cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1393390
title: Advance in understanding cis regulation of the plant gene with an emphasis on comparative genomics

description: This dataset is a list of <em>Arabidopsis thaliana</em> CNS sequences present in all three of the following CNS lists:
1) Haudry et al. (2013) An atalas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45:891-898.
2) PL3.0 (TAIR 10 version):
Turco et al. (2013) Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Frontiers in Plant Genetics and Genomics 4:170-180.
3) Van de Velde et al (2014) Inferences of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. Plant Cell 26:2729-2745.
CNS sequences found in all 3 CNS lists were identified using intersectBed from the BEDTools suite (Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842). 
CNSs from the verified list were assigned to an <em>Arabidopsis thaliana</em> gene based on their PL3.0 component. PL3.0 CNSs are defined as syntenic conserved noncoding regions between <em>Arabidopsis thaliana</em> and the early branching Brassicaceae <em>Aethionema</em> <em>arabicum</em>. Orthologous <em>Arabidopsis thaliana-Aethionema arabicum</em> genes were identified using a combination of CoGe: Synfind (Tang et al. (2011) BMC Bioinformatics 12:102) and the PL3.0 CNS pipeline (Turco et al. 2013). closestBed (Bedtools) was then used to map PL3.0 CNSs to the closest Arabidopsis thaliana gene which had an Aethionema arabicum ortholog. Distance to the nearest gene is included in the closestBed output. Proximal regions were defined as being 1000 bp upstream from the transcription start site (5' proximal) or 1000 bp downstream from the gene (3' proximal). For intragenic CNSs, a custom perlscript was used to identify the position of the CNS in introns vs UTRs. Overlap with UTRs and CDS regions was calculated using intersectBed (BEDTools) using bedfiles created from GFF "UTR" and "CDS" features. CNS sequences overlapping CDSs by 50% or more were given "CDS" designations. CNSs overlapping UTRs by 50% or more were given 5' or 3' UTR designations. 
Note: CNS assignments to <em>Arabidopsis thaliana</em> genes are best-guess computational assignments;  individual PL3.0 CNSs may in actuality function in regulating genes that are not the closest <em>Arabidopsis thaliana</em> gene with an A<em>ethionema arabicum</em> ortholog. This is particularly true for genes with complex regulation. In the GEvo links included in this spreadsheet these can often be seen as clusters of CNSs extending beyond the midpoint between two <em>Arabidopsis thaliana</em> genes. By adding additional orthologous genes to GEvo panels, it is often possible to assign a CNS to an <em>Arabidopsis thaliana</em> gene with greater confidence if only one of the two <em>Arabidopsis thaliana</em> genes is retained in all genomes along with the CNS.
DOI: 10.6084/m9.figshare.1393414
title: Syntheses and Crystal Structure of Three Novel Supramolecular Halides/Pseudohalides {(DMB)[Cu<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n,</sub>{(DMB)[Cu(SCN)<sub>4</sub>]}, and {(DMB)[Ag<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> Directed by Dicationic Template Possessing C2-Symmetry

description: Three novel hybrid complexes, namely{(DMB)[Cu<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> (<b>1</b>), {(DMB)[Cu(SCN)<sub>4</sub>]} (<b>2</b>), <b>and</b> {(DMB)[Ag<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> (<b>3</b>), have been synthesized via the self-assembly in DMF–methanol system based on multidentate ligand DMB, {DMB = α, α<i>′</i>- di(3-methylimidozole-1-yl)benzene dichloride}. Single-crystal X-ray diffraction analysis shows <b>1</b> and <b>3</b> are 1D supramolecules, whereas <b>2</b> is mononuclear. Electrostatic interactions between the organic counteranions and inorganic moieties are present and do the contribution to the crystal packing. These compounds have been further characterized by IR spectroscopy and thermostability properties.
DOI: 10.6084/m9.figshare.1393414.v1
title: Syntheses and Crystal Structure of Three Novel Supramolecular Halides/Pseudohalides {(DMB)[Cu<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n,</sub>{(DMB)[Cu(SCN)<sub>4</sub>]}, and {(DMB)[Ag<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> Directed by Dicationic Template Possessing C2-Symmetry

description: Three novel hybrid complexes, namely{(DMB)[Cu<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> (<b>1</b>), {(DMB)[Cu(SCN)<sub>4</sub>]} (<b>2</b>), <b>and</b> {(DMB)[Ag<sub>2</sub>(SCN)<sub>4</sub>]}<sub>n</sub> (<b>3</b>), have been synthesized via the self-assembly in DMF–methanol system based on multidentate ligand DMB, {DMB = α, α<i>′</i>- di(3-methylimidozole-1-yl)benzene dichloride}. Single-crystal X-ray diffraction analysis shows <b>1</b> and <b>3</b> are 1D supramolecules, whereas <b>2</b> is mononuclear. Electrostatic interactions between the organic counteranions and inorganic moieties are present and do the contribution to the crystal packing. These compounds have been further characterized by IR spectroscopy and thermostability properties.
DOI: 10.6084/m9.figshare.1394857
title: Geochemistry and petrogenesis of Permian granitoids in the northwestern margin of the North China Craton: insights from the Dongshengmiao pluton, Inner Mongolia

description: Permian granitoid emplacement represents one of the most important tectonothermal events in the northern margin of the North China Craton (NCC). In this study, we collected geochronological and geochemical data of the regional Permian granitoid in the northwestern margin of the NCC, and investigated the Dongshengmiao pluton, using it as an example to constrain the regional granitoid petrogenesis and its geodynamic settings. The Dongshengmiao pluton contains porphyritic granite and quartz diorite. LA-ICP-MS zircon U-Pb dating results have constrained the granitoid emplacement to be ca. 287‒275 Ma. The Dongshengmiao granitoids have a SiO<sub>2</sub> range of 58.4‒76.5%, moderate to high alkali content (Na<sub>2</sub>O + K<sub>2</sub>O = 5.16–7.94%), and are rich in large-ion lithophile elements (LILEs; e.g. Rb, Ba) and depleted in high-field strength elements (HFSEs; e.g. Nb, Ta, Ti). The zircons in quartz diorite have <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −15.6 to −11.1 with two-stage Hf model ages (T<sub>DM2</sub>) of 1997–2281 Ma, suggesting that the magma was derived from partial melting of old continental materials. In contrast, porphyritic granite shows variable Hf isotopic composition with <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −13.7 to −2.6 and T<sub>DM2</sub> of 1471–2167 Ma, indicating a heterogeneous magma source. Besides the Dongshengmiao pluton, all the Permian granitoids in the northwestern margin of the NCC exhibit similar geochemical characteristics, including enrichment in LILEs, depletion in Nb and Ta, and enriched Hf isotopic signatures. The comprehensive geochemical data indicate that these Permian granitoids are derived from magma mixing between dominant partial melting of ancient felsic crustal materials and minor juvenile basaltic magma. Tectonically, the Dongshengmiao and other granitoids in the northwestern margin of the NCC may have been formed in a post-collisional extensional setting.
DOI: 10.6084/m9.figshare.1394857.v1
title: Geochemistry and petrogenesis of Permian granitoids in the northwestern margin of the North China Craton: insights from the Dongshengmiao pluton, Inner Mongolia

description: Permian granitoid emplacement represents one of the most important tectonothermal events in the northern margin of the North China Craton (NCC). In this study, we collected geochronological and geochemical data of the regional Permian granitoid in the northwestern margin of the NCC, and investigated the Dongshengmiao pluton, using it as an example to constrain the regional granitoid petrogenesis and its geodynamic settings. The Dongshengmiao pluton contains porphyritic granite and quartz diorite. LA-ICP-MS zircon U-Pb dating results have constrained the granitoid emplacement to be ca. 287‒275 Ma. The Dongshengmiao granitoids have a SiO<sub>2</sub> range of 58.4‒76.5%, moderate to high alkali content (Na<sub>2</sub>O + K<sub>2</sub>O = 5.16–7.94%), and are rich in large-ion lithophile elements (LILEs; e.g. Rb, Ba) and depleted in high-field strength elements (HFSEs; e.g. Nb, Ta, Ti). The zircons in quartz diorite have <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −15.6 to −11.1 with two-stage Hf model ages (T<sub>DM2</sub>) of 1997–2281 Ma, suggesting that the magma was derived from partial melting of old continental materials. In contrast, porphyritic granite shows variable Hf isotopic composition with <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −13.7 to −2.6 and T<sub>DM2</sub> of 1471–2167 Ma, indicating a heterogeneous magma source. Besides the Dongshengmiao pluton, all the Permian granitoids in the northwestern margin of the NCC exhibit similar geochemical characteristics, including enrichment in LILEs, depletion in Nb and Ta, and enriched Hf isotopic signatures. The comprehensive geochemical data indicate that these Permian granitoids are derived from magma mixing between dominant partial melting of ancient felsic crustal materials and minor juvenile basaltic magma. Tectonically, the Dongshengmiao and other granitoids in the northwestern margin of the NCC may have been formed in a post-collisional extensional setting.
DOI: 10.6084/m9.figshare.1394857.v2
title: Geochemistry and petrogenesis of Permian granitoids in the northwestern margin of the North China Craton: insights from the Dongshengmiao pluton, Inner Mongolia

description: Permian granitoid emplacement represents one of the most important tectonothermal events in the northern margin of the North China Craton (NCC). In this study, we collected geochronological and geochemical data of the regional Permian granitoid in the northwestern margin of the NCC, and investigated the Dongshengmiao pluton, using it as an example to constrain the regional granitoid petrogenesis and its geodynamic settings. The Dongshengmiao pluton contains porphyritic granite and quartz diorite. LA-ICP-MS zircon U-Pb dating results have constrained the granitoid emplacement to be ca. 287‒275 Ma. The Dongshengmiao granitoids have a SiO<sub>2</sub> range of 58.4‒76.5%, moderate to high alkali content (Na<sub>2</sub>O + K<sub>2</sub>O = 5.16–7.94%), and are rich in large-ion lithophile elements (LILEs; e.g. Rb, Ba) and depleted in high-field strength elements (HFSEs; e.g. Nb, Ta, Ti). The zircons in quartz diorite have <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −15.6 to −11.1 with two-stage Hf model ages (T<sub>DM2</sub>) of 1997–2281 Ma, suggesting that the magma was derived from partial melting of old continental materials. In contrast, porphyritic granite shows variable Hf isotopic composition with <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −13.7 to −2.6 and T<sub>DM2</sub> of 1471–2167 Ma, indicating a heterogeneous magma source. Besides the Dongshengmiao pluton, all the Permian granitoids in the northwestern margin of the NCC exhibit similar geochemical characteristics, including enrichment in LILEs, depletion in Nb and Ta, and enriched Hf isotopic signatures. The comprehensive geochemical data indicate that these Permian granitoids are derived from magma mixing between dominant partial melting of ancient felsic crustal materials and minor juvenile basaltic magma. Tectonically, the Dongshengmiao and other granitoids in the northwestern margin of the NCC may have been formed in a post-collisional extensional setting.
DOI: 10.6084/m9.figshare.1394857.v3
title: Geochemistry and petrogenesis of Permian granitoids in the northwestern margin of the North China Craton: insights from the Dongshengmiao pluton, Inner Mongolia

description: Permian granitoid emplacement represents one of the most important tectonothermal events in the northern margin of the North China Craton (NCC). In this study, we collected geochronological and geochemical data of the regional Permian granitoid in the northwestern margin of the NCC, and investigated the Dongshengmiao pluton, using it as an example to constrain the regional granitoid petrogenesis and its geodynamic settings. The Dongshengmiao pluton contains porphyritic granite and quartz diorite. LA-ICP-MS zircon U-Pb dating results have constrained the granitoid emplacement to be ca. 287‒275 Ma. The Dongshengmiao granitoids have a SiO<sub>2</sub> range of 58.4‒76.5%, moderate to high alkali content (Na<sub>2</sub>O + K<sub>2</sub>O = 5.16–7.94%), and are rich in large-ion lithophile elements (LILEs; e.g. Rb, Ba) and depleted in high-field strength elements (HFSEs; e.g. Nb, Ta, Ti). The zircons in quartz diorite have <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −15.6 to −11.1 with two-stage Hf model ages (T<sub>DM2</sub>) of 1997–2281 Ma, suggesting that the magma was derived from partial melting of old continental materials. In contrast, porphyritic granite shows variable Hf isotopic composition with <i>ε</i><sub>Hf</sub>(<i>t</i>) values of −13.7 to −2.6 and T<sub>DM2</sub> of 1471–2167 Ma, indicating a heterogeneous magma source. Besides the Dongshengmiao pluton, all the Permian granitoids in the northwestern margin of the NCC exhibit similar geochemical characteristics, including enrichment in LILEs, depletion in Nb and Ta, and enriched Hf isotopic signatures. The comprehensive geochemical data indicate that these Permian granitoids are derived from magma mixing between dominant partial melting of ancient felsic crustal materials and minor juvenile basaltic magma. Tectonically, the Dongshengmiao and other granitoids in the northwestern margin of the NCC may have been formed in a post-collisional extensional setting.
DOI: 10.6084/m9.figshare.1394960
title: Deubiquitinating enzymes regulate PARK2-mediated mitophagy

description: The selective degradation of mitochondria by the process of autophagy, termed mitophagy, is one of the major mechanisms of mitochondrial quality control. The best-studied mitophagy pathway is the one mediated by PINK1 and PARK2/Parkin. From recent studies it has become clear that ubiquitin-ligation plays a pivotal role and most of the focus has been on the role of ubiquitination of mitochondrial proteins in mitophagy. Even though ubiquitination is a reversible process, very little is known about the role of deubiquitinating enzymes (DUBs) in mitophagy. Here, we report that 2 mitochondrial DUBs, USP30 and USP35, regulate PARK2-mediated mitophagy. We show that USP30 and USP35 can delay PARK2-mediated mitophagy using a quantitative mitophagy assay. Furthermore, we show that USP30 delays mitophagy by delaying PARK2 recruitment to the mitochondria during mitophagy. USP35 does not delay PARK2 recruitment, suggesting that it regulates mitophagy through an alternative mechanism. Interestingly, USP35 only associates with polarized mitochondria, and rapidly translocates to the cytosol during CCCP-induced mitophagy. It is clear that PARK2-mediated mitophagy is regulated at many steps in this important quality control pathway. Taken together, these findings demonstrate an important role of mitochondrial-associated DUBs in mitophagy. Because defects in mitochondria quality control are implicated in many neurodegenerative disorders, our study provides clear rationales for the design and development of drugs for the therapeutic treatment of neurodegenerative diseases such as Parkinson and Alzheimer diseases.
DOI: 10.6084/m9.figshare.1394960.v1
title: Deubiquitinating enzymes regulate PARK2-mediated mitophagy

description: The selective degradation of mitochondria by the process of autophagy, termed mitophagy, is one of the major mechanisms of mitochondrial quality control. The best-studied mitophagy pathway is the one mediated by PINK1 and PARK2/Parkin. From recent studies it has become clear that ubiquitin-ligation plays a pivotal role and most of the focus has been on the role of ubiquitination of mitochondrial proteins in mitophagy. Even though ubiquitination is a reversible process, very little is known about the role of deubiquitinating enzymes (DUBs) in mitophagy. Here, we report that 2 mitochondrial DUBs, USP30 and USP35 regulate PARK2-mediated mitophagy. We show that USP30 and USP35 can delay PARK2-mediated mitophagy using a quantitative mitophagy assay. Furthermore, we show that USP30 delays mitophagy by delaying PARK2 recruitment to the mitochondria during mitophagy. USP35 does not delay PARK2 recruitment, suggesting that it regulates mitophagy through an alternative mechanism. Interestingly, USP35 only associates with polarized mitochondria, and rapidly translocates to the cytosol during CCCP-induced mitophagy. It is clear that PARK2-mediated mitophagy is regulated at many steps in this important quality control pathway. Taken together, we have demonstrated an important role of mitochondrial-associated DUBs in mitophagy. Since defects in mitochondria quality control are implicated in many neurodegenerative disorders, our study provides clear rationales for the design and development of drugs for the therapeutic treatment of neurodegenerative diseases such as Parkinson and Alzheimer diseases.
DOI: 10.6084/m9.figshare.1394960.v2
title: Deubiquitinating enzymes regulate PARK2-mediated mitophagy

description: The selective degradation of mitochondria by the process of autophagy, termed mitophagy, is one of the major mechanisms of mitochondrial quality control. The best-studied mitophagy pathway is the one mediated by PINK1 and PARK2/Parkin. From recent studies it has become clear that ubiquitin-ligation plays a pivotal role and most of the focus has been on the role of ubiquitination of mitochondrial proteins in mitophagy. Even though ubiquitination is a reversible process, very little is known about the role of deubiquitinating enzymes (DUBs) in mitophagy. Here, we report that 2 mitochondrial DUBs, USP30 and USP35, regulate PARK2-mediated mitophagy. We show that USP30 and USP35 can delay PARK2-mediated mitophagy using a quantitative mitophagy assay. Furthermore, we show that USP30 delays mitophagy by delaying PARK2 recruitment to the mitochondria during mitophagy. USP35 does not delay PARK2 recruitment, suggesting that it regulates mitophagy through an alternative mechanism. Interestingly, USP35 only associates with polarized mitochondria, and rapidly translocates to the cytosol during CCCP-induced mitophagy. It is clear that PARK2-mediated mitophagy is regulated at many steps in this important quality control pathway. Taken together, these findings demonstrate an important role of mitochondrial-associated DUBs in mitophagy. Because defects in mitochondria quality control are implicated in many neurodegenerative disorders, our study provides clear rationales for the design and development of drugs for the therapeutic treatment of neurodegenerative diseases such as Parkinson and Alzheimer diseases.
DOI: 10.6084/m9.figshare.1394960.v3
title: Deubiquitinating enzymes regulate PARK2-mediated mitophagy

description: The selective degradation of mitochondria by the process of autophagy, termed mitophagy, is one of the major mechanisms of mitochondrial quality control. The best-studied mitophagy pathway is the one mediated by PINK1 and PARK2/Parkin. From recent studies it has become clear that ubiquitin-ligation plays a pivotal role and most of the focus has been on the role of ubiquitination of mitochondrial proteins in mitophagy. Even though ubiquitination is a reversible process, very little is known about the role of deubiquitinating enzymes (DUBs) in mitophagy. Here, we report that 2 mitochondrial DUBs, USP30 and USP35, regulate PARK2-mediated mitophagy. We show that USP30 and USP35 can delay PARK2-mediated mitophagy using a quantitative mitophagy assay. Furthermore, we show that USP30 delays mitophagy by delaying PARK2 recruitment to the mitochondria during mitophagy. USP35 does not delay PARK2 recruitment, suggesting that it regulates mitophagy through an alternative mechanism. Interestingly, USP35 only associates with polarized mitochondria, and rapidly translocates to the cytosol during CCCP-induced mitophagy. It is clear that PARK2-mediated mitophagy is regulated at many steps in this important quality control pathway. Taken together, these findings demonstrate an important role of mitochondrial-associated DUBs in mitophagy. Because defects in mitochondria quality control are implicated in many neurodegenerative disorders, our study provides clear rationales for the design and development of drugs for the therapeutic treatment of neurodegenerative diseases such as Parkinson and Alzheimer diseases.
DOI: 10.6084/m9.figshare.1396275
title: Cardiolipin remodeling by TAZ/tafazzin is selectively required for the initiation of mitophagy

description: Tafazzin (TAZ) is a phospholipid transacylase that catalyzes the remodeling of cardiolipin, a mitochondrial phospholipid required for oxidative phosphorylation. Mutations of TAZ cause Barth syndrome, which is characterized by mitochondrial dysfunction and dilated cardiomyopathy, leading to premature death. However, the molecular mechanisms underlying the cause of mitochondrial dysfunction in Barth syndrome remain poorly understood. Here we investigated the role of TAZ in regulating mitochondrial function and mitophagy. Using primary mouse embryonic fibroblasts (MEFs) with doxycycline-inducible knockdown of <i>Taz</i>, we showed that TAZ deficiency in MEFs caused defective mitophagosome biogenesis, but not other autophagic processes. Consistent with a key role of mitophagy in mitochondria quality control, TAZ deficiency in MEFs also led to impaired oxidative phosphorylation and severe oxidative stress. Together, these findings provide key insights on mitochondrial dysfunction in Barth syndrome, suggesting that pharmacological restoration of mitophagy may provide a novel treatment for this lethal condition.
DOI: 10.6084/m9.figshare.1396275.v1
title: Cardiolipin Remodeling by TAZ/Tafazzin Is Selectively Required for the Initiation of Mitophagy

description: ABSTRACTTafazzin (TAZ) is a phospholipid transacylase that catalyzes the remodeling of cardiolipin, a mitochondrial phospholipid required for oxidative phosphorylation. Mutations of TAZ cause Barth syndrome, which is characterized by mitochondrial dysfunction and dilated cardiomyopathy, leading to premature death. However, the molecular mechanisms underlying the cause of mitochondrial dysfunction in Barth syndrome remain poorly understood. Here we investigated the role of TAZ in regulating mitochondrial function and mitophagy. Using primary mouse embryonic fibroblasts (MEFs) with doxycycline-inducible knockdown of <i>Taz</i>, we showed that TAZ deficiency in MEFs caused defective mitophagosome biogenesis, but not other autophagic processes. Consistent with a key role of mitophagy in mitochondria quality control, TAZ deficiency in MEFs also led to impaired oxidative phosphorylation and severe oxidative stress. Together, these findings provide key insights on mitochondrial dysfunction in Barth syndrome, suggesting that pharmacological restoration of mitophagy may provide a novel treatment for this lethal condition.