cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1291199.v3
title: Metabolic reprogramming orchestrates cancer stem cell properties in nasopharyngeal carcinoma

description: Cancer stem cells (CSCs) represent a subpopulation of tumor cells endowed with self-renewal capacity and are considered as an underlying cause of tumor recurrence and metastasis. The metabolic signatures of CSCs and the mechanisms involved in the regulation of their stem cell-like properties still remain elusive. We utilized nasopharyngeal carcinoma (NPC) CSCs as a model to dissect their metabolic signatures and found that CSCs underwent metabolic shift and mitochondrial resetting distinguished from their differentiated counterparts. In metabolic shift, CSCs showed a greater reliance on glycolysis for energy supply compared with the parental cells. In mitochondrial resetting, the quantity and function of mitochondria of CSCs were modulated by the biogenesis of the organelles, and the round-shaped mitochondria were distributed in a peri-nuclear manner similar to those seen in the stem cells. In addition, we blocked the glycolytic pathway, increased the ROS levels, and depolarized mitochondrial membranes of CSCs, respectively, and examined the effects of these metabolic factors on CSC properties. Intriguingly, the properties of CSCs were curbed when we redirected the quintessential metabolic reprogramming, which indicates that the plasticity of energy metabolism regulated the balance between acquisition and loss of the stemness status. Taken together, we suggest that metabolic reprogramming is critical for CSCs to sustain self-renewal, deter from differentiation and enhance the antioxidant defense mechanism. Characterization of metabolic reprogramming governing CSC properties is paramount to the design of novel therapeutic strategies through metabolic intervention of CSCs.
DOI: 10.6084/m9.figshare.1291200.v3
title: CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor i with chromatin

description: Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase <i>CDC7</i>. Here we show that another kinase, <i>CDC28</i>, phosphorylates Cac1p on serines 94 and 515 in early S phase and regulates its association with chromatin, but not its association with PCNA. Mutations in the Cac1p-phosphorylation sites of <i>CDC28</i> but not of <i>CDC7</i> substantially reduce the <i>in vivo</i> phosphorylation of Cac1p. However, mutations in the putative <i>CDC7</i> target sites on Cac1p reduce its stability. The association of CAF-I with chromatin is impaired in a <i>cdc28–1</i> mutant and to a lesser extent in a <i>cdc7–1</i> mutant. In addition, mutations in the Cac1p-phosphorylation sites by both <i>CDC28</i> and <i>CDC7</i> reduce gene silencing at the telomeres. We propose that this phosphorylation represents a regulatory step in the recruitment of CAF-I to chromatin in early S phase that is distinct from the association of CAF-I with PCNA. Hence, we implicate <i>CDC28</i> in the regulation of chromatin reassembly during DNA replication. These findings provide novel mechanistic insights on the links between cell-cycle regulation, DNA replication and chromatin reassembly.
DOI: 10.6084/m9.figshare.1291198
title: ATM regulates cell fate choice upon p53 activation by modulating mitochondrial turnover and ROS levels

description: Despite extensive study, the mechanisms of cell fate choice upon p53 activation remain poorly understood. Using genome-wide shRNA screening, we recently identified the ATM kinase as synthetic lethal with Nutlin-3, an MDM2 inhibitor that leads to non-genotoxic p53 activation. Here, we demonstrate that while this synthetic lethal interaction relies upon components of both the intrinsic and extrinsic apoptotic pathways (e.g., BAX and BID), it is not due to significant ATM effects on the expression of p53 target genes. Instead, loss of ATM activity results in increased mitochondria and reactive oxygen species that drive apoptosis. Finally, we provide evidence that pharmacologic inhibition of ATM blocks autophagy in direct opposition to p53, which activates this process, and that inhibition of autophagy is sufficient to elicit an apoptotic response when combined with Nutlin-3.
DOI: 10.6084/m9.figshare.1291199.v2
title: Metabolic reprogramming orchestrates cancer stem cell properties in nasopharyngeal carcinoma

description: Cancer stem cells (CSCs) represent a subpopulation of tumor cells endowed with self-renewal capacity and are considered as an underlying cause of tumor recurrence and metastasis. The metabolic signatures of CSCs and the mechanisms involved in the regulation of their stem cell-like properties still remain elusive. We utilized nasopharyngeal carcinoma (NPC) CSCs as a model to dissect their metabolic signatures and found that CSCs underwent metabolic shift and mitochondrial resetting distinguished from their differentiated counterparts. In metabolic shift, CSCs showed a greater reliance on glycolysis for energy supply compared with the parental cells. In mitochondrial resetting, the quantity and function of mitochondria of CSCs were modulated by the biogenesis of the organelles, and the round-shaped mitochondria were distributed in a peri-nuclear manner similar to those seen in the stem cells. In addition, we blocked the glycolytic pathway, increased the ROS levels, and depolarized mitochondrial membranes of CSCs, respectively, and examined the effects of these metabolic factors on CSC properties. Intriguingly, the properties of CSCs were curbed when we redirected the quintessential metabolic reprogramming, which indicates that the plasticity of energy metabolism regulated the balance between acquisition and loss of the stemness status. Taken together, we suggest that metabolic reprogramming is critical for CSCs to sustain self-renewal, deter from differentiation and enhance the antioxidant defense mechanism. Characterization of metabolic reprogramming governing CSC properties is paramount to the design of novel therapeutic strategies through metabolic intervention of CSCs.
DOI: 10.6084/m9.figshare.1291200.v2
title: CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor i with chromatin

description: Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase <i>CDC7</i>. Here we show that another kinase, <i>CDC28</i>, phosphorylates Cac1p on serines 94 and 515 in early S phase and regulates its association with chromatin, but not its association with PCNA. Mutations in the Cac1p-phosphorylation sites of <i>CDC28</i> but not of <i>CDC7</i> substantially reduce the <i>in vivo</i> phosphorylation of Cac1p. However, mutations in the putative <i>CDC7</i> target sites on Cac1p reduce its stability. The association of CAF-I with chromatin is impaired in a <i>cdc28–1</i> mutant and to a lesser extent in a <i>cdc7–1</i> mutant. In addition, mutations in the Cac1p-phosphorylation sites by both <i>CDC28</i> and <i>CDC7</i> reduce gene silencing at the telomeres. We propose that this phosphorylation represents a regulatory step in the recruitment of CAF-I to chromatin in early S phase that is distinct from the association of CAF-I with PCNA. Hence, we implicate <i>CDC28</i> in the regulation of chromatin reassembly during DNA replication. These findings provide novel mechanistic insights on the links between cell-cycle regulation, DNA replication and chromatin reassembly.
DOI: 10.6084/m9.figshare.1291195
title: Qualifying Examination: Overlap graph-based sequence assembly in bioinformatics

description: This is my qualifying examination final report and presentation for the oral exam, presented at Michigan State University on August 29th. It reviews how the genome assembly problem formulation changed since the foundation of genome sequencing, with special attention to overlap graph-based sequence assembly. Three assemblers implementing this theoretical framework are reviewed, and a fourth one based on de Bruijn graph serves as a comparison between shared methods and differences on each approach. Finally possible directions for future works are discussed.
DOI: 10.6084/m9.figshare.1291193
title: Ethenoadenine Precursor 7,8-dihydro-7-hydroxy-imidazo[2,1-i]purine IRC

description: The reaction of chloroacetaldehyde with adenine to form ethenoadenine has been modelled: this is an intrinsic reaction coordinate for the dehydration reaction at the 6-31G(d) level of theory using the wB97X-D functional. When chloroacetaldehyde reacts with adenine to form ethenoadenine the reaction can proceed by one of two routes dependent upon the orientation of the chloroacetaldehyde molecule with the adenine molecule. This model is based upon an orientation which would form the intermediate 7,8-dihydro-7-hydroxy-imidazo[2,1-i]purine.
DOI: 10.6084/m9.figshare.1291192
title: Ethenoadenine Precursor 7,8-dihydro-7-hydroxy-imidazo[2,1-i]purine TS

description: The reaction of chloroacetaldehyde with adenine to form ethenoadenine has been modelled: this is a transition state structure at the 6-31G(d) level of theory using the wB97X-D functional. When chloroacetaldehyde reacts with adenine to form ethenoadenine the reaction can proceed by one of two routes dependent upon the orientation of the chloroacetaldehyde molecule with the adenine molecule. This model is based upon an orientation which would form the intermediate 7,8-dihydro-7-hydroxy-imidazo[2,1-i]purine.
DOI: 10.6084/m9.figshare.1291198.v1
title: ATM regulates cell fate choice upon p53 activation by modulating mitochondrial turnover and ROS levels

description: Despite extensive study, the mechanisms of cell fate choice upon p53 activation remain poorly understood. Using genome-wide shRNA screening, we recently identified the ATM kinase as synthetic lethal with Nutlin-3, an MDM2 inhibitor that leads to non-genotoxic p53 activation. Here, we demonstrate that while this synthetic lethal interaction relies upon components of both the intrinsic and extrinsic apoptotic pathways (e.g., BAX and BID), it is not due to significant ATM effects on the expression of p53 target genes. Instead, loss of ATM activity results in increased mitochondria and reactive oxygen species that drive apoptosis. Finally, we provide evidence that pharmacologic inhibition of ATM blocks autophagy in direct opposition to p53, which activates this process, and that inhibition of autophagy is sufficient to elicit an apoptotic response when combined with Nutlin-3.
DOI: 10.6084/m9.figshare.1291190
title: Identity elements for the aminoacylation of metazoan mitochondrial tRNA<sup>Arg</sup> have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment

description: Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA<sup>Ser</sup><sub>UCU</sub>. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.
DOI: 10.6084/m9.figshare.1291198.v3
title: ATM regulates cell fate choice upon p53 activation by modulating mitochondrial turnover and ROS levels

description: Despite extensive study, the mechanisms of cell fate choice upon p53 activation remain poorly understood. Using genome-wide shRNA screening, we recently identified the ATM kinase as synthetic lethal with Nutlin-3, an MDM2 inhibitor that leads to non-genotoxic p53 activation. Here, we demonstrate that while this synthetic lethal interaction relies upon components of both the intrinsic and extrinsic apoptotic pathways (e.g., BAX and BID), it is not due to significant ATM effects on the expression of p53 target genes. Instead, loss of ATM activity results in increased mitochondria and reactive oxygen species that drive apoptosis. Finally, we provide evidence that pharmacologic inhibition of ATM blocks autophagy in direct opposition to p53, which activates this process, and that inhibition of autophagy is sufficient to elicit an apoptotic response when combined with Nutlin-3.
DOI: 10.6084/m9.figshare.1291198.v2
title: ATM regulates cell fate choice upon p53 activation by modulating mitochondrial turnover and ROS levels

description: Despite extensive study, the mechanisms of cell fate choice upon p53 activation remain poorly understood. Using genome-wide shRNA screening, we recently identified the ATM kinase as synthetic lethal with Nutlin-3, an MDM2 inhibitor that leads to non-genotoxic p53 activation. Here, we demonstrate that while this synthetic lethal interaction relies upon components of both the intrinsic and extrinsic apoptotic pathways (e.g., BAX and BID), it is not due to significant ATM effects on the expression of p53 target genes. Instead, loss of ATM activity results in increased mitochondria and reactive oxygen species that drive apoptosis. Finally, we provide evidence that pharmacologic inhibition of ATM blocks autophagy in direct opposition to p53, which activates this process, and that inhibition of autophagy is sufficient to elicit an apoptotic response when combined with Nutlin-3.
DOI: 10.6084/m9.figshare.1291195.v1
title: Qualifying Examination

description: This is my qualifying examination final report and presentation for the oral exam, presented at Michigan State University on August 29th. It reviews how the genome assembly problem formulation changed since the foundation of genome sequencing, with special attention to overlap graph-based sequence assembly. Three assemblers implementing this theoretical framework are reviewed, and a fourth one based on de Bruijn graph serves as a comparison between shared methods and differences on each approach. Finally possible directions for future works are discussed.
DOI: 10.6084/m9.figshare.1291190.v1
title: Identity elements for the aminoacylation of metazoan mitochondrial tRNA<sup>Arg</sup> have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment

description: ABSTRACTEumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA<sup>Ser</sup><sub>UCU</sub>. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNA<sup>Arg</sup> in which the major identity elements permit the arginylation of all five encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNA<sup>Arg</sup><sub>UCG</sub> structural variants. The established identity elements are sufficient to maintain the fidelity of tRNA<sup>Ser</sup><sub>UCU</sub> reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNA<sup>Arg</sup><sub>UCG</sub> by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the two encoded tRNA<sup>Arg</sup><sub>UCG/UCU</sub> isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.
DOI: 10.6084/m9.figshare.1291195.v3
title: Qualifying Examination: Overlap graph-based sequence assembly in bioinformatics

description: This is my qualifying examination final report and presentation for the oral exam, presented at Michigan State University on August 29th. It reviews how the genome assembly problem formulation changed since the foundation of genome sequencing, with special attention to overlap graph-based sequence assembly. Three assemblers implementing this theoretical framework are reviewed, and a fourth one based on de Bruijn graph serves as a comparison between shared methods and differences on each approach. Finally possible directions for future works are discussed.
DOI: 10.6084/m9.figshare.1291195.v2
title: Qualifying Examination: Overlap graph-based sequence assembly in bioinformatics

description: This is my qualifying examination final report and presentation for the oral exam, presented at Michigan State University on August 29th. It reviews how the genome assembly problem formulation changed since the foundation of genome sequencing, with special attention to overlap graph-based sequence assembly. Three assemblers implementing this theoretical framework are reviewed, and a fourth one based on de Bruijn graph serves as a comparison between shared methods and differences on each approach. Finally possible directions for future works are discussed.
DOI: 10.6084/m9.figshare.1291190.v3
title: Identity elements for the aminoacylation of metazoan mitochondrial tRNA<sup>Arg</sup> have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment

description: Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA<sup>Ser</sup><sub>UCU</sub>. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.
DOI: 10.6084/m9.figshare.1291190.v2
title: Identity elements for the aminoacylation of metazoan mitochondrial tRNA<sup>Arg</sup> have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment

description: Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA<sup>Ser</sup><sub>UCU</sub>. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.