resistance associated
DOI: 10.6084/m9.figshare.12907482.v1
title: PDPK1 regulates autophagosome biogenesis by binding to PIK3C3

description: PDPK1 (3-phosphoinositide dependent protein kinase 1) is a phosphorylation-regulated kinase that plays a central role in activating multiple signaling pathways and cellular processes. Here, this study shows that PDPK1 turns on macroautophagy/autophagy as a SUMOylation-regulated kinase. <i>In vivo</i> data demonstrate that the SUMO modification of PDPK1 is a physiological feature in the brain and that it can be induced by viral infections. The SUMOylated PDPK1 regulates its own phosphorylation and subsequent activation of the AKT1 (AKT serine/threonine kinase 1)-MTOR (mechanistic target of rapamycin kinase) pathway. However, SUMOylation of PDPK1 is inhibited by binding to PIK3C3 (phosphatidylinositol 3-kinase catalytic subunit type 3). The nonSUMOylated PDPK1 then tethers LC3 to the endoplasmic reticulum to initiate autophagy, and it acts as a key component in forming the autophagic vacuole. Collectively, this study reveals the intricate molecular regulation of PDPK1 by post-translational modification in controlling autophagosome biogenesis, and it highlights the role of PDPK1 as a sensor of cellular stress and regulator of autophagosome biogenesis. <b>Abbreviations:</b> AKT1: AKT serine/threonine kinase 1; ATG14: autophagy related 14; Co-IP: co-immunoprecipitation; ER: endoplasmic reticulum; hpi: hours post-infection; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; pAb: polyclonal antibody; PDPK1: 3-phosphoinositide dependent protein kinase 1; PI3K: phosphoinositide 3-kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic, subunit type 3; RPS6KB1: ribosomal protein S6 kinase B1; SGK: serum/glucocorticoid regulated kinase; SQSTM1: sequestosome 1; SUMO: small ubiquitin like modifier; UBE2I/UBC9: ubiquitin conjugating enzyme E2 I; UVRAG: UV radiation resistance associated
DOI: 10.6084/m9.figshare.12907482.v3
title: PDPK1 regulates autophagosome biogenesis by binding to PIK3C3

description: PDPK1 (3-phosphoinositide dependent protein kinase 1) is a phosphorylation-regulated kinase that plays a central role in activating multiple signaling pathways and cellular processes. Here, this study shows that PDPK1 turns on macroautophagy/autophagy as a SUMOylation-regulated kinase. <i>In vivo</i> data demonstrate that the SUMO modification of PDPK1 is a physiological feature in the brain and that it can be induced by viral infections. The SUMOylated PDPK1 regulates its own phosphorylation and subsequent activation of the AKT1 (AKT serine/threonine kinase 1)-MTOR (mechanistic target of rapamycin kinase) pathway. However, SUMOylation of PDPK1 is inhibited by binding to PIK3C3 (phosphatidylinositol 3-kinase catalytic subunit type 3). The nonSUMOylated PDPK1 then tethers LC3 to the endoplasmic reticulum to initiate autophagy, and it acts as a key component in forming the autophagic vacuole. Collectively, this study reveals the intricate molecular regulation of PDPK1 by post-translational modification in controlling autophagosome biogenesis, and it highlights the role of PDPK1 as a sensor of cellular stress and regulator of autophagosome biogenesis. <b>Abbreviations:</b> AKT1: AKT serine/threonine kinase 1; ATG14: autophagy related 14; Co-IP: co-immunoprecipitation; ER: endoplasmic reticulum; hpi: hours post-infection; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; pAb: polyclonal antibody; PDPK1: 3-phosphoinositide dependent protein kinase 1; PI3K: phosphoinositide 3-kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic, subunit type 3; RPS6KB1: ribosomal protein S6 kinase B1; SGK: serum/glucocorticoid regulated kinase; SQSTM1: sequestosome 1; SUMO: small ubiquitin like modifier; UBE2I/UBC9: ubiquitin conjugating enzyme E2 I; UVRAG: UV radiation resistance associated
DOI: 10.6084/m9.figshare.12907482.v2
title: PDPK1 regulates autophagosome biogenesis by binding to PIK3C3

description: PDPK1 (3-phosphoinositide dependent protein kinase 1) is a phosphorylation-regulated kinase that plays a central role in activating multiple signaling pathways and cellular processes. Here, this study shows that PDPK1 turns on macroautophagy/autophagy as a SUMOylation-regulated kinase. <i>In vivo</i> data demonstrate that the SUMO modification of PDPK1 is a physiological feature in the brain and that it can be induced by viral infections. The SUMOylated PDPK1 regulates its own phosphorylation and subsequent activation of the AKT1 (AKT serine/threonine kinase 1)-MTOR (mechanistic target of rapamycin kinase) pathway. However, SUMOylation of PDPK1 is inhibited by binding to PIK3C3 (phosphatidylinositol 3-kinase catalytic subunit type 3). The nonSUMOylated PDPK1 then tethers LC3 to the endoplasmic reticulum to initiate autophagy, and it acts as a key component in forming the autophagic vacuole. Collectively, this study reveals the intricate molecular regulation of PDPK1 by post-translational modification in controlling autophagosome biogenesis, and it highlights the role of PDPK1 as a sensor of cellular stress and regulator of autophagosome biogenesis. <b>Abbreviations:</b> AKT1: AKT serine/threonine kinase 1; ATG14: autophagy related 14; Co-IP: co-immunoprecipitation; ER: endoplasmic reticulum; hpi: hours post-infection; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; pAb: polyclonal antibody; PDPK1: 3-phosphoinositide dependent protein kinase 1; PI3K: phosphoinositide 3-kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic, subunit type 3; RPS6KB1: ribosomal protein S6 kinase B1; SGK: serum/glucocorticoid regulated kinase; SQSTM1: sequestosome 1; SUMO: small ubiquitin like modifier; UBE2I/UBC9: ubiquitin conjugating enzyme E2 I; UVRAG: UV radiation resistance associated
DOI: 10.6084/m9.figshare.12907483
title: The DNA methyltransferase DNMT3A contributes to autophagy long-term memory

description: Macroautophagy/autophagy is a conserved catabolic pathway that targets cytoplasmic components for their degradation and recycling in an autophagosome-dependent lysosomal manner. Under physiological conditions, this process maintains cellular homeostasis. However, autophagy can be stimulated upon different forms of cellular stress, ranging from nutrient starvation to exposure to drugs. Thus, this pathway can be seen as a central component of the integrated and adaptive stress response. Here, we report that even brief induction of autophagy is coupled <i>in vitro</i> to a persistent downregulation of the expression of MAP1LC3 isoforms, which are key components of the autophagy core machinery. In fact, DNA-methylation mediated by <i>de novo</i> DNA methyltransferase DNMT3A of <i>MAP1LC3</i> loci upon autophagy stimulation leads to the observed long-term decrease of <i>MAP1LC3</i> isoforms at transcriptional level. Finally, we report that the downregulation of MAP1LC3 expression can be observed <i>in vivo</i> in zebrafish larvae and mice exposed to a transient autophagy stimulus. This epigenetic memory of autophagy provides some understanding of the long-term effect of autophagy induction and offers a possible mechanism for its decline upon aging, pathological conditions, or in response to treatment interventions. <b>Abbreviations:</b> ACTB: actin beta; ATG: autophagy-related; 5-Aza: 5-aza-2’-deoxycytidine; BafA1: bafilomycin A<sub>1</sub>; CBZ: carbamazepine; CDKN2A: cyclin dependent kinase inhibitor 2A; ChIP: chromatin immunoprecipitation; Clon.: clonidine; CpG: cytosine-guanine dinucleotide: DMSO: dimethyl sulfoxide; DNA: deoxyribonucleic acid; DNMT: DNA methyltransferase; DNMT1: DNA methyltransferase 1; DNMT3A: DNA methyltransferase alpha; DNMT3B: DNA methyltransferase beta; dpf: days post-fertilization; EBSS: Earle’s balanced salt solution; EM: Zebrafish embryo medium; GABARAP: GABA type A receptor associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GRO-Seq: Global Run-On sequencing; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; MAP1LC3B2: microtubule-associated protein 1 light chain 3 beta 2; MEM: minimum essential medium; MEF: mouse embryonic fibroblasts; mRNA: messenger RNA; MTOR: mechanistic target of rapamycin kinase; PBS: phosphate-buffered saline; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RT-qPCR: quantitative reverse transcription polymerase chain reaction; SQSTM1/p62: sequestosome 1; Starv.: starvation; Treh.: trehalose; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.12907483.v1
title: The DNA methyltransferase DNMT3A contributes to autophagy long-term memory

description: Macroautophagy/autophagy is a conserved catabolic pathway that targets cytoplasmic components for their degradation and recycling in an autophagosome-dependent lysosomal manner. Under physiological conditions, this process maintains cellular homeostasis. However, autophagy can be stimulated upon different forms of cellular stress, ranging from nutrient starvation to exposure to drugs. Thus, this pathway can be seen as a central component of the integrated and adaptive stress response. Here, we report that even brief induction of autophagy is coupled <i>in vitro</i> to a persistent downregulation of the expression of MAP1LC3 isoforms, which are key components of the autophagy core machinery. In fact, DNA-methylation mediated by <i>de novo</i> DNA methyltransferase DNMT3A of <i>MAP1LC3</i> loci upon autophagy stimulation leads to the observed long-term decrease of <i>MAP1LC3</i> isoforms at transcriptional level. Finally, we report that the downregulation of MAP1LC3 expression can be observed <i>in vivo</i> in zebrafish larvae and mice exposed to a transient autophagy stimulus. This epigenetic memory of autophagy provides some understanding of the long-term effect of autophagy induction and offers a possible mechanism for its decline upon aging, pathological conditions, or in response to treatment interventions. <b>Abbreviations:</b> ACTB: actin beta; ATG: autophagy-related; 5-Aza: 5-aza-2’-deoxycytidine; BafA1: bafilomycin A<sub>1</sub>; CBZ: carbamazepine; CDKN2A: cyclin dependent kinase inhibitor 2A; ChIP: chromatin immunoprecipitation; Clon.: clonidine; CpG: cytosine-guanine dinucleotide: DMSO: dimethyl sulfoxide; DNA: deoxyribonucleic acid; DNMT: DNA methyltransferase; DNMT1: DNA methyltransferase 1; DNMT3A: DNA methyltransferase alpha; DNMT3B: DNA methyltransferase beta; dpf: days post-fertilization; EBSS: Earle’s balanced salt solution; EM: Zebrafish embryo medium; GABARAP: GABA type A receptor associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GRO-Seq: Global Run-On sequencing; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; MAP1LC3B2: microtubule-associated protein 1 light chain 3 beta 2; MEM: minimum essential medium; MEF: mouse embryonic fibroblasts; mRNA: messenger RNA; MTOR: mechanistic target of rapamycin kinase; PBS: phosphate-buffered saline; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RT-qPCR: quantitative reverse transcription polymerase chain reaction; SQSTM1/p62: sequestosome 1; Starv.: starvation; Treh.: trehalose; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.11858922
title: Additional file 14 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 14. Prediction on the functional pathways of bacterial communities in wild and domesticated rice
DOI: 10.6084/m9.figshare.11858922.v1
title: Additional file 14 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 14. Prediction on the functional pathways of bacterial communities in wild and domesticated rice
DOI: 10.6084/m9.figshare.11858928
title: Additional file 15 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 15. Prediction on the functional redundancy of bacterial communities in wild and domesticated rice
DOI: 10.6084/m9.figshare.11858937
title: Additional file 16 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 16. Relative abundance and ecological guilds of fungal OTUs associated with 43 rice accessions
DOI: 10.6084/m9.figshare.11858937.v1
title: Additional file 16 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 16. Relative abundance and ecological guilds of fungal OTUs associated with 43 rice accessions
DOI: 10.6084/m9.figshare.7664711
title: Additional file 2: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Command lines of bacterial 16S amplicon sequencing analysis. (TXT 2 kb)
DOI: 10.6084/m9.figshare.7664711.v1
title: Additional file 2: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Command lines of bacterial 16S amplicon sequencing analysis. (TXT 2 kb)
DOI: 10.6084/m9.figshare.7664720
title: Additional file 3: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Sequence read numbers of the bacterial OTUs profiling (sequenced on a MiSeq PE250 sequencer at a depth of 29,718 sequences per sample). (XLS 882 kb)
DOI: 10.6084/m9.figshare.7664720.v1
title: Additional file 3: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Sequence read numbers of the bacterial OTUs profiling (sequenced on a MiSeq PE250 sequencer at a depth of 29,718 sequences per sample). (XLS 882 kb)
DOI: 10.6084/m9.figshare.7664723
title: Additional file 4: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic microbial taxonomic profiling (at genus level) (XLS 356 kb)
DOI: 10.6084/m9.figshare.7664723.v1
title: Additional file 4: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic microbial taxonomic profiling (at genus level) (XLS 356 kb)
DOI: 10.6084/m9.figshare.11859030
title: Additional file 1 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats

description: Supplementary tables.
DOI: 10.6084/m9.figshare.11859030.v1
title: Additional file 1 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats

description: Supplementary tables.
DOI: 10.6084/m9.figshare.7664726
title: Additional file 1: of Proliferative potential and resistance to immune checkpoint blockade in lung cancer patients

description: Table S1. Clinical characteristics. Table S2. RNA-seq gene function list. Table S3. Gene function analysis training set (Proportion test). Table S4. Gene function analysis training and test set combined (Proportion test). Table S5. Gene function analysis test set (Proportion test). Table S6. Accuracy for 10 proliferation immune-related genes. Table S7. Immunohistochemical assessment of Ki-67 positivity. Table S8. Disease control rate in cold tumors by proliferation status. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.7664726.v1
title: Additional file 1: of Proliferative potential and resistance to immune checkpoint blockade in lung cancer patients

description: Table S1. Clinical characteristics. Table S2. RNA-seq gene function list. Table S3. Gene function analysis training set (Proportion test). Table S4. Gene function analysis training and test set combined (Proportion test). Table S5. Gene function analysis test set (Proportion test). Table S6. Accuracy for 10 proliferation immune-related genes. Table S7. Immunohistochemical assessment of Ki-67 positivity. Table S8. Disease control rate in cold tumors by proliferation status. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.7664732
title: Additional file 5: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic bacterial taxonomic profiling (at genus level) (separated from the microbial taxonomic profiling) (XLS 355 kb)
DOI: 10.6084/m9.figshare.7664732.v1
title: Additional file 5: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic bacterial taxonomic profiling (at genus level) (separated from the microbial taxonomic profiling) (XLS 355 kb)
DOI: 10.6084/m9.figshare.7664738
title: Additional file 6: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: 16S rRNA gene sequences of the 12 isolated Streptomyces stains. (TXT 15 kb)
DOI: 10.6084/m9.figshare.7664738.v1
title: Additional file 6: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: 16S rRNA gene sequences of the 12 isolated Streptomyces stains. (TXT 15 kb)
DOI: 10.6084/m9.figshare.7664744
title: Additional file 7: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Estimated absolute abundance (EAA) of the metagenomic bacterial taxonomic profiling (at genus level) (XLS 354 kb)
DOI: 10.6084/m9.figshare.7664744.v1
title: Additional file 7: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Estimated absolute abundance (EAA) of the metagenomic bacterial taxonomic profiling (at genus level) (XLS 354 kb)
DOI: 10.6084/m9.figshare.19759532
title: Additional file 2 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 2: Table S1. The meta-data sheet of reported Kleaf.
DOI: 10.6084/m9.figshare.19759532.v1
title: Additional file 2 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 2: Table S1. The meta-data sheet of reported Kleaf.
DOI: 10.6084/m9.figshare.7664750
title: Additional file 8: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic microbial function profiling (KEGG orthology function category) (XLS 928 kb)
DOI: 10.6084/m9.figshare.7664750.v1
title: Additional file 8: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

description: Relative abundance of the metagenomic microbial function profiling (KEGG orthology function category) (XLS 928 kb)
DOI: 10.6084/m9.figshare.16577649
title: Sedimentary tectonic pattern of Wufeng and Longmaxi Formations in the northern margin of Sichuan Basin, South China

description: Organic-rich black shales in the Sichuan Basin from the Upper Ordovician and Lower Silurian are considered excellent source rocks and unconventional reservoirs of hydrocarbons in South China. The Wufeng and Longmaxi Formations in the Micangshan – Dabashan areas of the northern margin of Sichuan Basin were taken as the research objects. The purpose of this study is to reconstruct the sedimentary tectonic pattern of the Wufeng and Longmaxi Formations in the study area. First, the stratigraphic framework correlation and sedimentary facies analysis of Wufeng and Longmaxi Formations in the study area were carried out. Then, Mo/TOC and Al-Co[EF]×Mn[EF] geochemical indicators were used to identify the degree of water restricted during the deposition period. It was found that the thickness of black shale was relatively small near the uplift area. However, far away from the uplift area, from west to east, the black shale thickened and the TOC content increased gradually, which were controlled by the upwelling of continental margin and intracontinental depression. The results show that: (1) At the front edge of Micangshan, during the deposition period of Wufeng Formation, Fucheng and Qiaoting profiles were located in the intersection area of upwelling formed by two kinds of monsoon, which led to the long-term influence of upwelling in this area. The sedimentation period of Longmaxi Formation was mainly affected by ‘Xixiang Rise’, which led to the uplift of Wangcang and Nanjiang areas into islands. (2) At the front edge of Dabashan and Western Hubei – Eastern Chongqing areas, the Wufeng Formation presented a tectonic pattern of alternating uplift and depression. Due to the continuous compression of the Cathaysian Block from southeast to northwest, the Shizhu – Wuxi areas continued to subside during the deposition period of Longmaxi Formation, and the black shale was quite thick.